Publications

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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)

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).

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. Darrin York, Jian Ping Lu and Weitao Yang, "Density-functional Calculations of the Structure and Stability of C240 ", Phys. Rev. B. Rapid Communication, 49, 8526 (1993).

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

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 "Electronic Functional Theory of Molecules, Clusters, and Solids", pp 177-188, Edited by D.E. Ellis, Kluwer Academic Publishers (1994).

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, "An 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).

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(1996).

58. Wei Pan, Tianhai Zhu and Weitao Yang, "First-Principles Study of the Structural and Electronic Properties of Ethylene Adsorption on Si(100)-(2x1) Surface", J. Chem. Phys., 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).

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 and Weitao Yang. Fluctuations of conformations and charges of protein studied by linear-scaling quantum mechanical molecular dynamics simulation. J. Am Chem. Soc., pages xxx-xxx, 2000, submitted.

80.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).

81. 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).

82. 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).

83. 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).000).

84. 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).

85. 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).

86. Yingkai Zhang, Haiyan Liu and Weitao Yang, " Density Functional Theory QM/MM Study of the Reaction Mechanism of Triosephosphate Isomerase. Is There a Low-Barrier Hydrogen Bond Involved?", J. Am. Chem. Soc., submitted (2001).

87. Yingkai Zhang, Haiyan Liu and Weitao Yang, "Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions", invited paper, Springer Verlag's Lecture Notes Series in Computational Science & Engineering, (2002).

88. 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).

89. 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).

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

91. 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.

92. Paul W. Ayers and Weitao Yang. Density-Functional Theory. In Patrick Bultinck, Hans De Winter, Wilfried Langenaeker, and Jan P. Tollenaere, editors, Computational Medical Chemistry and Drug Discovery, pages 89-118. Marcel Dekker, Inc, New York, 2002.

93. 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.

94. 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).

95. 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).

96. 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.

97. 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.

98. 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).

99. 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.

100. Paul W. Ayers and Weitao Yang. "Legendre transform functionals for spin-density functional theory." J. Chem. Phys, 2003, submitted.

101. 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.

102. 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.

103. 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

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

105. 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.

106. Huasheng Feng, Jiang Bian, Lemin Li, and Weitao Yang. "An Efficient Algorithm for Nonorthogonal Localized Molecular Orbitals." J. Chem. Phys., 120-9458-9466, 2004.

107. Zhenyu Lu, Wieslaw Nowak, Gwangrog Lee, Piotr E. Marszalck, and Weitao Yang. "Complex Mechanics of Sugar Rings in Water Revealed by Quantum Mechanics Simulations." J. Am. Chem. Soc., 126-9033-9041, 2004.

108. 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.

109. 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.

110. 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.

111. 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.

112. 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.

113. 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.

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

115. 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.

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

117. 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.

118. 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.

119. H. Jiang and Weitao Yang. "Conjugate-Gradient Optimization Method for Orbital-Free Density Functional Calculations", Journal of Chemical Physics, 121(5): 2030-2036, 2004.

120. 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.

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

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

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

124. 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.

125. 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.

126. 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.

127. 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).

128. 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).

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

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

131. 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).

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

133. 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).

134. Qin Wu, Aron J. Cohen and Weitao Yang. "Analytic energy gradients of the optimized effective potential method" J. Chem. Phys, 123, 124111, (2005).

135. 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).

136. Rui Liu, San-Huang Ke, Weitao Yang, and Harold U. Baranger. "Organometallic molecular rectification" J. Chem. Phys., 124, 024718 (2006).

137. 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., 110 :2, 700-708, (2006).

138. 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).

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

140. 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).

141. San-Huang Ke, Weitao Yang, and Harold Baranger, "Nano-tube metal junctions: 2- and 3- terminal electrical transport", Los Alamos National Laboratory (2006).

142. Jungsan Sohn, Jerry Parks, Gregory Buhrman, Paul Brown, Kolbrun Kristjansdottir, Alexias Safi, Herbert Edelsbrunner, Weitao Yang and Johannes Rudolf, "Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate", Biochemistry, 44(50, 16563-16573, (2006).

143. Qin Wu, Aron Cohen and Weitao Yang. "Analytic energy gradients of the optimized effective potential method", Journ. Chem. Phys., 123(13), 134111/1--134111/10 (2006).

144. 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).

145. 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).

146. 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).

147. 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).

148. 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).

149. Paul Ayers and Weitao Yang. "Legendre-transform functionals for spin-density-functional theory", Journ. of Chem. Phys., 124(22), 224108-224123 , (2006).

150. 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).

151.Hu, H., Lu, Z.Y. and Yang, W.T. "QM/MM minimum free-energy path: Methodology and application to triosephosphate isomerase", Journal of Chemical Theory and Computation, 3 (2); 390-406, (2007)

152. 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.

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

154. 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)

155. Hu H, 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."
J Phys Chem A. (111(26):5685-91 (2007)

156. 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)

157. 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)

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

159.