Publications of David N. Beratan :chronological by type listing:
%%
@article{fds362659,
Author = {Aiello, CD and Abendroth, JM and Abbas, M and Afanasev, A and Agarwal,
S and Banerjee, AS and Beratan, DN and Belling, JN and Berche, B and Botana, A and Caram, JR and Celardo, GL and Cuniberti, G and Garcia-Etxarri, A and Dianat, A and Diez-Perez, I and Guo, Y and Gutierrez, R and Herrmann, C and Hihath, J and Kale, S and Kurian, P and Lai, Y-C and Liu, T and Lopez, A and Medina, E and Mujica, V and Naaman, R and Noormandipour, M and Palma, JL and Paltiel, Y and Petuskey, W and Ribeiro-Silva, JC and Saenz, JJ and Santos, EJG and Solyanik-Gorgone,
M and Sorger, VJ and Stemer, DM and Ugalde, JM and Valdes-Curiel, A and Varela, S and Waldeck, DH and Wasielewski, MR and Weiss, PS and Zacharias, H and Wang, QH},
Title = {A Chirality-Based Quantum Leap.},
Journal = {ACS nano},
Volume = {16},
Number = {4},
Pages = {4989-5035},
Year = {2022},
Month = {April},
url = {http://dx.doi.org/10.1021/acsnano.1c01347},
Abstract = {There is increasing interest in the study of chiral degrees
of freedom occurring in matter and in electromagnetic
fields. Opportunities in quantum sciences will likely
exploit two main areas that are the focus of this Review:
(1) recent observations of the chiral-induced spin
selectivity (CISS) effect in chiral molecules and engineered
nanomaterials and (2) rapidly evolving nanophotonic
strategies designed to amplify chiral light-matter
interactions. On the one hand, the CISS effect underpins the
observation that charge transport through nanoscopic chiral
structures favors a particular electronic spin orientation,
resulting in large room-temperature spin polarizations.
Observations of the CISS effect suggest opportunities for
spin control and for the design and fabrication of
room-temperature quantum devices from the bottom up, with
atomic-scale precision and molecular modularity. On the
other hand, chiral-optical effects that depend on both spin-
and orbital-angular momentum of photons could offer key
advantages in all-optical and quantum information
technologies. In particular, amplification of these chiral
light-matter interactions using rationally designed
plasmonic and dielectric nanomaterials provide approaches to
manipulate light intensity, polarization, and phase in
confined nanoscale geometries. Any technology that relies on
optimal charge transport, or optical control and readout,
including quantum devices for logic, sensing, and storage,
may benefit from chiral quantum properties. These properties
can be theoretically and experimentally investigated from a
quantum information perspective, which has not yet been
fully developed. There are uncharted implications for the
quantum sciences once chiral couplings can be engineered to
control the storage, transduction, and manipulation of
quantum information. This forward-looking Review provides a
survey of the experimental and theoretical fundamentals of
chiral-influenced quantum effects and presents a vision for
their possible future roles in enabling room-temperature
quantum technologies.},
Doi = {10.1021/acsnano.1c01347},
Key = {fds362659}
}
@article{fds231939,
Author = {Xiao, D and Bulat, FA and Yang, W and Beratan, DN},
Title = {A donor-nanotube paradigm for nonlinear optical
materials.},
Journal = {Nano letters},
Volume = {8},
Number = {9},
Pages = {2814-2818},
Year = {2008},
Month = {September},
ISSN = {1530-6984},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18698728},
Abstract = {Studies of the nonlinear electronic response of
donor/acceptor substituted nanotubes suggest a behavior that
is both surprising and qualitatively distinct from that in
conventional conjugated organic species. We find that the
carbon nanotubes serve as both electronic bridges and
acceptors, leading to a donor-nanotube paradigm for the
effective design of large first hyperpolarizabilities. We
also find that tuning the donor orientation, relative to the
nanotube, can significantly enhance the first
hyperpolarizability.},
Doi = {10.1021/nl801388z},
Key = {fds231939}
}
@article{fds222356,
Author = {Y. Zhang and C. Liu and A. Balaeff and S. S. Skourtis and D.N.
Beratan},
Title = {A flickering resonance mechanism for biological charge
transfer},
Journal = {PNAS},
Year = {2013},
Key = {fds222356}
}
@article{fds231926,
Author = {Hu, X and Hu, H and Beratan, DN and Yang, W},
Title = {A gradient-directed Monte Carlo approach for protein
design.},
Journal = {Journal of computational chemistry},
Volume = {31},
Number = {11},
Pages = {2164-2168},
Year = {2010},
Month = {August},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20186860},
Abstract = {We develop a new global optimization strategy,
gradient-directed Monte Carlo (GDMC) sampling, to optimize
protein sequence for a target structure using RosettaDesign.
GDMC significantly improves the sampling of sequence space,
compared to the classical Monte Carlo search protocol, for a
fixed backbone conformation as well as for the simultaneous
optimization of sequence and structure. As such, GDMC
sampling enhances the efficiency of protein
design.},
Doi = {10.1002/jcc.21506},
Key = {fds231926}
}
@article{fds335028,
Author = {Hu, X and Beratan, DN and Yang, W},
Title = {A gradient-directed Monte Carlo approach to molecular
design.},
Journal = {The Journal of chemical physics},
Volume = {129},
Number = {6},
Pages = {064102},
Year = {2008},
Month = {August},
url = {http://dx.doi.org/10.1063/1.2958255},
Abstract = {The recently developed linear combination of atomic
potentials (LCAP) approach [M. Wang et al., J. Am. Chem.
Soc. 128, 3228 (2006)] allows continuous optimization in a
discrete chemical space, and thus is useful in the design of
molecules for targeted properties. To address further
challenges arising from the rugged, continuous property
surfaces in the LCAP approach, we develop a
gradient-directed Monte Carlo (GDMC) strategy as an
augmentation to the original LCAP optimization method. The
GDMC method retains the power of exploring molecular space
by utilizing local gradient information computed from the
LCAP approach to jump between discrete molecular structures.
It also allows random MC moves to overcome barriers between
local optima on property surfaces. The combined GDMC-LCAP
approach is demonstrated here for optimizing nonlinear
optical properties in a class of donor-acceptor substituted
benzene and porphyrin frameworks. Specifically, one molecule
with four nitrogen atoms in the porphyrin ring was found to
have a larger first hyperpolarizability than structures with
the conventional porphyrin motif.},
Doi = {10.1063/1.2958255},
Key = {fds335028}
}
@article{fds231931,
Author = {Hu, X and Beratan, DN and Yang, W},
Title = {A gradient-directed Monte Carlo method for global
optimization in a discrete space: application to protein
sequence design and folding.},
Journal = {The Journal of chemical physics},
Volume = {131},
Number = {15},
Pages = {154117},
Year = {2009},
Month = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20568857},
Abstract = {We apply the gradient-directed Monte Carlo (GDMC) method to
select optimal members of a discrete space, the space of
chemically viable proteins described by a model Hamiltonian.
In contrast to conventional Monte Carlo approaches, our GDMC
method uses local property gradients with respect to
chemical variables that have discrete values in the actual
systems, e.g., residue types in a protein sequence. The
local property gradients are obtained from the interpolation
of discrete property values, following the linear
combination of atomic potentials scheme developed recently
[M. Wang et al., J. Am. Chem. Soc. 128, 3228 (2006)]. The
local property derivative information directs the search
toward the global minima while the Metropolis criterion
incorporated in the method overcomes barriers between local
minima. Using the simple HP lattice model, we apply the GDMC
method to protein sequence design and folding. The GDMC
algorithm proves to be particularly efficient, suggesting
that this strategy can be extended to other discrete
optimization problems in addition to inverse molecular
design.},
Doi = {10.1063/1.3236834},
Key = {fds231931}
}
@article{fds167393,
Author = {X. Hu and D.N. Beratan and W. Yang},
Title = {A gradient-directed Monte Caro method for global
optimization in discrete space: Application to protein
sequence design and folding},
Journal = {J. Chem. Phys},
Number = {131},
Pages = {154117},
Year = {2009},
Key = {fds167393}
}
@article{fds232055,
Author = {Skourtis, SS and Onuchic, JN and Beratan, DN},
Title = {A method to analyze multi-pathway effects on protein
mediated donor-acceptor coupling interactions},
Journal = {Inorganica Chimica Acta},
Volume = {243},
Number = {1-2},
Pages = {167-175},
Publisher = {Elsevier BV},
Year = {1996},
Month = {February},
url = {http://dx.doi.org/10.1016/0020-1693(96)04904-3},
Abstract = {Current strategies for analyzing donor-acceptor interactions
involve mapping the dominant coupling pathways or families
of pathways, followed by a numerical estimate of the
interaction mediated by the paths. This strategy succeeds
because it properly balances the through-bond versus
through-space aspects of the protein electron transfer
problem. Yet, existing analytical tools do not provide
general predictions of how specific protein motifs might
favor or disfavor electron transfer. This issue is best
addressed with methods that incorporate multiple interfering
pathways and that allow the coupling to be dissected
systematically into contributing factors. We present such a
method that probes collective effects arising from secondary
and tertiary motifs. This analysis indicates when (and why)
single pathway strategies succeed or fail. Applications of
this new method to model secondary structures are
described.},
Doi = {10.1016/0020-1693(96)04904-3},
Key = {fds232055}
}
@article{fds231885,
Author = {Skourtis, SS and Beratan, DN},
Title = {A molecular double slit paradigm},
Journal = {AIP Conference Proceedings},
Volume = {963},
Number = {2},
Pages = {809-812},
Publisher = {AIP},
Year = {2007},
Month = {December},
ISSN = {0094-243X},
url = {http://dx.doi.org/10.1063/1.2836214},
Abstract = {This contribution describes a simple model of a molecular
interferometer. We consider an electron transfer molecule
consisting of electron-donating and electron-acceptor parts
that are connected by a bridge. The bridge provides two
parallel tunneling pathways for electron transfer from donor
to acceptor. In each pathway the electron can interact with
a pathway-specific bridge vibration. We study electron
transfer from donor to acceptor mediated by inelastic
tunneling, where the tunneling electron exchanges energy
with the local bridge vibrations. When the tunneling
electron excites or is excited by a bridge vibration
specific to one of the tunneling pathways, the tunneling
pathway is "labeled" and the interference between tunneling
pathways is lost. We discuss types of molecules and
optical-spectroscopy experiments which could allow the
observation of this effect. © 2007 American Institute of
Physics.},
Doi = {10.1063/1.2836214},
Key = {fds231885}
}
@article{fds232044,
Author = {Hopfield, JJ and Onuchic, JN and Beratan, DN},
Title = {A molecular shift register based on electron
transfer.},
Journal = {Science (New York, N.Y.)},
Volume = {241},
Number = {4867},
Pages = {817-820},
Year = {1988},
Month = {August},
ISSN = {0036-8075},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17829175},
Abstract = {An electronic shift-register memory at the molecular level
is described. The memory elements are based on a chain of
electron-transfer molecules and the information is shifted
by photoinduced electron-transfer reactions. This device
integrates designed electronic molecules onto a very large
scale integrated (silicon microelectronic) substrate,
providing an example of a "molecular electronic device" that
could actually be made. The design requirements for such a
device and possible synthetic strategies are discussed.
Devices along these lines should have lower energy usage and
enhanced storage density.},
Doi = {10.1126/science.241.4867.817},
Key = {fds232044}
}
@article{fds337002,
Author = {Peters, JW and Beratan, DN and Bothner, B and Dyer, RB and Harwood, CS and Heiden, ZM and Hille, R and Jones, AK and King, PW and Lu, Y and Lubner,
CE and Minteer, SD and Mulder, DW and Raugei, S and Schut, GJ and Seefeldt,
LC and Tokmina-Lukaszewska, M and Zadvornyy, OA and Zhang, P and Adams,
MW},
Title = {A new era for electron bifurcation.},
Journal = {Current opinion in chemical biology},
Volume = {47},
Pages = {32-38},
Year = {2018},
Month = {December},
url = {http://dx.doi.org/10.1016/j.cbpa.2018.07.026},
Abstract = {Electron bifurcation, or the coupling of exergonic and
endergonic oxidation-reduction reactions, was discovered by
Peter Mitchell and provides an elegant mechanism to
rationalize and understand the logic that underpins the Q
cycle of the respiratory chain. Thought to be a unique
reaction of respiratory complex III for nearly 40 years,
about a decade ago Wolfgang Buckel and Rudolf Thauer
discovered that flavin-based electron bifurcation is also an
important component of anaerobic microbial metabolism. Their
discovery spawned a surge of research activity, providing a
basis to understand flavin-based bifurcation, forging
fundamental parallels with Mitchell's Q cycle and leading to
the proposal of metal-based bifurcating enzymes. New
insights into the mechanism of electron bifurcation provide
a foundation to establish the unifying principles and
essential elements of this fascinating biochemical
phenomenon.},
Doi = {10.1016/j.cbpa.2018.07.026},
Key = {fds337002}
}
@article{fds335026,
Author = {Ma, Z and Antoniou, P and Zhang, P and Skourtis, SS and Beratan,
DN},
Title = {A Nonequilibrium Molecular Dynamics Study of Infrared
Perturbed Electron Transfer.},
Journal = {Journal of chemical theory and computation},
Volume = {14},
Number = {9},
Pages = {4818-4832},
Year = {2018},
Month = {September},
url = {http://dx.doi.org/10.1021/acs.jctc.8b00001},
Abstract = {Infrared (IR) excitation is known to change
electron-transfer kinetics in molecules. We use
nonequilibrium molecular dynamics (NEqMD) simulations to
explore the molecular underpinnings of how vibrational
excitation may influence nonadiabatic electron-transfer.
NEqMD combines classical molecular dynamics simulations with
nonequilibrium semiclassical initial conditions to simulate
the dynamics of vibrationally excited molecules. We combine
NEqMD with electronic structure computations to probe IR
effects on electron transfer rates in two molecular species,
dimethylaniline-guanosine-cytidine-anthracene (DMA-GC-Anth)
and 4-(pyrrolidin-1-yl)phenyl-2,6,7-triazabicyclo[2.2.2]octatriene-10-cyanoanthracen-9-yl
(PP-BCN-CA). In DMA-GC-Anth, the simulations find that IR
excitation of the NH<sub>2</sub> scissoring motion and the
subsequent intramolecular vibrational energy redistribution
(IVR) do not significantly alter the mean-squared
donor-acceptor (DA) coupling interaction. This finding is
consistent with earlier computational analysis of static
systems. In PP-BCN-CA, IR excitation of the bridging C═N
bond changes the bridge-mediated coupling for charge
separation and recombination by ∼30-40%. The methods
described here enable detailed explorations of how IR
excitation may perturb charge-transfer processes at the
molecular scale.},
Doi = {10.1021/acs.jctc.8b00001},
Key = {fds335026}
}
@article{fds231980,
Author = {Onuchic, JN and Beratan, DN},
Title = {A predictive theoretical model for electron tunneling
pathways in proteins},
Journal = {The Journal of Chemical Physics},
Volume = {92},
Number = {1},
Pages = {722-733},
Publisher = {AIP Publishing},
Year = {1990},
Month = {January},
ISSN = {0021-9606},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000092000001000722000001&idtype=cvips},
Abstract = {A practical method is presented for calculating the
dependence of electron transfer rates on details of the
protein medium intervening between donor and acceptor. The
method takes proper account of the relative energetics and
mutual interactions of the donor, acceptor, and peptide
groups. It also provides a quantitative search scheme for
determining the important tunneling pathway(s) [specific
sequence (s) of localized bonding and antibonding orbitals
of the protein which dominate the donor-acceptor electronic
coupling] in native and tailored proteins, provides a tool
for designing new proteins with prescribed electron transfer
rates, and provides a consistent description of observed
electron transfer rates in existing redox labeled
metalloproteins and small molecule model compounds. © 1990
American Institute of Physics.},
Doi = {10.1063/1.458426},
Key = {fds231980}
}
@article{fds232056,
Author = {Perry, JL and Christensen, T and Goldsmith, MR and Toone, EJ and Beratan, DN and Simon, JD},
Title = {A protein-ligand ion pair stabilizes the binding of
Ochratoxin A to human serum albumin},
Journal = {J. Phys. Chem. B.},
Volume = {107},
Number = {31},
Pages = {7884-7888},
Year = {2003},
Abstract = {Ochratoxin A (OTA), a fungal metabolite of strains of
Penicillium and Aspergillus, binds in its dianion form to
Sudlow site I of human serum albumin (HSA) with high
affinity. In this study, isothermal calorimetry (ITC) is
used to study the binding of OTA and its O-methyl derivative
(MOA). Calculations of the equilibrium geometry of the
monoanion and dianion of OTA reveal only small structural
changes among the lowest energy conformers. The ITC data
show the binding of MOA, which lacks the phenolic proton of
OTA, is accompanied by the uptake of a proton from the
surrounding solvent. At pH 7.13, the binding of OTA is
accompanied by uptake of 0.43 ± 0.15 protons from the
solvent. At this pH, the monoanion (0.54) and dianion (0.46)
forms of OTA are both present in solution. However, the pKa
of the phenolic group of OTA decreases by more than three
units upon protein binding, and so all available OTA is
bound to the protein as the dianion. To account for the ITC
data, a model is proposed in which the proton is provided by
the phenolic moiety of OTA in the case of initial binding of
the monoanion, and a proton is taken up from the surrounding
solvent for initial binding of the dianion. The binding
constant of MOA is 2 orders of magnitude smaller than that
of OTA, indicating the ion pair between the phenoxide group
of OTA and the protonated amino acid is a major contributor
to the high binding affinity of OTA to HSA. To identify the
specific amino acid involved, the binding of OTA to bovine,
rat, and porcine serum albumins was examined. Deprotonation
of the monoanion of OTA occurred upon binding to all
species. Assuming the amino acid is conserved between
species and taking into account crystal structures of
ligands bound to site I of HSA and their ability to displace
OTA from HSA, either R218 or R257 is involved in the ion
pairing with OTA. These two amino acids sit across the
binding cavity from one other in site I.},
Key = {fds232056}
}
@article{fds348952,
Author = {Tong, J and Zhang, P and Zhang, L and Zhang, D and Beratan, DN and Song, H and Wang, Y and Li, T},
Title = {A Robust Bioderived Wavelength-Specific Photosensor Based on
BLUF Proteins.},
Journal = {Sensors and actuators. B, Chemical},
Volume = {310},
Pages = {127838},
Year = {2020},
Month = {May},
url = {http://dx.doi.org/10.1016/j.snb.2020.127838},
Abstract = {Photosensitive proteins are naturally evolved photosensors
that often respond to light signals of specific wavelengths.
However, their poor stability under ambient conditions
hinders their applications in non-biological settings. In
this proof-of-principle study, we grafted the blue light
using flavin (BLUF) protein reconstructed with flavin
adenine dinucleotide (FAD) or roseoflavin (RoF) onto
pristine graphene, and achieved selective sensitivity at 450
nm or 500 nm, respectively. We improved the thermal and
operational stability substantially via structure-guided
cross-linking, achieving 6-month stability under ambient
condition and normal operation at temperatures up to 200
°C. Furthermore, the device exhibited rare negative
photoconductivity behavior. The origins of this negative
photoconductivity behavior were elucidated via a combination
of experimental and theoretical analysis. In the
photoelectric conversion studies, holes from photoexcited
flavin migrated to graphene and recombined with electrons.
The device allows facile modulation and detection of charge
transfer, and provides a versatile platform for future
studies of photoinduced charge transfer in biosensors as
well as the development of stable wavelength-selective
biophotosensors.},
Doi = {10.1016/j.snb.2020.127838},
Key = {fds348952}
}
@article{fds340054,
Author = {Teo, RD and Smithwick, ER and Migliore, A and Beratan,
DN},
Title = {A single AT-GC exchange can modulate charge transfer-induced
p53-DNA dissociation.},
Journal = {Chemical communications (Cambridge, England)},
Volume = {55},
Number = {2},
Pages = {206-209},
Year = {2018},
Month = {December},
url = {http://dx.doi.org/10.1039/c8cc09048c},
Abstract = {Using molecular dynamics simulations and electronic
structure theory, we shed light on the charge dynamics that
causes the differential interaction of tumor suppressor
protein p53 with the p21 and Gadd45 genes in response to
oxidative stress. We show that the sequence dependence of
this selectivity results from competing charge transfer to
the protein and through the DNA, with implications on the
use of genome editing tools to influence the p53 regulatory
function.},
Doi = {10.1039/c8cc09048c},
Key = {fds340054}
}
@misc{fds370680,
Author = {Zusman, LD and Beratan, DN},
Title = {A three-state model for two-electron transfer
reactions.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {215},
Pages = {U235-U235},
Year = {1998},
Key = {fds370680}
}
@article{fds232018,
Author = {Prytkova, TR and Kurnikov, IV and Beratan, DN},
Title = {Ab initio based calculations of electron-transfer rates in
metalloproteins.},
Journal = {The journal of physical chemistry. B},
Volume = {109},
Number = {4},
Pages = {1618-1625},
Year = {2005},
Month = {February},
ISSN = {1520-6106},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16851133},
Abstract = {A long-standing challenge in electron-transfer theory is to
compute accurate rates of long-distance reactions in
proteins. We describe an ab initio Hartree-Fock approach to
compute electronic-coupling interactions and
electron-transfer rates in proteins that allows the
favorable comparison with experiment. The method includes
the following key features; each is essential for reliable
rate computations: (1) summing contributions over multiple
tunneling pathways, (2) averaging couplings over thermally
accessible protein conformations, (3) describing donor and
acceptor electronic structure explicitly, including
solvation effects, and averaging coupling over multiple
energy-level crossings of the nearly degenerate
donor-acceptor ligand-field states, and (4) eliminating
basis set artifacts associated with diffuse basis functions.
The strong dependence of coupling on donor-acceptor distance
and on pathway interferences causes large variations of the
computed electron-coupling values with protein geometry, and
the strongest coupled conformers dominate the
electron-transfer rate. As such, averaging over thermally
accessible conformers of the protein and of the redox
cofactors is essential. This approach was tested on six
ruthenium-modified azurin derivatives using the high
temperature nonadiabatic rate expression and compared with
simpler pathways, average barrier, and semiempirical INDO
models. Results of ab initio Hartree-Fock calculations with
a split-valence basis set are in good agreement with the
experimental rates. Predicted rates in the longer-distance
derivatives are underestimated by 3-8-fold. This analysis
indicates that the key ingredients needed for quantitatively
reliable protein electron-transfer rate calculations are
accessible.},
Doi = {10.1021/jp0457491},
Key = {fds232018}
}
@article{fds231870,
Author = {Kurnikov, IV and Beratan, DN},
Title = {Ab initio based effective Hamiltonians for long-range
electron transfer: Hartree-Fock analysis},
Journal = {Journal of Chemical Physics},
Volume = {105},
Number = {21},
Pages = {9561-9573},
Publisher = {AIP Publishing},
Year = {1996},
Month = {January},
ISSN = {0021-9606},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000105000021009561000001&idtype=cvips},
Abstract = {An ab initio electronic structure method is developed to
describe electron transfer in large systems. The method is
based on a molecular fragment effective Hamiltonian
approach. The strategy pieces together results of ab initio
quantum chemistry calculations on overlapping molecular
segments in order to build an effective Hamiltonian that
describes the long-range electronic interactions. This is
accomplished by constructing fragment effective Hamiltonians
that properly describe the electronic propagation
characteristics of each fragment (computed at the ab initio
Hartree-Fock level in an appropriate basis set). The
fragment effective Hamiltonian is projected onto the valence
orbital space of each fragment, and a relatively
well-localized set of effective interactions is obtained.
Combining these projected fragment Hamiltonians allows the
construction of a valence effective Hamiltonian for the
entire system. We find that the fragment Hamiltonian
matrices constructed in this way are transferable between
donor-acceptor systems with homologous electron-transfer
bridges. The overall strategy of fragmentation and
construction of valence effective Hamiltonians could enable
ab initio quality computations of long-range tunneling
interactions in macromolecules. We demonstrate the use of
the method in a series of electron-transfer model systems of
modest size. © 1996 American Institute of
Physics.},
Doi = {10.1063/1.472788},
Key = {fds231870}
}
@article{fds232031,
Author = {Priyadarshy, S and Therien, MJ and Beratan, DN},
Title = {Acetylenyl-linked, porphyrin-bridged, donor-acceptor
molecules: A theoretical analysis of the molecular first
hyperpolarizability in highly conjugated push-pull
chromophore structures},
Journal = {Journal of the American Chemical Society},
Volume = {118},
Number = {6},
Pages = {1504-1510},
Publisher = {American Chemical Society (ACS)},
Year = {1996},
Month = {February},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1996/118/i06/pdf/ja952690q.pdf},
Abstract = {We described the theoretical basis for the exceptionally
large molecular first hyperpolarizabilities inherent to
(5,15-diethynyl)porphinato)metal-bridged donor-acceptor
(D-A) molecules. β values relevant for hyper-Rayleigh
experiments are calculated at 1.064 and 0.830 μm for a
complex with such a structure, [5-((4'-dimethylamino)phenyl)ethynyl)-15-((4''-nitrophenyl)ethynyl)-10
,20-diphenylporphinato]zinc(II), and are 472 x 10-30 and
8152 x 10-30 cm5/esu, respectively. The values are 1 order
of magnitude larger than that calculated for any other
porphyrin bridged donor-acceptor chromophore studied to
date. The considerably enhanced hyperpolarizability arises
from the significant excited-state electronic asymmetry
manifest in such structures (derived from the strong
bridge-mediated D-A coupling enabled by the largely
porphyrin-based excited state) and the large bridge-centered
oscillator strength in this new class of D-bridge-A
molecules. Our analysis of NLO properties (based upon
INDO/SCI calculations within the sum over states formalism)
shows a sensitivity to the degree of cumulenic character in
the ground state. Calculations on structurally related
multiporphyrin systems suggest candidate chromophores with
further enhanced optical nonlinearities.},
Doi = {10.1021/ja952690q},
Key = {fds232031}
}
@article{fds369970,
Author = {Rousseau, BJG and Migliore, A and Stanley, RJ and Beratan,
DN},
Title = {Adenine Fine-Tunes DNA Photolyase's Repair
Mechanism.},
Journal = {The journal of physical chemistry. B},
Volume = {127},
Number = {13},
Pages = {2941-2954},
Year = {2023},
Month = {April},
url = {http://dx.doi.org/10.1021/acs.jpcb.3c00566},
Abstract = {The comparative study of DNA repair by mesophilic and
extremophilic photolyases helps us understand the evolution
of these enzymes and their role in preserving life on our
changing planet. The mechanism of repair of cyclobutane
pyrimidine dimer lesions in DNA by electron transfer from
the flavin adenine dinucleotide cofactor is the subject of
intense interest. The role of adenine in mediating this
process remains unresolved. Using microsecond molecular
dynamics simulations, we find that adenine mediates the
electron transfer in both mesophile and extremophile DNA
photolyases through a similar mechanism. In fact, in all
photolyases studied, the molecular conformations with the
largest electronic couplings between the enzyme cofactor and
DNA show the presence of adenine in 10-20% of the
strongest-coupling tunneling pathways between the atoms of
the electron donor and acceptor. Our theoretical analysis
finds that adenine serves the critical role of fine-tuning
rather than maximizing the donor-acceptor coupling within
the range appropriate for the repair function.},
Doi = {10.1021/acs.jpcb.3c00566},
Key = {fds369970}
}
@article{fds231975,
Author = {Onuchic, JN and Beratan, DN},
Title = {Adiabaticity criteria for outer-sphere bimolecular
electron-transfer reactions},
Journal = {Journal of Physical Chemistry},
Volume = {92},
Number = {17},
Pages = {4817-4820},
Publisher = {American Chemical Society (ACS)},
Year = {1988},
Month = {January},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1988/92/i17/pdf/j100328a001.pdf},
Abstract = {A model is presented for outer-sphere bimolecular
electron-transfer reactions which is correct in the
adiabatic, nonadiabatic, and intermediate dynamical regimes
for an overdamped solvent coordinate. From this model we
deduce the conditions for the transfer to be "adiabatic" or
"nonadiabatic". Evidence for the two regimes exists in the
experimental literature, so this work will provide guidance
for mapping out the transition between these regimes. The
time-scale separations needed to adequately describe the
process as an average over (distant dependent) unimolecular
rates are described. © 1988 American Chemical
Society.},
Doi = {10.1021/j100328a001},
Key = {fds231975}
}
@article{fds231976,
Author = {Beratan, DN and Onuchic, JN},
Title = {Adiabaticlty and nonadiabaticity in bimolecular outer-sphere
charge transfer reactions},
Journal = {The Journal of Chemical Physics},
Volume = {89},
Number = {10},
Pages = {6195-6203},
Publisher = {AIP Publishing},
Year = {1988},
Month = {January},
ISSN = {0021-9606},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000089000010006195000001&idtype=cvips},
Abstract = {A model for outer-sphere bimolecular electron transfer
reactions is presented which is based on a rate expression
correct in the adiabatic, nonadiabatic, and intermediate
dynamical regimes for an overdamped solvent coordinate. A
complete discussion of the time-scale separations needed to
define a bimolecular rate for these electron transfer
reactions is given. Bimolecular reaction rates are predicted
to display distinct solvent and electronic coupling
dependencies, defined by a few experimentally variable
parameters, which we now identify. Also, a significant
intermediate dynamical regime is predicted to exist in which
the rate is sensitive to both electronic coupling and
nuclear relaxation. Evidence that both extreme dynamical
regimes have been accessed experimentally is recalled, and
strategies are presented for fully mapping out the
dependence of rate on the electronic coupling and relaxation
times. © 1988 American Institute of Physics.},
Doi = {10.1063/1.455436},
Key = {fds231976}
}
@misc{fds370684,
Author = {KUHN, C and BERATAN, DN},
Title = {AN INVERSE STRATEGY FOR MOLECULAR DESIGN},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {210},
Pages = {120-INOR},
Year = {1995},
Key = {fds370684}
}
@article{fds231891,
Author = {De Mey and K and Clays, K and Therien, MJ and Beratan, DN and Asselberghs,
I},
Title = {Analysis of the unusual wavelength dependence of the first
hyperpolarizability of porphyrin derivatives},
Journal = {Proceedings of SPIE - The International Society for Optical
Engineering},
Volume = {7774},
Publisher = {SPIE},
Year = {2010},
Month = {October},
ISSN = {0277-786X},
url = {http://dx.doi.org/10.1117/12.859819},
Abstract = {Successfully predicting the frequency dispersion of
electronic hyperpolarizabilities is an unresolved challenge
in materials science and electronic structure theory. It has
been shown1 that the generalized Thomas-Kuhn sum rules
combined with linear absorption data and measured
hyperpolarizabilities at one or two frequencies, may be used
to predict the entire frequency-dependent electronic
hyperpolarizability spectrum. This treatment includes two-
and three-level contributions that arise from the lowest two
or three excited state manifolds, enabling us to describe
the unusual observed frequency dispersion of the dynamic
hyperpolarizability in high oscillator strength M-PZn
chromophores, where (porphinato)zinc(II) (PZn) and
metal(II)polypyridyl (M) units are connected via an ethyne
unit that aligns the high oscillator strength transition
dipoles of these components in a head-to-tail arrangement.
Importantly, this approach provides a quantitative scheme to
use linear optical absorption spectra and very few
individual hyperpolarizability values to predict the entire
frequency-dependent nonlinear optical response. In addition
we provide here experimental dynamic hyperpolarizability
values determined by hyper-Rayleigh scattering that
underscore the validity of our approach. © 2010
SPIE.},
Doi = {10.1117/12.859819},
Key = {fds231891}
}
@misc{fds22251,
Author = {J.N. Onuchic and D.N. Beratan},
Title = {Appendix A: Electron transfer rate calculations},
Pages = {273-283},
Booktitle = {Protein Electron Transfer},
Publisher = {bios Scientific Publishers, Oxford},
Editor = {D.S. Bendall},
Year = {1996},
Key = {fds22251}
}
@article{fds232050,
Author = {Marder, SR and Beratan, DN and Cheng, LT},
Title = {Approaches for optimizing the first electronic
hyperpolarizability of conjugated organic
molecules.},
Journal = {Science (New York, N.Y.)},
Volume = {252},
Number = {5002},
Pages = {103-106},
Year = {1991},
Month = {April},
ISSN = {0036-8075},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17739081},
Abstract = {A two-state, four-orbital, independent electron analysis of
the first optical molecular hyperpolarizability, beta, leads
to the prediction that |beta| maximizes at a combination of
donor and acceptor strengths for a given conjugated bridge.
Molecular design strategies that focus on the energetic
manipulations of the bridge states are proposed for the
optimization of beta. The limitations of molecular classes
based on common bridge structures are highlighted and more
promising candidates are described. Experimental results
supporting the validity of this approach are
presented.},
Doi = {10.1126/science.252.5002.103},
Key = {fds232050}
}
@article{fds343473,
Author = {Ru, X and Zhang, P and Beratan, DN},
Title = {Assessing Possible Mechanisms of Micrometer-Scale Electron
Transfer in Heme-Free Geobacter sulfurreducens
Pili.},
Journal = {The journal of physical chemistry. B},
Volume = {123},
Number = {24},
Pages = {5035-5047},
Year = {2019},
Month = {June},
url = {http://dx.doi.org/10.1021/acs.jpcb.9b01086},
Abstract = {The electrically conductive pili of Geobacter sulfurreducens
are of both fundamental and practical interest. They
facilitate extracellular and interspecies electron transfer
(ET) and also provide an electrical interface between living
and nonliving systems. We examine the possible mechanisms of
G. sulfurreducens electron transfer in regimes ranging from
incoherent to coherent transport. For plausible ET
parameters, electron transfer in G. sulfurreducens bacterial
nanowires mediated only by the protein is predicted to be
dominated by incoherent hopping between phenylalanine (Phe)
and tyrosine (Tyr) residues that are 3 to 4 Å apart, where
Phe residues in the hopping pathways may create delocalized
"islands." This mechanism could be accessible in the
presence of strong oxidants that are capable of oxidizing
Phe and Tyr residues. We also examine the physical
requirements needed to sustain biological respiration via
nanowires. We find that the hopping regimes with ET rates on
the order of 10<sup>8</sup> s<sup>-1</sup> between Phe
islands and Tyr residues, and conductivities on the order of
mS/cm, can support ET fluxes that are compatible with
cellular respiration rates, although sustaining this
delocalization in the heterogeneous protein environment may
be challenging. Computed values of fully coherent electron
fluxes through the pili are orders of magnitude too low to
support microbial respiration. We suggest experimental
probes of the transport mechanism based on mutant studies to
examine the roles of aromatic amino acids and yet to be
identified redox cofactors.},
Doi = {10.1021/acs.jpcb.9b01086},
Key = {fds343473}
}
@article{fds232013,
Author = {Zuber, G and Goldsmith, M-R and Beratan, DN and Wipf,
P},
Title = {Assignment of the absolute configuration of [n]-ladderanes
by TD-DFT optical rotation calculations.},
Journal = {Chirality},
Volume = {17},
Number = {8},
Pages = {507-510},
Year = {2005},
Month = {October},
ISSN = {0899-0042},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16121333},
Abstract = {In this study, we report theoretical specific rotation
values for a series of cis-/trans-alkylated-[5]-ladderanes
and cis-/trans-methylated-[n]-ladderanes. Using
time-dependent density functional response theory optical
rotation calculations, we can assign (+) and (-) optical
rotation signs to trans-(S)-alkyl-[5]-ladderane and
trans-(R)-alkyl-[5]-ladderane configurations, respectively.
In order to qualitatively validate our absolute
configuration predictions, we computed optical rotation
values at three different levels of theory--B3LYP, RI-BP86,
and Hartree-Fock--using the aug-cc-pVDZ basis set. We
observe a novel rung-parity-controlled oscillatory optical
rotatory phenomenon in our computations, which, to the best
of our knowledge, has never been reported or observed
before. Furthermore, this preliminary analysis of optical
rotation properties in this class of compounds should
facilitate the correct absolute stereochemical assignment of
natural and synthetic ladderanes, such as the trans-isomer
of pentacyclic C(20)-fatty acid methyl ester
(pentacycloanammoxic methyl ester), without the need for
derivatization, in particular for cases where NMR or X-ray
crystal structures are not readily available.},
Doi = {10.1002/chir.20190},
Key = {fds232013}
}
@article{fds232001,
Author = {Kondru, RK and Wipf, P and Beratan, DN},
Title = {Atomic contributions to the optical rotation angle as a
quantitative probe of molecular chirality.},
Journal = {Science (New York, N.Y.)},
Volume = {282},
Number = {5397},
Pages = {2247-2250},
Year = {1998},
Month = {December},
ISSN = {0036-8075},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9856945},
Abstract = {Chiral molecules are characterized by a specific rotation
angle, the angle through which plane-polarized light is
rotated on passing through an enantiomerically enriched
solution. Recent developments in methodology allow
computation of both the sign and the magnitude of these
rotation angles. However, a general strategy for assigning
the individual contributions that atoms and functional
groups make to the optical rotation angle and, more
generally, to the molecular chirality has remained elusive.
Here, a method to determine the atomic contributions to the
optical rotation angle is reported. This approach links
chemical structure with optical rotation angle and provides
a quantitative measure of molecular asymmetry propagation
from a center, axis, or plane of chirality.},
Doi = {10.1126/science.282.5397.2247},
Key = {fds232001}
}
@misc{fds370664,
Author = {Balabin, IA and Kawatsu, T and Beratan, DN},
Title = {Atomic scale simulations of sulfite oxidase structure and
function},
Journal = {BIOPHYSICAL JOURNAL},
Volume = {88},
Number = {1},
Pages = {15A-15A},
Year = {2005},
Key = {fds370664}
}
@article{fds349484,
Author = {Beratan, DN},
Title = {Autobiography of David N. Beratan.},
Journal = {The journal of physical chemistry. B},
Volume = {124},
Number = {17},
Pages = {3441-3446},
Year = {2020},
Month = {April},
url = {http://dx.doi.org/10.1021/acs.jpcb.0c02604},
Doi = {10.1021/acs.jpcb.0c02604},
Key = {fds349484}
}
@article{fds231919,
Author = {Balaeff, A and Craig, SL and Beratan, DN},
Title = {B-DNA to zip-DNA: simulating a DNA transition to a novel
structure with enhanced charge-transport
characteristics.},
Journal = {The journal of physical chemistry. A},
Volume = {115},
Number = {34},
Pages = {9377-9391},
Year = {2011},
Month = {September},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21598926},
Abstract = {The forced extension of a DNA segment is studied in a series
of steered molecular dynamics simulations, employing a broad
range of pulling forces. Throughout the entire force range,
the formation of a zipper-like (zip-) DNA structure is
observed. In that structure, first predicted by Lohikoski et
al., the bases of the DNA strands interdigitate with each
other and form a single-base aromatic stack. Similar motifs,
albeit only a few base pairs in extent, have been observed
in experimental crystal structures. Analysis of the dynamics
of structural changes in pulled DNA shows that S-form DNA,
thought to be adopted by DNA under applied force, serves as
an intermediate between B-DNA and zip-DNA. Therefore, the
phase transition plateau observed in force-extension curves
of DNA is suggested to reflect the B-DNA to zip-DNA
structural transition. Electronic structure analysis of
purine bases in zip-DNA indicates a several-fold to order of
magnitude increase in the π-π electronic coupling among
nearest-neighbor nucleobases, compared to B-DNA. We further
observe that zip-DNA does not require base pair
complementarity between DNA strands, and we predict that the
increased electronic coupling in zip-DNA will result in a
much higher rate of charge transfer through an all-purine
zip-DNA compared to B-DNA of equal length.},
Doi = {10.1021/jp110871g},
Key = {fds231919}
}
@article{fds232033,
Author = {Roitberg, AE and Holden, MJ and Mayhew, MP and Kurnikov, IV and Beratan,
DN and Vilker, VL},
Title = {Binding and Electron Transfer between Putidaredoxin and
Cytochrome P450cam. Theory and Experiments},
Journal = {Journal of the American Chemical Society},
Volume = {120},
Number = {35},
Pages = {8927-8932},
Publisher = {American Chemical Society (ACS)},
Year = {1998},
Month = {September},
ISSN = {0002-7863},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000075860100005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.1021/ja9739906},
Key = {fds232033}
}
@article{fds304358,
Author = {Perry, JL and Christensen, T and Goldsmith, MR and Toone, EJ and Beratan, DN and Simon, JD},
Title = {Binding of ochratoxin a to human serum albumin stabilized by
a protein-ligand ion pair},
Journal = {Journal of Physical Chemistry B},
Volume = {107},
Number = {31},
Pages = {7884-7888},
Publisher = {American Chemical Society (ACS)},
Year = {2003},
Month = {August},
url = {http://dx.doi.org/10.1021/jp034783x},
Abstract = {Ochratoxin A (OTA), a fungal metabolite of strains of
Penicillium and Aspergillus, binds in its dianion form to
Sudlow site I of human serum albumin (HSA) with high
affinity. In this study, isothermal calorimetry (ITC) is
used to study the binding of OTA and its O-methyl derivative
(MOA). Calculations of the equilibrium geometry of the
monoanion and dianion of OTA reveal only small structural
changes among the lowest energy conformers. The ITC data
show the binding of MOA, which lacks the phenolic proton of
OTA, is accompanied by the uptake of a proton from the
surrounding solvent. At pH 7.13, the binding of OTA is
accompanied by uptake of 0.43 ± 0.15 protons from the
solvent. At this pH, the monoanion (0.54) and dianion (0.46)
forms of OTA are both present in solution. However, the pKa
of the phenolic group of OTA decreases by more than three
units upon protein binding, and so all available OTA is
bound to the protein as the dianion. To account for the ITC
data, a model is proposed in which the proton is provided by
the phenolic moiety of OTA in the case of initial binding of
the monoanion, and a proton is taken up from the surrounding
solvent for initial binding of the dianion. The binding
constant of MOA is 2 orders of magnitude smaller than that
of OTA, indicating the ion pair between the phenoxide group
of OTA and the protonated amino acid is a major contributor
to the high binding affinity of OTA to HSA. To identify the
specific amino acid involved, the binding of OTA to bovine,
rat, and porcine serum albumins was examined. Deprotonation
of the monoanion of OTA occurred upon binding to all
species. Assuming the amino acid is conserved between
species and taking into account crystal structures of
ligands bound to site I of HSA and their ability to displace
OTA from HSA, either R218 or R257 is involved in the ion
pairing with OTA. These two amino acids sit across the
binding cavity from one other in site I.},
Doi = {10.1021/jp034783x},
Key = {fds304358}
}
@article{fds231883,
Author = {Perry, JL and Goldsmith, MR and Williams, TR and Radack, KP and Christensen, T and Gorham, J and Pasquinelli, MA and Toone, EJ and Beratan, DN and Simon, JD},
Title = {Binding of warfarin influences the acid-base equilibrium of
H242 in sudlow site I of human serum albumin.},
Journal = {Photochemistry and photobiology},
Volume = {82},
Number = {5},
Pages = {1365-1369},
Year = {2006},
Month = {September},
ISSN = {0031-8655},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16563025},
Abstract = {Sudlow Site I of human serum albumin (HSA) is located in
subdomain IIA of the protein and serves as a binding cavity
for a variety of ligands. In this study, the binding of
warfarin (W) is examined using computational techniques and
isothermal titration calorimetry (ITC). The structure of the
docked warfarin anion (W-) to Site I is similar to that
revealed by X-ray crystallography, with a calculated binding
constant of 5.8 x 10(5) M(-1). ITC experiments (pH 7.13 and
I = 0.1) carried out in three different buffers (MOPs,
phosphate and Tris) reveal binding of W- is accompanied by
uptake of 0.30+/-0.02 protons from the solvent. This
measurement suggests that the binding of W- is stabilized by
an ion-pair interaction between protonated H242 and the
phenoxide group of W-.},
Doi = {10.1562/2006-02-23-ra-811},
Key = {fds231883}
}
@article{fds231858,
Author = {Migliore, A and Polizzi, NF and Therien, MJ and Beratan,
DN},
Title = {Biochemistry and theory of proton-coupled electron
transfer.},
Journal = {Chemical reviews},
Volume = {114},
Number = {7},
Pages = {3381-3465},
Year = {2014},
Month = {April},
ISSN = {0009-2665},
url = {http://dx.doi.org/10.1021/cr4006654},
Doi = {10.1021/cr4006654},
Key = {fds231858}
}
@article{fds231955,
Author = {Skourtis, SS and Beratan, DN},
Title = {Biochemistry. Photosynthesis from the protein's
perspective.},
Journal = {Science (New York, N.Y.)},
Volume = {316},
Number = {5825},
Pages = {703-704},
Year = {2007},
Month = {May},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17478711},
Doi = {10.1126/science.1142330},
Key = {fds231955}
}
@article{fds231856,
Author = {Zhang, Y and Liu, C and Balaeff, A and Skourtis, SS and Beratan,
DN},
Title = {Biological charge transfer via flickering
resonance.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {111},
Number = {28},
Pages = {10049-10054},
Year = {2014},
Month = {July},
ISSN = {0027-8424},
url = {http://dx.doi.org/10.1073/pnas.1316519111},
Abstract = {Biological electron-transfer (ET) reactions are typically
described in the framework of coherent two-state electron
tunneling or multistep hopping. However, these ET reactions
may involve multiple redox cofactors in van der Waals
contact with each other and with vibronic broadenings on the
same scale as the energy gaps among the species. In this
regime, fluctuations of the molecular structures and of the
medium can produce transient energy level matching among
multiple electronic states. This transient degeneracy, or
flickering electronic resonance among states, is found to
support coherent (ballistic) charge transfer. Importantly,
ET rates arising from a flickering resonance (FR) mechanism
will decay exponentially with distance because the
probability of energy matching multiple states is
multiplicative. The distance dependence of FR transport thus
mimics the exponential decay that is usually associated with
electron tunneling, although FR transport involves real
carrier population on the bridge and is not a tunneling
phenomenon. Likely candidates for FR transport are
macromolecules with ET groups in van der Waals contact: DNA,
bacterial nanowires, multiheme proteins, strongly coupled
porphyrin arrays, and proteins with closely packed
redox-active residues. The theory developed here is used to
analyze DNA charge-transfer kinetics, and we find that
charge-transfer distances up to three to four bases may be
accounted for with this mechanism. Thus, the observed rapid
(exponential) distance dependence of DNA ET rates over
distances of ≲ 15 Å does not necessarily prove a
tunneling mechanism.},
Doi = {10.1073/pnas.1316519111},
Key = {fds231856}
}
@article{fds232038,
Author = {Babini, E and Bertini, I and Borsari, M and Capozzi, F and Luchinat, C and Zhang, X and Moura, GLC and Kurnikov, IV and Beratan, DN and Ponce, A and Di Bilio and AJ and Winkler, JR and Gray, HB},
Title = {Bond-mediated electron tunneling in ruthenium-modified
high-potential iron-sulfur protein [13]},
Journal = {Journal of the American Chemical Society},
Volume = {122},
Number = {18},
Pages = {4532-4533},
Publisher = {American Chemical Society (ACS)},
Year = {2000},
Month = {May},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/2000/122/i18/pdf/ja994472t.pdf},
Doi = {10.1021/ja994472t},
Key = {fds232038}
}
@article{fds231854,
Author = {Venkatramani, R and Wierzbinski, E and Waldeck, DH and Beratan,
DN},
Title = {Breaking the simple proportionality between molecular
conductances and charge transfer rates.},
Journal = {Faraday discussions},
Volume = {174},
Pages = {57-78},
Year = {2014},
Month = {January},
ISSN = {1359-6640},
url = {http://dx.doi.org/10.1039/c4fd00106k},
Abstract = {A theoretical framework is presented to describe and to
understand the observed relationship between molecular
conductances and charge transfer rates across molecular
bridges as a function of length, structure, and charge
transfer mechanism. The approach uses a reduced density
matrix formulation with a phenomenological treatment of
system-bath couplings to describe charge transfer kinetics
and a Green's function based Landauer-Buttiker method to
describe steady-state currents. Application of the framework
is independent of the transport regime and includes
bath-induced decoherence effects. This model shows that the
relationship between molecular conductances and charge
transfer rates follows a power-law. The nonlinear
rate-conductance relationship is shown to arise from
differences in the charge transport barrier heights and from
differences in environmental decoherence rates for the two
experiments. This model explains otherwise puzzling
correlations between molecular conductances and
electrochemical kinetics.},
Doi = {10.1039/c4fd00106k},
Key = {fds231854}
}
@article{fds231989,
Author = {Priyadarshy, S and Skourtis, SS and Risser, SM and Beratan,
DN},
Title = {Bridge-mediated electronic interactions: Differences between
Hamiltonian and Green function partitioning in a
non-orthogonal basis},
Journal = {Journal of Chemical Physics},
Volume = {104},
Number = {23},
Pages = {9473-9481},
Publisher = {AIP Publishing},
Year = {1996},
Month = {June},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000104000023009473000001&idtype=cvips},
Abstract = {An analysis of the partitioning (projection) technique is
given with emphasis on non-orthogonal basis sets. The
general expression for the effective Hamiltonian obtained
via Löwdin partitioning of the Schrödinger equation is
discussed in the context of semi-empirical theories and
electron transfer matrix elements. Numerous pitfalls in
calculations of matrix elements are pointed out. More
importantly, it is shown that contrary to the case of an
orthogonal basis, for a non-orthogonal basis Löwdin
partitioning of the Schrödinger equation and partitioning
of the Green function equation are not equivalent. The
latter method provides a more general prescription for
deriving effective Hamiltonians. Such Hamiltonians reproduce
the full propagation in the partitioned subspace. © 1996
American Institute of Physics.},
Doi = {10.1063/1.471690},
Key = {fds231989}
}
@article{fds232025,
Author = {Beratan, DN and Hopfield, JJ},
Title = {Calculation of Electron Tunneling Matrix Elements in Rigid
Systems: Mixed-Valence Dithiaspirocyclobutane
Molecules},
Journal = {Journal of the American Chemical Society},
Volume = {106},
Number = {6},
Pages = {1584-1594},
Publisher = {American Chemical Society (ACS)},
Year = {1984},
Month = {March},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1984/106/i06/pdf/ja00318a008.pdf},
Abstract = {A semiempirical model is presented which predicts
photoassisted electron-transfer rate dependence on distance
for redox groups connected by rigid polymeric linkers. The
model approximately reproduces the observed decay of the
optical tunneling matrix element with distance found for the
rigid ruthenium dithiaspiro mixed-valence complexes of
Stein, Lewis, Seitz, and Taube.1-3 The method calculates the
through-bond propagation of the wave function tail, by a
method which emphasizes obtaining the correct distance
dependence of the tunneling matrix element for these weakly
interacting donor-acceptor complexes. The method also allows
prediction of the magnitude of the matrix element, the
importance of hole or electron tunneling in the transport
process, the effect of donor and acceptor redox potential on
the matrix element, and the thermal tunneling matrix element
for these and other compounds. © 1984, American Chemical
Society. All rights reserved.},
Doi = {10.1021/ja00318a008},
Key = {fds232025}
}
@misc{fds22250,
Author = {D.N. Beratan and J.N. Onuchic},
Title = {Chapter 2: The protein bridge between redox
centers},
Pages = {23-42},
Booktitle = {Protein Electron Transfer},
Publisher = {BIOS Scientific Publishers, Oxford},
Editor = {D.S. Bendall},
Year = {1996},
Key = {fds22250}
}
@article{fds231888,
Author = {Mukhopadhyay, P and Zuber, G and Beratan, DN},
Title = {Characterizing aqueous solution conformations of a peptide
backbone with theoretical analysis of the Raman optical
activity spectra},
Journal = {Biophys. J.},
Volume = {95},
Number = {95},
Pages = {5574-5586},
Year = {2008},
url = {http://dx.doi.org/10.1529/biophysj.108.137596},
Abstract = {Mounting spectroscopic evidence indicates that alanine
predominantly adopts extended polyproline II (PPII)
conformations in short polypeptides. Here we analyze Raman
optical activity (ROA) spectra of N-acetylalanine-N'-methylamide
(Ala dipeptide) in H2O and D2O using density functional
theory on Monte Carlo (MC) sampled geometries to examine the
propensity of Ala dipeptide to adopt compact right-handed
(alpha(R)) and left-handed (alpha(L)) helical conformations.
The computed ROA spectra based on MC-sampled alpha(R) and
PPII peptide conformations contain all the key spectral
features found in the measured spectra. However, there is no
significant similarity between the measured and computed ROA
spectra based on the alpha(L)- and beta-conformations
sampled by the MC methods. This analysis suggests that Ala
dipeptide populates the alpha(R) and PPII conformations but
no substantial population of alpha(L)- or beta-structures,
despite sampling alpha(L)- and beta-structures in our MC
simulations. Thus, ROA spectra combined with the theoretical
analysis allow us to determine the dominant populated
structures. Including explicit solute-solvent interactions
in the theoretical analysis is essential for the success of
this approach.},
Doi = {10.1529/biophysj.108.137596},
Key = {fds231888}
}
@article{fds335027,
Author = {Beratan, DN and Naaman, R and Waldeck, DH},
Title = {Charge and spin transport through nucleic
acids},
Journal = {Current Opinion in Electrochemistry},
Volume = {4},
Number = {1},
Pages = {175-181},
Publisher = {Elsevier BV},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1016/j.coelec.2017.08.017},
Abstract = {Recent developments in our understanding of charge and spin
transport through nucleic acid duplexes are discussed.
Particular emphasis is placed on recent findings that point
to the importance of nucleobase fluctuations, transient but
extended length-scale electronic coherence, and
chiral-induced spin selectivity.},
Doi = {10.1016/j.coelec.2017.08.017},
Key = {fds335027}
}
@article{fds332971,
Author = {Sha, R and Xiang, L and Liu, C and Balaeff, A and Zhang, Y and Zhang, P and Li, Y and Beratan, DN and Tao, N and Seeman, NC},
Title = {Charge splitters and charge transport junctions based on
guanine quadruplexes.},
Journal = {Nature nanotechnology},
Volume = {13},
Number = {4},
Pages = {316-321},
Year = {2018},
Month = {April},
url = {http://dx.doi.org/10.1038/s41565-018-0070-x},
Abstract = {Self-assembling circuit elements, such as current splitters
or combiners at the molecular scale, require the design of
building blocks with three or more terminals. A promising
material for such building blocks is DNA, wherein multiple
strands can self-assemble into multi-ended junctions, and
nucleobase stacks can transport charge over long distances.
However, nucleobase stacking is often disrupted at junction
points, hindering electric charge transport between the two
terminals of the junction. Here, we show that a
guanine-quadruplex (G4) motif can be used as a connector
element for a multi-ended DNA junction. By attaching
specific terminal groups to the motif, we demonstrate that
charges can enter the structure from one terminal at one end
of a three-way G4 motif, and can exit from one of two
terminals at the other end with minimal carrier transport
attenuation. Moreover, we study four-way G4 junction
structures by performing theoretical calculations to assist
in the design and optimization of these connectors.},
Doi = {10.1038/s41565-018-0070-x},
Key = {fds332971}
}
@article{fds354754,
Author = {Bancroft, L and Zhang, J and Harvey, SM and Krzyaniak, MD and Zhang, P and Schaller, RD and Beratan, DN and Young, RM and Wasielewski,
MR},
Title = {Charge Transfer and Spin Dynamics in a Zinc Porphyrin Donor
Covalently Linked to One or Two Naphthalenediimide
Acceptors.},
Journal = {The journal of physical chemistry. A},
Volume = {125},
Number = {3},
Pages = {825-834},
Year = {2021},
Month = {January},
url = {http://dx.doi.org/10.1021/acs.jpca.0c10471},
Abstract = {Quantum coherence effects on charge transfer and spin
dynamics in a system having two degenerate electron
acceptors are studied using a zinc 5,10,15-tri(<i>n</i>-pentyl)-20-phenylporphyrin
(ZnP) electron donor covalently linked to either one or two
naphthalene-1,8:4,5-bis(dicarboximide) (NDI) electron
acceptors using an anthracene (An) spacer, ZnP-An-NDI
(<b>1</b>) and ZnP-An-NDI<sub>2</sub> (<b>2</b>),
respectively. Following photoexcitation of <b>1</b> and
<b>2</b> in toluene at 295 K, femtosecond transient
absorption spectroscopy shows that the electron transfer
(ET) rate constant for <b>2</b> is about three times larger
than that of <b>1</b>, which can be accounted for by the
statistical nature of incoherent ET as well as the electron
couplings for the charge separation reactions. In contrast,
the rate constant for charge recombination (CR) of <b>1</b>
is about 25% faster than that of <b>2</b>. Using femtosecond
transient infrared spectroscopy and theoretical analysis, we
find that the electron on NDI<sub>2</sub><sup>•-</sup> in
<b>2</b> localizes onto one of the two NDIs prior to CR,
thus precluding electronically coherent CR from
NDI<sub>2</sub><sup>•-</sup>. Conversely, CR in both
<b>1</b> and <b>2</b> is spin coherent as indicated by the
observation of a resonance in the <sup>3*</sup>ZnP yield
following CR as a function of applied magnetic field, giving
spin-spin exchange interaction energies of 2<i>J</i> = 210
and 236 mT, respectively, where the line width of the
resonance for <b>2</b> is greater than <b>1</b>. These data
show that while CR is a spin-coherent process, incoherent
hopping of the electron between the two NDIs in <b>2</b>,
consistent with the lack of delocalization noted above,
results in greater spin decoherence in <b>2</b> relative to
<b>1</b>.},
Doi = {10.1021/acs.jpca.0c10471},
Key = {fds354754}
}
@article{fds340999,
Author = {Teo, RD and Rousseau, BJG and Smithwick, ER and Di Felice and R and Beratan, DN and Migliore, A},
Title = {Charge Transfer between [4Fe4S] Proteins and DNA Is
Unidirectional: Implications for Biomolecular
Signaling.},
Journal = {Chem},
Volume = {5},
Number = {1},
Pages = {122-137},
Year = {2019},
Month = {January},
url = {http://dx.doi.org/10.1016/j.chempr.2018.09.026},
Abstract = {Recent experiments suggest that DNA-mediated charge
transport might enable signaling between the [4Fe4S]
clusters in the C-terminal domains of human DNA primase and
polymerase α, as well as the signaling between other
replication and repair high-potential [4Fe4S] proteins. Our
theoretical study demonstrates that the redox signaling
cannot be accomplished exclusively by DNA-mediated charge
transport because part of the charge transfer chain has an
unfavorable free energy profile. We show that hole or excess
electron transfer between a [4Fe4S] cluster and a nucleic
acid duplex through a protein medium can occur within
microseconds in one direction, while it is kinetically
hindered in the opposite direction. We present a set of
signaling mechanisms that may occur with the assistance of
oxidants or reductants, using the allowed charge transfer
processes. These mechanisms would enable the coordinated
action of [4Fe4S] proteins on DNA, engaging the [4Fe4S]
oxidation state dependence of the protein-DNA binding
affinity.},
Doi = {10.1016/j.chempr.2018.09.026},
Key = {fds340999}
}
@article{fds231853,
Author = {Beratan, DN and Liu, C and Migliore, A and Polizzi, NF and Skourtis, SS and Zhang, P and Zhang, Y},
Title = {Charge transfer in dynamical biosystems, or the treachery of
(static) images.},
Journal = {Accounts of chemical research},
Volume = {48},
Number = {2},
Pages = {474-481},
Year = {2015},
Month = {February},
ISSN = {0001-4842},
url = {http://dx.doi.org/10.1021/ar500271d},
Abstract = {CONSPECTUS: The image is not the thing. Just as a pipe
rendered in an oil painting cannot be smoked, quantum
mechanical coupling pathways rendered on LCDs do not convey
electrons. The aim of this Account is to examine some of our
recent discoveries regarding biological electron transfer
(ET) and transport mechanisms that emerge when one moves
beyond treacherous static views to dynamical frameworks.
Studies over the last two decades introduced both atomistic
detail and macromolecule dynamics to the description of
biological ET. The first model to move beyond the
structureless square-barrier tunneling description is the
Pathway model, which predicts how protein secondary motifs
and folding-induced through-bond and through-space tunneling
gaps influence kinetics. Explicit electronic structure
theory is applied routinely now to elucidate ET mechanisms,
to capture pathway interferences, and to treat redox
cofactor electronic structure effects. Importantly,
structural sampling of proteins provides an understanding of
how dynamics may change the mechanisms of biological ET, as
ET rates are exponentially sensitive to structure. Does
protein motion average out tunneling pathways? Do
conformational fluctuations gate biological ET? Are
transient multistate resonances produced by energy gap
fluctuations? These questions are becoming accessible as the
static view of biological ET recedes and dynamical
viewpoints take center stage. This Account introduces ET
reactions at the core of bioenergetics, summarizes our
team's progress toward arriving at an atomistic-level
description, examines how thermal fluctuations influence ET,
presents metrics that characterize dynamical effects on ET,
and discusses applications in very long (micrometer scale)
bacterial nanowires. The persistence of structural effects
on the ET rates in the face of thermal fluctuations is
considered. Finally, the flickering resonance (FR) view of
charge transfer is presented to examine how fluctuations
control low-barrier transport among multiple groups in van
der Waals contact. FR produces exponential distance
dependence in the absence of tunneling; the exponential
character emerges from the probability of matching multiple
vibronically broadened electronic energies within a
tolerance defined by the rms coupling among interacting
groups. FR thus produces band like coherent transport on the
nanometer length scale, enabled by conformational
fluctuations. Taken as a whole, the emerging context for ET
in dynamical biomolecules provides a robust framework to
design and interpret the inner workings of bioenergetics
from the molecular to the cellular scale and beyond, with
applications in biomedicine, biocatalysis, and energy
science.},
Doi = {10.1021/ar500271d},
Key = {fds231853}
}
@article{fds232015,
Author = {Lee, J and Balabin, IA and Beratan, DN and Lee, JG and Yates,
JT},
Title = {Charge transfer through chemisorbed organic molecules -
Neutralization of ionization processes at local sites in the
molecule},
Journal = {Chemical Physics Letters},
Volume = {412},
Number = {1-3},
Pages = {171-175},
Publisher = {Elsevier BV},
Year = {2005},
Month = {August},
url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6TFN-4GNKRVG-1-N&_cdi=5231&_user=38557&_orig=browse&_coverDate=08%2F25%2F2005&_sk=995879998&view=c&wchp=dGLzVlz-zSkzk&md5=7ddc456a040d0561556a211cb6c30a39&ie=/sdarticle.pdf},
Abstract = {The charge transfer through chemisorbed molecules has been
studied by using normally oriented pyridine and benzoate
molecules, chemisorbed on the Cu(1 1 0) surface. They yield
H+ ions from the outer three C-H bond locations when ionized
by electron impact. The local yield of these H+ ions allows
the determination of the rate of electron transport through
the molecule from the molecular contact point to the
ionization position, causing ion neutralization. A
superexchange (molecule-assisted tunneling) electron
transfer process is found to control the electron-transfer
event. © 2005 Elsevier B.V. All rights reserved.},
Doi = {10.1016/j.cplett.2005.05.101},
Key = {fds232015}
}
@article{fds231849,
Author = {Young, RM and Singh, APN and Thazhathveetil, AK and Cho, VY and Zhang,
Y and Renaud, N and Grozema, FC and Beratan, DN and Ratner, MA and Schatz,
GC and Berlin, YA and Lewis, FD and Wasielewski, MR},
Title = {Charge Transport across DNA-Based Three-Way
Junctions.},
Journal = {Journal of the American Chemical Society},
Volume = {137},
Number = {15},
Pages = {5113-5122},
Year = {2015},
Month = {April},
ISSN = {0002-7863},
url = {http://dx.doi.org/10.1021/jacs.5b00931},
Abstract = {DNA-based molecular electronics will require charges to be
transported from one site within a 2D or 3D architecture to
another. While this has been shown previously in linear,
π-stacked DNA sequences, the dynamics and efficiency of
charge transport across DNA three-way junction (3WJ) have
yet to be determined. Here, we present an investigation of
hole transport and trapping across a DNA-based three-way
junction systems by a combination of femtosecond transient
absorption spectroscopy and molecular dynamics simulations.
Hole transport across the junction is proposed to be gated
by conformational fluctuations in the ground state which
bring the transiently populated hole carrier nucleobases
into better aligned geometries on the nanosecond time scale,
thus modulating the π-π electronic coupling along the base
pair sequence.},
Doi = {10.1021/jacs.5b00931},
Key = {fds231849}
}
@article{fds232009,
Author = {Kondru, RK and Beratan, DN and Friestad, GK and Smith, AB and Wipf,
P},
Title = {Chiral action at a distance: remote substituent effects on
the optical activity of calyculins A and
B.},
Journal = {Organic letters},
Volume = {2},
Number = {11},
Pages = {1509-1512},
Year = {2000},
Month = {June},
ISSN = {1523-7060},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10841466},
Abstract = {[structure--see text] Calyculins A and B differ only by the
(E)- vs (Z)-configuration at C(2). Yet, they show a large
difference in optical rotations. We demonstrate a new
strategy that provides a physical analysis of this
long-range chiro-optical effect by Boltzmann-averaged atomic
contribution mapping. The polarizability characteristics of
the CN substituent rather than the perturbation of the
stereogenic centers or the introduction of asymmetry into
the polyene chain give rise to the remarkable difference in
rotation angles.},
Doi = {10.1021/ol005634p},
Key = {fds232009}
}
@article{fds231920,
Author = {Ben-Moshe, V and Beratan, DN and Nitzan, A and Skourtis,
SS},
Title = {Chiral control of current transfer in molecules.},
Journal = {Topics in current chemistry},
Volume = {298},
Number = {298},
Pages = {259-278},
Year = {2011},
Month = {January},
ISSN = {0340-1022},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21321805},
Abstract = {Electron transmission through chiral molecules induced by
circularly polarized light can be very different for mirror
image structures. This behavior is described in terms of
current transfer: the transfer of both charge and momentum.
We review recent theoretical developments on the theory of
current transfer and discuss related experimental studies of
electron transmission through chiral molecular structures
adsorbed on surfaces.},
Doi = {10.1007/128_2010_101},
Key = {fds231920}
}
@article{fds231946,
Author = {Skourtis, SS and Beratan, DN and Naaman, R and Nitzan, A and Waldeck,
DH},
Title = {Chiral control of electron transmission through
molecules.},
Journal = {Physical review letters},
Volume = {101},
Number = {23},
Pages = {238103},
Year = {2008},
Month = {December},
ISSN = {0031-9007},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19113598},
Abstract = {Electron transmission through chiral molecules induced by
circularly polarized light can be very different for
mirror-image structures, a peculiar fact given that the
electronic energy spectra of the systems are identical. We
propose that this asymmetry--as large as 10% for resonant
transport--arises from different dynamical responses of the
mirrored structures to coherent excitation. This behavior is
described in the context of a general novel phenomenon of
current transfer (transfer of charge with its momentum
information) and accounts for the observed asymmetry and its
dependence on structure.},
Doi = {10.1103/physrevlett.101.238103},
Key = {fds231946}
}
@article{fds327163,
Author = {Bloom, BP and Graff, BM and Ghosh, S and Beratan, DN and Waldeck,
DH},
Title = {Chirality Control of Electron Transfer in Quantum Dot
Assemblies.},
Journal = {Journal of the American Chemical Society},
Volume = {139},
Number = {26},
Pages = {9038-9043},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1021/jacs.7b04639},
Abstract = {Electron spin and molecular chirality are emerging as
factors that can be used effectively to direct charge flow
at the molecular scale. We report order of magnitude effects
of molecular chirality on electron-transfer rates between
quantum dots (QDs) in chiral QD assemblies. Indeed, both the
circular polarization of the light that excites the electron
donor and the imprinted chirality of the acceptor QDs affect
the dot-to-dot electron-transfer kinetics. We define a
polarization for the electron-transfer rate constant and
show that it correlates with the strength of the acceptor QD
circular dichroism (CD) spectrum. These findings imply that
the CD strength of the QD exciton transition(s) may be used
as a predictor for the spin-dependent electron transfer,
indicating that chiral imprinting of the dots may lie at the
origin of this phenomenon.},
Doi = {10.1021/jacs.7b04639},
Key = {fds327163}
}
@article{fds231936,
Author = {Balabin, IA and Yang, W and Beratan, DN},
Title = {Coarse-grained modeling of allosteric regulation in protein
receptors.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {106},
Number = {34},
Pages = {14253-14258},
Year = {2009},
Month = {August},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19706508},
Abstract = {Allosteric regulation provides highly specific ligand
recognition and signaling by transmembrane protein
receptors. Unlike functions of protein molecular machines
that rely on large-scale conformational transitions, signal
transduction in receptors appears to be mediated by more
subtle structural motions that are difficult to identify. We
describe a theoretical model for allosteric regulation in
receptors that addresses a fundamental riddle of signaling:
What are the structural origins of the receptor agonism
(specific signaling response to ligand binding)? The model
suggests that different signaling pathways in bovine
rhodopsin or human beta(2)-adrenergic receptor can be
mediated by specific structural motions in the receptors. We
discuss implications for understanding the receptor agonism,
particularly the recently observed "biased agonism"
(selected activation of specific signaling pathways), and
for developing rational structure-based drug-design
strategies.},
Doi = {10.1073/pnas.0901811106},
Key = {fds231936}
}
@article{fds315911,
Author = {Liu, C and Beratan, DN and Zhang, P},
Title = {Coarse-Grained Theory of Biological Charge Transfer with
Spatially and Temporally Correlated Noise.},
Journal = {The journal of physical chemistry. B},
Volume = {120},
Number = {15},
Pages = {3624-3633},
Year = {2016},
Month = {April},
ISSN = {1520-6106},
url = {http://dx.doi.org/10.1021/acs.jpcb.6b01018},
Abstract = {System-environment interactions are essential in determining
charge-transfer (CT) rates and mechanisms. We developed a
computationally accessible method, suitable to simulate CT
in flexible molecules (i.e., DNA) with hundreds of sites,
where the system-environment interactions are explicitly
treated with numerical noise modeling of time-dependent site
energies and couplings. The properties of the noise are
tunable, providing us a flexible tool to investigate the
detailed effects of correlated thermal fluctuations on CT
mechanisms. The noise is parametrizable by molecular
simulation and quantum calculation results of specific
molecular systems, giving us better molecular resolution in
simulating the system-environment interactions than sampling
fluctuations from generic spectral density functions. The
spatially correlated thermal fluctuations among different
sites are naturally built-in in our method but are not
readily incorporated using approximate spectral densities.
Our method has quantitative accuracy in systems with small
redox potential differences (<kbT) and provides qualitative
insights into systems with wide redox potential differences
(≫kbT). Specifically, we find that the temporal
correlations of site energies are critical in determining
the coherent-incoherent transition, while the role of
spatial correlations depends on the nature of the systems.
In a system with repeated bridge units of the same
chemistry, spatially correlated fluctuations enhance the
charge delocalization and charge-transfer rates; however, in
a system of units with different site energies, spatial
correlations slow the fluctuations to bring units into
degeneracy, in turn, slowing the charge-transfer rates. The
spatial and temporal correlations of condensed phase medium
fluctuations provide another source to control and tune the
kinetics and dynamics of charge-transfer
systems.},
Doi = {10.1021/acs.jpcb.6b01018},
Key = {fds315911}
}
@article{fds363347,
Author = {Shen, W and Teo, RD and Beratan, DN and Warren, JJ},
Title = {Cofactor Dynamics Couples the Protein Surface to the Heme in
Cytochrome c, Facilitating Electron
Transfer.},
Journal = {The journal of physical chemistry. B},
Volume = {126},
Number = {19},
Pages = {3522-3529},
Year = {2022},
Month = {May},
url = {http://dx.doi.org/10.1021/acs.jpcb.2c01632},
Abstract = {Electron transport through biomolecules and in biological
transport networks is of great importance to bioenergetics
and biocatalysis. More generally, it is of crucial
importance to understand how the pathways that connect
buried metallocofactors to other cofactors, and to protein
surfaces, affect the biological chemistry of
metalloproteins. In terms of electron transfer (ET), the
strongest coupling pathways usually comprise covalent and
hydrogen bonded networks, with a limited number of
through-space contacts. Herein, we set out to determine the
relative roles of hydrogen bonds involved in ET via an
established heme-to-surface tunneling pathway in cytochrome
(cyt) <i>c</i> (i.e., heme-W59-D60-E61-N62). A series of cyt
<i>c</i> variants were produced where a ruthenium
tris(diimine) photooxidant was placed at position 62 via
covalent modification of the N62C residue. Surprisingly,
variants where the H-bonding residues W59 and D60 were
replaced (i.e., W59F and D60A) showed no change in ET rate
from the ferrous heme to Ru(III). In contrast, changing the
composition of an alternative tunneling pathway (i.e.,
heme-M64-N63-C62) with the M64L substitution shows a factor
of 2 decrease in the rate of heme-to-Ru ET. This pathway
involves a through-space tunneling step between the heme and
M64 residue, and such steps are usually disfavored. To
rationalize why the heme-M64-N63-C62 is preferred, molecular
dynamics (MD) simulations and Pathways analysis were
employed. These simulations show that the change in heme-Ru
ET rates is attributed to different conformations with
compressed donor-acceptor distances, by ∼2 Å in pathway
distance, in the M64-containing protein as compared to the
M64L protein. The change in distance is correlated with
changes in the electronic coupling that are in accord with
the experimentally observed heme-Ru ET rates. Remarkably,
the M64L variation at the core of the protein translates to
changes in cofactor dynamics at the protein surface. The
surface changes identified by MD simulations include dynamic
anion-π and dipole-dipole interactions. These interactions
influence the strength of tunneling pathways and ET rates by
facilitating decreases in through-space tunneling distances
in key coupling pathways.},
Doi = {10.1021/acs.jpcb.2c01632},
Key = {fds363347}
}
@article{fds231893,
Author = {Skourtis, S and Beratan, DN and Waldeck, DH},
Title = {Coherence in electron tunneling pathways},
Journal = {Procedia Chemistry},
Volume = {3},
Number = {3},
Pages = {99-104},
Year = {2011},
url = {http://dx.doi.org/10.1016/j.proche.2011.08.016},
Abstract = {Central to the view of electron-transfer reactions is the
idea that nuclear motion generates a transition state
geometry at which the electron/hole amplitude propagates
coherently from the electron donor to the electron acceptor.
In the weakly coupled or nonadiabatic regime, the electron
amplitude tunnels through an electronic barrier between the
donor and acceptor. The structure of the barrier is
determined by the covalent and noncovalent interactions of
the bridge. Because the tunneling barrier depends on the
nuclear coordinates of the reactants (and on the surrounding
medium), the tunneling barrier is highly anisotropic, and it
is useful to identify particular routes, or pathways, along
which the transmission amplitude propagates. Moreover, when
more than one such pathway exists, and the paths give rise
to comparable transmission amplitude magnitudes, one may
expect to observe quantum interferences among pathways if
the propagation remains coherent. Given that the effective
tunneling barrier height and width are affected by the
nuclear positions, the modulation of the nuclear coordinates
will lead to a modulation of the tunneling barrier and hence
of the electron flow. For long distance electron transfer in
biological and biomimetic systems, nuclear fluctuations,
arising from flexible protein moieties and mobile water
bridges, can become quite significant. We discuss
experimental and theoretical results that explore the
quantum interferences among coupling pathways in
electron-transfer kinetics; we emphasize recent data and
theories associated with the signatures of chirality and
inelastic processes, which are manifested in the tunneling
pathway coherence (or absence of coherence).},
Doi = {10.1016/j.proche.2011.08.016},
Key = {fds231893}
}
@article{fds231940,
Author = {Keinan, S and Paquette, WD and Skoko, JJ and Beratan, DN and Yang, W and Shinde, S and Johnston, PA and Lazo, JS and Wipf,
P},
Title = {Computational design, synthesis and biological evaluation of
para-quinone-based inhibitors for redox regulation of the
dual-specificity phosphatase Cdc25B.},
Journal = {Organic & biomolecular chemistry},
Volume = {6},
Number = {18},
Pages = {3256-3263},
Year = {2008},
Month = {September},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18802630},
Abstract = {Quinoid inhibitors of Cdc25B were designed based on the
Linear Combination of Atomic Potentials (LCAP) methodology.
In contrast to a published hypothesis, the biological
activities and hydrogen peroxide generation in reducing
media of three synthetic models did not correlate with the
quinone half-wave potential, E(1/2).},
Doi = {10.1039/b806712k},
Key = {fds231940}
}
@misc{fds370668,
Author = {Liao, JL and Beratan, DN},
Title = {Computer modeling and simulation on ATP-driven large
conformational change in proteins},
Journal = {BIOPHYSICAL JOURNAL},
Volume = {86},
Number = {1},
Pages = {89A-89A},
Year = {2004},
Key = {fds370668}
}
@article{fds350998,
Author = {Xiang, L and Zhang, P and Liu, C and He, X and Li, HB and Li, Y and Wang, Z and Hihath, J and Kim, SH and Beratan, DN and Tao, N},
Title = {Conductance and configuration of molecular gold-water-gold
junctions under electric fields.},
Journal = {Matter},
Volume = {3},
Number = {1},
Pages = {166-179},
Year = {2020},
Month = {July},
url = {http://dx.doi.org/10.1016/j.matt.2020.03.023},
Abstract = {Water molecules can mediate charge transfer in biological
and chemical reactions by forming electronic coupling
pathways. Understanding the mechanism requires a
molecular-level electrical characterization of water. Here,
we describe the measurement of single water molecular
conductance at room temperature, characterize the structure
of water molecules using infrared spectroscopy, and perform
theoretical studies to assist in the interpretation of the
experimental data. The study reveals two distinct states of
water, corresponding to a parallel and perpendicular
orientation of the molecules. Water molecules switch from
parallel to perpendicular orientations on applying an
electric field, producing switching from high to low
conductance states, thus enabling the determination of
single water molecular dipole moments. The work further
shows that water-water interactions affect the atomic scale
configuration and conductance of water molecules. These
findings demonstrate the importance of the discrete nature
of water molecules in electron transfer and set limits on
water-mediated electron transfer rates.},
Doi = {10.1016/j.matt.2020.03.023},
Key = {fds350998}
}
@misc{fds370666,
Author = {Balabin, L and Kawatsu, T and Beratan, DN},
Title = {Conformational control of electron tunneling in sulfite
oxidase},
Journal = {BIOPHYSICAL JOURNAL},
Volume = {86},
Number = {1},
Pages = {473A-473A},
Year = {2004},
Key = {fds370666}
}
@article{fds231960,
Author = {Kawatsu, T and Beratan, DN and Kakitani, T},
Title = {Conformationally averaged score functions for electronic
propagation in proteins.},
Journal = {The journal of physical chemistry. B},
Volume = {110},
Number = {11},
Pages = {5747-5757},
Year = {2006},
Month = {March},
ISSN = {1520-6106},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16539520},
Abstract = {We explore the influence of conformational dynamics on
protein-mediated electron donor-acceptor interactions. We
introduce a thermally averaged score function to
characterize electronic propagation from redox cofactors
into the protein and solvent. The score function is explored
for myoglobin at the extended-Hückel level, and the results
are compared with those of simpler models. The
conformationally averaged quantum results are consistent
with the empirical analysis of the Pathways model. Notably,
subtle effects of quantum interference among multiple
coupling pathways that arise in static structures are
largely averaged out when protein thermal motion is
included. Propagation through bulk water near the
single-protein interface decays rapidly with
distance.},
Doi = {10.1021/jp052194g},
Key = {fds231960}
}
@article{fds231844,
Author = {Zhang, Y and Young, RM and Thazhathveetil, AK and Singh, APN and Liu, C and Berlin, YA and Grozema, FC and Lewis, FD and Ratner, MA and Renaud, N and Siriwong, K and Voityuk, AA and Wasielewski, MR and Beratan,
DN},
Title = {Conformationally Gated Charge Transfer in DNA Three-Way
Junctions.},
Journal = {The journal of physical chemistry letters},
Volume = {6},
Number = {13},
Pages = {2434-2438},
Year = {2015},
Month = {July},
url = {http://dx.doi.org/10.1021/acs.jpclett.5b00863},
Abstract = {Molecular structures that direct charge transport in two or
three dimensions possess some of the essential functionality
of electrical switches and gates. We use theory, modeling,
and simulation to explore the conformational dynamics of DNA
three-way junctions (TWJs) that may control the flow of
charge through these structures. Molecular dynamics
simulations and quantum calculations indicate that DNA TWJs
undergo dynamic interconversion among "well stacked"
conformations on the time scale of nanoseconds, a feature
that makes the junctions very different from linear DNA
duplexes. The studies further indicate that this
conformational gating would control charge flow through
these TWJs, distinguishing them from conventional (larger
size scale) gated devices. Simulations also find that
structures with polyethylene glycol linking groups
("extenders") lock conformations that favor CT for 25 ns or
more. The simulations explain the kinetics observed
experimentally in TWJs and rationalize their transport
properties compared with double-stranded
DNA.},
Doi = {10.1021/acs.jpclett.5b00863},
Key = {fds231844}
}
@article{fds231957,
Author = {Mukhopadhyay, P and Zuber, G and Wipf, P and Beratan,
DN},
Title = {Contribution of a solute's chiral solvent imprint to optical
rotation.},
Journal = {Angewandte Chemie (International ed. in English)},
Volume = {46},
Number = {34},
Pages = {6450-6452},
Year = {2007},
Month = {January},
ISSN = {1433-7851},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17645276},
Doi = {10.1002/anie.200702273},
Key = {fds231957}
}
@article{fds338026,
Author = {Seefeldt, LC and Peters, JW and Beratan, DN and Bothner, B and Minteer,
SD and Raugei, S and Hoffman, BM},
Title = {Control of electron transfer in nitrogenase.},
Journal = {Current opinion in chemical biology},
Volume = {47},
Pages = {54-59},
Year = {2018},
Month = {December},
url = {http://dx.doi.org/10.1016/j.cbpa.2018.08.011},
Abstract = {The bacterial enzyme nitrogenase achieves the reduction of
dinitrogen (N<sub>2</sub>) to ammonia (NH<sub>3</sub>)
utilizing electrons, protons, and energy from the hydrolysis
of ATP. Building on earlier foundational knowledge, recent
studies provide molecular-level details on how the energy of
ATP hydrolysis is utilized, the sequencing of multiple
electron transfer events, and the nature of energy
transduction across this large protein complex. Here, we
review the state of knowledge about energy transduction in
nitrogenase.},
Doi = {10.1016/j.cbpa.2018.08.011},
Key = {fds338026}
}
@article{fds232049,
Author = {Beratan, DN},
Title = {Controlled Electron Transfer for Molecular
Electronics},
Journal = {Molecular Crystals and Liquid Crystals Incorporating
Nonlinear Optics},
Volume = {190},
Number = {1},
Pages = {85-94},
Publisher = {Informa UK Limited},
Year = {1990},
Month = {October},
ISSN = {0140-6566},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1990EF05400010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.1080/00268949008047835},
Key = {fds232049}
}
@article{fds327360,
Author = {Liu, R and Bloom, BP and Waldeck, DH and Zhang, P and Beratan,
DN},
Title = {Controlling the Electron-Transfer Kinetics of Quantum-Dot
Assemblies},
Journal = {Journal of Physical Chemistry C},
Volume = {121},
Number = {27},
Pages = {14401-14412},
Publisher = {American Chemical Society (ACS)},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1021/acs.jpcc.7b02261},
Abstract = {Electron transfer theory is used to explore the
size-dependence of electron transfer (ET) between
dithiol-bridged quantum dots (QDs) and make predictions that
can be tested experimentally. Electronic couplings,
electronic densities of states, and reaction-free energies
are all found to be size-dependent and to influence the ET
rates. As the acceptor QD radius grows at fixed edge-to-edge
donor-acceptor distance, the reaction-free energy becomes
more negative. As a result, both electron and hole transfer
rates show a peak as a function of acceptor radius for donor
radii ranging from 9.5 to 21.5 Å however, this rate maximum
as a function of radius is weaker than that observed in
molecules, since the increasing acceptor density of states
partially compensates both the Marcus inverted effect and
the decreased electronic coupling with increasing radius.
The electronic coupling decreases as the donor radius grows
because the wave function probability density per surface
atom decreases and the acceptor density of states at the
donor's band edge energy decreases. The through-solvent and
through-bond electronic couplings have different
dependencies on QD radii, with a switch in the dominance of
the coupling mechanisms as the QD radius changes. For large
QDs, the through-solvent coupling dominates, so the
chemistry of the through-bond linkage does not strongly
influence the coupling. Finally, we discuss how the electron
and hole transfer rates can be matched by varying the QD
radii, thus providing an approach to optimize the
performance of solar cells based on type II QD
assemblies.},
Doi = {10.1021/acs.jpcc.7b02261},
Key = {fds327360}
}
@article{fds328571,
Author = {Bai, Y and Rawson, J and Roget, SA and Olivier, J-H and Lin, J and Zhang,
P and Beratan, DN and Therien, MJ},
Title = {Controlling the excited-state dynamics of low band gap,
near-infrared absorbers via proquinoidal unit
electronic structural modulation.},
Journal = {Chemical science},
Volume = {8},
Number = {9},
Pages = {5889-5901},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1039/c7sc02150j},
Abstract = {While the influence of proquinoidal character upon the
linear absorption spectrum of low optical bandgap
π-conjugated polymers and molecules is well understood, its
impact upon excited-state relaxation pathways and dynamics
remains obscure. We report the syntheses, electronic
structural properties, and excited-state dynamics of a
series of model highly conjugated near-infrared
(NIR)-absorbing chromophores based on a (porphinato)metal(ii)-proquinoidal
spacer-(porphinato)metal(ii) (<b>PM-Sp-PM</b>) structural
motif. A combination of excited-state dynamical studies and
time-dependent density functional theory calculations: (i)
points to the cardinal role that excited-state configuration
interaction (CI) plays in determining the magnitudes of
S<sub>1</sub> → S<sub>0</sub> radiative
(<i>k</i><sub>r</sub>), S<sub>1</sub> → T<sub>1</sub>
intersystem crossing (<i>k</i><sub>ISC</sub>), and
S<sub>1</sub> → S<sub>0</sub> internal conversion
(<i>k</i><sub>IC</sub>) rate constants in these
<b>PM-Sp-PM</b> chromophores, and (ii) suggests that a
primary determinant of CI magnitude derives from the
energetic alignment of the <b>PM</b> and <b>Sp</b> fragment
LUMOs (Δ<i>E</i><sub>L</sub>). These insights not only
enable steering of excited-state relaxation dynamics of high
oscillator strength NIR absorbers to realize either
substantial fluorescence or long-lived triplets
(<i>τ</i><sub>T<sub>1</sub></sub> > μs) generated at unit
quantum yield (<i>Φ</i><sub>ISC</sub> = 100%), but also
crafting of those having counter-intuitive properties: for
example, while (porphinato)platinum compounds are well known
to generate non-emissive triplet states (<i>Φ</i><sub>ISC</sub>
= 100%) upon optical excitation at ambient temperature,
diminishing the extent of excited-state CI in these systems
realizes long-wavelength absorbing heavy-metal fluorophores.
This work highlights approaches to: (i) modulate low-lying
singlet excited-state lifetime over the picosecond-to-nanosecond
time domain, (ii) achieve NIR fluorescence with quantum
yields up to 25%, (iii) tune the magnitude of
S<sub>1</sub>-T<sub>1</sub> ISC rate constant from
10<sup>9</sup> to 10<sup>12</sup> s<sup>-1</sup> and (iv)
realize T<sub>1</sub>-state lifetimes that range from ∼0.1
to several μs, for these model <b>PM-Sp-PM</b>
chromophores, and renders new insights to evolve bespoke
photophysical properties for low optical bandgap
π-conjugated polymers and molecules based on proquinoidal
conjugation motifs.},
Doi = {10.1039/c7sc02150j},
Key = {fds328571}
}
@article{fds231845,
Author = {D.N. Beratan},
Title = {Correction for Migliore et al., Sensing of molecules using
quantum dynamics.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {112},
Number = {25},
Pages = {E3310},
Year = {2015},
Month = {June},
ISSN = {0027-8424},
url = {http://dx.doi.org/10.1073/pnas.1509993112},
Doi = {10.1073/pnas.1509993112},
Key = {fds231845}
}
@article{fds231863,
Author = {Wang, Y and King, JR and Wu, P and Pelzman, DL and Beratan, DN and Toone,
EJ},
Title = {Correction to "Enthalpic Signature of Methonium Desolvation
Revealed in a Synthetic Host-Guest System Based on
Cucurbit[7]uril".},
Journal = {J Am Chem Soc},
Volume = {135},
Number = {46},
Pages = {17650},
Year = {2013},
Month = {November},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24215303},
Doi = {10.1021/ja408346j},
Key = {fds231863}
}
@article{fds316544,
Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Pham, TT and Mague,
JT and Donahue, JP and Schmehl, RH and Beratan, DN and Rubtsov,
IV},
Title = {Correction to "Evaluating the Extent of Intramolecular
Charge Transfer in the Excited States of Rhenium(I)
Donor-Acceptor Complexes with Time-Resolved Vibrational
Spectroscopy".},
Journal = {The journal of physical chemistry. B},
Volume = {120},
Number = {3},
Pages = {596},
Year = {2016},
Month = {January},
ISSN = {1520-6106},
url = {http://dx.doi.org/10.1021/acs.jpcb.5b12238},
Doi = {10.1021/acs.jpcb.5b12238},
Key = {fds316544}
}
@article{fds231897,
Author = {Wierzbinski, E and de Leon, A and Yin, X and Balaeff, A and Davis, KL and Rapireddy, S and Venkatramani, R and Keinan, S and Ly, DH and Madrid, M and Beratan, DN and Achim, C and Waldeck, DH},
Title = {Correction to effect of backbone flexibility on charge
transfer rates in Peptide nucleic Acid duplexes.},
Journal = {Journal of the American Chemical Society},
Volume = {134},
Number = {31},
Pages = {13141},
Year = {2012},
Month = {August},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22834983},
Doi = {10.1021/ja306598z},
Key = {fds231897}
}
@article{fds316543,
Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Schmehl, RH and Beratan, DN and Rubtsov, IV},
Title = {Correction to Full Electron Ligand-to-Ligand Charge Transfer
in a Compact Rhenium(I) Complex.},
Journal = {The journal of physical chemistry. A},
Volume = {120},
Number = {3},
Pages = {473},
Year = {2016},
Month = {January},
ISSN = {1089-5639},
url = {http://dx.doi.org/10.1021/acs.jpca.6b00093},
Doi = {10.1021/acs.jpca.6b00093},
Key = {fds316543}
}
@article{fds343569,
Author = {Teo, RD and Rousseau, BJG and Smithwick, ER and Felice, RD and Beratan,
DN and Migliore, A},
Title = {Correction: Charge Transfer between [4Fe4S] Proteins and DNA
Is Unidirectional: Implications for Biomolecular
Signaling.},
Journal = {Chem},
Volume = {5},
Number = {6},
Pages = {1682-1684},
Year = {2019},
Month = {June},
url = {http://dx.doi.org/10.1016/j.chempr.2019.05.016},
Abstract = {[This corrects the article PMC6350243.].},
Doi = {10.1016/j.chempr.2019.05.016},
Key = {fds343569}
}
@article{fds313541,
Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Schmehl, RH and Beratan, DN and Rubtsov, IV},
Title = {Correction: Electron transfer rate modulation in a compact
Re(i) donor-acceptor complex.},
Journal = {Dalton transactions (Cambridge, England :
2003)},
Volume = {45},
Number = {2},
Pages = {842},
Year = {2016},
Month = {January},
ISSN = {1477-9226},
url = {http://dx.doi.org/10.1039/c5dt90221e},
Abstract = {Correction for 'Electron transfer rate modulation in a
compact Re(i) donor-acceptor complex' by Yuankai Yue et al.,
Dalton Trans., 2015, 44, 8609-8616.},
Doi = {10.1039/c5dt90221e},
Key = {fds313541}
}
@article{fds370190,
Author = {Terai, K and Yuly, JL and Zhang, P and Beratan, DN},
Title = {Correlated particle transport enables biological free energy
transduction.},
Journal = {Biophysical journal},
Volume = {122},
Number = {10},
Pages = {1762-1771},
Year = {2023},
Month = {May},
url = {http://dx.doi.org/10.1016/j.bpj.2023.04.009},
Abstract = {Studies of biological transport frequently neglect the
explicit statistical correlations among particle site
occupancies (i.e., they use a mean-field approximation).
Neglecting correlations sometimes captures biological
function, even for out-of-equilibrium and interacting
systems. We show that neglecting correlations fails to
describe free energy transduction, mistakenly predicting an
abundance of slippage and energy dissipation, even for
networks that are near reversible and lack interactions
among particle sites. Interestingly, linear charge transport
chains are well described without including correlations,
even for networks that are driven and include site-site
interactions typical of biological electron transfer chains.
We examine three specific bioenergetic networks: a linear
electron transfer chain (as found in bacterial nanowires), a
near-reversible electron bifurcation network (as in complex
III of respiration and other recently discovered
structures), and a redox-coupled proton pump (as in complex
IV of respiration).},
Doi = {10.1016/j.bpj.2023.04.009},
Key = {fds370190}
}
@article{fds354265,
Author = {Teo, RD and Du, X and Vera, HLT and Migliore, A and Beratan,
DN},
Title = {Correlation between Charge Transport and Base Excision
Repair in the MutY-DNA Glycosylase.},
Journal = {The journal of physical chemistry. B},
Volume = {125},
Number = {1},
Pages = {17-23},
Year = {2021},
Month = {January},
url = {http://dx.doi.org/10.1021/acs.jpcb.0c08598},
Abstract = {Experimental evidence suggests that DNA-mediated redox
signaling between high-potential [Fe<sub>4</sub>S<sub>4</sub>]
proteins is relevant to DNA replication and repair
processes, and protein-mediated charge transfer (CT) between
[Fe<sub>4</sub>S<sub>4</sub>] clusters and nucleic acids is
a fundamental process of the signaling and repair
mechanisms. We analyzed the dominant CT pathways in the base
excision repair glycosylase MutY using molecular dynamics
simulations and hole hopping pathway analysis. We find that
the adenine nucleobase of the mismatched A·oxoG DNA base
pair facilitates [Fe<sub>4</sub>S<sub>4</sub>]-DNA CT prior
to adenine excision by MutY. We also find that the R153L
mutation in MutY (linked to colorectal adenomatous
polyposis) influences the dominant [Fe4S4]-DNA CT pathways
and appreciably decreases their effective CT
rates.},
Doi = {10.1021/acs.jpcb.0c08598},
Key = {fds354265}
}
@article{fds231956,
Author = {Prytkova, TR and Kurnikov, IV and Beratan, DN},
Title = {Coupling coherence distinguishes structure sensitivity in
protein electron transfer.},
Journal = {Science (New York, N.Y.)},
Volume = {315},
Number = {5812},
Pages = {622-625},
Year = {2007},
Month = {February},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17272715},
Abstract = {Quantum mechanical analysis of electron tunneling in nine
thermally fluctuating cytochrome b562 derivatives reveals
two distinct protein-mediated coupling limits. A
structure-insensitive regime arises for redox partners
coupled through dynamically averaged multiple-coupling
pathways (in seven of the nine derivatives) where heme-edge
coupling leads to the multiple-pathway regime. A
structure-dependent limit governs redox partners coupled
through a dominant pathway (in two of the nine derivatives)
where axial-ligand coupling generates the single-pathway
limit and slower rates. This two-regime paradigm provides a
unified description of electron transfer rates in 26
ruthenium-modified heme and blue-copper proteins, as well as
in numerous photosynthetic proteins.},
Doi = {10.1126/science.1134862},
Key = {fds231956}
}
@article{fds329887,
Author = {Polizzi, NF and Wu, Y and Lemmin, T and Maxwell, AM and Zhang, S-Q and Rawson, J and Beratan, DN and Therien, MJ and DeGrado,
WF},
Title = {De novo design of a hyperstable non-natural protein-ligand
complex with sub-Å accuracy.},
Journal = {Nature chemistry},
Volume = {9},
Number = {12},
Pages = {1157-1164},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1038/nchem.2846},
Abstract = {Protein catalysis requires the atomic-level orchestration of
side chains, substrates and cofactors, and yet the ability
to design a small-molecule-binding protein entirely from
first principles with a precisely predetermined structure
has not been demonstrated. Here we report the design of a
novel protein, PS1, that binds a highly electron-deficient
non-natural porphyrin at temperatures up to 100 °C. The
high-resolution structure of holo-PS1 is in sub-Å agreement
with the design. The structure of apo-PS1 retains the remote
core packing of the holoprotein, with a flexible binding
region that is predisposed to ligand binding with the
desired geometry. Our results illustrate the unification of
core packing and binding-site definition as a central
principle of ligand-binding protein design.},
Doi = {10.1038/nchem.2846},
Key = {fds329887}
}
@article{fds231843,
Author = {Polizzi, NF and Migliore, A and Therien, MJ and Beratan,
DN},
Title = {Defusing redox bombs?},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {112},
Number = {35},
Pages = {10821-10822},
Year = {2015},
Month = {September},
ISSN = {0027-8424},
url = {http://dx.doi.org/10.1073/pnas.1513520112},
Doi = {10.1073/pnas.1513520112},
Key = {fds231843}
}
@article{fds355937,
Author = {Valdiviezo, J and Clever, C and Beall, E and Pearse, A and Bae, Y and Zhang, P and Achim, C and Beratan, DN and Waldeck,
DH},
Title = {Delocalization-Assisted Transport through Nucleic Acids in
Molecular Junctions.},
Journal = {Biochemistry},
Volume = {60},
Number = {17},
Pages = {1368-1378},
Year = {2021},
Month = {May},
url = {http://dx.doi.org/10.1021/acs.biochem.1c00072},
Abstract = {The flow of charge through molecules is central to the
function of supramolecular machines, and charge transport in
nucleic acids is implicated in molecular signaling and DNA
repair. We examine the transport of electrons through
nucleic acids to understand the interplay of resonant and
nonresonant charge carrier transport mechanisms. This study
reports STM break junction measurements of peptide nucleic
acids (PNAs) with a G-block structure and contrasts the
findings with previous results for DNA duplexes. The
conductance of G-block PNA duplexes is much higher than that
of the corresponding DNA duplexes of the same sequence;
however, they do not display the strong even-odd dependence
conductance oscillations found in G-block DNA. Theoretical
analysis finds that the conductance oscillation magnitude in
PNA is suppressed because of the increased level of
electronic coupling interaction between G-blocks in PNA and
the stronger PNA-electrode interaction compared to that in
DNA duplexes. The strong interactions in the G-block PNA
duplexes produce molecular conductances as high as 3%
<i>G</i><sub>0</sub>, where <i>G</i><sub>0</sub> is the
quantum of conductance, for 5 nm duplexes.},
Doi = {10.1021/acs.biochem.1c00072},
Key = {fds355937}
}
@misc{fds22290,
Author = {D.N. Beratan and J.N. Onuchic and J.J. Hopfield},
Title = {Design of a molecular memory device based on electron
transfer reactions},
Pages = {331-357},
Booktitle = {Molecular Electronics: Science and Technology},
Publisher = {Engineering Foundation, New York},
Year = {1989},
Key = {fds22290}
}
@misc{fds22275,
Author = {D.N. Beratan and J.N. Onuchic and J.J. Hopefield},
Title = {Design of a molecular memory device: the electron transfer
shift register memory},
Pages = {107-118},
Booktitle = {Towards the Biochip},
Publisher = {World Publishing Company, New Jersey},
Editor = {C. Nicolini},
Year = {1990},
Key = {fds22275}
}
@misc{fds370703,
Author = {BERATAN, DN and ONUCHIC, JN and HOPFIELD, JJ},
Title = {DESIGN OF A TRUE MOLECULAR ELECTRONIC DEVICE - THE
ELECTRON-TRANSFER SHIFT REGISTER MEMORY},
Journal = {MOLECULAR ELECTRONICS : BIOSENSORS AND BIOCOMPUTERS},
Pages = {353-360},
Booktitle = {Molecular Electronics - Biosensors and Diocomputers},
Publisher = {Plenum Press},
Editor = {F.T. Hong},
Year = {1989},
ISBN = {0-306-43395-8},
Key = {fds370703}
}
@article{fds231896,
Author = {Jiang, N and Zuber, G and Keinan, S and Nayak, A and Yang, W and Therien,
MJ and Beratan, DN},
Title = {Design of coupled porphyrin chromophores with unusually
large hyperpolarizabilities},
Journal = {Journal of Physical Chemistry C},
Volume = {116},
Number = {17},
Pages = {9724-9733},
Publisher = {American Chemical Society (ACS)},
Year = {2012},
Month = {May},
ISSN = {1932-7447},
url = {http://dx.doi.org/10.1021/jp2115065},
Abstract = {Figure Persented: A new series of push-pull porphyrin-based
chromophores with unusually large static first
hyperpolarizabilities are designed on the basis of
coupled-perturbed Hartree-Fock and density functional
calculations. The proper combination of critical building
blocks, including a ruthenium(II) bisterpyridine complex,
proquinoidal thiadiazoloquinoxaline, and
(porphinato)zinc(II) units, gives rise to considerable
predicted enhancements of the static nonlinear optical (NLO)
response, computed to be as large as 11 300 × 10 -30 esu, 2
orders of magnitude larger than the benchmark
[5-((4′-(dimethylamino)phenyl)ethynyl)-15-((4″-nitrophenyl)ethynyl)
porphinato]zinc(II) chromophore. A two-state model was found
to be useful for the qualitative description of the first
hyperpolarizabilities in this class of NLO chromophores,
which are predicted to have hyperpolarizabilities
approaching the fundamental limit predicted to be attainable
by empirical theoretical models. © 2012 American Chemical
Society.},
Doi = {10.1021/jp2115065},
Key = {fds231896}
}
@misc{fds370699,
Author = {BERATAN, DN and CHENG, LT and MARDER, SR and MURDOCH, J and PERRY, JW and TIEMANN, BG and TSENG, JCC and VANDOREMAELE, G},
Title = {DESIGN OF NONLINEAR OPTICAL-MATERIALS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {202},
Pages = {173-BIOT},
Year = {1991},
Key = {fds370699}
}
@article{fds231961,
Author = {Wang, M and Hu, X and Beratan, DN and Yang, W},
Title = {Designing molecules by optimizing potentials.},
Journal = {Journal of the American Chemical Society},
Volume = {128},
Number = {10},
Pages = {3228-3232},
Year = {2006},
Month = {March},
ISSN = {0002-7863},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16522103},
Abstract = {The astronomical number of accessible discrete chemical
structures makes rational molecular design extremely
challenging. We formulate the design of molecules with
specific tailored properties as performing a continuous
optimization in the space of electron-nuclear attraction
potentials. The optimization is facilitated by using a
linear combination of atomic potentials (LCAP), a general
framework that creates a continuous property landscape from
an otherwise unlinked set of discrete molecular-property
values. A demonstration of this approach is given for the
optimization of molecular electronic polarizability and
hyperpolarizability. We show that the optimal structures can
be determined without enumerating and separately evaluating
the characteristics of the combinatorial number of possible
structures, a process that would be much slower. The LCAP
approach may be used with quantum or classical Hamiltonians,
suggesting possible applications to drug design and new
materials discovery.},
Doi = {10.1021/ja0572046},
Key = {fds231961}
}
@article{fds231953,
Author = {Keinan, S and Hu, X and Beratan, DN and Yang, W},
Title = {Designing molecules with optimal properties using the linear
combination of atomic potentials approach in an AM1
semiempirical framework.},
Journal = {The journal of physical chemistry. A},
Volume = {111},
Number = {1},
Pages = {176-181},
Year = {2007},
Month = {January},
ISSN = {1089-5639},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17201401},
Abstract = {The linear combination of atomic potentials (LCAP) approach
is implemented in the AM1 semiempirical framework and is
used to design molecular structures with optimized
properties. The optimization procedure uses property
derivative information to search molecular space and thus
avoid direct enumeration and evaluation of each molecule in
a library. Two tests are described: the optimization of
first hyperpolarizabilities of substituted aromatics and the
optimization of a figure of merit for n-type organic
semiconductors.},
Doi = {10.1021/jp0646168},
Key = {fds231953}
}
@article{fds332734,
Author = {Rousseau, BJG and Shafei, S and Migliore, A and Stanley, RJ and Beratan,
DN},
Title = {Determinants of Photolyase's DNA Repair Mechanism in
Mesophiles and Extremophiles.},
Journal = {Journal of the American Chemical Society},
Volume = {140},
Number = {8},
Pages = {2853-2861},
Year = {2018},
Month = {February},
url = {http://dx.doi.org/10.1021/jacs.7b11926},
Abstract = {Light-driven DNA repair by extremophilic photolyases is of
tremendous importance for understanding the early
development of life on Earth. The mechanism for flavin
adenine dinucleotide repair of DNA lesions is the subject of
debate and has been studied mainly in mesophilic species. In
particular, the role of adenine in the repair process is
poorly understood. Using molecular docking, molecular
dynamics simulations, electronic structure calculations, and
electron tunneling pathways analysis, we examined adenine's
role in DNA repair in four photolyases that thrive at
different temperatures. Our results indicate that the
contribution of adenine to the electronic coupling between
the flavin and the cyclobutane pyrimidine dimer lesion to be
repaired is significant in three (one mesophilic and two
extremophilic) of the four enzymes studied. Our analysis
suggests that thermophilic and hyperthermophilic photolyases
have evolved structurally to preserve the functional
position (and thus the catalytic function) of adenine at
their high temperatures of operation. Water molecules can
compete with adenine in establishing the strongest coupling
pathway for the electron transfer repair process, but the
adenine contribution remains substantial. The present study
also reconciles prior seemingly contradictory conclusions on
the role of adenine in mesophile electron transfer repair
reactions, showing how adenine-mediated superexchange is
conformationally gated.},
Doi = {10.1021/jacs.7b11926},
Key = {fds332734}
}
@article{fds232004,
Author = {Kondru, RK and Chen, CHT and Curran, DP and Beratan, DN and Wipf,
P},
Title = {Determination of the absolute configuration of
1,3,5,7-tetramethyl-1,3- dihydroindol-2-one by optical
rotation computation},
Journal = {Tetrahedron Asymmetry},
Volume = {10},
Number = {21},
Pages = {4143-4150},
Publisher = {Elsevier BV},
Year = {1999},
Month = {October},
url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6THT-3Y6HDKJ-G-Y&_cdi=5291&_user=38557&_orig=browse&_coverDate=10%2F29%2F1999&_sk=999899978&view=c&wchp=dGLbVlb-zSkWb&md5=6bd074b42cd870365d7f2e80a7606ca0&ie=/sdarticle.pdf},
Abstract = {The absolute configuration of 1,3,5,7-tetramethyl-1,3-dihydroindol-2-one
was determined by quantum chemical calculations of specific
rotation angles with coupled-perturbed Hartree-Fock methods.
The computation used molecular geometries obtained from ab
initio calculations as well as from molecular mechanics and
semi-empirical optimization. In addition to the dependence
on geometry optimization strategies, the basis set
dependence of the computed rotation angle was
examined.},
Doi = {10.1016/S0957-4166(99)00443-7},
Key = {fds232004}
}
@article{fds232039,
Author = {Specht, KM and Nam, J and Ho, DM and Berova, N and Kondru, RK and Beratan,
DN and Wipf, P and Pascal, RA and Kahne, D},
Title = {Determining absolute configuration in flexible molecules: a
case study.},
Journal = {Journal of the American Chemical Society},
Volume = {123},
Number = {37},
Pages = {8961-8966},
Year = {2001},
Month = {September},
ISSN = {0002-7863},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11552802},
Abstract = {Assigning absolute configuration of molecules continues to
be a major problem. Determining absolute configuration in
conformationally flexible systems is challenging, even for
experts. Here, we present a case study in which we use a
combination of molecular modeling, solution NMR, and X-ray
crystallography to illustrate why it is difficult to use
solution methods alone for configuration assignment. For the
case examined, a comparison of calculated and experimental
optical rotatory dispersion (ORD) data provides the most
straightforward way to assign the absolute
configuration.},
Doi = {10.1021/ja0104406},
Key = {fds232039}
}
@article{fds318055,
Author = {Skourtis, SS and Liu, C and Antoniou, P and Virshup, AM and Beratan,
DN},
Title = {Dexter energy transfer pathways.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {113},
Number = {29},
Pages = {8115-8120},
Year = {2016},
Month = {July},
url = {http://dx.doi.org/10.1073/pnas.1517189113},
Abstract = {Energy transfer with an associated spin change of the donor
and acceptor, Dexter energy transfer, is critically
important in solar energy harvesting assemblies, damage
protection schemes of photobiology, and organometallic
opto-electronic materials. Dexter transfer between
chemically linked donors and acceptors is bridge mediated,
presenting an enticing analogy with bridge-mediated electron
and hole transfer. However, Dexter coupling pathways must
convey both an electron and a hole from donor to acceptor,
and this adds considerable richness to the mediation
process. We dissect the bridge-mediated Dexter coupling
mechanisms and formulate a theory for triplet energy
transfer coupling pathways. Virtual donor-acceptor
charge-transfer exciton intermediates dominate at shorter
distances or higher tunneling energy gaps, whereas virtual
intermediates with an electron and a hole both on the bridge
(virtual bridge excitons) dominate for longer distances or
lower energy gaps. The effects of virtual bridge excitons
were neglected in earlier treatments. The two-particle
pathway framework developed here shows how Dexter
energy-transfer rates depend on donor, bridge, and acceptor
energetics, as well as on orbital symmetry and quantum
interference among pathways.},
Doi = {10.1073/pnas.1517189113},
Key = {fds318055}
}
@misc{fds370667,
Author = {Kawatsu, T and Beratan, DN},
Title = {Diffusion controlled intra-molecular electron transfer in
protein: A simple model of the sulfite oxidase},
Journal = {BIOPHYSICAL JOURNAL},
Volume = {86},
Number = {1},
Pages = {472A-472A},
Year = {2004},
Key = {fds370667}
}
@article{fds338391,
Author = {Bloom, BP and Liu, R and Zhang, P and Ghosh, S and Naaman, R and Beratan,
DN and Waldeck, DH},
Title = {Directing Charge Transfer in Quantum Dot
Assemblies.},
Journal = {Accounts of chemical research},
Volume = {51},
Number = {10},
Pages = {2565-2573},
Year = {2018},
Month = {October},
url = {http://dx.doi.org/10.1021/acs.accounts.8b00355},
Abstract = {The optical and electronic properties of semiconductor
quantum dots (QDs) make them attractive candidates for
applications in photovoltaics, spintronics, photocatalysis,
and optoelectronics. Understanding how to control the flow
of charge in QD assemblies is essential for realizing novel
applications. This Account explores some unique
characteristics of charge transport in QD dyads, triads, and
their assemblies. The emerging features of these assemblies
that provide new opportunities to manipulate charge flow at
the nanoscale are (1) cascading energy landscapes and band
offsets to inhibit charge recombination, (2) electrostatic
fields that direct charge flow through QD-QD and
QD-conjugated polymer junctions, and (3) QD chirality and
chiral imprinting that promotes vectorial electron and spin
selective transport. Charge flow kinetics is determined by a
combination of familiar electron transfer parameters
(reaction free energy, reorganization energy, and electronic
coupling), donor and acceptor electronic densities of
states, and internal electric fields. Electron transfer and
electronic structure theory, combined with kinetic modeling,
place the measured kinetics of QD electron transfer
donor-acceptor assemblies into a unified conceptual context.
The experimental transfer rates measured in these systems
depend upon structure and the internal electric fields that
are present in the assemblies. A negatively charged donor
and positively charged acceptor, for example, facilitates
(inhibits) electron (hole) transfer, while an electric field
of opposite orientation (reversal of charges) inhibits
(promotes) electron (hole) transfer. These and other
emerging rules that govern charge flow in NP assemblies
provide a strategy to design the directionality and yield of
interfacial charge transport. Chirality at the nanoscale can
induce spin selective charge transport, providing new ways
to direct charge (and spin) flow in QD assemblies.
Magnetoresistance and magnetic conductive probe atomic force
microscopy experiments show spin selective electron
transport for chirally imprinted QD assemblies. Photoinduced
electron transfer from achiral donor-QDs to chiral
acceptor-QDs depends on the electron spin and chiroptical
properties of the acceptor-QDs. These assemblies show
transport characteristics that correlate with features of
the QDs' circular dichroism spectra, presenting intriguing
challenges to theory, and indicating that spectroscopic
signatures may assist in the design and diagnosis of
functional molecular assemblies. Theoretical and
experimental studies of charge transport in well-defined QD
assemblies are establishing design principles for vectorial
charge transport and are also refining questions surrounding
the mechanism and control of these processes. These
intensified efforts are forging links between fundamental
discoveries regarding mechanism and practical applications
for these novel assembled nanostructures.},
Doi = {10.1021/acs.accounts.8b00355},
Key = {fds338391}
}
@article{fds362435,
Author = {Wiebelhaus, N and Singh, N and Zhang, P and Craig, SL and Beratan, DN and Fitzgerald, MC},
Title = {Discovery of the Xenon-Protein Interactome Using Large-Scale
Measurements of Protein Folding and Stability.},
Journal = {Journal of the American Chemical Society},
Volume = {144},
Number = {9},
Pages = {3925-3938},
Year = {2022},
Month = {March},
url = {http://dx.doi.org/10.1021/jacs.1c11900},
Abstract = {The intermolecular interactions of noble gases in biological
systems are associated with numerous biochemical responses,
including apoptosis, inflammation, anesthesia, analgesia,
and neuroprotection. The molecular modes of action
underlying these responses are largely unknown. This is in
large part due to the limited experimental techniques to
study protein-gas interactions. The few techniques that are
amenable to such studies are relatively low-throughput and
require large amounts of purified proteins. Thus, they do
not enable the large-scale analyses that are useful for
protein target discovery. Here, we report the application of
stability of proteins from rates of oxidation (SPROX) and
limited proteolysis (LiP) methodologies to detect
protein-xenon interactions on the proteomic scale using
protein folding stability measurements. Over 5000
methionine-containing peptides and over 5000 semi-tryptic
peptides, mapping to ∼1500 and ∼950 proteins,
respectively, in the yeast proteome, were assayed for
Xe-interacting activity using the SPROX and LiP techniques.
The SPROX and LiP analyses identified 31 and 60
Xe-interacting proteins, respectively, none of which were
previously known to bind Xe. A bioinformatics analysis of
the proteomic results revealed that these Xe-interacting
proteins were enriched in those involved in ATP-driven
processes. A fraction of the protein targets that were
identified are tied to previously established modes of
action related to xenon's anesthetic and organoprotective
properties. These results enrich our knowledge and
understanding of biologically relevant xenon interactions.
The sample preparation protocols and analytical
methodologies developed here for xenon are also generally
applicable to the discovery of a wide range of other
protein-gas interactions in complex biological mixtures,
such as cell lysates.},
Doi = {10.1021/jacs.1c11900},
Key = {fds362435}
}
@article{fds167395,
Author = {B.C. Rinderspacher and J. Andzelm and A. Rawlett and J. Dougherty and D.N. Beratan and W. Yang},
Title = {Discrete optimization of electronic hyperpolarizabilities in
a chemical subspace},
Journal = {J. Chem. Theory Comput},
Number = {5},
Pages = {3321-3329},
Year = {2009},
Key = {fds167395}
}
@article{fds231930,
Author = {Rinderspacher, BC and Andzelm, J and Rawlett, A and Dougherty, J and Beratan, DN and Yang, W},
Title = {Discrete optimization of electronic hyperpolarizabilities in
a chemical subspace},
Journal = {Army Research Laboratory Publication ARL-TR-4833},
Volume = {5},
Number = {12},
Pages = {3321-3329},
Year = {2009},
ISSN = {1549-9618},
url = {http://dx.doi.org/10.1021/ct900325p},
Abstract = {We introduce a general optimization algorithm based on an
interpolation of property values on a hypercube. Each vertex
of the hypercube represents a molecule, while the interior
of the interpolation represents a virtual superposition
("alchemical" mutation) of molecules. The resultant
algorithm is similar to branch-and-bound/tree-search
methods. We apply the algorithm to the optimization of the
first electronic hyperpolarizability for several tolane
libraries. The search includes structural and conformational
information. Geometries were optimized using the AM1
Hamiltonian, and first hyperpolarizabilities were computed
using the INDO/S method. Even for small libraries, a
significant improvement of the hyperpolarizability, up to a
factor of ca. 4, was achieved. The algorithm was validated
for efficiency and reproduced known experimental results.
The algorithm converges to a local optimum at a
computational cost on the order of the logarithm of the
library size, making large libraries accessible. For larger
libraries, the improvement was accomplished by performing
electronic structure calculations on less than 0.01% of the
compounds in the larger libraries. Alternation of electron
donating and accepting groups in the tolane scaffold was
found to produce candidates with large hyperpolarizabilities
consistently.},
Doi = {10.1021/ct900325p},
Key = {fds231930}
}
@article{fds231866,
Author = {Jiang, N and Kuznetsov, A and Nocek, JM and Hoffman, BM and Crane, BR and Hu, X and Beratan, DN},
Title = {Distance-independent charge recombination kinetics in
cytochrome c-cytochrome c peroxidase complexes: compensating
changes in the electronic coupling and reorganization
energies.},
Journal = {The journal of physical chemistry. B},
Volume = {117},
Number = {31},
Pages = {9129-9141},
Year = {2013},
Month = {August},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23895339},
Abstract = {Charge recombination rate constants vary no more than 3-fold
for interprotein ET in the Zn-substituted wild type (WT)
cytochrome c peroxidase (CcP):cytochrome c (Cc) complex and
in complexes with four mutants of the Cc protein (i.e.,
F82S, F82W, F82Y, and F82I), despite large differences in
the ET distance. Theoretical analysis indicates that charge
recombination for all complexes involves a combination of
tunneling and hopping via Trp191. For three of the five
structures (WT and F82S(W)), the protein favors hopping more
than that in the other two structures that have longer heme
→ ZnP distances (F82Y(I)). Experimentally observed
biexponential ET kinetics is explained by the complex
locking in alternative coupling pathways, where the acceptor
hole state is either primarily localized on ZnP (slow phase)
or on Trp191 (fast phase). The large conformational
differences between the CcP:Cc interface for the F82Y(I)
mutants compared to that the WT and F82S(W) complexes are
predicted to change the reorganization energies for the
CcP:Cc ET reactions because of changes in solvent exposure
and interprotein ET distances. Since the recombination
reaction is likely to occur in the inverted Marcus regime,
an increased reorganization energy compensates the decreased
role for hopping recombination (and the longer transfer
distance) in the F82Y(I) mutants. Taken together, coupling
pathway and reorganization energy effects for the five
protein complexes explain the observed insensitivity of
recombination kinetics to donor-acceptor distance and
docking pose and also reveals how hopping through aromatic
residues can accelerate long-range ET.},
Doi = {10.1021/jp401551t},
Key = {fds231866}
}
@article{fds315336,
Author = {Rupakheti, C and Al-Saadon, R and Zhang, Y and Virshup, AM and Zhang, P and Yang, W and Beratan, DN},
Title = {Diverse Optimal Molecular Libraries for Organic
Light-Emitting Diodes.},
Journal = {Journal of chemical theory and computation},
Volume = {12},
Number = {4},
Pages = {1942-1952},
Year = {2016},
Month = {April},
ISSN = {1549-9618},
url = {http://dx.doi.org/10.1021/acs.jctc.5b00829},
Abstract = {Organic light-emitting diodes (OLEDs) have wide-ranging
applications, from lighting to device displays. However, the
repertoire of organic molecules with efficient blue emission
is limited. To address this limitation, we have developed a
strategy to design property-optimized, diversity-oriented
libraries of structures with favorable fluorescence
properties. This approach identifies novel diverse candidate
organic molecules for blue emission with strong oscillator
strengths and low singlet-triplet energy gaps that favor
thermally activated delayed fluorescence (TADF)
emission.},
Doi = {10.1021/acs.jctc.5b00829},
Key = {fds315336}
}
@misc{fds370679,
Author = {Kurnikov, IV and Beratan, DN},
Title = {Divide-and-conquer approach to calculate electronic response
properties of macromolecules.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {215},
Pages = {U254-U254},
Year = {1998},
Key = {fds370679}
}
@article{fds318052,
Author = {Beratan, DN and Waldeck, DH},
Title = {DNA charge transfer: Hot holes break the speed
limit.},
Journal = {Nature chemistry},
Volume = {8},
Number = {11},
Pages = {992-993},
Year = {2016},
Month = {October},
url = {http://dx.doi.org/10.1038/nchem.2655},
Doi = {10.1038/nchem.2655},
Key = {fds318052}
}
@article{fds314839,
Author = {Zhang, Y and Zhang, WB and Liu, C and Zhang, P and Balaeff, A and Beratan,
DN},
Title = {DNA charge transport: Moving beyond 1D},
Journal = {Surface Science},
Volume = {652},
Pages = {33-38},
Publisher = {Elsevier BV},
Year = {2016},
Month = {October},
ISSN = {0039-6028},
url = {http://dx.doi.org/10.1016/j.susc.2016.03.011},
Abstract = {Charge transport across novel DNA junctions has been studied
for several decades. From early attempts to move charge
across DNA double crossover junctions to recent studies on
DNA three-way junctions and G4 motifs, it is becoming clear
that efficient cross-junction charge migration requires
strong base-to-base electronic coupling at the junction,
facilitated by favorable pi-stacking. We review recent
progress toward the goal of manipulating and controlling
charge transport through DNA junctions.},
Doi = {10.1016/j.susc.2016.03.011},
Key = {fds314839}
}
@article{fds231871,
Author = {Priyadarshy, S and Risser, SM and Beratan, DN},
Title = {DNA double helix mediated long range electron
transfer},
Journal = {Int. J. Quantum Chem. Quantun Biol. Symp.},
Volume = {60},
Number = {8},
Pages = {65-71},
Publisher = {WILEY},
Year = {1996},
url = {http://dx.doi.org/10.1002/(SICI)1097-461X(1996)60:8<1789::AID-QUA6>3.0.CO;2-U},
Abstract = {A theoretical analysis based upon large-scale
self-consistent Hartree-Fock calculations at a semiempirical
quantum theory level (CNDO/S) is performed to investigate
long-range electron transfer in a donor-DNA-acceptor
molecule, where the donor and acceptor moieties are tethered
to the DNA. The π-stacked base pairs are found to dominate
the long-range electronic coupling. Despite the π-electron
mediated coupling, the exponential distance decay constant
of the electron transfer rate is ∼ 1.2-1.6 Å-1, values
typical of electron transfer proteins. The calculated
long-range electron transfer rate of the order of 106 s-1
for a metal-to-metal distance of 21 Å is found to be in
agreement with kinetic measurements by Meade and Kayyem.
Based on the current analysis, the π-electrons dominate the
long-range electronic coupling interactions in DNA, but they
do not lead to one-dimensional molecular wire-like
properties. © 1996 John Wiley & Sons, Inc.},
Doi = {10.1002/(SICI)1097-461X(1996)60:8<1789::AID-QUA6>3.0.CO;2-U},
Key = {fds231871}
}
@article{fds231964,
Author = {Berlin, YA and Kurnikov, IV and Ratner, MA and Burin, AL and Beratan,
DN},
Title = {DNA electron transfer processes: Some theoretical
notions},
Journal = {Top. Curr. Chem.},
Volume = {237},
Pages = {1-36},
Publisher = {Springer Berlin Heidelberg},
Year = {2004},
url = {http://dx.doi.org/10.1007/b94471},
Doi = {10.1007/b94471},
Key = {fds231964}
}
@article{fds231990,
Author = {Priyadarshy, S and Risser, SM and Beratan, DN},
Title = {DNA is not a molecular wire: Protein-like electron-transfer
predicted for an extended π-electron system},
Journal = {Journal of Physical Chemistry},
Volume = {100},
Number = {44},
Pages = {17678-17682},
Publisher = {American Chemical Society (ACS)},
Year = {1996},
Month = {October},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1996/100/i44/pdf/jp961731h.pdf},
Abstract = {The earliest studies of electron-transfer proteins1 raised
the question of whether or not π-electron residues might
facilitate electron transport.2 Three recent long-range
electron-transfer experiments utilizing DNA bridges revisit
this provocative, yet unresolved, question.3,4,5 The
distance dependence of electron transfer in DNA is not a
matter of purely academic concern; it controls the mechanism
of DNA damage and repair in cells and is being exploited in
new molecular probes of DNA sequence. We present a
theoretical analysis based upon very large scale
self-consistent-field quantum calculation of all valence
electrons (as many as ∼3300) in these three systems This
computation is the first performed on such large
macromolecules and also the first to extract long-range
electronic interactions at this level of theory. DNA
electron transfer is found to be mediated by through-space
interactions between the π-electron-containing base pairs,
but the magnitude of the coupling facilitated by this
channel drops rapidly with distance, as a consequence of the
∼3.4 Å noncovalent gap between base pairs. These,
predictions are in agreement with most of the experimental
data. The rapid decay of electron-transfer rates with
distance computed here suggests that biologically controlled
DNA electron-transfer events, of importance in DNA repair,6
must function over relatively short range. Moreover, the
predicted distance dependence of electron transfer in DNA is
strikingly close to that found in proteins. © 1996 American
Chemical Society.},
Doi = {10.1021/jp961731h},
Key = {fds231990}
}
@article{fds232000,
Author = {Priyadarshy, S and Risser, SM and Beratan, DN},
Title = {DNA-mediated electron transfer},
Journal = {Journal of Biological Inorganic Chemistry},
Volume = {3},
Number = {2},
Pages = {196-200},
Publisher = {Springer Nature},
Year = {1998},
Month = {April},
url = {http://www.springerlink.com/media/2724vnyuxk1kbtm3ng86/contributions/l/w/r/6/lwr6ca0pguppb87d.pdf},
Abstract = {Electron transfer in DNA has been investigated for decades,
but recent experiments highlight our limited fundamental
understanding of these processes. Modern electron transfer
theory may help to address some of the open mechanistic
issues. We summarize and analyze the results of recent
experiments from a theoretical perspective. Future research
directions are suggested that might help to establish the
molecular mechanism(s) for long- range DNA electron
transfer.},
Doi = {10.1007/s007750050221},
Key = {fds232000}
}
@misc{fds370688,
Author = {PRIYADARSHY, S and RISSER, SM and BERATAN, DN},
Title = {DNA-MEDIATED LONG-RANGE ELECTRON-TRANSFER - BASES VS
BACKBONE},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {210},
Pages = {115-INOR},
Year = {1995},
Key = {fds370688}
}
@article{fds231873,
Author = {Beratan, DN and Priyadarshy, S and Risser, SM},
Title = {DNA: wire or insulator?},
Journal = {Chemistry and Biology},
Volume = {4},
Number = {1},
Pages = {3-8},
Year = {1997},
url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRP-4B616KK-BG-2&_cdi=6240&_user=38557&_coverDate=01%2F31%2F1997&_sk=%23TOC%236240%231997%23999959998%23473703%23FLP%23display%23Volume_4,_Issue_1,_Pages_1-85_(January_1997)%23tagged%23Volume%23first%3D4%23Issue%23first%3D1%23Pages%23first%3D1%23last%3D85%23date%23(January_1997)%23&view=c&_gw=y&wchp=dGLbVtb-zSkWW&md5=82145db032421c4f467734eb72ece26b&ie=/sdarticle.pdf},
Abstract = {DNA-based electron transfer reactions are seen in processes
such as biosynthesis and radiation damage/repair, but are
poorly understood. What kinds of experiments might tell us
how far and how fast electrons can travel in DNA? What does
modern theory predict?},
Doi = {10.1016/s1074-5521(97)90230-1},
Key = {fds231873}
}
@article{fds232041,
Author = {Aquino, AJA and Beroza, P and Beratan, DN and Onuchic,
JN},
Title = {Docking and electron transfer between cytochrome
c2 and the photosynthetic reaction
center},
Journal = {Chemical Physics},
Volume = {197},
Number = {3},
Pages = {277-288},
Publisher = {Elsevier BV},
Year = {1995},
Month = {August},
ISSN = {0301-0104},
url = {http://dx.doi.org/10.1016/0301-0104(95)00099-A},
Abstract = {Electron transfer between the proteins cytochrome c2 (cytc2)
and the photosynthetic reaction center (RC) was studied
using the pathways model of Beratan and Onuchic. To
investigate the protein structure dependence of this
electron transfer reaction, we separated the electronic
coupling decay between electron donor and acceptor into
three parts: (i) the coupling from the cytochrome heme to
the surface of the cytochrome, (ii) the coupling from the RC
surface to the bacteriochlorophyll dimer, and (iii) the
coupling from the surface of the cytochrome to the surface
of the reaction center. Calculating the coupling between the
surface amino acids and the redox center allows the simple
estimate of inter-protein electronic coupling, and, for a
given docked structure, provides a functional criterion for
evaluating that structure. The strongest heme to special
pair electron transfer pathway in Rps. viridis (an RC with
fixed heme-special pair structure) included surface residues
on the cytochrome and RC (when each was treated as a
separate protein), although it did not involve the most
strongly coupled surface atoms of the RC. To examine the
effect of docking orientation on electron transfer in Rb.
sphaeroides, in which the cytochrome is not bound to the RC,
we generated surface coupling maps of the electronic
coupling between the redox sites and solvent exposed atoms
in each protein. These maps were compared to individual
pathways calculated for two docked cytc2/RC structures, one
based on electrostatic complementarity, the other based on
maximizing electronic coupling. The electronic coupling
between donor and acceptor for these two docked structures
was remarkably similar, suggesting that efficient electron
transfer can be obtained from very different docked
orientations of the cytochrome. Other factors influencing
intermolecular electron transfer are discussed. ©
1995.},
Doi = {10.1016/0301-0104(95)00099-A},
Key = {fds232041}
}
@misc{fds370683,
Author = {ZUSMAN, LD and KURNIKOV, IV and BERATAN, DN and FARID,
RS},
Title = {DOES ELECTRON-TRANSFER THEORY EXPLAIN LARGE RATE DIFFERENCES
IN SINGLET AND TRIPLE EXCITED-STATE ELECTRON-TRANSFER
REACTIONS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {210},
Pages = {121-INOR},
Year = {1995},
Key = {fds370683}
}
@misc{fds318056,
Author = {Casimiro, DR and Beratan, DN and Onuchic, JN and Winkler, JR and Gray,
HB},
Title = {Donor-acceptor electronic coupling in ruthenium-modified
heme proteins},
Journal = {MECHANISTIC BIOINORGANIC CHEMISTRY},
Volume = {246},
Series = {ACS Symp. Series},
Pages = {471-485},
Booktitle = {Mechanistic Bioinorganic Chemistry},
Publisher = {AMER CHEMICAL SOC},
Editor = {Thorp, HH and Pecoraro, VL},
Year = {1995},
Month = {January},
ISBN = {0-8412-3062-5},
Key = {fds318056}
}
@misc{fds370693,
Author = {BERATAN, DN and RISSER, SM},
Title = {DONOR-ACCEPTOR INTERACTIONS IN COMPLEX METAL-CONTAINING
MOLECULES},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {206},
Pages = {483-INOR},
Year = {1993},
Key = {fds370693}
}
@article{fds304359,
Author = {Lewis, FD and Liu, J and Weigel, W and Rettig, W and Kurnikov, IV and Beratan, DN},
Title = {Donor-bridge-acceptor energetics determine the distance
dependence of electron tunneling in DNA.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {99},
Number = {20},
Pages = {12536-12541},
Year = {2002},
Month = {October},
ISSN = {0027-8424},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12228728},
Abstract = {Electron transfer (ET) processes in DNA are of current
interest because of their involvement in oxidative strand
cleavage reactions and their relevance to the development of
molecular electronics. Two mechanisms have been identified
for ET in DNA, a single-step tunneling process and a
multistep charge-hopping process. The dynamics of tunneling
reactions depend on both the distance between the electron
donor and acceptor and the nature of the molecular bridge
separating the donor and acceptor. In the case of protein
and alkane bridges, the distance dependence is not strongly
dependent on the properties of the donor and acceptor. In
contrast, we show here that the distance decay of DNA ET
rates varies markedly with the energetics of the donor and
acceptor relative to the bridge. Specifically, we find that
an increase in the energy of the bridge states by 0.25 eV (1
eV = 1.602 x 10(-19) J) relative to the donor and acceptor
energies for photochemical oxidation of nucleotides, without
changing the reaction free energy, results in an increase in
the characteristic exponential distance decay constant for
the ET rates from 0.71 to 1.1 A(-1). These results show
that, in the small tunneling energy gap regime of DNA ET,
the distance dependence is not universal; it varies strongly
with the tunneling energy gap. These DNA ET reactions fill a
"missing link" or transition regime between the large
barrier (rapidly decaying) tunneling regime and the (slowly
decaying) hopping regime in the general theory of
bridge-mediated ET processes.},
Doi = {10.1073/pnas.192432899},
Key = {fds304359}
}
@article{fds232035,
Author = {Liang, Z-X and Nocek, JM and Huang, K and Hayes, RT and Kurnikov, IV and Beratan, DN and Hoffman, BM},
Title = {Dynamic docking and electron transfer between Zn-myoglobin
and cytochrome b(5).},
Journal = {Journal of the American Chemical Society},
Volume = {124},
Number = {24},
Pages = {6849-6859},
Year = {2002},
Month = {June},
ISSN = {0002-7863},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12059205},
Abstract = {We present a broad study of the effect of neutralizing the
two negative charges of the Mb propionates on the
interaction and electron transfer (ET) between horse Mb and
bovine cyt b(5), through use of Zn-substituted Mb (ZnMb, 1)
to study the photoinitiated reaction, ((3)ZnP)Mb + Fe(3+)cyt
b(5) --> (ZnP)(+)Mb + Fe(2+)cyt b(5). The charge
neutralization has been carried out both by replacing the Mb
heme with zinc-deuteroporphyrin dimethylester (ZnMb(dme),
2), which replaces the charges by small neutral hydrophobic
patches, and also by replacement with the newly prepared
zinc-deuteroporphyrin diamide (ZnMb(diamide), 3), which
converts the charged groups to neutral, hydrophilic ones.
The effect of propionate neutralization on the conformation
of the zinc-porphyrin in the Mb heme pocket has been studied
by multinuclear NMR with an (15)N labeled zinc porphyrin
derivative (ZnMb((15)N-diamide), 4). The rates of
photoinitiated ET between the Mb's (1-3) and cyt b(5) have
been measured over a range of pH values and ionic strengths.
Isothermal titration calorimetry (ITC) and NMR methods have
been used to independently investigate the effect of charge
neutralization on Mb/b(5) binding. The neutralization of the
two heme propionates of ZnMb by formation of the heme
diester or, for the first time, the diamide increases the
second-order rate constant of the ET reaction between ZnMb
and cyt b(5) by as much as several 100-fold, depending on pH
and ionic strength, while causing negligible changes in
binding affinity. Brownian dynamic (BD) simulations and ET
pathway calculations provide insight into the protein
docking and ET process. The results support a new "dynamic
docking" paradigm for protein-protein reactions in which
numerous weakly bound conformations of the docked complex
contribute to the binding of cyt b(5) to Mb and Hb, but only
a very small subset of these are ET active, and this subset
does not include the conformations most favorable for
binding; the Mb surface is a large "target" with a small
"bullseye" for the cyt b(5) "arrow". This paradigm differs
sharply from the more familiar, "simple" docking within a
single, or narrow range of conformations, where binding
strength and ET reactivity increase in parallel. Likewise,
it is distinct from, although complementary to, the
well-known picture of conformational control of ET through
"gating", or a related picture of "conformational coupling".
The new model describes situations in which tight binding
does not correlate with efficient ET reactivity, and
explains how it is possible to modulate reactivity without
changing affinity. Such "decoupling" of reactivity from
binding clearly is of physiological relevance for the
reduction of met-Mb in muscle and of met-Hb in a red cell,
where tight binding of cyt b(5) to the high concentration of
ferrous-Mb/Hb would prevent the cytochrome from finding and
reducing the oxidized proteins; it likely is of
physiological relevance in other situations, as
well.},
Doi = {10.1021/ja0127032},
Key = {fds232035}
}
@article{fds304360,
Author = {Liang, Z-X and Kurnikov, IV and Nocek, JM and Mauk, AG and Beratan, DN and Hoffman, BM},
Title = {Dynamic docking and electron-transfer between cytochrome b5
and a suite of myoglobin surface-charge mutants.
Introduction of a functional-docking algorithm for
protein-protein complexes.},
Journal = {Journal of the American Chemical Society},
Volume = {126},
Number = {9},
Pages = {2785-2798},
Year = {2004},
Month = {March},
ISSN = {0002-7863},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14995196},
Abstract = {Horse myoglobin (Mb) provides a convenient "workbench" for
probing the effects of electrostatics on binding and
reactivity in the dynamic [Mb, cytochrome b(5)]
electron-transfer (ET) complex. We have combined mutagenesis
and heme neutralization to prepare a suite of six Mb
surface-charge variants: the [S92D]Mb and [V67R]Mb mutants
introduce additional charges on the "front" face, and
incorporation of the heme di-ester into each of these
neutralizes the charge on the heme propionates which further
increases the positive charge on the "front" face. For this
set of mutants, the nominal charge of Mb changes by -1 to +3
units relative to that for native Mb. For each member of
this set, we have measured the bimolecular quenching rate
constant (k(2)) for the photoinitiated (3)ZnDMb -->
Fe(3+)b(5) ET reaction as a function of ionic strength. We
find: (i) a dramatic decoupling of binding and reactivity,
in which k(2) varies approximately 10(3)-fold within the
suite of Mbs without a significant change in binding
affinity; (ii) the ET reaction occurs within the
"thermodynamic" or "rapid exchange" limit of the "Dynamic
Docking" model, in which a large ensemble of weakly bound
protein-protein configurations contribute to binding, but
only a few are reactive, as shown by the fact that the
zero-ionic-strength bimolecular rate constant varies
exponentially with the net charge on Mb; (iii) Brownian
dynamic docking profiles allow us to visualize the
microscopic basis of dynamic docking. To describe these
results we present a new theoretical approach which
mathematically combines PATHWAY donor/acceptor coupling
calculations with Poisson-Boltzmann-based electrostatics
estimates of the docking energetics in a Monte Carlo (MC)
sampling framework that is thus specially tailored to the
intermolecular ET problem. This procedure is extremely
efficient because it targets only the functionally active
complex geometries by introducing a "reactivity filter" into
the computations themselves, rather than as a subsequent
step. This efficiency allows us to employ more
computationally expensive and accurate methods to describe
the relevant intermolecular interaction energies and the
protein-mediated donor/acceptor coupling interactions. It is
employed here to compute the changes in the bimolecular rate
constant for ET between Mb and cyt b(5) upon variations in
the myoglobin surface charge, pH, and ionic
strength.},
Doi = {10.1021/ja038163l},
Key = {fds304360}
}
@misc{fds370704,
Author = {BERATAN, DN and ONUCHIC, JN},
Title = {DYNAMICAL EFFECTS ON BIMOLECULAR CHARGE-TRANSFER
REACTIONS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {195},
Pages = {171-PHYS},
Year = {1988},
Key = {fds370704}
}
@article{fds339224,
Author = {Skourtis, SS and Beratan, DN},
Title = {Editorial overview: Biological pathways for electrons,
protons and photo-excitations.},
Journal = {Current opinion in chemical biology},
Volume = {47},
Pages = {A1-A3},
Year = {2018},
Month = {December},
url = {http://dx.doi.org/10.1016/j.cbpa.2018.09.023},
Doi = {10.1016/j.cbpa.2018.09.023},
Key = {fds339224}
}
@article{fds231899,
Author = {Wierzbinski, E and de Leon, A and Yin, X and Balaeff, A and Davis, KL and Rapireddy, S and Venkatramani, R and Keinan, S and Ly, DH and Madrid, M and Beratan, DN and Achim, C and Waldeck, DH},
Title = {Effect of backbone flexibility on charge transfer rates in
peptide nucleic acid duplexes.},
Journal = {Journal of the American Chemical Society},
Volume = {134},
Number = {22},
Pages = {9335-9342},
Year = {2012},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22548314},
Abstract = {Charge transfer (CT) properties are compared between peptide
nucleic acid structures with an aminoethylglycine backbone
(aeg-PNA) and those with a γ-methylated backbone (γ-PNA).
The common aeg-PNA is an achiral molecule with a flexible
structure, whereas γ-PNA is a chiral molecule with a
significantly more rigid structure than aeg-PNA.
Electrochemical measurements show that the CT rate constant
through an aeg-PNA bridging unit is twice the CT rate
constant through a γ-PNA bridging unit. Theoretical
calculations of PNA electronic properties, which are based
on a molecular dynamics structural ensemble, reveal that the
difference in the CT rate constant results from the
difference in the extent of backbone fluctuations of aeg-
and γ-PNA. In particular, fluctuations of the backbone
affect the local electric field that broadens the energy
levels of the PNA nucleobases. The greater flexibility of
the aeg-PNA gives rise to more broadening, and a more
frequent appearance of high-CT rate conformations than in
γ-PNA.},
Doi = {10.1021/ja301677z},
Key = {fds231899}
}
@misc{fds370682,
Author = {KURNIKOV, IV and BERATAN, DN},
Title = {EFFECTIVE HAMILTONIAN APPROACH TO PROTEIN-MEDIATED
ELECTRON-TRANSFER},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {210},
Pages = {119-INOR},
Year = {1995},
Key = {fds370682}
}
@article{fds231898,
Author = {Lim, E and Kuznetsov, AE and Beratan, DN},
Title = {Effects of S-containing ligands on the structure and
electronic properties of CdnSen/CdnTen
nanoparticles (n = 3, 4, 6, and 9)},
Journal = {Chemical Physics},
Volume = {407},
Pages = {97-109},
Publisher = {Elsevier BV},
Year = {2012},
Month = {October},
ISSN = {0301-0104},
url = {http://dx.doi.org/10.1016/j.chemphys.2012.09.005},
Abstract = {To understand ligand capping effects on the structure and
electronic properties of CdnXn (X = Se, Te; n = 3, 4, 6, and
9) species, we performed density functional theory studies
of SCH2COOH-, SCH2CH2CO2H-, and SCH2CH 2NH2-capped
nanoparticles. CdnXn capping with all three capping groups
was found to produce significant NP distortions. All three
ligands destabilize the NP HOMOs and either stabilize or
destabilize their LUMOs, leading to closure of the HOMO/LUMO
gaps for all of the capped species, because the HOMO
destabilization effect is generally large than the LUMO
destabilization effect. The calculated absorption spectra of
bare and capped NPs, exemplified by CdnXn with n = 4 and 6,
show that all capping groups cause noticeable red shifts for
n = 4 and mostly blue shifts for n = 6. © 2012 Elsevier
B.V. All rights reserved.},
Doi = {10.1016/j.chemphys.2012.09.005},
Key = {fds231898}
}
@article{fds326592,
Author = {Beall, E and Ulku, S and Liu, C and Wierzbinski, E and Zhang, Y and Bae, Y and Zhang, P and Achim, C and Beratan, DN and Waldeck,
DH},
Title = {Effects of the Backbone and Chemical Linker on the Molecular
Conductance of Nucleic Acid Duplexes.},
Journal = {Journal of the American Chemical Society},
Volume = {139},
Number = {19},
Pages = {6726-6735},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1021/jacs.7b02260},
Abstract = {Scanning tunneling microscope break junction measurements
are used to examine how the molecular conductance of nucleic
acids depends on the composition of their backbone and the
linker group to the electrodes. Molecular conductances of 10
base pair long homoduplexes of DNA, aeg-PNA, γ-PNA, and a
heteroduplex of DNA/aeg-PNA with identical nucleobase
sequence were measured. The molecular conductance was found
to vary by 12 to 13 times with the change in backbone.
Computational studies show that the molecular conductance
differences between nucleic acids of different backbones
correlate with differences in backbone structural
flexibility. The molecular conductance was also measured for
duplexes connected to the electrode through two different
linkers, one directly to the backbone and one directly to
the nucleobase stack. While the linker causes an
order-of-magnitude increase in the overall conductance for a
particular duplex, the differences in the electrical
conductance with backbone composition are preserved. The
highest molecular conductance value, 0.06G<sub>0</sub>, was
measured for aeg-PNA duplexes with a base stack linker.
These findings reveal an important new strategy for creating
longer and more complex electroactive, nucleic acid
assemblies.},
Doi = {10.1021/jacs.7b02260},
Key = {fds326592}
}
@article{fds356168,
Author = {Yuly, JL and Zhang, P and Ru, X and Terai, K and Singh, N and Beratan,
DN},
Title = {Efficient and reversible electron bifurcation with either
normal or inverted potentials at the bifurcating
cofactor},
Journal = {Chem},
Volume = {7},
Number = {7},
Pages = {1870-1886},
Year = {2021},
Month = {July},
url = {http://dx.doi.org/10.1016/j.chempr.2021.03.016},
Abstract = {A longstanding mystery surrounding electron bifurcation is
the significance of inverted (or “crossed”) reduction
potentials of the two-electron bifurcating cofactor. Using a
many-electron open-system kinetic model, we show that
reversible and efficient electron bifurcation is possible
without inverted reduction potentials at the bifurcating
site if the absolute value of the difference between first
and second reduction potentials of the bifurcating species
is sufficiently large (on the scale of the redox-potential
span of the high- and low-potential branches). Surprisingly,
the case with strong, normally ordered potentials at the
bifurcating cofactor can produce electron bifurcation that
is just as effective as the case with strongly inverted
potentials. This finding amplifies the puzzle surrounding
the recruitment of inverted potentials in the few
well-characterized bifurcating systems of nature and
suggests that electron bifurcating cofactors without
strongly inverted potentials may yet be discovered.},
Doi = {10.1016/j.chempr.2021.03.016},
Key = {fds356168}
}
@article{fds346375,
Author = {Yuly, JL and Lubner, CE and Zhang, P and Beratan, DN and Peters,
JW},
Title = {Electron bifurcation: progress and grand
challenges.},
Journal = {Chemical communications (Cambridge, England)},
Volume = {55},
Number = {79},
Pages = {11823-11832},
Year = {2019},
Month = {October},
url = {http://dx.doi.org/10.1039/c9cc05611d},
Abstract = {Electron bifurcation moves electrons from a two-electron
donor to reduce two spatially separated one-electron
acceptors. If one of the electrons reduces a high-potential
(lower energy) acceptor, then the other electron may proceed
"uphill" to reduce a low-potential (higher energy) acceptor.
This mechanism is now considered the third mode of energy
transduction in biology, and offers promise for the
development of novel bioinspired energy conversion
strategies. Nature uses electron bifurcation to realize
highly sought-after reactions: reversible CO2 reduction,
nitrogen fixation, and hydrogen production. In this review,
we summarize the current understanding of electron
bifurcation, including both recent progress and outstanding
questions in understanding and developing artificial
electron bifurcation systems.},
Doi = {10.1039/c9cc05611d},
Key = {fds346375}
}
@article{fds328791,
Author = {Zhang, P and Yuly, JL and Lubner, CE and Mulder, DW and King, PW and Peters, JW and Beratan, DN},
Title = {Electron Bifurcation: Thermodynamics and Kinetics of
Two-Electron Brokering in Biological Redox
Chemistry.},
Journal = {Accounts of chemical research},
Volume = {50},
Number = {9},
Pages = {2410-2417},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1021/acs.accounts.7b00327},
Abstract = {How can proteins drive two electrons from a redox active
donor onto two acceptors at very different potentials and
distances? And how can this transaction be conducted without
dissipating very much energy or violating the laws of
thermodynamics? Nature appears to have addressed these
challenges by coupling thermodynamically uphill and downhill
electron transfer reactions, using two-electron donor
cofactors that have very different potentials for the
removal of the first and second electron. Although electron
bifurcation is carried out with near perfection from the
standpoint of energy conservation and electron delivery
yields, it is a biological energy transduction paradigm that
has only come into focus recently. This Account provides an
exegesis of the biophysical principles that underpin
electron bifurcation. Remarkably, bifurcating electron
transfer (ET) proteins typically send one electron uphill
and one electron downhill by similar energies, such that the
overall reaction is spontaneous, but not profligate.
Electron bifurcation in the NADH-dependent reduced
ferredoxin: NADP<sup>+</sup> oxidoreductase I (Nfn) is
explored in detail here. Recent experimental progress in
understanding the structure and function of Nfn allows us to
dissect its workings in the framework of modern ET theory.
The first electron that leaves the two-electron donor flavin
(L-FAD) executes a positive free energy "uphill" reaction,
and the departure of this electron switches on a second
thermodynamically spontaneous ET reaction from the flavin
along a second pathway that moves electrons in the opposite
direction and at a very different potential. The singly
reduced ET products formed from the bifurcating flavin are
more than two nanometers distant from each other. In Nfn,
the second electron to leave the flavin is much more
reducing than the first: the potentials are said to be
"crossed." The eventually reduced cofactors, NADH and
ferredoxin in the case of Nfn, perform crucial downstream
redox processes of their own. We dissect the thermodynamics
and kinetics of electron bifurcation in Nfn and find that
the key features of electron bifurcation are (1) spatially
separated transfer pathways that diverge from a two-electron
donor, (2) one thermodynamically uphill and one downhill
redox pathway, with a large negative shift in the donor's
reduction potential after departure of the first electron,
and (3) electron tunneling and activation factors that
enable bifurcation, producing a 1:1 partitioning of
electrons onto the two pathways. Electron bifurcation is
found in the CO<sub>2</sub> reducing pathways of
methanogenic archaea, in the hydrogen pathways of
hydrogenases, in the nitrogen fixing pathway of Fix, and in
the mitochondrial charge transfer chain of complex III,
cytochrome bc<sub>1</sub>. While crossed potentials may
offer the biological advantage of producing tightly
regulated high energy reactive species, neither kinetic nor
thermodynamic considerations mandate crossed potentials to
generate successful electron bifurcation. Taken together,
the theoretical framework established here, focusing on the
underpinning electron tunneling barriers and activation free
energies, explains the logic of electron bifurcation that
enables energy conversion and conservation in Nfn, points
toward bioinspired schemes to execute multielectron redox
chemistry, and establishes a roadmap for examining novel
electron bifurcation networks in nature.},
Doi = {10.1021/acs.accounts.7b00327},
Key = {fds328791}
}
@misc{fds22308,
Author = {D.N. Beratan and W.L. Luken},
Title = {Electron Correlation and the Chemical Bond},
Publisher = {Freewater Film Productions, Durham, NC},
Year = {1980},
Key = {fds22308}
}
@article{fds358329,
Author = {Valdiviezo, J and Zhang, P and Beratan, DN},
Title = {Electron ratcheting in self-assembled soft
matter.},
Journal = {The Journal of chemical physics},
Volume = {155},
Number = {5},
Pages = {055102},
Year = {2021},
Month = {August},
url = {http://dx.doi.org/10.1063/5.0044420},
Abstract = {Ratcheted multi-step hopping electron transfer systems can
plausibly produce directional charge transport over very
large distances without requiring a source-drain voltage
bias. We examine molecular strategies to realize ratcheted
charge transport based on multi-step charge hopping, and we
illustrate two ratcheting mechanisms with examples based on
DNA structures. The charge transport times and currents that
may be generated in these assemblies are also estimated
using kinetic simulations. The first ratcheting mechanism
described for nanoscale systems requires local electric
fields on the 10<sup>9</sup> V/m scale to realize nearly
100% population transport. The second ratcheting mechanism
for even larger systems, based on electrochemical gating, is
estimated to generate currents as large as 0.1 pA for DNA
structures that are a few μm in length with a gate voltage
of about 5 V, a magnitude comparable to currents measured
in DNA wires at the nanoscale when a source-drain voltage
bias of similar magnitude is applied, suggesting an approach
to considerably extend the distance range over which DNA
charge transport devices may operate.},
Doi = {10.1063/5.0044420},
Key = {fds358329}
}
@article{fds231959,
Author = {Kawatsu, T and Beratan, DN},
Title = {Electron transfer between cofactors in protein domains
linked by a flexible tether},
Journal = {Chemical Physics},
Volume = {326},
Number = {1},
Pages = {259-269},
Publisher = {Elsevier BV},
Year = {2006},
Month = {July},
ISSN = {0301-0104},
url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6TFM-4JBGJBR-2-4B&_cdi=5230&_user=38557&_orig=browse&_coverDate=07%2F11%2F2006&_sk=996739998&view=c&wchp=dGLbVzb-zSkWz&md5=4d2f73f773a8820794bf297c7a6a0854&ie=/sdarticle.pdf},
Abstract = {Some key electron-transfer (ET) proteins have domains
containing redox cofactors connected by a flexible tether.
The relative motion of the domains is essential for reaction
because of the strong ET rate dependence on distance. The
constrained conformational flexibility produces a kinetic
regime intermediate between "unimolecular" and
"bimolecular". We used a simple model for ET coupled to
conformational diffusion to explore the structure dependence
of the ET kinetics. The model describes the evolution of an
initially prepared reduced donor state, and recovers the
diffusion and electron tunneling-limited regimes. The
restriction of the conformational space imposed by the
tether introduces an entropic component to the effective
donor-acceptor interaction potential. As such, the tether
length may control the transition between the electron
tunneling and diffusion-limited regimes. © 2006 Elsevier
B.V. All rights reserved.},
Doi = {10.1016/j.chemphys.2006.01.020},
Key = {fds231959}
}
@article{fds232023,
Author = {Liang, ZX and Kurnikov, IV and Nocek, JM and Mauk, AG and Beratan, DN and Hoffman, BM},
Title = {Electron transfer between cytochrome b5 and a suite of
myoglobin surface-charge mutants; Introduction of a
funtional-docking algorithm for dynamically-docked
protein-protein complexes},
Journal = {J. Am. Chem. Soc.},
Volume = {126},
Number = {9},
Pages = {2785-2798},
Year = {2004},
ISSN = {0002-7863},
url = {http://pubs.acs.org/cgi-bin/article.cgi/jacsat/2004/126/i09/pdf/ja038163l.pdf},
Abstract = {Horse myoglobin (Mb) provides a convenient "workbench" for
probing the effects of electrostatics on binding and
reactivity in the dynamic [Mb, cytochrome b(5)]
electron-transfer (ET) complex. We have combined mutagenesis
and heme neutralization to prepare a suite of six Mb
surface-charge variants: the [S92D]Mb and [V67R]Mb mutants
introduce additional charges on the "front" face, and
incorporation of the heme di-ester into each of these
neutralizes the charge on the heme propionates which further
increases the positive charge on the "front" face. For this
set of mutants, the nominal charge of Mb changes by -1 to +3
units relative to that for native Mb. For each member of
this set, we have measured the bimolecular quenching rate
constant (k(2)) for the photoinitiated (3)ZnDMb -->
Fe(3+)b(5) ET reaction as a function of ionic strength. We
find: (i) a dramatic decoupling of binding and reactivity,
in which k(2) varies approximately 10(3)-fold within the
suite of Mbs without a significant change in binding
affinity; (ii) the ET reaction occurs within the
"thermodynamic" or "rapid exchange" limit of the "Dynamic
Docking" model, in which a large ensemble of weakly bound
protein-protein configurations contribute to binding, but
only a few are reactive, as shown by the fact that the
zero-ionic-strength bimolecular rate constant varies
exponentially with the net charge on Mb; (iii) Brownian
dynamic docking profiles allow us to visualize the
microscopic basis of dynamic docking. To describe these
results we present a new theoretical approach which
mathematically combines PATHWAY donor/acceptor coupling
calculations with Poisson-Boltzmann-based electrostatics
estimates of the docking energetics in a Monte Carlo (MC)
sampling framework that is thus specially tailored to the
intermolecular ET problem. This procedure is extremely
efficient because it targets only the functionally active
complex geometries by introducing a "reactivity filter" into
the computations themselves, rather than as a subsequent
step. This efficiency allows us to employ more
computationally expensive and accurate methods to describe
the relevant intermolecular interaction energies and the
protein-mediated donor/acceptor coupling interactions. It is
employed here to compute the changes in the bimolecular rate
constant for ET between Mb and cyt b(5) upon variations in
the myoglobin surface charge, pH, and ionic
strength.},
Doi = {10.1021/ja038163l},
Key = {fds232023}
}
@article{fds337577,
Author = {Teo, RD and Terai, K and Migliore, A and Beratan,
DN},
Title = {Electron transfer characteristics of 2'-deoxy-2'-fluoro-arabinonucleic
acid, a nucleic acid with enhanced chemical
stability.},
Journal = {Physical chemistry chemical physics : PCCP},
Volume = {20},
Number = {41},
Pages = {26063-26067},
Year = {2018},
Month = {November},
url = {http://dx.doi.org/10.1039/c8cp04816a},
Abstract = {The non-biological nucleic acid 2'-deoxy-2'-fluoro-arabinonucleic
acid (2'F-ANA) may be of use because of its higher chemical
stability than DNA in terms of resistance to hydrolysis and
nuclease degradation. In order to investigate the charge
transfer characteristics of 2'F-ANA, of relevance to
applications in nucleic acid-based biosensors and chip
technologies, we compare the electronic couplings for hole
transfer between stacked nucleobase pairs in DNA and 2'F-ANA
by carrying out density functional theory (DFT) calculations
on geometries taken from molecular dynamics simulations. We
find similar averages and distribution widths of the
base-pair couplings in the two systems. On the basis of this
result, 2'F-ANA is expected to have charge transfer
properties similar to those of DNA, while offering the
advantage of enhanced chemical stability. As such, 2'F-ANA
may serve as a possible alternative to DNA for use in a
broad range of nanobiotechnological applications.
Furthermore, we show that the (experimentally observed)
enhanced chemical stability resulting from the backbone
modifications does not cause reduced fluctuations of the
base-pair electronic couplings around the values found for
"ideal" B-DNA (with standard step parameter values). Our
study also supports the use of a DFT implementation, with
the M11 functional, of the wave function overlap method to
compute effective electronic couplings in nucleic acid
systems.},
Doi = {10.1039/c8cp04816a},
Key = {fds337577}
}
@article{fds231992,
Author = {Skourtis, SS and Beratan, DN},
Title = {Electron transfer contact maps},
Journal = {Journal of Physical Chemistry B},
Volume = {101},
Number = {7},
Pages = {1215-1234},
Publisher = {American Chemical Society (ACS)},
Year = {1997},
Month = {February},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcbfk/1997/101/i07/pdf/jp9619245.pdf},
Abstract = {An exact approach is introduced to establish and compare
quantitative structure-function relationships in electron
transfer proteins. The strategy is based on the idea of an
electron transfer contact map and is motivated by reduced
descriptions of 3D protein structure that emphasize the
folded conformation (ribbon drawings, distance contact maps,
and Ramachandran plots). Electron transfer contact maps
render the protein-mediated electronic coupling information
in a compact and transferable form. The method includes all
contributions of multiple interfering tunneling pathways to
the tunneling propagation and can be implemented at many
levels of electronic structure theory. Contact maps are used
to interpret the influence of mutations on electronic
propagation in model peptides.},
Doi = {10.1021/jp9619245},
Key = {fds231992}
}
@article{fds232030,
Author = {Risser, SM and Beratan, DN and Meade, TJ},
Title = {Electron Transfer in DNA: Predictions of Exponential Growth
and Decay of Coupling with Donor-Acceptor
Distance},
Journal = {Journal of the American Chemical Society},
Volume = {115},
Number = {6},
Pages = {2508-2510},
Publisher = {American Chemical Society (ACS)},
Year = {1993},
Month = {March},
ISSN = {0002-7863},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1993KU90200057&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.1021/ja00059a057},
Key = {fds232030}
}
@article{fds231915,
Author = {Venkatramani, R and Keinan, S and Balaeff, A and Beratan,
DN},
Title = {Electron transfer in nucleic acids: Black, white, and
gray},
Journal = {Coord. Chem. Revs.},
Number = {255},
Pages = {635-648},
Year = {2011},
Key = {fds231915}
}
@article{fds231997,
Author = {Zusman, LD and Beratan, DN},
Title = {Electron transfer in the photosynthetic reaction center:
mechanistic implications of mutagenesis studies.},
Journal = {Spectrochimica acta. Part A, Molecular and biomolecular
spectroscopy},
Volume = {54A},
Number = {9},
Pages = {1211-1218},
Year = {1998},
Month = {August},
ISSN = {1386-1425},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9734088},
Abstract = {A phenomenological analysis of the driving force effects in
photosynthetic reaction centers modified by mutagenesis and
also by chemical means is presented. Different parameter
sets associated with different mechanisms of electron
transfer are consistent with the mutagenesis experiments.
However, only one parameter set--connected with a sequential
mechanism of electron transfer--is consistent with all known
experimental data. Arguments explaining why the sequential
mechanism of electron transfer is selected by nature in the
wild type reaction center are provided. Why the driving
force of the wild type reaction center is about 0.25 eV is
explained and new driving force effects are
predicted.},
Doi = {10.1016/s1386-1425(98)00071-7},
Key = {fds231997}
}
@misc{fds370681,
Author = {Zusman, LD and Beratan, DN},
Title = {Electron transfer in the photosynthetic reaction center:
Mechanistic implications of mutagenesis studies.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {215},
Pages = {U190-U190},
Year = {1998},
Key = {fds370681}
}
@article{fds304365,
Author = {Zusman, LD and Beratan, DN},
Title = {Electron transfer in three-center chemical
systems},
Journal = {Journal of Chemical Physics},
Volume = {110},
Number = {21},
Pages = {10468-10481},
Publisher = {AIP Publishing},
Year = {1999},
Month = {June},
url = {http://dx.doi.org/10.1063/1.478976},
Abstract = {Electron transfer is examined in three redox center
(donor-bridge-acceptor) systems. Here, electron transfer
cannot be described as arising from one-dimensional
diffusional motion along the reaction coordinate. Instead,
two-dimensional diffusion over two statistically independent
reaction coordinates emerges. We show that electron transfer
in three-center systems can be reduced to electron transfer
between the pairs of adjacent centers. The interplay between
sequential and superexchange mechanisms is examined. New
expressions for the electron transfer rate, including
effects of the two-dimensional reaction coordinate and of
solvent dynamics, are derived. Using this analysis, new
driving force effects are predicted, and rich behavior is
revealed. © 1999 American Institute of Physics.},
Doi = {10.1063/1.478976},
Key = {fds304365}
}
@article{fds232002,
Author = {Zusman, LD and Beratan, DN},
Title = {Electron transfer in three-state systems},
Journal = {J. Chem. Phys.},
Volume = {110},
Number = {21},
Pages = {10468-10481},
Year = {1999},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000110000021010468000001&idtype=cvips},
Abstract = {Electron transfer is examined in three redox center
(donor-bridge-acceptor) systems. Here, electron transfer
cannot be described as arising from one-dimensional
diffusional motion along the reaction coordinate. Instead,
two-dimensional diffusion over two statistically independent
reaction coordinates emerges. We show that electron transfer
in three-center systems can be reduced to electron transfer
between the pairs of adjacent centers. The interplay between
sequential and superexchange mechanisms is examined. New
expressions for the electron transfer rate, including
effects of the two-dimensional reaction coordinate and of
solvent dynamics, are derived. Using this analysis, new
driving force effects are predicted, and rich behavior is
revealed. © 1999 American Institute of Physics.},
Key = {fds232002}
}
@article{fds231999,
Author = {Beratan, D and Skourtis, S},
Title = {Electron transfer mechanisms.},
Journal = {Current opinion in chemical biology},
Volume = {2},
Number = {2},
Pages = {235-243},
Year = {1998},
Month = {April},
url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRX-457KS2R-4K-1&_cdi=6246&_user=38557&_orig=browse&_coverDate=04%2F30%2F1998&_sk=999979997&view=c&wchp=dGLbVzz-zSkWz&md5=18303de1120376b338b92b2c589c551d&ie=/sdarticle.pdf},
Abstract = {The tunneling pathway framework description of protein
electron transfer reactions has prompted a lively discussion
of how structure and evolution influence electron transfer
rates. Recent protein and model system experiments,
performed in solution and in organized media, are providing
answers. The molecular mechanisms of DNA electron transfer
reactions are being probed as well with new theoretical and
experimental strategies.},
Doi = {10.1016/s1367-5931(98)80065-3},
Key = {fds231999}
}
@article{fds231852,
Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Schmehl, RH and Beratan, DN and Rubtsov, IV},
Title = {Electron transfer rate modulation in a compact Re(I)
donor-acceptor complex.},
Journal = {Dalton transactions (Cambridge, England :
2003)},
Volume = {44},
Number = {18},
Pages = {8609-8616},
Year = {2015},
Month = {May},
ISSN = {1477-9226},
url = {http://dx.doi.org/10.1039/c4dt02145b},
Abstract = {Formation of the charge transfer state with the rate
constant of (10 ps)(-1) has recently been reported for the
complex fac-[Re(I)(CO)3(DCEB)(3DMABN)] (ReEBA); where 3DMABN
is 3-dimethylaminobenzonitrile, serving as an electron
donor, and DCEB is 4,4'-(dicarboxyethyl)-2,2-bipyridine,
serving as an electron acceptor (Y. Yue et al., J. Phys.
Chem. A, 118, 10407). 3-Pulse UV-pump - IR-pump - IR-probe
spectroscopy is used in this work to study how the charge
separation reaction in ReEBA to form a ligand to ligand
charge transfer state (LLCT) can be modulated by vibrational
excitation of various modes of the complex. While no
significant rate modulation was found when the cyano group
stretching mode of the 3DMABN donor was excited, a sizable
effect was found when the ring stretching mode of the DCEB
acceptor was excited. The accumulation of the charge
separated state (LLCT state) in the 3-pulse experiment was
observed as a sharp excited-state vibrational peak of the
symmetric stretch of the three facial carbonyl groups,
νSS(CO). Modeling indicates that the rate of charge
separation is increased by ca. 28% when vibrational
excitation is present. The vibronic coupling signal of the
bpy ring mode and νSS(CO) as well as the energy transport
dynamics from bpy to carbonyl contributed to the 3-pulse
signal and was studied as well using the 3-pulse method.
Energy transport between the same modes in the ground
electronic state was measured by relaxation-assisted
two-dimensional infrared (RA 2DIR) spectroscopy. The energy
transport times of 4 ± 0.7 and 5 ± 1.5 ps were found for
the ground and excited electronic states.},
Doi = {10.1039/c4dt02145b},
Key = {fds231852}
}
@article{fds375213,
Author = {Mendis, KC and Li, X and Valdiviezo, J and Banziger, SD and Zhang, P and Ren, T and Beratan, DN and Rubtsov, IV},
Title = {Electron transfer rate modulation with mid-IR in
butadiyne-bridged donor-bridge-acceptor compounds.},
Journal = {Physical chemistry chemical physics : PCCP},
Volume = {26},
Number = {3},
Pages = {1819-1828},
Year = {2024},
Month = {January},
url = {http://dx.doi.org/10.1039/d3cp03175f},
Abstract = {Controlling electron transfer (ET) processes in
donor-bridge-acceptor (DBA) compounds by mid-IR excitation
can enhance our understanding of the ET dynamics and may
find practical applications in molecular sensing and
molecular-scale electronics. Alkyne moieties are attractive
to serve as ET bridges, as they offer the possibility of
fast ET and present convenient vibrational modes to perturb
the ET dynamics. Yet, these bridges introduce complexity
because of the strong torsion angle dependence of the ET
rates and transition dipoles among electronic states and a
shallow torsion barrier. In this study, we implemented
ultrafast 3-pulse laser spectroscopy to investigate how the
ET from the dimethyl aniline (D) electron donor to the
<i>N</i>-isopropyl-1,8-napthalimide (NAP) electron acceptor
can be altered by exciting the CC stretching mode
(<i>ν</i><sub>CC</sub>) of the butadiyne bridge linking
the donor and acceptor. The electron transfer was initiated
by electronically exciting the acceptor moiety at 400 nm,
followed by vibrational excitation of the alkyne,
<i>ν</i><sub>CC</sub>, and detecting the changes in the
absorption spectrum in the visible spectral region. The
experiments were performed at different delay times
<i>t</i><sub>1</sub> and <i>t</i><sub>2</sub>, which are the
delays between UV-mid-IR and mid-IR-Vis pulses,
respectively. Two sets of torsion-angle conformers were
identified, one featuring a very fast mean ET time of 0.63
ps (group A) and another featuring a slower mean ET time of
4.3 ps (group B), in the absence of the mid-IR excitation.
TD-DFT calculations were performed to determine key torsion
angle dependent molecular parameters, including the
electronic and vibrational transition dipoles, transition
frequencies, and electronic couplings. To describe the
3-pulse data, we developed a kinetic model that includes a
locally excited, acceptor-based S2 state, a charge separated
S1 state, and their vibrationally excited counterparts, with
either excited <i>ν</i><sub>CC</sub> (denoted as
S1A<sup>tr</sup>, S1B<sup>tr</sup>, S2A<sup>tr</sup>, and
S2B<sup>tr</sup>, where tr stands for the excited triplet
bond, <i>ν</i><sub>CC</sub>) or excited daughter modes
of the <i>ν</i><sub>CC</sub> relaxation
(S1A<sup>h</sup>, S1B<sup>h</sup>, S2A<sup>h</sup>, and
S2B<sup>h</sup>, where h stands for vibrationally hot
species). The kinetic model was solved analytically, and the
species-associated spectra (SAS) were determined numerically
using a matrix approach, treating first the experiments with
longer <i>t</i><sub>1</sub> delays and then using the
already determined SAS for modeling the experiments with
shorter <i>t</i><sub>1</sub> delays. Strong vibronic
coupling of <i>ν</i><sub>CC</sub> and of vibrationally
hot states makes the analysis complicated. Nevertheless, the
SAS were identified and the ET rates of the vibrationally
excited species, S2A<sup>tr</sup>, S2B<sup>tr</sup> and
S2B<sup>h</sup>, were determined. The results show that the
ET rate for the S2A species is <i>ca.</i> 1.2-fold slower
when the <i>ν</i><sub>CC</sub> mode is excited. The ET
rate for species S2B is slower by <i>ca.</i> 1.3-fold if the
compound is vibrationally hot and is essentially unchanged
when the <i>ν</i><sub>CC</sub> mode is excited. The SAS
determined for the tr and h species resemble the SAS for
their respective precursor species in the 2-pulse transient
absorption experiments, which validates the procedure used
and the results.},
Doi = {10.1039/d3cp03175f},
Key = {fds375213}
}
@misc{fds22196,
Author = {G.C. Walker and D.N. Beratan},
Title = {Electron Transfer Reactions},
Booktitle = {"Electron Transfer Reactions"},
Publisher = {Institute of Physics Press},
Editor = {J. Moore and N. Spencer},
Year = {2001},
Key = {fds22196}
}
@misc{fds222354,
Author = {D.N. Beratan and S.S. Skourtis},
Title = {Electron transfer through proteins},
Pages = {625-630},
Booktitle = {Encyclopedia of Biophysics},
Publisher = {Springer Verlag},
Editor = {G. Roberts and ed},
Year = {2013},
Key = {fds222354}
}
@misc{fds197284,
Author = {D.N. Beratan and S.S. Skourtis},
Title = {Electron transfer through proteins},
Booktitle = {Encyclopedia of Biophysics},
Publisher = {Springer Verlag},
Year = {2011},
Key = {fds197284}
}
@article{fds231859,
Author = {Winkler, JR and Gray, HB and Prytkova, TR and Kurnikov, IV and Beratan,
DN},
Title = {Electron Transfer through Proteins},
Pages = {15-33},
Booktitle = {Bioelectronics},
Publisher = {Wiley-VCH Verlag GmbH & Co. KGaA},
Editor = {I. Willner and E. Katz},
Year = {2005},
Month = {May},
url = {http://dx.doi.org/10.1002/352760376X.ch2},
Doi = {10.1002/352760376X.ch2},
Key = {fds231859}
}
@article{fds231981,
Author = {Onuchic, JN and De Andrade and PCP and Beratan, DN},
Title = {Electron tunneling pathways in proteins: A method to compute
tunneling matrix elements in very large systems},
Journal = {The Journal of Chemical Physics},
Volume = {95},
Number = {2},
Pages = {1131-1138},
Publisher = {AIP Publishing},
Year = {1991},
Month = {January},
ISSN = {0021-9606},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000095000002001131000001&idtype=cvips},
Abstract = {A tight-binding Hamiltonian and Dyson's equation method are
described that allow the computation of the tunneling matrix
elements between electron donor and acceptor sites in a
protein. The method is exact and computationally tractable.
The Green's function matrix elements of the bridge are
computed using a strategy that builds up the bridge one
orbital at a time, allowing inclusion of all orbitals on
proposed tunneling pathways and elsewhere. The tunneling
matrix element is determined directly from the bridge
Green's function. A simple representation of a helical
protein segment is used to illustrate the method and its
ability to include contributions from high-order
backscattering and multiple pathway interference in the
donor-acceptor coupling. © 1991 American Institute of
Physics.},
Doi = {10.1063/1.461142},
Key = {fds231981}
}
@article{fds232048,
Author = {Beratan, DN and Onuchic, JN},
Title = {Electron tunneling pathways in proteins: influences on the
transfer rate.},
Journal = {Photosynthesis research},
Volume = {22},
Number = {3},
Pages = {173-186},
Year = {1989},
Month = {December},
ISSN = {0166-8595},
url = {http://dx.doi.org/10.1007/bf00048296},
Abstract = {A strategy for calculating the tunneling matrix element
dependence on the medium intervening between donor and
acceptor in specific proteins is described. The scheme is
based on prior studies of small molecules and is general
enough to allow inclusion of through bond and through space
contributions to the electronic tunneling interaction. This
strategy should allow the prediction of relative electron
transfer rates in a number of proteins. It will therefore
serve as a design tool and will be explicitly testable, in
contrast with calculations on single molecules. As an
example, the method is applied to ruthenated myoglobin and
the tunneling matrix elements are estimated. Quantitative
improvements of the model are described and effects due to
motion of the bridging protein are discussed. The method
should be of use for designing target proteins having
tailored electron transfer rates for production with site
directed mutagenesis. The relevance of the technique to
understanding certain photosynthetic reaction center
electron transfer rates is discussed.},
Doi = {10.1007/bf00048296},
Key = {fds232048}
}
@misc{fds22279,
Author = {D.N. Beratan and J.N. Onuchic},
Title = {Electron tunneling pathways: from model compounds to
proteins},
Pages = {71-90},
Booktitle = {ACS Advance in Chemistry Series volume 228, Electron
transfer in organic, and biological systems},
Editor = {J.R. Bolton and N. Mataga and G. McLendon},
Year = {1991},
Key = {fds22279}
}
@article{fds231973,
Author = {Beratan, DN and Onuchic, JN and Hopfield, JJ},
Title = {Electron tunneling through covalent and noncovalent pathways
in proteins},
Journal = {The Journal of Chemical Physics},
Volume = {86},
Number = {8},
Pages = {4488-4498},
Publisher = {AIP Publishing},
Year = {1987},
Month = {January},
ISSN = {0021-9606},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000086000008004488000001&idtype=cvips},
Abstract = {A model is presented for electron tunneling in proteins
which allows the donor-acceptor interaction to be mediated
by the covalent bonds between amino acids and noncovalent
contacts between amino acid chains. The important tunneling
pathways are predicted to include mostly bonded groups with
less favorable nonbonded interactions being important when
the through bond pathway is prohibitively long. In some
cases, vibrational motion of nonbonded groups along the
tunneling pathway strongly inluences the temperature
dependence of the rate. Quantitative estimates for the sizes
of these noncovalent interactions are made and their role in
protein mediated electron transport is discussed. © 1987
American Institute of Physics.},
Doi = {10.1063/1.452723},
Key = {fds231973}
}
@misc{fds184126,
Author = {D.N. Beratan and S.S. Skourtis},
Title = {Electron tunneling through proteins},
Booktitle = {Encyclopedia of Biophysics (In Press)},
Publisher = {Springer Press},
Year = {2010},
Key = {fds184126}
}
@article{fds232026,
Author = {Beratan, DN},
Title = {Electron Tunneling through Rigid Molecular Bridges:
Bicyclo[2.2.2]octane},
Journal = {Journal of the American Chemical Society},
Volume = {108},
Number = {15},
Pages = {4321-4326},
Publisher = {American Chemical Society (ACS)},
Year = {1986},
Month = {January},
ISSN = {0002-7863},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1986/108/i15/pdf/ja00275a014.pdf},
Abstract = {Electron tunneling through polymers of bicyclo[2.2.2]octane
is studied. The repeating nature of the linker allows
prediction of the dependence of the tunneling matrix element
on distance and electronic energy by a semiempirical method
exploiting the translational symmetry of the linker.
Specific predictions for the dependence of rate on distance
are made for recently synthesized photosynthetic model
compounds containing porphyrins and quinones linked by this
bridge. A large difference between the decay of rate with
distance is predicted for the forward electron transfer in
these model compounds compared with the reverse electron
transfer. The effects of linker topology on the
donor-acceptor interaction in several linkers are compared,
and a heuristic rule is quantitated. The ability of the
[2.2.2] linker to mediate the donor-acceptor interaction is
shown to have an energy dependence determined by the
symmetry of the donor and acceptor orbitals relative to the
linker orbitals. © 1986, American Chemical Society. All
rights reserved.},
Doi = {10.1021/ja00275a014},
Key = {fds232026}
}
@article{fds375214,
Author = {Dunlap-Shohl, WA and Tabassum, N and Zhang, P and Shiby, E and Beratan,
DN and Waldeck, DH},
Title = {Electron-donating functional groups strengthen
ligand-induced chiral imprinting on CsPbBr3
quantum dots.},
Journal = {Scientific reports},
Volume = {14},
Number = {1},
Pages = {336},
Year = {2024},
Month = {January},
url = {http://dx.doi.org/10.1038/s41598-023-50595-2},
Abstract = {Chiral perovskite nanoparticles and films are promising for
integration in emerging spintronic and optoelectronic
technologies, yet few design rules exist to guide the
development of chiral material properties. The chemical
space of potential building blocks for these nanostructures
is vast, and the mechanisms through which organic ligands
can impart chirality to the inorganic perovskite lattice are
not well understood. In this work, we investigate how the
properties of chiral ammonium ligands, the most common
organic ligand type used with perovskites, affect the
circular dichroism of strongly quantum confined
CsPbBr<sub>3</sub> nanocrystals. We show that aromatic
ammonium ligands with stronger electron-donating groups lead
to higher-intensity circular dichroism associated with the
lowest-energy excitonic transition of the perovskite
nanocrystal. We argue that this behavior is best explained
by a modulation of the exciton wavefunction overlap between
the nanocrystal and the organic ligand, as the functional
groups on the ligand can shift electron density toward the
organic species-perovskite lattice interface to increase the
imprinting.},
Doi = {10.1038/s41598-023-50595-2},
Key = {fds375214}
}
@article{fds313865,
Author = {BERATAN, DN and ONUCHIC, JN},
Title = {ELECTRON-TRANSFER - FROM MODEL COMPOUNDS TO
PROTEINS},
Journal = {ADVANCES IN CHEMISTRY SERIES},
Number = {228},
Pages = {71-90},
Publisher = {AMER CHEMICAL SOC},
Year = {1991},
Month = {January},
ISSN = {0065-2393},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1991GD62900006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Key = {fds313865}
}
@misc{fds370707,
Author = {ONUCHIC, JN and BERATAN, DN and JORAN, AD and LELAND, BL and HOPFIELD,
JJ},
Title = {ELECTRON-TRANSFER IN PHOTOSYNTHETIC MODEL SYSTEMS -
EXPERIMENTS AND THEORY},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {192},
Pages = {363-INOR},
Year = {1986},
Key = {fds370707}
}
@misc{fds370686,
Author = {SKOURTIS, SS and BERATAN, DN},
Title = {ELECTRON-TRANSFER RAMACHANDRAN PLOTS - STRUCTURAL MOTIFS AND
ELECTRON PROPAGATION IN PROTEINS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {210},
Pages = {117-INOR},
Year = {1995},
Key = {fds370686}
}
@misc{fds370690,
Author = {ONUCHIC, JN and REGAN, JJ and SKOURTIS, SS and BERATAN,
DN},
Title = {ELECTRON-TUNNELING IN PROTEINS - SINGLE OR MULTIPLE
PATHWAYS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {208},
Pages = {78-PHYS},
Year = {1994},
Key = {fds370690}
}
@misc{fds370689,
Author = {BERATAN, DN and ONUCHIC, JN and CASIMIRO, DR and GRAY, HB and WINKLER,
JR},
Title = {ELECTRON-TUNNELING IN RUTHENIUM-MODIFIED
CYTOCHROME-C},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {208},
Pages = {357-PMSE},
Year = {1994},
Key = {fds370689}
}
@misc{fds370692,
Author = {RISSER, SM and REGAN, JJ and ONUCHIC, JN and BERATAN,
DN},
Title = {ELECTRON-TUNNELING PATHS IN MACROMOLECULES},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {206},
Pages = {82-PHYS},
Year = {1993},
Key = {fds370692}
}
@misc{fds370698,
Author = {BERATAN, DN},
Title = {ELECTRON-TUNNELING PATHWAYS IN NATIVE AND MODIFIED
PROTEINS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {202},
Pages = {133-BIOL},
Year = {1991},
Key = {fds370698}
}
@misc{fds370697,
Author = {LEITE, VP and BERATAN, DN and ONUCHIC, JN},
Title = {ELECTRON-TUNNELING PATHWAYS IN PROTEINS},
Journal = {FASEB JOURNAL},
Volume = {6},
Number = {1},
Pages = {A174-A174},
Booktitle = {Metal Ions in Biological Systems},
Publisher = {Marcel Dekker Press, New York},
Editor = {H. Sigel and A. Sigel},
Year = {1992},
Key = {fds370697}
}
@article{fds232040,
Author = {Beratan, DN and Onuchic, JN and Winkler, JR and Gray,
HB},
Title = {Electron-tunneling pathways in proteins.},
Journal = {Science (New York, N.Y.)},
Volume = {258},
Number = {5089},
Pages = {1740-1741},
Year = {1992},
Month = {December},
ISSN = {0036-8075},
url = {http://www.ncbi.nlm.nih.gov/pubmed/1334572},
Doi = {10.1126/science.1334572},
Key = {fds232040}
}
@article{fds304363,
Author = {Beratan, DN and Nelson Onuchic and J and Betts, JN and Bowler, BE and Gray,
HB},
Title = {Electron-Tunneling Pathways in Ruthenated
Proteins},
Journal = {Journal of the American Chemical Society},
Volume = {112},
Number = {22},
Pages = {7915-7921},
Publisher = {American Chemical Society (ACS)},
Year = {1990},
Month = {January},
ISSN = {0002-7863},
url = {http://dx.doi.org/10.1021/ja00178a011},
Abstract = {We implement a numerical algorithm to survey proteins for
electron-tunneling pathways. Insight is gained into the
nature of the mediation process in long-distance
electron-transfer reactions. The dominance of covalent and
hydrogen bond pathways is shown. The method predicts the
relative electronic couplings in ruthenated myoglobin and
cytochrome c consistent with measured electron-transfer
rates. It also allows the design of long-range
electron-transfer systems. Qualitative differences between
pathways arise from the protein secondary structure. Effects
of this sort are not predicted from simpler models that
neglect various details of the protein electronic structure.
© 1990, American Chemical Society. All rights
reserved.},
Doi = {10.1021/ja00178a011},
Key = {fds304363}
}
@book{fds197288,
Title = {Electronic and magnetic properties of chiral molecules and
supramolecular architectures},
Volume = {298},
Publisher = {Springer},
Editor = {D.N. Beratan},
Year = {2011},
Key = {fds197288}
}
@misc{fds370663,
Author = {Yates, JT and Lee, J and Lee, JG and Beratan, DN and Balabin,
I},
Title = {Electronic conductivity pathways in chemisorbed molecules:
Connections to molecular electronic issues.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {229},
Pages = {U631-U631},
Publisher = {AMER CHEMICAL SOC},
Year = {2005},
Month = {March},
Key = {fds370663}
}
@article{fds231985,
Author = {Risser, SM and Beratan, DN and Onuchic, JN},
Title = {Electronic coupling in starburst dendrimers},
Journal = {J. Phys. Chem.},
Volume = {97},
Number = {17},
Pages = {4523-4527},
Year = {1993},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1993/97/i17/pdf/j100119a045.pdf},
Abstract = {We describe the mechanism of electronic coupling in
starburst dendrimers, where each repeating unit is linked to
three or more nearest neighbors. The connectivity in these
molecules, which is that of a Bethe lattice or Cayley tree,
leads to localization of the electronic states even within
the "bands" of the material. This localization gives rise to
electronic coupling properties that are distinct from those
of the corresponding linear polymers. These differences are
evident in the predicted electron-transport properties of
the materials. When disorder is introduced to the structure,
however, the branched connectivity of the dendrimer can
enhance the probability of finding some strongly coupled
pathways between the core and surface sites of the
dendrimer. The unusual electron mediation properties of
these molecules make them particularly intriguing frameworks
for investigating the molecular control of electron
transport and, especially, the role that disorder can play
in establishing pathways for electronic communication in
macromolecules. © 1993 American Chemical
Society.},
Key = {fds231985}
}
@article{fds304364,
Author = {Risser, SM and Beratan, DN and Onuchic, JN},
Title = {Electronic coupling in starburst dendrimers: Connectivity,
disorder, and finite size effects in macromolecular Bethe
lattices},
Journal = {Journal of Physical Chemistry},
Volume = {97},
Number = {17},
Pages = {4523-4527},
Publisher = {American Chemical Society (ACS)},
Year = {1993},
Month = {January},
ISSN = {0022-3654},
url = {http://dx.doi.org/10.1021/j100119a045},
Abstract = {We describe the mechanism of electronic coupling in
starburst dendrimers, where each repeating unit is linked to
three or more nearest neighbors. The connectivity in these
molecules, which is that of a Bethe lattice or Cayley tree,
leads to localization of the electronic states even within
the "bands" of the material. This localization gives rise to
electronic coupling properties that are distinct from those
of the corresponding linear polymers. These differences are
evident in the predicted electron-transport properties of
the materials. When disorder is introduced to the structure,
however, the branched connectivity of the dendrimer can
enhance the probability of finding some strongly coupled
pathways between the core and surface sites of the
dendrimer. The unusual electron mediation properties of
these molecules make them particularly intriguing frameworks
for investigating the molecular control of electron
transport and, especially, the role that disorder can play
in establishing pathways for electronic communication in
macromolecules. © 1993 American Chemical
Society.},
Doi = {10.1021/j100119a045},
Key = {fds304364}
}
@article{fds318059,
Author = {BERATAN, DN},
Title = {ELECTRONIC HYPERPOLARIZABILITY AND CHEMICAL-STRUCTURE},
Journal = {ACS SYMPOSIUM SERIES},
Volume = {455},
Pages = {89-102},
Year = {1991},
Key = {fds318059}
}
@misc{fds22277,
Author = {D.N. Beratan},
Title = {Electronic hyperpolizability and chemical structure: a
tutorial},
Volume = {455},
Series = {ACS Symposium Series},
Pages = {89-102},
Booktitle = {New Materials for Nonlinear Optics},
Editor = {S.R. Marder and J.E. Sohn and G.D. Stucky},
Year = {1991},
Key = {fds22277}
}
@misc{fds370676,
Author = {Tong, GSM and Kurnikov, IV and Beratan, DN},
Title = {Electronic propagation in DNA.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {220},
Pages = {U226-U226},
Year = {2000},
Key = {fds370676}
}
@article{fds231977,
Author = {Hopfield, JJ and Onuchic, JN and Beratan, DN},
Title = {Electronic shift register memory based on molecular
electron-transfer reactions},
Journal = {Journal of Physical Chemistry},
Volume = {93},
Number = {17},
Pages = {6350-6357},
Publisher = {American Chemical Society (ACS)},
Year = {1989},
Month = {January},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1989/93/i17/pdf/j100354a017.pdf},
Abstract = {The design of a shift register memory at the molecular level
is described in detail. The memory elements are based on a
chain of electron-transfer molecules incorporated on a very
large scale integrated (VLSI) substrate, and the information
is shifted by photoinduced electron-transfer reactions. The
design requirements for such a system are discussed, and
several realistic strategies for synthesizing these systems
are presented. The immediate advantage of such a hybrid
molecular/VLSI device would arise from the possible
information storage density. The prospect of considerable
savings of energy per bit processed also exists. This
molecular shift register memory element design solves the
conceptual problems associated with integrating molecular
size components with larger (micron) size features on a
chip. © 1989 American Chemical Society.},
Doi = {10.1021/j100354a017},
Key = {fds231977}
}
@article{fds231914,
Author = {Wolak, MA and Balaeff, A and Gutmann, S and Helmrich, HJ and Vosloo, R and Beerbom, MM and Wierzbinski, E and Waldeck, DH and Bezer, S and Achim,
C and Beratan, DN and Schlaf, R},
Title = {Electronic structure of self-assembled peptide nucleic acid
thin films},
Journal = {Journal of Physical Chemistry C},
Volume = {115},
Number = {34},
Pages = {17123-17135},
Publisher = {American Chemical Society (ACS)},
Year = {2011},
Month = {September},
ISSN = {1932-7447},
url = {http://dx.doi.org/10.1021/jp201602j},
Abstract = {The electronic structure of self-assembled monolayers (SAMs)
of peptide nucleic acid (PNA) formed on Au substrates was
investigated. Cys-appended PNA 7-mers of thymine (Cys-T7)
were incubated on Au substrates in a nitrogen glovebox
attached to a photoemission spectrometer. Ultraviolet and
X-ray photoemission spectroscopy (UPS and XPS) measurements
on the resulting SAMs revealed the hole injection barrier at
the interface and the interface dipole. Electronic structure
calculations based on molecular dynamics sampling of the PNA
structure yielded the HOMO-LUMO gap and the electronic
density of states for PNA. Combined with the UPS data, the
theoretical calculation enabled estimation of the charge
injection barriers at the interface, as well as the
assignment of individual UP spectral features to specific
molecular orbitals. Interestingly, the dipole moment of the
PNA backbone is predicted to polarize PNA MOs, shifting the
preferred HOMO localization toward the C-terminus of PNA.
Control measurements on Cys-appended, abasic PNA backbone
7-mers (Cys-Bckb7) allowed the identification of the
emissions related to the PNA backbone in the UP spectra. The
orbital line-up at the interface between the Au substrate
and the Cys-PNA indicates a significant interface dipole
resulting in the alignment of the Au Fermi level near the
center of the PNA HOMO-LUMO gap. This alignment causes large
charge injection barriers for both holes and electrons, and
thus impedes charge transfer from Au into the Cys-PNA SAM.
© 2011 American Chemical Society.},
Doi = {10.1021/jp201602j},
Key = {fds231914}
}
@misc{fds370673,
Author = {Kurnikov, IV and Beratan, DN},
Title = {Electrostatic and electron transfer coupling control in the
mechanism of energy transduction of nitrogenase.},
Journal = {BIOPHYSICAL JOURNAL},
Volume = {80},
Number = {1},
Pages = {42A-42A},
Year = {2001},
Key = {fds370673}
}
@article{fds232037,
Author = {Liang, ZX and Nocek, JM and Kurnikov, IV and Beratan, DN and Hoffman,
BM},
Title = {Electrostatic control of electron transfer between myoglobin
and cytochrome b5: Effect of methylating the heme
propionates of Zn-myoglobin [16]},
Journal = {Journal of the American Chemical Society},
Volume = {122},
Number = {14},
Pages = {3552-3553},
Publisher = {American Chemical Society (ACS)},
Year = {2000},
Month = {April},
ISSN = {0002-7863},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/2000/122/i14/pdf/ja993951p.pdf},
Doi = {10.1021/ja993951p},
Key = {fds232037}
}
@misc{fds370675,
Author = {Hoffman, B and Nocek, JM and Liang, ZX and Leesch, VW and Kurnikov, IV and Beratan, DN},
Title = {Electrostatic control of electron transfer within protein
complexes.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {220},
Pages = {U450-U450},
Year = {2000},
Key = {fds370675}
}
@article{fds350772,
Author = {Zheng, L and Migliore, A and Beratan, DN},
Title = {Electrostatic Field-Induced Oscillator Strength Focusing in
Molecules.},
Journal = {The journal of physical chemistry. B},
Volume = {124},
Number = {29},
Pages = {6376-6388},
Year = {2020},
Month = {July},
url = {http://dx.doi.org/10.1021/acs.jpcb.0c04783},
Abstract = {The development of light-harvesting devices based on
molecular materials depends critically on the ability to
focus the electronic oscillator strength of molecules into
the UV-vis spectral window. Typical molecular chromophores
have only about 1% of their total electronic oscillator
strength in this spectral region and thus perform at a small
fraction of their possible effectiveness. This theoretical
study finds that the electronic oscillator strength of
polyenes in the UV-vis region may be enhanced by 1 order of
magnitude using electrostatic fields, motivating specific
experimental studies of oscillator strength focusing. We
find scaling relationships between the polyene length, the
intensity of the applied field, and the field-induced
increase in oscillator strength that are useful for the
implementation of light-harvesting strategies based on
polyenes.},
Doi = {10.1021/acs.jpcb.0c04783},
Key = {fds350772}
}
@misc{fds370670,
Author = {Beratan, DN},
Title = {Electrostatics, electron tunneling, and energy transduction
in biomolecules.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {223},
Pages = {C52-C52},
Year = {2002},
Key = {fds370670}
}
@article{fds231934,
Author = {Hu, X and Beratan, DN and Yang, W},
Title = {Emergent strategies for inverse molecular
design},
Journal = {Science in China B: Chemistry},
Volume = {52},
Number = {52},
Pages = {1769-1776},
Publisher = {Springer Nature},
Year = {2009},
ISSN = {1006-9291},
url = {http://dx.doi.org/10.1007/s11426-009-0260-3},
Abstract = {Molecular design is essential and ubiquitous in chemistry,
physics, biology, and material science. The immense space of
available candidate molecules requires novel optimization
strategies and algorithms for exploring the space and
achieving efficient and effective molecular design. This
paper summarizes the current progress toward developing
practical theoretical optimization schemes for molecular
design. In particular, we emphasize emergent strategies for
inverse molecular design. Several representative design
examples, based on recently developed strategies, are
described to demonstrate the principles of inverse molecular
design. © 2009 Science in China Press and Springer Berlin
Heidelberg.},
Doi = {10.1007/s11426-009-0260-3},
Key = {fds231934}
}
@misc{fds370672,
Author = {Kurnikova, MG and Roitberg, AE and Beratan, DN},
Title = {Energetic analysis of F1 ATP synthase conformations and
substrate binding.},
Journal = {BIOPHYSICAL JOURNAL},
Volume = {80},
Number = {1},
Pages = {500A-500A},
Year = {2001},
Key = {fds370672}
}
@article{fds357371,
Author = {Yuly, JL and Zhang, P and Beratan, DN},
Title = {Energy transduction by reversible electron
bifurcation},
Journal = {Current Opinion in Electrochemistry},
Volume = {29},
Year = {2021},
Month = {October},
url = {http://dx.doi.org/10.1016/j.coelec.2021.100767},
Abstract = {Electron bifurcation is a biological energy conversion
process that oxidizes a two-electron donor at medium
potential, coupled to the reduction of a high- and a
low-potential acceptor species. This process is often fully
reversible (can occur close to ΔG≈0), allowing the
creation of strong reductants with minimal free energy cost,
using compounds with higher reduction potentials. For many
years, the internal workings of electron bifurcating enzymes
were poorly understood, especially regarding how
short-circuit reactions are prevented. Recently, a conserved
energy landscape was proposed to naturally insulate against
short-circuit reactions, enabling efficient and reversible
electron bifurcation (the reversible EB scheme). We review
the physical principles that underpin the EB scheme,
describe how the reversible EB scheme is distinct from
previous views, and outline questions that remain
open.},
Doi = {10.1016/j.coelec.2021.100767},
Key = {fds357371}
}
@article{fds337001,
Author = {Seefeldt, LC and Hoffman, BM and Peters, JW and Raugei, S and Beratan,
DN and Antony, E and Dean, DR},
Title = {Energy Transduction in Nitrogenase.},
Journal = {Accounts of chemical research},
Volume = {51},
Number = {9},
Pages = {2179-2186},
Year = {2018},
Month = {September},
url = {http://dx.doi.org/10.1021/acs.accounts.8b00112},
Abstract = {Nitrogenase is a complicated two-component enzyme system
that uses ATP binding and hydrolysis energy to achieve one
of the most difficult chemical reactions in nature, the
reduction of N<sub>2</sub> to NH<sub>3</sub>. One component
of the Mo-based nitrogenase system, Fe protein, delivers
electrons one at a time to the second component, the
catalytic MoFe protein. This process occurs through a series
of synchronized events collectively called the "Fe protein
cycle". Elucidating details of the events associated with
this cycle has constituted an important challenge in
understanding the nitrogenase mechanism. Electron delivery
is a multistep process involving three metal clusters with
intra- and interprotein events. It is proposed that the
first electron transfer event is a gated intraprotein
transfer of one electron from the MoFe protein P-cluster to
the FeMo cofactor. Measurement of the effect of osmotic
pressure on the rate of this electron transfer process
revealed that it is gated by protein conformational changes.
This first electron transfer is activated by binding of the
Fe protein containing two bound ATP molecules. The mechanism
of how this protein-protein association triggers electron
transfer remains unknown. The second electron transfer event
is proposed to be a rapid interprotein "backfill" with
transfer of one electron from the reduced Fe protein 4Fe-4S
cluster to the oxidized P-cluster. In this way, electron
delivery can be viewed as a case of "deficit spending". Such
a deficit-spending electron transfer process can be
envisioned as a way to achieve one-direction electron flow,
limiting the potential for back electron flow. Hydrolysis of
two ATP molecules associated with the Fe protein occurs
after the electron transfer and therefore is not used to
directly drive the electron transfer. Rather, ATP hydrolysis
is proposed to contribute to relaxation of the "activated"
conformational state associated with the ATP form of the
complex, with the free energy from ATP hydrolysis being used
to pay back energy associated with component protein
association and electron transfer. Release of inorganic
phosphate (Pi) and protein-protein dissociation follow
electron transfer and ATP hydrolysis. The rate-limiting step
for the Fe protein cycle is not dissociation of the two
proteins, as previously believed, but rather is release of
Pi after ATP hydrolysis, which is then followed by rapid
protein-protein complex dissociation. Nitrogenase is
composed of two catalytic halves that do not function
independently but rather exhibit anticooperative nuclear
motion in which electron transfer in one-half of the complex
partially inhibits electron transfer and ATP hydrolysis in
the other half. Calculations indicated the existence of
anticooperative interactions across the entire nitrogenase
complex, suggesting a mechanism for the control of events on
opposite ends of this large complex. The mechanistic
necessity for this anticooperative process remains unknown.
This Account presents a working model for how all of these
processes work together in the nitrogenase "machine" to
transduce the energy from ATP binding and hydrolysis to
drive N<sub>2</sub> reduction.},
Doi = {10.1021/acs.accounts.8b00112},
Key = {fds337001}
}
@article{fds318054,
Author = {Liu, C and Xiang, L and Zhang, Y and Zhang, P and Beratan, DN and Li, Y and Tao, N},
Title = {Engineering nanometre-scale coherence in soft
matter.},
Journal = {Nature chemistry},
Volume = {8},
Number = {10},
Pages = {941-945},
Year = {2016},
Month = {October},
url = {http://dx.doi.org/10.1038/nchem.2545},
Abstract = {Electronic delocalization in redox-active polymers may be
disrupted by the heterogeneity of the environment that
surrounds each monomer. When the differences in monomer
redox-potential induced by the environment are small (as
compared with the monomer-monomer electronic interactions),
delocalization persists. Here we show that guanine (G) runs
in double-stranded DNA support delocalization over 4-5
guanine bases. The weak interaction between delocalized G
blocks on opposite DNA strands is known to support partially
coherent long-range charge transport. The
molecular-resolution model developed here finds that the
coherence among these G blocks follows an even-odd
orbital-symmetry rule and predicts that weakening the
interaction between G blocks exaggerates the resistance
oscillations. These findings indicate how sequence can be
exploited to change the balance between coherent and
incoherent transport. The predictions are tested and
confirmed using break-junction experiments. Thus, tailored
orbital symmetry and structural fluctuations may be used to
produce coherent transport with a length scale of multiple
nanometres in soft-matter assemblies, a length scale
comparable to that of small proteins.},
Doi = {10.1038/nchem.2545},
Key = {fds318054}
}
@article{fds343688,
Author = {Polizzi, NF and Jiang, T and Beratan, DN and Therien,
MJ},
Title = {Engineering opposite electronic polarization of singlet and
triplet states increases the yield of high-energy
photoproducts.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {116},
Number = {29},
Pages = {14465-14470},
Year = {2019},
Month = {July},
url = {http://dx.doi.org/10.1073/pnas.1901752116},
Abstract = {Efficient photosynthetic energy conversion requires
quantitative, light-driven formation of high-energy,
charge-separated states. However, energies of high-lying
excited states are rarely extracted, in part because the
congested density of states in the excited-state manifold
leads to rapid deactivation. Conventional photosystem
designs promote electron transfer (ET) by polarizing excited
donor electron density toward the acceptor ("one-way" ET), a
form of positive design. Curiously, negative design
strategies that explicitly avoid unwanted side reactions
have been underexplored. We report here that electronic
polarization of a molecular chromophore can be used as both
a positive and negative design element in a light-driven
reaction. Intriguingly, prudent engineering of polarized
excited states can steer a "U-turn" ET-where the excited
electron density of the donor is initially pushed away from
the acceptor-to outcompete a conventional one-way ET scheme.
We directly compare one-way vs. U-turn ET strategies via a
linked donor-acceptor (DA) assembly in which selective
optical excitation produces donor excited states polarized
either toward or away from the acceptor. Ultrafast
spectroscopy of DA pinpoints the importance of realizing
donor singlet and triplet excited states that have opposite
electronic polarizations to shut down intersystem crossing.
These results demonstrate that oppositely polarized
electronically excited states can be employed to steer
photoexcited states toward useful, high-energy products by
routing these excited states away from states that are
photosynthetic dead ends.},
Doi = {10.1073/pnas.1901752116},
Key = {fds343688}
}
@article{fds231868,
Author = {Wang, Y and King, JR and Wu, P and Pelzman, DL and Beratan, DN and Toone,
EJ},
Title = {Enthalpic signature of methonium desolvation revealed in a
synthetic host-guest system based on cucurbit[7]uril.},
Journal = {Journal of the American Chemical Society},
Volume = {135},
Number = {16},
Pages = {6084-6091},
Year = {2013},
Month = {April},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23510488},
Abstract = {Methonium (N(+)Me3) is an organic cation widely distributed
in biological systems. As an organic cation, the binding of
methonium to protein receptors requires the removal of a
positive charge from water. The appearance of methonium in
biological transmitters and receptors seems at odds with the
large unfavorable desolvation free energy reported for
tetramethylammonium (TMA(+)), a frequently utilized
surrogate of methonium. Here, we report an experimental
system that facilitates incremental internalization of
methonium within the molecular cavity of cucurbit[7]uril
(CB[7]). Using a combination of experimental and
computational studies, we show that the transfer of
methonium from bulk water (partially solvated methonium
state) to the CB[7] cavity (mostly desolvated methonium
state) is accompanied by a remarkably small desolvation
enthalpy of just 0.5 ± 0.3 kcal·mol(-1), a value
significantly less endothermic than those values suggested
from gas-phase model studies. Our results are in accord with
neutron scattering measurements that suggest methonium
produces only a minimal perturbation in the bulk water
structure, which highlights the limitations of gas-phase
models. More surprisingly, the incremental withdrawal of the
methonium surface from water produces a nonmonotonic
response in desolvation enthalpy. A partially desolvated
state exists, in which a portion of the methonium group
remains exposed to solvent. This structure incurs an
increased enthalpic penalty of ~3 kcal·mol(-1) compared to
other solvation states. We attribute this observation to the
pre-encapsulation dewetting of the methonium surface.
Together, our results offer a rationale for the wide
distribution of methonium in a biological context and
suggest limitations to computational estimates of binding
affinities based on simple parametrization of
solvent-accessible surface area.},
Doi = {10.1021/ja311327v},
Key = {fds231868}
}
@article{fds222353,
Author = {Y. Wang and J.R. King and P. Wu and D.L. Pelzman and D.N. Beratan and E.J. Toone},
Title = {Enthalpic signature of methonium desolvation revealed in a
synthetic host-guest system based on curcurbit[7]uril},
Journal = {J. Am. Chem. Soc.},
Number = {135},
Pages = {6084-6091},
Year = {2013},
Key = {fds222353}
}
@article{fds231879,
Author = {Goldsmith, MR and Jayasuriya, N and Beratan, DN and Wipf,
P},
Title = {Erratum: Optical rotation of noncovalent aggregates (Journal
of the American Chemical Society (2003) 125
(15696-15697))},
Journal = {Journal of the American Chemical Society},
Volume = {126},
Number = {30},
Pages = {9464},
Publisher = {American Chemical Society (ACS)},
Year = {2004},
Month = {August},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja047614e},
Doi = {10.1021/ja047614e},
Key = {fds231879}
}
@article{fds231864,
Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Pham, TT and Mague,
JT and Donahue, JP and Schmehl, RH and Beratan, DN and Rubtsov,
IV},
Title = {Evaluating the extent of intramolecular charge transfer in
the excited states of rhenium(I) donor-acceptor complexes
with time-resolved vibrational spectroscopy.},
Journal = {The journal of physical chemistry. B},
Volume = {117},
Number = {49},
Pages = {15903-15916},
Year = {2013},
Month = {December},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24117405},
Abstract = {Excited states in transition-metal complexes, even in those
featuring ligands with strong electron donating and
accepting properties, often involve only partial charge
transfer between the donor and acceptor ligands. The
excited-state properties of [Re(bpy)(CO)3L](+) compounds
were studied, where L is 4-dimethylaminobenzonitrile
(Re4DMABN), 3-dimethylaminobenzonitrile (Re3DMABN), and
benzonitrile (ReBN) using time-resolved infrared (TRIR) and
electronic spectroscopy methods as well as electronic
structure computations. The DMABN complexes exhibit strongly
solvent-dependent luminescence; the excited state lifetime
decreases from microseconds in dichloromethane to several
nanoseconds in mixed MeOH:DCM (1:1) solvent. Despite the
similarities in the solvent dependence of the excited state
dynamics and redox properties for Re3DMABN and Re4DMABN, the
nature of the lowest energy excited states formed in these
two compounds is drastically different. For example, the
lowest energy excited state for Re4DMABN in the mixed
solvent is assigned to the (4DMABN → bpy) ligand-to-ligand
charge transfer (LLCT) state featuring partial charge
transfer character. An equilibrium between a 3DMABN
intraligand triplet ((3)IL) and a metal-ligand-to-ligand
charge transfer (MLLCT) state is found for Re3DMABN in the
mixed solvent with the latter at ca. 400 cm(-1) lower
energy. The origin of such a drastic difference between the
states involved in Re4DMABN and Re3DMABN is attributed to a
difference in the energies of polarized quinoidal resonance
structures in 4DMABN and 3DMABN ligands.},
Doi = {10.1021/jp409628e},
Key = {fds231864}
}
@article{fds231921,
Author = {Venkatramani, R and Davis, KL and Wierzbinski, E and Bezer, S and Balaeff, A and Keinan, S and Paul, A and Kocsis, L and Beratan, DN and Achim, C and Waldeck, DH},
Title = {Evidence for a near-resonant charge transfer mechanism for
double-stranded peptide nucleic acid.},
Journal = {Journal of the American Chemical Society},
Volume = {133},
Number = {1},
Pages = {62-72},
Year = {2011},
Month = {January},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21141966},
Abstract = {We present evidence for a near-resonant mechanism of charge
transfer in short peptide nucleic acid (PNA) duplexes
obtained through electrochemical, STM break junction
(STM-BJ), and computational studies. A seven base pair
(7-bp) PNA duplex with the sequence (TA)(3)-(XY)-(TA)(3) was
studied, in which XY is a complementary nucleobase pair. The
experiments showed that the heterogeneous charge transfer
rate constant (k(0)) and the single-molecule conductance
(σ) correlate with the oxidation potential of the purine
base in the XY base pair. The electrochemical measurements
showed that the enhancement of k(0) is independent, within
experimental error, of which of the two PNA strands contains
the purine base of the XY base pair. 7-bp PNA duplexes with
one or two GC base pairs had similar measured k(0) and
conductance values. While a simple superexchange model,
previously used to rationalize charge transfer in single
stranded PNA (Paul et al. J. Am. Chem. Soc. 2009, 131,
6498-6507), describes some of the experimental observations,
the model does not explain the absence of an enhancement in
the experimental k(0) and σ upon increasing the G content
in the duplexes from one to two. Moreover, the superexchange
model is not consistent with other studies (Paul et al. J.
Phys. Chem. B 2010, 114, 14140), that showed a hopping
charge transport mechanism is likely important for PNA
duplexes longer than seven base pairs. A quantitative
computational analysis shows that a near-resonant charge
transfer regime, wherein a mix of superexchange and hopping
mechanisms are expected to coexist, can rationalize all of
the experimental results.},
Doi = {10.1021/ja107622m},
Key = {fds231921}
}
@article{fds359453,
Author = {Nayak, A and Park, J and De Mey and K and Hu, X and Beratan, DN and Clays, K and Therien, MJ},
Title = {Excited-State Dynamics and Nonlinear Optical Properties of
Hyperpolarizable Chromophores Based on Conjugated
Bis(terpyridyl)Ru(II) and Palladium and Platinum Porphyrinic
Components: Impact of Heavy Metals upon Supermolecular
Electro-Optic Properties.},
Journal = {Inorganic chemistry},
Volume = {60},
Number = {20},
Pages = {15404-15412},
Year = {2021},
Month = {October},
url = {http://dx.doi.org/10.1021/acs.inorgchem.1c02041},
Abstract = {A new series of strongly coupled oscillators based upon
(porphinato)Pd, (porphinato)Pt, and bis(terpyridyl)ruthenium(II)
building blocks is described. These <b>RuPPd</b>,
<b>RuPPt</b>, <b>RuPPdRu</b>, and <b>RuPPtRu</b>
chromophores feature bis(terpyridyl)Ru(II) moieties
connected to the (porphinato)metal unit via an ethyne linker
that bridges the 4'-terpyridyl and porphyrin macrocycle
<i>meso</i>-carbon positions. Pump-probe transient optical
data demonstrate sub-picosecond excited singlet-to-triplet-state
relaxation. The relaxed lowest-energy triplet
(T<sub>1</sub>) excited states of these chromophores feature
absorption manifolds that span the 800-1200 nm spectral
region, microsecond triplet-state lifetimes, and large
absorptive extinction coefficients [ε(T<sub>1</sub> →
T<sub><i>n</i></sub>) > 4 × 10<sup>4</sup> M<sup>-1</sup>
cm<sup>-1</sup>]. Dynamic hyperpolarizability
(β<sub>λ</sub>) values were determined from hyper-Rayleigh
light scattering (HRS) measurements carried out at several
incident irradiation wavelengths over the 800-1500 nm
spectral region. Relative to benchmark <b>RuPZn</b> and
<b>RuPZnRu</b> chromophores which showed large
β<sub>HRS</sub> values over the 1200-1600 nm range,
<b>RuPPd</b>, <b>RuPPt</b>, <b>RuPPdRu</b>, and
<b>RuPPtRu</b> displayed large β<sub>HRS</sub> values over
the 850-1200 nm region. Generalized Thomas-Kuhn sum (TKS)
rules and experimental hyperpolarizability values were
utilized to determine excited state-to-excited state
transition dipole terms from experimental electronic
absorption data and thus assessed frequency-dependent
β<sub>λ</sub> values, including two- and three-level
contributions for both β<sub><i>zzz</i></sub> and
β<sub><i>xzx</i></sub> tensor components to the
<b>RuPPd</b>, <b>RuPPt</b>, <b>RuPPdRu</b>, and
<b>RuPPtRu</b> hyperpolarizability spectra. These analyses
qualitatively rationalize how the β<sub><i>zzz</i></sub>
and β<sub><i>xzx</i></sub> tensor elements influence the
observed irradiation wavelength-dependent
hyperpolarizability magnitudes. The TKS analysis suggests
that supermolecules related to <b>RuPPd</b>, <b>RuPPt</b>,
<b>RuPPdRu</b>, and <b>RuPPtRu</b> will likely feature
intricate dependences of experimentally determined
β<sub>HRS</sub> values as a function of irradiation
wavelength that derive from substantial singlet-triplet
mixing, and complex interactions among multiple different β
tensor components that modulate the long wavelength regime
of the nonlinear optical response.},
Doi = {10.1021/acs.inorgchem.1c02041},
Key = {fds359453}
}
@misc{fds370687,
Author = {PRIYADARSHY, S and GRABE, MD and BERATAN, DN},
Title = {EXCITONIC AND THROUGH-BOND COUPLING IN YNE BRIDGED
PORPHYRINS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {210},
Pages = {116-INOR},
Year = {1995},
Key = {fds370687}
}
@article{fds231912,
Author = {Balabin, IA and Hu, X and Beratan, DN},
Title = {Exploring biological electron transfer pathway dynamics with
the Pathways plugin for VMD.},
Journal = {Journal of computational chemistry},
Volume = {33},
Number = {8},
Pages = {906-910},
Year = {2012},
Month = {March},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22298319},
Abstract = {We describe the new Pathways plugin for the molecular
visualization program visual molecular dynamics. The plugin
identifies and visualizes tunneling pathways and pathway
families in biomolecules, and calculates relative electronic
couplings. The plugin includes unique features to estimate
the importance of individual atoms for mediating the
coupling, to analyze the coupling sensitivity to thermal
motion, and to visualize pathway fluctuations. The Pathways
plugin is open source software distributed under the terms
of the GNU's Not Unix (GNU) public license.},
Doi = {10.1002/jcc.22927},
Key = {fds231912}
}
@article{fds231943,
Author = {Balamurugan, D and Yang, W and Beratan, DN},
Title = {Exploring chemical space with discrete, gradient, and hybrid
optimization methods.},
Journal = {The Journal of chemical physics},
Volume = {129},
Number = {17},
Pages = {174105},
Year = {2008},
Month = {November},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19045331},
Abstract = {Discrete, gradient, and hybrid optimization methods are
applied to the challenge of discovering molecules with
optimized properties. The cost and performance of the
approaches were studied using a tight-binding model to
maximize the static first electronic hyperpolarizability of
molecules. Our analysis shows that discrete branch and bound
methods provide robust strategies for inverse chemical
design involving diverse chemical structures. Based on the
linear combination of atomic potentials, a hybrid
discrete-gradient optimization strategy significantly
improves the performance of the gradient methods. The hybrid
method performs better than dead-end elimination and
competes with branch and bound and genetic algorithms. The
branch and bound methods for these model Hamiltonians are
more cost effective than genetic algorithms for
moderate-sized molecular optimization.},
Doi = {10.1063/1.2987711},
Key = {fds231943}
}
@article{fds231951,
Author = {Zuber, G and Wipf, P and Beratan, DN},
Title = {Exploring the optical activity tensor by anisotropic
Rayleigh optical activity scattering.},
Journal = {Chemphyschem : a European journal of chemical physics and
physical chemistry},
Volume = {9},
Number = {2},
Pages = {265-271},
Year = {2008},
Month = {February},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18219646},
Abstract = {Rayleigh optical activity (RayOA) spectroscopy promises to
provide an elegant and robust analytical method to probe
molecular stereochemistry. A careful selection of RayOA
variants such as right-angle depolarized ICP (incident
circular polarization) or backscattering DCP(I) (in-phase
dual circular polarization) allows analysis of the
anisotropic component of the scattered light. In this study,
we show that calculated anisotropic Rayleigh optical
activity quantities provide key advantages over isotropic
chiroptical quantities (such as optical rotation and RayOA
variants dominated by isotropic invariants): 1) higher
sensitivity for probing the chiroptical tensor G', 2)
reduced dependence on small geometry changes, and 3) much
less stringent computational demand for predicting an
accurate sign than for optical rotation. Moreover, the
stereochemical information provided by anisotropic RayOA and
its invariants can be used to develop chirality descriptors
because of the apparent correlation between
structure/stereochemistry and the sign and magnitude of the
anisotropic Rayleigh optical activity quantities.},
Doi = {10.1002/cphc.200700660},
Key = {fds231951}
}
@article{fds231970,
Author = {Beratan, DN and Hopfield, JJ},
Title = {Failure of the Born-Oppenheimer and Franck-Condon
approximations for long distance electron transfer rate
calculations},
Journal = {The Journal of Chemical Physics},
Volume = {81},
Number = {12},
Pages = {5753-5759},
Publisher = {AIP Publishing},
Year = {1984},
Month = {January},
ISSN = {0021-9606},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000081000012005753000001&idtype=cvips},
Abstract = {Quantum mechanical and semiclassical formulations of
nonadiabatic electron transfer theory are usually
implemented within a Born-Oppenheimer regime. Calculations
on real weakly interacting systems are so difficult that
this approximation is rarely questioned. The
Born-Oppenheimer approximation becomes qualitatively wrong
for electron transfers at very large distances. A model
vibronic problem is exactly solved and compared with the
Born-Oppenheimer result. Rate expressions are derived from
the wave functions using the "golden rule" approximation.
Electron propagation is intimately correlated with nuclear
motion so that the vibrational energy left on the donor
critically affects the electronic decay length. Several
deviations from the usual predictions appear for transfers
over very large distances. © 1984 American Institute of
Physics.},
Doi = {10.1063/1.447627},
Key = {fds231970}
}
@misc{fds313868,
Author = {REGAN, JJ and BETTS, JN and BERATAN, DN and ONUCHIC,
JN},
Title = {FINDING ELECTRON-TRANSFER PATHWAYS},
Journal = {PRINCETON LECTURES ON BIOPHYSICS},
Pages = {175-195},
Booktitle = {Princeton Lectures on Biophysics},
Publisher = {WORLD SCIENTIFIC PUBL CO PTE LTD},
Editor = {Bialek, W},
Year = {1992},
Month = {January},
ISBN = {981-02-1325-5},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1992BZ88Z00004&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Key = {fds313868}
}
@misc{fds370695,
Author = {REGAN, JJ and BERATAN, DN and ONUCHIC, JN},
Title = {FINDING ELECTRON-TRANSFER PATHWAYS IN PROTEINS},
Journal = {BIOPHYSICAL JOURNAL},
Volume = {64},
Number = {2},
Pages = {A129-A129},
Year = {1993},
Key = {fds370695}
}
@article{fds231886,
Author = {Skourtis, SS and Prytkova, T and Beratan, DN},
Title = {Flavin Charge Transfer Transitions Assist DNA Photolyase
Electron Transfer.},
Journal = {AIP conference proceedings},
Volume = {963},
Pages = {674-677},
Year = {2007},
Month = {January},
ISSN = {0094-243X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23226907},
Abstract = {This contribution describes molecular dynamics,
semi-empirical and ab-initio studies of the primary
photo-induced electron transfer reaction in DNA photolyase.
DNA photolyases are FADH(-)-containing proteins that repair
UV-damaged DNA by photo-induced electron transfer. A DNA
photolyase recognizes and binds to cyclobutatne pyrimidine
dimer lesions of DNA. The protein repairs a bound lesion by
transferring an electron to the lesion from FADH(-), upon
photo-excitation of FADH(-) with 350-450 nm light. We
compute the lowest singlet excited states of FADH(-) in DNA
photolyase using INDO/S configuration interaction,
time-dependent density-functional, and time-dependent
Hartree-Fock methods. The calculations identify the lowest
singlet excited state of FADH(-) that is populated after
photo-excitation and that acts as the electron donor. For
this donor state we compute conformationally-averaged
tunneling matrix elements to empty electron- acceptor states
of a thymine dimer bound to photolyase. The conformational
averaging involves different FADH(-) - thymine dimer
confromations obtained from molecular dynamics simulations
of the solvated protein with a thymine dimer docked in its
active site. The tunneling matrix element computations use
INDO/S-level Green's function, energy splitting, and
Generalized Mulliken-Hush methods. These calculations
indicate that photo-excitation of FADH(-) causes a π →
π(*) charge-transfer transition that shifts electron
density to the side of the flavin isoalloxazine ring that is
adjacent to the docked thymine dimer. This shift in electron
density enhances the FADH(-) - to - dimer electronic
coupling, thus inducing rapid electron transfer.},
Doi = {10.1063/1.2836174},
Key = {fds231886}
}
@article{fds231917,
Author = {Carias, H and Beratan, DN and Skourtis, SS},
Title = {Floquet analysis for vibronically modulated electron
tunneling.},
Journal = {The journal of physical chemistry. B},
Volume = {115},
Number = {18},
Pages = {5510-5518},
Year = {2011},
Month = {May},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21476504},
Abstract = {Electron tunneling provides the primary reaction channel for
electron transfer (ET) in many molecular systems. The
analysis of such systems therefore requires the
consideration of electronic coherence and interference
effects. A model system for which tunneling may be either
symmetry forbidden or allowed is considered here in the
presence of a driving infrared (IR) field. It was previously
shown that inelastic tunneling allows ET in the symmetry
forbidden system via vibronic interactions. We show here
that explicit considerations of IR interactions with these
systems further changes the ET kinetics. Analysis in the
framework of Floquet theory reveals that interaction with an
IR field may increase the probability of inelastic tunneling
and thus enhance the ET rate for a system in which elastic
ET is forbidden. It is shown that IR driving of a nuclear
oscillator promotes the oscillator into excited states that
couple more strongly to the tunneling electron. Furthermore,
it is shown that IR driving may suppress the ET rate in this
same system, depending on system energetics. In a model
where elastic tunneling is symmetry allowed, we examine
vibronic modulation of ET in the Floquet framework. ET rates
are computed for symmetry allowed and forbidden model
systems, and vibronic interactions are found to suppress or
enhance ET in both systems. The inelastic ET rate may be
enhanced over 4 orders of magnitude in the symmetry
disfavored case or suppressed by 15% in the same system.
Effects of IR on ET rates in the symmetry-allowed system are
weaker with enhancements up to 34% over the undriven rate
and suppression of about 3% with IR driving present. This
study is the first theoretical and computational exploration
of ET rate control by IR irradiation of the
bridge.},
Doi = {10.1021/jp111097a},
Key = {fds231917}
}
@article{fds231922,
Author = {Skourtis, SS and Waldeck, DH and Beratan, DN},
Title = {Fluctuations in biological and bioinspired electron-transfer
reactions.},
Journal = {Annual review of physical chemistry},
Volume = {61},
Number = {61},
Pages = {461-485},
Year = {2010},
Month = {January},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20192814},
Abstract = {Central to theories of electron transfer (ET) is the idea
that nuclear motion generates a transition state that
enables electron flow to proceed, but nuclear motion also
induces fluctuations in the donor-acceptor (DA) electronic
coupling that is the rate-limiting parameter for
nonadiabatic ET. The interplay between the DA energy gap and
DA coupling fluctuations is particularly noteworthy in
biological ET, where flexible protein and mobile water
bridges take center stage. Here, we discuss the critical
timescales at play for ET reactions in fluctuating media,
highlighting issues of the Condon approximation, average
medium versus fluctuation-controlled electron tunneling,
gated and solvent relaxation controlled electron transfer,
and the influence of inelastic tunneling on electronic
coupling pathway interferences. Taken together, one may use
this framework to establish principles to describe how
macromolecular structure and structural fluctuations
influence ET reactions. This framework deepens our
understanding of ET chemistry in fluctuating media.
Moreover, it provides a unifying perspective for biophysical
charge-transfer processes and helps to frame new questions
associated with energy harvesting and transduction in
fluctuating media.},
Doi = {10.1146/annurev.physchem.012809.103436},
Key = {fds231922}
}
@article{fds232011,
Author = {Kurnikov, IV and Charnley, AK and Beratan, DN},
Title = {From ATP to electron transfer: Electrostatics and
free-energy transduction in nitrogenase},
Journal = {Journal of Physical Chemistry B},
Volume = {105},
Number = {23},
Pages = {5359-5367},
Publisher = {American Chemical Society (ACS)},
Year = {2001},
Month = {June},
ISSN = {1089-5647},
url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2001/105/i23/pdf/jp002540o.pdf},
Abstract = {Nitrogenase consists of two proteins that work in concert to
reduce atmospheric dinitrogen to a biologically useful form,
ammonia (Curr. Opin. Chem. Bio. 2000, 4, 559-566; Chem. Rev.
1996, 96, 2965-2982). The smaller of the proteins (the
so-called Fe protein) shuttles high-energy electrons to the
larger subunit (the so-called MoFe protein) where the
reduction of dinitrogen molecules takes place. The Fe
protein catalyzes the hydrolysis of two MgATP molecules per
electron transferred to the MoFe protein. The physical
mechanism that couples the ATP hydrolysis and
electron-transfer reactions in nitrogenase is one of the
"great mysteries" of nitrogen fixation. Our goal is to
describe the free-energy transformations that occur in
nitrogenase based upon theoretical analysis of structural
and electrochemical data. The electrostatic and
thermodynamic analysis described here, made possible by
recent X-ray structural data (and motivated by closely
related electrochemical studies: Biochemistry 1997, 36,
12976-12983; FEBS Lett. 1998, 432, 55-58), shows that the
ATP hydrolysis energy in nitrogenase serves the purpose of
increasing the driving force of the electron-transfer
reaction in and protein-protein complex. MgATP binding
induces conformational changes and protein-protein
association. The protein-protein docking excludes water from
the negatively charged [Fe4S4]S4cys redox cofactor that lies
near the Fe-protein surface, boosting its energy through
diminished solvation. We estimated the induced
redox-potential change to be equal to or larger than
one-third of an electronvolt, which is roughly the energy
associated with the hydrolysis of one MgATP molecule.
Nitrogenase appears, therefore, to employ a relatively
simple ATP hydrolysis coupled redox cofactor desolvation
mechanism to energize, and thus to accelerate, interprotein
electron transfer. Our analysis also indicates that
electrostatic interactions play an important role in the
substitution of MgADP by MgATP upon reduction of the
[Fe4S4]S4cys cluster in the Fe protein. The nitrogenase
scheme of energy conversion may suggest alternative
strategies for the design of new molecular
devices.},
Doi = {10.1021/jp002540o},
Key = {fds232011}
}
@article{fds231855,
Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Schmehl, RH and Beratan, DN and Rubtsov, IV},
Title = {Full-electron ligand-to-ligand charge transfer in a compact
Re(I) complex.},
Journal = {The journal of physical chemistry. A},
Volume = {118},
Number = {45},
Pages = {10407-10415},
Year = {2014},
Month = {November},
ISSN = {1089-5639},
url = {http://dx.doi.org/10.1021/jp5039877},
Abstract = {Ligand-to-ligand charge transfer (LLCT) states in transition
metal complexes are often characterized by fractional
electron transfer due to coupling of the LLCT state with
many other states via the metal. We designed and
characterized a compact Re(I) complex that displays
essentially full-electron charge transfer in the LLCT
excited state. The complex, [Re(DCEB)(CO)3(L)](+) (DCEB =
4,4'-dicarboxyethyl-2,2'-bipyridine), referred to as ReEBA,
features two redox active ligands with strong electron
accepting (DCEB) and electron donating (L is
3-dimethylaminobenzonitrile (3DMABN)) properties. The lowest
energy excited state formed with a ca. 10 ps time constant
and was characterized as the full-electron 3DMABN → DCEB
LLCT state using time-resolved infrared spectroscopy (TRIR),
transient absorption spectroscopy, and DFT computations.
Analysis of a range of vibrational modes helped to assign
the charge transfer characteristics of the complex. The LLCT
state lifetime in ReEBA shows a strong dependence on the
solvent polarity and features solvent dependent frequency
shifts for several vibrational reporters. The formation of a
full-electron LLCT state (∼92%) was enabled by tuning the
redox properties of the electron accepting ligand (DCEB) and
simultaneously decoupling the redox active group of the
electron donating ligand (3DMABN) from the metal center.
This strategy is generally applicable for designing compact
transition metal complexes that have full-electron LLCT
states.},
Doi = {10.1021/jp5039877},
Key = {fds231855}
}
@article{fds232014,
Author = {Zheng, J and Kang, YK and Therien, MJ and Beratan,
DN},
Title = {Generalized Mulliken-Hush analysis of electronic coupling
interactions in compressed pi-stacked porphyrin-bridge-quinone
systems.},
Journal = {Journal of the American Chemical Society},
Volume = {127},
Number = {32},
Pages = {11303-11310},
Year = {2005},
Month = {August},
ISSN = {0002-7863},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16089459},
Abstract = {Donor-acceptor interactions were investigated in a series of
unusually rigid, cofacially compressed pi-stacked
porphyrin-bridge-quinone systems. The two-state generalized
Mulliken-Hush (GMH) approach was used to compute the
coupling matrix elements. The theoretical coupling values
evaluated with the GMH method were obtained from
configuration interaction calculations using the INDO/S
method. The results of this analysis are consistent with the
comparatively soft distance dependences observed for both
the charge separation and charge recombination reactions.
Theoretical studies of model structures indicate that the
phenyl units dominate the mediation of the donor-acceptor
coupling and that the relatively weak exponential decay of
rate with distance arises from the compression of this
pi-electron stack.},
Doi = {10.1021/ja050984y},
Key = {fds232014}
}
@article{fds231882,
Author = {Skourtis, SS and Beratan, DN},
Title = {Guest editorial: Electron transfer},
Journal = {Molecular Simulation},
Volume = {32},
Number = {9},
Pages = {675-676},
Publisher = {Informa UK Limited},
Year = {2006},
Month = {August},
ISSN = {0892-7022},
url = {http://dx.doi.org/10.1080/08927020600991120},
Doi = {10.1080/08927020600991120},
Key = {fds231882}
}
@article{fds231945,
Author = {Beratan, DN and Balabin, IA},
Title = {Heme-copper oxidases use tunneling pathways.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {105},
Number = {2},
Pages = {403-404},
Year = {2008},
Month = {January},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18180451},
Doi = {10.1073/pnas.0711343105},
Key = {fds231945}
}
@article{fds231950,
Author = {Parks, JM and Kondru, RK and Hua, H and Beratan, DN and Yang,
W},
Title = {Hepatitis C virus NS5B polymerase: Important roles of the
internal energy and van der Waals interactions from QM/MM
calculations},
Journal = {J.Phys.Chem.B},
Number = {112},
Pages = {3168-3176},
Year = {2008},
Key = {fds231950}
}
@article{fds231887,
Author = {Parks, JM and Kondru, RK and Hu, H and Beratan, DN and Yang,
W},
Title = {Hepatitis C virus NS5B polymerase: QM/MM calculations show
the important role of the internal energy in ligand
binding.},
Journal = {The journal of physical chemistry. B},
Volume = {112},
Number = {10},
Pages = {3168-3176},
Year = {2008},
Month = {March},
ISSN = {1520-6106},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18271573},
Abstract = {The inter- and intramolecular interactions that determine
the experimentally observed binding mode of the ligand
(2Z)-2-(benzoylamino)-3-[4-(2-bromophenoxy)phenyl]-2-propenoate
in complex with hepatitis C virus NS5B polymerase have been
studied using QM/MM calculations. DFT-based QM/MM
optimizations were performed on a number of ligand
conformers in the protein-ligand complex. Using these
initial poses, our aim is 2-fold. First, we identify the
minimum energy pose. Second, we dissect the energetic
contributions to this pose using QM/MM methods. The study
reveals the critical importance of internal energy for the
proper energy ranking of the docked poses. Using this
protocol, we successfully identified three poses that have
low RMSD with respect to the crystallographic structure from
among the top 20 initially docked poses. We show that the
most important energetic component contributing to binding
for this particular protein-ligand system is the
conformational (i.e., QM internal) energy.},
Doi = {10.1021/jp076885j},
Key = {fds231887}
}
@article{fds231994,
Author = {Skourtis, SS and Beratan, DN},
Title = {High and low resolution theories of protein electron
transfer},
Journal = {Journal of Biological Inorganic Chemistry},
Volume = {2},
Number = {3},
Pages = {378-386},
Publisher = {Springer Nature},
Year = {1997},
Month = {January},
url = {http://www.springerlink.com/media/e3d054fexk6qwlcbrqau/contributions/g/l/8/9/gl89l5vjc3awtg6f.pdf},
Abstract = {Protein-mediated electronic interactions facilitate
biological electron transfer (ET) reactions. Theory and
experiment are being used extensively to establish
atomic-scale descriptions of these reactions. The last 20
years have seen a progression of descriptions ranging from
square barrier protein approximations to tunneling Pathway
models, and recently to valence orbital Hamiltonian methods.
Pathway connectivity, reflecting a protein's secondary and
tertiary motif, is predicted (and was recently confirmed) to
determine the ET rate. A critical challenge now is to
extract from more detailed orbital descriptions, with
millions of interaction elements between orbitals,
predictions of how primary sequence and folding-induced
contacts influence electron transfer rates. Electron
transfer contact maps reduce the orbital interaction
information in a manner that allows ready interpretation in
the context of protein motifs and mutations. We discuss
these modern models for protein ET and the reduced views
that are being derived from them.},
Doi = {10.1007/s007750050147},
Key = {fds231994}
}
@article{fds232012,
Author = {Kurnikov, IV and Tong, GSM and Madrid, M and Beratan,
DN},
Title = {Hole size and energetics in double helical DNA: Competition
between quantum delocalization and solvation
localization},
Journal = {Journal of Physical Chemistry B},
Volume = {106},
Number = {1},
Pages = {7-10},
Publisher = {American Chemical Society (ACS)},
Year = {2002},
Month = {January},
ISSN = {1089-5647},
url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2002/106/i01/pdf/jp0132329.pdf},
Abstract = {The transition between single step long-range tunneling and
multistep hopping transport in DNA electron transfer depends
on a myriad of factors including sequence, distance,
conformation, solvation and, consequently, hole state
energetics. We show that the solvation energetics of hole
(radical cation) states in DNA is comparable to the quantum
delocalization energetics of the hole. That is, the
solvation forces that tend to localize the hole compete with
the quantum effects that give rise to hole delocalization.
The net result is that the hole states are predicted to be
relatively compact (one to three base pairs in length) and
that the "trap depth" of these holes is expected to be much
shallower than anticipated by gas-phase quantum chemical
analysis of base stacks. This analysis predicts guanine
oxidation potential dependence on the length of GC runs to
be modest (differences <0.1 V for holes from one to three
base pairs). The lowering of the trapped hole binding energy
has significant implications for the structure and mobility
of hole states in DNA.},
Doi = {10.1021/jp0132329},
Key = {fds232012}
}
@article{fds337038,
Author = {Ma, Z and Lin, Z and Lawrence, CM and Rubtsov, IV and Antoniou, P and Skourtis, SS and Zhang, P and Beratan, DN},
Title = {How can infra-red excitation both accelerate and slow charge
transfer in the same molecule?},
Journal = {Chemical science},
Volume = {9},
Number = {30},
Pages = {6395-6405},
Year = {2018},
Month = {August},
url = {http://dx.doi.org/10.1039/c8sc00092a},
Abstract = {A UV-IR-Vis 3-pulse study of infra-red induced changes to
electron transfer (ET) rates in a donor-bridge-acceptor
species finds that charge-separation rates are slowed, while
charge-recombination rates are accelerated as a result of IR
excitation during the reaction. We explore the underpinning
mechanisms for this behavior, studying IR-induced changes to
the donor-acceptor coupling, to the validity of the Condon
approximation, and to the reaction coordinate distribution.
We find that the dominant IR-induced rate effects in the
species studied arise from changes to the density of states
in the Marcus curve crossing region. That is, IR
perturbation changes the probability of accessing the
activated complex for the ET reactions. IR excitation
diminishes the population of the activated complex for
forward (activationless) ET, thus slowing the rate. However,
IR excitation increases the population of the activated
complex for (highly activated) charge recombination ET, thus
accelerating the charge recombination rate.},
Doi = {10.1039/c8sc00092a},
Key = {fds337038}
}
@misc{fds370678,
Author = {Beratan, DN and Kurnikov, IV},
Title = {How does nitrogenase work?.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {218},
Pages = {U485-U486},
Year = {1999},
Key = {fds370678}
}
@article{fds231968,
Author = {Liao, J-L and Beratan, DN},
Title = {How does protein architecture facilitate the transduction of
ATP chemical-bond energy into mechanical work? The cases of
nitrogenase and ATP binding-cassette proteins.},
Journal = {Biophysical journal},
Volume = {87},
Number = {2},
Pages = {1369-1377},
Year = {2004},
Month = {August},
ISSN = {0006-3495},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15298939},
Abstract = {Transduction of adenosine triphosphate (ATP) chemical-bond
energy into work to drive large-scale conformational changes
is common in proteins. Two specific examples of
ATP-utilizing proteins are the nitrogenase iron protein and
the ATP binding-cassette transporter protein, BtuCD.
Nitrogenase catalyzes biological nitrogen fixation whereas
BtuCD transports vitamin B(12) across membranes. Both
proteins drive their reactions with ATP. To interpret how
the mechanical force generated by ATP binding and hydrolysis
is propagated in these proteins, a coarse-grained elastic
network model is employed. The analysis shows that subunits
of the proteins move against each other in a concerted
manner. The lowest-frequency modes of the nitrogenase iron
protein and of the ATP binding-cassette transporter BtuCD
protein are found to link the functionally critical domains,
and these modes are suggested to be responsible for (at
least the initial stages) large-scale ATP-coupled
conformational changes.},
Doi = {10.1529/biophysj.103.038653},
Key = {fds231968}
}
@article{fds231929,
Author = {Yuan, L and Seo, J-S and Kang, NS and Keinan, S and Steele, SE and Michelotti, GA and Wetsel, WC and Beratan, DN and Gong, Y-D and Lee, TH and Hong, J},
Title = {Identification of 3-hydroxy-2-(3-hydroxyphenyl)-4H-1-benzopyran-4-ones
as isoform-selective PKC-zeta inhibitors and potential
therapeutics for psychostimulant abuse.},
Journal = {Mol Biosyst},
Volume = {5},
Number = {9},
Pages = {927-930},
Year = {2009},
Month = {September},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19668856},
Abstract = {From a screen of small molecule libraries to identify
potential therapeutics for psychostimulant abuse,
3-hydroxy-2-(3-hydroxyphenyl)-4H-1-benzopyran-4-ones were
shown to be isoform-selective PKC-zeta inhibitors.},
Doi = {10.1039/b903036k},
Key = {fds231929}
}
@article{fds167397,
Author = {L. Yuan and J. Seo and N.S. Kang and S. Keinan and S.E. Steele and G.A.
Michelotti, W.C. Wetsel and D.N. Beratan and Y-D. Gong and T.H. Lee and J. Hong},
Title = {Identification of 3-Hydroxy-2-(3-Hydroxyphenyl)-4H-1-Benzopyran-4-Ones
as Isoform-Selective PKC-ζ Inhibitors and Potential
Therapeutics for Psychostimulant Abuse},
Journal = {Mol. BioSyst},
Number = {5},
Pages = {927-930},
Year = {2009},
Key = {fds167397}
}
@article{fds333776,
Author = {Liu, R and Bloom, BP and Waldeck, DH and Zhang, P and Beratan,
DN},
Title = {Improving Solar Cell Performance Using Quantum Dot Triad
Charge-Separation Engines},
Journal = {Journal of Physical Chemistry C},
Volume = {122},
Number = {11},
Pages = {5924-5934},
Publisher = {American Chemical Society (ACS)},
Year = {2018},
Month = {March},
url = {http://dx.doi.org/10.1021/acs.jpcc.8b00010},
Abstract = {We use kinetic modeling to explore the current-voltage,
power-voltage, and power conversion efficiency
characteristics of quantum dot dyads and triads as possible
light absorption and charge separation engines in quantum
dot, bulk heterojunction solar cells. The external and
internal power conversion quantum efficiencies are
significantly enhanced by introducing a third quantum dot
between the donor and acceptor quantum dots. Given the
constraint of comparable charge-recombination and
charge-separation rates, open-circuit voltages for triads
are predicted to be about 10%-17% larger than those for
dyads, and short-circuit currents for triads are about 400%
larger than those for dyads. These improvements in the
efficiencies can be further enhanced by tuning the band-edge
energy offset of the middle-position quantum dot from its
neighbors. The band-edge energies of the middle quantum dot
should be tuned so that they form a cascading band-edge
energy alignment from the band-edge energies of the left
CdTe QD to the right CdSe QD. To produce the most favorable
solar cell performance, the middle quantum dot's conduction
(valence) band edge should be closer to the right quantum
dot's band edge when the charge recombination rates are low
(high) and near the conduction (valence) band edge of the
left quantum dot when the charge recombination rates are
high (low). This analysis identifies important strategies to
design multi-QD assemblies for solar energy harvesting and
conversion.},
Doi = {10.1021/acs.jpcc.8b00010},
Key = {fds333776}
}
@article{fds362434,
Author = {Liu, KT and Beratan, DN and Zhang, P},
Title = {Improving the efficiency of open-quantum-system simulations
using matrix product states in the interaction
picture},
Journal = {Physical Review A},
Volume = {105},
Number = {3},
Year = {2022},
Month = {March},
url = {http://dx.doi.org/10.1103/PhysRevA.105.032406},
Abstract = {Modeling open quantum systems-quantum systems coupled to a
bath-is of value in condensed-matter theory, cavity quantum
electrodynamics, nanosciences, and biophysics. The real-time
simulation of open quantum systems was advanced
significantly by the recent development of chain mapping
techniques and the use of matrix product states that exploit
the intrinsic entanglement structure in open quantum
systems. The computational cost of simulating open quantum
systems, however, remains high when the bath is excited to
high-lying quantum states. We develop an approach to reduce
the computational costs in such cases. The interaction
representation for the open quantum system is used to
distribute excitations among the bath degrees of freedom so
that the occupation of each bath oscillator is ensured to be
low. The interaction picture also causes the matrix
dimensions to be much smaller in a matrix product state of a
chain-mapped open quantum system than in the Schrödinger
picture. Using the interaction representation accelerates
the calculations by one to two orders of magnitude over the
existing matrix-product-state method. In the regime of
strong system-bath coupling and high temperatures, the
speedup can be as large as three orders of magnitude. The
approach developed here is especially promising to simulate
the dynamics of open quantum systems in high-temperature and
strong-coupling regimes.},
Doi = {10.1103/PhysRevA.105.032406},
Key = {fds362434}
}
@article{fds304361,
Author = {Skourtis, SS and Waldeck, DH and Beratan, DN},
Title = {Inelastic electron tunneling erases coupling-pathway
interferences},
Journal = {Journal of Physical Chemistry B},
Volume = {108},
Number = {40},
Pages = {15511-15518},
Publisher = {American Chemical Society (ACS)},
Year = {2004},
Month = {October},
ISSN = {1520-6106},
url = {http://dx.doi.org/10.1021/jp0485340},
Abstract = {Theoretical analysis of nonadiabatic electron-transfer
reactions in molecules usually assumes that electron
amplitude propagates coherently from the reductant to the
oxidant via covalent and noncovalent coupling pathways. We
show that when the tunneling electron excites local bridge
vibrations (inelastic tunneling), the excitation "labels"
the physical pathway traversed. As such, the coherence among
the bridge-mediated tunneling pathways is destroyed. We
illustrate this effect using a simple model Hamiltonian and
show how the donor-acceptor interaction, and thus the
electron-transfer rate, is modified by inelastic effects.
Pathway coherence loss provides a mechanism to relax
orbital-symmetry constraints on electron-transfer reactions.
This effect may be of particular significance in
macromolecules with destructively interfering pathways or
low tunneling barriers. Pathway decoherence that arises from
inelastic effects in molecules is analogous to coherence
loss in mesoscopic "which way" interferometers and might
provide an approach to gate electron flow in molecular-scale
devices.},
Doi = {10.1021/jp0485340},
Key = {fds304361}
}
@article{fds231978,
Author = {Beratan, DN},
Title = {Influence of gap states on the nonresonant second
hyperpolarizabilities of conjugated organic
polymers},
Journal = {Journal of physical chemistry},
Volume = {93},
Number = {10},
Pages = {3915-3920},
Publisher = {American Chemical Society (ACS)},
Year = {1989},
Month = {January},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1989/93/i10/pdf/j100347a012.pdf},
Abstract = {The presence of conjugation and substitution defects
introduces 'gap states' in finite polyenes that are shown to
influence the size and sign of the second molecular
hyperpolarizability, γxxxx. Using a one-electron
tight-binding model, we calculate the dependence of γxxxx
on the defect-state occupancy and energy in finite polyenes.
Defects can cause a significant decrease or enhancement of
γxxxx by impeding charge delocalization or by creating
partly filled bands (mimicking the one-band limit),
respectively. Concomitant sign changes in γxxxx are
predicted. Calculations of these effects are made for
molecules in which a central atom's identity and electron
occupancy are varied. The results suggest strategies for
designing molecules that can be either photochemically or
electrochemically switched between states with considerably
different second hyperpolarizabilities.},
Doi = {10.1021/j100347a012},
Key = {fds231978}
}
@article{fds232047,
Author = {Beratan, DN and Onuchic, JN and Hopfield, JJ},
Title = {Information storage at the molecular level: the design of a
molecular shift register memory},
Journal = {Journal of the British Interplanetary Society},
Volume = {42},
Pages = {468-473},
Year = {1989},
Key = {fds232047}
}
@article{fds231910,
Author = {Keinan, S and Nocek, JM and Hoffman, BM and Beratan,
DN},
Title = {Interfacial hydration, dynamics and electron transfer:
multi-scale ET modeling of the transient [myoglobin,
cytochrome b5] complex.},
Journal = {Physical chemistry chemical physics : PCCP},
Volume = {14},
Number = {40},
Pages = {13881-13889},
Year = {2012},
Month = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22955681},
Abstract = {Formation of a transient [myoglobin (Mb), cytochrome b(5)
(cyt b(5))] complex is required for the reductive repair of
inactive ferri-Mb to its functional ferro-Mb state. The [Mb,
cyt b(5)] complex exhibits dynamic docking (DD), with its
cyt b(5) partner in rapid exchange at multiple sites on the
Mb surface. A triple mutant (Mb(3M)) was designed as part of
efforts to shift the electron-transfer process to the simple
docking (SD) regime, in which reactive binding occurs at a
restricted, reactive region on the Mb surface that dominates
the docked ensemble. An electrostatically-guided brownian
dynamics (BD) docking protocol was used to generate an
initial ensemble of reactive configurations of the complex
between unrelaxed partners. This ensemble samples a broad
and diverse array of heme-heme distances and orientations.
These configurations seeded all-atom constrained molecular
dynamics simulations (MD) to generate relaxed complexes for
the calculation of electron tunneling matrix elements
(T(DA)) through tunneling-pathway analysis. This procedure
for generating an ensemble of relaxed complexes combines the
ability of BD calculations to sample the large variety of
available conformations and interprotein distances, with the
ability of MD to generate the atomic level information,
especially regarding the structure of water molecules at the
protein-protein interface, that defines electron-tunneling
pathways. We used the calculated T(DA) values to compute ET
rates for the [Mb(wt), cyt b(5)] complex and for the complex
with a mutant that has a binding free energy strengthened by
three D/E → K charge-reversal mutations, [Mb(3M), cyt
b(5)]. The calculated rate constants are in agreement with
the measured values, and the mutant complex ensemble has
many more geometries with higher T(DA) values than does the
wild-type Mb complex. Interestingly, water plays a double
role in this electron-transfer system, lowering the
tunneling barrier as well as inducing protein interface
remodeling that screens the repulsion between the
negatively-charged propionates of the two
hemes.},
Doi = {10.1039/c2cp41949a},
Key = {fds231910}
}
@article{fds367942,
Author = {Chowdhury, SN and Zhang, P and Beratan, DN},
Title = {Interference between Molecular and Photon Field-Mediated
Electron Transfer Coupling Pathways in Cavities
br},
Journal = {JOURNAL OF PHYSICAL CHEMISTRY LETTERS},
Year = {2022},
url = {http://dx.doi.org/10.1021/acs.jpclett.2c024969822J},
Doi = {10.1021/acs.jpclett.2c024969822J},
Key = {fds367942}
}
@article{fds367470,
Author = {Chowdhury, SN and Zhang, P and Beratan, DN},
Title = {Interference between Molecular and Photon Field-Mediated
Electron Transfer Coupling Pathways in Cavities.},
Journal = {The journal of physical chemistry letters},
Volume = {13},
Number = {42},
Pages = {9822-9828},
Year = {2022},
Month = {October},
url = {http://dx.doi.org/10.1021/acs.jpclett.2c02496},
Abstract = {Cavity polaritonics creates novel opportunities to direct
chemical reactions. Electron transfer (ET) reactions are
among the simplest reactions, and they underpin energy
conversion. New strategies to manipulate and direct electron
flow at the nanoscale are of particular interest in
biochemistry, energy science, bioinspired materials science,
and chemistry. We show that optical cavities can modulate
electron transfer pathway interferences and ET rates in
donor-bridge-acceptor (DBA) systems. We derive the rate for
DBA electron transfer when the molecules are coupled to
cavity modes, emphasizing novel cavity-induced pathway
interferences with the molecular electronic coupling
pathways, as these interferences allow a new kind of ET rate
tuning. The interference between the cavity-induced coupling
pathways and the intrinsic molecular coupling pathway is
dependent on the cavity properties. Thus, manipulating the
interference between the cavity-induced DA coupling and the
bridge-mediated coupling offers an approach to direct and
manipulate charge flow at the nanoscale.},
Doi = {10.1021/acs.jpclett.2c02496},
Key = {fds367470}
}
@article{fds376669,
Author = {Sun, R and Park, KS and Comstock, AH and McConnell, A and Chen, Y-C and Zhang, P and Beratan, D and You, W and Hoffmann, A and Yu, Z-G and Diao, Y and Sun, D},
Title = {Inverse chirality-induced spin selectivity effect in chiral
assemblies of π-conjugated polymers.},
Journal = {Nature materials},
Year = {2024},
Month = {March},
url = {http://dx.doi.org/10.1038/s41563-024-01838-8},
Abstract = {Coupling of spin and charge currents to structural chirality
in non-magnetic materials, known as chirality-induced spin
selectivity, is promising for application in spintronic
devices at room temperature. Although the chirality-induced
spin selectivity effect has been identified in various
chiral materials, its Onsager reciprocal process, the
inverse chirality-induced spin selectivity effect, remains
unexplored. Here we report the observation of the inverse
chirality-induced spin selectivity effect in chiral
assemblies of π-conjugated polymers. Using spin-pumping
techniques, the inverse chirality-induced spin selectivity
effect enables quantification of the magnitude of the
longitudinal spin-to-charge conversion driven by
chirality-induced spin selectivity in different chiral
polymers. By widely tuning conductivities and supramolecular
chiral structures via a printing method, we found a very
long spin relaxation time of up to several nanoseconds
parallel to the chiral axis. Our demonstration of the
inverse chirality-induced spin selectivity effect suggests
possibilities for elucidating the puzzling interplay between
spin and chirality, and opens a route for spintronic
applications using printable chiral assemblies.},
Doi = {10.1038/s41563-024-01838-8},
Key = {fds376669}
}
@article{fds231900,
Author = {De Vleeschouwer and F and Yang, W and Beratan, DN and Geerlings, P and De
Proft, F},
Title = {Inverse design of molecules with optimal reactivity
properties: acidity of 2-naphthol derivatives.},
Journal = {Physical chemistry chemical physics : PCCP},
Volume = {14},
Number = {46},
Pages = {16002-16013},
Year = {2012},
Month = {December},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23089917},
Abstract = {The design of molecules with optimal properties is an
important challenge in chemistry because of the
astronomically large number of possible stable structures
that is accessible in chemical space. This obstacle can be
overcome through inverse molecular design. In inverse
design, one uses the computation of certain indices to
design molecules with an optimal target property. In this
study, for the first time, inverse design was used to
optimize reactivity properties of molecules. Specifically,
we optimized the acidity of substituted 2-naphthols, both in
the ground and the excited state. Substituted 2-naphthols
belong to the class of photoacids, showing enhanced acidity
when excited from the singlet ground state to the first
singlet excited state. The focus of this work is the ground
state. As a measure of acidity, three different properties
are optimized: the charge on the hydroxyl hydrogen atom of
the acid, the charge on the negatively charged oxygen atom
of the conjugate base and the energy difference between acid
and conjugate base. Both the practical use of the
methodology and the results for ground and excited states
are discussed.},
Doi = {10.1039/c2cp42623d},
Key = {fds231900}
}
@article{fds231949,
Author = {Xiao, D and Yang, W and Beratan, DN},
Title = {Inverse molecular design in a tight-binding
framework.},
Journal = {The Journal of chemical physics},
Volume = {129},
Number = {4},
Pages = {044106},
Year = {2008},
Month = {July},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18681633},
Abstract = {The number of chemical species of modest molecular weight
that can be accessed with known synthetic methods is
astronomical. An open challenge is to explore this space in
a manner that will enable the discovery of molecular species
and materials with optimized properties. Recently, an
inverse molecular design strategy, the linear combination of
atomic potentials (LCAP) approach [J. Am. Chem. Soc. 128,
3228 (2006)] was developed to optimize electronic
polarizabilities and first hyperpolarizabilities. Here,
using a simple tight-binding (TB) approach, we show that
continuous optimization can be carried out on the LCAP
surface successfully to explore vast chemical libraries of
10(2) to 10(16) extended aromatic compounds. We show that
the TB-LCAP optimization is not only effective in locating
globally optimal structures based on their electronic
polarizabilities and first hyperpolarizabilities, but also
is straightforwardly extended to optimize transition dipole
moments and HOMO-LUMO energy gaps. This approach finds
optimal structures among 10(4) candidates with about 40
individual molecular property calculations. As such, for
structurally similar molecular candidates, the TB-LCAP
approach may provide an effective means to identify
structures with optimal properties.},
Doi = {10.1063/1.2955756},
Key = {fds231949}
}
@article{fds231988,
Author = {Kuhn, C and Beratan, DN},
Title = {Inverse strategies for molecular design},
Journal = {Journal of Physical Chemistry},
Volume = {100},
Number = {25},
Pages = {10595-10599},
Publisher = {American Chemical Society (ACS)},
Year = {1996},
Month = {June},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1996/100/i25/pdf/jp960518i.pdf},
Abstract = {An "inverse" molecular design strategy is described to
assist in the development of new molecules with optimized
properties. This approach is based on a molecular orbital
view and can be used to tailor ground state or excited state
properties subject to particular constraints. In this
scheme, wave functions are sought that optimize a chemical
or electronic property, and then a Hamiltonian is
constructed that generates these optimized wave functions.
Analysis of the chemical properties in the optimized systems
may suggest new synthetic targets. Examples are presented
that optimize the transition dipole moment in some simple
structures. © 1996 American Chemical Society.},
Doi = {10.1021/jp960518i},
Key = {fds231988}
}
@article{fds231928,
Author = {Keinan, S and Venkatramani, R and Balaeff, A and Beratan,
DN},
Title = {Is MD geometry sampling sufficient for nucleobase electronic
structure analysis of et reactions? Comparing classical MD
and QM/MM methods},
Journal = {Journal of Physical Chemistry C},
Volume = {114},
Number = {48},
Pages = {20496-20502},
Publisher = {American Chemical Society (ACS)},
Year = {2010},
Month = {December},
ISSN = {1932-7447},
url = {http://dx.doi.org/10.1021/jp104919g},
Abstract = {It has been shown in many experimental studies that one of
the major charge-transfer mechanisms in nucleic acids is
that by positive charge carriers (holes), residing
predominantly on G bases. Theoretical charge-transfer
calculations often use Koopmans' theorem to approximate the
relaxed doublet cation hole energies from simulations of the
neutral ground state (GS). An assumption in these
calculations is that the geometry and interactions of the
doublet cation (DC) hole with the solvent is the same as
that for the neutral GS. Here, we simulate the DC hole on
solvated G and A nucleobases using combined quantum
mechanics/molecular mechanics (QM/MM) methods and compare
the geometries and electronic structure of the charged bases
to those of the neutral bases. We also study the effects of
the solvent environment on the nucleobase electronic
structure and estimate the size of the smallest solvent
shell that needs to be included in order to achieve
convergence of the nucleobase energy levels. We find that
Koopmans' theorem based methods provide a satisfactory
description of the nucleobase energy levels, with the
largest deviation (̃0.1eV) for charged bases in explicit
water. We also find that the size of the solvent shell is
crucial for describing the nucleobase electronic structure.
When the solvent is properly accounted for, we find that the
average energy separation between the hole energy levels on
isolated G and A is ̃0.2 eV, and the hole energy levels
fluctuate by ̃0.3 eV. These findings suggest important
corrections to earlier theoretical studies that
overestimated the hole energy separation among nucleobases
and underestimated or neglected the base energy distribution
due to thermal fluctuations of the nucleobases and their
environment. Our results further suggest that hopping charge
transport plays an important role even at short distances.
© 2010 American Chemical Society.},
Doi = {10.1021/jp104919g},
Key = {fds231928}
}
@article{fds326931,
Author = {Nayak, A and Park, J and De Mey and K and Hu, X and Duncan, TV and Beratan,
DN and Clays, K and Therien, MJ},
Title = {Large Hyperpolarizabilities at Telecommunication-Relevant
Wavelengths in Donor-Acceptor-Donor Nonlinear Optical
Chromophores.},
Journal = {ACS central science},
Volume = {2},
Number = {12},
Pages = {954-966},
Year = {2016},
Month = {December},
url = {http://dx.doi.org/10.1021/acscentsci.6b00291},
Abstract = {Octopolar <i>D</i><sub>2</sub>-symmetric chromophores, based
on the MPZnM supermolecular motif in which
(porphinato)zinc(II) (PZn) and ruthenium(II) polypyridyl (M)
structural units are connected via ethyne linkages, were
synthesized. These structures take advantage of
electron-rich <i>meso</i>-arylporphyrin or electron-poor
<i>meso</i>-(perfluoroalkyl)porphyrin macrocycles,
unsubstituted terpyridyl and 4'-pyrrolidinyl-2,2';6',2″-terpyridyl
ligands, and modulation of metal(II) polypyridyl-to-(porphinato)zinc
connectivity, to probe how electronic and geometric factors
impact the measured hyperpolarizability. Transient
absorption spectra obtained at early time delays
(<i>t</i><sub>delay</sub> < 400 fs) demonstrate fast
excited-state relaxation, and formation of a highly
polarized T<sub>1</sub> excited state; the T<sub>1</sub>
states of these chromophores display expansive, intense
T<sub>1</sub> → T <sub><i>n</i></sub> absorption manifolds
that dominate the 800-1200 nm region of the NIR, long (μs)
triplet-state lifetimes, and unusually large NIR excited
absorptive extinction coefficients [ε(T<sub>1</sub> → T
<sub><i>n</i></sub> ) ∼ 10<sup>5</sup> M<sup>-1</sup>
cm<sup>-1</sup>]. Dynamic hyperpolarizability
(β<sub>λ</sub>) values were determined from hyper-Rayleigh
light scattering (HRS) measurements, carried out at multiple
incident irradiation wavelengths spanning the 800-1500 nm
spectral domain. The measured β<sub>HRS</sub> value (4600
± 1200 × 10<sup>-30</sup> esu) for one of these complexes,
RuPZnRu, is the largest yet reported for any chromophore at
a 1500 nm irradiation wavelength, highlighting that
appropriate engineering of strong electronic coupling
between multiple charge-transfer oscillators provides a
critical design strategy to realize octopolar NLO
chromophores exhibiting large β<sub>HRS</sub> values at
telecom-relevant wavelengths. Generalized Thomas-Kuhn sum
(TKS) rules were utilized to compute the effective
excited-state-to-excited-state transition dipole moments
from experimental linear-absorption spectra; these data were
then utilized to compute hyperpolarizabilities as a function
of frequency, that include two- and three-state
contributions for both β <sub><i>zzz</i></sub> and β
<sub><i>xzx</i></sub> tensor components to the RuPZnRu
hyperpolarizability spectrum. This analysis predicts that
the β <sub><i>zzz</i></sub> and β <sub><i>xzx</i></sub>
tensor contributions to the RuPZnRu hyperpolarizability
spectrum maximize near 1550 nm, in agreement with
experimental data. The TKS analysis suggests that relative
to analogous dipolar chromophores, octopolar supermolecules
will be likely characterized by more intricate dependences
of the measured hyperpolarizability upon irradiation
wavelength due to the interactions among multiple different
β tensor components.},
Doi = {10.1021/acscentsci.6b00291},
Key = {fds326931}
}
@article{fds366126,
Author = {Georgieva, ZN and Zhang, Z and Zhang, P and Bloom, BP and Beratan, DN and Waldeck, DH},
Title = {Ligand Coverage and Exciton Delocalization Control Chiral
Imprinting in Perovskite Nanoplatelets},
Journal = {Journal of Physical Chemistry C},
Volume = {126},
Number = {37},
Pages = {15986-15995},
Year = {2022},
Month = {January},
url = {http://dx.doi.org/10.1021/acs.jpcc.2c04192},
Abstract = {Chiral perovskites have recently generated significant
interest, yet little is known about how their chiro-optical
properties arise. In this study, chiral methylammonium lead
halide perovskite nanoplatelets (NPLs) with varied halide
and ligand compositions are prepared by using direct
synthetic methods. Circular dichroism (CD) and 1H NMR
studies find a nonlinear relationship between the
chiroptical properties and the ratio of chiral
phenylethylammonium (PEA) to achiral octylamine (OA) ligands
on the NPL surface. We use density functional theory (DFT)
computations and a chiral imprinted particle-in-a-box model
to rationalize the experimentally observed CD spectra, and
we find that the saturation of the induced chirality depends
on the size of the perovskite exciton relative to the size
of the ligand moleclues. Temperature-dependent CD and 1H NMR
studies, combined with DFT analysis, show that both the CD
intensity and sign depend strongly on the structure and
orientation of the ligands. This work reveals the complex
nature of chiral imprinting in perovskite nanostructures and
establishes a simple physical model for ligand-induced
chiral imprinting to guide the further development of chiral
materials.},
Doi = {10.1021/acs.jpcc.2c04192},
Key = {fds366126}
}
@article{fds285284,
Author = {Bloom, BP and Zhao, LB and Wang, Y and Waldeck, DH and Liu, R and Zhang, P and Beratan, DN},
Title = {Ligand-induced changes in the characteristic size-dependent
electronic energies of CdSe nanocrystals},
Journal = {Journal of Physical Chemistry C},
Volume = {117},
Number = {43},
Pages = {22401-22411},
Publisher = {American Chemical Society (ACS)},
Year = {2013},
Month = {October},
ISSN = {1932-7447},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000326608200031&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {This work explores the electronic energy of CdSe
nanoparticles as a function of nanoparticle (NP) size and
capping ligand. Differential pulse voltammetry was used to
determine the valence band edge of CdSe NPs that are capped
with three different ligands (aniline, thiophenol, and
phenylphosphonic acid), and the experimental values are
compared with DFT calculations. These results show how the
energy position and the size-dependent behavior of the
energy bands of CdSe can be modulated by the chemical nature
of the capping ligand. The computations underscore how the
nature of the highest lying filled states of the
nanoparticle can change with ligand type and how this can
explain differences between previously reported
size-dependent data on similar systems. The findings show
that both the ligand and quantum confinement effects should
be accounted for in modeling size-dependent effects for
different NP-ligand systems. © 2013 American Chemical
Society.},
Doi = {10.1021/jp403164w},
Key = {fds285284}
}
@article{fds222349,
Author = {B.P. Bloom and J-B. Zhao and Y. Wang and D.H. Waldeck and R. Liu and P.
Zhang and D.N. Beratan},
Title = {Ligand-induced changes in the characteristic size-dependent
electronic energies of CdSe nanocrystals},
Journal = {J. Phys Chem. C},
Year = {2013},
url = {http://dx.doi.org/10.1021/jp403164w},
Doi = {10.1021/jp403164w},
Key = {fds222349}
}
@article{fds222350,
Author = {J. Lin and X. Hu and P. Zhang and A. Van Rynbach and D.N. Beratan and C.
Kent, B. Mehl and J. Papanikolas and T.J. Meyer and Thomas and W. Lin and S.S. Skourtis and M. Constantinou},
Title = {Ligand-induced changes in the characteristic size-dependent
electronic energies of CdSe nanocrystals},
Journal = {J. Phys Chem. C},
Year = {2013},
url = {http://dx.doi.org/10.1021/jp401515r},
Doi = {10.1021/jp401515r},
Key = {fds222350}
}
@article{fds231971,
Author = {Beratan, DN and Onuchic, JN and Hopfield, JJ},
Title = {Limiting forms of the tunneling matrix element in the long
distance bridge mediated electron transfer
problem},
Journal = {The Journal of Chemical Physics},
Volume = {83},
Number = {10},
Pages = {5325-5329},
Publisher = {AIP Publishing},
Year = {1985},
Month = {January},
ISSN = {0021-9606},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000083000010005325000001&idtype=cvips},
Abstract = {A simple model is presented for long distance electron
transfer through a bridging medium. Assumptions about the
bridge mediated interaction, inherent in many other models,
are shown to be limits of the more general problem. The
relative importance of through bond and through space
coupling is discussed. © 1985 American Institute of
Physics.},
Doi = {10.1063/1.449694},
Key = {fds231971}
}
@article{fds231958,
Author = {Kazmin, D and Prytkova, T and Cook, CE and Wolfinger, R and Chu, T-M and Beratan, D and Norris, JD and Chang, C-Y and McDonnell,
DP},
Title = {Linking ligand-induced alterations in androgen receptor
structure to differential gene expression: a first step in
the rational design of selective androgen receptor
modulators.},
Journal = {Mol Endocrinol},
Volume = {20},
Number = {6},
Pages = {1201-1217},
Year = {2006},
Month = {June},
ISSN = {0888-8809},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16574741},
Abstract = {We have previously identified a family of novel androgen
receptor (AR) ligands that, upon binding, enable AR to adopt
structures distinct from that observed in the presence of
canonical agonists. In this report, we describe the use of
these compounds to establish a relationship between AR
structure and biological activity with a view to defining a
rational approach with which to identify useful selective AR
modulators. To this end, we used combinatorial peptide phage
display coupled with molecular dynamic structure analysis to
identify the surfaces on AR that are exposed specifically in
the presence of selected AR ligands. Subsequently, we used a
DNA microarray analysis to demonstrate that differently
conformed receptors facilitate distinct patterns of gene
expression in LNCaP cells. Interestingly, we observed a
complete overlap in the identity of genes expressed after
treatment with mechanistically distinct AR ligands. However,
it was differences in the kinetics of gene regulation that
distinguished these compounds. Follow-up studies, in
cell-based assays of AR action, confirmed the importance of
these alterations in gene expression. Together, these
studies demonstrate an important link between AR structure,
gene expression, and biological outcome. This relationship
provides a firm underpinning for mechanism-based screens
aimed at identifying SARMs with useful clinical
profiles.},
Doi = {10.1210/me.2005-0309},
Key = {fds231958}
}
@article{fds232042,
Author = {Luken, WL and Beratan, DN},
Title = {Localized orbitals and the Fermi hole},
Journal = {Theoretica Chimica Acta},
Volume = {61},
Number = {3},
Pages = {265-281},
Publisher = {Springer Nature America, Inc},
Year = {1982},
Month = {May},
ISSN = {0040-5744},
url = {http://dx.doi.org/10.1007/BF00550971},
Abstract = {The relationship between localized orbitals and the Fermi
hole is demonstrated with contour maps of the Fermi hole in
the water molecule. These contour maps indicate the presence
of regions in which the Fermi hole is relatively stable,
regions in which the shape of the Fermi hole changes
rapidly, and regions in which the Fermi hole follows the
probe electron smoothly. If a single orbital dominates any
region of space, the Fermi hole resembles that orbital for
any position of the probe electron in the dominated region.
© 1982 Springer-Verlag.},
Doi = {10.1007/BF00550971},
Key = {fds232042}
}
@misc{fds370706,
Author = {BERATAN, DN},
Title = {LONG-DISTANCE BRIDGE MEDIATED ELECTRON-TRANSFER IN RIGID
MODEL SYSTEMS AND FLOPPY REAL SYSTEMS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {192},
Pages = {34-PHYS},
Year = {1986},
Key = {fds370706}
}
@article{fds232045,
Author = {Cowan, JA and Upmacis, RK and Beratan, DN and Onuchic, JN and Gray,
HB},
Title = {Long-range electron transfer in myoglobin.},
Journal = {Annals of the New York Academy of Sciences},
Volume = {550},
Pages = {68-84},
Year = {1988},
Month = {January},
ISSN = {0077-8923},
url = {http://www.ncbi.nlm.nih.gov/pubmed/3245652},
Abstract = {The distance and driving-force dependences of electron
transfer (ET) in a set of four surface-ruthenated
myoglobins, in which the heme prosthetic group has been
systematically replaced by a series of metalloporphyrins of
differing excited-state redox potentials, have provided
information on the magnitude [Hab(12.7 A) approximately 6.3
x 10(-3) cm-1] and decay [beta approximately 0.8 A-1, where
kET alpha exp [-beta(d - do)]] of protein-mediated
donor-acceptor electronic coupling. A reorganization energy
lambda approximately 1.3 eV, due to coordination and
solvation changes both at and between the ET sites, has been
estimated using a rate expression that allows
electron-vibration coupling to classical and quantum
mechanical modes. The contribution to lambda from the
porphyrin and peptide matrix is approximately 0.7 eV.
Specific electron-tunneling pathways in the protein have
been evaluated.},
Doi = {10.1111/j.1749-6632.1988.tb35324.x},
Key = {fds232045}
}
@misc{fds370696,
Author = {WINKLER, JR and BERATAN, DN and GRAY, HB},
Title = {LONG-RANGE ELECTRON-TRANSFER IN PROTEINS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {203},
Pages = {7-CHED},
Year = {1992},
Key = {fds370696}
}
@misc{fds370685,
Author = {CURRY, WB and DEFOREST, SA and GRABE, MD and BERATAN,
DN},
Title = {LONG-RANGE ELECTRON-TRANSFER IN RPS VIRIDIS PHOTOSYNTHETIC
REACTION-CENTER AND HORSE HEART CYTOCHROME-C},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {210},
Pages = {118-INOR},
Year = {1995},
Key = {fds370685}
}
@article{fds231966,
Author = {Skourtis, SS and Waldeck, DH and Beratan, DN},
Title = {Loss of Pathway Coherence in Inelastic Bridge-mediated
Electron Transfer},
Journal = {J. Phys. Chem. B},
Volume = {108},
Number = {40},
Pages = {15511-15518},
Year = {2004},
ISSN = {1520-6106},
url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2004/108/i40/pdf/jp0485340.pdf},
Abstract = {Theoretical analysis of nonadiabatic electron-transfer
reactions in molecules usually assumes that electron
amplitude propagates coherently from the reductant to the
oxidant via covalent and noncovalent coupling pathways. We
show that when the tunneling electron excites local bridge
vibrations (inelastic tunneling), the excitation "labels"
the physical pathway traversed. As such, the coherence among
the bridge-mediated tunneling pathways is destroyed. We
illustrate this effect using a simple model Hamiltonian and
show how the donor-acceptor interaction, and thus the
electron-transfer rate, is modified by inelastic effects.
Pathway coherence loss provides a mechanism to relax
orbital-symmetry constraints on electron-transfer reactions.
This effect may be of particular significance in
macromolecules with destructively interfering pathways or
low tunneling barriers. Pathway decoherence that arises from
inelastic effects in molecules is analogous to coherence
loss in mesoscopic "which way" interferometers and might
provide an approach to gate electron flow in molecular-scale
devices.},
Doi = {10.1021/jp0485340},
Key = {fds231966}
}
@article{fds232028,
Author = {Betts, JN and Beratan, DN and Onuchic, JN},
Title = {Mapping Electron Tunneling Pathways: An Algorithm that Finds
the “Minimum Length”/Maximum Coupling Pathway between
Electron Donors and Acceptors in Proteins},
Journal = {Journal of the American Chemical Society},
Volume = {114},
Number = {11},
Pages = {4043-4046},
Publisher = {American Chemical Society (ACS)},
Year = {1992},
Month = {May},
ISSN = {0002-7863},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1992/114/i11/pdf/ja00037a004.pdf},
Abstract = {The covalent, hydrogen bonded, and van der Waals
connectivity of proteins can be represented with geometrical
objects called graphs. In these graphs, vertices represent
bonds and the connections between them, edges, represent
bond-bond interactions. We describe a model in which edge
lengths are associated with the wave function decay between
interacting pairs of bonds, and a minimum distance
graph-search algorithm is used to find the pathways that
dominate electron donor-acceptor interactions in these
molecules. Predictions of relative electron transfer rates
can be made from these pathway lengths. The results are
consistent with many experimentally measured
electron-transfer rates, although some anomalies exist.
Presentation of the pathway coupling between the donor (or
acceptor) and every other atom in a given protein as a
color-coded map provides a design tool for tailored
electron-transfer proteins. © 1992, American Chemical
Society. All rights reserved.},
Doi = {10.1021/ja00037a004},
Key = {fds232028}
}
@article{fds345382,
Author = {Teo, RD and Wang, R and Smithwick, ER and Migliore, A and Therien, MJ and Beratan, DN},
Title = {Mapping hole hopping escape routes in proteins.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {116},
Number = {32},
Pages = {15811-15816},
Year = {2019},
Month = {August},
url = {http://dx.doi.org/10.1073/pnas.1906394116},
Abstract = {A recently proposed oxidative damage protection mechanism in
proteins relies on hole hopping escape routes formed by
redox-active amino acids. We present a computational tool to
identify the dominant charge hopping pathways through these
residues based on the mean residence times of the
transferring charge along these hopping pathways. The
residence times are estimated by combining a kinetic model
with well-known rate expressions for the charge-transfer
steps in the pathways. We identify the most rapid hole
hopping escape routes in cytochrome P450 monooxygenase,
cytochrome <i>c</i> peroxidase, and benzylsuccinate synthase
(BSS). This theoretical analysis supports the existence of
hole hopping chains as a mechanism capable of providing hole
escape from protein catalytic sites on biologically relevant
timescales. Furthermore, we find that pathways involving the
[4Fe4S] cluster as the terminal hole acceptor in BSS are
accessible on the millisecond timescale, suggesting a
potential protective role of redox-active cofactors for
preventing protein oxidative damage.},
Doi = {10.1073/pnas.1906394116},
Key = {fds345382}
}
@article{fds365682,
Author = {Parker, KA and Schultz, JD and Singh, N and Wasielewski, MR and Beratan,
DN},
Title = {Mapping Simulated Two-Dimensional Spectra to Molecular
Models Using Machine Learning.},
Journal = {The journal of physical chemistry letters},
Volume = {13},
Number = {32},
Pages = {7454-7461},
Year = {2022},
Month = {August},
url = {http://dx.doi.org/10.1021/acs.jpclett.2c01913},
Abstract = {Two-dimensional (2D) spectroscopy encodes molecular
properties and dynamics into expansive spectral data sets.
Translating these data into meaningful chemical insights is
challenging because of the many ways chemical properties can
influence the spectra. To address the task of extracting
chemical information from 2D spectroscopy, we study the
capacity of simple feedforward neural networks (NNs) to map
simulated 2D electronic spectra to underlying physical
Hamiltonians. We examined hundreds of simulated 2D spectra
corresponding to monomers and dimers with varied
Franck-Condon active vibrations and monomer-monomer
electronic couplings. We find the NNs are able to correctly
characterize most Hamiltonian parameters in this study with
an accuracy above 90%. Our results demonstrate that NNs can
aid in interpreting 2D spectra, leading from spectroscopic
features to underlying effective Hamiltonians.},
Doi = {10.1021/acs.jpclett.2c01913},
Key = {fds365682}
}
@article{fds318053,
Author = {Polizzi, NF and Therien, MJ and Beratan, DN},
Title = {Mean First-Passage Times in Biology.},
Journal = {Israel journal of chemistry},
Volume = {56},
Number = {9-10},
Pages = {816-824},
Year = {2016},
Month = {November},
url = {http://dx.doi.org/10.1002/ijch.201600040},
Abstract = {Many biochemical processes, such as charge hopping or
protein folding, can be described by an average timescale to
reach a final state, starting from an initial state. Here,
we provide a pedagogical treatment of the mean first-passage
time (MFPT) of a physical process, which depends on the
number of intervening states between the initial state and
the target state. Our aim in this tutorial review is to
provide a clear development of the mean first-passage time
formalism and to show some of its practical utility. The
MFPT treatment can provide a useful link between microscopic
rates and the average timescales often probed by
experiment.},
Doi = {10.1002/ijch.201600040},
Key = {fds318053}
}
@article{fds359873,
Author = {Roy, S and Zheng, L and Silberbush, O and Engel, M and Atsmon-Raz, Y and Miller, Y and Migliore, A and Beratan, DN and Ashkenasy,
N},
Title = {Mechanism of Side Chain-Controlled Proton Conductivity in
Bioinspired Peptidic Nanostructures.},
Journal = {The journal of physical chemistry. B},
Volume = {125},
Number = {46},
Pages = {12741-12752},
Year = {2021},
Month = {November},
url = {http://dx.doi.org/10.1021/acs.jpcb.1c08857},
Abstract = {Bioinspired peptide assemblies are promising candidates for
use as proton-conducting materials in electrochemical
devices and other advanced technologies. Progress toward
applications requires establishing foundational
structure-function relationships for transport in these
materials. This experimental-theoretical study sheds light
on how the molecular structure and proton conduction are
linked in three synthetic cyclic peptide nanotube assemblies
that comprise the three canonical basic amino acids (lysine,
arginine, and histidine). Experiments find an order of
magnitude higher proton conductivity for lysine-containing
peptide assemblies compared to histidine and arginine
containing assemblies. The simulations indicate that, upon
peptide assembly, the basic amino acid side chains are close
enough to enable direct proton transfer. The proton transfer
kinetics is determined in the simulations to be governed by
the structure and flexibility of the side chains. Together,
experiments and theory indicate that the proton mobility is
the main determinant of proton conductivity, critical for
the performance of peptide-based devices.},
Doi = {10.1021/acs.jpcb.1c08857},
Key = {fds359873}
}
@misc{fds154734,
Author = {D.N. Beratan},
Title = {Methods and systems for selecting molecular structures,”
provisional patent application, submitted 2/16/07; patent
filed 6/12/08},
Year = {2008},
Key = {fds154734}
}
@misc{fds370702,
Author = {BERATAN, DN and ONUCHIC, JN},
Title = {MODELS FOR PREDICTING ELECTRON-TUNNELING PATHWAYS IN
PROTEINS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {198},
Pages = {85-PHYS},
Year = {1989},
Key = {fds370702}
}
@misc{fds370705,
Author = {BERATAN, DN and ONUCHIC, JN},
Title = {MODELS FOR PROTEIN FACILITATED ELECTRON-TRANSFER
REACTIONS},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {193},
Pages = {21-INOR},
Year = {1987},
Key = {fds370705}
}
@article{fds231933,
Author = {Lin, Z and Lawrence, CM and Xiao, D and Kireev, VV and Skourtis, SS and Sessler, JL and Beratan, DN and Rubtsov, IV},
Title = {Modulating unimolecular charge transfer by exciting bridge
vibrations.},
Journal = {Journal of the American Chemical Society},
Volume = {131},
Number = {50},
Pages = {18060-18062},
Year = {2009},
Month = {December},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19928957},
Abstract = {Ultrafast UV-vibrational spectroscopy was used to
investigate how vibrational excitation of the bridge changes
photoinduced electron transfer between donor
(dimethylaniline) and acceptor (anthracene) moieties bridged
by a guanosine-cytidine base pair (GC). The charge-separated
(CS) state yield is found to be lowered by high-frequency
bridge mode excitation. The effect is linked to a dynamic
modulation of the donor-acceptor coupling interaction by
weakening of H-bonding and/or by disruption of the bridging
base-pair planarity.},
Doi = {10.1021/ja907041t},
Key = {fds231933}
}
@article{fds232027,
Author = {Onuchic, JN and Beratan, DN},
Title = {Molecular Bridge Effects on Distant Charge
Tunneling},
Journal = {Journal of the American Chemical Society},
Volume = {109},
Number = {22},
Pages = {6771-6778},
Publisher = {American Chemical Society (ACS)},
Year = {1987},
Month = {October},
ISSN = {0002-7863},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1987/109/i22/pdf/ja00256a035.pdf},
Abstract = {The question arises as to whether different hydrocarbon
bridges should give different electron-transfer rates. We
answer this question on the basis of energetic and
topological (interference) effects that can be gleaned from
one-electron models. A discussion of model compound
electron-transfer rates based on this interpretation is
given. The approximations implicit in the periodic models
used here (and in previous work) are carefully justified. ©
1987, American Chemical Society. All rights
reserved.},
Doi = {10.1021/ja00256a035},
Key = {fds232027}
}
@misc{fds313866,
Author = {Beratan, DN},
Title = {Molecular control of electron transfer events within and
between biomolecules},
Journal = {MOLECULAR ELECTRONICS: BIO-SENSORS AND BIO-COMPUTERS},
Volume = {96},
Pages = {227-236},
Booktitle = {Molecular electronics: biosensors and biocomputers},
Publisher = {SPRINGER},
Editor = {Barsanti, L and Evangelista, V and Gualtieri, P and Passarelli, V and Vestri, S},
Year = {2003},
Month = {January},
ISBN = {1-4020-1211-X},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000183158700007&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Key = {fds313866}
}
@misc{fds26206,
Author = {D.N. Beratan},
Title = {Molecular control of electron tunneling processes},
Publisher = {Chapter 3.2 in IBC Molecular Nanotechology Conference
Proceedings, IBC Press},
Year = {1997},
Key = {fds26206}
}
@article{fds231947,
Author = {Keinan, S and Therien, MJ and Beratan, DN and Yang,
W},
Title = {Molecular design of porphyrin-based nonlinear optical
materials.},
Journal = {The journal of physical chemistry. A},
Volume = {112},
Number = {47},
Pages = {12203-12207},
Year = {2008},
Month = {November},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18973325},
Abstract = {Nonlinear optical chromophores containing
(porphyrinato)Zn(II), proquinoid, and (terpyridyl)metal(II)
building blocks were optimized in a library containing
approximately 10(6) structures using the linear combination
of atomic potentials (LCAP) methodology. We report here the
library design and molecular property optimizations. Two
basic structural types of large beta(0) chromophores were
examined: linear and T-shaped motifs. These T-shaped
geometries suggest a promising NLO chromophoric architecture
for experimental investigation and further support the value
of performing LCAP searches in large chemical
spaces.},
Doi = {10.1021/jp806351d},
Key = {fds231947}
}
@misc{fds22271,
Author = {D.N. Beratan},
Title = {Molecular electronic device concepts},
Volume = {10},
Pages = {411-417},
Booktitle = {1992 Encyclopedia of Physical Science and
Technology},
Publisher = {Academic Press},
Year = {1992},
Key = {fds22271}
}
@misc{fds22280,
Author = {D.N. Beratan},
Title = {Molecular electronic device concepts},
Pages = {359-364},
Booktitle = {1991 Encyclopedia of Physical Science and Technology
Yearbook},
Publisher = {Academic Press},
Year = {1991},
Key = {fds22280}
}
@article{fds232053,
Author = {Waldeck, DH and Beratan, DN},
Title = {Molecular electronics: observation of molecular
rectification.},
Journal = {Science (New York, N.Y.)},
Volume = {261},
Number = {5121},
Pages = {576-577},
Year = {1993},
Month = {July},
ISSN = {0036-8075},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17758166},
Doi = {10.1126/science.261.5121.576},
Key = {fds232053}
}
@misc{fds370671,
Author = {Kurnikov, IV and Liang, ZX and Nocek, JM and Hoffman, BM and Beratan,
DN},
Title = {Monte-Carlo simulations of bimolecular electron transfer
between myoglobin and cytochrome B5.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {221},
Pages = {U397-U397},
Year = {2001},
Key = {fds370671}
}
@misc{fds22198,
Author = {S.S. Skourtis and D.N. Beratan},
Title = {Multi-center and multi-electron transfer in
biology},
Journal = {Electron Transfer Reaction},
Volume = {1},
Series = {Electron Transfer Reaction},
Pages = {109-125},
Booktitle = {Theory & Principles},
Editor = {Wiley-VCH (Weinheim), V. Balzani},
Year = {2001},
Key = {fds22198}
}
@article{fds359452,
Author = {Beratan, DN},
Title = {Multiple hops move electrons from bacteria to
rocks.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {118},
Number = {42},
Pages = {e2115620118},
Year = {2021},
Month = {October},
url = {http://dx.doi.org/10.1073/pnas.2115620118},
Doi = {10.1073/pnas.2115620118},
Key = {fds359452}
}
@article{fds350771,
Author = {Teo, RD and Migliore, A and Beratan, DN},
Title = {Mutation effects on charge transport through the p58c
iron-sulfur protein.},
Journal = {Chemical science},
Volume = {11},
Number = {27},
Pages = {7076-7085},
Year = {2020},
Month = {July},
url = {http://dx.doi.org/10.1039/d0sc02245d},
Abstract = {Growing experimental evidence indicates that iron-sulfur
proteins play key roles in DNA repair and replication. In
particular, charge transport between [Fe<sub>4</sub>S<sub>4</sub>]
clusters, mediated by proteins and DNA, may convey signals
to coordinate enzyme action. Human primase is a well studied
[Fe<sub>4</sub>S<sub>4</sub>] protein, and its p58c domain
(which contains an [Fe<sub>4</sub>S<sub>4</sub>] cluster)
plays a role in the initiation of DNA replication. The Y345C
mutation in p58c is linked to gastric tumors and may
influence the protein-mediated charge transport. The
complexity of protein-DNA systems, and the intricate
electronic structure of [Fe<sub>4</sub>S<sub>4</sub>]
clusters, have impeded progress into understanding
functional charge transport in these systems. In this study,
we built force fields to describe the high potential
[Fe<sub>4</sub>S<sub>4</sub>] cluster in both oxidation
states. The parameterization is compatible with AMBER force
fields and enabled well-balanced molecular dynamics
simulations of the p58c-RNA/DNA complex relevant to the
initiation of DNA replication. Using the molecular mechanics
Poisson-Boltzmann and surface area solvation method on the
molecular dynamics trajectories, we find that the p58c
mutation induces a modest change in the p58c-duplex binding
free energy in agreement with recent experiments. Through
kinetic modeling and analysis, we identify key features of
the main charge transport pathways in p58c. In particular,
we find that the Y345C mutation partially changes the
composition and frequency of the most efficient (and
potentially relevant to the biological function) charge
transport pathways between the [Fe<sub>4</sub>S<sub>4</sub>]
cluster and the duplex. Moreover, our approach sets the
stage for a deeper understanding of functional charge
transfer in [Fe<sub>4</sub>S<sub>4</sub>] protein-DNA
complexes.},
Doi = {10.1039/d0sc02245d},
Key = {fds350771}
}
@article{fds231916,
Author = {Contreras García and J and Keinan, S and Beratan, DN and Yang, W and Johnson, ER and Chaudret, R},
Title = {NCIPLOT: a program for plotting non-covalent interaction
regions},
Journal = {J. Chem. Theory Comput.},
Volume = {7},
Number = {7},
Pages = {625-632},
Year = {2011},
ISSN = {1549-9618},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21516178},
Abstract = {Non-covalent interactions hold the key to understanding many
chemical, biological, and technological problems. Describing
these non-covalent interactions accurately, including their
positions in real space, constitutes a first step in the
process of decoupling the complex balance of forces that
define non-covalent interactions. Because of the size of
macromolecules, the most common approach has been to assign
van der Waals interactions (vdW), steric clashes (SC), and
hydrogen bonds (HBs) based on pairwise distances between
atoms according to their van der Waals radii. We recently
developed an alternative perspective, derived from the
electronic density: the Non-Covalent Interactions (NCI)
index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has
the dual advantages of being generally transferable to
diverse chemical applications and being very fast to
compute, since it can be calculated from promolecular
densities. Thus, NCI analysis is applicable to large
systems, including proteins and DNA, where analysis of
non-covalent interactions is of great potential value. Here,
we describe the NCI computational algorithms and their
implementation for the analysis and visualization of weak
interactions, using both self-consistent fully
quantum-mechanical, as well as promolecular, densities. A
wide range of options for tuning the range of interactions
to be plotted is also presented. To demonstrate the
capabilities of our approach, several examples are given
from organic, inorganic, solid state, and macromolecular
chemistry, including cases where NCI analysis gives insight
into unconventional chemical bonding. The NCI code and its
manual are available for download at http://www.chem.duke.edu/~yang/software.htm.},
Doi = {10.1021/ct100641a},
Key = {fds231916}
}
@article{fds232010,
Author = {Perry, TL and Dickerson, A and Khan, AA and Kondru, RK and Beratan, DN and Wipf, P and Kelly, M and Hamann, MT},
Title = {New peroxylactones from the Jamaican sponge Plakinastrella
onkodes, with inhibitory activity against the AIDS
opportunistic parasitic infection Toxoplasma
gondii},
Journal = {Tetrahedron},
Volume = {57},
Number = {8},
Pages = {1483-1487},
Publisher = {Elsevier BV},
Year = {2001},
Month = {February},
ISSN = {0040-4020},
url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6THR-42G08W1-5-C&_cdi=5289&_user=38557&_orig=browse&_coverDate=02%2F18%2F2001&_sk=999429991&view=c&wchp=dGLbVtz-zSkzS&md5=9131454337d1599a42c0349a9dc1187a&ie=/sdarticle.pdf},
Abstract = {An analysis of the chemical constituents of Plakinastrella
onkodes collected in Jamaica yielded three cyclic peroxides,
including the known plakortolide (1) and two new analogs of
1. The absolute configuration of plakortolide G
((3R,4R,6R,8S)-3) was determined by ab initio optical
rotation computations using a coupled Hartree-Fock (CHF)
method implemented in CADPAC. Plakortolide (1) (J. Org.
Chem. 1980, 45, 3396) and plakortolide G (3) exhibited
potent inhibitory activity against the protozoan Toxoplasma
gondii in HFF cells and represent the first marine natural
products reported with T. gondii inhibitory activity. ©
2001 Elsevier Science Ltd.},
Doi = {10.1016/S0040-4020(00)01134-0},
Key = {fds232010}
}
@article{fds231974,
Author = {Beratan, DN and Onuchic, JN and Perry, JW},
Title = {Nonlinear susceptibilities of finite conjugated organic
polymers},
Journal = {Journal of Physical Chemistry},
Volume = {91},
Number = {11},
Pages = {2696-2698},
Publisher = {American Chemical Society (ACS)},
Year = {1987},
Month = {January},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1987/91/i11/pdf/j100295a009.pdf},
Abstract = {Tight-binding calculations of the length dependence of the
third-order molecular hyperpolarizability for polyenes and
polyynes are reported. The π-electron wave functions were
determined by exploiting the limited translational symmetry
of the molecules. Perturbation theory was used to calculate
the longitudinal component of the electronic nonresonant
hyperpolarizability. To our knowledge, this is the first
two-"band" calculation of third-order hyperpolarizabilities
on finite π-electron systems of varying length. In contrast
to the results of the one-"band" models, the
hyperpolarizability densities increase rapidly and then,
after about 10-15 repeating units, approach an asymptotic
value. © 1987 American Chemical Society.},
Doi = {10.1021/j100295a009},
Key = {fds231974}
}
@article{fds231894,
Author = {Venkatramani, R and Keinan, S and Balaeff, A and Beratan,
DN},
Title = {Nucleic Acid Charge Transfer: Black, White and
Gray.},
Journal = {Coordination chemistry reviews},
Volume = {255},
Number = {7-8},
Pages = {635-648},
Year = {2011},
Month = {April},
ISSN = {0010-8545},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21528017},
Abstract = {Theoretical studies of charge transport in deoxyribonucleic
acid (DNA) and peptide nucleic acid (PNA) indicate that
structure and dynamics modulate the charge transfer rates,
and that different members of a structural ensemble support
different charge transport mechanisms. Here, we review the
influences of nucleobase geometry, electronic structure,
solvent environment, and thermal conformational fluctuations
on the charge transfer mechanism. We describe an emerging
framework for understanding the diversity of charge
transport mechanisms seen in nucleic acids.},
Doi = {10.1016/j.ccr.2010.12.010},
Key = {fds231894}
}
@article{fds333775,
Author = {Peters, JW and Beratan, DN and Schut, GJ and Adams,
MWW},
Title = {On the nature of organic and inorganic centers that
bifurcate electrons, coupling exergonic and endergonic
oxidation-reduction reactions.},
Journal = {Chemical communications (Cambridge, England)},
Volume = {54},
Number = {33},
Pages = {4091-4099},
Year = {2018},
Month = {April},
url = {http://dx.doi.org/10.1039/c8cc01530a},
Abstract = {Bifurcating electrons to couple endergonic and exergonic
electron-transfer reactions has been shown to have a key
role in energy conserving redox enzymes. Bifurcating enzymes
require a redox center that is capable of directing electron
transport along two spatially separate pathways. Research
into the nature of electron bifurcating sites indicates that
one of the keys is the formation of a low potential
oxidation state to satisfy the energetics required of the
endergonic half reaction, indicating that any redox center
(organic or inorganic) that can exist in multiple oxidation
states with sufficiently separated redox potentials should
be capable of electron bifurcation. In this Feature Article,
we explore a paradigm for bifurcating electrons down
independent high and low potential pathways, and describe
redox cofactors that have been demonstrated or implicated in
driving this unique biochemistry.},
Doi = {10.1039/c8cc01530a},
Key = {fds333775}
}
@article{fds323625,
Author = {Polizzi, NF and Beratan, DN},
Title = {Open-Access, Interactive Explorations for Teaching and
Learning Quantum Dynamics},
Journal = {Journal of Chemical Education},
Volume = {92},
Number = {12},
Pages = {2161-2164},
Publisher = {American Chemical Society (ACS)},
Year = {2015},
Month = {November},
url = {http://dx.doi.org/10.1021/acs.jchemed.5b00662},
Abstract = {While the research field of quantum dynamics (QD) benefits
from advances in modern computational power, the educational
field of QD paradoxically does not. We have developed an
open-access, interactive, electronic notebook that leverages
a user-friendly interface to engage a new generation of
visual learners with QD. We begin each topic (e.g.,
adiabaticity, light-matter interactions, and relaxation
processes) with essential questions, issues, and background
that orient the learner; we then move directly to visual
explorations of the phenomena, where the learner can
immediately manipulate parameters that control and drive the
physics. This notebook requires only a computer that can run
Wolfram's computable document format (CDF) files (both the
notebook and CDF player are free) and enables learning in a
variety of contexts and grade levels: flipped classrooms,
small groups, and high school students through advanced
researchers. Without sacrificing rigor, Quantum
Dynamics...with the Dynamics! (QDWD) aims to develop
physical intuition and is built in the spirit of hands-on
experimentation with immediate and visual results. The
hierarchical structure of QDWD lends itself to
differentiated instruction, where a motivated or advanced
student can explore the computer code, mathematical
formalism, and underpinning physics.},
Doi = {10.1021/acs.jchemed.5b00662},
Key = {fds323625}
}
@article{fds231874,
Author = {Beratan, DN and Kondru, RK and Wipf, P},
Title = {Optical activity: From structure - Function to structure
prediction},
Journal = {ACS Symposium Series},
Volume = {810},
Pages = {104-118},
Year = {2002},
Month = {January},
ISSN = {0097-6156},
url = {http://dx.doi.org/10.1021/bk-2002-0810.ch008},
Abstract = {Optical rotation is easily measured and provides a
comprehensive probe of molecular dissymmetry. Reliable
calculations of optical rotation angles are now accessible
for organic molecules. These calculations have allowed us to
establish new computational approaches to assign the
absolute stereochemistry of complex natural products. These
methods also allow us to pinpoint chemical group
contributions to optical rotation, resulting in assignment
of how particular dissymmetric structural elements influence
the sign and the magnitude of optical rotations. This
chapter reviews our recent developments in computing optical
rotation angles for natural products, in using this data to
assign absolute stereochemistry, and in establishing
structure-property relations for rotation
angles.},
Doi = {10.1021/bk-2002-0810.ch008},
Key = {fds231874}
}
@misc{fds370677,
Author = {Beratan, DN and Kondru, RK and Wipf, P},
Title = {Optical activity: From structure-function to structure
prediction.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {219},
Pages = {U348-U348},
Year = {2000},
Key = {fds370677}
}
@article{fds232036,
Author = {Ribe, S and Kondru, RK and Beratan, DN and Wipf, P},
Title = {Optical rotation computation, total synthesis, and
stereochemistry assignment of the marine natural product
pitiamide A},
Journal = {Journal of the American Chemical Society},
Volume = {122},
Number = {19},
Pages = {4608-4617},
Publisher = {American Chemical Society (ACS)},
Year = {2000},
Month = {May},
ISSN = {0002-7863},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/2000/122/i19/pdf/ja9945313.pdf},
Abstract = {We report the joint application of ab initio computations
and total synthesis to assign the absolute configuration of
a new natural product. The expected specific rotations of
the (7S,10R)- and (7R,10R)-isomers of pitiamide A in a CHCl3
solvent continuum model were determined as +8 and - 39,
respectively, by CADPAC calculations of the
electric-dipole-magnetic- dipole polarizability tensor.
Total syntheses of these two stereoisomers of the marine
metabolite were achieved by a convergent strategy that
utilized Evans' oxazolidinone alkylation, a novel
water-accelerated modification of Negishi's
zirconocene-catalyzed asymmetric carbometalation as well as
an unusual segment condensation via Mitsunobu alkylation of
a nosyl-activated amide. The experimental optical rotation
measurements confirmed the results of the computational
optical rotation predictions. On the basis of NMR
comparisons, the configuration of pitiamide A was assigned
as (7R,10R). These studies highlight the considerable
structural significance of [α](D) data, but, because the
optical rotation of the natural product was different from
either synthetic diastereomer, our work serves also as an
illustration of potential problems with obtaining accurate
experimental [α](D) data for natural samples.},
Doi = {10.1021/ja9945313},
Key = {fds232036}
}
@article{fds232024,
Author = {Goldsmith, M-R and Jayasuriya, N and Beratan, DN and Wipf,
P},
Title = {Optical rotation of noncovalent aggregates.},
Journal = {Journal of the American Chemical Society},
Volume = {125},
Number = {51},
Pages = {15696-15697},
Year = {2003},
Month = {December},
ISSN = {0002-7863},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14677931},
Abstract = {Dilute solutions of (R)-(-)-pantolactone in CCl4 were
studied by polarimetry in conjunction with theoretical
calculations of [alpha]D. Our data demonstrate that the
self-association of a chiral solute results in a change in
[alpha]D that can be accounted for by the presence of
hydrogen-bonded dimeric species. The theoretical analysis
predicts a concentration-dependent specific rotation in good
agreement with experiment. Further exploration of monomer
and dimer [alpha]D differences, through atomic map analysis,
reveals large contributions to [alpha]D from the
hydrogen-bonded hydroxyl groups in the tightly-coupled
dimer. This study extends the computation of chiroptical
properties to the accurate concentration-dependent
prediction of [alpha]D for noncovalently interacting
self-associating species.},
Doi = {10.1021/ja0376893},
Key = {fds232024}
}
@article{fds231932,
Author = {Mukhopadhyay, P and Wipf, P and Beratan, DN},
Title = {Optical signatures of molecular dissymmetry: combining
theory with experiments to address stereochemical
puzzles.},
Journal = {Accounts of chemical research},
Volume = {42},
Number = {6},
Pages = {809-819},
Year = {2009},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19378940},
Abstract = {Modern chemistry emerged from the quest to describe the
three-dimensional structure of molecules: van't Hoff's
tetravalent carbon placed symmetry and dissymmetry at the
heart of chemistry. In this Account, we explore how modern
theory, synthesis, and spectroscopy can be used in concert
to elucidate the symmetry and dissymmetry of molecules and
their assemblies. Chiroptical spectroscopy, including
optical rotatory dispersion (ORD), electronic circular
dichroism (ECD), vibrational circular dichroism (VCD), and
Raman optical activity (ROA), measures the response of
dissymmetric structures to electromagnetic radiation. This
response can in turn reveal the arrangement of atoms in
space, but deciphering the molecular information encoded in
chiroptical spectra requires an effective theoretical
approach. Although important correlations between ECD and
molecular stereochemistry have existed for some time, a
battery of accurate new theoretical methods that link a much
wider range of chiroptical spectroscopies to structure have
emerged over the past decade. The promise of this field is
considerable: theory and spectroscopy can assist in
assigning the relative and absolute configurations of
complex products, revealing the structure of noncovalent
aggregates, defining metrics for molecular diversity based
on polarization response, and designing chirally imprinted
nanomaterials. The physical organic chemistry of chirality
is fascinating in its own right: defining atomic and group
contributions to optical rotation (OR) is now possible.
Although the common expectation is that chiroptical response
is determined solely by a chiral solute's electronic
structure in a given environment, chiral imprinting effects
on the surrounding medium and molecular assembly can, in
fact, dominate the chiroptical signatures. The theoretical
interpretation of chiroptical markers is challenging because
the optical properties are subtle, resulting from the strong
electric dipole and the weaker electric quadrupole and
magnetic dipole perturbations by the electromagnetic field.
Moreover, OR arises from a combination of nearly canceling
contributions to the electronic response. Indeed, the
challenge posed by the chiroptical properties delayed the
advent of even qualitatively accurate descriptions for some
chiroptical signatures until the past decade when, for
example, prediction of the observed sign of experimental OR
became accessible to theory. The computation of chiroptical
signatures, in close coordination with synthesis and
spectroscopy, provides a powerful framework to diagnose and
interpret the dissymmetry of chemical structures and
molecular assemblies. Chiroptical theory now produces new
schemes to elucidate structure, to describe the specific
molecular sources of chiroptical signatures, and to assist
in our understanding of how dissymmetry is templated and
propagated in the condensed phase.},
Doi = {10.1021/ar8002859},
Key = {fds231932}
}
@article{fds184132,
Author = {Y. Xing and T-H. Park and R. Venkatramani and S. Keinan and D.N.
Beratan, M.J. Therien and E. Borguet},
Title = {Optimizing single molecule conductivity of conjugated
organic oligomers with conjugated carbodithioate
linkers},
Journal = {J. Am. Chem. Soc.},
Number = {132},
Pages = {7946-7956},
Year = {2010},
Key = {fds184132}
}
@article{fds231924,
Author = {Xing, Y and Park, T-H and Venkatramani, R and Keinan, S and Beratan, DN and Therien, MJ and Borguet, E},
Title = {Optimizing single-molecule conductivity of conjugated
organic oligomers with carbodithioate linkers.},
Journal = {Journal of the American Chemical Society},
Volume = {132},
Number = {23},
Pages = {7946-7956},
Year = {2010},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20433175},
Abstract = {In molecular electronics, the linker group, which attaches
the functional molecular core to the electrode, plays a
crucial role in determining the overall conductivity of the
molecular junction. While much focus has been placed on
optimizing molecular core conductivity, there have been
relatively few attempts at designing optimal linker groups
to metallic or semiconducting electrodes. The vast majority
of molecular electronic studies use thiol linker groups;
work probing alternative amine linker systems has only
recently been explored. Here, we probe single-molecule
conductances in phenylene-ethynylene molecules terminated
with thiol and carbodithioate linkers, experimentally using
STM break-junction methods and theoretically using a
nonequilibrium Green's function approach. Experimental
studies demonstrate that the carbodithioate linker augments
electronic coupling to the metal electrode and lowers the
effective barrier for charge transport relative to the
conventional thiol linker, thus enhancing the conductance of
the linker-phenylene-ethynylene-linker unit; these data
underscore that phenylene-ethynylene-based structures are
more highly conductive than originally appreciated in
molecular electronics applications. The theoretical analysis
shows that the nature of sulfur hybridization in these
species is responsible for the order-of-magnitude increased
conductance in carbodithioate-terminated systems relative to
identical conjugated structures that feature classic thiol
linkers, independent of the mechanism of charge transport.
Interestingly, in these systems, the tunneling current is
not dominated by the frontier molecular orbitals. While
barriers <k(B)T are expected to produce low beta values, we
show that the competition between tunneling and resonant
transport processes allows barriers >>k(B)T to produce the
low beta values seen in our experiments. Taken together,
these experimental and theoretical studies indicate a
promising role for carbodithioate-based connectivity in
molecular-scale electronics applications involving metallic
and semiconducting electrodes.},
Doi = {10.1021/ja909559m},
Key = {fds231924}
}
@misc{fds370700,
Author = {MARDER, SR and BERATAN, DN and CHENG, LT and TIEMANN,
BG},
Title = {OPTIMIZING THE 2ND-ORDER OPTICAL NONLINEARITIES OF
ORGANIC-MOLECULES},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {201},
Pages = {163-INOR},
Year = {1991},
Key = {fds370700}
}
@article{fds347152,
Author = {Kang, YK and Zheng, J and Rubtsov, IV and Beratan, DN and Therien,
MJ},
Title = {Orientational Dependence of Cofacial Porphyrin-Quinone
Electronic Interactions within the Strong Coupling
Regime},
Journal = {J. Am. Chem. Soc.},
Volume = {123},
Number = {49},
Pages = {10456-10462},
Year = {2008},
url = {http://dx.doi.org/10.1021/acs.jpcb.9b07627},
Abstract = {We examine the relative magnitudes of electronic coupling
HDA in two face-to-face rigid and diastereomeric
(porphinato)zinc(II)-quinone (PZn-Q) assemblies, 1β-ZnA and
1β-ZnB, in which the six quinonyl carbon atoms lie in
virtually identical arrangements relative to the PZn plane
at sub-van der Waals donor-acceptor (D-A) interplanar
separations. Steady-state and time-resolved transient
optical data and computational studies show that minor
differences in relative D-A cofacial orientation give rise
to disparate HDA magnitudes for both photoinduced charge
separation (CS) and thermal charge recombination (CR).
Time-dependent density functional theory (TDDFT)
computations illuminate the nature of direct charge transfer
states and the electronic structural factors that give rise
to these differential HDAs. These data show more extensive
mixing of locally excited (LE) and CS states in 1β-ZnA
relative to 1β-ZnB and that these HDA differences track the
magnitudes of electronic coupling matrix elements determined
from steady-state electronic spectral data and thermal CR
rate constants measured via pump-probe spectroscopy.
Collectively, this work shows that electron transfer
dynamics may be manipulated in cofacial D-A systems, even at
sub-van der Waals contact, provided that conformational
rigidity precludes structural fluctuations that modulate D-A
interactions on the charge transfer time
scale.},
Doi = {10.1021/acs.jpcb.9b07627},
Key = {fds347152}
}
@article{fds356972,
Author = {Pastore, AJ and Teo, RD and Montoya, A and Burg, MJ and Twahir, UT and Bruner, SD and Beratan, DN and Angerhofer, A},
Title = {Oxalate decarboxylase uses electron hole hopping for
catalysis.},
Journal = {The Journal of biological chemistry},
Volume = {297},
Number = {1},
Pages = {100857},
Year = {2021},
Month = {July},
url = {http://dx.doi.org/10.1016/j.jbc.2021.100857},
Abstract = {The hexameric low-pH stress response enzyme oxalate
decarboxylase catalyzes the decarboxylation of the oxalate
mono-anion in the soil bacterium Bacillus subtilis. A single
protein subunit contains two Mn-binding cupin domains, and
catalysis depends on Mn(III) at the N-terminal site. The
present study suggests a mechanistic function for the
C-terminal Mn as an electron hole donor for the N-terminal
Mn. The resulting spatial separation of the radical
intermediates directs the chemistry toward decarboxylation
of the substrate. A π-stacked tryptophan pair (W96/W274)
links two neighboring protein subunits together, thus
reducing the Mn-to-Mn distance from 25.9 Å (intrasubunit)
to 21.5 Å (intersubunit). Here, we used theoretical
analysis of electron hole-hopping paths through redox-active
sites in the enzyme combined with site-directed mutagenesis
and X-ray crystallography to demonstrate that this
tryptophan pair supports effective electron hole hopping
between the C-terminal Mn of one subunit and the N-terminal
Mn of the other subunit through two short hops of
∼8.5 Å. Replacement of W96, W274, or both with
phenylalanine led to a large reduction in catalytic
efficiency, whereas replacement with tyrosine led to
recovery of most of this activity. W96F and W96Y mutants
share the wildtype tertiary structure. Two additional
hole-hopping networks were identified leading from the Mn
ions to the protein surface, potentially protecting the
enzyme from high Mn oxidation states during turnover. Our
findings strongly suggest that multistep hole-hopping
transport between the two Mn ions is required for enzymatic
function, adding to the growing examples of proteins that
employ aromatic residues as hopping stations.},
Doi = {10.1016/j.jbc.2021.100857},
Key = {fds356972}
}
@article{fds231982,
Author = {Onuchic, JN and Beratan, DN and Winkler, JR and Gray,
HB},
Title = {Pathway analysis of protein electron-transfer
reactions.},
Journal = {Annual review of biophysics and biomolecular
structure},
Volume = {21},
Pages = {349-377},
Year = {1992},
Month = {January},
ISSN = {1056-8700},
url = {http://www.ncbi.nlm.nih.gov/pubmed/1326356},
Doi = {10.1146/annurev.bb.21.060192.002025},
Key = {fds231982}
}
@article{fds232054,
Author = {Curry, WB and Grabe, MD and Kurnikov, IV and Skourtis, SS and Beratan,
DN and Regan, JJ and Aquino, AJ and Beroza, P and Onuchic,
JN},
Title = {Pathways, pathway tubes, pathway docking, and propagators in
electron transfer proteins.},
Journal = {Journal of bioenergetics and biomembranes},
Volume = {27},
Number = {3},
Pages = {285-293},
Year = {1995},
Month = {June},
ISSN = {0145-479X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8847342},
Abstract = {The simplest views of long-range electron transfer utilize
flat one-dimensional barrier tunneling models, neglecting
structural details of the protein medium. The pathway model
of protein electron transfer reintroduces structure by
distinguishing between covalent bonds, hydrogen bonds, and
van der Waals contacts. These three kinds of interactions in
a tunneling pathway each have distinctive decay factors
associated with them. The distribution and arrangement of
these bonded and nonbonded contacts in a folded protein
varies tremendously between structures, adding a richness to
the tunneling problem that is absent in simpler views. We
review the pathway model and the predictions that it makes
for protein electron transfer rates in small proteins,
docked proteins, and the photosynthetic reactions center. We
also review the formulation of the protein electron transfer
problem as an effective two-level system. New multi-pathway
approaches and improved electronic Hamiltonians are
described briefly as well.},
Doi = {10.1007/bf02110098},
Key = {fds232054}
}
@article{fds231948,
Author = {Balabin, IA and Beratan, DN and Skourtis, SS},
Title = {Persistence of structure over fluctuations in biological
electron-transfer reactions.},
Journal = {Physical review letters},
Volume = {101},
Number = {15},
Pages = {158102},
Year = {2008},
Month = {October},
ISSN = {0031-9007},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18999647},
Abstract = {In the soft-wet environment of biomolecular electron
transfer, it is possible that structural fluctuations could
wash out medium-specific electronic effects on electron
tunneling rates. We show that beyond a transition distance
(2-3 A in water and 6-7 A in proteins), fluctuation
contributions to the mean-squared donor-to-acceptor
tunneling matrix element are likely to dominate over the
average matrix element. Even though fluctuations dominate
the tunneling mechanism at larger distances, we find that
the protein fold is "remembered" by the electronic coupling,
and structure remains a key determinant of electron transfer
kinetics.},
Doi = {10.1103/physrevlett.101.158102},
Key = {fds231948}
}
@article{fds344730,
Author = {Ashfold, M and Bender, J and Beratan, DN and Bradforth, S and Cina, J and Datta, A and Dawlaty, J and Dill, R and Dodin, A and Duchi, M and Estergreen, L and Fleming, G and Frankcombe, T and Gate, G and Gessner,
O and Ginsberg, N and Grieco, C and Haggmark, M and Hammes-Schiffer, S and Huxter, V and Kellogg, M and Korovina, N and Lee, Y and Mahl, J and Morenz,
K and Ogilvie, J and Oliver, TAA and Penfold, T and Persson, P and Schwartz, B and Son, M and Stavros, V and Steen, C and Thompson, M and Wasielewski, M and Weiss, E and Woolley, J},
Title = {Photo-induced electron transfer: general
discussion.},
Journal = {Faraday discussions},
Volume = {216},
Pages = {434-459},
Year = {2019},
Month = {July},
url = {http://dx.doi.org/10.1039/c9fd90029b},
Doi = {10.1039/c9fd90029b},
Key = {fds344730}
}
@article{fds167417,
Author = {R. Venkatramani and D.Y. Zang and C. Oh and J. Grote and D.
Beratan},
Title = {Photoconductivity and current-voltage characteristics in
thin DNA},
Journal = {Proceedings of SPIE-The Society of Photo-Optical
Instrumentation Engineers, 7403, 74030B-1 to
74030B-12},
Year = {2009},
Key = {fds167417}
}
@article{fds231889,
Author = {Venkatramani, R and Zang, DY and Oh, C and Grote, J and Beratan,
D},
Title = {Photoconductivity and current-voltage characteristics of
thin DNA films: Experiments and modeling},
Journal = {Proceedings of SPIE - The International Society for Optical
Engineering},
Volume = {7403},
Publisher = {SPIE},
Year = {2009},
Month = {January},
ISSN = {0277-786X},
url = {http://dx.doi.org/10.1117/12.831024},
Abstract = {We report experimental observations and theoretical modeling
of an unusual photoelectric effect in deoxyribonucleic acid
(DNA) thin-film devices, under visible and near-infrared
illumination. The devices also show diode-type rectifying
current-voltage (I-V) characteristics. An equivalent circuit
model was constructed that fits the experimental data, and
physical processes likely to arise in the devices are
discussed. We envisage the formation of a Schottky barrier
at the DNA film-metal interface and infer that the
photoresponse arises from photoinjection of electrons from
the metal into the DNA film. © 2009 SPIE.},
Doi = {10.1117/12.831024},
Key = {fds231889}
}
@article{fds313542,
Author = {Polizzi, NF and Eibling, MJ and Perez-Aguilar, JM and Rawson, J and Lanci, CJ and Fry, HC and Beratan, DN and Saven, JG and Therien,
MJ},
Title = {Photoinduced Electron Transfer Elicits a Change in the
Static Dielectric Constant of a de Novo Designed
Protein.},
Journal = {Journal of the American Chemical Society},
Volume = {138},
Number = {7},
Pages = {2130-2133},
Year = {2016},
Month = {February},
ISSN = {0002-7863},
url = {http://dx.doi.org/10.1021/jacs.5b13180},
Abstract = {We provide a direct measure of the change in effective
dielectric constant (ε(S)) within a protein matrix after a
photoinduced electron transfer (ET) reaction. A linked
donor-bridge-acceptor molecule, PZn-Ph-NDI, consisting of a
(porphinato)Zn donor (PZn), a phenyl bridge (Ph), and a
naphthalene diimide acceptor (NDI), is shown to be a "meter"
to indicate protein dielectric environment. We calibrated
PZn-Ph-NDI ET dynamics as a function of solvent dielectric,
and computationally de novo designed a protein SCPZnI3 to
bind PZn-Ph-NDI in its interior. Mapping the protein ET
dynamics onto the calibrated ET catalogue shows that SCPZnI3
undergoes a switch in the effective dielectric constant
following photoinduced ET, from ε(S) ≈ 8 to ε(S) ≈
3.},
Doi = {10.1021/jacs.5b13180},
Key = {fds313542}
}
@article{fds231954,
Author = {Prytkova, TR and Beratan, DN and Skourtis, SS},
Title = {Photoselected electron transfer pathways in DNA
photolyase.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {104},
Number = {3},
Pages = {802-807},
Year = {2007},
Month = {January},
ISSN = {0027-8424},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17209014},
Abstract = {Cyclobutane dimer photolyases are proteins that bind to
UV-damaged DNA containing cyclobutane pyrimidine dimer
lesions. They repair these lesions by photo-induced electron
transfer. The electron donor cofactor of a photolyase is a
two-electron-reduced flavin adenine dinucleotide (FADH(-)).
When FADH(-) is photo-excited, it transfers an electron from
an excited pi --> pi* singlet state to the pyrimidine dimer
lesion of DNA. We compute the lowest excited singlet states
of FADH(-) using ab initio (time-dependent density
functional theory and time-dependent Hartree-Fock), and
semiempirical (INDO/S configuration interaction) methods.
The calculations show that the two lowest pi --> pi* singlet
states of FADH(-) are localized on the side of the flavin
ring that is proximal to the dimer lesion of DNA. For the
lowest-energy donor excited state of FADH(-), we compute the
conformationally averaged electronic coupling to acceptor
states of the thymine dimer. The coupling calculations are
performed at the INDO/S level, on donor-acceptor cofactor
conformations obtained from molecular dynamics simulations
of the solvated protein with a thymine dimer docked in its
active site. These calculations demonstrate that the
localization of the (1)FADH(-)* donor state on the flavin
ring enhances the electronic coupling between the flavin and
the dimer by permitting shorter electron-transfer pathways
to the dimer that have single through-space jumps.
Therefore, in photolyase, the photo-excitation itself
enhances the electron transfer rate by moving the electron
towards the dimer.},
Doi = {10.1073/pnas.0605319104},
Key = {fds231954}
}
@article{fds231913,
Author = {Polizzi, NF and Skourtis, SS and Beratan, DN},
Title = {Physical constraints on charge transport through bacterial
nanowires.},
Journal = {Faraday discussions},
Volume = {155},
Pages = {43-62},
Year = {2012},
Month = {January},
ISSN = {1359-6640},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22470966},
Abstract = {Extracellular appendages of the dissimilatory metal-reducing
bacterium Shewanella oneidensis MR-1 were recently shown to
sustain currents of 10(10) electrons per second over
distances of 0.5 microns [El-Naggar et al., Proc. Natl.
Acad. Sci. U. S. A., 2010, 107, 18127]. However, the
identity of the charge localizing sites and their
organization along the "nanowire" remain unknown. We use
theory to predict redox cofactor separation distances that
would permit charge flow at rates of 10(10) electrons per
second over 0.5 microns for voltage biases of < or = IV,
using a steady-state analysis governed by a non-adiabatic
electron transport mechanism. We find the observed currents
necessitate a multi-step hopping transport mechanism, with
charge localizing sites separated by less than 1 nm and
reorganization energies that rival the lowest known in
biology.},
Doi = {10.1039/c1fd00098e},
Key = {fds231913}
}
@article{fds231944,
Author = {Hatcher, E and Balaeff, A and Keinan, S and Venkatramani, R and Beratan,
DN},
Title = {PNA versus DNA: effects of structural fluctuations on
electronic structure and hole-transport mechanisms.},
Journal = {Journal of the American Chemical Society},
Volume = {130},
Number = {35},
Pages = {11752-11761},
Year = {2008},
Month = {September},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18693722},
Abstract = {The effects of structural fluctuations on charge transfer in
double-stranded DNA and peptide nucleic acid (PNA) are
investigated. A palindromic sequence with two guanine bases
that play the roles of hole donor and acceptor, separated by
a bridge of two adenine bases, was analyzed using combined
molecular dynamics (MD) and quantum-chemical methods.
Surprisingly, electronic structure calculations on
individual MD snapshots show significant frontier orbital
electronic population on the bridge in approximately 10% of
the structures. Electron-density delocalization to the
bridge is found to be gated by fluctuations of the covalent
conjugated bond structure of the aromatic rings of the
nucleic bases. It is concluded, therefore, that both thermal
hopping and superexchange should contribute significantly to
charge transfer even in short DNA/PNA fragments. PNA is
found to be more flexible than DNA, and this flexibility is
predicted to produce larger rates of charge
transfer.},
Doi = {10.1021/ja802541e},
Key = {fds231944}
}
@article{fds352770,
Author = {Bai, S and Zhang, P and Beratan, DN},
Title = {Predicting Dexter Energy Transfer Interactions from
Molecular Orbital Overlaps},
Journal = {Journal of Physical Chemistry C},
Volume = {124},
Number = {35},
Pages = {18956-18960},
Year = {2020},
Month = {September},
url = {http://dx.doi.org/10.1021/acs.jpcc.0c06694},
Abstract = {Dexter energy transfer (DET), also known as spin forbidden
energy transfer (e.g., 3D1A → 1D3A), is undergoing a
resurgence of interest because of its utility in energy
science, photocatalysis, and biomedical imaging. The DET
reactions enable exciton fission and fusion and have been
recently used to facilitate nanoscale imaging of protein
assemblies on cell surfaces. While DET and Förster energy
transfer rates are often well described using Fermi's golden
rule, the donor-acceptor couplings for DET may be
bridge-state-mediated and depend on the electronic structure
of and interactions among the donor, bridge, and acceptor.
We provide a simple approach to approximate DET couplings
using a product of molecular orbital overlap factors. This
approach may be used to guide the design of DET systems with
targeted energy-transfer kinetics.},
Doi = {10.1021/acs.jpcc.0c06694},
Key = {fds352770}
}
@article{fds231925,
Author = {Hu, X and Xiao, D and Keinan, S and Asselberghs, I and Therien, MJ and Clays, K and Yang, W and Beratan, DN},
Title = {Predicting the Frequency Dispersion of Electronic
Hyperpolarizabilities on the Basis of Absorption Data and
Thomas-Kuhn Sum Rules},
Journal = {J. Phys. Chem. C},
Volume = {114},
Number = {114},
Pages = {2349-2359},
Publisher = {American Chemical Society (ACS)},
Year = {2010},
ISSN = {1932-7447},
url = {http://hdl.handle.net/10161/4078 Duke open
access},
Abstract = {Successfully predicting the frequency dispersion of
electronic hyperpolarizabilities is an unresolved challenge
in materials science and electronic structure theory. We
show that the generalized Thomas-Kuhn sum rules, combined
with linear absorption data and measured hyperpolarizability
at one or two frequencies, may be used to predict the entire
frequency-dependent electronic hyperpolarizability spectrum.
This treatment includes two- and three-level contributions
that arise from the lowest two or three excited electronic
state manifolds, enabling us to describe the unusual
observed frequency dispersion of the dynamic
hyperpolarizability in high oscillator strength M-PZn
chromophores, where (porphinato)zinc(II) (PZn) and
metal(II)polypyridyl (M) units are connected via an ethyne
unit that aligns the high oscillator strength transition
dipoles of these components in a head-to-tail arrangement.
We show that some of these structures can possess very
similar linear absorption spectra yet manifest dramatically
different frequency dependent hyperpolarizabilities, because
of three-level contributions that result from excited
state-to excited state transition dipoles among charge
polarized states. Importantly, this approach provides a
quantitative scheme to use linear optical absorption spectra
and very limited individual hyperpolarizability measurements
to predict the entire frequency-dependent nonlinear optical
response. Copyright © 2010 American Chemical
Society.},
Doi = {10.1021/jp911556x},
Key = {fds231925}
}
@article{fds232017,
Author = {Skourtis, SS and Balabin, IA and Kawatsu, T and Beratan,
DN},
Title = {Protein dynamics and electron transfer: electronic
decoherence and non-Condon effects.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {102},
Number = {10},
Pages = {3552-3557},
Year = {2005},
Month = {March},
ISSN = {0027-8424},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15738409},
Abstract = {We compute the autocorrelation function of the
donor-acceptor tunneling matrix element <T(DA)(t)T(DA)(0)>
for six Ru-azurin derivatives. Comparison of this decay time
to the decay time of the time-dependent Franck-Condon factor
{computed by Rossky and coworkers [Lockwood, D. M., Cheng,
Y.-K. & Rossky, P. J. (2001) Chem. Phys. Lett. 345,
159-165]} reveals the extent to which non-Condon effects
influence the electron-transfer rate. <T(DA)(t)T(DA)(0)> is
studied as a function of donor-acceptor distance, tunneling
pathway structure, tunneling energy, and temperature to
explore the structural and dynamical origins of non-Condon
effects. For azurin, the correlation function is remarkably
insensitive to tunneling pathway structure. The decay time
is only slightly shorter than it is for solvent-mediated
electron transfer in small organic molecules and originates,
largely, from fluctuations of valence angles rather than
bond lengths.},
Doi = {10.1073/pnas.0409047102},
Key = {fds232017}
}
@article{fds232051,
Author = {Beratan, DN and Betts, JN and Onuchic, JN},
Title = {Protein electron transfer rates set by the bridging
secondary and tertiary structure.},
Journal = {Science (New York, N.Y.)},
Volume = {252},
Number = {5010},
Pages = {1285-1288},
Year = {1991},
Month = {May},
ISSN = {0036-8075},
url = {http://www.ncbi.nlm.nih.gov/pubmed/1656523},
Abstract = {The rate of long-distance electron transfer in proteins
rapidly decreases with distance, which is indicative of an
electron tunneling process. Calculations predict that the
distance dependence of electron transfer in native proteins
is controlled by the protein's structural motif. The helix
and sheet content of a protein and the tertiary arrangement
of these secondary structural units define the distance
dependence of electronic coupling in that protein. The
calculations use a tunneling pathway model applied
previously with success to ruthenated proteins. The analysis
ranks the average distance decay constant for electronic
coupling in electron transfer proteins and identifies the
amino acids that are coupled to the charge localization site
more strongly or weakly than average for their
distance.},
Doi = {10.1126/science.1656523},
Key = {fds232051}
}
@article{fds231984,
Author = {Regan, JJ and Risser, SM and Beratan, DN and Onuchic,
JN},
Title = {Protein electron transport: Single versus multiple
pathways},
Journal = {Journal of Physical Chemistry},
Volume = {97},
Number = {50},
Pages = {13083-13088},
Publisher = {American Chemical Society (ACS)},
Year = {1993},
Month = {January},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1993/97/i50/pdf/j100152a009.pdf},
Abstract = {Pathway analysis provides a tool for the design of tailored
electron-transfer proteins and is a useful starting point
from which to build up multipathway views of electron
mediation that include the influence of interference and all
of the chemical tunability that is accessible. We present a
new theoretical strategy to determine when a single-pathway
picture is sufficient or when one must consider multiple
paths. A definition of a single pathway in the context of a
Green's function formalism is presented. To illustrate these
effects, examples are given for cytochrome c. We also show
that full protein Green's function calculations can be
carried out at the tight-binding (extended-Hückel) level on
cytochrome c including all valence orbitals of the protein.
Although many questions remain about appropriate
parameterization, the simple Pathway prediction that
proteins are not structureless isotropic electron-transfer
barriers holds as multiple pathways are included in the
calculations and backscattering of electron amplitude within
and between pathways is added. © 1993 American Chemical
Society.},
Doi = {10.1021/j100152a009},
Key = {fds231984}
}
@article{fds231952,
Author = {Zöllner, A and Pasquinelli, MA and Bernhardt, R and Beratan,
DN},
Title = {Protein phosphorylation and intermolecular electron
transfer: a joint experimental and computational study of a
hormone biosynthesis pathway.},
Journal = {Journal of the American Chemical Society},
Volume = {129},
Number = {14},
Pages = {4206-4216},
Year = {2007},
Month = {April},
ISSN = {0002-7863},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17358057},
Abstract = {Protein phosphorylation is a common regulator of enzyme
activity. Chemical modification of a protein surface,
including phosphorylation, could alter the function of
biological electron-transfer reactions. However, the
sensitivity of intermolecular electron-transfer kinetics to
post-translational protein modifications has not been widely
investigated. We have therefore combined experimental and
computational studies to assess the potential role of
phosphorylation in electron-transfer reactions. We
investigated the steroid hydroxylating system from bovine
adrenal glands, which consists of adrenodoxin (Adx),
adrenodoxin reductase (AdR), and a cytochrome P450, CYP11A1.
We focused on the phosphorylation of Adx at Thr-71, since
this residue is located in the acidic interaction domain of
Adx, and a recent study has demonstrated that this residue
is phosphorylated by casein kinase 2 (CK2) in vitro.1
Optical biosensor experiments indicate that the presence of
this phosphorylation slightly increases the binding affinity
of oxidized Adx with CYP11A1ox but not AdRox. This tendency
was confirmed by KA values extracted from Adx
concentration-dependent stopped-flow experiments that
characterize the interaction between AdRred and Adxox or
between Adxred and CYP11A1ox. In addition, acceleration of
the electron-transfer kinetics measured with stopped-flow is
seen only for the phosphorylated Adx-CYP11A1 reaction.
Biphasic reaction kinetics are observed only when Adx is
phosphorylated at Thr-71, and the Brownian dynamics (BD)
simulations suggest that this phosphorylation may enhance
the formation of a secondary Adx-CYP11A1 binding complex
that provides an additional electron-transfer pathway with
enhanced coupling.},
Doi = {10.1021/ja064803j},
Key = {fds231952}
}
@misc{fds22225,
Author = {D.N. Beratanand S.S. Skourtis},
Title = {Protein-mediated electron transfer: pathways, orbital
interactions and contact maps},
Pages = {9-27},
Booktitle = {Biological electron-transfer chains: genetics, composition
and mode of operation},
Publisher = {Kluwer Academic Publishers, Dordrecht, The
Netherlands},
Editor = {G.W. Canters and E. Vigenboom},
Year = {1998},
Key = {fds22225}
}
@misc{fds370665,
Author = {Prytkova, TR and Kurnikov, IV and Beratan, DN},
Title = {Quantitave prediction of electron-transfer rates in
metallo-proteins.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {227},
Pages = {U1013-U1013},
Year = {2004},
Key = {fds370665}
}
@article{fds342752,
Author = {Bai, S and Zhang, P and Antoniou, P and Skourtis, SS and Beratan,
DN},
Title = {Quantum interferences among Dexter energy transfer
pathways.},
Journal = {Faraday discussions},
Volume = {216},
Pages = {301-318},
Year = {2019},
Month = {July},
url = {http://dx.doi.org/10.1039/c9fd00007k},
Abstract = {Dexter energy transfer in chemical systems moves an exciton
(i.e., an electron-hole pair) from a donor chromophore to an
acceptor chromophore through a bridge by a combination of
bonded and non-bonded interactions. The transition is
enabled by both one-electron/one-particle and
two-electron/two-particle interaction mechanisms. Assuming
that there is no real intermediate state population of an
electron, hole, or exciton in the bridge, the transport
involves two states that are coupled non-adiabatically. As
such, coherent quantum interferences arise among the Dexter
energy coupling pathways. These interferences, while related
to well understood interferences in single-electron
transfer, are much richer because of their two particle
nature: the transfer of a triplet exciton involves the net
transfer of both an electron and a hole. Despite this
additional complexity, simple rules can govern Dexter
coupling pathway interferences in special cases. As in the
case of single-electron transfer, identical parallel
coupling pathways can be constructively interfering and may
enhance the Dexter transfer rate. Because of the virtual
particle combinatorics associated with two-particle
superexchange, two parallel Dexter coupling routes may be
expected to enhance Dexter couplings by more than a factor
of two. We explore Dexter coupling pathway interferences in
non-covalent assemblies, employing a method that enables the
assessment of Dexter coupling pathway strengths and
interferences, in the context of one-particle and
two-particle coupling interactions.},
Doi = {10.1039/c9fd00007k},
Key = {fds342752}
}
@article{fds371416,
Author = {Sun, K and Fang, C and Kang, M and Zhang, Z and Zhang, P and Beratan, DN and Brown, KR and Kim, J},
Title = {Quantum Simulation of Polarized Light-Induced Electron
Transfer with a Trapped-Ion Qutrit System.},
Journal = {The journal of physical chemistry letters},
Volume = {14},
Number = {26},
Pages = {6071-6077},
Year = {2023},
Month = {July},
url = {http://dx.doi.org/10.1021/acs.jpclett.3c01166},
Abstract = {Electron transfer within and between molecules is crucial in
chemistry, biochemistry, and energy science. This study
describes a quantum simulation method that explores the
influence of light polarization on electron transfer between
two molecules. By implementing precise and coherent control
among the quantum states of trapped atomic ions, we can
induce quantum dynamics that mimic the electron-transfer
dynamics in molecules. We use three-level systems (qutrits),
rather than traditional two-level systems (qubits), to
enhance the simulation efficiency and realize high-fidelity
simulations of electron-transfer dynamics. We treat the
quantum interference between the electron coupling pathways
from a donor with two degenerate excited states to an
acceptor and analyze the transfer efficiency. We also
examine the potential error sources that enter the quantum
simulations. The trapped-ion systems have favorable scalings
with system size compared to those of classical computers,
promising access to richer electron-transfer
simulations.},
Doi = {10.1021/acs.jpclett.3c01166},
Key = {fds371416}
}
@article{fds231911,
Author = {Beratan, DN and Onuchic, JN},
Title = {Redox redux.},
Journal = {Physical chemistry chemical physics : PCCP},
Volume = {14},
Number = {40},
Pages = {13728},
Year = {2012},
Month = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22960628},
Doi = {10.1039/c2cp90148j},
Key = {fds231911}
}
@article{fds365681,
Author = {Peterson, EJ and Rawson, J and Beratan, DN and Zhang, P and Therien,
MJ},
Title = {Regulating Singlet-Triplet Energy Gaps through
Substituent-Driven Modulation of the Exchange and Coulomb
Interactions.},
Journal = {Journal of the American Chemical Society},
Volume = {144},
Number = {34},
Pages = {15457-15461},
Year = {2022},
Month = {August},
url = {http://dx.doi.org/10.1021/jacs.2c06713},
Abstract = {Control of the singlet-triplet energy gap
(Δ<i>E</i><sub>ST</sub>) is central to realizing productive
energy conversion reactions, photochemical reaction
trajectories, and emergent applications that exploit
molecular spin physics. Despite this, no systematic methods
have been defined to tune Δ<i>E</i><sub>ST</sub> in simple
molecular frameworks, let alone by an approach that also
holds chromophore size and electronic structural parameters
(such as the HOMO-LUMO gap) constant. Using a combination of
molecular design, photophysical and potentiometric
experiments, and quantum chemical analyses, we show that the
degree of electron-electron repulsion in excited singlet and
triplet states may be finely controlled through the
substitution pattern of a simple porphyrin absorber,
enabling regulation of relative electronically excited
singlet and triplet state energies by the designed
restriction of the electron-electron Coulomb (<i>J</i>) and
exchange (<i>K</i>) interaction magnitudes. This approach
modulates the Δ<i>E</i><sub>ST</sub> magnitude by
controlling the densities of state in the occupied and
virtual molecular orbital manifolds, natural transition
orbital polarization, and the relative contributions of one
electron transitions involving select natural transition
orbital pairs. This road map, which regulates electron
density overlaps in the occupied and virtual states that
define the singlet and triplet wave functions of these
chromophores, enables new approaches to preserve excitation
energy despite intersystem crossing.},
Doi = {10.1021/jacs.2c06713},
Key = {fds365681}
}
@article{fds349327,
Author = {Jin, Y and Ru, X and Su, NQ and Mei, Y and Beratan, DN and Zhang, P and Yang,
W},
Title = {Revisiting the Hole Size in Double Helical DNA with
Localized Orbital Scaling Corrections.},
Journal = {The journal of physical chemistry. B},
Volume = {124},
Number = {16},
Pages = {3428-3435},
Year = {2020},
Month = {April},
url = {http://dx.doi.org/10.1021/acs.jpcb.0c03112},
Abstract = {The extent of electronic wave function delocalization for
the charge carrier (electron or hole) in double helical DNA
plays an important role in determining the DNA charge
transfer mechanism and kinetics. The size of the charge
carrier's wave function delocalization is regulated by the
solvation induced localization and the quantum
delocalization among the π stacked base pairs at any
instant of time. Using a newly developed localized orbital
scaling correction (LOSC) density functional theory method,
we accurately characterized the quantum delocalization of
the hole wave function in double helical B-DNA. This
approach can be used to diagnose the extent of
delocalization in fluctuating DNA structures. Our studies
indicate that the hole state tends to delocalize among 4
guanine-cytosine (GC) base pairs and among 3 adenine-thymine
(AT) base pairs when these adjacent bases fluctuate into
degeneracy. The relatively small delocalization in AT base
pairs is caused by the weaker π-π interaction. This extent
of delocalization has significant implications for assessing
the role of coherent, incoherent, or flickering coherent
carrier transport in DNA.},
Doi = {10.1021/acs.jpcb.0c03112},
Key = {fds349327}
}
@article{fds231890,
Author = {Paul, A and Bezer, S and Venkatramani, R and Kocsis, L and Wierzbinski,
E and Balaeff, A and Keinan, S and Beratan, DN and Achim, C and Waldeck,
DH},
Title = {Role of nucleobase energetics and nucleobase interactions in
single-stranded peptide nucleic acid charge
transfer.},
Journal = {Journal of the American Chemical Society},
Volume = {131},
Number = {18},
Pages = {6498-6507},
Year = {2009},
Month = {May},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19382798},
Abstract = {Self-assembled monolayers of single-stranded (ss) peptide
nucleic acids (PNAs) containing seven nucleotides (TTTXTTT),
a C-terminus cysteine, and an N-terminus ferrocene redox
group were formed on gold electrodes. The PNA monomer group
(X) was selected to be either cytosine (C), thymine (T),
adenine (A), guanine (G), or a methyl group (Bk). The charge
transfer rate through the oligonucleotides was found to
correlate with the oxidation potential of X. Kinetic
measurements and computational studies of the ss-PNA
fragments show that a nucleobase mediated charge transport
mechanism in the deep tunneling superexchange regime can
explain the observed dependence of the kinetics of charge
transfer on the PNA sequence. Theoretical analysis suggests
that the charge transport is dominantly hole-mediated and
takes place through the filled bridge orbitals. The
strongest contribution to conductance comes from the highest
filled orbitals (HOMO, HOMO-1, and HOMO-2) of individual
bases, with a rapid drop off in contributions from lower
lying filled orbitals. Our studies further suggest that the
linear correlation observed between the experimental charge
transfer rates and the oxidation potential of base X arises
from weak average interbase couplings and similar stacking
geometries for the four TTTXTTT systems.},
Doi = {10.1021/ja9000163},
Key = {fds231890}
}
@article{fds231938,
Author = {Paul, and Bezer, S and Venkatramani, R and Kocsis, L and Wierzbinski,
E and Balaeff, A and Keinan, S and Beratan, DN and Achim, C and Waldeck,
DH},
Title = {Role of Nucleobase Energetics in Single Stranded Peptide
Nucleic Acid Charge Transfer},
Journal = {J. Am. Chem. Soc},
Number = {131},
Pages = {6498-6507},
Year = {2009},
Key = {fds231938}
}
@article{fds232043,
Author = {Perry, JW and Stiegman, AE and Marder, SR and Coulter, DR and Beratan,
DN and Brinza, DE and Klavetter, FL and Grubbs, RH},
Title = {Second and third order nonlinear optical properties of
conjugated molecules and polymers},
Journal = {Proceedings of SPIE-The Society of Photo-Optical
Instrumentation Engineers},
Volume = {971},
Pages = {17-24},
Publisher = {SPIE},
Year = {1988},
url = {http://dx.doi.org/10.1117/12.948211},
Abstract = {Second and third order nonlinear optical properties of some
newly synthesized organic molecules and polymers are
reported. Powder second harmonic generation efficiencies of
up to 200 times urea have been realized for asymmetric
donor-acceptor acetylenes. Third harmonic generation x(3)s
have been determined for a series of small conjugated
molecules in solution. THG x(3)s have also been determined
for a series of soluble conjugated copolymers prepared using
ring-openinig metathesis polymerization. The results are
discussed in terms of relevant molecular and/or macroscopic
structural features of these conjugated organic materials.
© 1988 SPIE.},
Doi = {10.1117/12.948211},
Key = {fds232043}
}
@article{fds231906,
Author = {Wolfgang, J and Risser, SM and Priyadarshy, S and Beratan,
DN},
Title = {Secondary structure conformations and long range electronic
interactions in oligopeptides},
Journal = {J. Phys. Chem. B.},
Volume = {101},
Number = {15},
Pages = {2987-2991},
Publisher = {American Chemical Society (ACS)},
Year = {1997},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcbfk/1997/101/i15/pdf/jp963771r.pdf},
Abstract = {Combined quantum mechanical coupling calculations and
molecular dynamics simulations were performed to examine the
role of modest geometrical fluctuations of peptide secondary
structures on long range electronic interactions in
oligopeptides. Molecular dynamics simulations were performed
to obtain typical relevant conformations of oligopeptides,
and self-consistent Hartree-Fock calculations at the
semiempirical quantum theory level were performed to extract
the long range electronic propagation. Initial α-helical
oligopeptides show dominant hole-mediated coupling over a
large tunneling energy range, while the initial extended
conformation oligopeptides have more nearly equal
contributions from both hole and electron mechanisms. Modest
geometrical fluctuations lead to changes in the character of
long range electronic interactions. The computations
highlight the danger of drawing conclusions from electronic
structure calculations of electronic coupling in peptide
model systems on the basis of computations on single
geometries.},
Doi = {10.1021/jp963771r},
Key = {fds231906}
}
@article{fds231848,
Author = {Migliore, A and Naaman, R and Beratan, DN},
Title = {Sensing of molecules using quantum dynamics.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {112},
Number = {19},
Pages = {E2419-E2428},
Year = {2015},
Month = {May},
ISSN = {0027-8424},
url = {http://dx.doi.org/10.1073/pnas.1502000112},
Abstract = {We design sensors where information is transferred between
the sensing event and the actuator via quantum relaxation
processes, through distances of a few nanometers. We thus
explore the possibility of sensing using intrinsically
quantum mechanical phenomena that are also at play in
photobiology, bioenergetics, and information processing.
Specifically, we analyze schemes for sensing based on charge
transfer and polarization (electronic relaxation) processes.
These devices can have surprising properties. Their
sensitivity can increase with increasing separation between
the sites of sensing (the receptor) and the actuator (often
a solid-state substrate). This counterintuitive response and
other quantum features give these devices favorable
characteristics, such as enhanced sensitivity and
selectivity. Using coherent phenomena at the core of
molecular sensing presents technical challenges but also
suggests appealing schemes for molecular sensing and
information transfer in supramolecular structures.},
Doi = {10.1073/pnas.1502000112},
Key = {fds231848}
}
@article{fds232016,
Author = {Lin, J and Beratan, DN},
Title = {Simulation of electron transfer between cytochrome C2 and
the bacterial photosynthetic reaction center: Brownian
dynamics analysis of the native proteins and double
mutants.},
Journal = {The journal of physical chemistry. B},
Volume = {109},
Number = {15},
Pages = {7529-7534},
Year = {2005},
Month = {April},
ISSN = {1520-6106},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16851864},
Abstract = {Electron transfer is essential for bacterial photosynthesis
which converts light energy into chemical energy. This paper
theoretically studies the interprotein electron transfer
from cytochrome c(2) of Rhodobacter capsulatus to the
photosynthetic reaction center of Rhodobacter sphaeroides in
native and mutated systems. Brownian dynamics is used with
an exponential distance-dependent electron-transfer rate
model to compute bimolecular rate constants, which are
consistent with experimental data when reasonable prefactors
and decay constants are used. Interestingly, switching of
the reaction mechanism from the diffusion-controlled limit
in the native proteins to the activation-controlled limit in
one of the mutants (DK(L261)/KE(C99)) was found. We also
predict that the second-order rate for the native reaction
center/cytochrome c(2) system will decrease with increasing
ionic strength, a characteristic of electrostatically
controlled docking.},
Doi = {10.1021/jp045417w},
Key = {fds232016}
}
@article{fds303173,
Author = {Galperin, M and Beratan, DN},
Title = {Simulation of scanning tunneling microscope images of
1,3-cyclohexadiene bound to a silicon surface.},
Journal = {The journal of physical chemistry. B},
Volume = {109},
Number = {4},
Pages = {1473-1480},
Year = {2005},
Month = {February},
ISSN = {1520-6106},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16851118},
Abstract = {Scanning tunneling microscope (STM) images of
1,3-cyclohexadiene bound to silicon are interpreted using a
nonequilibrium Green's function method. The resolution of
the carbon-carbon double bond for positive bias voltages but
not for negative bias voltages is explained using a
quasiprobability density analysis. The asymmetry in the
images arises from the system's voltage dependent electronic
structure. A pi* orbital is found to be responsible for the
empty state STM images of the carbon-carbon double bond,
which is observed experimentally. The pi orbital relevant
for the opposite bias does not produce an STM image sharply
localized in the bond region because the molecule induces a
Si-surface dipole dependent on the bias. The dipole voltage
dependence arises from molecular charging. This result
emphasizes the importance of simulating the molecule as an
element in an open quantum system.},
Doi = {10.1021/jp045783f},
Key = {fds303173}
}
@article{fds232019,
Author = {Galperin, M and Beratan, DN},
Title = {Simulation of STM images of 1,4 cyclohexadiene bound to a
silicon surface},
Journal = {J. Phys. Chem B},
Volume = {109},
Number = {4},
Pages = {1473-1480},
Year = {2005},
ISSN = {1520-6106},
url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2005/109/i04/pdf/jp045783f.pdf},
Abstract = {Scanning tunneling microscope (STM) images of
1,3-cyclohexadiene bound to silicon are interpreted using a
nonequilibrium Green's function method. The resolution of
the carbon-carbon double bond for positive bias voltages but
not for negative bias voltages is explained using a
quasiprobability density analysis. The asymmetry in the
images arises from the system's voltage dependent electronic
structure. A pi* orbital is found to be responsible for the
empty state STM images of the carbon-carbon double bond,
which is observed experimentally. The pi orbital relevant
for the opposite bias does not produce an STM image sharply
localized in the bond region because the molecule induces a
Si-surface dipole dependent on the bias. The dipole voltage
dependence arises from molecular charging. This result
emphasizes the importance of simulating the molecule as an
element in an open quantum system.},
Doi = {10.1021/jp045783f},
Key = {fds232019}
}
@article{fds231941,
Author = {He, W and Hatcher, E and Balaeff, A and Beratan, DN and Gil, RR and Madrid,
M and Achim, C},
Title = {Solution structure of a peptide nucleic acid duplex from NMR
data: features and limitations.},
Journal = {Journal of the American Chemical Society},
Volume = {130},
Number = {40},
Pages = {13264-13273},
Year = {2008},
Month = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18781753},
Abstract = {This paper describes the results of a 1D and 2D NMR
spectroscopy study of a palindromic 8-base pair PNA duplex
GGCATGCC in H2O and H2O-D2O solutions. The (1)H NMR peaks
have been assigned for most of the protons of the six
central base pairs, as well as for several amide protons of
the backbone. The resulting 36 interbase and base-backbone
distance restraints were used together with Watson-Crick
restraints to generate the PNA duplex structure in the
course of 10 independent simulated annealing runs followed
by restrained molecular dynamics (MD) simulations in
explicit water. The resulting PNA structures correspond to a
P-type helix with helical parameters close to those observed
in the crystal structures of PNA. Based on the current
limited number of restraints obtained from NMR spectra,
alternative structures obtained by MD from starting PNA
models based on DNA cannot be ruled out and are also
discussed.},
Doi = {10.1021/ja800652h},
Key = {fds231941}
}
@article{fds231884,
Author = {Mukhopadhyay, P and Zuber, G and Goldsmith, M-R and Wipf, P and Beratan,
DN},
Title = {Solvent effect on optical rotation: A case study of
methyloxirane in water.},
Journal = {Chemphyschem : a European journal of chemical physics and
physical chemistry},
Volume = {7},
Number = {12},
Pages = {2483-2486},
Year = {2006},
Month = {December},
ISSN = {1439-4235},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17072929},
Doi = {10.1002/cphc.200600477},
Key = {fds231884}
}
@article{fds231972,
Author = {Onuchic, JN and Beratan, DN and Hopfield, JJ},
Title = {Some aspects of electron-transfer reaction
dynamics},
Journal = {Journal of Physical Chemistry},
Volume = {90},
Number = {16},
Pages = {3707-3721},
Publisher = {American Chemical Society (ACS)},
Year = {1986},
Month = {January},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1986/90/i16/pdf/j100407a045.pdf},
Abstract = {We prissent a simple, but complete, quantum mechanical model
for electron transfer. It contains the elements necessary to
calculate a rate: electron, reaction coordinate(s), and
bath. The completeness of the model allows analysis of the
dynamical aspects of the transfer (validity of the
nonadiabatic, Born-Oppenheimer, and Condon approximations,
for example). Interaction between the reaction coordinate(s)
and the bath is discussed for "weak" and "strong" coupling,
and the rate expression is derived in these limits. A model
for donor and acceptor vibronic wave functions is solved
exactly by using a molecular orbital approach. The rates are
calculated from these states and a comparison with the
standard Born-Oppenheimer/Condon result is made. The nature
of the "inverted" effect is found to depend on transfer
distance and details of the vibronic coupling. © 1986
American Chemical Society.},
Doi = {10.1021/j100407a045},
Key = {fds231972}
}
@misc{fds370708,
Author = {ONUCHIC, JN and BERATAN, DN},
Title = {SOME ASPECTS OF ELECTRON-TRANSFER REACTION
DYNAMICS},
Journal = {BIOPHYSICAL JOURNAL},
Volume = {49},
Number = {2},
Pages = {A483-A483},
Year = {1986},
Key = {fds370708}
}
@article{fds231923,
Author = {Ben-Moshe, V and Nitzan, A and Skourtis, SS and Beratan,
DN},
Title = {Steady-state theory of current transfer},
Journal = {Journal of Physical Chemistry C},
Volume = {114},
Number = {17},
Pages = {8005-8013},
Publisher = {American Chemical Society (ACS)},
Year = {2010},
Month = {May},
ISSN = {1932-7447},
url = {http://hdl.handle.net/10161/4066 Duke open
access},
Abstract = {Current transfer is defined as a charge-transfer process
where the transferred charge carries information about its
original motion. We have recently suggested that such
transfer causes the asymmetry observed in electron transfer
induced by circularly polarized light through helical wires.
This paper presents the steady-state theory of current
transfer within a tight binding model of coupled wires
systems. The asymmetry in the system response to a steady
current imposed in a particular direction on one of the
wires is used to define the efficiency of current transfer.
© 2010 American Chemical Society.},
Doi = {10.1021/jp100661f},
Key = {fds231923}
}
@article{fds231935,
Author = {Beratan, DN and Skourtis, SS and Balabin, IA and Balaeff, A and Keinan,
S and Venkatramani, R and Xiao, D},
Title = {Steering electrons on moving pathways.},
Journal = {Accounts of chemical research},
Volume = {42},
Number = {10},
Pages = {1669-1678},
Year = {2009},
Month = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19645446},
Abstract = {Electron transfer (ET) reactions provide a nexus among
chemistry, biochemistry, and physics. These reactions
underpin the "power plants" and "power grids" of
bioenergetics, and they challenge us to understand how
evolution manipulates structure to control ET kinetics.
Ball-and-stick models for the machinery of electron
transfer, however, fail to capture the rich electronic and
nuclear dynamics of ET molecules: these static
representations disguise, for example, the range of
thermally accessible molecular conformations. The influence
of structural fluctuations on electron-transfer kinetics is
amplified by the exponential decay of electron tunneling
probabilities with distance, as well as the delicate
interference among coupling pathways. Fluctuations in the
surrounding medium can also switch transport between
coherent and incoherent ET mechanisms--and may gate ET so
that its kinetics is limited by conformational
interconversion times, rather than by the intrinsic ET time
scale. Moreover, preparation of a charge-polarized donor
state or of a donor state with linear or angular momentum
can have profound dynamical and kinetic consequences. In
this Account, we establish a vocabulary to describe how the
conformational ensemble and the prepared donor state
influence ET kinetics in macromolecules. This framework is
helping to unravel the richness of functional biological ET
pathways, which have evolved within fluctuating
macromolecular structures. The conceptual framework for
describing nonadiabatic ET seems disarmingly simple: compute
the ensemble-averaged (mean-squared) donor-acceptor (DA)
tunneling interaction, <H(DA)(2)>, and the Franck-Condon
weighted density of states, rho(FC), to describe the rate,
(2pi/variant Planck's over 2pi)<H(DA)(2)>rho(FC). Modern
descriptions of the thermally averaged electronic coupling
and of the Franck-Condon factor establish a useful
predictive framework in biology, chemistry, and nanoscience.
Describing the influence of geometric and energetic
fluctuations on ET allows us to address a rich array of
mechanistic and kinetic puzzles. How strongly is a protein's
fold imprinted on the ET kinetics, and might thermal
fluctuations "wash out" signatures of structure? What is the
influence of thermal fluctuations on ET kinetics beyond
averaging of the tunneling barrier structure? Do electronic
coupling mechanisms change as donor and acceptor reposition
in a protein, and what are the consequences for the ET
kinetics? Do fluctuations access minority species that
dominate tunneling? Can energy exchanges between the
electron and bridge vibrations generate vibronic signatures
that label some of the D-to-A pathways traversed by the
electron, thus eliminating unmarked pathways that would
otherwise contribute to the DA coupling (as in other "which
way" or double-slit experiments)? Might medium fluctuations
drive tunneling-hopping mechanistic transitions? How does
the donor-state preparation, in particular, its polarization
toward the acceptor and its momentum characteristics (which
may introduce complex rather than pure real relationships
among donor orbital amplitudes), influence the electronic
dynamics? In this Account, we describe our recent studies
that address puzzling questions of how conformational
distributions, excited-state polarization, and electronic
and nuclear dynamical effects influence ET in
macromolecules. Indeed, conformational and dynamical effects
arise in all transport regimes, including the tunneling,
resonant transport, and hopping regimes. Importantly, these
effects can induce switching among ET mechanisms.},
Doi = {10.1021/ar900123t},
Key = {fds231935}
}
@article{fds231869,
Author = {Virshup, AM and Contreras-García, J and Wipf, P and Yang, W and Beratan, DN},
Title = {Stochastic voyages into uncharted chemical space produce a
representative library of all possible drug-like
compounds.},
Journal = {Journal of the American Chemical Society},
Volume = {135},
Number = {19},
Pages = {7296-7303},
Year = {2013},
Month = {May},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23548177},
Abstract = {The "small molecule universe" (SMU), the set of all
synthetically feasible organic molecules of 500 Da molecular
weight or less, is estimated to contain over 10(60)
structures, making exhaustive searches for structures of
interest impractical. Here, we describe the construction of
a "representative universal library" spanning the SMU that
samples the full extent of feasible small molecule
chemistries. This library was generated using the newly
developed Algorithm for Chemical Space Exploration with
Stochastic Search (ACSESS). ACSESS makes two important
contributions to chemical space exploration: it allows the
systematic search of the unexplored regions of the small
molecule universe, and it facilitates the mining of chemical
libraries that do not yet exist, providing a near-infinite
source of diverse novel compounds.},
Doi = {10.1021/ja401184g},
Key = {fds231869}
}
@article{fds231902,
Author = {Beratan, DN},
Title = {Strategies for the 'molecular engineering' of chemical,
electronic, and optical devices},
Journal = {Proceedings of the Intersociety Energy Conversion
Engineering Conference},
Volume = {3},
Pages = {519-520},
Year = {1990},
Month = {December},
Abstract = {Theoretical chemistry is assisting in the design of new
materials for biocatalysis, ultrasmall-scale electronic
devices, and nonlinear optics. The author discusses of the
kinds of molecular design and property prediction problems
which have recently been attacked using these techniques.
The role of theoretical chemistry for developing the
structure-property relationships in families of small
molecules with novel optical properties is
discussed.},
Key = {fds231902}
}
@article{fds231850,
Author = {Rupakheti, C and Virshup, A and Yang, W and Beratan,
DN},
Title = {Strategy to discover diverse optimal molecules in the small
molecule universe.},
Journal = {Journal of chemical information and modeling},
Volume = {55},
Number = {3},
Pages = {529-537},
Year = {2015},
Month = {March},
ISSN = {1549-9596},
url = {http://dx.doi.org/10.1021/ci500749q},
Abstract = {The small molecule universe (SMU) is defined as a set of
over 10(60) synthetically feasible organic molecules with
molecular weight less than ∼500 Da. Exhaustive
enumerations and evaluation of all SMU molecules for the
purpose of discovering favorable structures is impossible.
We take a stochastic approach and extend the ACSESS
framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 ,
7296 - 7303 ) to develop diversity oriented molecular
libraries that can generate a set of compounds that is
representative of the small molecule universe and that also
biases the library toward favorable physical property
values. We show that the approach is efficient compared to
exhaustive enumeration and to existing evolutionary
algorithms for generating such libraries by testing in the
NKp fitness landscape model and in the fully enumerated
GDB-9 chemical universe containing 3 × 10(5)
molecules.},
Doi = {10.1021/ci500749q},
Key = {fds231850}
}
@article{fds232003,
Author = {Kondru, RK and Wipf, P and Beratan, DN},
Title = {Structural and Conformational Dependence of Optical Rotation
Angles},
Journal = {Journal of Physical Chemistry A},
Volume = {103},
Number = {33},
Pages = {6603-6611},
Publisher = {American Chemical Society (ACS)},
Year = {1999},
Month = {August},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcafh/1999/103/i33/pdf/jp990697e.pdf},
Abstract = {The ability to compute and to interpret optical rotation
angles of chiral molecules is of great value in assigning
relative and absolute stereochemistry. The molar rotations
for an indoline and an azetidine, as well as for menthol and
menthone, were calculated using ab inito methods and
compared to the experimental values. In one case the
calculated rotation angle allowed the assignment of the
absolute configuration of a heterocycle of unknown
stereochemistry. The critical importance of Boltzmann
averaging of conformers for reliable prediction of the
optical rotation angle was established. Comparisons between
static-field and time-dependent methods were made pointing
to the limits and validity of the methods as electronic
resonance is approached. A protocol analogous to population
analysis was used to analyze atomic contributions to the
rotation angle in specific conformers. The combination of
atomic contribution maps and conformational analysis may
provide an indirect tool to assist in three-dimensional
structure determination.},
Doi = {10.1021/jp990697e},
Key = {fds232003}
}
@article{fds231857,
Author = {Kuznetsov, AE and Beratan, DN},
Title = {Structural and electronic properties of bare and capped Cd
33Se33 and Cd33Te33
quantum dots},
Journal = {Journal of Physical Chemistry C},
Volume = {118},
Number = {13},
Pages = {7094-7109},
Publisher = {American Chemical Society (ACS)},
Year = {2014},
Month = {April},
ISSN = {1932-7447},
url = {http://dx.doi.org/10.1021/jp4007747},
Abstract = {We performed comparative DFT (B3LYP/Lanl2dz) studies of the
structural and electronic properties of bare and NH3-,
SCH3-, and OPH3-capped Cd33Se33 and Cd33Te 33 quantum dots
(QDs). The capping groups were chosen as simple models for
capping ligands used broadly in experiments. We explored the
effects of the capping ligands, coordinated to the QDs via
N, S, and O atoms, on the stabilization/destabilization of
the QD HOMO and LUMO energies, and on the HOMO/LUMO energy
related quantities: vertical ionization potentials and
electron affinities. The effects of solvents commonly used
in experimental studies of capped QDs (water, toluene, and
acetonitrile) on QD structures and electronic properties
were investigated as well. Analysis of the bare and capped
QD frontier orbital composition was performed using the
projected density of states approach. We also studied
Cd33Se33 and Cd 33Te33 QDs capped with N(CH3)3 and SCH2CO2H
ligands. © 2014 American Chemical Society.},
Doi = {10.1021/jp4007747},
Key = {fds231857}
}
@article{fds231895,
Author = {Kuznetsov, AE and Balamurugan, D and Skourtis, SS and Beratan,
DN},
Title = {Structural and electronic properties of bare and capped Cd
nSen/CdnTen
Nanoparticles (n = 6, 9)},
Journal = {Journal of Physical Chemistry C},
Volume = {116},
Number = {12},
Pages = {6817-6830},
Publisher = {American Chemical Society (ACS)},
Year = {2012},
Month = {March},
ISSN = {1932-7447},
url = {http://dx.doi.org/10.1021/jp2109187},
Abstract = {Relationships between structures and properties (energy
gaps, vertical ionization potentials (IPv), vertical
electron affinities (EA v), and ligand binding energies) in
small capped CdSe/CdTe nanoparticles (NPs) are poorly
understood. We have performed the first systematic density
functional theory (DFT) (B3LYP/Lanl2dz) study of the
structural (geometries and ligand binding energies) and
electronic (HOMO/LUMO energy gaps, IPsv, and EAsv)
properties of Cd nSen/CdnTen NPs (n = 6, 9), both bare and
capped with NH3, SCH3, and OPH3 ligands. NH3 and OPH3
ligands cause HOMO/LUMO energy destabilization in capped
NPs, more pronounced for the LUMOs than for the HOMOs.
Orbital destabilization drastically reduces both the IPv and
EA v of the NPs compared with the bare species. For SCH
3-capped Cd6X6 NPs, formation of expanded structures was
found to be preferable to crystal-like structures. SCH 3
groups cause destabilization of the HOMOs of the capped NPs
and stabilization of their LUMOs, which indicates a
reduction of the IPv of the capped NPs compared with the
bare species. For the Cd9X 9 NPs, similar trends in
stabilization/destabilization of frontier orbitals were
observed in comparison with the capped Cd6X6 species. Also,
pinning of the HOMO energies was observed for the NH 3- and
SCH3-capped NPs as a function of a NP size. © 2012 American
Chemical Society.},
Doi = {10.1021/jp2109187},
Key = {fds231895}
}
@article{fds222357,
Author = {A. Kuznetsov and D.N. Beratan},
Title = {Structural and Electronic Properties of Bare and Capped
Cd33Se33/Cd33Te33 Nanoparticles},
Journal = {J. Phys. Chem. C},
Year = {2013},
Key = {fds222357}
}
@misc{fds313867,
Author = {BERATAN, DN and ONUCHIC, JN},
Title = {STRUCTURAL CONTROL OF ELECTRON-TRANSFER IN
PROTEINS},
Journal = {MOLECULAR BASIS OF OXIDATIVE DAMAGE BY LEUKOCYTES},
Pages = {57-67},
Booktitle = {The molecular basis of oxidative damage by
leukocytes},
Publisher = {CRC PRESS INC},
Editor = {Jesaitis, AJ and Dratz, EA},
Year = {1992},
Month = {January},
ISBN = {0-8493-6363-2},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1992BX45G00005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Key = {fds313867}
}
@article{fds232046,
Author = {Beratan, DN and Lee, MA and Allender, DW and Risser,
S},
Title = {Structural dependence of the pi-electron contributions to
the optical second hyperpolarizability of linear conjugated
organic molecules},
Journal = {Proceedings of SPIE - The International Society for Optical
Engineering},
Volume = {1080},
Pages = {101-107},
Publisher = {SPIE},
Year = {1989},
Month = {July},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1989BP78U00013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {Tight-binding (molecular orbital) models of conjugated
organic molecules were used to predict structure-activity
correlations for molecules with large electronic
hyperpolarizabilities [1]. The dependence of the nonresonant
second hyperpolarizability on chain length and molecular
substituents was investigated. The calculations point out
the influence of bond alternation and the presence of
substitutional (and conjugation) “defects” on the size,
sign, and chain length dependence of the molecular (and the
bulk) hyperpolarizability. It is hoped that the calculations
will provide guidance for future chemical synthesis by
presenting strategies for systematically tuning the size and
sign of the hyperpolarizability. © 1989
SPIE.},
Doi = {10.1117/12.976406},
Key = {fds232046}
}
@article{fds231907,
Author = {Kurnikov, IV and Zusman, LD and Kurnikova, MG and Farid, RS and Beratan,
DN},
Title = {Structural fluctuations, spin, reorganization energy, and
tunneling energy control of intramolecular electron
transfer: The surprising case of electron transfer in a
d8-d8 bimetallic system},
Journal = {Chemtracts},
Volume = {11},
Number = {5},
Pages = {359-365},
Year = {1998},
Month = {May},
Abstract = {Theoretical analysis of the ET rates in di-iridium complexes
with covalently linked pyridinium acceptors has shown the
crucial role of the conformational dynamics. ET is fast
enough to occur in the extended conformations of molecules
with short spacers while it is gated by the conformational
changes in species with longer, more flexible, spacers.
Reorganization energies and electronic coupling were
calculated to be larger then expected from the analysis of
the singlet ET rate dependence on the reaction driving force
indicating that all the ET reactions studied occur in the
normal Marcus region. Electronic coupling is almost the same
for the reaction from the spin-singlet and -triplet excited
states of the Ir2 unit. A dip on the dependence of the
electroniccoupling term on the tunneling energy was
predicted.},
Key = {fds231907}
}
@article{fds232032,
Author = {Kurnikov, IV and Zusman, LD and Kurnikova, MG and Farid, RS and Beratan,
DN},
Title = {Structural fluctuations, spin, reorganization energy, and
tunneling energy control of intramolecular electron
transfer: The surprising case of electron transfer in a
d8-d8 bimetallic system},
Journal = {Journal of the American Chemical Society},
Volume = {119},
Number = {24},
Pages = {5690-5700},
Publisher = {American Chemical Society (ACS)},
Year = {1997},
Month = {June},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1997/119/i24/pdf/ja970309r.pdf},
Abstract = {A considerable body of unimolecular electron-transfer rate
data has been reported recently for Ir2 excited-state donors
linked to substituted pyridinium acceptors. These data pose
a substantial paradox. Simple analysis suggested that
donor-acceptor coupling matrix elements differ by 1 order of
magnitude for the excited triplet and singlet states. Yet,
there is no fundamental reason to expect this large
electronic coupling dependence on spin state. We offer an
alternative self-consistent interpretation based on a hybrid
theoretical analysis that includes ab initio quantum
calculations of electronic couplings, molecular dynamics
simulations of molecular geometries, and Poisson-Boltzmann
computations of reorganization energies. Taken together the
analysis provides a detailed comprehensive interpretation of
these reactions. In our analysis, we reach the conclusions:
(1) that reorganization energies in these systems (~1.3-1.7
eV) are larger than expected from simple analysis of
experiments, (2) that electronic couplings (~0.005-0.02 eV)
are also larger than previously believed and differ only by
a factor of 2 for singlet and triplet states, (3) that the
molecules have access to multiple conformations differing
both in reorganization energy and electronic coupling, and
explicit treatment of this flexibility is crucial to
interpret the rate data, and (4) that a considerable dip is
expected in the donor- acceptor coupling dependence on
tunneling energy, associated with destructively interfering
electron and hole-mediated coupling pathways, which probably
leads to a small observed ET rate in one of the compounds.
Taken together, this analysis explains most of the
experimental data. Fundamental arguments and detailed
computations show that the influence of donor spin state on
long-range electronic interactions is relatively weak. Many
of the molecular aspects that establish the ET
characteristics of these molecules exist in other semirigid
model compounds, making this hybrid theoretical strategy of
general interest.},
Doi = {10.1021/ja970309r},
Key = {fds232032}
}
@article{fds231996,
Author = {Zusman, LD and Beratan, DN},
Title = {Structure of the electrical double layer in high-temperature
superconductors. Origin of the dip in the double-layer
capacitance near the superconducting transition},
Journal = {Journal of Physical Chemistry B},
Volume = {101},
Number = {36},
Pages = {7095-7099},
Publisher = {American Chemical Society (ACS)},
Year = {1997},
Month = {September},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcbfk/1997/101/i36/pdf/jp971026o.pdf},
Abstract = {A theory of the electrical double layer in high-temperature
superconductors is developed in the context of a modified
Ginzburg-Landau equation. Potential and excess charge
distributions inside the electrode are computed. These
distributions are shown to be characterized by a new
fundamental length parameter. This length diverges when the
electrode temperature approaches the superconducting
critical temperature. The capacitance of the electrical
double layer is found to be inversely proportional to this
length. On the basis of this analysis, the origin of an
experimentally observed dip in the double-layer capacitance
is explained. The dependence of this capacitance dip on the
external field is predicted.},
Doi = {10.1021/jp971026o},
Key = {fds231996}
}
@article{fds231967,
Author = {Perry, JL and Goldsmith, MR and Peterson, MA and Beratan, DN and Wozniak, G and Rüker, F and Simon, JD},
Title = {Structure of the ochratoxin a binding site within human
serum albumin},
Journal = {Journal of Physical Chemistry B},
Volume = {108},
Number = {43},
Pages = {16960-16964},
Publisher = {American Chemical Society (ACS)},
Year = {2004},
Month = {October},
ISSN = {1520-6106},
url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2004/108/i43/pdf/jp0480652.pdf},
Abstract = {The binding site of ochratoxin A (OTA) within domain 2A of
human serum albumin (HSA) is examined by theoretical
simulations and site-directed mutagenesis experiments. The
calculated binding constant, based on docking experiments
and theoretical affinity constants derived from the
empirical free energy of binding as implemented in AutoDock
3.0, for the OTA dianion (3.7 × 10 6 M -1) is in good
agreement with experimental value of 5.2 × 10 6 M -1. The
carboxy terminus of OTA associates with R218 and R222 of the
protein. Binding is reduced by over an order of magnitude
for the mutant R218A in both experiments and theoretical
simulations. The carbonyl of the lactone and the phenolic
group of OTA are in close proximity to R257. The
experimental binding constant of OTA to the R257A mutant is
1.6 × 10 5 M -1, over an order of magnitude smaller than
for the wild-type protein. The predicted binding constant
based on a comparison of the lowest-energy conformer from
docking studies performed in AutoDock 3.0 of OTA to the
R257A mutant (8.3 × 10 4 M -1) is also in good agreement
with the experimental result. R257 clearly plays an
important role in the binding of the isocoumarin ring of OTA
by serving as a proton acceptor and stabilizing the binding
through the creation of an ion pair with the phenoxide group
on OTA.},
Doi = {10.1021/jp0480652},
Key = {fds231967}
}
@misc{fds318057,
Author = {MARDER, SR and CHENG, LT and BERATAN, DN},
Title = {STRUCTURE PROPERTY RELATIONSHIPS FOR MOLECULAR 2ND-ORDER
NONLINEAR OPTICS},
Journal = {MOLECULAR ELECTRONICS - SCIENCE AND TECHNOLOGY},
Volume = {262},
Series = {American Institute of Physics Conference
Proceedings},
Pages = {252-264},
Publisher = {AIP PRESS},
Editor = {AVIRAM, A},
Year = {1992},
Month = {January},
ISBN = {1-56396-041-9},
Key = {fds318057}
}
@misc{fds22276,
Author = {S.R. Marder and B.G. Tiemann and D.N. Beratan and L-T. Cheng and W.
Tam},
Title = {Structure property relationships for organic and
oranometallic materials with second-order
nonlinearities},
Pages = {165-175},
Booktitle = {Organic Materials for Nonlinear Optics, II},
Publisher = {Royal Society of Chemistry, Cambridge},
Editor = {R.A. hann and D. Bloor},
Year = {1991},
Key = {fds22276}
}
@misc{fds313864,
Author = {MARDER, SR and BERATAN, DN and TIEMANN, BG and CHENG, LT and TAM,
W},
Title = {STRUCTURE PROPERTY RELATIONSHIPS FOR ORGANIC AND
ORGANOMETALLIC MATERIALS WITH 2ND-ORDER OPTICAL
NONLINEARITIES},
Journal = {ORGANIC MATERIALS FOR NON-LINEAR OPTICS II},
Volume = {91},
Pages = {165-175},
Publisher = {ROYAL SOC CHEMISTRY},
Editor = {HANN, RA and BLOOR, D},
Year = {1991},
Month = {January},
ISBN = {0-85186-397-3},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1991BU63Y00021&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Key = {fds313864}
}
@article{fds232029,
Author = {Risser, SM and Beratan, DN and Marder, SR},
Title = {Structure-Function Relationships for β, the First Molecular
Hyperpolarizability},
Journal = {Journal of the American Chemical Society},
Volume = {115},
Number = {17},
Pages = {7719-7728},
Publisher = {American Chemical Society (ACS)},
Year = {1993},
Month = {August},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1993/115/i17/pdf/ja00070a016.pdf},
Abstract = {A four-orbital model is used to map the overall dependence
of β, the first electronic hyperpolarizability, on chemical
parameters such as donor/acceptor strength and coupling
between bridge and donor/acceptor orbitals. These
calculations are used to develop general structure-property
relationships for β and to demonstrate the physical origin
of maxima, minima, and zeros in β. Comparison with
multiorbital calculations on specific molecules show that
the general relationships apply to more complex structures
as well. A number of strategies for manipulating β by
varying molecular structure emerge from the analysis. We
show that the absolute maxima in the β surfaces fall
outside of the range that has been probed using conventional
organic donors and acceptors. © 1993, American Chemical
Society. All rights reserved.},
Doi = {10.1021/ja00070a016},
Key = {fds232029}
}
@article{fds231969,
Author = {Marder, SR and Cheng, LTA and Tiemann, BG and Beratan,
DN},
Title = {Structure/property relationships for molecular second-order
nonlinear optics (Invited Paper)},
Journal = {Proceedings of SPIE - The International Society for Optical
Engineering},
Volume = {1560},
Pages = {86-97},
Publisher = {SPIE},
Year = {1991},
Month = {December},
url = {http://spiedl.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PSISDG001560000001000086000001&idtype=cvips&prog=normal},
Abstract = {Using a two-state model, it was recently shown that there is
an optimal combination of donor and acceptor strengths for a
given bridge that will maximize the first molecular
electronic hyperpolarizability (β). To date, molecules with
sufficiently strong donors and acceptors have not been
synthesized to reach this ideal point. Here we outline
synthetic strategies that lead to molecules where β is
optimized by tuning the degree of bond alternation in the
π-electron system between the donor and acceptor.
Implementation of this strategy relies on the realization
that molecules with strongly aromatic end groups will not
have the correct balance of two limiting charge transfer
resonance forms in the ground state to achieve the degree of
bond alternation required to optimize the molecular
hyperpolarizability. Electric field induced second harmonic
generation studies on organic molecules with various bridge
structures support our hypothesis.},
Doi = {10.1117/12.50708},
Key = {fds231969}
}
@article{fds367317,
Author = {Liu, KT and Song, FF and Beratan, DN and Zhang, P},
Title = {Suppressing the entanglement growth in matrix product state
evolution of quantum systems through nonunitary similarity
transformations},
Journal = {Physical Review B},
Volume = {106},
Number = {10},
Year = {2022},
Month = {September},
url = {http://dx.doi.org/10.1103/PhysRevB.106.104306},
Abstract = {In strong-coupling regimes, quantum dynamical effects can
alter conventional physics described by perturbation
theories, but the dynamical simulations of these quantum
systems using matrix product states - such as multilevel
vibronic systems that are relevant to energy and electron
transfer reactions - suffer from rapid entanglement growth
during their real-time evolution, impeding explorations of
spectra, dynamics, and kinetics. We examine the possibility
of using nonunitary transformations to alter dynamical
entanglement growth in matrix-product-state simulations of
quantum systems, using the spin-boson model to showcase the
reduced entanglement. By appropriately choosing the
transformation, the entanglement growth rate is suppressed,
improving the efficiency of quantum dynamical simulations.
Entanglement control is achieved by the transformation-induced
biased transitions among the system quantum states, and by
"projecting"(approximately) the system quantum state to one
of the eigenstates of the system-bath coupling operator,
thus controlling the energy exchange between the system and
the bath. The transformation can be applied to quantum
many-body systems, including spin chains and multilevel
vibronic systems; the approach improves the numerical
efficiency of the matrix product state simulations.},
Doi = {10.1103/PhysRevB.106.104306},
Key = {fds367317}
}
@article{fds349326,
Author = {Li, X and Valdiviezo, J and Banziger, SD and Zhang, P and Ren, T and Beratan, DN and Rubtsov, IV},
Title = {Symmetry controlled photo-selection and charge separation in
butadiyne-bridged donor-bridge-acceptor compounds.},
Journal = {Physical chemistry chemical physics : PCCP},
Volume = {22},
Number = {17},
Pages = {9664-9676},
Year = {2020},
Month = {May},
url = {http://dx.doi.org/10.1039/d0cp01235a},
Abstract = {Electron transfer (ET) in donor-bridge-acceptor (DBA)
compounds depends strongly on the structural and electronic
properties of the bridge. Among the bridges that support
donor-acceptor conjugation, alkyne bridges have attractive
and unique properties: they are compact, possess linear
structure permitting access to high symmetry DBA molecules,
and allow torsional motion of D and A, especially for longer
bridges. We report conformation dependent electron transfer
dynamics in a set of novel DBA compounds featuring butadiyne
(C4) bridge, N-isopropyl-1,8-napthalimide (NAP) acceptors,
and donors that span a range of reduction potentials
(trimethyl silane (Si-C4-NAP), phenyl (Ph-C4-NAP), and
dimethyl aniline (D-C4-NAP)). Transient mid-IR absorption
spectra of the C[triple bond, length as m-dash]C bridge
stretching modes, transient spectra in the visible range,
and TD-DFT calculations were used to decipher the ET
mechanisms. We found that the electronic excited state
energies and, especially, the transition dipoles (S0 → Sn)
depend strongly on the dihedral angle (θ) between D and A
and the frontier orbital symmetry, offering an opportunity
to photo-select particular excited states with specific
ranges of dihedral angles by exciting at chosen wavelengths.
For example, excitation of D-C4-NAP at 400 nm predominantly
prepares an S1 excited state in the planar conformations (θ
∼ 0) but selects an S2 state with θ ∼ 90°, indicating
the dominant role of the molecular symmetry in the
photophysics. Moreover, the symmetry of the frontier
orbitals of such DBA compounds not only defines the
photo-selection outcome, but also determines the rate of the
S2 → S1 charge separation reaction. Unprecedented
variation of the S2-S1 electronic coupling with θ by over
four orders of magnitude results in slow ET at θ ca. 0°
and 90° but extremely fast ET at θ of 20-60°. The unique
features of high-symmetry alkyne bridged DBA structures
enable frequency dependent ET rate selection and make this
family of compounds promising targets for the vibrational
excitation control of ET kinetics.},
Doi = {10.1039/d0cp01235a},
Key = {fds349326}
}
@article{fds231927,
Author = {Hammill, JT and Contreras García and J and Virshup, AM and Beratan, DN and Yang, W and Wipf, P},
Title = {Synthesis and chemical diversity analysis of
bicyclo[3.3.1]non-3-en-2-ones},
Journal = {Tetrahedron},
Volume = {66},
Number = {66},
Pages = {5852-5862},
Year = {2010},
ISSN = {0040-4020},
url = {http://dx.doi.org/10.1016/j.tet.2010.04.112},
Abstract = {Functionalized bicyclo[3.3.1]non-3-en-2-ones are obtained
from commercially available phenols by a hypervalent iodine
oxidation, enone epoxidation, epoxide thiolysis, and
intramolecular aldol reaction sequence. Reaction
optimization studies identified room temperature as well as
microwave-mediated procedures, providing moderate to good
yields (57%-88%) in the thiophenol-mediated epoxide opening
and intramolecular aldol reaction. In addition, the
isolation of a key intermediate and in situ NMR studies
supported the mechanistic hypothesis. The bicyclic ring
products occupy novel chemical space according to ChemGPS
and Chemaxon chemical diversity and cheminformatics
analyses.},
Doi = {10.1016/j.tet.2010.04.112},
Key = {fds231927}
}
@article{fds304357,
Author = {Kondru, RK and Lim, S and Wipf, P and Beratan, DN},
Title = {Synthetic and model computational studies of molar rotation
additivity for interacting chiral centers: a reinvestigation
of van't Hoff's principle.},
Journal = {Chirality},
Volume = {9},
Number = {5-6},
Pages = {469-477},
Year = {1997},
Month = {January},
ISSN = {0899-0042},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9329177},
Abstract = {When plane-polarized light impinges on a solution of
optically active molecules, the polarization of the light
that emerges is rotated. This simple phenomenon arises from
the interaction of light with matter and is well understood,
in principle, van't Hoff's rule of optical superposition
correlates the molar rotation with the individual
contributions to optical activity of isolated centers of
asymmetry. This straightforward empirical additivity rule is
rarely used for structure elucidation nowadays because of
its limitations in the assessment of conformationally
restricted or interacting chiral centers. However,
additivity can be used successfully to assign the
configuration of complex natural products such as
hennoxazole A if appropriate synthetic partial structures
are available. Therefore, van't Hoff's principle is a
powerful stereochemical complement to natural products'
total synthesis. The quest for reliable quantitative methods
to calculate the angle of rotation a priori has been
underway for a long time. Both classical and quantum methods
for calculating molar rotation have been developed. Of
particular practical importance for determining the absolute
structure of molecules by calculation is the manner in which
interactions between multiple chiral centers in a single
molecule are included, leading to additive or non-additive
optical rotation angles. This problem is addressed here
using semi-empirical electronic structure models and the
Rosenfeld equation.},
Doi = {10.1002/(sici)1520-636x(1997)9:5/6<469::aid-chir13>3.0.co;2-},
Key = {fds304357}
}
@article{fds231993,
Author = {Kondru, RK and Lim, S and Wipf, P and Beratan, DN},
Title = {Synthetic and model computational studies of optical angle
additivity for interacting chiral centers: A reinvestigation
of van't Hoff's principle},
Journal = {Chirality},
Volume = {9},
Number = {5-6},
Pages = {468-477},
Year = {1997},
ISSN = {0899-0042},
url = {http://www3.interscience.wiley.com/cgi-bin/fulltext/54386/PDFSTART},
Abstract = {When plane-polarized light impinges on a solution of
optically active molecules, the polarization of the light
that emerges is rotated. This simple phenomenon arises from
the interaction of light with matter and is well understood,
in principle, van't Hoff's rule of optical superposition
correlates the molar rotation with the individual
contributions to optical activity of isolated centers of
asymmetry. This straightforward empirical additivity rule is
rarely used for structure elucidation nowadays because of
its limitations in the assessment of conformationally
restricted or interacting chiral centers. However,
additivity can be used successfully to assign the
configuration of complex natural products such as
hennoxazole A if appropriate synthetic partial structures
are available. Therefore, van't Hoff's principle is a
powerful stereochemical complement to natural products'
total synthesis. The quest for reliable quantitative methods
to calculate the angle of rotation a priori has been
underway for a long time. Both classical and quantum methods
for calculating molar rotation have been developed. Of
particular practical importance for determining the absolute
structure of molecules by calculation is the manner in which
interactions between multiple chiral centers in a single
molecule are included, leading to additive or non-additive
optical rotation angles. This problem is addressed here
using semi-empirical electronic structure models and the
Rosenfeld equation.},
Doi = {10.1002/(SICI)1520-636X(1997)9:5/6<469::AID-CHIR13>3.0.CO;2-},
Key = {fds231993}
}
@article{fds362912,
Author = {Roy, PP and Kundu, S and Valdiviezo, J and Bullard, G and Fletcher, JT and Liu, R and Yang, S-J and Zhang, P and Beratan, DN and Therien, MJ and Makri, N and Fleming, GR},
Title = {Synthetic Control of Exciton Dynamics in Bioinspired
Cofacial Porphyrin Dimers.},
Journal = {Journal of the American Chemical Society},
Volume = {144},
Number = {14},
Pages = {6298-6310},
Year = {2022},
Month = {April},
url = {http://dx.doi.org/10.1021/jacs.1c12889},
Abstract = {Understanding how the complex interplay among excitonic
interactions, vibronic couplings, and reorganization energy
determines coherence-enabled transport mechanisms is a grand
challenge with both foundational implications and potential
payoffs for energy science. We use a combined experimental
and theoretical approach to show how a modest change in
structure may be used to modify the exciton delocalization,
tune electronic and vibrational coherences, and alter the
mechanism of exciton transfer in covalently linked cofacial
Zn-porphyrin dimers (<i>meso-beta</i> linked
<i>AB</i><sub><i>m-β</i></sub> and <i>meso-meso</i> linked
<i>AA</i><sub><i>m-m</i></sub>). While both
<i>AB</i><sub><i>m-β</i></sub> and <i>AA</i><sub><i>m-m</i></sub>
feature zinc porphyrins linked by a 1,2-phenylene bridge,
differences in the interporphyrin connectivity set the
lateral shift between macrocycles, reducing electronic
coupling in <i>AB</i><sub><i>m-β</i></sub> and resulting in
a localized exciton. Pump-probe experiments show that the
exciton dynamics is faster by almost an order of magnitude
in the strongly coupled <i>AA</i><sub><i>m-m</i></sub>
dimer, and two-dimensional electronic spectroscopy (2DES)
identifies a vibronic coherence that is absent in
<i>AB</i><sub><i>m-β</i></sub>. Theoretical studies
indicate how the interchromophore interactions in these
structures, and their system-bath couplings, influence
excitonic delocalization and vibronic coherence-enabled
rapid exciton transport dynamics. Real-time path integral
calculations reproduce the exciton transfer kinetics
observed experimentally and find that the linking-modulated
exciton delocalization strongly enhances the contribution of
vibronic coherences to the exciton transfer mechanism, and
that this coherence accelerates the exciton transfer
dynamics. These benchmark molecular design, 2DES, and
theoretical studies provide a foundation for directed
explorations of nonclassical effects on exciton dynamics in
multiporphyrin assemblies.},
Doi = {10.1021/jacs.1c12889},
Key = {fds362912}
}
@article{fds232021,
Author = {Zuber, G and Goldsmith, M-R and Hopkins, TD and Beratan, DN and Wipf,
P},
Title = {Systematic assignment of the configuration of flexible
natural products by spectroscopic and computational methods:
the bistramide C analysis.},
Journal = {Organic letters},
Volume = {7},
Number = {23},
Pages = {5269-5272},
Year = {2005},
Month = {November},
ISSN = {1523-7060},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16268555},
Abstract = {[reaction: see text] The combination of NMR NOE, chemical
shift, and J-coupling measurements with molar rotation and
circular dichroism (CD) determinations, including RI-DFT
BP86/aug-cc-pVDZ calculations, reduced a candidate pool of
1024 possible stereoisomers of (+)-bistramide C to a single
absolute configuration assignment for the 10 stereogenic
carbons of the marine natural product.},
Doi = {10.1021/ol052154v},
Key = {fds232021}
}
@article{fds356973,
Author = {Sang, Y and Mishra, S and Tassinari, F and Karuppannan, SK and Carmieli,
R and Teo, RD and Migliore, A and Beratan, DN and Gray, HB and Pecht, I and Fransson, J and Waldeck, DH and Naaman, R},
Title = {Temperature Dependence of Charge and Spin Transfer in
Azurin.},
Journal = {The journal of physical chemistry. C, Nanomaterials and
interfaces},
Volume = {125},
Number = {18},
Pages = {9875-9883},
Year = {2021},
Month = {May},
url = {http://dx.doi.org/10.1021/acs.jpcc.1c01218},
Abstract = {The steady-state charge and spin transfer yields were
measured for three different Ru-modified azurin derivatives
in protein films on silver electrodes. While the
charge-transfer yields exhibit weak temperature dependences,
consistent with operation of a near activation-less
mechanism, the spin selectivity of the electron transfer
improves as temperature increases. This enhancement of spin
selectivity with temperature is explained by a vibrationally
induced spin exchange interaction between the Cu(II) and its
chiral ligands. These results indicate that distinct
mechanisms control charge and spin transfer within proteins.
As with electron charge transfer, proteins deliver polarized
electron spins with a yield that depends on the protein's
structure. This finding suggests a new role for protein
structure in biochemical redox processes.},
Doi = {10.1021/acs.jpcc.1c01218},
Key = {fds356973}
}
@misc{fds370691,
Author = {SKOURTIS, SS and BERATAN, DN and ONUCHIC, JN},
Title = {THE 2-STATE REDUCTION IN BRIDGE-MEDIATED
ELECTRON-TRANSFER},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {206},
Pages = {85-PHYS},
Year = {1993},
Key = {fds370691}
}
@misc{fds154732,
Author = {I.A. Balabin and D.N. Beratan and S.S. Skourtis},
Title = {The chemical roles of water in biological electron
transfer},
Booktitle = {Wiley Encyclopedia of Chemical Biology, Vol.
1},
Editor = {T.P. Begley},
Year = {2008},
url = {http://mrw.interscience.wiley.com/emrw/9780470048672/home/},
Key = {fds154732}
}
@misc{fds370701,
Author = {BERATAN, DN},
Title = {THE CHEMICAL-STRUCTURE DEPENDENCE OF ELECTRONIC
HYPERPOLARIZABILITIES},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {199},
Pages = {16-INOR},
Year = {1990},
Key = {fds370701}
}
@article{fds231962,
Author = {Goldsmith, M-R and George, CB and Zuber, G and Naaman, R and Waldeck,
DH and Wipf, P and Beratan, DN},
Title = {The chiroptical signature of achiral metal clusters induced
by dissymmetric adsorbates.},
Journal = {Physical chemistry chemical physics : PCCP},
Volume = {8},
Number = {1},
Pages = {63-67},
Year = {2006},
Month = {January},
ISSN = {1463-9076},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16482245},
Abstract = {Using a dissymmetrically-perturbed particle-in-a-box model,
we demonstrate that the induced optical activity of chiral
monolayer protected clusters, such as Whetten's Au28(SG)16
glutathione-passivated gold nanoclusters (J. Phys. Chem. B,
2000, 104, 2630-2641), could arise from symmetric metal
cores perturbed by a dissymmetric or chiral field
originating from the adsorbates. This finding implies that
the electronic states of the nanocluster core are chiral,
yet the lattice geometries of these cores need not be
geometrically distorted by the chiral adsorbates. Based on
simple chiral monolayer protected cluster models, we
rationalize how the adsorption pattern of the tethering
sulfur atoms has a substantial effect on the induced CD in
the NIR spectral region, and we show how the chiral image
charge produced in the core provides a convenient means of
visualizing dissymmetric perturbations to the achiral gold
nanocluster core.},
Doi = {10.1039/b511563a},
Key = {fds231962}
}
@article{fds231965,
Author = {Rubtsov, IV and Kang, YK and Redmore, NP and Allen, RM and Zheng, J and Beratan, DN and Therien, MJ},
Title = {The degree of charge transfer in ground and charge-separated
states revealed by ultrafast visible pump/mid-IR probe
spectroscopy.},
Journal = {Journal of the American Chemical Society},
Volume = {126},
Number = {16},
Pages = {5022-5023},
Year = {2004},
Month = {April},
ISSN = {0002-7863},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15099057},
Abstract = {We demonstrate a new femtosecond visible pump/mid-IR probe
spectroscopic approach to assess directly the ground- and
excited-state degrees of charge transfer (CT) in
donor-spacer-acceptor (D-Sp-A) structures. Two classes of
(porphinato)zinc(II) (PZn)-based D-Sp-A compounds with
either quinonyl (Q) or N-(N'-octyl)pyromellitic diimide (PI)
electron acceptors were interrogated. Carbonyl antisymmetric
stretching mode frequency domain transient-IR spectra of
these species were recorded and analyzed for the Q/PI
moieties. These data show that the acceptor mode frequency
shift, DeltanuA, determined by this method provides a more
accurate measure of the degree of CT in ground and
charge-separated states relative to other techniques which
rely on the ground-state frequency shift alone. This
approach enables determination of new experimental
benchmarks to test the power of complimentary computational
methods and provides a means to probe the degree of CT in
transitions that either overlap strongly with other bands or
possess low oscillator strength.},
Doi = {10.1021/ja030674k},
Key = {fds231965}
}
@misc{fds22240,
Author = {J. N. Onuchic and S.M. Risser and S.S. Skourtis and D.N.
Beratan},
Title = {The design of starburst dendrimer electron transfer
systems},
Pages = {369-379},
Booktitle = {Molecular Electronics},
Publisher = {Chemistry for the 21st Century Series, Blackwell Science,
Oxford, Chapter 12},
Editor = {M. Ratner and J. Jortner},
Year = {1997},
Key = {fds22240}
}
@article{fds231865,
Author = {Skourtis, SS and Lin, J and Beratan, DN},
Title = {The effects of bridge motion on electron transfer reactions
mediated by tunneling},
Pages = {357-382},
Booktitle = {Modern Methods for Theoretical Physical Chemistry of
Biopolymers},
Publisher = {Elsevier},
Editor = {E.B. Starikov and J.P. Lewis and S. Tanaka},
Year = {2006},
Month = {December},
url = {http://dx.doi.org/10.1016/B978-044452220-7/50082-4},
Abstract = {This chapter provides an in-depth review of recent
developments associated with dynamical effects on electron
transfer (ET) processes. It discusses the regimens of
validity for standard rate formulations and presents in
detail the explicit examples of dynamically coupled electron
transfer reactions. It also discusses methods for the
computation of tunneling matrix elements, bridge mediated
electron transfer rates for fluctuating bridges, the
influence of tunneling matrix element fluctuations on the ET
rate, the qualitative picture of tunneling matrix element
fluctuation effects on the ET rate, quantum nuclear motion
and inelastic tunneling, tunneling through a bridge with
large conformational freedom, and bimolecular ET kinetics:
exploring numerous protein-protein conformations and aqueous
coupling pathways between proteins. In conclusion, the
theoretical framework and specific applications outlined
show a richness that emerges as bridge dynamical effects are
added explicitly to the considerations of electron transfer
kinetics. Quantum interferences can be manipulated by
inelastic tunneling effects; reaction mechanisms can be
switched, and bridge-mediated tunneling can be dominated by
minority population species. © 2006 Elsevier B.V. All
rights reserved.},
Doi = {10.1016/B978-044452220-7/50082-4},
Key = {fds231865}
}
@misc{fds43098,
Author = {S.S. Skourtis and J. Lin and D.N. Beratan},
Title = {The effects of bridge motion on electron transfer reactions
mediated by tunneling},
Booktitle = {Modern Methods for Theoretical Physical Chemistry of
Biopolymers},
Editor = {E.B. Starikov and S. Tanaka and J.P. Lewis},
Year = {2005},
Key = {fds43098}
}
@article{fds304362,
Author = {Lin, J and Balabin, IA and Beratan, DN},
Title = {The nature of aqueous tunneling pathways between
electron-transfer proteins.},
Journal = {Science (New York, N.Y.)},
Volume = {310},
Number = {5752},
Pages = {1311-1313},
Year = {2005},
Month = {November},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16311331},
Abstract = {Structured water molecules near redox cofactors were found
recently to accelerate electron-transfer (ET) kinetics in
several systems. Theoretical study of interprotein electron
transfer across an aqueous interface reveals three
distinctive electronic coupling mechanisms that we describe
here: (i) a protein-mediated regime when the two proteins
are in van der Waals contact; (ii) a structured
water-mediated regime featuring anomalously weak distance
decay at relatively close protein-protein contact distances;
and (iii) a bulk water-mediated regime at large distances.
Our analysis explains a range of otherwise puzzling
biological ET kinetic data and provides a framework for
including explicit water-mediated tunneling effects on ET
kinetics.},
Doi = {10.1126/science.1118316},
Key = {fds304362}
}
@article{fds232008,
Author = {Lee, M and Shephard, MJ and Risser, SM and Priyadarshy, S and Paddon-Row, MN and Beratan, DN},
Title = {The nature of tunnel splitting mediated by stacked
aromatics},
Journal = {Journal of Physical Chemistry A},
Volume = {104},
Number = {32},
Pages = {7593-7599},
Publisher = {American Chemical Society (ACS)},
Year = {2000},
Month = {August},
ISSN = {1089-5639},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcafh/2000/104/i32/pdf/jp994372+.pdf},
Abstract = {We have examined the distance and orientation dependence of
the energy splitting, ΔE(π*), between the two lowest-lying
unoccupied molecular orbitals of a pair of
tetracyanoethylene (TCNE) molecules bridged by a stack of
noncovalently bonded benzene rings; the stack length ranged
from one to. six benzene molecules. The distance between
ring planes was fixed at 3.4 Å, while the orientation of
the rings and of the TCNE molecules was varied. The
magnitude of the splitting energy was found to decay
exponentially with increasing stack length, r; ΔE(π*) = A
exp(-0.5βer), with the damping factor, βe, ranging in
value from 1.1 to 1.6 Å-1, as might be anticipated for
instances where the "tunneling energy" lies several electron
volts away from the frontier orbitals of the π-electron
stack. Both ab initio and semiempirical computations predict
a weak dependence of the coupling upon the orientation of
the rings. The ab initio HF/3-21G calculations give βe
values approximately 20% smaller than those values found in
semiempirical computations using π-stacks in which the
separation between adjacent benzene molecules (3.4 Å) is
typical of stacked aromatic systems. This is due to the
improved capability of the 3-21G basis set to treat the
nearest-neighbor inter-ring orbital interactions, compared
to the more contracted complete neglect of differential
overlap (CNDO) basis set. Comparison to calculations with a
more extended basis shows the 3-21G basis is accurate for
rings separated by up to 4.0 Å, but for larger separations,
ab initio calculations require the use of diffuse functions
to properly describe the exponential decay of the
interaction. © 2000 American Chemical Society.},
Doi = {10.1021/jp994372+},
Key = {fds232008}
}
@article{fds232006,
Author = {Jones, ML and Kurnikov, IV and Beratan, DN},
Title = {The nature of tunneling pathway and average packing density
models for protein-mediated electron transfer},
Journal = {Journal of Physical Chemistry A},
Volume = {106},
Number = {10},
Pages = {2002-2006},
Publisher = {American Chemical Society (ACS)},
Year = {2002},
Month = {March},
ISSN = {1089-5639},
url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcafh/2002/106/i10/pdf/jp0133743.pdf},
Abstract = {The last 30 years have witnessed the development of
increasingly successful theoretical approaches to predicting
how a protein's chemical composition and three-dimensional
structure influence its propensity to mediate
electron-transfer reactions. Analysis has progressed from
uniform-barrier models that neglect atomic detail, to
pathway models that incorporate the specific nature of the
bonding and the protein fold, to multipathway models that
add coherently the contributions of pathways, to methods
that average over accessible geometries. Large-scale
electronic structure methods remain of somewhat limited use
because: the demands of geometry sampling and electronic
structure calculation are considerable, especially for
slower ET events; qualitative new insights arising from the
more intensive analysis have been moderate; and
structure-function relations become increasingly difficult
to derive from more complex models. For these reasons,
simple models remain both useful and popular. The simplest
structured-protein models employ tunneling pathway and
average packing density analysis. These methods are derived
from the same protein physics: electronic interactions decay
much more rapidly through-space than through-bond. We show
that for the majority of 38 donor-acceptor pairs in 28
proteins with determined X-ray structures, the two models
are in qualitative agreement. However, for five of these
donor-acceptor pairs, the pathway and the average packing
density predictions are qualitatively different. The
structural reasons for these differences are clear: (1)
strong coupling pathways may exist in regions of
unremarkable packing density, (2) explicit water molecules
added to the X-ray structures can eliminate otherwise costly
through-space jumps, (3) strong pathways situated beyond the
zone sampled in average packing density analysis can
dominate. We suggest that the instances of substantial
differences between the two models can be used to probe ET
tunneling mechanism. Differences, where they exist, point to
specific t structural motifs where pathway effects
associated with a protein s three-dimensional structure
might play a central role in ET kinetics.},
Doi = {10.1021/jp0133743},
Key = {fds232006}
}
@article{fds231867,
Author = {Wierzbinski, E and Venkatramani, R and Davis, KL and Bezer, S and Kong,
J and Xing, Y and Borguet, E and Achim, C and Beratan, DN and Waldeck,
DH},
Title = {The single-molecule conductance and electrochemical
electron-transfer rate are related by a power
law.},
Journal = {ACS nano},
Volume = {7},
Number = {6},
Pages = {5391-5401},
Year = {2013},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23692478},
Abstract = {This study examines quantitative correlations between
molecular conductances and standard electrochemical rate
constants for alkanes and peptide nucleic acid (PNA)
oligomers as a function of the length, structure, and charge
transport mechanism. The experimental data show a power-law
relationship between conductances and charge transfer rates
within a given class of molecules with the same bridge
chemistry, and a lack of correlation when a more diverse
group of molecules is compared, in contrast with some
theoretical predictions. Surprisingly, the PNA duplexes
exhibit the lowest charge-transfer rates and the highest
molecular conductances. The nonlinear rate-conductance
relationships for structures with the same bridging
chemistries are attributed to differences in the
charge-mediation characteristics of the molecular bridge,
energy barrier shifts and electronic dephasing, in the two
different experimental settings.},
Doi = {10.1021/nn401321k},
Key = {fds231867}
}
@article{fds232052,
Author = {Skourtis, SS and Beratan, DN and Onuchic, JN},
Title = {The two-state reduction for electron and hole transfer in
bridge-mediated electron-transfer reactions},
Journal = {Chemical Physics},
Volume = {176},
Number = {2-3},
Pages = {501-520},
Publisher = {Elsevier BV},
Year = {1993},
Month = {October},
ISSN = {0301-0104},
url = {http://dx.doi.org/10.1016/0301-0104(93)80258-B},
Abstract = {We present a unified analysis of the two-state reduction in
bridge-mediated electron transfer for both electron and hole
transfer. The parameter that characterizes the leading error
associated with a two-state reduction is derived in the
energy and time domains. A precise definition of the
tunnelling energy is given. We also derive analytically the
regimes of validity of the two-state reduction and we
interpret it in terms of the time evolution of the purely
electronic part of the electron-transfer probability. ©
1993.},
Doi = {10.1016/0301-0104(93)80258-B},
Key = {fds232052}
}
@misc{fds370674,
Author = {Beratan, DN and Kurnikov, IV and Tong, GSM},
Title = {Theoretical approaches to biological electron transfer in
multi-component systems.},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {220},
Pages = {U461-U461},
Year = {2000},
Key = {fds370674}
}
@misc{fds370669,
Author = {Pasquinelli, MA and Beratan, DN},
Title = {Theoretical studies of the effects of phosphorylation on
protein electron transfer chains},
Journal = {BIOPHYSICAL JOURNAL},
Volume = {84},
Number = {2},
Pages = {149A-150A},
Year = {2003},
Key = {fds370669}
}
@article{fds32269,
Author = {S.S. Skourtis and D.N. Beratan},
Title = {Theories of structure-function relationships for
bridge-mediated electron transfer},
Volume = {106},
Pages = {377-452},
Booktitle = {Adv. Chem. Phys.},
Year = {1999},
Key = {fds32269}
}
@article{fds231908,
Author = {Skourtis, SS and Beratan, DN},
Title = {Theories of structure-function relationships for
bridge-mediated electron transfer reactions},
Journal = {Advances in Chemical Physics},
Volume = {106},
Pages = {377-452},
Publisher = {JOHN WILEY & SONS INC},
Year = {1999},
Month = {December},
ISSN = {0065-2385},
url = {http://dx.doi.org/10.1002/9780470141656.ch8},
Doi = {10.1002/9780470141656.ch8},
Key = {fds231908}
}
@article{fds231991,
Author = {Nocek, JM and Zhou, JS and De Forest and S and Priyadarshy, S and Beratan,
DN and Onuchic, JN and Hoffman, BM},
Title = {Theory and Practice of Electron Transfer within Proteinminus
signProtein Complexes: Application to the Multidomain
Binding of Cytochrome c by Cytochrome c Peroxidase.},
Journal = {Chemical reviews},
Volume = {96},
Number = {7},
Pages = {2459-2490},
Year = {1996},
Month = {November},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11848833},
Doi = {10.1021/cr9500444},
Key = {fds231991}
}
@article{fds232034,
Author = {Kondru, RK and Wipf, P and Beratan, DN},
Title = {Theory-assisted determination of absolute stereochemistry
for complex natural products via computation of molar
rotation angles [17]},
Journal = {Journal of the American Chemical Society},
Volume = {120},
Number = {9},
Pages = {2204-2205},
Publisher = {American Chemical Society (ACS)},
Year = {1998},
Month = {March},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1998/120/i09/pdf/ja973690o.pdf},
Doi = {10.1021/ja973690o},
Key = {fds232034}
}
@article{fds231995,
Author = {Zusman, LD and Beratan, DN},
Title = {Three-state model for two-electron transfer
reactions},
Journal = {Journal of Physical Chemistry A},
Volume = {101},
Number = {22},
Pages = {4136-4141},
Publisher = {American Chemical Society (ACS)},
Year = {1997},
Month = {May},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcafh/1997/101/i22/pdf/jp970123e.pdf},
Abstract = {Much of electron transfer based catalysis relies upon
multielectron rather than single-electron transfer
processes. If the multielectron events proceed through
stable one-electron intermediates, conventional theory
describes the events However, when an unstable one-electron
intermediate plays a role, when a stable intermediate lives
for a brief period of time, or when concerted multielectron
events occur, the electronic coupling and free energy
dependence of the rate is distinct from that arising in
one-electron theories. We describe several new features that
can arise in multielectron processes, predict their
experimental signature, and show how these ideas can be
applied to specific experimental systems.},
Doi = {10.1021/jp970123e},
Key = {fds231995}
}
@misc{fds22297,
Author = {D.N. Beratan and J.N. Onuchic and J.J. Hopfield},
Title = {Through bond and through space limits of the long distance
electron transfer problem},
Pages = {488},
Booktitle = {Protein Structure, Molecular and Electronic
Reactivity},
Editor = {R. Austin and et al.},
Year = {1987},
Key = {fds22297}
}
@article{fds231892,
Author = {Beratan, DN and Naaman, R and Waldeck, DH},
Title = {Topics in Current Chemistry: Preface},
Journal = {Topics in Current Chemistry},
Volume = {298},
Pages = {ix-x},
Year = {2011},
Month = {February},
ISSN = {0340-1022},
Key = {fds231892}
}
@misc{fds370662,
Author = {Beratan, D},
Title = {Toward a theory of infra-red perturbed electron transfer
reactions},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {255},
Year = {2018},
Key = {fds370662}
}
@article{fds232020,
Author = {Zuber, G and Goldsmith, M-R and Beratan, DN and Wipf,
P},
Title = {Towards Raman optical activity calculations of large
molecules.},
Journal = {Chemphyschem : a European journal of chemical physics and
physical chemistry},
Volume = {6},
Number = {4},
Pages = {595-597},
Year = {2005},
Month = {April},
ISSN = {1439-4235},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15881572},
Doi = {10.1002/cphc.200400544},
Key = {fds232020}
}
@article{fds231861,
Author = {Lin, J and Hu, X and Zhang, P and Van Rynbach and A and Beratan, DN and Kent,
CA and Mehl, BP and Papanikolas, JM and Meyer, TJ and Lin, W and Skourtis,
SS and Constantinou, M},
Title = {Triplet excitation energy dynamics in metal-organic
frameworks},
Journal = {Journal of Physical Chemistry C},
Volume = {117},
Number = {43},
Pages = {22250-22259},
Publisher = {American Chemical Society (ACS)},
Year = {2013},
Month = {October},
ISSN = {1932-7447},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000326608200013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {Metal-organic frameworks (MOFs) are appealing candidates for
use in energy harvesting and concentrating because of their
high chromophore density and structural tunability. The
ability to engineer electronic excitation energy transport
pathways is of particular interest for designing energy
harvesting materials. In this study, theoretical analysis
was performed on energy transfer in MOFs that contain light
absorbing ruthenium complexes that serve as hopping
intermediates for energy transfer kinetics and energy
trapping osmium complexes. We find that the excitation
transport kinetics is well described by a Dexter (exchange)
triplet-to-triplet energy transfer mechanism with multistep
incoherent exciton hopping. The modeling combines ab initio
electronic structure theory with kinetic network analysis.
The sensitivity of Dexter mechanism energy transfer to
framework structure establishes different kinds of energy
transport paths in the different structures. For example,
the mixed Ru/Os MOF structures described here establish one
or three-dimensional hopping networks. As such, Dexter
mechanism energy harvesting materials may be amenable to
designing structures that can spatially direct exciton
energy along specific pathways for energy delivery to
reaction centers. © 2013 American Chemical
Society.},
Doi = {10.1021/jp401515r},
Key = {fds231861}
}
@article{fds232005,
Author = {Lewis, FD and Liu, J and Weigel, W and Retting, W and Kurnikov, IV and Beratan, DN},
Title = {Tunneling energy controls DNA electron transfer distance
dependence},
Journal = {Proc. Natl. Acad. Sci. (USA)},
Volume = {99},
Number = {20},
Pages = {12536-12541},
Year = {2002},
ISSN = {0027-8424},
url = {http://www.pnas.org/cgi/content/full/99/20/12536},
Abstract = {Electron transfer (ET) processes in DNA are of current
interest because of their involvement in oxidative strand
cleavage reactions and their relevance to the development of
molecular electronics. Two mechanisms have been identified
for ET in DNA, a single-step tunneling process and a
multistep charge-hopping process. The dynamics of tunneling
reactions depend on both the distance between the electron
donor and acceptor and the nature of the molecular bridge
separating the donor and acceptor. In the case of protein
and alkane bridges, the distance dependence is not strongly
dependent on the properties of the donor and acceptor. In
contrast, we show here that the distance decay of DNA ET
rates varies markedly with the energetics of the donor and
acceptor relative to the bridge. Specifically, we find that
an increase in the energy of the bridge states by 0.25 eV (1
eV = 1.602 x 10(-19) J) relative to the donor and acceptor
energies for photochemical oxidation of nucleotides, without
changing the reaction free energy, results in an increase in
the characteristic exponential distance decay constant for
the ET rates from 0.71 to 1.1 A(-1). These results show
that, in the small tunneling energy gap regime of DNA ET,
the distance dependence is not universal; it varies strongly
with the tunneling energy gap. These DNA ET reactions fill a
"missing link" or transition regime between the large
barrier (rapidly decaying) tunneling regime and the (slowly
decaying) hopping regime in the general theory of
bridge-mediated ET processes.},
Doi = {10.1073/pnas.192432899},
Key = {fds232005}
}
@article{fds232007,
Author = {Tong, GSM and Kurnikov, IV and Beratan, DN},
Title = {Tunneling energy effects on GC oxidation in
DNA},
Journal = {Journal of Physical Chemistry B},
Volume = {106},
Number = {9},
Pages = {2381-2392},
Publisher = {American Chemical Society (ACS)},
Year = {2002},
Month = {March},
ISSN = {1089-5647},
url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2002/106/i09/pdf/jp013387g.pdf},
Abstract = {Hole-mediated electronic couplings, reorganization energies,
and electron transfer (ET) rates are examined theoretically
for hole-transfer reactions in DNA. Electron transfer rates
are found to depend critically on the energy gap between the
donor/acceptor states and the intervening bases-the
tunneling energy gap. The calculated distance decay exponent
for the square of the electronic coupling, β, for hole
transfer between GC base pairs (and pi-electron D/A pairs)
ranges from 0.95 to 1.5 Å-1 in the model structures as the
tunneling energy gap varies from 0.3 to 0.8 eV (which we
argue is the range of energy gaps for GC oxidation probed in
recent experiments). We show that the tunneling energy gap
depends on the ET reorganization energy, which itself grows
rapidly with distance for ET over 1-5 base pairs. Inclusion
of the distance dependence of reorganization energies for
these hole transfer reactions gives the tunneling rates an
apparent decay exponent of ∼1.5-2.5 Å-1. We show that ET
rates observed in DNA across one and two base pairs are
reasonably well described with single-step ET theories,
using our calculated couplings and reorganization energies.
However, the computed single-step tunneling (superexchange)
ET rates for donor and acceptor species separated by three
or more base pairs are much smaller than observed. We
conclude that longer-distance ET probably proceeds through
thermal population of intermediate hole states of the
bridging bases. Switching between mechanisms as distance
grows beyond a few base pairs is likely to be a general
characteristic of ET in small tunneling energy gap
systems.},
Doi = {10.1021/jp013387g},
Key = {fds232007}
}
@article{fds231983,
Author = {Beratan, DN and Betts, JN and Onuchic, JN},
Title = {Tunneling pathway and redox-state-dependent electronic
couplings at nearly fixed distance in electron-transfer
proteins},
Journal = {Journal of Physical Chemistry},
Volume = {96},
Number = {7},
Pages = {2852-2855},
Publisher = {American Chemical Society (ACS)},
Year = {1992},
Month = {January},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1992/96/i07/pdf/j100186a014.pdf},
Abstract = {The tunneling pathway model for electron transfer, which
accounts for the unique covalent, hydrogen-bonded, and van
der Waals contacts linking donor and acceptor in a protein,
gives a consistent description of electron-transfer rates in
ruthenated proteins (cytochrome c, myoglobin, and cytochrome
b5), while simpler exponential decay models are not fully
adequate. We report several new testable predictions of the
pathway model relating electron-transfer rates to protein
structure. The analysis predicts qualitative differences in
the distance dependence of protein electron transfer at
short (<5 Å) vs long distance, differences in the nature of
the coupling through α-helix vs β-sheet, and the
possibility of switching electronic coupling upon
oxidation/reduction or ligation/deligation in
metalloproteins. © 1992 American Chemical
Society.},
Doi = {10.1021/j100186a014},
Key = {fds231983}
}
@misc{fds370694,
Author = {RISSER, SM and REGAN, JJ and ONUCHIC, JN and BERATAN,
DN},
Title = {TUNNELING PATHWAYS IN MACROMOLECULES},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {205},
Pages = {197-INOR},
Year = {1993},
Key = {fds370694}
}
@article{fds231904,
Author = {Onuchic, JN and Beratan, D},
Title = {Tunneling pathways in proteins: From biology to molecular
electronics},
Journal = {Proceedings of the Annual Conference on Engineering in
Medicine and Biology},
Number = {pt 4},
Pages = {1764-1765},
Year = {1990},
Month = {December},
Abstract = {A method is presented for the calculation of tunneling
matrix elements for electron transfer in proteins. The
concept of a tunneling pathway is introduced and its
importance in mediating this coupling is described. Comments
are presented on how, using the knowledge about electron
transfer reactions, a molecular shift register memory has
been designed. Similar to photosynthetic structures, these
shift register memories have to separate charge (fast
forward electron transfer) much faster than the charge
separated states are able to recombine (slow reverse
electron transfer). This device demonstrates the importance
of understanding how controlled electron transfer reactions
work for developing new kinds of technology.},
Key = {fds231904}
}
@article{fds231963,
Author = {Jianping, L and Beratan, DN},
Title = {Tunneling while pulling: The dependence of tunneling current
on end-to-end distance in a flexible molecule},
Journal = {Journal of Physical Chemistry A},
Volume = {108},
Number = {26},
Pages = {5655-5661},
Publisher = {American Chemical Society (ACS)},
Year = {2004},
Month = {July},
ISSN = {1089-5639},
url = {http://dx.doi.org/10.1021/jp0379502},
Abstract = {Most molecules access a broad range of conformations at room
temperature. Since electron-tunneling interactions are
exponentially sensitive to geometry changes, thermal
fluctuations are expected to have a large influence on
room-temperature tunneling currents and scanning tunneling
microscope images. We explore the influence of
conformational freedom on tunneling currents in a simple
model for tunneling mediated by a single small molecule that
bridges between a model tip and substrate. The tip and
substrate are described as semi-infinite structures. The
bridging molecule and the metals are all described with
tight-binding Hamiltonians. The conformationally averaged
tunneling matrix element, proportional to the tunneling
currents, is computed from thermally accessible molecular
conformations. We vary the sulfur-to-sulfur separation
distance in -S-(CH 2) 8-S- (n-octanedithiol) and, at each of
these separations, compute the family of thermally
accessible conformers. The two sulfur atoms are constrained
to positions along a line perpendicular to the substrate
surface. The conformationally averaged tunneling current
computed for each fixed sulfur-to-sulfur distance is
predicted to display an average distance dependence that is
strikingly similar to the decay found in experiments
performed on families of extended ("all trans") n-alkanes.
That is, the tunneling current is predicted to decay
exponentially with a decay parameter of ∼1.0 Å -1 based
on the tip to substrate distance. This observation supports
the notion that the most strongly coupled conformers in the
ensemble dominate the STM tunneling current. This conclusion
is also consistent with the analysis of protein
electron-transfer systems, where thermal fluctuations are
predicted to shorten coupling pathways and to minimize the
influence on the rate of destructive interferences among
multiple coupling pathways.},
Doi = {10.1021/jp0379502},
Key = {fds231963}
}
@article{fds231937,
Author = {Xiao, D and Skourtis, SS and Rubtsov, IV and Beratan,
DN},
Title = {Turning charge transfer on and off in a molecular
interferometer with vibronic pathways.},
Journal = {Nano letters},
Volume = {9},
Number = {5},
Pages = {1818-1823},
Year = {2009},
Month = {May},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19435376},
Abstract = {Inelastic electron-transfer kinetics in molecules with
electron donor and acceptor units connected by a bridge is
expected to be sensitive to bridge-localized vibronic
interactions. Here, we show how inelastic electron transfer
may be turned on and off in a double-slit style experiment
that uses the molecule as an interferometer. We describe
donor-acceptor interactions in terms of interfering vibronic
coupling pathways that can be actively selected ("labeled")
when pathway-specific vibrations are excited by infrared
radiation. Thus, inelastic tunneling may be actively
controlled, and we suggest strategies for building molecular
scale quantum interferometers and switches based on this
phenomenon.},
Doi = {10.1021/nl8037695},
Key = {fds231937}
}
@article{fds362029,
Author = {Ko, C-H and Zhu, Q and Tassinari, F and Bullard, G and Zhang, P and Beratan, DN and Naaman, R and Therien, MJ},
Title = {Twisted molecular wires polarize spin currents at room
temperature.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {119},
Number = {6},
Pages = {e2116180119},
Year = {2022},
Month = {February},
url = {http://dx.doi.org/10.1073/pnas.2116180119},
Abstract = {A critical spintronics challenge is to develop molecular
wires that render efficiently spin-polarized currents.
Interplanar torsional twisting, driven by chiral
binucleating ligands in highly conjugated molecular wires,
gives rise to large near-infrared rotational strengths. The
large scalar product of the electric and magnetic dipole
transition moments ([Formula: see text]), which are evident
in the low-energy absorptive manifolds of these wires, makes
possible enhanced chirality-induced spin selectivity-derived
spin polarization. Magnetic-conductive atomic force
microscopy experiments and spin-Hall devices demonstrate
that these designs point the way to achieve high spin
selectivity and large-magnitude spin currents in chiral
materials.},
Doi = {10.1073/pnas.2116180119},
Key = {fds362029}
}
@article{fds231851,
Author = {Lin, J and Balamurugan, D and Zhang, P and Skourtis, SS and Beratan,
DN},
Title = {Two-Electron Transfer Pathways.},
Journal = {The journal of physical chemistry. B},
Volume = {119},
Number = {24},
Pages = {7589-7597},
Year = {2015},
Month = {June},
ISSN = {1520-6106},
url = {http://dx.doi.org/10.1021/jp511429z},
Abstract = {The frontiers of electron-transfer chemistry demand that we
develop theoretical frameworks to describe the delivery of
multiple electrons, atoms, and ions in molecular systems.
When electrons move over long distances through high
barriers, where the probability for thermal population of
oxidized or reduced bridge-localized states is very small,
the electrons will tunnel from the donor (D) to acceptor
(A), facilitated by bridge-mediated superexchange
interactions. If the stable donor and acceptor redox states
on D and A differ by two electrons, it is possible that the
electrons will propagate coherently from D to A. While
structure-function relations for single-electron
superexchange in molecules are well established, strategies
to manipulate the coherent flow of multiple electrons are
largely unknown. In contrast to one-electron superexchange,
two-electron superexchange involves both one- and
two-electron virtual intermediate states, the number of
virtual intermediates increases very rapidly with system
size, and multiple classes of pathways interfere with one
another. In the study described here, we developed simple
superexchange models for two-electron transfer. We explored
how the bridge structure and energetics influence
multielectron superexchange, and we compared two-electron
superexchange interactions to single-electron superexchange.
Multielectron superexchange introduces interference between
singly and doubly oxidized (or reduced) bridge virtual
states, so that even simple linear donor-bridge-acceptor
systems have pathway topologies that resemble those seen for
one-electron superexchange through bridges with multiple
parallel pathways. The simple model systems studied here
exhibit a richness that is amenable to experimental
exploration by manipulating the multiple pathways, pathway
crosstalk, and changes in the number of donor and acceptor
species. The features that emerge from these studies may
assist in developing new strategies to deliver multiple
electrons in condensed-phase redox systems, including
multiple-electron redox species, multimetallic/multielectron
redox catalysts, and multiexciton excited
states.},
Doi = {10.1021/jp511429z},
Key = {fds231851}
}
@article{fds231987,
Author = {Zusman, LD and Beratan, DN},
Title = {Two-electron transfer reactions in polar
solvents},
Journal = {Journal of Chemical Physics},
Volume = {105},
Number = {1},
Pages = {165-176},
Publisher = {AIP Publishing},
Year = {1996},
Month = {January},
url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000105000001000165000001&idtype=cvips},
Abstract = {Chemical, biological, and electrode based electron transfer
(ET) processes involve multielectron events. However, an
adequate framework in which to describe these complex
reactions does not yet exist. A theory for two-electron
transfer reactions in Debye solvents is developed. The
theory is formulated by generalizing Zusman's model of ET
reactions [L. D. Zusman, Chem. Phys. 49, 295 (1980)] to
those involving three parabolic wells: One for the doubly
reduced donor, one for the singly reduced donor/singly
reduced acceptor, and one for the doubly reduced acceptor.
The ET processes are described in terms of diffusional
motion along a one-dimensional reaction coordinate with
tunneling transitions at the intersection points of the
parabolas. Two competing mechanisms of two-electron transfer
arise. One is a process with two sequential single electron
steps D=A→D-A-→DA=. The other involves ET in one
concerted two-electron step (D=A→DA=). The general rate
expressions for two-electron transfer are obtained. When the
stepwise mechanism dominates, the free energy of activation
is predicted to depend upon the driving forces of the two
sequential steps but is independent of the overall driving
force of the reaction. When concerted two-electron transfer
dominates, the Marcus relation is obtained with a
reorganization energy associated with the shift of two
electrons. The dynamical solvent effect in two-electron ET
processes is predicted to be unusual. Two distinct regimes
exist, each with essentially linear 1/γL dependence (with
γL the solvent longitudinal relaxation time): one for slow
solvents and one for fast solvents. A combination of solvent
and free energy studies could be used to elucidate the
mechanism of multielectron processes in chemical and
biological systems. © 1996 American Institute of
Physics.},
Doi = {10.1063/1.471862},
Key = {fds231987}
}
@article{fds231918,
Author = {Susumu, K and Fisher, JAN and Zheng, J and Beratan, DN and Yodh, AG and Therien, MJ},
Title = {Two-photon absorption properties of proquinoidal D-A-D and
A-D-A quadrupolar chromophores.},
Journal = {The journal of physical chemistry. A},
Volume = {115},
Number = {22},
Pages = {5525-5539},
Year = {2011},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21568299},
Abstract = {We report the synthesis, one- and two-photon absorption
spectroscopy, fluorescence, and electrochemical properties
of a series of quadrupolar molecules that feature
proquinoidal π-aromatic acceptors. These quadrupolar
molecules possess either donor-acceptor-donor (D-A-D) or
acceptor-donor-acceptor (A-D-A) electronic motifs, and
feature 4-N,N-dihexylaminophenyl, 4-dodecyloxyphenyl,
4-(N,N-dihexylamino)benzo[c][1,2,5]thiadiazolyl or
2,5-dioctyloxyphenyl electron donor moieties and
benzo[c][1,2,5]thiadiazole (BTD) or 6,7-bis(3',7'-dimethyloctyl)[1,2,5]thiadiazolo[3,4-g]quinoxaline
(TDQ) electron acceptor units. These conjugated structures
are highly emissive in nonpolar solvents and exhibit large
spectral red-shifts of their respective lowest energy
absorption bands relative to analogous reference compounds
that incorporate phenylene components in place of BTD and
TDQ moieties. BTD-based D-A-D and A-D-A chromophores exhibit
increasing fluorescence emission red-shifts, and a
concomitant decrease of the fluorescence quantum yield
(Φ(f)) with increasing solvent polarity; these data
indicate that electronic excitation augments
benzothiadiazole electron density via an internal charge
transfer mechanism. The BTD- and TDQ-containing structures
exhibit blue-shifted two-photon absorption (TPA) spectra
relative to their corresponding one-photon absorption (OPA)
spectra, and display high TPA cross sections (>100 GM)
within these spectral windows. D-A-D and A-D-A structures
that feature more extensive conjugation within this series
of compounds exhibit larger TPA cross sections consistent
with computational simulation. Factors governing TPA
properties of these quadrupolar chromophores are discussed
within the context of a three-state model.},
Doi = {10.1021/jp2000738},
Key = {fds231918}
}
@article{fds231901,
Author = {Beratan, DN and Hopfield, JJ and Onuchic, JN},
Title = {Ultrasmall memories based on electron transfer
reactions},
Journal = {Annual International Conference of the IEEE Engineering in
Medicine and Biology - Proceedings},
Volume = {11 pt 4},
Pages = {1322},
Publisher = {IEEE},
Year = {1989},
Month = {December},
url = {http://dx.doi.org/10.1109/iembs.1989.96217},
Abstract = {Summary form only given. An electronic shift register memory
at the molecular level is described. The memory elements are
based on a chain of electron transfer molecules, and the
information is shifted by photoinduced electron transfer
reactions. This device integrates designed electronic
molecules onto a very-large-scale integrated (silicon
microelectronic) substrate, providing an example of a
molecular electronic device.},
Doi = {10.1109/iembs.1989.96217},
Key = {fds231901}
}
@article{fds351428,
Author = {Yuly, JL and Zhang, P and Lubner, CE and Peters, JW and Beratan,
DN},
Title = {Universal free-energy landscape produces efficient and
reversible electron bifurcation.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {117},
Number = {35},
Pages = {21045-21051},
Year = {2020},
Month = {September},
url = {http://dx.doi.org/10.1073/pnas.2010815117},
Abstract = {For decades, it was unknown how electron-bifurcating systems
in nature prevented energy-wasting short-circuiting
reactions that have large driving forces, so synthetic
electron-bifurcating molecular machines could not be
designed and built. The underpinning free-energy landscapes
for electron bifurcation were also enigmatic. We predict
that a simple and universal free-energy landscape enables
electron bifurcation, and we show that it enables
high-efficiency bifurcation with limited short-circuiting
(the EB scheme). The landscape relies on steep free-energy
slopes in the two redox branches to insulate against
short-circuiting using an electron occupancy blockade
effect, without relying on nuanced changes in the
microscopic rate constants for the short-circuiting
reactions. The EB scheme thus unifies a body of observations
on biological catalysis and energy conversion, and the
scheme provides a blueprint to guide future campaigns to
establish synthetic electron bifurcation
machines.},
Doi = {10.1073/pnas.2010815117},
Key = {fds351428}
}
@article{fds346844,
Author = {Banziger, SD and Li, X and Valdiviezo, J and Zeller, M and Zhang, P and Beratan, DN and Rubtsov, IV and Ren, T},
Title = {Unsymmetrical Bis-Alkynyl Complexes Based on
Co(III)(cyclam): Synthesis, Ultrafast Charge Separation, and
Analysis.},
Journal = {Inorganic chemistry},
Volume = {58},
Number = {22},
Pages = {15487-15497},
Year = {2019},
Month = {November},
url = {http://dx.doi.org/10.1021/acs.inorgchem.9b02557},
Abstract = {Donor-bridge-acceptor (D-B-A) systems with a polarizable
bridge can afford rapid photoinduced electron transfer
dynamics that may be susceptible to rate modulation by
infrared excitation. We describe the synthesis,
characterization, and electronic structure of a class of
readily assembled D-B-A structures linked by a cobalt cyclam
bridge. The reaction between [Co(cyclam)Cl<sub>2</sub>]Cl
and 4-ethynyl-<i>N</i>-isopropyl-1,8-naphthalimide
(HC<sub>2</sub>NAP<sup>iPr</sup>) yields
[Co(cyclam)(C<sub>2</sub>NAP<sup>iPr</sup>)Cl]Cl (<b>1</b>),
which reacts with LiC<sub>2</sub>Y at -78 °C to afford
[Co(cyclam)(C<sub>2</sub>NAP<sup>iPr</sup>)(C<sub>2</sub>D)]Cl
with D as C<sub>6</sub>H<sub>4</sub>-4-NMe<sub>2</sub>
(<b>2a</b>), NAP<sup>iPr</sup> (<b>2b</b>), Ph (<b>2c</b>),
and C<sub>6</sub>H<sub>4</sub>-4-N(4-MeOPh)<sub>2</sub>
(<b>2d</b>). Molecular structures of <b>1</b> and <b>2a</b>
were established using single-crystal X-ray diffraction,
while the redox properties and fluorescence profiles of
compounds <b>1</b> and <b>2</b> were examined using
voltammetric and steady-state emission techniques,
respectively. The electronic structures and photophysical
properties of these compounds were studied using density
functional theory and time-dependent density functional
theory methods. The excited-state dynamics of compounds
<b>1</b>, <b>2a</b>, and <b>2d</b> were explored using
femtosecond transient absorption spectroscopy with 400 nm
excitation and detection in both the visible and mid-IR
spectral regions. Formation of a long-lived excited state
was complete within 20 ps of excitation in all three
compounds. Ultrafast spectral changes observed in <b>2a</b>
and <b>2d</b> within the first 20 ps indicated the formation
of a charge separated state (CS state, D<sup>+</sup>-B-A<sup>-</sup>)
with characteristic times of less than 0.1 and 0.25 ps,
respectively. The CS state undergoes rapid charge
recombination (8 ps in <b>2a</b> and 4 ps in <b>2d</b>). The
CS dynamics is facilitated by the Co center, which mixes the
bright NAP-centered electronic state with a pure CS state.
The mixing strength depends on the donor energetics and
conformation, which significantly influences the charge
transfer dynamics in <b>2a</b> and <b>2d</b>.},
Doi = {10.1021/acs.inorgchem.9b02557},
Key = {fds346844}
}
@article{fds231998,
Author = {Kumar, K and Kurnikov, IV and Beratan, DN and Waldeck, DH and Zimmt,
MB},
Title = {Use of modern electron transfer theories to determine
electronic coupling matrix elements in intramolecular
systems},
Journal = {Journal of Physical Chemistry A},
Volume = {102},
Number = {28},
Pages = {5529-5541},
Publisher = {American Chemical Society (ACS)},
Year = {1998},
Month = {July},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcafh/1998/102/i28/pdf/jp980113t.pdf},
Abstract = {The dependence of the donor/acceptor electronic coupling on
the topology of donor-bridge-acceptor (DBA) molecules is
probed experimentally and theoretically. The temperature
dependence of photoinduced electron-transfer rate constants
is analyzed with a semiclassical electron-transfer model to
extract the donor/acceptor electronic coupling matrix
elements |V| and the low-frequency reorganization energy at
295 K, λ0(295 K), for four rigid DBA molecules. The
sensitivity of the electronic coupling |V| to the models and
parameters used to fit the data are extensively
investigated. The treatment of the low-frequency
reorganization energy's temperature dependence has a
significant impact on the analysis. The identity of the
principal coupling pathways is determined for molecular
linkages that propagate symmetry allowed donor/acceptor
interactions and molecular linkages that propagate symmetry
forbidden donor/acceptor interactions. For the symmetry
forbidden case, these analyses demonstrate that solvent
molecules provide the dominant coupling pathway in the
nine-bond bridge, C-shaped molecule 2 but do not
significantly influence |V| across the seven-bond, linear
bridge in 1.},
Doi = {10.1021/jp980113t},
Key = {fds231998}
}
@article{fds231847,
Author = {Antoniou, P and Ma, Z and Zhang, P and Beratan, DN and Skourtis,
SS},
Title = {Vibrational control of electron-transfer reactions: a
feasibility study for the fast coherent transfer
regime.},
Journal = {Physical chemistry chemical physics : PCCP},
Volume = {17},
Number = {46},
Pages = {30854-30866},
Year = {2015},
Month = {December},
ISSN = {1463-9076},
url = {http://dx.doi.org/10.1039/c5cp00610d},
Abstract = {Molecular vibrations and electron-vibrational interactions
are central to the control of biomolecular electron and
energy-transfer rates. The vibrational control of molecular
electron-transfer reactions by infrared pulses may enable
the precise probing of electronic-vibrational interactions
and of their roles in determining electron-transfer
mechanisms. This type of electron-transfer rate control is
advantageous because it does not alter the electronic state
of the molecular electron-transfer system or irreversibly
change its molecular structure. For bridge-mediated
electron-transfer reactions, infrared (vibrational)
excitation of the bridge linking the electron donor to the
electron acceptor was suggested as being capable of
influencing the electron-transfer rate by modulating the
bridge-mediated donor-to-acceptor electronic coupling. This
kind of electron-transfer experiment has been realized,
demonstrating that bridge-mediated electron-transfer rates
can be changed by exciting vibrational modes of the bridge.
Here, we use simple models and ab initio computations to
explore the physical constraints on one's ability to
vibrationally perturb electron-transfer rates using infrared
excitation. These constraints stem from the nature of
molecular vibrational spectra, the strengths of the
electron-vibrational coupling, and the interaction between
molecular vibrations and infrared radiation. With these
constraints in mind, we suggest parameter regimes and
molecular architectures that may enhance the vibrational
control of electron transfer for fast coherent
electron-transfer reactions.},
Doi = {10.1039/c5cp00610d},
Key = {fds231847}
}
@article{fds342308,
Author = {Michaeli, K and Beratan, DN and Waldeck, DH and Naaman,
R},
Title = {Voltage-induced long-range coherent electron transfer
through organic molecules.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {116},
Number = {13},
Pages = {5931-5936},
Year = {2019},
Month = {March},
url = {http://dx.doi.org/10.1073/pnas.1816956116},
Abstract = {Biological structures rely on kinetically tuned charge
transfer reactions for energy conversion, biocatalysis, and
signaling as well as for oxidative damage repair. Unlike
man-made electrical circuitry, which uses metals and
semiconductors to direct current flow, charge transfer in
living systems proceeds via biomolecules that are nominally
insulating. Long-distance charge transport, which is
observed routinely in nucleic acids, peptides, and proteins,
is believed to arise from a sequence of thermally activated
hopping steps. However, a growing number of experiments find
limited temperature dependence for electron transfer over
tens of nanometers. To account for these observations, we
propose a temperature-independent mechanism based on the
electric potential difference that builds up along the
molecule as a precursor of electron transfer. Specifically,
the voltage changes the nature of the electronic states away
from being sharply localized so that efficient resonant
tunneling across long distances becomes possible without
thermal assistance. This mechanism is general and is
expected to be operative in molecules where the electronic
states densely fill a wide energy window (on the scale of
electronvolts) above or below the gap between the
highest-occupied molecular orbital (HOMO) and the lowest
unoccupied molecular orbital (LUMO). We show that this
effect can explain the temperature-independent charge
transport through DNA and the strongly voltage-dependent
currents that are measured through organic semiconductors
and peptides.},
Doi = {10.1073/pnas.1816956116},
Key = {fds342308}
}
@article{fds232022,
Author = {Lin, J and Balabin, IA and Beratan, DN},
Title = {Water -mediated tunneling between proteins},
Journal = {Science},
Volume = {310},
Number = {5752},
Pages = {1311-1313},
Year = {2005},
url = {http://www.sciencemag.org/cgi/reprint/310/5752/1311.pdf},
Abstract = {Structured water molecules near redox cofactors were found
recently to accelerate electron-transfer (ET) kinetics in
several systems. Theoretical study of interprotein electron
transfer across an aqueous interface reveals three
distinctive electronic coupling mechanisms that we describe
here: (i) a protein-mediated regime when the two proteins
are in van der Waals contact; (ii) a structured
water-mediated regime featuring anomalously weak distance
decay at relatively close protein-protein contact distances;
and (iii) a bulk water-mediated regime at large distances.
Our analysis explains a range of otherwise puzzling
biological ET kinetic data and provides a framework for
including explicit water-mediated tunneling effects on ET
kinetics.},
Doi = {10.1126/science.1118316},
Key = {fds232022}
}
@article{fds231986,
Author = {Risser, SM and Beratan, DN},
Title = {What is the anharmonicity of a molecule's electronic wave
function?},
Journal = {Journal of Physical Chemistry},
Volume = {99},
Number = {7},
Pages = {1935-1942},
Publisher = {American Chemical Society (ACS)},
Year = {1995},
Month = {January},
ISSN = {0022-3654},
url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1995/99/i07/pdf/j100007a024.pdf},
Abstract = {The dependence of a classical spring's hyperpolarizabilities
on its anharmonicity constants is known, defining a simple
structure-property relationship. Corresponding
structure-property relationships for the electronic
hyperpolarizabilities of quantum many-particle systems,
molecules, remain elusive. The quasi-harmonic behavior of
molecular electronic polarization is disguised by the
Coulombic nature of the interaction potential. Yet, to the
extent that a perturbation theory description of electronic
hyperpolarizability is appropriate, the quantum electronic
hyperpolarizability problem maps onto a single-particle
effective anharmonic oscillator hamiltonian. Here, we derive
this relationship, which provides a means of establishing
the effective anharmonic oscillator constants for a
molecule. We calculate these electronic anharmonicities
analytically and show results for some simple hamiltonians.
One barrier to the design of chemical chromophores with
tailored nonlinear optical coefficients is an understanding
of how molecular structure influences hyperpolarizability.
Restating the problem in terms of anharmonicities
demystifies the source and magnitude of the electronic
hyperpolarizabilities. © 1995 American Chemical
Society.},
Doi = {10.1021/j100007a024},
Key = {fds231986}
}
@article{fds314840,
Author = {Zheng, L and Polizzi, NF and Dave, AR and Migliore, A and Beratan,
DN},
Title = {Where Is the Electronic Oscillator Strength? Mapping
Oscillator Strength across Molecular Absorption
Spectra.},
Journal = {The journal of physical chemistry. A},
Volume = {120},
Number = {11},
Pages = {1933-1943},
Year = {2016},
Month = {March},
ISSN = {1089-5639},
url = {http://dx.doi.org/10.1021/acs.jpca.6b00692},
Abstract = {The effectiveness of solar energy capture and conversion
materials derives from their ability to absorb light and to
transform the excitation energy into energy stored in free
carriers or chemical bonds. The Thomas-Reiche-Kuhn (TRK) sum
rule mandates that the integrated (electronic) oscillator
strength of an absorber equals the total number of electrons
in the structure. Typical molecular chromophores place only
about 1% of their oscillator strength in the UV-vis window,
so individual chromophores operate at about 1% of their
theoretical limit. We explore the distribution of oscillator
strength as a function of excitation energy to understand
this circumstance. To this aim, we use familiar
independent-electron model Hamiltonians as well as
first-principles electronic structure methods. While model
Hamiltonians capture the qualitative electronic spectra
associated with π electron chromophores, these Hamiltonians
mistakenly focus the oscillator strength in the fewest
low-energy transitions. Advanced electronic structure
methods, in contrast, spread the oscillator strength over a
very wide excitation energy range, including transitions to
Rydberg and continuum states, consistent with experiment.
Our analysis rationalizes the low oscillator strength in the
UV-vis spectral region in molecules, a step toward the goal
of oscillator strength manipulation and focusing.},
Doi = {10.1021/acs.jpca.6b00692},
Key = {fds314840}
}
@misc{fds370661,
Author = {Beratan, D},
Title = {Where's my oscillator strength?},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {255},
Year = {2018},
Key = {fds370661}
}
@article{fds343568,
Author = {Beratan, DN},
Title = {Why Are DNA and Protein Electron Transfer So
Different?},
Journal = {Annual review of physical chemistry},
Volume = {70},
Pages = {71-97},
Year = {2019},
Month = {June},
url = {http://dx.doi.org/10.1146/annurev-physchem-042018-052353},
Abstract = {The corpus of electron transfer (ET) theory provides
considerable power to describe the kinetics and dynamics of
electron flow at the nanoscale. How is it, then, that
nucleic acid (NA) ET continues to surprise, while
protein-mediated ET is relatively free of mechanistic
bombshells? I suggest that this difference originates in the
distinct electronic energy landscapes for the two classes of
reactions. In proteins, the donor/acceptor-to-bridge energy
gap is typically several-fold larger than in NAs. NA ET can
access tunneling, hopping, and resonant transport among the
bases, and fluctuations can enable switching among
mechanisms; protein ET is restricted to tunneling among
redox active cofactors and, under strongly oxidizing
conditions, a few privileged amino acid side chains. This
review aims to provide conceptual unity to DNA and protein
ET reaction mechanisms. The establishment of a unified
mechanistic framework enabled the successful design of NA
experiments that switch electronic coherence effects on and
off for ET processes on a length scale of multiple
nanometers and promises to provide inroads to directing and
detecting charge flow in soft-wet matter.},
Doi = {10.1146/annurev-physchem-042018-052353},
Key = {fds343568}
}
@article{fds357539,
Author = {Ru, X and Crane, BR and Zhang, P and Beratan, DN},
Title = {Why Do Most Aromatics Fail to Support Hole Hopping in the
Cytochrome c Peroxidase-Cytochrome c
Complex?},
Journal = {The journal of physical chemistry. B},
Volume = {125},
Number = {28},
Pages = {7763-7773},
Year = {2021},
Month = {July},
url = {http://dx.doi.org/10.1021/acs.jpcb.1c05064},
Abstract = {Electron transport through aromatic species (especially
tryptophan and tyrosine) plays a central role in water
splitting, redox signaling, oxidative damage protection, and
bioenergetics. The cytochrome <i>c</i> peroxidase
(CcP)-cytochrome <i>c</i> (Cc) complex (CcP:Cc) is used
widely to study interprotein electron transfer (ET)
mechanisms. Tryptophan 191 (Trp191) of CcP supports hole
hopping charge recombination in the CcP:Cc complex.
Experimental studies find that when Trp191 is substituted by
tyrosine, phenylalanine, or redox-active aniline derivatives
bound in the W191G cavity, enzymatic activity and charge
recombination rates both decrease. Theoretical analysis of
these CcP:Cc complexes finds that the ET kinetics depend
strongly on the chemistry of the modified Trp site. The
computed electronic couplings in the W191F and W191G species
are orders of magnitude smaller than in the native protein,
due largely to the absence of a hopping intermediate and the
large tunneling distance. Small molecules bound in the W191G
cavity are weakly coupled electronically to the Cc heme, and
the structural disorder of the guest molecule in the binding
pocket may contribute further to the lack of enzymatic
activity. The couplings in W191Y are not substantially
weakened compared to the native species, but the redox
potential difference for tyrosine vs tryptophan oxidation
accounts for the slower rate in the Tyr mutant. Thus,
theoretical analysis explains why only the native Trp
supports rapid hole hopping in the CcP:Cc complex. Favorable
free energies and electronic couplings are essential for
establishing an efficient hole hopping relay in this
protein-protein complex.},
Doi = {10.1021/acs.jpcb.1c05064},
Key = {fds357539}
}