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1.  Robert G. Parr and Weitao Yang. “Density-Functional Approach to the Frontier-Electron Theory of Chemical Reactivity”, J. Am. Chem. Soc. 106, 4049 (1984).

2.  Weitao Yang, Robert G. Parr and R. Pucci, “Electron Density, Kohn-Sham Frontier Orbitals, and Fukui Functions”, J. Chem. Phys. 81, 2862 (1984).


3.  Mel Levy, Weitao Yang and Robert G. Parr, “A New Functional with Homogeneous Coordinate Scaling in Density-Functional Theory: F[*,*]”, J. Chem. Phys. 83, 2334 (1985).

4.  Weitao Yang, Chengteh Lee and Swapan K. Ghosh, “Molecular Softness as the Average of Atomic Softnesses: Companion Principle to the Geometric Mean Principle for Electronegativity Equalization”, J. Phys. Chem. 89, 5412 (1985).

5.  Weitao Yang and Robert G. Parr, “Hardness, Softness, and Fukui Function in the Electronic Theory of Metals and Catalysis”, Proc. Natl. Acad. Sci. USA 82, 6723 (1985)


6. Weitao Yang and John E. Harriman, “Analysis of the Kinetic Energy Functional in Density-Functional Theory”, J. Chem. Phys. 84, 3320 (1986).

7. Weitao Yang, “Gradient Correction in Thomas-Fermi Theory”, Phys. Rev. A 34, 4575 (1986).

8. Weitao Yang, Robert G. Parr and Chengteh Lee, “Various Functionals for the Kinetic Energy Density of an Atom or Molecule”, Phys. Rev. A 34, 4586 (1986).

9. 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. 108, 5708 ( 1986).


10. Wenhui Xue and Weitao Yang, “Application of a Scaled Particle Theory to Polar Solute System and Calculation of the Salt Effect Constant”, Acta Physico-Chimica Sinica, 3, 258 (1987) (pdf)

11. Weitao Yang, “Ab Initio Approach for Many-Electron System Without Invoking Orbitals: An Integral Formulation of Density-Functional Theory”, Phys. Rev. Lett. 59, 1569 (1987).

12. Weitao Yang, Robert G. Parr and Lieve Uytterhoeven, “New Relation Between Hardness and Compressibility of Minerals”, Physics and Chemistry of Minerals, 15, 191 (1987). [PDF]

13. Weitao Yang, “Some Remarks on Scaling Relations in Density-Functional Theory”, P499 in Density Matrices and Density-Functionals, Edited by R. Erdahl and V. H. Smith, Jr., D. Reidel Publishing Company, Dordrecht, Holland (1987).


14. Chengteh Lee, Weitao Yang and Robert G. Parr, “Local Softness and Chemical Reactivity in the Molecules CO, SCN, and H CO”, Theochem 163, 305 (1988).

15. 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 37, 785 (1988).

16. Weitao Yang, “Ab Initio Approach for Many-Electron Systems Without Invoking Orbitals: An Integral Formulation of Density-Functional Theory”, Phys. Rev. A 38, 5494 (1988).

17. Weitao Yang, “Thermal Properties of Many-Electron Systems: An Integral Formulation of Density-Functional Theory”, Phys. Rev. A 38, 5504 (1988).

18. Weitao Yang, “Dynamic Linear Response of Many-Electron Systems: An Integral Formulation of Density-Functional Theory”, Phys. Rev. A 38, 5512 (1988).

19. Weitao Yang and Andrew C. Peet, “The Collocation Method for Bound Solutions of the Schroedinger Equation”, Chem. Phys. Lett. 153, 98 (1988).


20. R.G. Parr and W. Yang, “Density-Functional Theory of Atoms and Molecules.” Oxford University Press, New York, NY, 1989.

21. 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. 90, 1746 (1989).

22. 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. 91, 6598 ( 1989).

23. 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. 91, 3504 (1989).

24. 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. 91, 7537 ( 1989).


25. 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. 38, 819 (1990).

26. Weitao Yang, “Integral Formulation of Density-Functional Theory”, Adv. Quantum Chem. 21, 293 (1990) edited by Samuel B. Trickey. (Invited paper to commemorate the 25th Anniversary of the Hohenberg-Kohn theorem.)

27. 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. 92, 522 (1990).


28. Weitao Yang, “A Local Projection Method for the Linear Combination of Atomic Orbital Implementation of Density-Functional Theory”, J. Chem. Phys. 94, 1208 (1991).

29. Weitao Yang, “Direct Calculation of Electron Density in Density-Functional Theory”, Phys. Rev. Letts. 66, 1438 (1991).

30. Weitao Yang, “Direct Calculation of Electron Density in Density-Functional Theory: Implementation for Benzene and a Tetrapeptide”, Phys. Rev. A 44, 7823 (1991).


31. Chengteh Lee and Weitao Yang, “The Divide-and-Conquer Density-Functional Approach: Molecular Internal Rotation and Density of States”, J. Chem. Phys. 96, 2408–2411 (1992).

32. T. Daniel Crawford and Weitao Yang, “The Hartley Basis Functions and Transform: Alternatives to Plane Wares and Fourier Transform,” Chem. Phys. Lett. 192, 45 ( 1992).

33. Weitao Yang, “Electron Density as the Basic Variable: a Divide-and-Conquer Approach to the Ab Initio Computation of Large Molecules”, Journal of Molecular Structure/THEOCHEM 255, 461 (1992). Invited paper for the special issue on “Electron Density and Chemical Reactions”.


34. R. J. Bemish, P. A. Block, L.G. Pedersen, Weitao Yang and R. E. Miller, “The Ar-C2H2 Intermolecular Potential from High Resolution Spectroscopy and ab initio Theory: A Case for Multi-Center Interactions”, J. Chem. Phys. 99, 8585 (1993).

35. Chengteh Lee, George Fitzgerald and Weitao Yang, “Nonlocal Density Functional Calculations: Comparison of Two Implementation Schemes”, J. Chem. Phys. 98, 2971 (1993).

36. Weitao Yang, “Density-Functional Theory of Large Systems: A Divide-and-Conquer Approach”, page 367, in Condensed-Matter Theories vol. 8, edited by L. Blum and F. B. Malik, Plenum Press (1993)

37. Tianhai Zhu, Chengteh Lee and Weitao Yang, “Examination of Several Exchange – Correlation Energy Functionals by Accurate Self-Consistent Atomic Calculations”, J. Chem. Phys. 98 (6), 4814 (1993).


38. Darrin York, Jian Ping Lu and Weitao Yang, “Density-functional Calculations of the Structure and Stability of C240 “, Phys. Rev. B. Rapid Communication, 49(12), 8526-8528 (1994).

39. Jian Ping Lu and Weitao Yang, “The Shape of Large Single- and Multiple-Shell Fullerenes”, Phys. Rev. B, 49, 11421(1994).

40. Weitao Yang and Zhongxiang Zhou, “Electronic Structure of Solid-State Systems via the Divide-and-Conquer Method”, Invited chapter in “Density Functional Theory of Molecules, Clusters, and Solids”, pp 177-188, Edited by D.E. Ellis, Kluwer Academic Publishers (1994). (pdf)

41. Darrin York and Weitao Yang, “The Fast Fourier Poisson Method for Calculating Ewald Sums”, J. Chem. Phys., 101, 3298 (1994).

42. Tianhai Zhu and Weitao Yang, “Structure of the Ammonia Dimer Studied by Density-Functional Theory”, The International Journal of Quantum Chemistry, 49, 613(1994).


43. 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., 102, 7549(1995).

44. Pan Wei and Weitao Yang, “Structure and Stability of Molybdenum Carbide Clusters (MoC4)n (n=1 to 4) and Their Anions”, Phys. Rev. B, 51, 7224(1995).

45. R. G. Parr and Weitao Yang, “Density-Functional Theory of the Electronic Structure of Molecules”, Ann. Rev. Phys. Chem., 46, 701(1995).

46. Jose M. Perez-Jorda and Weitao Yang, “An Algorithm for 3D numerical integration that scale linearly with the size of the molecule”, Chem. Phys. Lett., 241,469(1995).

47. Jose M. Perez-Jorda and Weitao Yang, “A Simple O( N log N) Algorithm for the Rapid Evaluation of Particle-Particle Interactions”, Chem. Phys. Lett., 247, 484(1995).

48. Weitao Yang and Taisung Lee, “A Density-Matrix Divide-and-Conquer Approach for Electronic Structure Calculations of Large Molecules”, J. Chem. Phys., 103, 5674 (1995).

49. Darrin M. York, Weitao Yang, Hsing Lee, Tom Darden and Lee Pedersen, “Towards the Accurate Modeling of DNA: the Importance of Long Range Electrostatics”, J. Am. Chem. Soc, Communication, 117, 5001-5002(1995). (pdf)

50. Qingsheng Zhao and Weitao Yang, “Analytical Energy Gradients and Geometry Optimization in the Divide-and-Conquer Method for Large Molecules”, J. Chem. Phys., 102, 9598(1995).


51. Tai-Sung Lee, Darrin York and Weitao Yang, “Linear-Scaling Semiempirical Quantum Calculations for Macromolecules”, J. Chem. Phys. 105, 2744(1996).

52. Haihong Ni, Darrin York, Lee Bartolotti, Richard Wells and Weitao Yang, “Density Functinoal Study of the Geometries, Stabilities and Bond Energies of III-V(13-15) Four-Membered Ring Compounds”, J. Am. Chem. Soc., 118, 5732(1996).

53. Jose M. Perez-Jorda and Weitao Yang, “A Concise Redefinition of the Solid Spherical Harmonics and its Use in the fast Multipole Methods”, J. Chem. Phys., 104, 8003(1996).

54. Darrin York, Tai-Sung Lee and Weitao Yang, “Quantum Mechanical Study of Aqueous Polarization Effects on Biological Macromolecules”, J. Am. Chem. Soc., Communication, 118, 10940(1996).

55. Darrin York and Weitao Yang, “A Chemical Potential Equalization Method for Molecular Simulations”, J. Chem. Phys., 104, 159(1996).

56. Darrin York, Tai-Sung Lee and Weitao Yang, “Parameterization and Efficient Implementation of a Solvent Model for Linear-Scaling Semiempirical Quantum Mechanical calculations of Biological Macromolecules”, Chem. Phys. Lett. 263, 297 (1996).

57. Tianhai Zhu, Wei Pan and Weitao Yang, “Structure of Solid-State Systems from Embedded-Cluster Calculations: a Divide-and-Conquer Approach”, Phys. Rev. B., 53, 12713(199


58. Wei Pan, Tianhai Zhu and Weitao Yang, “First-Principles Study of the Structural and Electronic Properties of Ethylene Adsorption on Si(100)-(2×1) Surface”, J. Chem. Phys., 107, 3981-3985 (1997).

59. Jose M. Perez-Jorda and Weitao Yang, “Fast Evaluation of the Coulomb Energy for Electron Densities”, J. Chem. Phys., 107, 1218-1226 (1997).

60. Weitao Yang, “Absolute Energy Minimum Principles for Linear Scaling Quantum Mechanical Calculations”, Phys. Rev. B. 56, 9294-9297 (1997).

61. Yingkai Zhang, Wei Pan and Weitao Yang, “Describing van der Waals Interaction in Diatomic Molecules with Generalized Gradient Approximations: the ole of the Exchange Functional”, J. Chem. Phys., 107, 7921-7925 (1997).

62. Tianhai Zhu, Wei Pan and Weitao Yang, “Divide-and-Conquer Calculations for Clean Surfaces and Surface Adsorption”, Theo. Chem. Account., 96, 2-6 (1997).


63. Tai-Sung Lee and Weitao Yang, “A Frozen Density Matrix Approach for Electronic Structure Calculations”, Int. J. Quantum Chem., 69, 397–404 (1998).

64. Tai-Sung Lee, James P. Lewis and Weitao Yang, “Linear-Scaling Quantum Mechanical Calculations of Biological Molecules: The Divide-and-Conquer Approach”, invited article, Computational Materials Science, 12, 259–277(1998).

65. James P. Lewis, Charles W. Carter, Jr., 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., 120, 5407–5410(1998).

66. Wei Pan, Tai-Sung Lee and Weitao Yang, “A Parallel Implementation of Divide-and-Conquer Semiempirical Quantum Chemistry Calculations”, J. Comp. Chem. 19, 1101(1998).

67. Jose M. Perez-Jorda and Weitao Yang, “On the Scaling of Multipole Methods for Particle-Particle Interactions”, Chem. Phys. Lett., 282, 71–78 (1998).

68. Weitao Yang. “Generalized adiabatic connection in density functional theory”. J. Chem. Phys., 109: 10107-10110, 1998.

69. Weitao Yang and Jose M. Perez-Jorda, “Linear Scaling Methods for Electronic Structure Calculations”, 1496–1513, Encyclopedia of Computational Chemistry, edited by Paul v. R. Schleyer, John Wiley & Sons, New York (1998). Published Online: 15 APR 2002, DOI: 10.1002/0470845015.cla005m

70. Weitao Yang, Mel Levy and S. Trickey “Special Issue: Symposium on density functional and applications (Part I of II) – Introduction”, Int. J. Quantum Chem., 69-227-227. (1998).

71. Darrin York, Taisung Lee and Weitao Yang, “Quantum Mechanical Treatment of Biological Macromolecules in Solution Using Linear-Scaling electronic Structure Methods”, Phys. Rev. Lett., 80, 5011–5014(1998).

72. Yingkai Zhang and Weitao Yang, “A Challenge for Density Functionals: Self-interaction Error Increases for Systems with a Noninteger Number of Electrons”, J. Chem. Phys. 109, 2604–2608 (1998).

73. Yingkai Zhang and Weitao Yang, “Comment on ‘Generalized Gradient Approximation Made Simple'”, Phys. Rev. Lett., 80, 890 (1998).


74. James P. Lewis, Shubin Liu, Taisung Lee and Weitao Yang, “A Linear-Scaling Quantum Mechanical Investigation of Cytidine Deaminase”, invited article, J. Comp. Phys. 151, 242–263(1999).

75. 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, 14, 53–61(1999).

76. Yingkai Zhang, Taisung Lee and Weitao Yang, “A Pseudo-Bond Approach To Combining Quantum Mechanical And Molecualr Mechanical Methods”, J. Chem. Phys., 110, 46–54 (1999).


77. 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, 79, 325–329 (2000).

78. Shubin Liu, Jose M. Perez-Jorda and Weitao Yang, ” Nonothorgonal Localized Molecular Orbitals in Electronic Structure Theory”, J. Chem. Phys., 112, 1634–1644(2000).

79. 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., 122, 6560(2000).

80. 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., 84, 5172–5175(2000).

81. 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., 103, 346–348(2000).

82. 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. 112, 3483–3492 (2000).


83. Haiyan Liu, Marcus Elstner, Efthimios Kaxiras,Thomas Frauenheim, Jan Hermans and Weitao Yang, “Quantum Mechanics Simulation of Protein Dynamics on Long Time Scale Made Possible”, in press, Proteins (2001). PROTEINS:Structure,Function,and Genetics 44,484-489(2001).

84. 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, 105(27), 6437-6444 (2001).


85. Yingkai Zhang, Haiyan Liu and Weitao Yang, “Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions”, invited paper, chapter in book, Computational Methods for Macromolecules: Challenges and Applications, editors Tamar Schlick and Hin Hark Gan, 2000. Springer Verlag’s Lecture Notes Series in Computational Science & Engineering, (2002), pages332-354.

86. Qin Wu and Weitao Yang, “An Empirical Correction to Density Functional Theory for van der Waals Interactions”, J. Chem. Phys., 116 (2), 515-524 (2002).

87. Zhenyu Lu, Haiyan Liu, Marcus Elstner and Weitao Yang, “Parameterization of COSMO Solvent Model for Self-Consistent Charge Density-Functional Based Tight-Binding Calculations”, Reviews In Modern Quantum Chemistry: A Celebration Of The Contributions Of R. G. PARR, Editor: K.D.Sen, (2002). (pdf)

88. Weitao Yang and Qin Wu, “A Direct Method for Optimizing Effective Potentials in Density Functional Theory,” Phys. Rev. Lett., 89, 143002 1-4 (2002).

89. Qiang Xue and Weitao Yang. “Distributed Electronic Structure Calculations with Divide-and-Conquer Approach.” In Work-in-Progress Session of the PACT’02 Conference, Charlottesville, VA, Sept. 2002.


. Qin Wu, Paul W. Ayers, and Weitao Yang. “Density Functional Theory Calculations with Correct Long Range Potentials”. J. Chem. Phys., 119(6): 2978-2990, 2003.

91. Qin Wu and Weitao Yang, “A Direct Optimization Method for Calculating Density Functionals and Exchange-Correlation Potentials from Electron Densities,” J. Chem. Phys., 118 (6), 2498-2509 ( 2003).

92. 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., 90 (2), 026806 1-4 ( 2003).

93. G. A. Cisneros, H. Liu, Y. Zhang, and W. Yang “Ab-initio QM/MM Study Shows There is no General Acid in the Reaction Catalyzed by 4-Oxalocrotonate Tautomerase”, J. Am. Chem. Soc., 125 (34), 10384-10393, 2003.

94. San-Huang Ke, Harold U. Baranger, and Weitao Yang. Additional energies of fullerences and carbon nanotubes as quantum dots: the role of symmetry. Phys Rev. Lett., 91(11): 116803-1–116803-4, 2003.

95. Jun-ya Hasegawa, Mayumi Ishida, Hiroshi Nakatsuji, Zhenyu Lu, Haiyan Liu and Weitao Yang, “Energetics of the Electron Transfer from Bacteriopheiophytin to Ubiquinone in the Photosynthetic Reaction Center of Rhodopseudomonoas Viridis: Theoretical Study,” J. Phys. Chem. B, 107 (3) 838-847 (2003).

96. Paula Mori-Sanchez, Qin Wu, and Weitao Yang. “Accurate Polymer Polarizabilities with Exact Exchange Density Functional Theory.” J. Chem. Phys. 119(21):11001-11004, 2003.

97. Qin Wu and Weitao Yang. Algebraic equation and iterative optimization for the optimized effective potential in density functional theory. J. Theo. Comp. Chem., 2(4): 627-638, 2003.

98. Hong Jiang, Harold U. Baranger, and Weitao Yang. Density functional theory simulation of large quantum dots. Phys. Rev. B, 68:165337-1–165337-9, 2003.

99. Laurel A. Goj, Andres Cisneros, Weitao Yang, and Ross A. Widenhoefer. “Dramatic Effect of Homoallylic Substitution on the Rate of Palladiumcatalyzed Diene Cycloisomerization.” Journal of Organometallic Chemistry, 687:498-507, 2003. Erratum


100. Li Xie, Haiyan Liu, and Weitao Yang. “Adapting the Nudged Elastic Band Method for Determining Minimum-Energy.” J. Chem. Phys., 120:8039-8052, 2004.

101. Weitao Yang, Paul W. Ayers, and Qin Wu. “Potential Functionals: Dual to Density Functionals and Solution to the V-Representability Problem.” Phys. Rev. Lett., 92:146404-1-146404-4, 2004.

102. Huasheng Feng, Jiang Bian, Lemin Li, and Weitao Yang. “An Efficient Method for Constructing Nonorthogonal Localized Molecular Orbitals.” J. Chem. Phys., 120-9458-9466, 2004.

103. Zhenyu Lu, Wieslaw Nowak, Gwangrog Lee, Piotr E. Marszalck, and Weitao Yang. “Elastic Properties of Single Amylase Chains in Water: a Quantum Mechanical and AFM study.” J. Am. Chem. Soc., 126 (29)-9033-9041, 2004.

104. San-Huang Ke, Harold U. Baranger, and Weitao Yang. “Electron Transport Through Molecules: Self-Consistent and Non-Self-Consistent Approaches.” Phys. Rev. B, 70(8), Article No. 085410, 2004.

105. Hong Jiang, Denis Ullmo, Weitao Yang, and Harold U. Baranger. “Electron-Electron Interactions in Isolated and Realistic Quantum Dots: A Density Functional Theory Study.” Phys. Rev. B, 69:235326-1-235336-10, 2004.

106. Haiyan 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., 121:697-706, 2004.

107. Zhenyu Lu and Weitao Yang. “Reaction Path Potential for Complex Systems Derived from Ab Initio QM/MM Calculations.” J. Chem. Phys., 121:89-100, 2004.

108. 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., 121-101-107, 2004.

109. San-Huang Ke, Harold U. Baranger, and Weitao Yang. “Molecular Conductance: Chemical Trends of Anchoring Groups.” J. Am. Chem. Soc., 126(48) 15897-15904, 2004.

110. Hong, Ziang and Weitao Yang. “Conjugate-Gradient Optimization Method for Orbital-Free Density Functional Calculations.” J. Chem. Phys., 121:2030-2036, 2004.

111. Gerardo A. 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, 43:6885-689, 2004.

112. Dennis Ulmo, Hong Jiang, Weitao Yang, and Harold Baranger. “Landau Fermi Liquid Picture of Spin Density Dots”. Phys. Rev. B, 70(205309) 2004.

113. Aron J. Cohen, Qin Wu, and Weitao Yang. “Calculation of Nuclear Magnetic Resonance Shielding Constants Using Potential Based Methods”. Chem. Phys. Lett, 399(1-3): 84-88, 2004.

114. L. A. Goj, G. A. Cisneros, Weitao Yang, and Ross A. Widenhoefer. “Dramatic Effect of Homoallylic Substitution on the Rate of Palladium-Catalyzed Diene Cycloisomerization”, Journal of Organometallic Chemistry, 689(17): 2845, 2004.

115. Paul W. Ayers and Weitao Yang. “Density-functional theory.” In Patrick Bultinck, Hans de Winter, Wilfried Langenaeker, and Jan P. Tollenaere, editors, Computational Medicinal Chemistry and Drug Discovery, pages 80-118. Marcel Dekker, Inc., New York, NY, 2004.


116. Rui Liu, San-Huang Ke, Harold U. Baranger, and Weitao Yang. “Intermolecular Effect in Molecular Electronics”. J. Chem. Phys, 122, 044703, 2005.

117. San-Huang Ke, Harold U. Baranger, and Weitao Yang. “Contact Atomic Structure and Electron Transport Through Molecules.” J. Chem. Phys., 122, 074404, 2005.

118. Hong Jiang, Dennis Ulmo, Weitao Yang, and Harold Baranger. “Scrambling and Gate Effects in Realistic Quantum Dots.” Phys. Rev. B, 71, 085313, 2005.

119. Stephanie A. Getty, Chaiwat Engtrakul, Lixin Wang, Rui Liu, San-Huang Ke, Harold U. Baranger, Weitao Yang, Michael S. Fuhrer, and Lawrence R. Sita. “Near-Perfect Conduction Through a Ferrocene-Based Molecular Wire”. Phys. Rev. Lett. B, 2005, 71, 241401(R), 2005.

120 San-Huang Ke, Harold U. Baranger, and Weitao Yang. “Electron Transport Through Molecules: Gate-Induced Polarization and Potential Shift”. Phys. Rev. B, 71, 113401, 2005.

121. Wu, Qin, Aron J. Cohen and Weitao Yang. “Excitation energies from time-dependent density functional theory with accurate exchange-correlation potentials”. Molecular Physics, (103), No 6-8, 711-717, 2005.

122. Cisneros, Andres, 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”. Journ. Chem. Phys.,122, 114502 (2005).

123. Denis Ullmo, Hong Jiang, Weitao Yang, and Harold U. Baranger “Interactions and broken time-reversal symmetry in chaotic quantum dots”. Phys. Rev. B., 71, 201310 (2005).

124. Rui Liu, San-Huang Ke, Harold U. Baranger “Organometallic spintronics: dicobaltocene switch”. NANO Letters, 5(10), 1959 (2005).

125. San-Huang Ke, Harold U. Baranger and Weitao Yang “Models of electrodes and contacts in molecular electronics”. Journ. Chem. Phys. 123, 114701 (2005).

126. Paula Mori-Sanchez, Qin Wu, and Weitao Yang “Orbital-dependent correlation energy in density-functional theory based on a second-order perturbation approach: success and failure”. Journ. Chem. Phys. 123, 062204 (2005).

127. Hao Hu and Weitao Yang, “Dual-topology/dual-coordinatr free-energy simulation using QM/MM force field” J. Chem. Phys., 123 041102 (2005).

128. Felipe Bulat, Alejandro Toro-Labbe, Benoit Champagne, Bernard Kirtman and Weitao Yang. “Density-functional theory (hyper) polarizabilities of push-pull conjugated systems: treatment of exact exchange and role of correlation” J. Chem. Phys., 123, 014319 (2005).

129. Qin Wu, Aron J. Cohen and Weitao Yang. “Analytic energy gradients of the optimized effective potential method” J. Chem. Phys, 123, 124111, (2005).doi:10.1063/1.1989310 (10 pages) Online Publication Date: 5 October 2005 | Cited 2 times

130. Jungsan Sohn, Jerry Parks, Gregory Buhrman, Paul Brown, Kolbrun Kristjansdottir, Alexias Safi, Herbert Edelsbrunner, Weitao Yang and Johannes Rudolph. “Experimental validation of the docking orientation of cdc25 witth its cdk2-cyca protein substrate” Biochemistry, 44(50), 16563-16573, (2005).


131. Paul Ayers and Weitao Yang. “Legendre-transform functionals for spin-density-functional theory”, Journ. of Chem. Phys., 124(22), 224108-224123 , (2006). doi:10.1063/1.2200884 (15 pages) | Cited 13 times Online Publication Date: 13 June 2006

132. Steven Burger and Weitao Yang. “A combined explicit-implicit method for high accuracy reaction path integration“, Journ of Chem. Phys., 124(22), 224102-224112, (2006).

133. Steven K. Burger and Weitao Yang. “Quadratic string method for determining the minimum-energy path based on multiobjective optimization”, J. Chem. Phys., 124, 054109, (2006).

134. Steven K. Burger and Weitao Yang. “Automatic integration of the reaction path using diagonally imlicit runge-kutta methods”, J. Chem. Phys., 125 (24), 244108, (2006).

135. B. Champagne, F A. Bulat, W Yang, S Bonness, and B Kirtman, “Density functional theory investigation of the polarizability and second hyperpolarizability of polydiacetylene and polybutatriene chains: Treatment of exact exchange and role of correlation,” J. Chem. Phys. 125, (19) 194114 (2006); doi:10.1063/1.2388262 (9 pages) Online Publication Date: 21 November 2006| Cited 23 times

136. G.A. Cisneros, M. Wang, P. Silinski, M.C. Fitzgerald, and W. Yang. “Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase”, J. Phys. Chem.A, 110 :2, 700-708, (2006). Publication Date (Web): October 14, 2005 (Article) DOI: 10.1021/jp0543328

137. Takumi Hori, Hideaki Takahashi, Masayoshi Nakano, Tomoshige Nitta and Weitao Yang, “A QM/MM study combined with the theory of energy representation: solvation free energies for anti/syn acetic acids in aqueous solution“, Chem. Phys. Letters, 124(5), (2006).

138. S. H. Ke, H. U. Baranger, and W. T. Yang. “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, 3(5):819-823, 2006.

139. San-H. Ke, Weitao Yang, and Harold Baranger, “Nano-tube metal junctions: 2- and 3- terminal electrical transport”, J Chem Phys 124(18):181102, (2006). J. Chem. Phys. 124, 181102 (2006); doi:10.1063/1.2200356 (5 pages) | Cited 9 times.Online Publication Date: 10 May 2006

140. P. Lin, W. T. Yang, L. C. Pedersen, M. Negishi, and L. G. Pedersen. “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, 106(14):2981-2998, 2006.

141. Rui Liu, San-Huang Ke, Weitao Yang, and Harold U. Baranger. “Organometallic molecular rectification” J. Chem. Phys., 124 (2), 024718 (2006). doi:10.1063/1.2141955 (5 pages) | Cited 17 times Online Publication Date: 11 January 2006

142. Rui Liu, San-Huang Ke, Harold Baranger and Weitao Yang. “Negative differential resistance and hysteresis through an organometallic molecule from molecular-level crossing“, Journal Am.Chem. Soc., 128(19), 6274-6275, (2006).

143. Zhenyu Lu, Hao Hu, Weitao Yang, and Piotr E. Marszalek. Simulating Force-Induced Conformational Transitions in Polysaccharides with the SMD Replica Exchange Method. Biophys J. 2006 September 15; 91(6): L57–L59. Published online 2006 July 7. doi: 10.1529/biophysj.106.090324. PMCID: PMC1557546

144. Paula Mori-Sanchez, Aron Cohen, and Weitao Yang. “Self-interaction free-exchange correlational functional for thermochemistry and kinetics“, Journ. Chem. Phys., 124(9), 091102/1-091102/4, (2006).

145. P. Mori-Sanchez, A. J. Cohen, and W. T. Yang. “Many-electron self-interaction error in approximate density functionals.” J. Chem. Phys. 125 (20), 201102 (2006); doi:10.1063/1.2403848 (4 pages) | Online Publication Date: 28 November 2006 Cited 77 times

146. Mingliang Wang, Zhenyu Lu and Weitao Yang. “Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase“, Journal of Chem. Phys., 124(12), 124516/1–124516/8, (2006).

147. Mingliang Wang, Xiangqian Hu, David Beratan and Weitao Yang. “Designing molecules by optimizing potentials”, JACS, 128(10), 3228-3232, (2006).

148. Qingmin Zhang, Zhenyu Lu, Hao Hu, Weitao Yang, and Piotr E. Marxzalek. “Direct detection of the formation of v-amylose helix by single molecule force spectroscopy”, J. Am. Chem. Soc., 128, 9387-9393, (2006).


149. Cohen, A. J. Mori-Sanchez, P. and Yang, W. T. “Development of exchange-correlation functionals with minimal many-electron self-interaction error“, Journal of Chemical Physics, 126(19), 191109-191114, (2007).

150. F. A. Bulat, T. Heaton-Burgess, A. J. Cohen, and W. T. Yang. “Optimized effective potentials from electron densities in finite basis sets.” J. Chem. Phys. 127 (17), 174101 (2007); doi:10.1063/1.2800021 (9 pages) | Cited 8 times Online Publication Date: 1 November 2007

151. S. K. Burger and W. Yang. “Sequential quadratic programming method for determining the minimum energy path.” J. Chem. Phys. 127 (16), 164107 (2007); doi:10.1063/1.2780147 (7 pages) | Online Publication Date: 23 October 2007, Cited 6 times

152. Hu, H., Lu, Z.Y. and Yang, W.T. “QM/MM minimum free-energy path: Methodology and application to triosephosphate isomerase“,J Chem Theory Comput. 2007 March; 3(2): 390–406. doi: 10.1021/ct600240y. PMCID: PMC2600730.

153. H. Hu, Z. Y. Lu, and W. T. Yang. “Fitting molecular electrostatic potentials from quantum mechanical calculations.” Journal of Chemical Theory and Computation, 3(3):1004-1013, 2007.

154. S. H. Ke, H. U. Baranger, and W. Yang. “Electron transport through single conjugated organic  molecules: Basis set effects in ab initio calculations.” J. Chem. Phys. 127 (14), 144107 (2007); doi:10.1063/1.2770718 (6 pages) Online Publication Date: 12 October 2007 | Cited 7 times

155.   S. H. Ke, H. U. Baranger, and W. T. Yang. “Contact transparency of nanotube-molecule-nanotube junctions.” Physical Review Letters, 99(14):146802, 2007.

156. R. Liu, S. H. Ke, W. Yang, and H. U. Baranger. “Cobaltocene as a spin filter.” J. Chem. Phys. 127(14), 141104 (2007); doi:10.1063/1.2796151 (4 pages) | Cited 8 times Online Publication Date: 10 October 2007

157. 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, 46(24):10252-10260, 2007.

158. 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.” J Phys Chem A. (2007) 111(1):176-81.

159. Heaton-Burgess, T. Bulat, F. A., Yang, W. T. “Optimized effective potentials in finite basis sets.” Physical Review Letters, 98 (25), ;256401 (2007)

160. Ke, S. H., Baranger H. U., Yang, W. T., “Role of the exchange-correlation potential in ab initio electron transport calculations.” Journal of Chemical Physics, 126 (20) ; 201102 (2007)

161. Hao Hu, Zhenyu Lu, Marcus Elstner, Jan Hermans, and Weitao Yang. Simulating water with the SCCDFTB method: from molecular clusters to the liquid state. J Phys Chem A. Author manuscript; available in PMC 2008 August 21. PMCID: PMC2518942 Published in final edited form as: J Phys Chem A. 2007 July 5; 111(26): 5685–5691. Published online 2007 May 3. doi: 10.1021/jp070308d.

162. Cohen AJ, Mori-Sanchez P, Yang W. “Assessment and formal properties of exchange-correlation functionals constructed from the adiabatic connection.”
J Chem Phys. 127(3):034101. (2007)

163. Hori T, Takahashi H, Furukawa S, 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.” J Phys Chem B. 111(3):581-8. (2007)

164. Heaton-Burgess T, Ayers P, Yang W. “Spin-potential functional formalism for current-carrying noncollinear magnetic systems.” Phys Rev Lett. 98(3):036403. (2007)


165. Hu, H, Boone, A, Yang, W., Mechanism of OMP Decarboxylation in Orotidine 5′-Monophosphate Decarboxylase. J Am Chem Soc. 2008 Oct 8. [Epub ahead of print] PMID: 18839943 [PubMed – as supplied by publisher]

166. Ke, SH, Yang, WT, Baranger, H., Quantum-interference-controlled molecular electronics.

167. 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. Org Biomol Chem. 2008 Sep 21;6(18):3256-63. Epub 2008 Jul 15. PMID: 18802630 [PubMed – in process]

168. Xiao DQ, Bulat FA, Yang WT, Beratan DN., A donor-nanotube paradigm for nonlinear optical materials Nano Lett., 2008, 8 (9), pp 2814–2818 DOI: 10.1021/nl801388z Publication Date (Web): August 12, 2008

172. Hu XQ, Beratan DN, Yang WT, “A gradient-directed Monte Carlo approach to molecular design” J. Chem. Phys. 129 (6), 064102 (2008); doi:10.1063/1.2958255 (9 pages) | Cited 7 times Online Publication Date: 8 August 2008

173. Li Z, Wang CY, Zhang X, Ke SH, Yang WT, Transport properties of an armchair carbon nanotube with a double vacancy under stretching, JOURNAL OF PHYSICS-CONDENSED MATTER   Volume: 20   Issue: 34 Article Number: 345225   Published: AUG 27 2008

174. Fujimoto, K, Yang, WT, Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg(2+)-sensitive dye. Chem Phys. 2008 Aug 7;129(5):054102. PMID: 18698883 [PubMed – indexed for MEDLINE]

175. Xiao DQ, Yang WT, Beratan DN: Inverse molecular design in a tight-binding framework, JOURNAL OF CHEMICAL PHYSICS   Volume: 129   Issue: 4 Article Number: 044106   Published: JUL 28 2008

176. Cohen AJ, Mori-Sanchez P, Yang WT, Insights into current limitations of density functional theory, Source: SCIENCE   Volume: 321   Issue: 5890   Pages: 792-794   Published: AUG 8 2008

177. Burger SK, Yang WT , Linear-scaling quantum calculations using non-orthogonal localized molecular orbitals, JOURNAL OF PHYSICS-CONDENSED MATTER   Volume: 20   Issue: 29 Article Number: 294209   Published: JUL 23 2008

178. Zeng XC, Hu XQ, Hu H, Cohen AJ, Yang WT, Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach. J Chem Phys. 2008 Mar 28;128(12):124510. PMID: 18376946 [PubMed – indexed for MEDLINE]

179. Heaton-Burgess T, Cohen, AJ, Yang W, Davidson ER, Size extensivity of the direct optimized effective potential method. J Chem Phys. 2008 Mar 21;128(11):114702. PMID: 18361596 [PubMed – indexed for MEDLINE]

180. 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. Phys Chem B. 2008 Mar 13;112(10):3168-76. Epub 2008 Feb 14. PMID: 18271573 [PubMed – indexed for MEDLINE]

181. 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. J Chem Phys. 2008 Jan 21;128(3):034105. PMID: 18205486 [PubMed – indexed for MEDLINE]

182. Ayers, P.W., Yang, W, Bartolotti, L., Fukui Function, Chapter 18 of Chemical Reactivity Theory: A Density Functional View, Chattaraj ed. 21.9.2008

183. Qingmin Zhang, Zhenyu Lu, Hao Hu, Weitao Yang, and Piotr E Marszalek. Direct Detection of the Formation of V-Amylose Helix by Single Molecule Force Spectroscopy. J Am Chem Soc. Author manuscript; available in PMC 2008 August 30. PMCID: PMC2527463 Published in final edited form as: J Am Chem Soc. 2006 July 26; 128(29): 9387–9393. doi: 10.1021/ja057693+.

184. Johnson ER, Mori-Sánchez P, Cohen AJ, Yang W., Delocalization errors in density functionals and implications for main-group thermochemistry. J Chem Phys. 2008 Nov 28;129(20):204112. PMID: 19045857 [PubMed]

185 . Balamurugan D, Yang W, Beratan DN., Exploring chemical space with discrete, gradient, and hybrid optimization methods. J Chem Phys. 2008 Nov 7;129(17):174105. PMID: 19045331 [PubMed – indexed for MEDLINE]

186. Parks JM, Hu H, Cohen AJ, Yang W. A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes. J Chem Phys. 2008 Oct 21;129(15):154106. PMID: 19045175 [PubMed – indexed for MEDLINE]

186. Cohen AJ, Mori-Sánchez P, Yang W. Fractional spins and static correlation error in density functional theory. J Chem Phys. 2008 Sep 28;129(12):121104. PMID: 19044996 [PubMed]

187. Heaton-Burgess T, Yang W. Optimized effective potentials from arbitrary basis sets. J Chem Phys. 2008 Nov 21;129(19):194102. PMID: 19026040 [PubMed]

188. F. A. Bulat, S. H. Ke, W. Yang, and L. Couchman. “Lead-molecule coupling effects on the distortion  dependent conductance of carbon nanotubes.” Physical Review B, 77(15):153401, 2008.

189. 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, 59:573-601,  2008.

190. 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, 112(47):12203-12207, 2008.

191. 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,  47(22) :4200-4203, 2008.

192. 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, 100(14):146401,   2008.


193. 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. Bioorg Med Chem Lett. 2009 Apr 22. [Epub ahead of print] PMID: 19423348 [PubMed – as supplied by publisher]

194. 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. J Chem Phys. 2009 Apr 28;130(16):164111. PMID: 19405565 [PubMed – indexed for MEDLINE]

195. Bulat FA, Couchman L, Yang W., Contact geometry and conductance of crossed nanotube junctions under pressure., Nano Lett. 2009 May;9(5):1759-63., PMID: 19331377 [PubMed]

196. 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. J Phys Chem B. 2009 Apr 16;113(15):5217-24. PMID: 19301836 [PubMed – indexed for MEDLINE]

197. Mori-Sánchez P, Cohen AJ, Yang W., Discontinuous nature of the exchange-correlation functional in strongly correlated systems. Phys Rev Lett. 2009 Feb 13;102(6):066403. Epub 2009 Feb 13. PMID: 19257614 [PubMed]

198. Ke SH, Yang W, Curtarolo S, Baranger HU. Thermopower of molecular junctions: an ab initio study. Nano Lett. 2009 Mar;9(3):1011-4. PMID: 19203208 [PubMed – indexed for MEDLINE]

199. Balabin IA, Yang W, Beratan DN., Coarse-grained modeling of allosteric regulation in protein receptors. Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14253-8. Epub 2009 Aug 12.PMID: 19706508 [PubMed – indexed for MEDLINE]

200. 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. J Chem Phys. 2009 Oct 21;131(15):154117. PMID: 20568857 [PubMed – indexed for MEDLINE] Free PMC Article Related citations

201. G. ANDRES CISNEROS and WEI Tao YANG. “Comparison ofreaction barriers in energy and free  energy for enzyme catalysis.” In D.M. York and T.-S. Lee, editors, Multi-scale Quantum Models for Biocatalysis, pages 57-78. Springer-Verlag, London, 2009.

202. 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, 5(4):786-792, 2009.

203. 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, 898(1- 3):17-30, 2009.

204. X. Q. Hu, D. N. Beratan, and W. T. Yang. “Emergent strategies for inverse molecular design.” Science in China Series B-Chemistry, 52(11): 1769-1776, 2009.

205. 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, 69(3):375-382, 2009.

206.   P. Mori-Sanchez, A. J. Cohen, and W. T. Yang. “Discontinuous nature of the exchange-correlation functional in strongly correlated systems.” Physical Review Letters, 102(6), 2009.

207. 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, 5(12):3321-3329, 2009.


208. Cui G, Fang W, Yang W., Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals. Phys Chem Chem Phys. 2010 Jan 14;12(2):416-21. Epub 2009 Nov 13.PMID: 20023819 [PubMed]

209. Hu H, Yang W., Elucidating Solvent Contributions to Solution Reactions with Ab Initio QM/MM Methods (dagger). J Phys Chem B. 2010 Mar 4;114(8):2755-9.PMID: 20121225 [PubMed – in process]

210. Hu X, Yang W., Accelerating self-consistent field convergence with the augmented Roothaan-Hall energy function. J Chem Phys. 2010 Feb 7;132(5):054109.PMID: 20136307 [PubMed – in process]

211. Zeng X, Hu H, Zhou HX, Marszalek PE, Yang W., Equilibrium sampling for biomolecules under mechanical tension.Biophys J. 2010 Feb 17;98(4):733-40. PMID: 20159170 [PubMed – in process]

212. Hu X, Hu H, Beratan DN, Yang W., A gradient-directed Monte Carlo approach for protein design. J Comput Chem. 2010 Feb 23. [Epub ahead of print] PMID: 20186860 [PubMed – indexed for MEDLINE] ] Related citations

213. Cui G, Fang W, Yang W. , Efficient Construction of Nonorthogonal Localized Molecular Orbitals in large Systems (dagger). J Phys Chem A. 2010 Jun 15. [Epub ahead of print] J Phys Chem A. 2010 Aug 26;114(33):8878-83. PMID: 20550205 [PubMed] Related citations

214. Ke SH, Liu R, Yang W, Baranger H U., Time-dependent transport through molecular junctions. J Chem Phys. 2010 Jun 21;132(23):234105. PMID: 20572687 [PubMed]  Related citations

215. Johnson ER, Keinan S, Mori-Sánchez P, Contreras-García J, Cohen AJ, Yang W. “Revealing noncovalent interactions. “J Am Chem Soc. 2010 May 12;132(18):6498-506.PMID: 20394428 [PubMed – indexed for MEDLINE] Related citations

216. 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. Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7225-9. Epub 2010 Apr 1, doi: 10.1073/pnas.1001132107. PMCID: PMC2867729 PMID 20360565 [PubMed – indexed for MEDLINE] supplementary material

217. Zheng X, Ke SH, Yang W. Conductive junctions with parallel graphene sheets. J Chem Phys. 2010 Mar 21;132(11):114703.PMID: 20331312 [PubMed – indexed for MEDLINE]

218. 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. J Chem Phys. 2010 Jun 21;132(23):234113. PMID: 20572695 [PubMed]

219. Lee W, Zeng X, Zhou HX, Bennett V, Yang W, Marszalek PE., Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations. J Biol Chem. 2010 Dec 3;285(49):38167-72. Epub 2010 Sep 24. PMID: 20870713 [PubMed – indexed for MEDLINE] Related citations

220. Johnson ER, Yang W, Davidson ER., Spin-state splittings, highest-occupied-molecular-orbital and lowest-unoccupied-molecular-orbital energies, and chemical hardness. J Chem Phys. 2010 Oct 28;133(16):164107. PMID: 21033775 [PubMed – in process] Related citations

221. 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. J Am Chem Soc. 2010 Dec 13. [Epub ahead of print] PMID: 21142157 [PubMed – as supplied by publisher] Related citations

222. G. L. Cui and W. T. Yang. Challenges with range-separated exchange-correlation functionals in time dependent density functional theory calculations. Molecular Physics, 108(19-20):2745-2750, 2010. DOI: 10.1080/00268976.2010.523442

223. X. Q. Hu, D. Q. Xiao, S. Keinan, 1. Asselberghs, M. J. Therien, K. Clays, W. T. Yang, and D. N. Beratan. Predicting the frequency dispersion of electronic hyperpolarizabilities on the basis of absorption data and thomas-kuhn sum rules. Journal of Physical Chemistry C, 114(5):2349-2359, 2010.

224. Jared T. Hammill, Julia Contreras-García, Aaron M. Virshup, David N. Beratan, Weitao Yang,and Peter Wipf,
Synthesis and chemical diversity analysis of bicyclo[3.3.1]non-3-en-2-ones, Tetrahedron, 66, ( 31), July 2010, Pages 5852-5862, PMID 20798897 [PubMed] Related citations


225. Sun Z, Yang W. Communication: An exact short-time solver for the time-dependent Schrodinger equation. J Chem Phys. 2011 Jan 28;134(4):041101. PMID: 21280676 [PubMed – in process] doi:10.1063/1.3549570 (4 pagesRelated citations

226. Ess DH, Johnson ER, Hu X, Yang W., Singlet-triplet energy gaps for diradicals from fractional-spin density-functional theory. J Phys Chem A. 2011 Jan 13;115(1):76-83. Epub 2010 Dec 9. PMID: 21141988 [PubMed – in process] Related citations

227. Shenvi N, Subotnik JE, Yang W. Simultaneous-trajectory surface hopping: A parameter-free algorithm for implementing decoherence in nonadiabatic dynamics. J Chem Phys. 2011 Apr 14;134(14):144102. PMID: 21495737 [PubMed-in process]
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228. Contreras-García J, Johnson ER, Keinan S, Chaudret R, Piquemal JP, Beratan DN, Yang W., NCIPLOT: a program for plotting non-covalent interaction regions. J Chem Theory Comput. 2011 Mar 8;7(3):625-632. PMID: 21516178 [PubMed] Related citations

229. Tam ES, Parks JJ, Shum WW, Zhong YW, Santiago-Berríos MB, Zheng X, Yang W, Chan GK, Abruña HD, Ralph DC. “Single-Molecule Conductance of Pyridine-Terminated Dithienylethene Switch Molecules,” ACS Nano 5 (6) June 2011 5115-5123. [Epub ahead of print May 23] PMID: 21574612 [PubMed – as supplied by publisher] Related citations Times Cited: 0      References: 46       

230. Cui, GL; Yang, WT, Conical intersections in solution: Formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method. JOURNAL OF CHEMICAL PHYSICS   Volume: 134   Issue: 20   Article Number: 204115   Published: 2011 PMID: 21639432 [PubMed – in process]

231. Lin, XS ; Hu, XQ ; Concepcion, JJ; Chen, ZF ; Liu, SB; Meyer, TJ.); Yang, WT , Catalytic mechanism for single-site water oxidation process: A theoretical study. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  Volume: 241   Meeting Abstract: 88-CATL   Published: MAR 27 2011

232. Keinan, S ; Contreras-Garcia, J ; Wipf, P ; Yang, WT ; Beratan, DN (Beratan, David N.), Predicating BBB permeability for quinoline methanol based antimalarial agents. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  Volume: 241   Meeting Abstract: 86-COMP   Published: MAR 27 2011

233. Contreras-Garcia, J ; Johnson, ER ; Keinan, S ; Beratan, DN ; Yang, WT , From density to scoring functions: Revealing non covalent interactions. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  Volume: 241   Meeting Abstract: 276-COMP   Published: MAR 27 2011

234. Hu, XQ; Jin, YD ; Zeng, XC ; Hu, H; Yang, WT , Density fragment interaction approach for condensed phase applications, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  Volume: 241   Meeting Abstract: 7-PHYS   Published: MAR 27 2011

235. Zeng, XC; Hu, XQ; Hu, H; Yang, WT, Ab initio QM/MM calculation of electron transfer rate constant, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  Volume: 241   Meeting Abstract: 64-PHYS   Published: MAR 27 2011

236. Zheng, Xiao, Cohen, AJ, Mori-Sanchez, P, Hu, XQ, Yang, W, Improving band gap prediction in density functioal theory from molecules to solids. Physical Review Letters 107 (2) 107.026403 July 7, 2011 epub 2011 July 7 PMID: 21797627, [PubMed – in process]

237. Shenvi, Neil, Bubotnik, Joseph E, Yang, Weitao, “Phase-corrected surface hopping: Correcting the phase evolution of the electronic wavefunction,” JOURNAL OF CHEMICAL PHYSICS  Volume: 135   Issue: 2     Article Number: 024101  
 DOI: 10.1063/1.3603447   Published: JUL 14 2011 ]     Citation MapCitation Map

238. Contreras-García J, Yang W, Johnson ER. “Analysis of Hydrogen-Bond Interaction Potentials from the Electron Density: Integration of Noncovalent Interaction Regions.” J Phys Chem A. 2011 Nov 17;115(45):12983-90. Epub 2011 Jul 25.. [Epub ahead of print] PMID: 21786796
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239. Wu, Pan, Hu, XQ, Yang, WT, “λ Metadynamics Approach to Compute absolute Solvation Free Energy.” J Phys Chem Letters 2 (17): 2099-2103 10.1021/jz200808x Sept 1, 2011 ISSN: 1948-7185

240. Cohen AJ, Mori-Sánchez P, Yang W. “Challenges for Density Functional Theory.” Chem Rev. 2011 Dec 22. [Epub ahead of print] No abstract available. PMID: 22191548 [PubMed – as supplied by publisher]

241. Shenvi, N; Yang, WT, “An algebraic operator approach to electronic structure,” JOURNAL OF CHEMICAL PHYSICS, Volume: 135   Issue: 24     Article Number: 244111   DOI: 10.1063/1.3671388   Part: Part 2011   Published: DEC 28 2011, ISSN: 0021-9606 Article Number: 244111 Unique ID: WOS:000298640500014, PMID: 22225148 [PubMed – in process]


242. Cho, Jinhyun, Lin, Qiubao, Yang, Sungwoo, Simmons, Jay G., Jr., Cheng, Yingwen, Lin, Erica, Yang, Jianqiu, Foreman, John V, Everitt, Henry O., Yang, Weitao, Kim, Jungsang, Liu, Jie, Sulfur-doped zinc oxide (ZnO) Nanostars: Synthesis and simulation of growth mechanism, NANO RESEARCH  Volume: 5   Issue: 1   Pages: 20-26   DOI: 10.1007/s12274-011-0180-3   Published: JAN 2012

243.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. Phys Chem Chem Phys. 2012 Feb 14;14(6):1827-45. Epub 2012 Jan 10. PMID: 22234283 [PubMed – indexed for MEDLINE]

244. Lee W, Zeng X, Rotolo K, Yang M, Schofield CJ, Bennett V, Yang W, Marszalek PE. Mechanical anisotropy of ankyrin repeats. Biophys J. 2012 Mar 7;102(5):1118-26. Epub 2012 Mar 6. PMID: 22404934[PubMed – indexed for MEDLINE]

245. 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. J Phys Chem B. 2012 Jun 14;116(23):6889-97. Epub 2012 Mar 28. PMID: 22417185 [PubMed – in process]

246. Hu X, Jin Y, Zeng X, Hu H, Yang W. Liquid water simulations with the density fragment interaction approach. Phys Chem Chem Phys. 2012 Jun 7;14(21):7700-9. Epub 2012 Apr 2. PMID: 22466097 [PubMed – in process]

247. Yang W, Cohen AJ, De Proft F, Geerlings P. Analytical evaluation of Fukui functions and real-space linerar response function. J Chem Phys. 2012 Apr 14;136(14):144110. PMID: 22502504 [PubMed – in process]

248. Yang, W, Cohen, AJ, Mori-Sanchez P, Derivative discontinuity, bandgap and lowest unoccupied molecular orbital in density functional theory. J Chem Phys. 2012 May 28;136(20):204111. PMID: 22667544 [PubMed – as supplied by publisher]

249. 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. Proc Natl Acad Sci U S A. 2012 May 21. [Epub ahead of print] PMID: 22615356 [PubMed – as supplied by publisher]

250. Xu Y, Wang BJ, Ke SH, Yang W, Alzahrani AZ. Highly tunable spin-dependent electron transport through carbon atomic chains connecting two zigzag graphene nanoribbons. J Chem Phys. 2012 Sep 14;137(10):104107. doi: 10.1063/1.4752197. PMID: 22979850 [PubMed] Related citations

251. Peng D, Hu X, Devarajan D, Ess DH, Johnson ER, Yang W. Variational fractional-spin density-functional theory for diradicals. J Chem Phys. 2012 Sep 21;137(11):114112. PMID: 22998254 [PubMed] Related citations

252. 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. Phys Chem Chem Phys. 2012 Dec 14;14(46):16002-13. doi: 10.1039/c2cp42623d. PMID: 23089917 [PubMed – in process] Related citations

253. Gillet N, Chaudret R, Contreras-Garcίa J, Yang W, Silvi B, Piquemal JP. Coupling quantum interpretative techniques: another look at chemical mechanisms in organic reactions. J Chem Theory Comput. 2012 Nov 13;8(11):3993-3997. Epub 2012 Sep 18. PMID: 23185140 [PubMed]

254. Zheng X, Liu M, Johnson ER, Contreras-García J, Yang W. Delocalization error of density-functional approximations: a distinct manifestation in hydrogen molecular chains. J Chem Phys. 2012 Dec 7 ;137(21):214106. doi: 10.1063/1.4768673. PMID: 23231216 [PubMed – in process] Related citations

255. Shenvi N, Yang W. Achieving partial decoherence in surface hopping through phase correction. J Chem Phys. 2012 Dec 14;137(22):22A528. doi: 10.1063/1.4746407. PMID: 23249065 [PubMed – in process] Related citations

256. Peng, D, Zhao, B, Cohen, A.J., Hu, X., Yang, W, Optimized effective potential for calculations with orbital-free potential functionals. Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, 2012 May 9; vol 110, issue 9-10, Special Issue: Quantum Molecular Dynamics: a Festschrift in Honour of William H. Miller. DOI: 10.1080/00268976.2012.681310


257. Chaudret R, Parks JM, Yang W. Pseudobond parameters for QM∕MM studies involving nucleosides, nucleotides, and their analogs. J Chem Phys. 2013 Jan 28;138(4):045102. doi: 10.1063/1.4772182. PMID: 23387624 [PubMed – in process] Related citations

258. De Vleeschouwer F, Chankisjijev A, Yang W, Geerlings P, De Proft F., Pushing the boundaries of intrinsically stable radicals: inverse design using the thiadiazinyl radical as a template. J Org Chem. 2013 Apr 5;78(7):3151-8. doi: 10.1021/jo400101d. Epub 2013 Mar 13. PMID: 23461465. [PubMed – in process] Related citations

259. 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. J Am Chem Soc. 2013 Apr 2. [Epub ahead of print] PMID: 23548177, [PubMed – as supplied by publisher]

260. Zheng X, Zhou T, Yang W. A nonempirical scaling correction approach for density functional methods involving substantial amount of Hartree-Fock exchange. J Chem Phys. 2013 May 7;138(17):174105. doi: 10.1063/1.4801922. PMID: 23656112 [PubMed – in process]

261. Peng D, Yang W. Fukui function and response function for nonlocal and fractional systems. J Chem Phys. 2013 May 14;138(18):184108. doi: 10.1063/1.4803101. PMID: 23676030 [PubMed – in process]

262. Yang, Yang; van Aggelen, Helen; Steinmann, Stephan N, W. Yang. Benchmark tests and spin adaptation for the particle-particle random phase approximation. J Chem Phys. 2013 Nov. 7; 139 ( 17) : 174110; DOI: 10.1063/1.4828728 test

263. Wang, Jun; Yang, Weitao, Concerted Proton Transfer Mechanism of Clostridium thermocellum Ribose-5-phosphate Isomerase, J Phys Chem B, 117 (32) 9354-9361 AUG 15 2013
Times Cited: 0, DOI: 10.1021/jp404948c test

264. Zhang, Du; Steinmann, Stephan N.; Yang, Weitao, Dynamical second-order Bethe-Salpeter equation kernel: A method for electronic excitation beyond the adiabatic approximation, J Chemical Phys, Oct. 2013, 139 ( 15) : 154109 OCT 21 2013, Times Cited: 0, DOI: 10.1063/1.4824907 test

265. Peng, Liang; Gu, Feng Long; Yang, Weitao, Effective preconditioning for ab initio ground state energy minimization with non-orthogonal localized molecular orbitals, P Chemistry Chem Physics 15 (37): 15518-15527 July 2013. Times Cited: 0, DOI: 10.1039/c3cp52989d test

266. Peng, Degao; Steinmann, Stephan N.; van Aggelen, Helen; Yang, W., Equivalence of particle-particle random phase approximation correlation energy and ladder-coupled-cluster doubles, J Chem Phys 139 (10), 104112, SEP 14 2013, Times Cited: 2, DOI: 10.1063/1.4820556text

267. van Aggelen, Helen; Yang, Yang; Yang, Weitao, Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random-phase approximation, Phys Rev 88 ( 3) SEP 24 2013, Times Cited: 0 DOI: 10.1103/PhysRevA.88.030501 text

268. Yang, Weitao; Mori-Sanchez, Paula; Cohen, Aron J. Extension of many-body theory and approximate density functionals to fractional charges and fractional spins, J Chemical Phys; 139 ( 10); 104114: SEP 14 2013, Times Cited: 0, DOI: 10.1063/1.4817183 text

269. Peng, Degao; Yang, Weitao, Fukui function and response function for nonlocal and fractional systems,
J Chem Phys: 138 ( 18); 184108, MAY 14 2013 Times Cited: 2, DOI: 10.1063/1.4803101 text

270. Scholl, Zackary N.; Yang, Weitao; Marszalek, Piotr E. Improving Single Molecule Force Spectroscopy through Automated Real-Time Data Collection and Quantification of Experimental Conditions
Biophys J: 104 ( 2) 512A, JAN 29 2013, Times Cited: 0