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. Ke, S-H; Baranger, HU; Yang, W, Molecular conductance: chemical trends of anchoring groups., Journal of the American Chemical Society, vol. 126 no. 48 (December, 2004), pp. 15897-15904 [15571415], [doi] [abs] .
  2. Cohen, AJ; Wu, Q; Yang, W, Calculation of nuclear magnetic resonance shielding constants using potential-based methods, Chemical Physics Letters, vol. 399 no. 1-3 (2004), pp. 84-88 [doi] [abs] .
Preprints
  1. Scholl, ZN; Li, Q; Yang, W; Marszalek, P, Single-Molecule Force-Spectroscopy Reveals the Calcium Dependency of Folding Intermediates in the Multidomain Protein S, Biophysical Journal, vol. 110 no. 3 (February, 2016), pp. 393a-393a [doi] .
  2. Wang, W; Li, Z; Yang, W, Angular momentum dependent field emission energy distribution, IVNC 2015 - Technical Digest: 28th International Vacuum Nanoelectronics Conference (August, 2015), pp. 30-31 [doi] [abs] .
  3. Scholl, ZN; Yang, W; Marszalek, P, N-terminal Domain Of Luciferase Controls Misfolding Avoidance, Protein Science : a Publication of the Protein Society, vol. 23 (July, 2014), pp. 249-249 .
  4. Yang, W, Mechanism of catalytic reactions and redox processes for solar fuel with multiscale QM/MM simulation, Abstracts of Papers of the American Chemical Society, vol. 246 (September, 2013) .
  5. Yang, W, Progress in exchange-correlation energy functionals, Abstracts of Papers of the American Chemical Society, vol. 242 (August, 2011) .
  6. Rinderspacher, BC; Beratan, DN; Yang, W, CINF 71-Inverse design of host-guest complexes in competitive binding problems, Abstracts of Papers of the American Chemical Society, vol. 236 (August, 2008) .
  7. Cohen, AJ; Mori-Sanchez, P; Heaton-Burgess, T; Bulat, FA; Yang, W, COMP 436-Accurate density functionals addressing the self-interaction error and potential functional formalism, Abstracts of Papers of the American Chemical Society, vol. 234 (August, 2007) .
  8. Yang, WT; Lu, ZY; Wang, ML, Reaction path potential for simulation of chemical reactions in enzymes derived from ab initio QM/MM calculations, Abstracts of Papers of the American Chemical Society, vol. 228 (August, 2004), pp. U247-U247 [Gateway.cgi] .
Journal Articles
  1. Shen, L; Zeng, X; Hu, H; Hu, X; Yang, W, Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants., Journal of Chemical Theory and Computation (August, 2018) [doi] [abs] .
  2. Sutton, C; Yang, Y; Zhang, D; Yang, W, Single, Double Electronic Excitations and Exciton Effective Conjugation Lengths in π-Conjugated Systems., The Journal of Physical Chemistry Letters, vol. 9 no. 14 (July, 2018), pp. 4029-4036 [doi] [abs] .
  3. Wang, H; Yang, W, Force Field for Water Based on Neural Network., The Journal of Physical Chemistry Letters, vol. 9 no. 12 (June, 2018), pp. 3232-3240 [doi] [abs] .
  4. Al-Saadon, R; Sutton, C; Yang, W, Accurate Treatment of Charge-Transfer Excitations and Thermally Activated Delayed Fluorescence Using the Particle-Particle Random Phase Approximation., Journal of Chemical Theory and Computation, vol. 14 no. 6 (June, 2018), pp. 3196-3204 [doi] [abs] .
  5. Zhang, D; Yang, X; Zheng, X; Yang, W, Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies, Molecular Physics, vol. 116 no. 7-8 (April, 2018), pp. 927-934 [doi] .
  6. Contreras-García, J; Yang, W, Perspective: Chemical information encoded in electron density, Wuli Huaxue Xuebao/ Acta Physico Chimica Sinica, vol. 34 no. 6 (March, 2018), pp. 567-580 [doi] [abs] .
  7. Li, C; Zheng, X; Su, NQ; Yang, W, Localized orbital scaling correction for systematic elimination of delocalization error in density functional approximations, National Science Review, vol. 5 no. 2 (March, 2018), pp. 203-215 [doi] .
  8. Zhang, X; Li, X; Reish, ME; Zhang, D; Su, NQ; Gutiérrez, Y; Moreno, F; Yang, W; Everitt, HO; Liu, J, Plasmon-Enhanced Catalysis: Distinguishing Thermal and Nonthermal Effects., Nano Letters, vol. 18 no. 3 (March, 2018), pp. 1714-1723 [doi] [abs] .
  9. Shen, L; Yang, W, Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks., Journal of Chemical Theory and Computation, vol. 14 no. 3 (March, 2018), pp. 1442-1455 [doi] [abs] .
  10. Li, G; Zhang, D; Yu, Y; Huang, S; Yang, W; Cao, L, Activating MoS2 for pH-Universal Hydrogen Evolution Catalysis., Journal of the American Chemical Society, vol. 139 no. 45 (November, 2017), pp. 16194-16200 [doi] [abs] .
  11. Jin, Y; Zhang, D; Chen, Z; Su, NQ; Yang, W, Generalized Optimized Effective Potential for Orbital Functionals and Self-Consistent Calculation of Random Phase Approximations., The Journal of Physical Chemistry Letters, vol. 8 no. 19 (October, 2017), pp. 4746-4751 [doi] [abs] .
  12. Jin, Y; Yang, Y; Zhang, D; Peng, D; Yang, W, Excitation energies from particle-particle random phase approximation with accurate optimized effective potentials., The Journal of Chemical Physics, vol. 147 no. 13 (October, 2017), pp. 134105 [doi] [abs] .
  13. Wu, J; Shen, L; Yang, W, Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations., The Journal of Chemical Physics, vol. 147 no. 16 (October, 2017), pp. 161732 [doi] [abs] .
  14. Peng, D; Li, S; Peng, L; Gu, FL; Yang, W, Time-Dependent Coupled Perturbed Hartree-Fock and Density-Functional-Theory Approach for Calculating Frequency-Dependent (Hyper)Polarizabilities with Nonorthogonal Localized Molecular Orbitals., Journal of Chemical Theory and Computation, vol. 13 no. 9 (September, 2017), pp. 4101-4112 [doi] [abs] .
  15. Chen, Z; Zhang, D; Jin, Y; Yang, Y; Su, NQ; Yang, W, Multireference Density Functional Theory with Generalized Auxiliary Systems for Ground and Excited States., The Journal of Physical Chemistry Letters, vol. 8 no. 18 (September, 2017), pp. 4479-4485 [doi] [abs] .
  16. Zhang, D; Su, NQ; Yang, W, Accurate Quasiparticle Spectra from the T-Matrix Self-Energy and the Particle-Particle Random Phase Approximation., The Journal of Physical Chemistry Letters, vol. 8 no. 14 (July, 2017), pp. 3223-3227 [doi] [abs] .
  17. Li, C; Lu, J; Yang, W, On extending Kohn-Sham density functionals to systems with fractional number of electrons., The Journal of Chemical Physics, vol. 146 no. 21 (June, 2017), pp. 214109 [doi] [abs] .
  18. Scholl, ZN; Yang, W; Marszalek, PE, Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase., Biophysical Journal, vol. 112 no. 9 (May, 2017), pp. 1829-1840 [doi] [abs] .
  19. Lewis, CA; Shen, L; Yang, W; Wolfenden, R, Three Pyrimidine Decarboxylations in the Absence of a Catalyst., Biochemistry, vol. 56 no. 10 (March, 2017), pp. 1498-1503 [doi] [abs] .
  20. Perdew, JP; Yang, W; Burke, K; Yang, Z; Gross, EKU; Scheffler, M; Scuseria, GE; Henderson, TM; Zhang, IY; Ruzsinszky, A; Peng, H; Sun, J; Trushin, E; Görling, A, Understanding band gaps of solids in generalized Kohn-Sham theory., Proceedings of the National Academy of Sciences of the United States of America, vol. 114 no. 11 (March, 2017), pp. 2801-2806 [doi] [abs] .
  21. Yang, Y; Dominguez, A; Zhang, D; Lutsker, V; Niehaus, TA; Frauenheim, T; Yang, W, Charge transfer excitations from particle-particle random phase approximation-Opportunities and challenges arising from two-electron deficient systems., The Journal of Chemical Physics, vol. 146 no. 12 (March, 2017), pp. 124104 [doi] [abs] .
  22. Zhang, X; Li, X; Zhang, D; Su, NQ; Yang, W; Everitt, HO; Liu, J, Product selectivity in plasmonic photocatalysis for carbon dioxide hydrogenation., Nature Communications, vol. 8 (February, 2017), pp. 14542 [doi] [abs] .
  23. Li, C; Yang, W, On the piecewise convex or concave nature of ground state energy as a function of fractional number of electrons for approximate density functionals., The Journal of Chemical Physics, vol. 146 no. 7 (February, 2017), pp. 074107 [doi] [abs] .
  24. Li, G; Zhang, D; Qiao, Q; Yu, Y; Peterson, D; Zafar, A; Kumar, R; Curtarolo, S; Hunte, F; Shannon, S; Zhu, Y; Yang, W; Cao, L, All The Catalytic Active Sites of MoS2 for Hydrogen Evolution., Journal of the American Chemical Society, vol. 138 no. 51 (December, 2016), pp. 16632-16638 [doi] [abs] .
  25. Zhang, D; Yang, W, Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation., The Journal of Chemical Physics, vol. 145 no. 14 (October, 2016), pp. 144105 [doi] [abs] .
  26. Shen, L; Wu, J; Yang, W, Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks., Journal of Chemical Theory and Computation, vol. 12 no. 10 (October, 2016), pp. 4934-4946 [doi] [abs] .
  27. Yang, Y; Davidson, ER; Yang, W, Nature of ground and electronic excited states of higher acenes., Proceedings of the National Academy of Sciences of the United States of America, vol. 113 no. 35 (August, 2016), pp. E5098-E5107 [doi] [abs] .
  28. Scholl, ZN; Li, Q; Yang, W; Marszalek, PE, Single-molecule Force Spectroscopy Reveals the Calcium Dependence of the Alternative Conformations in the Native State of a βγ-Crystallin Protein., The Journal of Biological Chemistry, vol. 291 no. 35 (August, 2016), pp. 18263-18275 [doi] [abs] .
  29. Yang, Y; Shen, L; Zhang, D; Yang, W, Conical Intersections from Particle-Particle Random Phase and Tamm-Dancoff Approximations., The Journal of Physical Chemistry Letters, vol. 7 no. 13 (July, 2016), pp. 2407-2411 [doi] [abs] .
  30. Wang, H; Yang, W, Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory., The Journal of Chemical Physics, vol. 144 no. 22 (June, 2016), pp. 224107 [doi] [abs] .
  31. Yang, Y; Burke, K; Yang, W, Accurate atomic quantum defects from particle–particle random phase approximation, Molecular Physics, vol. 114 no. 7-8 (April, 2016), pp. 1189-1198 [doi] .
  32. Rupakheti, C; Al-Saadon, R; Zhang, Y; Virshup, AM; Zhang, P; Yang, W; Beratan, DN, Diverse Optimal Molecular Libraries for Organic Light-Emitting Diodes., Journal of Chemical Theory and Computation, vol. 12 no. 4 (April, 2016), pp. 1942-1952 [doi] [abs] .
  33. Shen, L; Yang, W, Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations., Journal of Chemical Theory and Computation, vol. 12 no. 4 (April, 2016), pp. 2017-2027 [doi] [abs] .
  34. Li, C; Lu, J; Yang, W, Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals., The Journal of Chemical Physics, vol. 143 no. 22 (December, 2015), pp. 224110 [doi] [abs] .
  35. Zheng, X; Li, C; Zhang, D; Yang, W, Scaling correction approaches for reducing delocalization error in density functional approximations, Science China Chemistry, vol. 58 no. 12 (December, 2015), pp. 1825-1844 [doi] .
  36. Yang, Y; Peng, D; Davidson, ER; Yang, W, Singlet-triplet energy gaps for diradicals from particle-particle random phase approximation., The Journal of Physical Chemistry A, vol. 119 no. 20 (May, 2015), pp. 4923-4932 [doi] [abs] .
  37. Zhang, D; Zheng, X; Li, C; Yang, W, Orbital relaxation effects on Kohn-Sham frontier orbital energies in density functional theory., The Journal of Chemical Physics, vol. 142 no. 15 (April, 2015), pp. 154113 [doi] [abs] .
  38. Li, S; Hu, L; Peng, L; Yang, W; Gu, FL, Coupled-Perturbed SCF Approach for Calculating Static Polarizabilities and Hyperpolarizabilities with Nonorthogonal Localized Molecular Orbitals., Journal of Chemical Theory and Computation, vol. 11 no. 3 (March, 2015), pp. 923-931 [doi] [abs] .
  39. Rupakheti, C; Virshup, A; Yang, W; Beratan, DN, Strategy to discover diverse optimal molecules in the small molecule universe., Journal of Chemical Information and Modeling, vol. 55 no. 3 (March, 2015), pp. 529-537 [doi] [abs] .
  40. Scholl, ZN; Yang, W; Marszalek, PE, Direct observation of multimer stabilization in the mechanical unfolding pathway of a protein undergoing oligomerization., Acs Nano, vol. 9 no. 2 (February, 2015), pp. 1189-1197 [doi] [abs] .
  41. Li, C; Zheng, X; Cohen, AJ; Mori-Sánchez, P; Yang, W, Local scaling correction for reducing delocalization error in density functional approximations., Physical Review Letters, vol. 114 no. 5 (February, 2015), pp. 053001 [doi] [abs] .
  42. Scholl, ZN; Yang, W; Marszalek, PE, Chaperones rescue luciferase folding by separating its domains., The Journal of Biological Chemistry, vol. 290 no. 2 (January, 2015), pp. 883-883 [doi] .
  43. Zhang, D; Peng, D; Zhang, P; Yang, W, Analytic gradients, geometry optimization and excited state potential energy surfaces from the particle-particle random phase approximation., Physical Chemistry Chemical Physics : Pccp, vol. 17 no. 2 (January, 2015), pp. 1025-1038 [doi] [abs] .
  44. Peng, D; Yang, Y; Zhang, P; Yang, W, Restricted second random phase approximations and Tamm-Dancoff approximations for electronic excitation energy calculations., The Journal of Chemical Physics, vol. 141 no. 21 (December, 2014), pp. 214102 [doi] [abs] .
  45. Guo, H; Xie, D; Yang, W, A tribute to Guosen Yan, Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol. 133 no. 12 (December, 2014) [doi] .
  46. Su, NQ; Yang, W; Mori-Sánchez, P; Xu, X, Fractional charge behavior and band gap predictions with the XYG3 type of doubly hybrid density functionals., The Journal of Physical Chemistry A, vol. 118 no. 39 (October, 2014), pp. 9201-9211 [doi] [abs] .
  47. Scholl, ZN; Yang, W; Marszalek, PE, Chaperones rescue luciferase folding by separating its domains., The Journal of Biological Chemistry, vol. 289 no. 41 (October, 2014), pp. 28607-28618 [doi] [abs] .
  48. Yang, Y; Peng, D; Lu, J; Yang, W, Excitation energies from particle-particle random phase approximation: Davidson algorithm and benchmark studies., The Journal of Chemical Physics, vol. 141 no. 12 (September, 2014), pp. 124104 [doi] [abs] .
  49. Li, Y; Nese, A; Hu, X; Lebedeva, NV; LaJoie, TW; Burdyńska, J; Stefan, MC; You, W; Yang, W; Matyjaszewski, K; Sheiko, SS, Shifting Electronic Structure by Inherent Tension in Molecular Bottlebrushes with Polythiophene Backbones, Acs Macro Letters, vol. 3 no. 8 (August, 2014), pp. 738-742 [doi] .
  50. Shenvi, N; van Aggelen, H; Yang, Y; Yang, W, Tensor hypercontracted ppRPA: reducing the cost of the particle-particle random phase approximation from O(r(6)) to O(r(4))., The Journal of Chemical Physics, vol. 141 no. 2 (July, 2014), pp. 024119 [doi] [abs] .
  51. Yang, W, Preface: Special topic on advances in density functional theory., The Journal of Chemical Physics, vol. 140 no. 18 (May, 2014), pp. 18A101 [doi] [abs] .
  52. van Aggelen, H; Yang, Y; Yang, W, Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random phase approximation., The Journal of Chemical Physics, vol. 140 no. 18 (May, 2014), pp. 18A511 [doi] [abs] .
  53. Peng, D; van Aggelen, H; Yang, Y; Yang, W, Linear-response time-dependent density-functional theory with pairing fields., The Journal of Chemical Physics, vol. 140 no. 18 (May, 2014), pp. 18A522 [doi] [abs] .
  54. Chaudret, R; Contreras-Garcia, J; Delcey, M; Parisel, O; Yang, W; Piquemal, J-P, Revisiting H2O Nucleation around Au(+) and Hg(2+): The Peculiar "Pseudo-Soft" Character of the Gold Cation., Journal of Chemical Theory and Computation, vol. 10 no. 5 (May, 2014), pp. 1900-1909 [doi] [abs] .
  55. Yu, Y; Huang, S-Y; Li, Y; Steinmann, SN; Yang, W; Cao, L, Layer-Dependent Electrocatalysis of MoS 2 for Hydrogen Evolution, Nano Letters, vol. 14 no. 2 (February, 2014), pp. 553-558 [doi] .
  56. Franks, AT; Peng, D; Yang, W; Franz, KJ, Characterization of a photoswitching chelator with light-modulated geometric, electronic, and metal-binding properties., Inorganic Chemistry, vol. 53 no. 3 (February, 2014), pp. 1397-1405 [doi] [abs] .
  57. Yang, Y; Van Aggelen, H; Yang, W, Double, Rydberg and charge transfer excitations from pairing matrix fluctuation and particle-particle random phase approximation, The Journal of Chemical Physics, vol. 139 no. 22 (December, 2013) [doi] [abs] .
  58. Yang, Y; van Aggelen, H; Yang, W, Double, Rydberg and charge transfer excitations from pairing matrix fluctuation and particle-particle random phase approximation., The Journal of Chemical Physics, vol. 139 no. 22 (December, 2013), pp. 224105 [24329054], [doi] [abs] .
  59. Yang, Y; van Aggelen, H; Steinmann, SN; Peng, D; Yang, W, Benchmark tests and spin adaptation for the particle-particle random phase approximation., The Journal of Chemical Physics, vol. 139 no. 17 (November, 2013), pp. 174110 [24206290], [doi] [abs] .
  60. Zhang, D; Steinmann, SN; Yang, W, Dynamical second-order Bethe-Salpeter equation kernel: a method for electronic excitation beyond the adiabatic approximation., The Journal of Chemical Physics, vol. 139 no. 15 (October, 2013), pp. 154109 [24160502], [doi] [abs] .
  61. Peng, D; Steinmann, SN; van Aggelen, H; Yang, W, Equivalence of particle-particle random phase approximation correlation energy and ladder-coupled-cluster doubles., The Journal of Chemical Physics, vol. 139 no. 10 (September, 2013), pp. 104112 [24050333], [doi] [abs] .
  62. van Aggelen, H; Yang, Y; Yang, W, Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random-phase approximation, Physical Review A, vol. 88 no. 3 (September, 2013), pp. 030501 [doi] [abs] .
  63. Yang, W; Mori-Sánchez, P; Cohen, AJ, Extension of many-body theory and approximate density functionals to fractional charges and fractional spins., The Journal of Chemical Physics, vol. 139 no. 10 (September, 2013), pp. 104114 [24050335], [doi] [abs] .
  64. Steinmann, SN; Yang, W, Wave function methods for fractional electrons., The Journal of Chemical Physics, vol. 139 no. 7 (August, 2013), pp. 074107 [23968072], [doi] [abs] .
  65. Shenvi, N; van Aggelen, H; Yang, Y; Yang, W; Schwerdtfeger, C; Mazziotti, D, The tensor hypercontracted parametric reduced density matrix algorithm: coupled-cluster accuracy with O(r(4)) scaling., The Journal of Chemical Physics, vol. 139 no. 5 (August, 2013), pp. 054110 [23927246], [doi] [abs] .
  66. Wang, J; Yang, W, Concerted proton transfer mechanism of Clostridium thermocellum ribose-5-phosphate isomerase., Journal of Physical Chemistry B, vol. 117 no. 32 (August, 2013), pp. 9354-9361 [23875675], [doi] [abs] .
  67. Peng, D; Yang, W, Fukui function and response function for nonlocal and fractional systems., The Journal of Chemical Physics, vol. 138 no. 18 (May, 2013), pp. 184108 [23676030], [doi] [abs] .
  68. Virshup, AM; Contreras-García, J; Wipf, P; Yang, W; Beratan, DN, Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds., Journal of the American Chemical Society, vol. 135 no. 19 (May, 2013), pp. 7296-7303 [23548177], [doi] [abs] .
  69. Zheng, X; Zhou, T; Yang, W, A nonempirical scaling correction approach for density functional methods involving substantial amount of Hartree-Fock exchange., The Journal of Chemical Physics, vol. 138 no. 17 (May, 2013), pp. 174105 [doi] [abs] .
  70. Wu, P; Chaudret, R; Hu, X; Yang, W, Noncovalent Interaction Analysis in Fluctuating Environments., Journal of Chemical Theory and Computation, vol. 9 no. 5 (May, 2013), pp. 2226-2234 [doi] [abs] .
  71. Scholl, ZN; Yang, W; Marszalek, PE, Improving Single Molecule Force Spectroscopy through Automated Real-Time Data Collection and Quantification of Experimental Conditions, Biophysical Journal, vol. 104 no. 2 (January, 2013), pp. 512A-512A [Gateway.cgi], [doi] .
  72. Chaudret, R; Parks, JM; Yang, W, Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs., The Journal of Chemical Physics, vol. 138 no. 4 (January, 2013), pp. 045102 [23387624], [doi] [abs] .
  73. Peng, L; Gu, FL; Yang, W, Effective preconditioning for ab initio ground state energy minimization with non-orthogonal localized molecular orbitals, Physical Chemistry Chemical Physics : Pccp, vol. 15 no. 37 (2013), pp. 15518-15527 [doi] [abs] .
  74. Jin, Y; Johnson, ER; Hu, X; Yang, W; Hu, H, Contributions of Pauli repulsions to the energetics and physical properties computed in QM/MM methods, Journal of Computational Chemistry, vol. 34 no. 27 (2013), pp. 2380-2388 [doi] [abs] .
  75. Vleeschouwer, FD; Chankisjijev, A; Yang, W; Geerlings, P; Proft, FD, Pushing the boundaries of intrinsically stable radicals: Inverse design using the thiadiazinyl radical as a template, The Journal of Organic Chemistry, vol. 78 no. 7 (2013), pp. 3151-3158 [doi] [abs] .
  76. De Vleeschouwer, F; Yang, W; Beratan, DN; Geerlings, P; De Proft, F, Inverse design of molecules with optimal reactivity properties: acidity of 2-naphthol derivatives., Physical Chemistry Chemical Physics, vol. 14 no. 46 (December, 2012), pp. 16002-16013 [23089917], [doi] [abs] .
  77. Zeng, X; Hu, X; Yang, W, Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru(2+)-Ru(3+) Self-Exchange Electron Transfer., Journal of Chemical Theory and Computation, vol. 8 no. 12 (December, 2012), pp. 4960-4967 [doi] [abs] .
  78. Shenvi, N; Yang, W, Achieving partial decoherence in surface hopping through phase correction., The Journal of Chemical Physics, vol. 137 no. 22 (December, 2012), pp. 22A528 [23249065], [doi] [abs] .
  79. Gillet, N; Chaudret, R; Contreras-Garcίa, J; Yang, W; Silvi, B; Piquemal, J-P, Coupling quantum interpretative techniques: another look at chemical mechanisms in organic reactions., Journal of Chemical Theory and Computation, vol. 8 no. 11 (November, 2012), pp. 3993-3997 [doi] [abs] .
  80. Peng, D; Hu, X; Devarajan, D; Ess, DH; Johnson, ER; Yang, W, Variational fractional-spin density-functional theory for diradicals., The Journal of Chemical Physics, vol. 137 no. 11 (September, 2012), pp. 114112 [22998254], [doi] [abs] .
  81. Johnson, ER; Contreras-García, J; Yang, W, Density-Functional Errors in Alkanes: A Real-Space Perspective., Journal of Chemical Theory and Computation, vol. 8 no. 8 (August, 2012), pp. 2676-2681 [doi] [abs] .
  82. Hu, X; Jin, Y; Zeng, X; Hu, H; Yang, W, Liquid water simulations with the density fragment interaction approach., Physical Chemistry Chemical Physics, vol. 14 no. 21 (June, 2012), pp. 7700-7709 [22466097], [doi] [abs] .
  83. Wu, P; Cisneros, GA; Hu, H; Chaudret, R; Hu, X; Yang, W, Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways., Journal of Physical Chemistry B, vol. 116 no. 23 (June, 2012), pp. 6889-6897 [22417185], [doi] [abs] .
  84. Yang, W; Cohen, AJ; Mori-Sánchez, P, Derivative discontinuity, bandgap and lowest unoccupied molecular orbital in density functional theory., The Journal of Chemical Physics, vol. 136 no. 20 (May, 2012), pp. 204111 [22667544], [doi] [abs] .
  85. Yang, W; Cohen, AJ; De Proft, F; Geerlings, P, Analytical evaluation of Fukui functions and real-space linear response function., The Journal of Chemical Physics, vol. 136 no. 14 (April, 2012), pp. 144110 [22502504], [doi] [abs] .
  86. Lee, W; Zeng, X; Rotolo, K; Yang, M; Schofield, CJ; Bennett, V; Yang, W; Marszalek, PE, Mechanical anisotropy of ankyrin repeats., Biophysical Journal, vol. 102 no. 5 (March, 2012), pp. 1118-1126 [22404934], [doi] [abs] .
  87. Cohen, AJ; Mori-Sánchez, P; Yang, W, Challenges for density functional theory., Chemical Reviews, vol. 112 no. 1 (January, 2012), pp. 289-320 [doi] [abs] .
  88. Yang, W; Mori-Sanchez, P; Cohen, AJ, Insight and progress in density functional theory, Aip Conference Proceedings, vol. 1504 (2012), pp. 605-606 [doi] [abs] .
  89. Sun, Z; Yang, W; Zhang, DH, Higher-order split operator schemes for solving the Schrödinger equation in the time-dependent wave packet method: Applications to triatomic reactive scattering calculations, Physical Chemistry Chemical Physics : Pccp, vol. 14 no. 6 (2012), pp. 1827-1845 [doi] [abs] .
  90. Mori-Sánchez, P; Cohen, AJ; Yang, W, Failure of the random-phase-approximation correlation energy, Physical Review A, vol. 85 no. 4 (2012) [doi] [abs] .
  91. Peng, D; Zhao, B; Cohen, AJ; Hu, X; Yang, W, Optimized effective potential for calculations with orbital-free potential functionals, Molecular Physics, vol. 110 no. 9-10 (2012), pp. 925-934 [doi] [abs] .
  92. Xu, Y; Wang, B-J; Ke, S-H; Yang, W; Alzahrani, AZ, Highly tunable spin-dependent electron transport through carbon atomic chains connecting two zigzag graphene nanoribbons, The Journal of Chemical Physics, vol. 137 no. 10 (2012) [doi] [abs] .
  93. Lin, X; Hu, X; Concepcion, JJ; Chen, Z; Liu, S; Meyer, TJ; Yang, W, Theoretical study of catalytic mechanism for single-site water oxidation process, Proceedings of the National Academy of Sciences of the United States of America, vol. 109 no. 39 (2012), pp. 15669-15672 [doi] [abs] .
  94. Zheng, X; Liu, M; Johnson, ER; Contreras-García, J; Yang, W, Delocalization error of density-functional approximations: A distinct manifestation in hydrogen molecular chains, The Journal of Chemical Physics, vol. 137 no. 21 (2012) [doi] [abs] .
  95. Cho, J; Lin, Q; Yang, S; Jr, JGS; Cheng, Y; Lin, E; Yang, J; Foreman, JV; Everitt, HO; Yang, W; Kim, J; Liu, J, Sulfur-doped zinc oxide (ZnO) Nanostars: Synthesis and simulation of growth mechanism, Nano Research, vol. 5 no. 1 (2012), pp. 20-26 [doi] [abs] .
  96. Jiang, N; Zuber, G; Keinan, S; Nayak, A; Yang, W; Therien, MJ; Beratan, DN, Design of coupled porphyrin chromophores with unusually large hyperpolarizabilities, The Journal of Physical Chemistry C, vol. 116 no. 17 (2012), pp. 9724-9733 [doi] [abs] .
  97. Zhang, J; Yang, W; Piquemal, J-P; Ren, P, Modeling structural coordination and ligand binding in zinc proteins with a polarizable potential, Journal of Chemical Theory and Computation, vol. 8 no. 4 (2012), pp. 1314-1324 [doi] [abs] .
  98. Shenvi, N; Yang, W, An algebraic operator approach to electronic structure., The Journal of Chemical Physics, vol. 135 no. 24 (December, 2011), pp. 244111 [22225148], [doi] [abs] .
  99. Contreras-García, J; Yang, W; Johnson, ER, Analysis of hydrogen-bond interaction potentials from the electron density: integration of noncovalent interaction regions., The Journal of Physical Chemistry A, vol. 115 no. 45 (November, 2011), pp. 12983-12990 [21786796], [doi] [abs] .
  100. Wu, P; Hu, X; Yang, W, λ-Meta Dynamics Approach To Compute Absolute Solvation Free Energy., The Journal of Physical Chemistry Letters, vol. 2 no. 17 (September, 2011), pp. 2099-2103 [Gateway.cgi], [doi] [abs] .
  101. Zheng, X; Cohen, AJ; Mori-Sanchez, P; Hu, X; Yang, W, Improving Band Gap Prediction in Density Functional Theory from Molecules to Solids, Physical Review Letters, vol. 107 no. 2 (July, 2011), pp. 026403 [21797627], [doi] [abs] .
  102. Shenvi, N; Subotnik, JE; Yang, W, Phase-corrected surface hopping: correcting the phase evolution of the electronic wavefunction., The Journal of Chemical Physics, vol. 135 no. 2 (July, 2011), pp. 024101 [21766919], [doi] [abs] .
  103. Tam, ES; Parks, JJ; Shum, WW; Zhong, Y-W; Santiago-Berríos, MB; Zheng, X; Yang, W; Chan, GK-L; Abruña, HD; Ralph, DC, Single-molecule conductance of pyridine-terminated dithienylethene switch molecules., Acs Nano, vol. 5 no. 6 (June, 2011), pp. 5115-5123 [doi] [abs] .
  104. Cui, G; Yang, W, Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method., The Journal of Chemical Physics, vol. 134 no. 20 (May, 2011), pp. 204115 [21639432], [doi] [abs] .
  105. Shenvi, N; Subotnik, JE; Yang, W, Simultaneous-trajectory surface hopping: a parameter-free algorithm for implementing decoherence in nonadiabatic dynamics., The Journal of Chemical Physics, vol. 134 no. 14 (April, 2011), pp. 144102 [21495737], [doi] [abs] .
  106. Contreras-García, J; Johnson, ER; Keinan, S; Chaudret, R; Piquemal, J-P; Beratan, DN; Yang, W, NCIPLOT: a program for plotting non-covalent interaction regions., Journal of Chemical Theory and Computation, vol. 7 no. 3 (March, 2011), pp. 625-632 [21516178], [doi] [abs] .
  107. Sun, Z; Yang, W, Communication: An exact short-time solver for the time-dependent Schrödinger equation., The Journal of Chemical Physics, vol. 134 no. 4 (January, 2011), pp. 041101 [21280676], [doi] [abs] .
  108. Sun, Z; Yang, W, An exact short-time solver for the time-dependent Schrodinger equation, The Journal of Chemical Physics, vol. 134 no. 4 (January, 2011), pp. 041101 [Gateway.cgi], [doi] .
  109. Hu, X; Hu, H; Melvin, JA; Clancy, KW; McCafferty, DG; Yang, W, Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation., Journal of the American Chemical Society, vol. 133 no. 3 (January, 2011), pp. 478-485 [21142157], [doi] [abs] .
  110. Ess, DH; Johnson, ER; Hu, X; Yang, W, Singlet-triplet energy gaps for diradicals from fractional-spin density-functional theory., The Journal of Physical Chemistry A, vol. 115 no. 1 (January, 2011), pp. 76-83 [doi] [abs] .
  111. Lin, X; Hu, X; Concepcion, JJ; Chen, Z; Liu, S; Meyer, TJ; Yang, W, Catalytic mechanism for single-site water oxidation process: A theoretical study, Abstracts of Papers of the American Chemical Society (2011) [abs] .
  112. Wu, P; Hu, X; Yang, W, λ-metadynamics approach to compute absolute solvation free energy, The Journal of Physical Chemistry Letters, vol. 2 no. 17 (2011), pp. 2099-2103 [doi] [abs] .
  113. Lee, W; Zeng, X; Zhou, H-X; Bennett, V; Yang, W; Marszalek, PE, Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations, The Journal of Biological Chemistry, vol. 286 no. 10 (2011), pp. 8708- [doi] .
  114. Lee, W; Zeng, X; Zhou, H-X; Bennett, V; Yang, W; Marszalek, PE, Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations., The Journal of Biological Chemistry, vol. 285 no. 49 (December, 2010), pp. 38167-38172 [20870713], [doi] [abs] .
  115. Cui, G; Yang, W, Challenges with range-separated exchange-correlation functionals in time-dependent density functional theory calculations, Molecular Physics, vol. 108 no. 19-20 (October, 2010), pp. 2745-2750 [doi] [abs] .
  116. Cui, G; Fang, W; Yang, W, Efficient construction of nonorthogonal localized molecular orbitals in large systems., The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory, vol. 114 no. 33 (August, 2010), pp. 8878-8883 [20550205], [doi] [abs] .
  117. Hu, X; Hu, H; Beratan, DN; Yang, W, A gradient-directed Monte Carlo approach for protein design., Journal of Computational Chemistry, vol. 31 no. 11 (August, 2010), pp. 2164-2168 [20186860], [doi] [abs] .
  118. Heaton-Burgess, T; Yang, W, Structural manifestation of the delocalization error of density functional approximations: C(4N+2) rings and C(20) bowl, cage, and ring isomers., The Journal of Chemical Physics, vol. 132 no. 23 (June, 2010), pp. 234113 [20572695], [doi] [abs] .
  119. Ke, S-H; Liu, R; Yang, W; Baranger, HU, Time-dependent transport through molecular junctions., The Journal of Chemical Physics, vol. 132 no. 23 (June, 2010), pp. 234105 [20572687], [doi] [abs] .
  120. Johnson, ER; Keinan, S; Mori-Sánchez, P; Contreras-García, J; Cohen, AJ; Yang, W, Revealing noncovalent interactions., Journal of the American Chemical Society, vol. 132 no. 18 (May, 2010), pp. 6498-6506 [20394428], [doi] [abs] .
  121. Chen, Z; Concepcion, JJ; Hu, X; Yang, W; Hoertz, PG; Meyer, TJ, Concerted O atom-proton transfer in the O-O bond forming step in water oxidation., Proceedings of the National Academy of Sciences of the United States of America, vol. 107 no. 16 (April, 2010), pp. 7225-7229 [doi] [abs] .
  122. Zheng, X; Ke, S-H; Yang, W, Conductive junctions with parallel graphene sheets., The Journal of Chemical Physics, vol. 132 no. 11 (March, 2010), pp. 114703 [20331312], [doi] [abs] .
  123. Zeng, X; Hu, H; Zhou, H-X; Marszalek, PE; Yang, W, Equilibrium sampling for biomolecules under mechanical tension., Biophysical Journal, vol. 98 no. 4 (February, 2010), pp. 733-740 [20159170], [doi] [abs] .
  124. Hu, X; Xiao, D; Keinan, S; Asselberghs, I; Therien, MJ; Clays, K; Yang, W; Beratan, DN, Predicting the Frequency Dispersion of Electronic Hyperpolarizabilities on the Basis of Absorption Data and Thomas−Kuhn Sum Rules, The Journal of Physical Chemistry C, vol. 114 no. 5 (February, 2010), pp. 2349-2359 [repository], [doi] [abs] .
  125. Hu, X; Yang, W, Accelerating self-consistent field convergence with the augmented Roothaan-Hall energy function., The Journal of Chemical Physics, vol. 132 no. 5 (February, 2010), pp. 054109 [20136307], [doi] [abs] .
  126. Cui, G; Fang, W; Yang, W, Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals., Physical Chemistry Chemical Physics, vol. 12 no. 2 (January, 2010), pp. 416-421 [20023819], [doi] [abs] .
  127. Hu, H; Yang, W, Elucidating solvent contributions to solution reactions with Ab initio QM/MM methods, Journal of Physical Chemistry B, vol. 114 no. 8 (2010), pp. 2755-2759 [repository], [doi] [abs] .
  128. Johnson, ER; Yang, W; Davidson, ER, Spin-state splittings, highest-occupied-molecular-orbital and lowest-unoccupied-molecular-orbital energies, and chemical hardness, The Journal of Chemical Physics, vol. 133 no. 16 (2010) [repository], [doi] [abs] .
  129. Hammill, JT; Contreras-García, J; Virshup, AM; Beratan, DN; Yang, W; Wipf, P, Synthesis and chemical diversity analysis of bicyclo[3.3.1]non-3-en-2-ones, Tetrahedron, vol. 66 no. 31 (2010), pp. 5852-5862 [doi] [abs] .
  130. Hu, X; Beratan, DN; Yang, W, A gradient-directed Monte Carlo method for global optimization in a discrete space: application to protein sequence design and folding., The Journal of Chemical Physics, vol. 131 no. 15 (October, 2009), pp. 154117 [20568857], [doi] [abs] .
  131. Balabin, IA; Yang, W; Beratan, DN, Coarse-grained modeling of allosteric regulation in protein receptors., Proc Natl Acad Sci U S A, vol. 106 no. 34 (August, 2009), pp. 14253-14258 [19706508], [doi] [abs] .
  132. Balabin, IA; Yang, W; Beratan, DN, Modeling allosteric regulation in GPCRs: Toward rational structure-based drug design, Abstracts of Papers of the American Chemical Society, vol. 238 (August, 2009) [Gateway.cgi] .
  133. Yang, W, Free energies and mechanisms of chemical reactions in enzymes and in solution with QMMM minimum free energy path, Abstracts of Papers of the American Chemical Society, vol. 238 (August, 2009) .
  134. Kasper, AC; Moon, EJ; Hu, X; Park, Y; Wooten, CM; Kim, H; Yang, W; Dewhirst, MW; Hong, J, Analysis of HIF-1 inhibition by manassantin A and analogues with modified tetrahydrofuran configurations., Bioorganic & Medicinal Chemistry Letters, vol. 19 no. 14 (July, 2009), pp. 3783-3786 [19423348], [doi] [abs] .
  135. Bulat, FA; Couchman, L; Yang, W, Contact geometry and conductance of crossed nanotube junctions under pressure., Nano Letters, vol. 9 no. 5 (May, 2009), pp. 1759-1763 [19331377], [doi] [abs] .
  136. Zeng, X; Hu, H; Hu, X; Yang, W, Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method., The Journal of Chemical Physics, vol. 130 no. 16 (April, 2009), pp. 164111 [19405565], [doi] [abs] .
  137. Parks, JM; Hu, H; Rudolph, J; Yang, W, 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 (April, 2009), pp. 5217-5224 [19301836], [doi] [abs] .
  138. Ke, S-H; Yang, W; Curtarolo, S; Baranger, HU, Thermopower of molecular junctions: an ab initio study., Nano Letters, vol. 9 no. 3 (March, 2009), pp. 1011-1014 [19203208], [doi] [abs] .
  139. Mori-Sánchez, P; Cohen, AJ; Yang, W, Discontinuous nature of the exchange-correlation functional in strongly correlated systems., Physical Review Letters, vol. 102 no. 6 (February, 2009), pp. 066403 [19257614], [doi] [abs] .
  140. Rinderspacher, BC; Andzelm, J; Rawlett, A; Dougherty, J; Beratan, DN; Yang, W, Discrete optimization of electronic hyperpolarizabilities in a chemical subspace, Journal of Chemical Theory and Computation, vol. 5 no. 12 (2009), pp. 3321-3329 [doi] [abs] .
  141. Li, Z; Wang, C-Y; Ke, S-H; Yang, W, First-principles study for transport properties of defective carbon nanotubes with oxygen adsorption, The European Physical Journal B, vol. 69 no. 3 (2009), pp. 375-382 [doi] [abs] .
  142. Hu, X; Beratan, DN; Yang, W, Emergent strategies for inverse molecular design, Science in China Series B-Chemistry, vol. 52 no. 11 (2009), pp. 1769-1776 [doi] [abs] .
  143. Hu, H; Yang, W, 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 [doi] [abs] .
  144. Cohen, AJ; Mori Sanchez, P; Yang, WT, Second-order perturbation theory with fractional charges and fractional spins, Journal of Chemical Theory and Computation, vol. 5 no. 5 (2009), pp. 786-792 [doi] [abs] .
  145. Cohen, AJ; Mori-Sánchez, P; Yang, W, Second-order perturbation theory with fractional charges and fractional spins, Journal of Chemical Theory and Computation, vol. 5 no. 4 (2009), pp. 786-792 [doi] [abs] .
  146. Keinan, S; Therien, MJ; Beratan, DN; Yang, W, Molecular design of porphyrin-based nonlinear optical materials., The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory, vol. 112 no. 47 (November, 2008), pp. 12203-12207 [18973325], [doi] [abs] .
  147. Heaton-Burgess, T; Yang, W, Optimized effective potentials from arbitrary basis sets., The Journal of Chemical Physics, vol. 129 no. 19 (November, 2008), pp. 194102 [19026040], [doi] [abs] .
  148. Balamurugan, D; Yang, W; Beratan, DN, Exploring chemical space with discrete, gradient, and hybrid optimization methods., The Journal of Chemical Physics, vol. 129 no. 17 (November, 2008), pp. 174105 [19045331], [doi] [abs] .
  149. Hu, H; Boone, A; Yang, W, Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase., Journal of the American Chemical Society, vol. 130 no. 44 (November, 2008), pp. 14493-14503 [18839943], [doi] [abs] .
  150. Johnson, ER; Mori-Sánchez, P; Cohen, AJ; Yang, W, Delocalization errors in density functionals and implications for main-group thermochemistry., The Journal of Chemical Physics, vol. 129 no. 20 (November, 2008), pp. 204112 [19045857], [doi] [abs] .
  151. Heaton Burgess, T; Yang, WT, Optimized effective potentials from arbitrary basis sets, Journal of Chemical Physics, vol. 129 (November, 2008), pp. 194102 .
  152. Parks, JM; Hu, H; Cohen, AJ; Yang, W, A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes., The Journal of Chemical Physics, vol. 129 no. 15 (October, 2008), pp. 154106 [19045175], [doi] [abs] .
  153. Ke, S-H; Yang, W; Baranger, HU, Quantum-interference-controlled molecular electronics., Nano Letters, vol. 8 no. 10 (October, 2008), pp. 3257-3261 [18803424], [doi] [abs] .
  154. Keinan, S; Paquette, WD; Skoko, JJ; Beratan, DN; Yang, W; Shinde, S; Johnston, PA; Lazo, JS; Wipf, P, 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 no. 18 (September, 2008), pp. 3256-3263 [18802630], [doi] [abs] .
  155. Xiao, D; Bulat, FA; Yang, W; Beratan, DN, A donor-nanotube paradigm for nonlinear optical materials., Nano Letters, vol. 8 no. 9 (September, 2008), pp. 2814-2818 [18698728], [doi] [abs] .
  156. Cohen, AJ; Mori-Sánchez, P; Yang, W, Fractional spins and static correlation error in density functional theory., The Journal of Chemical Physics, vol. 129 no. 12 (September, 2008), pp. 121104 [19044996], [doi] [abs] .
  157. Hu, X; Beratan, DN; Yang, W, A gradient-directed Monte Carlo approach to molecular design., The Journal of Chemical Physics, vol. 129 no. 6 (August, 2008), pp. 064102 [18715046], [doi] [abs] .
  158. Fujimoto, K; Yang, W, Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg(2+)-sensitive dye., The Journal of Chemical Physics, vol. 129 no. 5 (August, 2008), pp. 054102 [18698883], [doi] [abs] .
  159. Cohen, AJ; Mori-Sánchez, P; Yang, W, Insights into current limitations of density functional theory., Science (New York, N.Y.), vol. 321 no. 5890 (August, 2008), pp. 792-794 [18687952], [doi] [abs] .
  160. Xiao, D; Yang, W; Beratan, DN, Inverse molecular design in a tight-binding framework., The Journal of Chemical Physics, vol. 129 no. 4 (July, 2008), pp. 044106 [18681633], [doi] [abs] .
  161. Mori-Sánchez, P; Cohen, AJ; Yang, W, Localization and delocalization errors in density functional theory and implications for band-gap prediction., Physical Review Letters, vol. 100 no. 14 (April, 2008), pp. 146401 [18518055], [doi] [abs] .
  162. Zeng, X; Hu, H; Hu, X; Cohen, AJ; Yang, W, Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach., The Journal of Chemical Physics, vol. 128 no. 12 (March, 2008), pp. 124510 [18376946], [doi] [abs] .
  163. Parks, JM; Kondru, RK; Hu, H; Beratan, DN; Yang, W, 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 no. 10 (March, 2008), pp. 3168-3176 [18271573], [doi] [abs] .
  164. Heaton-Burgess, T; Cohen, AJ; Yang, W; Davidson, ER, Size extensivity of the direct optimized effective potential method., The Journal of Chemical Physics, vol. 128 no. 11 (March, 2008), pp. 114702 [18361596], [doi] [abs] .
  165. Hu, H; Lu, Z; Parks, JM; Burger, SK; Yang, W, 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., The Journal of Chemical Physics, vol. 128 no. 3 (January, 2008), pp. 034105 [18205486], [doi] [abs] .
  166. Hu, H; Yang, W, 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 (January, 2008), pp. 573-601 [18393679], [doi] [abs] .
  167. Li, Z; Wang, C-Y; Zhang, X; Ke, S-H; Yang, W, First-principles study for transport properties of armchair carbon nanotubes with a double vacancy under strain, Journal of Applied Physics, vol. 103 no. 11 (2008) [doi] [abs] .
  168. Bulat, FA; Ke, S-H; Yang, W; Couchman, L, Lead-molecule coupling effects on the distortion-dependent conductance of carbon nanotubes, Physical Review B, vol. 77 no. 15 (2008) [doi] [abs] .
  169. Li, Z; Wang, C-Y; Zhang, X; Ke, S-H; Yang, W, Transport properties of an armchair carbon nanotube with a double vacancy under stretching, Journal of Physics. Condensed Matter : an Institute of Physics Journal, vol. 20 no. 34 (2008), pp. 345225 [doi] [abs] .
  170. Lee, H; Kim, KW; Park, J; Kim, H; Kim, S; Kim, D; Hu, X; Yang, W; Hong, J, 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 [doi] [abs] .
  171. Cohen, AJ; Mori-Sánchez, P; Yang, W, Fractional charge perspective on the band gap in density-functional theory, Physical Review B, vol. 77 no. 11 (2008), pp. 115123 [doi] [abs] .
  172. Burger, SK; Yang, W, Linear-scaling quantum calculations using non-orthogonal localized molecular orbitals, Journal of Physics. Condensed Matter : an Institute of Physics Journal, vol. 20 no. 29 (2008), pp. 294209 [doi] [abs] .
  173. Bulat, FA; Heaton-Burgess, T; Cohen, AJ; Yang, W, Optimized effective potentials from electron densities in finite basis sets., The Journal of Chemical Physics, vol. 127 no. 17 (November, 2007), pp. 174101 [17994801], [doi] [abs] .
  174. Burger, SK; Yang, W, Sequential quadratic programming method for determining the minimum energy path., The Journal of Chemical Physics, vol. 127 no. 16 (October, 2007), pp. 164107 [17979319], [doi] [abs] .
  175. Liu, R; Ke, S-H; Yang, W; Baranger, HU, Cobaltocene as a spin filter., The Journal of Chemical Physics, vol. 127 no. 14 (October, 2007), pp. 141104 [17935378], [doi] [abs] .
  176. Ke, S-H; Baranger, HU; Yang, W, Contact transparency of nanotube-molecule-nanotube junctions., Physical Review Letters, vol. 99 no. 14 (October, 2007), pp. 146802 [17930697], [doi] [abs] .
  177. Ke, S-H; Baranger, HU; Yang, W, Electron transport through single conjugated organic molecules: basis set effects in ab initio calculations., The Journal of Chemical Physics, vol. 127 no. 14 (October, 2007), pp. 144107 [17935386], [doi] [abs] .
  178. Parks, JM; Hu, H; Kondru, R; Yang, W, COMP 244-Nature of ligand binding in HCV polymerase: Characterization of specific interactions from QM/MM calculations, Abstracts of Papers of the American Chemical Society, vol. 234 (August, 2007) [Gateway.cgi] .
  179. Zeng, X; Hu, H; Yang, W, PHYS 124-QM/MM calculation of electron transfer process: Fractional number of electrons approach, Abstracts of Papers of the American Chemical Society, vol. 234 (August, 2007) .
  180. Hu, H; Yang, W, PHYS 301-Free energies of chemical reactions in enzyme and in solution, Abstracts of Papers of the American Chemical Society, vol. 234 (August, 2007) .
  181. Hu, H; Lu, Z; Elstner, M; Hermans, J; Yang, W, Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state., The Journal of Physical Chemistry A, vol. 111 no. 26 (July, 2007), pp. 5685-5691 [17474727], [doi] [abs] .
  182. Cohen, AJ; Mori-Sánchez, P; Yang, W, Assessment and formal properties of exchange-correlation functionals constructed from the adiabatic connection., The Journal of Chemical Physics, vol. 127 no. 3 (July, 2007), pp. 034101 [17655425], [doi] [abs] .
  183. Heaton-Burgess, T; Bulat, FA; Yang, W, Optimized effective potentials in finite basis sets., Physical Review Letters, vol. 98 no. 25 (June, 2007), pp. 256401 [17678039], [doi] [abs] .
  184. Ke, S-H; Baranger, HU; Yang, W, Role of the exchange-correlation potential in ab initio electron transport calculations., The Journal of Chemical Physics, vol. 126 no. 20 (May, 2007), pp. 201102 [17552745], [doi] [abs] .
  185. Cohen, AJ; Mori-Sánchez, P; Yang, W, Development of exchange-correlation functionals with minimal many-electron self-interaction error., The Journal of Chemical Physics, vol. 126 no. 19 (May, 2007), pp. 191109 [17523789], [doi] [abs] .
  186. Hu, H; Lu, Z; Yang, W, QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase., Journal of Chemical Theory and Computation, vol. 3 no. 2 (March, 2007), pp. 390-406 [19079734], [doi] [abs] .
  187. Heaton-Burgess, T; Ayers, P; Yang, W, Spin-potential functional formalism for current-carrying noncollinear magnetic systems., Physical Review Letters, vol. 98 no. 3 (January, 2007), pp. 036403 [17358702], [doi] [abs] .
  188. Keinan, S; Hu, X; Beratan, DN; Yang, W, Designing molecules with optimal properties using the linear combination of atomic potentials approach in an AM1 semiempirical framework., The Journal of Physical Chemistry A, vol. 111 no. 1 (January, 2007), pp. 176-181 [17201401], [doi] [abs] .
  189. Wang, W; Qiao, J; Wang, L; Duan, L; Zhang, D; Yang, W; Qiu, Y, Synthesis, structures, and optical properties of cadmium iodide/phenethylamine hybrid materials with controlled structures and emissions, Inorganic Chemistry, vol. 46 no. 24 (2007), pp. 10252-10260 [doi] [abs] .
  190. Ke, S-H; Baranger, HU; Yang, W, Role of the exchange-correlation potential in ab initio electron transport calculations, Journal of Chemical Physics, vol. 126 no. 20 (2007), pp. 201102/1-201102/4 [17552745], [doi] [abs] .
  191. Hu, H; Lu, Z; Yang, W, Fitting molecular electrostatic potentials from quantum mechanical calculations, Journal of Chemical Theory and Computation, vol. 3 no. 3 (2007), pp. 1004-1013 [doi] [abs] .
  192. Hori, T; Takahashi, H; Furukawa, S-I; Nakano, M; Yang, W, 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, vol. 111 no. 3 (2007), pp. 581-588 [doi] [abs] .
  193. Burger, SK; Yang, W, Automatic integration of the reaction path using diagonally implicit Runge-Kutta methods., The Journal of Chemical Physics, vol. 125 no. 24 (December, 2006), pp. 244108 [17199341], [doi] [abs] .
  194. Mori-Sánchez, P; Cohen, AJ; Yang, W, Many-electron self-interaction error in approximate density functionals., The Journal of Chemical Physics, vol. 125 no. 20 (November, 2006), pp. 201102 [17144681], [doi] [abs] .
  195. Lu, Z; Hu, H; Yang, W; Marszalek, PE, Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method., Biophysical Journal, vol. 91 no. 6 (September, 2006), pp. L57-L59 [16829559], [doi] [abs] .
  196. Zhang, Q; Lu, Z; Hu, H; Yang, W; Marszalek, PE, Direct detection of the formation of V-amylose helix by single molecule force spectroscopy., Journal of the American Chemical Society, vol. 128 no. 29 (July, 2006), pp. 9387-9393 [16848474], [doi] [abs] .
  197. Burger, SK; Yang, W, A combined explicit-implicit method for high accuracy reaction path integration., The Journal of Chemical Physics, vol. 124 no. 22 (June, 2006), pp. 224102 [16784258], [doi] [abs] .
  198. Liu, R; Ke, S-H; Baranger, HU; Yang, W, Negative differential resistance and hysteresis through an organometallic molecule from molecular-level crossing., Journal of the American Chemical Society, vol. 128 no. 19 (May, 2006), pp. 6274-6275 [16683765], [doi] [abs] .
  199. Ke, S-H; Yang, W; Baranger, HU, Nanotube-metal junctions: 2- and 3-terminal electrical transport., The Journal of Chemical Physics, vol. 124 no. 18 (May, 2006), pp. 181102 [16709090], [doi] [abs] .
  200. Wang, M; Lu, Z; Yang, W, Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase., The Journal of Chemical Physics, vol. 124 no. 12 (March, 2006), pp. 124516 [16599706], [doi] [abs] .
  201. Mori-Sánchez, P; Cohen, AJ; Yang, W, Self-interaction-free exchange-correlation functional for thermochemistry and kinetics., The Journal of Chemical Physics, vol. 124 no. 9 (March, 2006), pp. 91102 [16526838], [doi] [abs] .
  202. Wang, M; Hu, X; Beratan, DN; Yang, W, Designing molecules by optimizing potentials., Journal of the American Chemical Society, vol. 128 no. 10 (March, 2006), pp. 3228-3232 [16522103], [doi] [abs] .
  203. Burger, SK; Yang, W, Quadratic string method for determining the minimum-energy path based on multiobjective optimization., The Journal of Chemical Physics, vol. 124 no. 5 (February, 2006), pp. 054109 [16468853], [doi] [abs] .
  204. Cisneros, GA; Wang, M; Silinski, P; Fitzgerald, MC; Yang, W, Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase., The Journal of Physical Chemistry A, vol. 110 no. 2 (January, 2006), pp. 700-708 [16405343], [doi] [abs] .
  205. Liu, R; Ke, S-H; Yang, W; Baranger, HU, Organometallic molecular rectification., The Journal of Chemical Physics, vol. 124 no. 2 (January, 2006), pp. 024718 [16422637], [doi] [abs] .
  206. Champagne, B; Bulat, FA; Yang, W; Bonness, S; Kirtman, B, Density functional theory investigation of the polarizability and second hyperpolarizability of polydiacetylene and polybutatriene chains: Treatment of exact exchange and role of correlation, The Journal of Chemical Physics, vol. 125 no. 19 (2006) [doi] [abs] .
  207. Ke, S-H; Baranger, HU; Yang, W, Development of ab initio calculation for electron transport and the effects of lead and contact structures in molecular electronics, Journal of computational and theoretical nanoscience, vol. 3 no. 5 (2006), pp. 819-823 [doi] [abs] .
  208. Hori, T; Takahashi, H; Nakano, M; Nitta, T; Yang, W, A QM/MM study combined with the theory of energy representation: Solvation free energies for anti/syn acetic acids in aqueous solution, Chemical Physics Letters, vol. 419 no. 1-3 (2006), pp. 240-244 [doi] [abs] .
  209. Ayers, PW; Yang, W, Legendre-transform functionals for spin-density-functional theory, The Journal of Chemical Physics, vol. 124 no. 22 (2006), pp. 224108 [doi] [abs] .
  210. Ping, L; Yang, W; Pedersen, LC; Negishi, M; Pedersen, LG, Searching for the minimum energy path in the sulfuryl transfer reaction catalyzed by human estrogen sulfotransferase: Role of enzyme dynamics, International Journal of Quantum Chemistry, vol. 106 no. 14 (2006), pp. 2981-2998 [doi] [abs] .
  211. Sohn, J; Parks, JM; Buhrman, G; Brown, P; Kristjánsdóttir, K; Safi, A; Edelsbrunner, H; Yang, W; Rudolph, J, Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate., Biochemistry, vol. 44 no. 50 (December, 2005), pp. 16563-16573 [16342947], [doi] [abs] .
  212. Liu, R; Ke, S-H; Baranger, HU; Yang, W, Organometallic spintronics: dicobaltocene switch., Nano Letters, vol. 5 no. 10 (October, 2005), pp. 1959-1962 [16218717], [doi] [abs] .
  213. Wu, Q; Cohen, AJ; Yang, W, Analytic energy gradients of the optimized effective potential method., The Journal of Chemical Physics, vol. 123 no. 13 (October, 2005), pp. 134111 [16223279], [doi] [abs] .
  214. Ke, S-H; Baranger, HU; Yang, W, Models of electrodes and contacts in molecular electronics., The Journal of Chemical Physics, vol. 123 no. 11 (September, 2005), pp. 114701 [16392577] [abs] .
  215. Mori-Sánchez, P; Wu, Q; Yang, W, Orbital-dependent correlation energy in density-functional theory based on a second-order perturbation approach: success and failure., The Journal of Chemical Physics, vol. 123 no. 6 (August, 2005), pp. 62204 [16122290], [doi] [abs] .
  216. Hu, H; Yang, W, Dual-topology/dual-coordinate free-energy simulation using QM/MM force field., The Journal of Chemical Physics, vol. 123 no. 4 (July, 2005), pp. 041102 [16095339], [doi] [abs] .
  217. Cisneros, GA; Liu, H; Lu, Z; Yang, W, Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods., The Journal of Chemical Physics, vol. 122 no. 11 (March, 2005), pp. 114502 [15836224], [doi] [abs] .
  218. Ke, S-H; Baranger, HU; Yang, W, Contact atomic structure and electron transport through molecules., The Journal of Chemical Physics, vol. 122 no. 7 (February, 2005), pp. 074704 [15743262], [doi] [abs] .
  219. Liu, R; Ke, S-H; Baranger, HU; Yang, W, Intermolecular effect in molecular electronics., The Journal of Chemical Physics, vol. 122 no. 4 (January, 2005), pp. 44703 [15740279], [doi] [abs] .
  220. 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 .
  221. Ullmo, D; Jiang, H; Yang, W; Baranger, HU, Interactions and broken time-reversal symmetry in chaotic quantum dots, Physical Review B - Condensed Matter and Materials Physics, vol. 71 no. 20 (2005) [doi] [abs] .
  222. Jiang, H; Ullmo, D; Yang, W; Baranger, HU, Scrambling and gate-induced fluctuations in realistic quantum dots, Physical Review B, vol. 71 no. 8 (2005) [doi] [abs] .
  223. Bulat, FA; Toro-Labb́, A; Champagne, B; Kirtman, B; Yang, W, Density-functional theory (hyper)polarizabilities of push-pull π -conjugated systems: Treatment of exact exchange and role of correlation, The Journal of Chemical Physics, vol. 123 no. 1 (2005) [doi] [abs] .
  224. Wu, Q; Cohen, AJ; Yang, W, Analytic energy gradients of the optimized effective potential method, J. Chem. Phys., vol. 123 no. 134111/1-134111/10 (2005), pp. 134111 [16223279], [doi] [abs] .
  225. Getty, SA; Engtrakul, C; Wang, L; Liu, R; Ke, S-H; Baranger, HU; Yang, W; Fuhrer, MS; Sita, LR, Near-perfect conduction through a ferrocene-based molecular wire, Physical Review B, vol. 71 no. 24 (2005) [doi] [abs] .
  226. Bulat, FA; Toro-Labbe, A; Champagne, B; Kirtman, B; Yang, W, 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 .
  227. Wu, Q; Cohen, AJ; Yang, W, Excitation energies from time-dependent density functional theory with accurate exchange-correlation potentials, Molecular Physics, vol. 103 no. 6-8 (2005), pp. 711-717 [doi] [abs] .
  228. Ke, S-H; Baranger, HU; Yang, W, Electron transport through molecules: Gate-induced polarization and potential shift, Physical Review B, vol. 71 no. 11 (2005), pp. 113401/1-113401/4 [doi] [abs] .
  229. Ke, S-H; Baranger, H; Yang, W, "Contact Atomic Structure and Electron Transport Through Molecules", J. Chem. Phys., vol. 122 no. 7 (2005), pp. 114502/1-114502/7 [15743262], [doi] [abs] .
  230. Ulmo, D; Jiang, H; Yang, W; Baranger, H, "Landau Fermi Liquid Picture of Spin Density Functional Theory: Strutinsky Approach to Quantum Dots", Phys. Rev. B., Rapid Communication, vol. 71 no. 20 (2005), pp. 201310/1-201310/4 [doi] [abs] .
  231. Mori-Sánchez, P; Wu, Q; Yang, W, Orbital-dependent correlation energy in density-functional theory based on a second-order perturbation approach: success and failure., The Journal of Chemical Physics, vol. 123 no. 6 (2005), pp. 62204- [abs] .
  232. Cisneros, GA; Liu, H; Lu, Z; Yang, W, Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods., The Journal of Chemical Physics, vol. 122 no. 11 (2005), pp. 114502- [abs] .
  233. Jiang, H; Yang, W, Conjugate-gradient optimization method for orbital-free density functional calculations., The Journal of Chemical Physics, vol. 121 no. 5 (August, 2004), pp. 2030-2036 [15260756], [doi] [abs] .
  234. Lu, Z; Yang, W, Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations., The Journal of Chemical Physics, vol. 121 no. 1 (July, 2004), pp. 89-100 [15260525], [doi] [abs] .
  235. Wang, M; Lu, Z; Yang, W, Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method., The Journal of Chemical Physics, vol. 121 no. 1 (July, 2004), pp. 101-107 [15260526], [doi] [abs] .
  236. Lu, Z; Nowak, W; Lee, G; Marszalek, PE; Yang, W, Elastic properties of single amylose chains in water: a quantum mechanical and AFM study., Journal of the American Chemical Society, vol. 126 no. 29 (July, 2004), pp. 9033-9041 [15264836], [doi] [abs] .
  237. Cisneros, GA; Wang, M; Silinski, P; Fitzgerald, MC; Yang, W, The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment., Biochemistry, vol. 43 no. 22 (June, 2004), pp. 6885-6892 [15170325], [doi] [abs] .
  238. Jiang, H; Ullmo, D; Yang, W; Baranger, HU, Scrambling and Gate Effects in Realistic Quantum Dots, vol. 71 (May, 2004), pp. 085313/1-085313/6 [0405262v2], [doi] [abs] .
  239. Yang, W; Ayers, PW; Wu, Q, Potential functionals: dual to density functionals and solution to the v-representability problem., Physical Review Letters, vol. 92 no. 14 (April, 2004), pp. 146404 [15089563], [doi] [abs] .
  240. Feng, H; Bian, J; Li, L; Yang, W, An efficient method for constructing nonorthogonal localized molecular orbitals, The Journal of Chemical Physics, vol. 120 no. 20 (2004), pp. 9458-9466 [doi] [abs] .
  241. Xie, L; Liu, H; Yang, W, Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes, The Journal of Chemical Physics, vol. 120 no. 17 (2004), pp. 8039-8052 [doi] [abs] .
  242. Goj, LA; Cisneros, GA; Yang, W; Widenhoefer, RA, Erratum: "Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization" (Journal of Organometallic Chemistry (2003) vol. 687 (498-507) 10.1016/j.jorganchem.2003.09.046), Journal of Organometallic Chemistry, vol. 689 no. 17 (2004), pp. 2845- [doi] .
  243. Jiang, H; Ullmo, D; Yang, W; Baranger, HU, Electron-electron interactions in isolated and realistic quantum dots: A density functional theory study, Physical Review. B, Condensed Matter, vol. 69 no. 23 (2004), pp. 235326-1-235326-10 [doi] [abs] .
  244. Ke, S-H; Baranger, HU; Yang, W, Electron transport through molecules: Self-consistent and non-self-consistent approaches, Physical Review B - Condensed Matter and Materials Physics, vol. 70 no. 8 (2004), pp. 085410-1-085410-12 [doi] [abs] .
  245. Wang, M; Lu, Z; Yang, W, "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 no. 1 (2004), pp. 101-107 [15260526], [doi] [abs] .
  246. Lu, Z; Yang, W, "Reaction Path Potential for Complex Systems Derived From ab initioqm/mm Calculations", J. Chem. Phys., vol. 121 no. 1 (2004), pp. 89-100 [15260525], [doi] [abs] .
  247. Liu, H; Lu, Z; Cisneros, GA; Yang, W, Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions, The Journal of Chemical Physics, vol. 121 no. 2 (2004), pp. 697-706 [doi] [abs] .
  248. Lu, Z; Nowak, W; Lee, G; Marszalek, P; Yang, W, "Elastic Properties of Single Amylose Chains in Water", J. Am. Chem. Soc., vol. 126 no. 29 (2004), pp. 9033-9041 [15264836], [doi] [abs] .
  249. Ullmo, D; Jiang, H; Yang, W; Baranger, HU, Landau Fermi-liquid picture of spin density functional theory: Strutinsky approach to quantum dots, Physical Review. B, Condensed Matter, vol. 70 no. 20 (2004), pp. 205309-1-205309-15 [doi] [abs] .
  250. Wu, Q; Yang, WT, Algebraic equation and iterative optimization for the optimized effective potential in density functional theory, Journal of Theoretical and Computational Chemistry, vol. 2 no. 4 (December, 2003), pp. 627-638 [Gateway.cgi], [doi] .
  251. Jiang, H; Baranger, HU; Yang, WT, Density-functional theory simulation of large quantum dots, Physical Review B, vol. 68 no. 16 (October, 2003), pp. 1653371-1653379 [Gateway.cgi], [doi] [abs] .
  252. Cisneros, GA; Liu, H; Zhang, Y; Yang, W, Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase., Journal of the American Chemical Society, vol. 125 no. 34 (August, 2003), pp. 10384-10393 [12926963], [doi] [abs] .
  253. Jiang, H; Baranger, HU; Yang, W, Spin and conductance-peak-spacing distributions in large quantum dots: a density-functional theory study., Physical Review Letters, vol. 90 no. 2 (January, 2003), pp. 026806 [12570571], [doi] [abs] .
  254. Goj, LA; Cisneros, GA; Yang, W; Widenhoefer, RA, Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization, Journal of Organometallic Chemistry, vol. 687 no. 2 (2003), pp. 498-507 [doi] [abs] .
  255. Jiang, H; Baranger, HU; Yang, W, Desnity functional theory simulation of large quantum dots, Phys. Rev. B., vol. 68 (2003), pp. 165337-1-165337-9 .
  256. Mori-Sánchez, P; Wu, Q; Yang, W, Accurate polymer polarizabilities with exact exchange density-functional theory, Journal of Chemical Physics, vol. 119 no. 21 (2003), pp. 11001-11004 [doi] [abs] .
  257. Hasegawa, J-Y; Ishida, M; Nakatsuji, H; Lu, Z; Liu, H; Yang, W, Energetics of the electron transfer from bacteriopheophytin to ubiquinone in the photosynthetic reaction center for Rhodopseudomonas viridis: Theoretical study, Journal of Physical Chemistry B, vol. 107 no. 3 (2003), pp. 838-847 [doi] [abs] .
  258. Ke, S-H; Baranger, HU; Yang, W, Addition Energies of Fullerenes and Carbon Nanotubes as Quantum Dots, Phys. Rev. Lett., vol. 91 no. 11 (2003), pp. 116803 [14525451], [doi] [abs] .
  259. Wu, Q; Yang, W, A direct optimization method for calculating density functionals and exchange-correlation potentials from electron densities, Journal of Chemical Physics, vol. 118 no. 6 (2003), pp. 2498-2509 [doi] [abs] .
  260. Wu, Q; Ayers, PW; Yang, W, Density-functional theory calculations with correct long-range potentials, Journal of Chemical Physics, vol. 119 no. 6 (2003), pp. 2978-2990 [doi] [abs] .
  261. Jiang, H; Baranger, HU; Yang, W, Density-functional theory simulation of large quantum dots, Physical Review. B, Condensed Matter, vol. 68 no. 16 (2003), pp. 1653371-1653379 [abs] .
  262. Yang, W; Wu, Q, Direct method for optimized effective potentials in density-functional theory., Physical Review Letters, vol. 89 no. 14 (September, 2002), pp. 143002 [12366042], [doi] [abs] .
  263. 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) .
  264. Yang, W; Lee, H-W; Hellinga, H; Yang, JJ, Structural analysis, identification, and design of calcium-binding sites in proteins., Proteins, vol. 47 no. 3 (May, 2002), pp. 344-356 [doi] [abs] .
  265. Lu, ZY; Liu, HY; Yang, WT, A QM/MM study on the structure and catalysis mechanism of PDE4B., Abstracts of Papers of the American Chemical Society, vol. 223 (April, 2002), pp. C76-C76 .
  266. Cisneros, GA; Liu, HY; Zhang, YK; Yang, WT, QM/MM study of the reaction mechanism of 4-oxalocrotonate tautomerase., Abstracts of Papers of the American Chemical Society, vol. 223 (April, 2002), pp. C78-C78 [Gateway.cgi] .
  267. Yang, WT; Zhang, YK; Liu, HY, Developments and applications of a DFT QM/MM free energy method for simulation of chemical reactions in enzymes., Abstracts of Papers of the American Chemical Society, vol. 223 (April, 2002), pp. C89-C89 [Gateway.cgi] .
  268. 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 .
  269. Wu, Q; Yang, W, Empirical correction to density functional theory for van der Waals interactions, Journal of Chemical Physics, vol. 116 no. 2 (2002), pp. 515-524 [doi] [abs] .
  270. Wu, Q; Yang, W, An Empirical Correction to Density Functional Theory for van der Waals Interactions, J. Chem. Phys., vol. 116 (2002), pp. 515-524 .
  271. Liu, H; Elstner, M; Kaxiras, E; Frauenheim, T; Hermans, J; Yang, W, Quantum mechanics simulation of protein dynamics on long timescale., Proteins, vol. 44 no. 4 (September, 2001), pp. 484-489 [11484226] [abs] .
  272. 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 .
  273. Baik, M-H; Silverman, JS; Yang, IV; Ropp, PA; Szalai, VA; Yang, W; Thorp, HH, Using density functional theory to design DNA base analogues with low oxidation potentials, Journal of Physical Chemistry B, vol. 105 no. 27 (2001), pp. 6437-6444 [doi] [abs] .
  274. Yang, W; Zhang, Y; Ayers, PW, Degenerate ground states and a fractional number of electrons in density and reduced density matrix functional theory, Physical Review Letters, vol. 84 no. 22 (May, 2000), pp. 5172-5175 [10990895], [doi] [abs] .
  275. Zhang, YK; Yang, WT, Perspective on "Density-functional theory for fractional particle number: derivative discontinuities of the energy" Perdew JP, Parr RG, Levy M, Balduz JL Jr, Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol. 103 no. 3-4 (February, 2000), pp. 346-348 [Gateway.cgi], [doi] [abs] .
  276. 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 .
  277. Liu, H; Zhang, Y; Yang, W, How is the active site of enolase organized to catalyze two different reaction steps?, Journal of the American Chemical Society, vol. 122 no. 28 (2000), pp. 6560-6570 [doi] [abs] .
  278. Enkvist, C; Zhang, Y; Yang, W, Density functional study of a weakly hydrogen-bonded benzene-ammonia complex: The importance of the exchange functional, International Journal of Quantum Chemistry, vol. 79 no. 5 (2000), pp. 325-329 [doi] [abs] .
  279. Liu, H; Zhang, Y; Yang, W, 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 .
  280. Zhang, Y; Liu, H; Yang, W, 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, Journal of Chemical Physics, vol. 112 no. 8 (2000), pp. 3483-3492 [abs] .
  281. Enkvist, C; Zhang, Y; Yang, W, 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 .
  282. Liu, S; Pérez-Jordâ, JM; Yang, W, Nonorthogonal localized molecular orbitals in electronic structure theory, Journal of Chemical Physics, vol. 112 no. 4 (2000), pp. 1634-1644 [abs] .
  283. Zhang, Y; Lee, T; Yang, W, A psuedo-bond approach to combining quantum mechanical and molecular mechanical methods, J. Chem. Phys., vol. 110 no. 1 (1999), pp. 46-54 [doi] [abs] .
  284. Little, SB; Rabinowitz, JR; Wei, P; Yang, W, A comparison of calculated and experimental geometries for crowded polycyclic aromatic hydrocarbons and their metabolites, Polycyclic Aromatic Compounds, vol. 1999 no. 14-15 (1999), pp. 53-61 [abs] .
  285. Lewis, JP; Liu, S; Lee, T-S; Yang, W, A Linear-Scaling Quantum Mechanical Investigation of Cytidine Deaminase, Journal of Computational Physics, vol. 151 no. 1 (1999), pp. 242-263(invited article.) [doi] [abs] .
  286. Zhang, Y; Lee, T-S; Yang, W, A pseudobond approach to combining quantum mechanical and molecular mechanical methods, Journal of Chemical Physics, vol. 110 no. 1 (1999), pp. 46-54 [doi] [abs] .
  287. Zhang, Y; Yang, W, A challenge for density functionals: Self-interaction error increases for systems with a noninteger number of electrons, The Journal of Chemical Physics, vol. 109 no. 7 (August, 1998), pp. 2604-2608 [doi] [abs] .
  288. Yang, WT; Levy, M; Trickey, S, Special issue: Symposium on density functional and applications (Part I of II) - Introduction, International Journal of Quantum Chemistry, vol. 69 no. 3 (August, 1998), pp. 227-227 [Gateway.cgi] .
  289. Acker, JC; Marks, LB; Spencer, DP; Yang, W; Avery, MA; Dodge, RK; Rosner, GL; Dewhirst, MW, Serial in vivo observations of cerebral vasculature after treatment with a large single fraction of radiation., Radiation Research, vol. 149 no. 4 (April, 1998), pp. 350-359 [9525499], [doi] [abs] .
  290. Lewis, JP; Carter, CW; Hermans, J; Pan, W; Lee, TS; Yang, WT, Quantum mechanical methods for large biomolecular systems: Applications in the study of the cytidine deaminase enzyme, Biophysical Journal, vol. 74 no. 2 (February, 1998), pp. A132-A132 [Gateway.cgi] .
  291. Zhang, YK; Yang, WT, Comment on "Generalized gradient approximation made simple", Physical Review Letters, vol. 80 no. 4 (January, 1998), pp. 890-890 [Gateway.cgi], [doi] .
  292. York, DM; Lee, T-S; Yang, W, Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods, Physical Review Letters, vol. 80 no. 22 (1998), pp. 5011-5014 [abs] .
  293. Yang, W; Levy, M; Trickey, S, Symposium on density functional and applications (part 1 of ii) - introduction, Int. J. Quantum Chem., vol. 69 (1998), pp. 227 .
  294. Yang, W, Generalized adiabatic connection in density functional theory, Journal of Chemical Physics, vol. 109 no. 23 (1998), pp. 10107-10110 [doi] [abs] .
  295. Pérez-Jordá, JM; Yang, W, On the scaling of multipole methods for particle-particle interactions, Chemical Physics Letters, vol. 282 no. 1 (1998), pp. 71-78 [abs] .
  296. Pan, W; Lee, T-S; Yang, W, Parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations, Journal of Computational Chemistry, vol. 19 no. 9 (1998), pp. 1101-1109 [abs] .
  297. Lewis, JP; Jr, CWC; Hermans, J; Pan, W; Lee, T-S; Yang, W, Active species for the ground-state complex of cytidine deaminase: A linear-scaling quantum mechanical investigation, Journal of the American Chemical Society, vol. 120 no. 22 (1998), pp. 5407-5410 [doi] [abs] .
  298. Lee, T-S; Lewis, JP; Yang, W, Linear-scaling quantum mechanical calculations of biological molecules: The divide-and-conquer approach, Computational Materials Science, vol. 12 no. 3 (1998), pp. 259-277(invited article.) [abs] .
  299. Lee, T-S; Yang, W, Frozen density matrix approach for electronic structure calculations, International Journal of Quantum Chemistry, vol. 69 no. 3 (1998), pp. 397-404 [abs] .
  300. Zhu, TH; Pan, W; Yang, WT, Divide-and-conquer calculations for clean surfaces and surface adsorption, Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol. 96 no. 1 (April, 1997), pp. 2-6 [Gateway.cgi], [doi] .
  301. Zhang, Y; Pan, W; Yang, W, Describing van der Waals interaction in diatomic molecules with generalized gradient approximations: The role of the exchange functional, The Journal of Chemical Physics, vol. 107 no. 19 (1997), pp. 7921-7925 [abs] .
  302. Yang, W, Absolute-energy-minimum principles for linear-scaling electronic-structure calculations, Physical Review B - Condensed Matter and Materials Physics, vol. 56 no. 15 (1997), pp. 9294-9297 [abs] .
  303. Pérez-Jordá, JM; Yang, W, Fast evaluation of the Coulomb energy for electron densities, Journal of Chemical Physics, vol. 107 no. 4 (1997), pp. 1218-1226 [abs] .
  304. Pan, W; Zhu, T; Yang, W, First-principles study of the structural and electronic properties of ethylene adsorption on Si(100)-(2×1) surface, The Journal of Chemical Physics, vol. 107 no. 10 (1997), pp. 3981-3985 [abs] .
  305. Zhu, T; Pan, W; Yang, W, Structure of solid-state systems from embedded-cluster calculations: A divide-and-conquer approach, Physical Review B - Condensed Matter and Materials Physics, vol. 53 no. 19 (1996), pp. 12713-12724 [abs] .
  306. York, DM; Lee, T-S; Yang, W, Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules, Chemical Physics Letters, vol. 263 no. 1-2 (1996), pp. 297-304 [abs] .
  307. York, DM; Yang, W, A chemical potential equalization method for molecular simulations, The Journal of Chemical Physics, vol. 104 no. 1 (1996), pp. 159-172 [abs] .
  308. York, DM; Lee, T-S; Yang, W, Quantum mechanical study of aqueous polarization effects on biological macromolecules, Journal of the American Chemical Society, vol. 118 no. 44 (1996), pp. 10940-10941 [doi] .
  309. Pérez-Jordá, JM; Yang, W, A concise redefinition of the solid spherical harmonics and its use in fast multipole methods, Journal of Chemical Physics, vol. 104 no. 20 (1996), pp. 8003-8006 [abs] .
  310. Ni, H; York, DM; Bartolotti, L; Wells, RL; Yang, W, Density-functional study of the geometries, stabilities, and bond energies of group III-V (13-15) four-membered-ring compounds, Journal of the American Chemical Society, vol. 118 no. 24 (1996), pp. 5732-5736 [doi] [abs] .
  311. Lee, T-S; York, DM; Yang, W, Linear-scaling semiempirical quantum calculations for macromolecules, Journal of Chemical Physics, vol. 105 no. 7 (1996), pp. 2744-2750 [abs] .
  312. Wei, P; Yang, W, Structure and stability of molybdenum carbide clusters (MoC4)n (n=1 to 4) and their anions, Physical Review. B, Condensed Matter, vol. 51 no. 11 (1995), pp. 7224-7230 [doi] [abs] .
  313. Zhao, Q; Yang, W, Analytical energy gradients and geometry optimization in the divide-and-conquer method for large molecules, The Journal of Chemical Physics, vol. 102 no. 24 (1995), pp. 9598-9603 [abs] .
  314. York, DM; Yang, W; Lee, H; Darden, T; Pedersen, LG, Toward the accurate modeling of DNA: The importance of long-range electrostatics, Journal of the American Chemical Society, vol. 117 no. 17 (1995), pp. 5001-5002 .
  315. Yang, W; Lee, T-S, A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules, The Journal of Chemical Physics, vol. 103 no. 13 (1995), pp. 5674-5678 [abs] .
  316. Pérez-Jordá, J; Yang, W, A simple O(N log N) algorithm for the rapid evaluation of particle-particle interactions, Chemical Physics Letters, vol. 247 no. 4-6 (1995), pp. 484-490 [abs] .
  317. Pérez-Jorda, J; Yang, W, An algorithm for 3D numerical integration that scales linearly with the size of the molecule, Chemical Physics Letters, vol. 241 no. 4 (1995), pp. 469-476 [abs] .
  318. Parr, RG; Yang, W, Density-functional theory of the electronic structure of molecules, Annual Review of Physical Chemistry, vol. 46 no. 1 (1995), pp. 701-728 [abs] .
  319. Lee, T-S; York, DM; Yang, W, A new definition of atomic charges based on a variational principle for the electrostatic potential energy, The Journal of Chemical Physics, vol. 102 no. 19 (1995), pp. 7549-7556 [abs] .
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  323. York, D; Lu, JP; Yang, W, Density-functional calculations of the structure and stability of C240, Physical Review. B, Condensed Matter, vol. 49 no. 12 (1994), pp. 8526-8528 [doi] [abs] .
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  326. Bemish, RJ; Block, PA; Pedersen, LG; Weitao, Y; Miller, RE, The Ar-C2H2 intermolecular potential from high resolution spectroscopy and ab initio theory: A case for multicenter interactions, The Journal of Chemical Physics, vol. 99 no. 11 (1993), pp. 8585-8598 [abs] .
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  330. LEE, CT; YANG, WT, THE DIVIDE-AND-CONQUER DENSITY-FUNCTIONAL APPROACH - MOLECULAR INTERNAL-ROTATION AND DENSITY OF STATES, The Journal of Chemical Physics, vol. 96 no. 3 (February, 1992), pp. 2408-2411 [Gateway.cgi], [doi] .
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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 .