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Publications of Weitao Yang    :chronological  combined  bibtex listing:

Books

  1. W. Yang, Special issue: Symposium on density functional and applications (Part I of II), Int. J. Quantum Chem., vol. 69 (1998)
  2. R.G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules (1989), Oxford University Press, New York

Papers Accepted

  1. San-Huang Ke, Harold Baranger and Weitao Yang, "Molecular Conductance: Chemical Trends of Anchoring Groups", J. Am. Chem. Soc. (2004)
  2. Aron Cohen, Qin Wu and Weitao Yang, "Calculation of Nuclear Magnetic Resonance Sheilding Constants Using Potential Based Methods", Chem. Phys. Lett. (2004)

Journal Articles

  1. J. Contreras-Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J. P. Piquemal, D. N. Beratan, and W. T. Yang, Nciplot: A program for plotting noncovalent interaction regions., Journal of Chemical Theory and Computation no. 7 (2011), pp. 625-632
  2. J. Contreras-Garcia, W. T. Yang, and E. R. Johnson, Analysis of hydrogen-bond interaction potentials from the electron density: Integration of noncovalent interaction regions., Journal of Physical Chemistry A no. 115 (2011), pp. 12983-12990
  3. G. L. Cui and W. T. Yang, Conical intersections in solution: Formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method, Journal of Chemical Physics no. 134 (2011), pp. 204115
  4. D. H. Ess, E. R. Johnson, X. Q. Hu, and W. T. Yang, Singlet-triplet energy gaps for diradicals from fractional-spin density-functional theory, Journal of Physical Chemistry A no. 115 (2011), pp. 76-83
  5. X. Q. Hu, H. Hu, J. A. Melvin, K. W. Clancy, D. G. McCafferty, and W. T. Yang, Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: A qm/mm simulation, Journal of the American Chemical Society no. 133 (2011), pp. 478-485
  6. N. Shenvi, J. E. Subotnik, and W. T. Yang, Simultaneous-trajectory surface hopping: A parameterfree algorithm for implementing decoherence in nonadiabatic dynamics, Journal of Chemical Physics no. 134 (2011), pp. 144102
  7. N. Shenvi, J. E. Subotnik, and W. T. Yang, Phase-corrected surface hopping: Correcting the phase evolution of the electronic wavefunction, Journal of Chemical Physics no. 135 (2011), pp. 024101
  8. Z. G. Sun and W. T. Yang, An exact short-time solver for the time-dependent schrodinger equation, Journal of Chemical Physics no. 134 (2011), pp. 041101
  9. E. S. Tam, J. J. Parks, W. W. Shum, Y. W. Zhong, M. B. Santiago-Berrios, X. Zheng, W. T. Yang, G. K. L. Chan, H. D. Abruna, and D. C. Ralph, Single-molecule conductance of pyridine-terminated dithienylethene switch molecules, ACS Nano no. 5 (2011), pp. 5115-5123
  10. P. Wu, X. Q. Hu, and W. T. Yang, lambda-metadynamics approach to compute absolute solvation free energy, Journal of Physical Chemistry Letters no. 2 (2011), pp. 2099-2103
  11. X. Zheng, A. J. Cohen, P. Mori-Sanchez, X. Q. Hu, and W. T. Yang, Improving band gap prediction in density functional theory from molecules to solids, Physical Review Letters no. 107 (2011), pp. 026403
  12. I. A. Balabin, W. T. Yang, and D. N. Beratan, Coarse-grained modeling of allosteric regulation in protein receptors, Proceedings of the National Academy of Sciences of the United States of America no. 34 (2009), pp. 14253-14258
  13. F. A. Bulat, L. Couchman, and W. T. Yang, Contact geometry and conductance of crossed nanotube junctions under pressure, Nano Letters, vol. 9 no. 5 (2009), pp. 1759-1763
  14. A. J. Cohen, P. Mori-Sanchez, and W. T. Yang, Second-order perturbation theory with fractional charges and fractional spins, Journal of Chemical Theory and Computation, vol. 5 no. 5 (2009), pp. 786–792
  15. X. Q. Hu, D. N. Beratan, and W. T. Yang, A gradient-directed monte carlo method for global optimization in a discrete space: Application to protein sequence design and folding, Journal of Chemical Physics, vol. 131 no. 15 (2009), pp. 154117
  16. H. Hu and W. T. Yang, Development and application of ab initio qm/mm methods for mechanistic simulation of reactions in solution and in enzymes, Journal of Molecular Structure-Theochem, vol. 898 no. 1-3 (2009), pp. 17-30
  17. X. Q. Hu, D. N. Beratan, and W. T. Yang, Emergent strategies for inverse molecular design, Science in China Series B-Chemistry, vol. 52 no. 11 (2009), pp. 1769-1776
  18. A. C. Kasper, E. J. Moon, X. Q. Hu, Y. Park, C. M. Wooten, H. Kim, W. T. Yang, M. W. Dewhirst, and J. Y. Hong, Analysis of hif-1 inhibition by manassantin a and analogues with modified tetrahydrofuran configurations, Bioorganic & Medicinal Chemistry Letters, vol. 19 no. 14 (2009), pp. 3783-3786
  19. S. H. Ke, M. Yang, S. Curtarolo, and H. U. Baranger, “Thermopower of molecular junctions: An ab initio study, Nano Letters, vol. 9 no. 3 (2009), pp. 1011-1014
  20. Z. Li, C. Y. Wang, S. H. Ke, and W. Yang, “First-principles study for transport properties of defective carbon nanotubes with oxygen adsorption, European Physical Journal B, vol. 69 no. 3 (2009), pp. 375-382
  21. P. Mori-Sanchez, A. J. Cohen, and W. T. Yang, “Discontinuous nature of the exchange-correlation functional in strongly correlated systems, Physical Review Letters, vol. 102 (2009), pp. 066403
  22. J. M. Parks, H. Hu, J. Rudolph, and W. T. Yang, Mechanism of cdc25b phosphatase with the small molecule substrate p-nitrophenyl phosphate from qm/mm-mfep calculations, Journal of Physical Chemistry B, vol. 113 no. 15 (2009), pp. 5217-5224
  23. B. C. Rinderspacher, J. Andzelm, A. Rawlett, J. Dougherty, D. N. Beratan, and W. T. Yang, Discrete optimization of electronic hyperpolarizabilities in a chemical subspace, Journal of Chemical Theory and Computation, vol. 5 no. 12 (2009), pp. 3321-3329
  24. X. C. Zeng, H. Hu, X. Q. Hu, and W. T. Yang, Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method, Journal of Chemical Physics, vol. 130 no. 16 (2009), pp. 164111
  25. T. Heaton-Burgess and W. T. Yang, Optimized effective potentials from arbitrary basis sets, Journal of Chemical Physics, vol. 129 (November, 2008), pp. 194102
  26. H. Hu, A. Boone, and W. T. Yang, Mechanism of omp decarboxylation in orotidine 5 ’-monophosphate decarboxylase, Journal of the American Chemical Society, vol. 130 (November, 2008), pp. 14493-14503
  27. D. Balamurugan, W. T. Yang, and D. N. Beratan, Exploring chemical space with discrete, gradient, and hybrid optimization methods, Journal of Chemical Physics, vol. 129 (November, 2008), pp. 174105
  28. E. R. Johnson, P. Mori-Sanchez, A. J. Cohen, and W. T. Yang, Delocalization errors in density functionals and implications for main-group thermochemistry, Journal of Chemical Physics, vol. 129 (November, 2008), pp. 204112
  29. S. Keinan, M. J. Therien, D. N. Beratan, and W. T. Yang, Molecular design of porphyrin-based nonlinear optical materials, Journal of Physical Chemistry A, vol. 112 (November, 2008), pp. 12203-12207
  30. S. H. Ke, W. T. Yang, and H. U. Baranger, Quantum-interference-controlled molecular electronics, Nano Letters, vol. 8 (October, 2008), pp. 3257-3261
  31. J. M. Parks, H. Hu, A. J. Cohen, and W. T. Yang, A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes, Journal of Chemical Physics, vol. 129 (October, 2008), pp. 154106
  32. A. J. Cohen, P. Mori-Sanchez, and W. T. Yang, Fractional spins and static correlation error in density functional theory, Journal of Chemical Physics, vol. 129 (September, 2008), pp. 121104
  33. S. Keinan, W. D. Paquette, J. J. Skoko, D. N. Beratan, W. T. Yang, S. Shinde, P. A. Johnston, J. S. Lazo, and P. Wipf, Computational design, synthesis and biological evaluation of para-quinone-based inhibitors for redox regulation of the dual-specificity phosphatase cdc25b, Organic & Biomolecular Chemistry, vol. 6 (September, 2008), pp. 3256-3263
  34. D. Q. Xiao, F. A. Bulat, W. T. Yang, and D. N. Beratan, A donor-nanotube paradigm for nonlinear optical materials, Nano Letters, vol. 8 (September, 2008), pp. 2814-2818
  35. A. J. Cohen, P. Mori-Sanchez, and W. T. Yang, Insights into current limitations of density functional theory, Science, vol. 321 (August, 2008), pp. 792-794
  36. K. Fujimoto and W. T. Yang, Density-fragment interaction approach for quantum-mechanical/molecularmechanical calculations with application to the excited states of a mg2+-sensitive dye, Journal of Chemical Physics, vol. 129 (August, 2008), pp. 054102
  37. X. Q. Hu, D. N. Beratan, and W. T. Yang, A gradient-directed monte carlo approach to molecular design, Journal of Chemical Physics, vol. 129 (August, 2008), pp. 064102
  38. Z. Li, C. Y. Wang, X. Zhang, S. H. Ke, and W. T. Yang, Transport properties of an armchair carbon nanotube with a double vacancy under stretching, Journal of Physics-Condensed Matter, vol. 20 (August, 2008), pp. 345225
  39. S. K. Burger and W. T. Yang, Linear-scaling quantum calculations using non-orthogonal localized molecular orbitals, Journal of Physics-Condensed Matter, vol. 20 (July, 2008), pp. 294209
  40. D. Q. Xiao, W. T. Yang, and D. N. Beratan, Inverse molecular design in a tight-binding framework, Journal of Chemical Physics, vol. 129 (July, 2008), pp. 044106
  41. P. Mori-Sanchez, A. J. Cohen, and W. T. Yang, Localization and delocalization errors in density functional theory and implications for band-gap prediction, Physical Review Letters, vol. 100 (April, 2008), pp. 146401
  42. T. Heaton-Burgess, A. J. Cohen, W. T. Yang, and E. R. Davidson, Size extensivity of the direct optimized effective potential method, Journal of Chemical Physics, vol. 128 (March, 2008), pp. 114702
  43. A. J. Cohen, P. Mori-Sanchez, and W. T. Yang, Fractional charge perspective on the band gap in density-functional theory, Physical Review B, vol. 77 (March, 2008), pp. 115123
  44. J. M. Parks, R. K. Kondru, H. Hu, D. N. Beratan, and W. T. Yang, Hepatitis c virus ns5b polymerase: Qm/mm calculations show the important role of the internal energy in ligand binding, Journal of Physical Chemistry B, vol. 112 (March, 2008), pp. 3168-3176
  45. X. C. Zeng, H. Hu, X. Q. Hu, A. J. Cohen, and W. T. Yang, Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach, Journal of Chemical Physics, vol. 128 (March, 2008), pp. 124510
  46. H. Hu, Z. Y. Lu, J. M. Parks, S. K. Burger, and W. T. Yang, Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface, Journal of Chemical Physics, vol. 128 (January, 2008), pp. 034105
  47. H. Hu and W. T. Yang, Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods, Annual Review of Physical Chemistry, vol. 59 (2008), pp. 573-601
  48. H. Lee, K. W. Kim, J. Park, H. Kim, S. Kim, D. Kim, X. Q. Hu, W. T. Yang, and J. Y. Hong, A general strategy for construction of both 2,6-cis-and 2,6-trans-disubstituted tetrahydropyrans: Substrate-controlled asymmetric total synthesis of (+)-scanlonenyne, Angewandte Chemie-International Edition, vol. 47 no. 22 (2008), pp. 4200-4203
  49. S. K. Burger and W. Yang, Sequential quadratic programming method for determining the minimum energy path, J. Chem. Phys., vol. 127 (2007), pp. 164107/1-164107/7
  50. A. J. Cohen, P. Mori-Sanchez, and W. Yang, Assessment and formal properties of exchange-correlation functionals constructed from the adiabatic connection, J. Chem. Phys., vol. 127 no. 3 (2007), pp. 034101-034101/03410114
  51. A. J. Cohen, P. Mori-Sanchez, and W. Yang, Development of exchange-correlation functionals with minimal many-electron self-interaction error, J. Chem. Phys., vol. 126 (2007), pp. 191109/1-191109/5
  52. T. Heaton-Burgess, P. Ayers, and W. Yang, Spin-potential functional formalism for current-carrying noncollinear magnetic systems, Physical Review Letters, vol. 98 (2007), pp. 36403
  53. T. Heaton-Burgess, F. A. Bulat, and W. Yang, Optimized effective potentials in finite basis sets, Phys. Rev. Lett., vol. 98 (2007), pp. 256401/1-256401/4
  54. T. Hori, H. Takahashi, S. I. Furukawa, M. Nakano, and W. Yang, Computational study on the relative acidity of acetic acid by the qm/mm method combined with the theory of energy representation, Journal of Physical Chemistry B no. 111 (2007), pp. 581-588
  55. H. Hu, Z. Lu, and W. Yang, Fitting molecular electrostatic potentials from quantum mechanical calculations, Journal of Chemical Theory and Computation, vol. 3 (2007), pp. 1004-1013
  56. H. Hu, Z. Y. Lu, and W. T. Yang, Qm/mm minimum free-energy path: Methodology and application to triosephosphate isomerase, Journal of Chemical Theory and Computation, vol. 3 (2007), pp. 390-406
  57. H. Hu, Z. Lu, M. Elstner, J. Hermans, and W. Yang, Simulating water with the self-consistent-charge density functional tight binding method: From molecular clusters to the liquid state, Journal of Physical Chemistry A, vol. 111 (2007), pp. 5685-5691
  58. S.-H. Ke, H. U. Baranger, and W. Yang, Electron transport through single conjugated organic molecules: Basis set effects in ab initio calculations, Journal of Chemical Physics, vol. 127 (2007), pp. 144107/1-144107/6
  59. S.-H. Ke, H. U. Baranger, and W. Yang, Contact transparency of nanotube-molecule-nanotube junctions, Physical Review Letters, vol. 99 (2007), pp. 146802/1-146802/4
  60. S.-H. Ke, H. U. Baranger, and W. Yang, Role of the exchange-correlation potential in ab initio electron transport calculations, Journal of Chemical Physics, vol. 126 (2007), pp. 201102/1-201102/4
  61. S. Keinan, X. Q. Hu, D. N. Beratan, and W. T. Yang, Designing molecules with optimal properties using the linear combination of atomic potentials approach in an am1 semiempirical framework, Journal of Physical Chemistry A, vol. 111 (2007), pp. 176-181
  62. R. Liu, S.-H. Ke, W. Yang, and H. U. Baranger, Cobaltocene as a spin filter, Journal of Chemical Physics, vol. 127 (2007), pp. 141104/1-141104/4
  63. W. Wang, J. Qiao, L. D. Wang, L. A. Duan, D. Q. Zhang, W. T. Yang, and Y. Qiu, Synthesis, structures, and optical properties of cadmium iodide/phenethylamine hybrid materials with controlled structures and emissions, Inorganic Chemistry, vol. 46 (2007), pp. 10252-10260
  64. F. A. Bulat, T. Heaton-Burgess, A. J. Cohen, and W. T. Yang, Optimized effective potentials from electron densities in finite basis sets, Journal of Chemical Physics, vol. 127 (2007), pp. 174101
  65. Dennis Ulmo, Hong Jiang, Weitao Yang and Harold Baranger, "Landau Fermi Liquid Picture of Spin Density Functional Theory: Strutinsky Approach to Quantum Dots", Phys. Rev. B., Rapid Communication, vol. 71 (2005), pp. 201310/1-201310/4
  66. San-Huang Ke, Harold Baranger and Weitao Yang, "Contact Atomic Structure and Electron Transport Through Molecules", J. Chem. Phys., vol. 122 (2005), pp. 114502/1-114502/7
  67. Hong Jiang, Dennis Ulmo, Weitao Yang and Harold Baranger, "Scrambling and Gate Effects in Realistic Quantum Dots", Phys. Rev. B, vol. 71 (2005), pp. 085313/1-085313/6
  68. Rui Liu, San-Huang Ke, Harold Baranger and Weitao Yang, "Intermolecular Effect in Molecular Electronics", J. Chem. Phys., vol. 122 (2005), pp. 044703/1-044703/4
  69. San-Huang Ke, Harold Baranger and Weitao Yang, "Electron Transport Through Molecules: Gate Induced Polarization and Potential Shift", Phys. Rev. B, vol. 71 (2005), pp. 113401/1-113401/4
  70. Rui Liu, San-Huang Ke, Harold Baranger and Weitao Yang, Organometallic spintronics: Dibobaltocene switch, Nano Lett. (Communication), vol. 5 (2005), pp. 1959-1962
  71. Paula Mor-Sanchez, Qin Wu and Weitao Yang, Orbital-dependent correlation energy in density-functional theory based on a second-order perturbation approach: success and failure, J. Chem. Phys., vol. 123 (2005), pp. 062204/1-062204/14
  72. San-Huang Ke, Rui Liu, Harold U. Baranger and Weitao Yang, Models of electrodes and contacts in molecular electronics, J. Chem. Phys., vol. 123 (2005), pp. 114701/1-114701/8
  73. G. Andres Cisneros, Haiyan Liu, Zhenyu Lu and Weitao Yang, Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain of replicas" methods, J. Chem. Phys., vol. 122 (2005), pp. 114502/1-114502/7
  74. Qin Wu, Aron J. Cohen and Weitao Yang, Excitation energies from time-dependent density functional theory with accurate exchange-correlation potentials, Mol. Phys., vol. 103 (2005), pp. 711-717
  75. Felipe A. Bulat, Alejandro Toro-Labbe, Benoit Champagne, Bernard Kirtman and Weitao Yang, Dft (hyper)polarizabilities of push-pull pi-conjugated systems, treatment of exact exchange and role correlation, J. Chem. Phys., vol. 123 (2005), pp. 014319/1-014319/7
  76. Stephanie A. Getty, Chaiwat Engtrakul, Lixin Wang, Rui Liu, San-Huang Ke, Harold U. Baranger, Weitao Yang, Michal S. Fuhrer and Lawrence R. Sita, Near-perfect conduction through a ferrocence-based molecular wire, Phys. Rev. B., vol. 71 (2005), pp. 241401 (R)/1-241401(R)/4
  77. Hao Hu and Weitao Yang, Dual-topology-dual-coordinate free energy simulation using qm/mm force field, J. Chem. Phys. Communication, vol. 123 (2005), pp. 041102/1-041102/4
  78. Qin Wu, Aron J. Cohen and Weitao Yang, Analytic energy gradients of the optimized effective potential method, J. Chem. Phys., vol. 123 no. 134111/1-134111/10 (2005)
  79. J. Sohn, J. Parks, P. Burham, G. Brown, K. Kristjansdottir, A. Safi, H. Edelsbrunner, W. Yang and J. Rudolph, Experimental Validation of the Docking Orientation of Cdc25 with its Cdk2/CycA Protein Substrate, Biochemistry, vol. 44 (2005), pp. 16563-16573
  80. W. Yang, P. Ayers and Q. Wu, "Potential Functionals: Dual to Density Functionals and Solution to the v-representability problem", Phys. Rev. Lett., vol. 92 (2004), pp. 146404-1-146404-4
  81. Zhenyu Lu, Wieslaw Nowak, Gwangrog Lee, Piotr Marszalek and Wietao Yang, "Elastic Properties of Single Amylose Chains in Water", J. Am. Chem. Soc., vol. 126 (2004), pp. 9033-9041
  82. Hiayan Liu, Zhenyu Lu, G. Andres Cisneros and Weitao Yang, "Parallel Iterative Reaction Path Optimization in ab initio Quantum Mechanical/Molecular Mechanical Modeling of Enzyme Reaction", J. Chem. Phys., vol. 121 (2004), pp. 697-706
  83. Zhenyu Lu and Weitao Yang, "Reaction Path Potential for Complex Systems Derived From ab initioqm/mm Calculations", J. Chem. Phys., vol. 121 (2004), pp. 89-100
  84. Mingliang Wang, Zhenyu Lu and Weitao Yang, "Transmission Coefficient Calculation for Proton Transfer in Triosephosphate Isomerase on the Reaction Path Potential Generated from ab initio qm/mm Calculations", J. Chem. Phys., vol. 121 (2004), pp. 101-107
  85. Hong Jiang and Weitao Yang, "Conjugate-gradient Optimization Method for Orbital-free Density Functional Calculations", J. Chem. Phys., vol. 121 (2004), pp. 2030-2036
  86. Gerardo Cisneros, Min Wang, Peter Silinski, Michael C. Fitzgerald and Weitao Yang, "The Protein Backbone Makes Important Contributions to 4-oxalocrotonate tautomerase Enzyme Catalysis: Understanding from Theory and Experiment", Biochemistry, vol. 43 (2004), pp. 6885-6889
  87. Qin Wu, Paul W. Ayers, and Weitao Yang, Density functional theory calculations with correct long range potentials, J. Chem. Phys., vol. 119 (2003), pp. 2978-2990
  88. Qin Wu and Weitao Yang, A direct optimization method for calculating density functionals and exchange correlation potentials from electron densities, J. Chem. Phys., vol. 118 no. 6 (2003), pp. 2498-2509
  89. Hong Jiang, Harold U Baranger, and Weitao Yang, Spin and conductance-peak-spacing distributions in large quantum dots: A density functional theory study, Phys. Rev. Lett, vol. 90 no. 2 (2003), pp. 02806-1-02806-4
  90. G. Andres Cisneros, Haiyan Liu, Yinkai Zhang, and Weitao Yang, Ab initio qm/mm study shows that there is no general acid in the reaction catalized by 4-oxalocrotonate tautomerase, J. Am. Chem. Soc., vol. 125 (2003), pp. 10384-10393
  91. San-Huang Ke, Harold U. Baranger, and Weitao Yang, Additional energies of fullerenes and carbon nanotubes as quantum dots: the role of symmetry, Phys. Rev. Lett., vol. 91 no. 11 (2003), pp. 116803-1-116803-4
  92. Jun ya Hasegawa, Mayumi Ishida, Hiroshi Nakatsuji, Zhenyu Lu, and Weitao Yang, Energetics of the electron transfer from bacteriopheophytin to ubiquinone in the photosynthetic reaction center for Rhodopseudomonas Viridis: Theoretical study, J. Phys. Chem. B., vol. 107 (2003), pp. 838-847
  93. Paula Mori-Sanchez, Qin Wu, and Weitao Yang, Accurate polymer polarizabilities with exact exchange density functional theory, J. Chem. Phys., vol. 119 no. 21 (2003), pp. 11001-11004
  94. Qin Wu and Weitao Yang, Algebraic equation and iterative optimization for the optimized effective potential in density functional theory, J. Theo Comp. Chem., vol. 2 no. 4 (2003), pp. 627-638
  95. Hong Jiang, Harold U Baranger, and Weitao Yang, Density functional theory simulation of large quantum dots, Phys. Rev. B., vol. 68 (2003), pp. 165337-1-165337-9
  96. Hong Jiang, Harold U Baranger, and Weitao Yang, Desnity functional theory simulation of large quantum dots, Phys. Rev. B., vol. 68 (2003), pp. 165337-1-165337-9
  97. Laurel A. Goj, Andrés Cisneros, Weitao Yang, and Ross A. Widenhoefer, Dramatic effect of homoallylic substitution on the rate of palladiumcatalyzed diene cycloisomerization, Organometallic Chemistry, vol. 687 (2003), pp. 498-507
  98. Qiang Xue and Weitao Yang, Distributed electronic structure calculations with divide-and-conquer approach, Work-in-Progress Session of the PACT-02 Conference, Charlottesville, VA (September, 2002)
  99. Qin Wu and Weitao Yang, An Empirical Correction to Density Functional Theory for van der Waals Interactions, J. Chem. Phys., vol. 116 (2002), pp. 515-524
  100. Qin Wu and Weitao Yang, An empirical correction to density functional theory for van der waals interactions, J. Chem. Phys., vol. 116 (2002), pp. 515-524
  101. Weitao Yang and Qin Wu, Direct method for optimized effective potentials in density functional theory, Phys. Rev. Lett., vol. 89 (2002), pp. 143002-1-143002-4
  102. Mu-Hyun Baik, Joel S. Silverman, Ivana V. Yang, Patricia A. Ropp, Veronika A. Szalai, Weitao Yang, and H. Holden Thorp, Using Density Functional Theory To Design DNA Base Analogues with Low Oxidation Potentials, The Journal of Physical Chemistry B, vol. 105 no. 27 (2001), pp. 6437-6444
  103. Haiyan Liu, Marcus Elstner, Efthimios Kaxiras, Thomas Frauenheim, Jan Hermans, and Weitao Yang, Quantum mechanics simulation of protein dynamics on long timescale, PROTEINS: Structure, Function, and Genetics, vol. 44 (2001), pp. 484-489
  104. Mu-Hyun Baik, Joel S. Silverman, Patricia A. Ropp, Ivana V. Yang, Veronika A. Szalai, Weitao Yang, and H. Holden Thorp, Using density functional theory to design dna base analogues with low oxidation potentials, J. Phys. Chem. B., vol. 105 no. 27 (2001), pp. 6437-6444
  105. Shubin Liu, Jose M. Perez-Jorda and Weitao Yang, Nonothorgonal Localized Molecular Orbitals in Electronic Structure Theory, J. Chem. Phys., vol. 112 (2000), pp. 1634--1644
  106. Weitao Yang, Yingkai Zhang, and Paul Ayers, Degenerate Ground States and Fractional Number of Electrons in Density and Reduced Density Matrix Functional Theory, Phys. Rev. Lett., vol. 84 (2000), pp. 5172--5175
  107. Christer Enkvist, Yingkai Zhang, Weitao Yang, Density Functional Study of A Weakly Hydrogen Bonded System: the Benzene-Ammonia Complex, The International Journal of Quantum Chemistry, vol. 79 (2000), pp. 325--329
  108. Yingkai Zhang, Haiyan Liu and Weitao Yang, Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface, J. Chem. Phys., vol. 112 (2000), pp. 3483--3492
  109. Haiyan Liu ,Yingkai Zhang, and Weitao Yang, How is the active-site of enolase organized to achieve overall efficiency in catalyzing a two step reaction, J. Am. Chem. Soc., vol. 122 (2000), pp. 6560
  110. Yingkai Zhang and Weitao Yang, Perspective on 'Density-Functional Theory for Fractional Particle Number:Derivative Discontinuities of the Energy' by J.P. Perdew, R.G. Parr, M. Levy and J.L. Balduz,Jr., Theo. Chem. Account., vol. 103 (2000), pp. 346--348
  111. Stephen B. Little, James R. Rabinowitz, Pan Wei, and Weitao Yang, A comparison of calculated and experimental geometries of crowded polycyclic aromatic hydrocarbons and their metabolites, Polycyclic Aromatic Compounds, vol. 14 (2000), pp. 53-61
  112. Haiyan Liu, Yingkai Zhang, and Weitao Yang, How is the active-site of enolase organized to achieve overall efficiency in catalyzing a two step reaction, J. Am. Chem. Soc., vol. 122 (2000), pp. 6560-6570
  113. James P. Lewis, Shubin Liu, Taisung Lee, and Weitao Yang, A linear-scaling quantum mechanical investigation of cytidine deaminase, J. Comp. Phys., vol. 151 (1999), pp. 242-263 (invited article.)
  114. Yingkai Zhang, Taisung Lee, and Weitao Yang, A psuedo-bond approach to combining quantum mechanical and molecular mechanical methods, J. Chem. Phys., vol. 110 (1999), pp. 46-54
  115. Tai-Sung Lee and Weitao Yang, A frozen density matrix approach for electronic structure calculations, Int. J. Quantum Chem., vol. 69 (1998), pp. 397-404
  116. Tai-Sung Lee, James P. Lewis, and Weitao Yang, Linear-scaling quantum mechanical calculations of biological molecules: The divide-and-conquer approach, Computational Materials Science, vol. 12 (1998), pp. 259-277 (invited article.)
  117. James P. Lewis, Jr., Charles W. Carter, Jan Hermans, Wei Pan, Tai-Sung Lee, and Weitao Yang, Active species for the ground-state complex of cytidine deaminase: A linear-scaling quantum mechanical investigation, J. Am. Chem. Soc., vol. 120 (1998), pp. 5407-5410
  118. Wei Pan, Tai-Sung Lee, and Weitao Yang, A parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations, J. Comp. Chem., vol. 19 (1998), pp. 1101-1107
  119. José M. Pérez-Jordá and Weitao Yang, On the scaling of multiple methods for particle-particle interactions, Chem. Phys. Lett., vol. 282 (1998), pp. 71-78
  120. Weitao Yang, Generalized adiabatic connections in density functional theory, J. Chem. Phys., vol. 109 (1998), pp. 10107-10110
  121. Weitao Yang, Mel Levy, and S. Trickey, Symposium on density functional and applications (part 1 of ii) - introduction, Int. J. Quantum Chem., vol. 69 (1998), pp. 227
  122. Darrin York, Taisung Lee, and Weitao Yang, Quantum mechanical treatment of biological macro-molecules in solution using linear-scaling electronic structure methods, Phys. Rev. Lett., vol. 80 (1998), pp. 5011-5014
  123. Yingkai Zhang and Weitao Yang, A challenge for density functionals: Self-interaction error increases for systems with a nonintegar number of electrons, J. Chem. Phys., vol. 109 (1998), pp. 2604-2608
  124. Yingkai Zhang and Weitao Yang, Comment on 'generalized gradient approximation made simple', Phys. Rev. Lett., vol. 80 (1998), pp. 890
  125. Wei Pan, Tianhai Zhu, and Weitao Yang, First-principles study of the structural and electronic properties of ethylene adsorption on si(100)-(2x1) surface, J. Chem. Phys., vol. 107 (1997), pp. 3981-3985
  126. José M. Pérez-Jordá and Weitao Yang, Fast evaluation of the coulomb energy for electron densities, J. Chem. Phys., vol. 107 (1997), pp. 1218-1226
  127. Weitao Yang, Absolute energy minimum princples for linear-scaling electronic structure calculations, Phys. Rev. B., vol. 56 (1997), pp. 9294-9297
  128. Yingkai Zhang, Wei Pan, and Weitao Yang, Describing van der waals interaction in diatomic molecules with generalized gradient approximations: the role of the exchange functional, J. Chem. Phys., vol. 107 (1997), pp. 7921-7925
  129. Tianhai Zhu, Wei Pan, and Weitao Yang, Divide-and-conquer calculations for clean surfaces and surface adsorption, Theo. Chem. Acc., vol. 96 (1997), pp. 2-6
  130. Tai-Sung Lee, Darrin York, and Weitao Yang, Linear-scaling semiemperical quantum calculations for macromolecules, J. Chem. Phys., vol. 105 (1996), pp. 2744-2750
  131. Haihong Ni, Darrin York, Lee Bartolotti, Richard Wells, and Weitao Yang, Density functional study of the geometries, stabilities and bond energies of iii-v(13-15) four-membered ring compounds, J. Am. Chem. Soc., vol. 118 (1996), pp. 5732-5736
  132. José M. Pérez-Jordá and Weitao Yang, A concise redefinition of the solid spherical harmonics and its use in fast multipole methods, J. Chem. Phys., vol. 104 no. 20 (1996), pp. 8003-8006
  133. Darrin York, Tai-Sung Lee, and Weitao Yang, Quantum mechanical study of aqueous polarization effects on biological macromolecules, J. Am. Chem. Soc. Comm., vol. 118 (1996), pp. 10940-10941
  134. Darrin York and Weitao Yang, A chemical equalization method for molecular simulations, J. Chem. Phys., vol. 104 (1996), pp. 159-172
  135. Darrin York, Tai-Sung Lee, and Weitao Yang, Parameterization and efficient implementation of a solvent model for linear-scaling semiemperical quantum mechanical calculations of biological macro-molecules, Chem. Phys. Lett., vol. 263 (1996), pp. 297-304
  136. Tianhai Zhu, Wei Pan, and Weitao Yang, Structure of solid-state systems from embedded-cluster calculations: a divide-and-conquer approach, Phys. Rev. B., vol. 53 (1996), pp. 12713-12724
  137. Taisung Lee, Darrin York, and Weitao Yang, A new definition of atomic charges based on a variational principle for the electrostatic potential energy, J. Chem. Phys., vol. 102 (1995), pp. 7549-7556
  138. Wei Pan and Weitao Yang, Structure and stability of molybdenum carbide clusters (moc4)n(n = 1to4) and their anions, Phys. Rev. B., vol. 51 (1995), pp. 7224-7230
  139. R.G. Parr and Weitao Yang, Density-functional theory of the electronic structure of molecules, Ann. Rev. Phys. Chem., vol. 46 (1995), pp. 701-728
  140. José M. Pérez-Jordá and Weitao Yang, An algorithm for 3d numerical integration that scales linearly with the size of the molecule, Chem. Phys. Lett., vol. 241 (1995), pp. 469-476
  141. José M. Pérez-Jordá and Weitao Yang, A simple o(n log n) algorithm for the rapid evaluation of particle-particle interactions, Chem. Phys. Lett., vol. 247 (1995), pp. 484-490
  142. Weitao Yang and Tai-Sung Lee, A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules, J. Chem. Phys., vol. 103 (1995), pp. 5674-5678
  143. Darrin M. York, Weitao Yang, Hsing Lee, Tom Darden, and Lee Pedersen, Towards the accurate modeling of dna: the importance of long range electrostatistics, J. Am. Chem. Soc., vol. 117 (1995), pp. 5001-5002
  144. Qingsheng Zhao and Weitao Yang, Analytical energy gradients and geometry optimization in the divide-and-conquer method for large molecules, J. Chem. Phys., vol. 102 (1995), pp. 9598-9603
  145. Jian Ping Lu and Weitao Yang, The shape of large single- and multiple-shell fullerenes, Phys. Rev. B., vol. 49 (1994), pp. 11421-11424
  146. D. York and W. Yang, The fast fourier poisson method for calculating ewald sums, J. Chem. Phys., vol. 101 no. 4 (1994), pp. 3298-3300
  147. Tianhai Zhu and Weitao Yang, Structure of the ammonia dimer studied by density-functional theory, Int. J. Quantum Chem., vol. 49 (1994), pp. 613-623
  148. R.J. Bemish, P.A. Block, L.G. Pedersen, Weitao Yang, and R.E. Miller, The ar-c2h2 inter-molecular potential from high resolution spectroscopy and ab initio theory: A case for multi-center interactions, J. Chem. Phys., vol. 99 (1993), pp. 8593-8598
  149. Chengteh Lee, George Fitzgerald, and Weitao Yang, Nonlocal density functional calculations: Comparison of two implementation schemes, J. Chem. Phys., vol. 98 (1993), pp. 2971-2974
  150. Darrin York, Jian Ping Lu, and Weitao Yang, Density-functional calculations of the structure and stability of c240, Phys. Rev. B., vol. 49 (1993), pp. 8526-8528
  151. Tianhai Zhu, Chengteh Lee, and Weitao Yang, Examination of several exchange-correlation energy functionals by accurate self-consistent atomic calculations, J. Chem. Phys., vol. 98 (1993), pp. 4814-4821 (Erratum: J. Chem. Phys. 99, 4329 (1993).)
  152. T. Daniel Crawford and Weitao Yang, The hartley basis functions and transform: Alternatives to plane wares and fourier transform, Chem. Phys. Lett., vol. 192 (1992), pp. 45-48
  153. Chengteh Lee and Weitao Lee, The divide-functional approach: molecular internal rotation and density of states, J. Chem. Phys., vol. 96 (1992), pp. 2408-2411
  154. Weitao Yang, Electron density as the basic variable: a divide-and-conquer approach to the ab initio computation of large molecules, J. Mol. Struc./THEOCHEM, vol. 255 (1992), pp. 461-479 (Invited paper for the special issue on "Electron Density and Chemical Reactions".)
  155. Weitao Yang, A local projection method for the linear combination of atomic orbital implementation of density-functional theory, J. Chem. Phys., vol. 94 (1991), pp. 1208
  156. Weitao Yang, Direct calculation of electron density in density-functional theory, Phys. Rev. Lett., vol. 66 (1991), pp. 1438-1441
  157. Weitao Yang, Direct calculation of electron density in density-functional theory: implementation for benzene and a tetrapeptide, Phys. Rev. A., vol. 44 (1991), pp. 7823-7826
  158. Robert C. Morrison, Weitao Yang, Robert G. Parr, and Chengteh Lee, Approximate density matrices and wigner distribution functions from density, kinetic energy density and idempotency constraints, Int. J. Quantum Chem., vol. 38 (1990), pp. 819
  159. Weitao Yang, Integral formulation of density-functional theory, edited by Samuel B. Trickey, Density Functional Theory of Many-Fermion Systems, vol. 21 (1990), pp. 293 (Invited paper.)
  160. Weitao Yang and Andrew C. Peet, A method for calculating vibrational bound states by iterative solution of the collocation equations constructed from localized basis sets, J. Chem. Phys., vol. 92 (1990), pp. 522
  161. Andrew C. Peet and Weitao Yang, The collocation method for calculating vibrational bound states of molecular systems-with application to ar-hcl, J. Chem. Phys., vol. 90 (1989), pp. 1746
  162. Andrew C. Peet and Weitao Yang, An adapted form of the collocation method for calculating energy levels of rotating atom-diatom complexes, J. Chem. Phys., vol. 91 (1989), pp. 6598
  163. Weitao Yang and William H. Miller, Block lanczos approach combined with matrix continued fraction for the s-matrix kohn variational principle in quantum scattering, J. Chem. Phys., vol. 91 (1989), pp. 3504
  164. Weitao Yang, Andrew C. Peet, and William H. Miller, A collocation approach for quantum scattering based on the s-matrix version of the kohn variational principle, J. Chem. Phys., vol. 91 (1989), pp. 7537
  165. Chengteh Lee, Weitao Yang, and Robert G. Parr, Local softness and chemical reactivity in the molecules co, scn, and h co, vol. 163 (1988), pp. 305
  166. Chengteh Lee, Weitao Yang, and Robert G. Parr, Development of the colle-salvetti correlation energy formula into a functional of the electron density, Phys. Rev. B., vol. 37 (1988), pp. 785
  167. Weitao Yang, Ab initio approac for many-electron systems without invoking orbitals: An integral formulation of density-functional theory, Phys. Rev. A., vol. 38 (1988), pp. 5494
  168. Weitao Yang, Thermal properties of many-electron systems: An integral formulation of density-functional theory, Phys. Rev. A., vol. 38 (1988), pp. 5504
  169. Weitao Yang, Dynamic linear response of many-electron systems: An integral formulation of density-functional theory, Phys. Rev. A., vol. 38 (1988), pp. 5512
  170. Weitao Yang and Andrew C. Peet, The collocation method for bound solutions of the schroedinger equation, Chem. Phys. Lett., vol. 153 (1988), pp. 98
  171. Wenhui Xue and Weitao Yang, Application of a scaled particle theory to polar solute system and calculation of the salt effect constant, Acta Physica-Chimica Sinica, vol. 3 (1987), pp. 258
  172. Weitao Yang, Ab initio approach for many-electon system without invoking orbitals: An integral formulation of density-functional theory, Phys. Rev. Lett., vol. 59 (1987), pp. 1569
  173. Weitao Yang, Robert G. Parr, and Lieve Uytterhoeven, New relation between hardness and compressibility of minerals, Phys. and Chem. of Minerals, vol. 15 (1987), pp. 191
  174. Weitao Yang and John E. Harriman, Analysis of the kinetic energy functional in density-functional theory, J. Chem. Phys., vol. 84 (1986), pp. 3320
  175. Weitao Yang, Gradient correction in thomas-fermi theory, Phys. Rev. A., vol. 34 (1986), pp. 4575
  176. Weitao Yang, Robert G. Parr, and Chengteh Lee, Various functionals for the kinetic energy density of an atom or molecule, Phys. Rev. A., vol. 34 (1986), pp. 4586
  177. Weitao Yang and Wilfried J. Mortier, The use of global and local molecular parameters for the analysis of the gas-phase basicity of amines, J. Am. Chem. Soc., vol. 108 (1986), pp. 5708
  178. Mel Levy, Weitao Yang, and Robert G. Parr, A new functional with homogeneous coordinate scaling in density-functional theory: f[ρ,λ], J. Chem. Phys., vol. 83 (1985), pp. 2334
  179. Weitao Yang, Chengteh Lee, and Swapan K. Ghosh, Molecular softness as the average of atomic softness: Companion principle to the geometric mean principle for electonegativity equalization, J. Phys. Chem., vol. 89 (1985), pp. 5412
  180. Weitao Yang and Robert G. Parr, Hardness, softness, and fukui function in the electronic theory of metals and catalysis, Proc. Natl. Acadm. Sci, USA, vol. 82 (1985), pp. 6723
  181. Robert G. Parr and Weitao Yang, Density-functional approach to the frontier-electron theory of chemical rectivity, J. Am. Chem. Soc., vol. 106 (1984), pp. 4049
  182. Weitao Yang, Robert G. Parr, and R. Pucci, Electron density, kohn-sham frontier orbitals, and fukai functions, J. Chem. Phys., vol. 81 (1984), pp. 2862

Chapter in Book

  1. G. A. CISNEROS and W. T. YANG, Comparison of reaction barriers in energy and free energy for enzyme catalysis, in Multi-scale Quantum Models for Biocatalysis, edited by D. York and T.-S. Lee (2009), pp. 57-78, London: Springer-Verlag
  2. Paul W. Ayers and Weitao Yang, Density-functional theory, in Computational Medicinal Chemistry and Drug Discovery, edited by Wilfried Langenaeker (2003)
  3. Yingkai Zhang, Haiyan Liu, and Weitao Yang, Ab initio qm/mm and free energy calculations of enzyme reactions, in Computational Methods for Macromolecules-Challenges and Applications, Springer Verlag's Lecture Notes Series in Computational Science and Engineering, edited by T. Schlick and H.H. Gan (2002), pp. 332=354, Springer, New York
  4. Zhenyu Lu, Haiyan Liu, Marcus Elstner, and Weitao Yang, Parameterization of cosmo solvent model for self-consistent charge density-functional based tight-binding calculations, in Reviews in Modern Quantum Chemistry: A Celebration Of The Contributions of R.G. PARR, edited by K.D. Sen (2002), pp. 1606-1614, World Scientific, Singapore
  5. Weitao Yang and José M. Pérez-Jordá, Linear scaling methods for electronic structure calculations, in Encyclopedia of Computational Chemistry, edited by P.v.R. Schleyer (1998), pp. 1496-1513, John Wiley & Sons
  6. Weitao Yang and Zhongxiang Zhou, Electronic structure of solid-state systems via the divide-and-conquer method, in Electronic Functional Theory of Molecules, Clusters, and Solids, edited by D.E. Ellis (1994), pp. 177-188, Kluwer Academic Publishers, Dordrecht
  7. Weitao Yang, Density-functional theory of large systems: a divide-and-conquer approach, in Condensed-Matter Theories, edited by L. Blum and F.B. Malik, vol. 8 (1993), pp. 367-372, Plenum Press, Berlin
  8. Weitao Yang, Some remarks on scaling relations in density-functional theory, in Density Matrices and Density-Functionals, edited by R. Erdahl and Jr. V. H. Smith (1987), pp. 499-506, D. Reidel Publishing Company, Dordrecht, Holland