Weitao Yang | Scholars@Duke

Weitao Yang
Philip Handler Professor of Chemistry in Trinity College of Arts and Sciences

Prof. Yang, the Philip Handler Professor of Chemistry, is developing methods for quantum mechanical calculations of large systems and carrying out quantum mechanical simulations of biological systems and nanostructures. His group has developed the linear scaling methods for electronic structure calculations and more recently the QM/MM methods for simulations of chemical reactions in enzymes.

Current Appointments & Affiliations

Philip Handler Professor of Chemistry in Trinity College of Arts and Sciences, Chemistry, Trinity College of Arts & Sciences 2003
Professor of Chemistry, Chemistry, Trinity College of Arts & Sciences 1999
Professor in the Department of Physics, Physics, Trinity College of Arts & Sciences 2012
Faculty Network Member of The Energy Initiative, Duke University Energy Initiative, Initiatives 2012

Contact Information

5310 French Family Science Center, Durham, NC 27708
Box 90346, Durham, NC 27708-0346
weitao.yang@duke.edu (919) 660-1562
Yang Research Group

Background
Education, Training, & Certifications
- Ph.D., University of North Carolina at Chapel Hill 1986
- B.S., Peking University (China) 1982
Duke Appointment History
- Associate Professor with Tenure, Chemistry, Trinity College of Arts & Sciences 1995 - 1999
- Assistant Professor, Chemistry, Trinity College of Arts & Sciences 1989 - 1995
Recognition
In the News
- APR 28, 2017
  
  Energy Initiative Awards Seven New Seed Grants
- FEB 23, 2017
  
  Light-Driven Reaction Converts Carbon Dioxide Into Fuel
- MAY 18, 2015
  
  Weitao Yang on Knowing How Electrons Behave
Awards & Honors
Research
Selected Grants
- Molecular Mechanisms of Spontaneous and Hsp70-assisted Renaturation of Misfolded Proteins awarded by National Science Foundation 2018 - 2021
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Center for Complex Materials from First Principles (CCM) awarded by Temple University 2018 - 2020
- Localized Orbital Scaling Correction for Periodic Systems awarded by Molecular Sciences Software Institute 2018 - 2019
- Computer Simulations of Enzymes awarded by National Institutes of Health 2000 - 2019
- Vectorial Folding of Large, Multidomain Proteins awarded by National Science Foundation 2015 - 2018
- Center for the Computational Design of Functional Layered Materials awarded by Temple University 2014 - 2018
- Development and Applications of Density Functional Methods for Large Systems awarded by National Science Foundation 2006 - 2018
- Theory Assisted Library and Inverse Design for Materials Optimization awarded by Samsung Electronics Co., Ltd. 2013 - 2016
- Structural Biology and Biophysics Training Program awarded by National Institutes of Health 1994 - 2015
- Vectorial Folding of Protiens and Nascent Polypeptide Chains by AFM and Computer Simulations awarded by National Science Foundation 2011 - 2014
- Theory and Design of Molecular Electronics for Sensor Applications awarded by Office of Naval Research 2009 - 2014
- Conformations of Polysaccharides and Nucleic Acids by Single Molecule Force Spectroscopy awarded by National Science Foundation 2007 - 2011
- Coherence and Correlations in Electronic Nanostructures awarded by National Science Foundation 2005 - 2009
- Development and Applications of Density Functional Methods for Large Systems awarded by National Science Foundation 2003 - 2007
- Coherence and Correlation in Electronic Nanostructures awarded by National Science Foundation 2001 - 2006
- Individual National Research Service Award (Postdoctoral Fellowship) awarded by National Institutes of Health 2001 - 2002
- Development and Applications of Density Functional Methods for Large Systems awarded by National Science Foundation 1998 - 2002
- (96-1022) Symposium on Density Functional Theory and Applications awarded by National Science Foundation 1997 - 1998
- (97-0336) The Divide and Conquer Density Functional Approach for Large Molecules and for Molecules on Surface awarded by National Science Foundation 1995 - 1998
- (94-0956) The Divide-and-Conquer Density Functional Approach for Large Molecules and for Molecules on Surfaces awarded by National Science Foundation 1995 - 1997
- (96-0290) The Divide and Conquer Density Functional Approach for Large Molecules and for Molecules on Surfaces awarded by National Science Foundation 1995 - 1997
- (93-0470) Quantum Molecular Modeling with Massively Parallel Computers: A Divide-and-Conquer Approach awarded by Environmental Protection Agency 1993 - 1996
- (95-0940) Quantum Molecular Modeling with Massively Parallel Computers: A Divide-and-Conquer Approach awarded by Environmental Protection Agency 1993 - 1996
- (91-0382) Applying Density-Functional Theory to Large Molecules: Theoretical and Computational Development awarded by National Science Foundation 1991 - 1993
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Wang, W, Yang, W, and Li, Z. "Field Electron Emission Images Far Away from a Semi-Infinitely Long Emitter: A Multiscale Simulation." The Journal of Physical Chemistry C 122, no. 48 (December 6, 2018): 27754-27760. Full Text
  - Su, NQ, Li, C, and Yang, W. "Describing strong correlation with fractional-spin correction in density functional theory." Proceedings of the National Academy of Sciences of the United States of America 115, no. 39 (September 10, 2018): 9678-9683. Full Text
  - Shen, L, Zeng, X, Hu, H, Hu, X, and Yang, W. "Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants." Journal of Chemical Theory and Computation 14, no. 9 (September 2018): 4948-4957. Full Text
  - Sutton, C, Yang, Y, Zhang, D, and Yang, W. "Single, Double Electronic Excitations and Exciton Effective Conjugation Lengths in π-Conjugated Systems." The Journal of Physical Chemistry Letters 9, no. 14 (July 6, 2018): 4029-4036. Full Text
  - Wang, H, and Yang, W. "Force Field for Water Based on Neural Network." The Journal of Physical Chemistry Letters 9, no. 12 (June 4, 2018): 3232-3240. Full Text
  - Al-Saadon, R, Sutton, C, and 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 14, no. 6 (June 2018): 3196-3204. Full Text
  - Zhang, D, Yang, X, Zheng, X, and Yang, W. "Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies." Molecular Physics 116, no. 7-8 (April 18, 2018): 927-934. Full Text
  - Contreras-García, J, and Yang, W. "Perspective: Chemical information encoded in electron density." Wuli Huaxue Xuebao/ Acta Physico Chimica Sinica 34, no. 6 (March 20, 2018): 567-580. Full Text
  - Li, C, Zheng, X, Su, NQ, and Yang, W. "Localized orbital scaling correction for systematic elimination of delocalization error in density functional approximations." National Science Review 5, no. 2 (March 1, 2018): 203-215. Full Text
  - Shen, L, and Yang, W. "Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks." Journal of Chemical Theory and Computation 14, no. 3 (March 2018): 1442-1455. Full Text
  - Zhang, X, Li, X, Reish, ME, Zhang, D, Su, NQ, Gutiérrez, Y, Moreno, F, Yang, W, Everitt, HO, and Liu, J. "Plasmon-Enhanced Catalysis: Distinguishing Thermal and Nonthermal Effects." Nano Letters 18, no. 3 (March 2018): 1714-1723. Full Text
  - Li, G, Zhang, D, Yu, Y, Huang, S, Yang, W, and Cao, L. "Activating MoS2 for pH-Universal Hydrogen Evolution Catalysis." Journal of the American Chemical Society 139, no. 45 (November 2, 2017): 16194-16200. Full Text
  - Jin, Y, Yang, Y, Zhang, D, Peng, D, and Yang, W. "Excitation energies from particle-particle random phase approximation with accurate optimized effective potentials." The Journal of chemical physics 147, no. 13 (October 2017): 134105-. Full Text
  - Jin, Y, Zhang, D, Chen, Z, Su, NQ, and Yang, W. "Generalized Optimized Effective Potential for Orbital Functionals and Self-Consistent Calculation of Random Phase Approximations." The journal of physical chemistry letters 8, no. 19 (October 2017): 4746-4751. Full Text
  - Wu, J, Shen, L, and Yang, W. "Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations." The Journal of chemical physics 147, no. 16 (October 2017): 161732-. Full Text
  - Chen, Z, Zhang, D, Jin, Y, Yang, Y, Su, NQ, and Yang, W. "Multireference Density Functional Theory with Generalized Auxiliary Systems for Ground and Excited States." The journal of physical chemistry letters 8, no. 18 (September 2017): 4479-4485. Full Text
  - Peng, D, Li, S, Peng, L, Gu, FL, and 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 13, no. 9 (September 2017): 4101-4112. Full Text
  - Zhang, D, Su, NQ, and Yang, W. "Accurate Quasiparticle Spectra from the T-Matrix Self-Energy and the Particle-Particle Random Phase Approximation." The journal of physical chemistry letters 8, no. 14 (July 2017): 3223-3227. Full Text
  - Li, C, Lu, J, and Yang, W. "On extending Kohn-Sham density functionals to systems with fractional number of electrons." The Journal of Chemical Physics 146, no. 21 (June 2017): 214109-. Full Text
  - Scholl, ZN, Yang, W, and Marszalek, PE. "Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase." Biophysical Journal 112, no. 9 (May 2017): 1829-1840. Full Text
  - Lewis, CA, Shen, L, Yang, W, and Wolfenden, R. "Three Pyrimidine Decarboxylations in the Absence of a Catalyst." Biochemistry 56, no. 10 (March 6, 2017): 1498-1503. Full Text
  - 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, and 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 114, no. 11 (March 6, 2017): 2801-2806. Full Text
  - Yang, Y, Dominguez, A, Zhang, D, Lutsker, V, Niehaus, TA, Frauenheim, T, and 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 146, no. 12 (March 2017): 124104-null. Full Text
  - Zhang, X, Li, X, Zhang, D, Su, NQ, Yang, W, Everitt, HO, and Liu, J. "Product selectivity in plasmonic photocatalysis for carbon dioxide hydrogenation." Nature Communications 8 (February 23, 2017): 14542-null. Full Text Open Access Copy
  - Li, C, and 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 146, no. 7 (February 2017): 074107-null. Full Text
  - Li, G, Zhang, D, Qiao, Q, Yu, Y, Peterson, D, Zafar, A, Kumar, R, Curtarolo, S, Hunte, F, Shannon, S, Zhu, Y, Yang, W, and Cao, L. "All The Catalytic Active Sites of MoS2 for Hydrogen Evolution." Journal of the American Chemical Society 138, no. 51 (December 15, 2016): 16632-16638. Full Text
  - Shen, L, Wu, J, and Yang, W. "Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks." Journal of Chemical Theory and Computation 12, no. 10 (October 2016): 4934-4946. Full Text
  - Zhang, D, and Yang, W. "Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation." The Journal of Chemical Physics 145, no. 14 (October 2016): 144105-null. Full Text
  - Yang, Y, Davidson, ER, and 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 113, no. 35 (August 15, 2016): E5098-E5107. Full Text
  - Scholl, ZN, Li, Q, Yang, W, and 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 291, no. 35 (August 2016): 18263-18275. Full Text
  - Yang, Y, Shen, L, Zhang, D, and Yang, W. "Conical Intersections from Particle-Particle Random Phase and Tamm-Dancoff Approximations." The journal of physical chemistry letters 7, no. 13 (July 2016): 2407-2411. Full Text
  - Wang, H, and Yang, W. "Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory." The Journal of Chemical Physics 144, no. 22 (June 2016): 224107-null. Full Text
  - Yang, Y, Burke, K, and Yang, W. "Accurate atomic quantum defects from particle–particle random phase approximation." Molecular Physics 114, no. 7-8 (April 17, 2016): 1189-1198. Full Text
  - Rupakheti, C, Al-Saadon, R, Zhang, Y, Virshup, AM, Zhang, P, Yang, W, and Beratan, DN. "Diverse Optimal Molecular Libraries for Organic Light-Emitting Diodes." Journal of Chemical Theory and Computation 12, no. 4 (April 2016): 1942-1952. Full Text
  - Shen, L, and 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 12, no. 4 (April 2016): 2017-2027. Full Text
  - Li, C, Lu, J, and Yang, W. "Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals." The Journal of chemical physics 143, no. 22 (December 2015): 224110-. Full Text
  - Zheng, X, Li, C, Zhang, D, and Yang, W. "Scaling correction approaches for reducing delocalization error in density functional approximations." Science China Chemistry 58, no. 12 (December 2015): 1825-1844. Full Text
  - Yang, Y, Peng, D, Davidson, ER, and Yang, W. "Singlet-triplet energy gaps for diradicals from particle-particle random phase approximation." The Journal of Physical Chemistry. A 119, no. 20 (May 2015): 4923-4932. Full Text
  - Zhang, D, Zheng, X, Li, C, and Yang, W. "Orbital relaxation effects on Kohn-Sham frontier orbital energies in density functional theory." The Journal of Chemical Physics 142, no. 15 (April 2015): 154113-null. Full Text
  - Li, S, Hu, L, Peng, L, Yang, W, and Gu, FL. "Coupled-Perturbed SCF Approach for Calculating Static Polarizabilities and Hyperpolarizabilities with Nonorthogonal Localized Molecular Orbitals." Journal of Chemical Theory and Computation 11, no. 3 (March 2015): 923-931. Full Text
  - Rupakheti, C, Virshup, A, Yang, W, and Beratan, DN. "Strategy to discover diverse optimal molecules in the small molecule universe." Journal of Chemical Information and Modeling 55, no. 3 (March 2015): 529-537. Full Text
  - Scholl, ZN, Yang, W, and Marszalek, PE. "Direct observation of multimer stabilization in the mechanical unfolding pathway of a protein undergoing oligomerization." ACS nano 9, no. 2 (February 10, 2015): 1189-1197. Full Text
  - Li, C, Zheng, X, Cohen, AJ, Mori-Sánchez, P, and Yang, W. "Local scaling correction for reducing delocalization error in density functional approximations." Physical Review Letters 114, no. 5 (February 4, 2015): 053001-null. Full Text
  - Scholl, ZN, Yang, W, and Marszalek, PE. "Chaperones rescue luciferase folding by separating its domains." Journal of Biological Chemistry 290, no. 2 (January 9, 2015): 883-883. Full Text
  - Zhang, D, Peng, D, Zhang, P, and Yang, W. "Analytic gradients, geometry optimization and excited state potential energy surfaces from the particle-particle random phase approximation." Physical chemistry chemical physics : PCCP 17, no. 2 (January 2015): 1025-1038. Full Text
  - Guo, H, Xie, D, and Yang, W. "A tribute to Guosen Yan." Theoretical Chemistry Accounts 133, no. 12 (December 2014). Full Text
  - Peng, D, Yang, Y, Zhang, P, and Yang, W. "Restricted second random phase approximations and Tamm-Dancoff approximations for electronic excitation energy calculations." The Journal of chemical physics 141, no. 21 (December 2014): 214102-. Full Text
  - Scholl, ZN, Yang, W, and Marszalek, PE. "Chaperones rescue luciferase folding by separating its domains." The Journal of Biological Chemistry 289, no. 41 (October 2014): 28607-28618. Full Text
  - Su, NQ, Yang, W, Mori-Sánchez, P, and Xu, X. "Fractional charge behavior and band gap predictions with the XYG3 type of doubly hybrid density functionals." The Journal of Physical Chemistry. A 118, no. 39 (October 2014): 9201-9211. Full Text
  - Yang, Y, Peng, D, Lu, J, and Yang, W. "Excitation energies from particle-particle random phase approximation: Davidson algorithm and benchmark studies." The Journal of Chemical Physics 141, no. 12 (September 2014): 124104-null. Full Text
  - Li, Y, Nese, A, Hu, X, Lebedeva, NV, LaJoie, TW, Burdyńska, J, Stefan, MC, You, W, Yang, W, Matyjaszewski, K, and Sheiko, SS. "Shifting Electronic Structure by Inherent Tension in Molecular Bottlebrushes with Polythiophene Backbones." Acs Macro Letters 3, no. 8 (August 19, 2014): 738-742. Full Text
  - Shenvi, N, van Aggelen, H, Yang, Y, and 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 141, no. 2 (July 2014): 024119-. Full Text
  - Chaudret, R, Contreras-Garcia, J, Delcey, M, Parisel, O, Yang, W, and 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 10, no. 5 (May 2014): 1900-1909. Full Text
  - Peng, D, van Aggelen, H, Yang, Y, and Yang, W. "Linear-response time-dependent density-functional theory with pairing fields." The Journal of Chemical Physics 140, no. 18 (May 2014): 18A522-null. Full Text
  - Yang, W. "Preface: Special topic on advances in density functional theory." The Journal of chemical physics 140, no. 18 (May 2014): 18A101-. Full Text
  - van Aggelen, H, Yang, Y, and Yang, W. "Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random phase approximation." The Journal of Chemical Physics 140, no. 18 (May 2014): 18A511-null. Full Text
  - Yu, Y, Huang, S-Y, Li, Y, Steinmann, SN, Yang, W, and Cao, L. "Layer-Dependent Electrocatalysis of MoS2 for Hydrogen Evolution." Nano Letters 14, no. 2 (February 12, 2014): 553-558. Full Text
  - Franks, AT, Peng, D, Yang, W, and Franz, KJ. "Characterization of a photoswitching chelator with light-modulated geometric, electronic, and metal-binding properties." Inorganic Chemistry 53, no. 3 (February 2014): 1397-1405. Full Text
  - "Double, Rydberg and charge transfer excitations from pairing matrix fluctuation and particle-particle random phase approximation." Journal of Chemical Physics 139, no. 22 (December 14, 2013). Full Text
  - Yang, Y, van Aggelen, H, and Yang, W. "Double, Rydberg and charge transfer excitations from pairing matrix fluctuation and particle-particle random phase approximation." The Journal of Chemical Physics 139, no. 22 (December 2013): 224105-null. Full Text
  - "Benchmark tests and spin adaptation for the particle-particle random phase approximation." Journal of Chemical Physics 139, no. 17 (November 7, 2013). Full Text
  - Yang, Y, van Aggelen, H, Steinmann, SN, Peng, D, and Yang, W. "Benchmark tests and spin adaptation for the particle-particle random phase approximation." J Chem Phys 139, no. 17 (November 7, 2013): 174110-. Full Text Link to Item
  - Zhang, D, Steinmann, SN, and Yang, W. "Dynamical second-order Bethe-Salpeter equation kernel: a method for electronic excitation beyond the adiabatic approximation." J Chem Phys 139, no. 15 (October 21, 2013): 154109-. Full Text Link to Item
  - Jin, Y, Johnson, ER, Hu, X, Yang, W, and Hu, H. "Contributions of Pauli repulsions to the energetics and physical properties computed in QM/MM methods." Journal of Computational Chemistry 34, no. 27 (October 2013): 2380-2388. Full Text
  - "Extension of many-body theory and approximate density functionals to fractional charges and fractional spins." Journal of Chemical Physics 139, no. 10 (September 14, 2013). Full Text
  - "Equivalence of particle-particle random phase approximation correlation energy and ladder-coupled-cluster doubles." Journal of Chemical Physics 139, no. 10 (September 14, 2013). Full Text
  - Peng, D, Steinmann, SN, van Aggelen, H, and Yang, W. "Equivalence of particle-particle random phase approximation correlation energy and ladder-coupled-cluster doubles." The Journal of Chemical Physics 139, no. 10 (September 2013): 104112-null. Full Text
  - Yang, W, Mori-Sánchez, P, and Cohen, AJ. "Extension of many-body theory and approximate density functionals to fractional charges and fractional spins." The Journal of Chemical Physics 139, no. 10 (September 2013): 104114-null. Full Text
  - "Wave function methods for fractional electrons." Journal of Chemical Physics 139, no. 7 (August 21, 2013). Full Text
  - Steinmann, SN, and Yang, W. "Wave function methods for fractional electrons." J Chem Phys 139, no. 7 (August 21, 2013): 074107-. Full Text Link to Item
  - "The tensor hypercontracted parametric reduced density matrix algorithm: Coupled-cluster accuracy with O(r⁴) scaling." Journal of Chemical Physics 139, no. 5 (August 7, 2013). Full Text
  - Shenvi, N, van Aggelen, H, Yang, Y, Yang, W, Schwerdtfeger, C, and Mazziotti, D. "The tensor hypercontracted parametric reduced density matrix algorithm: coupled-cluster accuracy with O(r(4)) scaling." J Chem Phys 139, no. 5 (August 7, 2013): 054110-. Full Text Link to Item
  - Wang, J, and Yang, W. "Concerted proton transfer mechanism of Clostridium thermocellum ribose-5-phosphate isomerase." The Journal of Physical Chemistry. B 117, no. 32 (August 2, 2013): 9354-9361. Full Text
  - Peng, D, and Yang, W. "Fukui function and response function for nonlocal and fractional systems." J Chem Phys 138, no. 18 (May 14, 2013): 184108-. Full Text Link to Item
  - Virshup, AM, Contreras-García, J, Wipf, P, Yang, W, and Beratan, DN. "Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds." Journal of the American Chemical Society 135, no. 19 (May 2, 2013): 7296-7303. Full Text
  - Wu, P, Chaudret, R, Hu, X, and Yang, W. "Noncovalent Interaction Analysis in Fluctuating Environments." Journal of Chemical Theory and Computation 9, no. 5 (May 2013): 2226-2234. Full Text
  - Zheng, X, Zhou, T, and Yang, W. "A nonempirical scaling correction approach for density functional methods involving substantial amount of Hartree-Fock exchange." The Journal of Chemical Physics 138, no. 17 (May 2013): 174105-null. Full Text
  - Chaudret, R, Parks, JM, and Yang, W. "Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs." J Chem Phys 138, no. 4 (January 28, 2013): 045102-. Full Text Link to Item
  - Jin, Y, Johnson, ER, Hu, X, Yang, W, and Hu, H. "Contributions of Pauli repulsions to the energetics and physical properties computed in QM/MM methods." Journal of Computational Chemistry 34, no. 27 (2013): 2380-2388. Full Text
  - Peng, L, Gu, FL, and Yang, W. "Effective preconditioning for ab initio ground state energy minimization with non-orthogonal localized molecular orbitals." Physical Chemistry Chemical Physics 15, no. 37 (2013): 15518-15527. Full Text
  - Vleeschouwer, FD, Chankisjijev, A, Yang, W, Geerlings, P, and Proft, FD. "Pushing the boundaries of intrinsically stable radicals: Inverse design using the thiadiazinyl radical as a template." Journal of Organic Chemistry 78, no. 7 (2013): 3151-3158. Full Text
  - De Vleeschouwer, F, Yang, W, Beratan, DN, Geerlings, P, and De Proft, F. "Inverse design of molecules with optimal reactivity properties: acidity of 2-naphthol derivatives." Phys Chem Chem Phys 14, no. 46 (December 14, 2012): 16002-16013. Full Text Link to Item
  - Shenvi, N, and Yang, W. "Achieving partial decoherence in surface hopping through phase correction." The Journal of Chemical Physics 137, no. 22 (December 2012): 22A528-null. Full Text
  - Zeng, X, Hu, X, and 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 8, no. 12 (December 2012): 4960-4967. Full Text
  - Zheng, X, Liu, M, Johnson, ER, Contreras-García, J, and Yang, W. "Delocalization error of density-functional approximations: a distinct manifestation in hydrogen molecular chains." The Journal of Chemical Physics 137, no. 21 (December 2012): 214106-null. Full Text
  - Gillet, N, Chaudret, R, Contreras-Garcίa, J, Yang, W, Silvi, B, and Piquemal, J-P. "Coupling quantum interpretative techniques: another look at chemical mechanisms in organic reactions." Journal of Chemical Theory and Computation 8, no. 11 (November 2012): 3993-3997. Full Text
  - Lin, X, Hu, X, Concepcion, JJ, Chen, Z, Liu, S, Meyer, TJ, and 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 109, no. 39 (September 2012): 15669-15672. Full Text
  - Peng, D, Hu, X, Devarajan, D, Ess, DH, Johnson, ER, and Yang, W. "Variational fractional-spin density-functional theory for diradicals." The Journal of Chemical Physics 137, no. 11 (September 2012): 114112-null. Full Text
  - Johnson, ER, Contreras-García, J, and Yang, W. "Density-Functional Errors in Alkanes: A Real-Space Perspective." Journal of Chemical Theory and Computation 8, no. 8 (August 2, 2012): 2676-2681. Full Text
  - Hu, X, Jin, Y, Zeng, X, Hu, H, and Yang, W. "Liquid water simulations with the density fragment interaction approach." Physical Chemistry Chemical Physics : Pccp 14, no. 21 (June 2012): 7700-7709. Full Text
  - Wu, P, Cisneros, GA, Hu, H, Chaudret, R, Hu, X, and Yang, W. "Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways." The Journal of Physical Chemistry. B 116, no. 23 (June 2012): 6889-6897. Full Text
  - Peng, D, Zhao, B, Cohen, AJ, Hu, X, and Yang, W. "Optimized effective potential for calculations with orbital-free potential functionals." Molecular Physics 110, no. 9-10 (May 10, 2012): 925-934. Full Text
  - Jiang, N, Zuber, G, Keinan, S, Nayak, A, Yang, W, Therien, MJ, and Beratan, DN. "Design of Coupled Porphyrin Chromophores with Unusually Large Hyperpolarizabilities." The Journal of Physical Chemistry C 116, no. 17 (May 3, 2012): 9724-9733. Full Text
  - Yang, W, Cohen, AJ, and Mori-Sánchez, P. "Derivative discontinuity, bandgap and lowest unoccupied molecular orbital in density functional theory." The Journal of Chemical Physics 136, no. 20 (May 2012): 204111-null. Full Text
  - Zhang, J, Yang, W, Piquemal, J-P, and Ren, P. "Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential." Journal of Chemical Theory and Computation 8, no. 4 (April 10, 2012): 1314-1324. Full Text
  - Yang, W, Cohen, AJ, De Proft, F, and Geerlings, P. "Analytical evaluation of Fukui functions and real-space linear response function." The Journal of Chemical Physics 136, no. 14 (April 2012): 144110-null. Full Text
  - Lee, W, Zeng, X, Rotolo, K, Yang, M, Schofield, CJ, Bennett, V, Yang, W, and Marszalek, PE. "Mechanical anisotropy of ankyrin repeats." Biophys J 102, no. 5 (March 7, 2012): 1118-1126. Full Text Link to Item
  - Cohen, AJ, Mori-Sánchez, P, and Yang, W. "Challenges for Density Functional Theory." Chemical Reviews 112, no. 1 (January 11, 2012): 289-320. Full Text
  - Cho, J, Lin, Q, Yang, S, Simmons, JG, Cheng, Y, Lin, E, Yang, J, Foreman, JV, Everitt, HO, Yang, W, Kim, J, and Liu, J. "Sulfur-doped zinc oxide (ZnO) Nanostars: Synthesis and simulation of growth mechanism." Nano Research 5, no. 1 (January 2012): 20-26. Full Text
  - Cohen, AJ, Mori-Sánchez, P, and Yang, W. "Challenges for density functional theory." Chemical Reviews 112, no. 1 (January 2012): 289-320. Full Text
  - Sun, Z, Yang, W, and 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 14, no. 6 (2012): 1827-1845. Full Text
  - Xu, Y, Wang, B-J, Ke, S-H, Yang, W, and Alzahrani, AZ. "Highly tunable spin-dependent electron transport through carbon atomic chains connecting two zigzag graphene nanoribbons." Journal of Chemical Physics 137, no. 10 (2012). Full Text
  - Yang, W, Mori-Sanchez, P, and Cohen, AJ. "Insight and progress in density functional theory." (2012). Full Text
  - Shenvi, N, and Yang, W. "An algebraic operator approach to electronic structure." J Chem Phys 135, no. 24 (December 28, 2011): 244111-. Full Text Link to Item
  - Contreras-García, J, Yang, W, and Johnson, ER. "Analysis of hydrogen-bond interaction potentials from the electron density: integration of noncovalent interaction regions." The Journal of Physical Chemistry. A 115, no. 45 (November 2011): 12983-12990. Full Text
  - Wu, P, Hu, X, and Yang, W. "λ-Meta Dynamics Approach To Compute Absolute Solvation Free Energy." The Journal of Physical Chemistry Letters 2, no. 17 (September 2011): 2099-2103. Full Text
  - Meyer, TJ, and Yang, W. "Catalytic mechanism for single-site water oxidation process: A theoretical study." Acs National Meeting Book of Abstracts (August 25, 2011).
  - Zheng, X, Cohen, AJ, Mori-Sanchez, P, Hu, X, and Yang, W. "Improving Band Gap Prediction in Density Functional Theory from Molecules to Solids." PHYSICAL REVIEW LETTERS 107, no. 2 (July 7, 2011). Full Text Link to Item
  - Zheng, X, Cohen, AJ, Mori-Sánchez, P, Hu, X, and Yang, W. "Improving band gap prediction in density functional theory from molecules to solids." Physical Review Letters 107, no. 2 (July 7, 2011): 026403-null. Full Text
  - Shenvi, N, Subotnik, JE, and Yang, W. "Phase-corrected surface hopping: correcting the phase evolution of the electronic wavefunction." The Journal of Chemical Physics 135, no. 2 (July 2011): 024101-null. Full Text
  - Tam, ES, Parks, JJ, Shum, WW, Zhong, Y-W, Santiago-Berríos, MB, Zheng, X, Yang, W, Chan, GK-L, Abruña, HD, and Ralph, DC. "Single-molecule conductance of pyridine-terminated dithienylethene switch molecules." Acs Nano 5, no. 6 (June 2011): 5115-5123. Full Text
  - Cui, G, and Yang, W. "Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method." J Chem Phys 134, no. 20 (May 28, 2011): 204115-. Full Text Link to Item
  - Shenvi, N, Subotnik, JE, and Yang, W. "Simultaneous-trajectory surface hopping: a parameter-free algorithm for implementing decoherence in nonadiabatic dynamics." The Journal of Chemical Physics 134, no. 14 (April 2011): 144102-null. Full Text
  - Lee, W, Zeng, X, Zhou, H-X, Bennett, V, Yang, W, and Marszalek, PE. "Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations." Journal of Biological Chemistry 286, no. 10 (March 11, 2011): 8708.3-8708. Full Text
  - Contreras-García, J, Johnson, ER, Keinan, S, Chaudret, R, Piquemal, J-P, Beratan, DN, and Yang, W. "NCIPLOT: a program for plotting non-covalent interaction regions." Journal of Chemical Theory and Computation 7, no. 3 (March 2011): 625-632. Full Text
  - Sun, Z, and Yang, W. "Communication: An exact short-time solver for the time-dependent Schrödinger equation." J Chem Phys 134, no. 4 (January 28, 2011): 041101-. Full Text Link to Item
  - Ess, DH, Johnson, ER, Hu, X, and Yang, W. "Singlet-triplet energy gaps for diradicals from fractional-spin density-functional theory." The Journal of Physical Chemistry. A 115, no. 1 (January 2011): 76-83. Full Text
  - Hu, X, Hu, H, Melvin, JA, Clancy, KW, McCafferty, DG, and Yang, W. "Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation." Journal of the American Chemical Society 133, no. 3 (January 2011): 478-485. Full Text
  - Sun, Z, and Yang, W. "Communication: An exact short-time solver for the time-dependent Schrödinger equation." The Journal of Chemical Physics 134, no. 4 (January 2011): 041101-null. Full Text
  - Wu, P, Hu, X, and Yang, W. "λ-metadynamics approach to compute absolute solvation free energy." Journal of Physical Chemistry Letters 2, no. 17 (2011): 2099-2103. Full Text
  - Lee, W, Zeng, X, Zhou, H-X, Bennett, V, Yang, W, and Marszalek, PE. "Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations." The Journal of Biological Chemistry 285, no. 49 (December 2010): 38167-38172. Full Text
  - Cui, G, and Yang, W. "Challenges with range-separated exchange-correlation functionals in time-dependent density functional theory calculations." Molecular Physics 108, no. 19-20 (October 10, 2010): 2745-2750. Full Text
  - Cui, G, Fang, W, and Yang, W. "Efficient construction of nonorthogonal localized molecular orbitals in large systems." J Phys Chem A 114, no. 33 (August 26, 2010): 8878-8883. Full Text Open Access Copy Link to Item
  - Hu, X, Hu, H, Beratan, DN, and Yang, W. "A gradient-directed Monte Carlo approach for protein design." J Comput Chem 31, no. 11 (August 2010): 2164-2168. Full Text Link to Item
  - Heaton-Burgess, T, and 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 132, no. 23 (June 21, 2010): 234113-. Full Text Open Access Copy Link to Item
  - Ke, S-H, Liu, R, Yang, W, and Baranger, HU. "Time-dependent transport through molecular junctions." J Chem Phys 132, no. 23 (June 21, 2010): 234105-. Full Text Open Access Copy Link to Item
  - Johnson, ER, Keinan, S, Mori-Sánchez, P, Contreras-García, J, Cohen, AJ, and Yang, W. "Revealing noncovalent interactions." Journal of the American Chemical Society 132, no. 18 (May 2010): 6498-6506. Full Text Open Access Copy
  - Chen, Z, Concepcion, JJ, Hu, X, Yang, W, Hoertz, PG, and 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 107, no. 16 (April 2010): 7225-7229. Full Text
  - Zheng, X, Ke, S-H, and Yang, W. "Conductive junctions with parallel graphene sheets." J Chem Phys 132, no. 11 (March 21, 2010): 114703-. Full Text Open Access Copy Link to Item
  - Hu, H, and Yang, W. "Elucidating solvent contributions to solution reactions with ab initio QM/MM methods." The Journal of Physical Chemistry. B 114, no. 8 (March 2010): 2755-2759. Full Text Open Access Copy
  - Hu, X, Xiao, D, Keinan, S, Asselberghs, I, Therien, MJ, Clays, K, Yang, W, and 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 114, no. 5 (February 11, 2010): 2349-2359. Full Text Open Access Copy
  - Hu, X, and Yang, W. "Accelerating self-consistent field convergence with the augmented Roothaan-Hall energy function." J Chem Phys 132, no. 5 (February 7, 2010): 054109-. Full Text Open Access Copy Link to Item
  - Zeng, X, Hu, H, Zhou, H-X, Marszalek, PE, and Yang, W. "Equilibrium sampling for biomolecules under mechanical tension." Biophysical Journal 98, no. 4 (February 2010): 733-740. Full Text
  - Cui, G, Fang, W, and Yang, W. "Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals." Phys Chem Chem Phys 12, no. 2 (January 14, 2010): 416-421. Full Text Open Access Copy Link to Item
  - Hammill, JT, Contreras-García, J, Virshup, AM, Beratan, DN, Yang, W, and Wipf, P. "Synthesis and chemical diversity analysis of bicyclo[3.3.1]non-3-en-2-ones." Tetrahedron 66, no. 31 (2010): 5852-5862. Full Text
  - Johnson, ER, Yang, W, and Davidson, ER. "Spin-state splittings, highest-occupied-molecular-orbital and lowest-unoccupied-molecular-orbital energies, and chemical hardness." Journal of Chemical Physics 133, no. 16 (2010). Full Text Open Access Copy
  - Rinderspacher, BC, Andzelm, J, Rawlett, A, Dougherty, J, Beratan, DN, and Yang, W. "Discrete Optimization of Electronic Hyperpolarizabilities in a Chemical Subspace." Journal of Chemical Theory and Computation 5, no. 12 (December 2009): 3321-3329. Full Text
  - Hu, X, Beratan, DN, and Yang, W. "Emergent strategies for inverse molecular design." Science in China Series B: Chemistry 52, no. 11 (November 2009): 1769-1776. Full Text
  - Hu, X, Beratan, DN, and 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 131, no. 15 (October 21, 2009): 154117-. Full Text Link to Item
  - Balabin, IA, Yang, W, and Beratan, DN. "Coarse-grained modeling of allosteric regulation in protein receptors." Proc Natl Acad Sci U S A 106, no. 34 (August 25, 2009): 14253-14258. Full Text Link to Item
  - Balabin, IA, Yang, W, and Beratan, DN. "Modeling allosteric regulation in GPCRs: Toward rational structure-based drug design." ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 238 (August 16, 2009). Link to Item
  - 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 238 (August 16, 2009). Link to Item
  - Kasper, AC, Moon, EJ, Hu, X, Park, Y, Wooten, CM, Kim, H, Yang, W, Dewhirst, MW, and Hong, J. "Analysis of HIF-1 inhibition by manassantin A and analogues with modified tetrahydrofuran configurations." Bioorg Med Chem Lett 19, no. 14 (July 15, 2009): 3783-3786. Full Text Link to Item
  - Li, Z, Wang, C-Y, Ke, S-H, and Yang, W. "First-principles study for transport properties of defective carbon nanotubes with oxygen adsorption." The European Physical Journal B 69, no. 3 (June 2009): 375-382. Full Text
  - Bulat, FA, Couchman, L, and Yang, W. "Contact geometry and conductance of crossed nanotube junctions under pressure." Nano Lett 9, no. 5 (May 2009): 1759-1763. Full Text Link to Item
  - Cohen, AJ, Mori-Sánchez, P, and Yang, W. "Second-Order Perturbation Theory with Fractional Charges and Fractional Spins." Journal of Chemical Theory and Computation 5, no. 4 (April 2009): 786-792. Full Text
  - Parks, JM, Hu, H, Rudolph, J, and Yang, W. "Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations." The Journal of Physical Chemistry. B 113, no. 15 (April 2009): 5217-5224. Full Text
  - Zeng, X, Hu, H, Hu, X, and Yang, W. "Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method." The Journal of Chemical Physics 130, no. 16 (April 2009): 164111-null. Full Text
  - Hu, H, and Yang, W. "Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes." Theochem 898, no. 1-3 (March 2009): 17-30. Full Text
  - Ke, S-H, Yang, W, Curtarolo, S, and Baranger, HU. "Thermopower of molecular junctions: an ab initio study." Nano Lett 9, no. 3 (March 2009): 1011-1014. Full Text Link to Item
  - Mori-Sanchez, P, Cohen, AJ, and Yang, W. "Discontinuous Nature of the Exchange-Correlation Functional in Strongly Correlated Systems." PHYSICAL REVIEW LETTERS 102, no. 6 (February 13, 2009). Full Text Link to Item
  - Mori-Sánchez, P, Cohen, AJ, and Yang, W. "Discontinuous nature of the exchange-correlation functional in strongly correlated systems." Physical Review Letters 102, no. 6 (February 13, 2009): 066403-null. Full Text
  - Cohen, AJ, Mori Sanchez, P, and Yang, WT. "Second-order perturbation theory with fractional charges and fractional spins." Journal of Chemical Theory and Computation 5, no. 5 (2009): 786-792. (Academic Article)
  - Keinan, S, Therien, MJ, Beratan, DN, and Yang, W. "Molecular design of porphyrin-based nonlinear optical materials." J Phys Chem A 112, no. 47 (November 27, 2008): 12203-12207. Full Text Link to Item
  - Heaton-Burgess, T, and Yang, W. "Optimized effective potentials from arbitrary basis sets." J Chem Phys 129, no. 19 (November 21, 2008): 194102-. Full Text Link to Item
  - Balamurugan, D, Yang, W, and Beratan, DN. "Exploring chemical space with discrete, gradient, and hybrid optimization methods." J Chem Phys 129, no. 17 (November 7, 2008): 174105-. Full Text Link to Item
  - Heaton Burgess, T, and Yang, WT. "Optimized eﬀective potentials from arbitrary basis sets." Journal of Chemical Physics 129 (November 2008): 194102-. (Academic Article)
  - Hu, H, Boone, A, and Yang, W. "Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase." Journal of the American Chemical Society 130, no. 44 (November 2008): 14493-14503. Full Text
  - Johnson, ER, Mori-Sánchez, P, Cohen, AJ, and Yang, W. "Delocalization errors in density functionals and implications for main-group thermochemistry." The Journal of Chemical Physics 129, no. 20 (November 2008): 204112-null. Full Text
  - Ke, S-H, Yang, W, and Baranger, HU. "Quantum-interference-controlled molecular electronics." Nano Lett 8, no. 10 (October 2008): 3257-3261. Full Text Link to Item
  - Parks, JM, Hu, H, Cohen, AJ, and Yang, W. "A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes." The Journal of Chemical Physics 129, no. 15 (October 2008): 154106-null. Full Text
  - Cohen, AJ, Mori-Sánchez, P, and Yang, W. "Fractional spins and static correlation error in density functional theory." The Journal of Chemical Physics 129, no. 12 (September 2008): 121104-null. Full Text
  - Keinan, S, Paquette, WD, Skoko, JJ, Beratan, DN, Yang, W, Shinde, S, Johnston, PA, Lazo, JS, and 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 6, no. 18 (September 2008): 3256-3263. Full Text
  - Xiao, D, Bulat, FA, Yang, W, and Beratan, DN. "A donor-nanotube paradigm for nonlinear optical materials." Nano Letters 8, no. 9 (September 2008): 2814-2818. Full Text
  - Li, Z, Wang, C-Y, Zhang, X, Ke, S-H, and Yang, W. "Transport properties of an armchair carbon nanotube with a double vacancy under stretching." Journal of Physics: Condensed Matter 20, no. 34 (August 27, 2008): 345225-345225. Full Text
  - Hu, X, Beratan, DN, and Yang, W. "A gradient-directed Monte Carlo approach to molecular design." J Chem Phys 129, no. 6 (August 14, 2008): 064102-null. Full Text Link to Item
  - Cohen, AJ, Mori-Sánchez, P, and Yang, W. "Insights into current limitations of density functional theory." Science (New York, N.Y.) 321, no. 5890 (August 2008): 792-794. Full Text
  - Fujimoto, K, and 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 129, no. 5 (August 2008): 054102-null. Full Text
  - Xiao, D, Yang, W, and Beratan, DN. "Inverse molecular design in a tight-binding framework." The Journal of Chemical Physics 129, no. 4 (July 2008): 044106-null. Full Text
  - Li, Z, Wang, C-Y, Zhang, X, Ke, S-H, and Yang, W. "First-principles study for transport properties of armchair carbon nanotubes with a double vacancy under strain." Journal of Applied Physics 103, no. 11 (June 2008): 113714-113714. Full Text
  - Mori-Sánchez, P, Cohen, AJ, and Yang, W. "Localization and delocalization errors in density functional theory and implications for band-gap prediction." Physical Review Letters 100, no. 14 (April 7, 2008): 146401-null. Full Text
  - Heaton-Burgess, T, Cohen, AJ, Yang, W, and Davidson, ER. "Size extensivity of the direct optimized effective potential method." The Journal of Chemical Physics 128, no. 11 (March 2008): 114702-null. Full Text
  - Parks, JM, Kondru, RK, Hu, H, Beratan, DN, and Yang, W. "Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding." The Journal of Physical Chemistry. B 112, no. 10 (March 2008): 3168-3176. Full Text
  - Zeng, X, Hu, H, Hu, X, Cohen, AJ, and Yang, W. "Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach." The Journal of Chemical Physics 128, no. 12 (March 2008): 124510-null. Full Text
  - Burger, SK, and Yang, W. "Linear-scaling quantum calculations using non-orthogonal localized molecular orbitals." Journal of Physics Condensed Matter 20, no. 29 (2008). Full Text
  - Hu, H, Lu, Z, Parks, JM, Burger, SK, and 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 128, no. 3 (January 2008): 034105-null. Full Text
  - Hu, H, and 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 59 (January 2008): 573-601. (Review) Full Text
  - Lee, H, Kim, KW, Park, J, Kim, H, Kim, S, Kim, D, Hu, X, Yang, W, and 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 47, no. 22 (2008): 4200-4203. Full Text
  - Bulat, FA, Heaton-Burgess, T, Cohen, AJ, and Yang, W. "Optimized effective potentials from electron densities in finite basis sets." The Journal of Chemical Physics 127, no. 17 (November 2007): 174101-null. Full Text
  - Burger, SK, and Yang, W. "Sequential quadratic programming method for determining the minimum energy path." J Chem Phys 127, no. 16 (October 28, 2007): 164107-. Full Text Link to Item
  - Liu, R, Ke, S-H, Yang, W, and Baranger, HU. "Cobaltocene as a spin filter." J Chem Phys 127, no. 14 (October 14, 2007): 141104-. Full Text Link to Item
  - Ke, S-H, Baranger, HU, and Yang, W. "Contact transparency of nanotube-molecule-nanotube junctions." Phys Rev Lett 99, no. 14 (October 5, 2007): 146802-. Full Text Link to Item
  - Ke, S-H, Baranger, HU, and Yang, W. "Electron transport through single conjugated organic molecules: basis set effects in ab initio calculations." The Journal of Chemical Physics 127, no. 14 (October 2007): 144107-null. Full Text
  - Hu, H, and Yang, W. "PHYS 301-Free energies of chemical reactions in enzyme and in solution." ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 234 (August 19, 2007). Link to Item
  - Parks, JM, Hu, H, Kondru, R, and 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 234 (August 19, 2007). Link to Item
  - Zeng, X, Hu, H, and Yang, W. "PHYS 124-QM/MM calculation of electron transfer process: Fractional number of electrons approach." ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 234 (August 19, 2007). Link to Item
  - Cohen, AJ, Mori-Sánchez, P, and Yang, W. "Assessment and formal properties of exchange-correlation functionals constructed from the adiabatic connection." The Journal of Chemical Physics 127, no. 3 (July 2007): 034101-null. Full Text
  - Hu, H, Lu, Z, Elstner, M, Hermans, J, and 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 111, no. 26 (July 2007): 5685-5691. Full Text
  - Heaton-Burgess, T, Bulat, FA, and Yang, W. "Optimized effective potentials in finite basis sets." Physical Review Letters 98, no. 25 (June 20, 2007): 256401-null. Full Text
  - Ke, S-H, Baranger, HU, and Yang, W. "Role of the exchange-correlation potential in ab initio electron transport calculations." J Chem Phys 126, no. 20 (May 28, 2007): 201102-. Full Text Link to Item
  - Cohen, AJ, Mori-Sánchez, P, and Yang, W. "Development of exchange-correlation functionals with minimal many-electron self-interaction error." The Journal of Chemical Physics 126, no. 19 (May 2007): 191109-null. Full Text
  - Hu, H, Lu, Z, and Yang, W. "QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase." J Chem Theory Comput 3, no. 2 (March 2007): 390-406. Full Text Link to Item
  - Heaton-Burgess, T, Ayers, P, and Yang, W. "Spin-potential functional formalism for current-carrying noncollinear magnetic systems." PHYSICAL REVIEW LETTERS 98, no. 3 (January 19, 2007). Full Text Link to Item
  - Heaton-Burgess, T, Ayers, P, and Yang, W. "Spin-potential functional formalism for current-carrying noncollinear magnetic systems." Phys Rev Lett 98, no. 3 (January 19, 2007): 036403-. Full Text Link to Item
  - Hori, T, Takahashi, H, Furukawa, S-I, Nakano, M, and 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 111, no. 3 (2007): 581-588. Full Text
  - Hu, H, Lu, Z, and Yang, W. "Fitting molecular electrostatic potentials from quantum mechanical calculations." Journal of Chemical Theory and Computation 3, no. 3 (2007): 1004-1013. Full Text
  - Ke, S-H, Baranger, HU, and Yang, W. "Role of the exchange-correlation potential in ab initio electron transport calculations." Journal of Chemical Physics 126 (2007): 201102/1-201102/4. (Academic Article)
  - Keinan, S, Hu, X, Beratan, DN, and 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 111, no. 1 (January 2007): 176-181. Full Text
  - Wang, W, Qiao, J, Wang, L, Duan, L, Zhang, D, Yang, W, and Qiu, Y. "Synthesis, structures, and optical properties of cadmium iodide/phenethylamine hybrid materials with controlled structures and emissions." Inorganic Chemistry 46, no. 24 (2007): 10252-10260. Full Text
  - Burger, SK, and Yang, W. "Automatic integration of the reaction path using diagonally implicit Runge-Kutta methods." J Chem Phys 125, no. 24 (December 28, 2006): 244108-. Full Text Link to Item
  - Mori-Sánchez, P, Cohen, AJ, and Yang, W. "Many-electron self-interaction error in approximate density functionals." The Journal of Chemical Physics 125, no. 20 (November 2006): 201102-null. Full Text
  - Ke, S-H, Baranger, HU, and 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 3, no. 5 (October 1, 2006): 819-823. Full Text
  - Lu, Z, Hu, H, Yang, W, and Marszalek, PE. "Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method." Biophys J 91, no. 6 (September 15, 2006): L57-L59. Full Text Link to Item
  - Zhang, Q, Lu, Z, Hu, H, Yang, W, and Marszalek, PE. "Direct detection of the formation of V-amylose helix by single molecule force spectroscopy." Journal of the American Chemical Society 128, no. 29 (July 2006): 9387-9393. Full Text
  - Burger, SK, and Yang, W. "A combined explicit-implicit method for high accuracy reaction path integration." J Chem Phys 124, no. 22 (June 14, 2006): 224102-. Full Text Link to Item
  - Burger, SK, and Yang, WT. "A combined explicit-implicit method for high accuracy reaction path integration." JOURNAL OF CHEMICAL PHYSICS 124, no. 22 (June 14, 2006). Full Text Link to Item
  - Liu, R, Ke, S-H, Baranger, HU, and Yang, W. "Negative differential resistance and hysteresis through an organometallic molecule from molecular-level crossing." J Am Chem Soc 128, no. 19 (May 17, 2006): 6274-6275. Full Text Link to Item
  - Ke, S-H, Yang, W, and Baranger, HU. "Nanotube-metal junctions: 2- and 3-terminal electrical transport." J Chem Phys 124, no. 18 (May 14, 2006): 181102-. Full Text Link to Item
  - Wang, ML, Hu, XQ, Beratan, DN, and Yang, WT. "Designing molecules by optimizing potentials." JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 128, no. 10 (March 15, 2006): 3228-3232. Full Text Link to Item
  - Mori-Sánchez, P, Cohen, AJ, and Yang, W. "Self-interaction-free exchange-correlation functional for thermochemistry and kinetics." The Journal of Chemical Physics 124, no. 9 (March 2006): 91102-null. Full Text
  - Wang, M, Hu, X, Beratan, DN, and Yang, W. "Designing molecules by optimizing potentials." Journal of the American Chemical Society 128, no. 10 (March 2006): 3228-3232. Full Text
  - Wang, M, Lu, Z, and Yang, W. "Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase." The Journal of Chemical Physics 124, no. 12 (March 2006): 124516-null. Full Text
  - Burger, SK, and Yang, W. "Quadratic string method for determining the minimum-energy path based on multiobjective optimization." J Chem Phys 124, no. 5 (February 7, 2006): 054109-. Full Text Link to Item
  - Burger, SK, and Yang, WT. "Quadratic string method for determining the minimum-energy path based on multiobjective optimization." JOURNAL OF CHEMICAL PHYSICS 124, no. 5 (February 7, 2006). Full Text Link to Item
  - Hori, T, Takahashi, H, Nakano, M, Nitta, T, and 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 419, no. 1-3 (February 2006): 240-244. Full Text
  - Cisneros, GA, Wang, M, Silinski, P, Fitzgerald, MC, and Yang, W. "Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase." J Phys Chem A 110, no. 2 (January 19, 2006): 700-708. Full Text Link to Item
  - Liu, R, Ke, S-H, Yang, W, and Baranger, HU. "Organometallic molecular rectification." J Chem Phys 124, no. 2 (January 14, 2006): 024718-. Full Text Link to Item
  - Ayers, PW, and Yang, W. "Legendre-transform functionals for spin-density-functional theory." Journal of Chemical Physics 124, no. 22 (2006). Full Text
  - Champagne, B, Bulat, FA, Yang, W, Bonness, S, and 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." Journal of Chemical Physics 125, no. 19 (2006). Full Text
  - Lin, P, Yang, W, Pedersen, LC, Negishi, M, and 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 106, no. 14 (2006): 2981-2998. Full Text
  - Sohn, J, Parks, JM, Buhrman, G, Brown, P, Kristjánsdóttir, K, Safi, A, Edelsbrunner, H, Yang, W, and Rudolph, J. "Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate." Biochemistry 44, no. 50 (December 20, 2005): 16563-16573. Full Text Link to Item
  - Liu, R, Ke, S-H, Baranger, HU, and Yang, W. "Organometallic spintronics: dicobaltocene switch." Nano Lett 5, no. 10 (October 2005): 1959-1962. Full Text Link to Item
  - Wu, Q, Cohen, AJ, and Yang, W. "Analytic energy gradients of the optimized effective potential method." The Journal of Chemical Physics 123, no. 13 (October 2005): 134111-null. Full Text
  - Ke, S-H, Baranger, HU, and Yang, W. "Models of electrodes and contacts in molecular electronics." J Chem Phys 123, no. 11 (September 15, 2005): 114701-. Link to Item
  - Mori-Sánchez, P, Wu, Q, and 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 123, no. 6 (August 2005): 62204-null. Full Text
  - Hu, H, and Yang, W. "Dual-topology/dual-coordinate free-energy simulation using QM/MM force field." J Chem Phys 123, no. 4 (July 22, 2005): 041102-. Full Text Link to Item
  - Wu, Q, Cohen, AJ, and Yang *, W. "Excitation energies from time-dependent density functional theory with accurate exchange-correlation potentials." Molecular Physics 103, no. 6-8 (March 20, 2005): 711-717. Full Text
  - "Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods." Journal of Chemical Physics 122, no. 11 (March 15, 2005). Full Text
  - Cisneros, GA, Liu, H, Lu, Z, and 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." J Chem Phys 122, no. 11 (March 15, 2005): 114502-. Full Text Link to Item
  - Ke, S-H, Baranger, HU, and Yang, W. "Contact atomic structure and electron transport through molecules." J Chem Phys 122, no. 7 (February 15, 2005): 074704-. Full Text Link to Item
  - Liu, R, Ke, S-H, Baranger, HU, and Yang, W. "Intermolecular effect in molecular electronics." J Chem Phys 122, no. 4 (January 22, 2005): 44703-. Full Text Link to Item
  - Bulat, FA, Toro-Labbe, A, Champagne, B, Kirtman, B, and Yang, W. "Dft (hyper)polarizabilities of push-pull pi-conjugated systems, treatment of exact exchange and role correlation." J. Chem. Phys. 123 (2005): 014319/1-014319/7. (Academic Article)
  - Bulat, FA, Toro-Labb́, A, Champagne, B, Kirtman, B, and Yang, W. "Density-functional theory (hyper)polarizabilities of push-pull π -conjugated systems: Treatment of exact exchange and role of correlation." Journal of Chemical Physics 123, no. 1 (2005). Full Text
  - Jiang, H, Ullmo, D, Yang, W, and Baranger, HU. "Scrambling and gate-induced fluctuations in realistic quantum dots." Physical Review B - Condensed Matter and Materials Physics 71, no. 8 (2005). Full Text
  - Ke, S-H, Baranger, H, and Yang, W. ""Contact Atomic Structure and Electron Transport Through Molecules"." J. Chem. Phys. 122 (2005): 114502/1-114502/7. (Academic Article)
  - Mori-Sánchez, P, Wu, Q, and 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 123, no. 6 (2005): 62204--.
  - Ulmo, D, Jiang, H, Yang, W, and Baranger, H. ""Landau Fermi Liquid Picture of Spin Density Functional Theory: Strutinsky Approach to Quantum Dots"." Phys. Rev. B., Rapid Communication 71 (2005): 201310/1-201310/4. (Academic Article)
  - Wu, Q, Cohen, AJ, and Yang, W. "Analytic energy gradients of the optimized effective potential method." J. Chem. Phys. 123, no. 134111/1-134111/10 (2005). (Academic Article)
  - Ke, S-H, Baranger, HU, and Yang, W. "Molecular conductance: chemical trends of anchoring groups." Journal of the American Chemical Society 126, no. 48 (December 2004): 15897-15904. Full Text
  - Cohen, AJ, Wu, Q, and Yang, W. "Calculation of nuclear magnetic resonance shielding constants using potential-based methods." Chemical Physics Letters 399, no. 1-3 (November 2004): 84-88. Full Text
  - Goj, LA, Cisneros, GA, Yang, W, and Widenhoefer, RA. "Erratum to “Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization” [J. Organomet. Chem. 687 (2003) 498–507]." Journal of Organometallic Chemistry 689, no. 17 (September 2004): 2845-2845. Full Text
  - Jiang, H, and Yang, W. "Conjugate-gradient optimization method for orbital-free density functional calculations." J Chem Phys 121, no. 5 (August 1, 2004): 2030-2036. Full Text Link to Item
  - Lu, Z, Nowak, W, Lee, G, Marszalek, PE, and Yang, W. "Elastic properties of single amylose chains in water: a quantum mechanical and AFM study." Journal of the American Chemical Society 126, no. 29 (July 2004): 9033-9041. Full Text
  - Lu, Z, and Yang, W. "Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations." J Chem Phys 121, no. 1 (July 1, 2004): 89-100. Full Text Link to Item
  - Wang, M, Lu, Z, and Yang, W. "Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method." J Chem Phys 121, no. 1 (July 1, 2004): 101-107. Full Text Link to Item
  - Cisneros, GA, Wang, M, Silinski, P, Fitzgerald, MC, and Yang, W. "The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment." Biochemistry 43, no. 22 (June 2004): 6885-6892. Full Text
  - Yang, W, Ayers, PW, and Wu, Q. "Potential functionals: dual to density functionals and solution to the v-representability problem." Phys Rev Lett 92, no. 14 (April 9, 2004): 146404-. Full Text Link to Item
  - Feng, H, Bian, J, Li, L, and Yang, W. "An efficient method for constructing nonorthogonal localized molecular orbitals." Journal of Chemical Physics 120, no. 20 (2004): 9458-9466. Full Text
  - Liu, H, Lu, Z, Cisneros, GA, and Yang, W. "Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions." Journal of Chemical Physics 121, no. 2 (2004): 697-706. Full Text
  - Lu, Z, Nowak, W, Lee, G, Marszalek, P, and Yang, W. ""Elastic Properties of Single Amylose Chains in Water"." J. Am. Chem. Soc. 126 (2004): 9033-9041. (Academic Article)
  - Lu, Z, and Yang, W. ""Reaction Path Potential for Complex Systems Derived From ab initioqm/mm Calculations"." J. Chem. Phys. 121 (2004): 89-100. (Academic Article)
  - Wang, M, Lu, Z, and 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. 121 (2004): 101-107. (Academic Article)
  - Xie, L, Liu, H, and Yang, W. "Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes." Journal of Chemical Physics 120, no. 17 (2004): 8039-8052. Full Text
  - Goj, LA, Cisneros, GA, Yang, W, and Widenhoefer, RA. "Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization." Journal of Organometallic Chemistry 687, no. 2 (December 2003): 498-507. Full Text
  - Mori-Sánchez, P, Wu, Q, and Yang, W. "Accurate polymer polarizabilities with exact exchange density-functional theory." The Journal of Chemical Physics 119, no. 21 (December 2003): 11001-11004. Full Text
  - WU, QIN, and YANG, WEITAO. "ALGEBRAIC EQUATION AND ITERATIVE OPTIMIZATION FOR THE OPTIMIZED EFFECTIVE POTENTIAL IN DENSITY FUNCTIONAL THEORY." Journal of Theoretical and Computational Chemistry 02, no. 04 (December 2003): 627-638. Full Text
  - Ke, S-H, Baranger, HU, and Yang, W. "Addition energies of fullerenes and carbon nanotubes as quantum dots: the role of symmetry." Phys Rev Lett 91, no. 11 (September 12, 2003): 116803-. Full Text Link to Item
  - Cisneros, GA, Liu, H, Zhang, Y, and Yang, W. "Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase." J Am Chem Soc 125, no. 34 (August 27, 2003): 10384-10393. Full Text Link to Item
  - Wu, Q, Ayers, PW, and Yang, W. "Density-functional theory calculations with correct long-range potentials." The Journal of Chemical Physics 119, no. 6 (August 8, 2003): 2978-2990. Full Text
  - Jiang, H, Baranger, HU, and Yang, W. "Spin and conductance-peak-spacing distributions in large quantum dots: a density-functional theory study." Phys Rev Lett 90, no. 2 (January 17, 2003): 026806-. Full Text Link to Item
  - Hasegawa, J-Y, Ishida, M, Nakatsuji, H, Lu, Z, Liu, H, and Yang, W. "Energetics of the Electron Transfer from Bacteriopheophytin to Ubiquinone in the Photosynthetic Reaction Center ofRhodopseudomonas Viridis: Theoretical Study." The Journal of Physical Chemistry B 107, no. 3 (January 2003): 838-847. Full Text
  - Jiang, H, Baranger, HU, and Yang, W. "Desnity functional theory simulation of large quantum dots." Phys. Rev. B. 68 (2003). (Academic Article)
  - Jiang, H, Baranger, HU, and Yang, W. "Density-functional theory simulation of large quantum dots." Physical Review B - Condensed Matter and Materials Physics 68, no. 16 (2003): 1653371-1653379.
  - Ke, S-H, Baranger, HU, and Yang, W. "Addition Energies of Fullerenes and Carbon Nanotubes as Quantum Dots." Phys. Rev. Lett. 91 (2003): 116803-. (Academic Article) Link to Item
  - Wu, Q, and Yang, W. "A direct optimization method for calculating density functionals and exchange–correlation potentials from electron densities." The Journal of Chemical Physics 118, no. 6 (2003): 2498-2498. Full Text
  - Yang, W, and Wu, Q. "Direct method for optimized effective potentials in density-functional theory." Phys Rev Lett 89, no. 14 (September 30, 2002): 143002-. Full Text Link to Item
  - Yang, W, Lee, H-W, Hellinga, H, and Yang, JJ. "Structural analysis, identification, and design of calcium-binding sites in proteins." Proteins 47, no. 3 (May 2002): 344-356. Full Text
  - Cisneros, GA, Liu, HY, Zhang, YK, and Yang, WT. "QM/MM study of the reaction mechanism of 4-oxalocrotonate tautomerase." ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 223 (April 7, 2002): C78-C78. Link to Item
  - Lu, ZY, Liu, HY, and Yang, WT. "A QM/MM study on the structure and catalysis mechanism of PDE4B." ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 223 (April 7, 2002): C76-C76. Link to Item
  - Yang, WT, Zhang, YK, and 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 223 (April 7, 2002): C89-C89. Link to Item
  - Wu, Q, and Yang, W. "Empirical correction to density functional theory for van der Waals interactions." The Journal of Chemical Physics 116, no. 2 (January 8, 2002): 515-524. Full Text
  - Wu, Q, and Yang, W. "An Empirical Correction to Density Functional Theory for van der Waals Interactions." J. Chem. Phys. 116 (2002): 515-524. (Academic Article)
  - Liu, H, Elstner, M, Kaxiras, E, Frauenheim, T, Hermans, J, and Yang, W. "Quantum mechanics simulation of protein dynamics on long timescale." Proteins 44, no. 4 (September 2001): 484-489. Full Text
  - Baik, M-H, Silverman, JS, Yang, IV, Ropp, PA, Szalai, VA, Yang, W, and Thorp, HH. "Using Density Functional Theory To Design DNA Base Analogues with Low Oxidation Potentials." The Journal of Physical Chemistry B 105, no. 27 (July 2001): 6437-6444. Full Text
  - Liu, H, Zhang, Y, and Yang, W. "How Is the Active Site of Enolase Organized To Catalyze Two Different Reaction Steps?." Journal of the American Chemical Society 122, no. 28 (July 2000): 6560-6570. Full Text
  - Yang, W, Zhang, Y, and Ayers, PW. "Degenerate ground states and a fractional number of electrons in density and reduced density matrix functional theory." Physical Review Letters 84, no. 22 (May 2000): 5172-5175. Full Text
  - Zhang, Y, Liu, H, and Yang, W. "Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combinedab initioQM/MM potential energy surface." The Journal of Chemical Physics 112, no. 8 (February 22, 2000): 3483-3492. Full Text
  - Zhang, YK, and 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 103, no. 3-4 (February 2000): 346-348. Full Text Link to Item
  - Enkvist, C, Zhang, Y, and Yang, W. "Density Functional Study of A Weakly Hydrogen Bonded System: the Benzene-Ammonia Complex." The International Journal of Quantum Chemistry 79 (2000): 325-329. (Academic Article)
  - Enkvist, C, Zhang, Y, and Yang, W. "Density functional study of a weakly hydrogen-bonded benzene-ammonia complex: The importance of the exchange functional." International Journal of Quantum Chemistry 79, no. 5 (2000): 325-329. Full Text
  - Liu, H, Zhang, Y, and Yang, W. "How is the active-site of enolase organized to achieve overall efficiency in catalyzing a two step reaction." J. Am. Chem. Soc. 122 (2000): 6560-. (Academic Article)
  - Little, SB, Rabinowitz, JR, Wei, P, and Yang, W. "A Comparison of Calculated and Experimental Geometries for Crowded polycyclic Aromatic Hydrocarbons and their Metabolites." Polycyclic Aromatic Compounds 14, no. 1-4 (December 1999): 53-61. Full Text
  - Lewis, JP, Liu, S, Lee, T-S, and Yang, W. "A Linear-Scaling Quantum Mechanical Investigation of Cytidine Deaminase." Journal of Computational Physics 151, no. 1 (1999): 242-263. Full Text
  - Zhang, Y, Lee, T, and Yang, W. "A psuedo-bond approach to combining quantum mechanical and molecular mechanical methods." J. Chem. Phys. 110 (1999): 46-54. (Academic Article)
  - Zhang, Y, Lee, T-S, and Yang, W. "A pseudobond approach to combining quantum mechanical and molecular mechanical methods." The Journal of Chemical Physics 110, no. 1 (January 1999): 46-54. Full Text
  - Yang, W. "Generalized adiabatic connection in density functional theory." The Journal of Chemical Physics 109, no. 23 (December 15, 1998): 10107-10110. Full Text
  - Lee, T-S, Lewis, JP, and Yang, W. "Linear-scaling quantum mechanical calculations of biological molecules: The divide-and-conquer approach." Computational Materials Science 12, no. 3 (October 1998): 259-277. Full Text
  - Yang, WT, Levy, M, and Trickey, S. "Special issue: Symposium on density functional and applications (Part I of II) - Introduction." INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 69, no. 3 (August 15, 1998): 227-227. Link to Item
  - Zhang, Y, and Yang, W. "A challenge for density functionals: Self-interaction error increases for systems with a noninteger number of electrons." The Journal of Chemical Physics 109, no. 7 (August 15, 1998): 2604-2608. Full Text
  - Pan, W, Lee, T-S, and Yang, W. "Parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations." Journal of Computational Chemistry 19, no. 9 (July 15, 1998): 1101-1109. Full Text
  - Lewis, JP, Carter,, CW, Hermans, J, Pan, W, Lee, T-S, and Yang, W. "Active Species for the Ground-State Complex of Cytidine Deaminase: A Linear-Scaling Quantum Mechanical Investigation." Journal of the American Chemical Society 120, no. 22 (June 1998): 5407-5410. Full Text
  - Acker, JC, Marks, LB, Spencer, DP, Yang, W, Avery, MA, Dodge, RK, Rosner, GL, and Dewhirst, MW. "Serial in vivo observations of cerebral vasculature after treatment with a large single fraction of radiation." Radiation Research 149, no. 4 (April 1998): 350-359. Full Text
  - Lewis, JP, Carter, CW, Hermans, J, Pan, W, Lee, TS, and Yang, WT. "Quantum mechanical methods for large biomolecular systems: Applications in the study of the cytidine deaminase enzyme." BIOPHYSICAL JOURNAL 74, no. 2 (February 1998): A132-A132. Link to Item
  - Lee, T-S, and Yang, W. "Frozen density matrix approach for electronic structure calculations." International Journal of Quantum Chemistry 69, no. 3 (1998): 397-404. Full Text
  - Pérez-Jordá, JM, and Yang, W. "On the scaling of multipole methods for particle–particle interactions." Chemical Physics Letters 282, no. 1 (January 1998): 71-78. Full Text
  - Yang, W, Levy, M, and Trickey, S. "Symposium on density functional and applications (part 1 of ii) - introduction." Int. J. Quantum Chem. 69 (1998): 227-. (Academic Article)
  - Zhang, Y, Pan, W, and 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 107, no. 19 (November 15, 1997): 7921-7925. Full Text
  - Pan, W, Zhu, T, and 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 107, no. 10 (September 8, 1997): 3981-3985. Full Text
  - Pérez-Jordá, JM, and Yang, W. "Fast evaluation of the Coulomb energy for electron densities." The Journal of Chemical Physics 107, no. 4 (July 22, 1997): 1218-1226. Full Text
  - Zhu, T, Pan, W, and Yang, W. "Divide-and-conquer calculations for clean surfaces and surface adsorption." Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) 96, no. 1 (April 28, 1997): 2-6. Full Text
  - York, DM, Lee, T-S, and Yang, W. "Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules." Chemical Physics Letters 263, no. 1-2 (December 1996): 297-304. Full Text
  - Lee, TS, York, DM, and Yang, W. "Linear‐scaling semiempirical quantum calculations for macromolecules." The Journal of Chemical Physics 105, no. 7 (August 15, 1996): 2744-2750. Full Text
  - Pérez‐Jordá, JM, and Yang, W. "A concise redefinition of the solid spherical harmonics and its use in fast multipole methods." The Journal of Chemical Physics 104, no. 20 (May 22, 1996): 8003-8006. Full Text
  - Ni, H, York, DM, Bartolotti, L, Wells, RL, and 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 118, no. 24 (January 1996): 5732-5736. Full Text
  - York, DM, Lee, T-S, and Yang, W. "Quantum Mechanical Study of Aqueous Polarization Effects on Biological Macromolecules." Journal of the American Chemical Society 118, no. 44 (January 1996): 10940-10941. Full Text
  - York, DM, and Yang, W. "A chemical potential equalization method for molecular simulations." The Journal of Chemical Physics 104, no. 1 (January 1996): 159-172. Full Text
  - Pérez-Jordá, J, and Yang, W. "A simple O(N log N) algorithm for the rapid evaluation of particle-particle interactions." Chemical Physics Letters 247, no. 4-6 (December 1995): 484-490. Full Text
  - Yang, W, and Lee, TS. "A density‐matrix divide‐and‐conquer approach for electronic structure calculations of large molecules." The Journal of Chemical Physics 103, no. 13 (October 1995): 5674-5678. Full Text
  - Pérez-Jorda, J, and Yang, W. "An algorithm for 3D numerical integration that scales linearly with the size of the molecule." Chemical Physics Letters 241, no. 4 (July 1995): 469-476. Full Text
  - Zhao, Q, and Yang, W. "Analytical energy gradients and geometry optimization in the divide‐and‐conquer method for large molecules." The Journal of Chemical Physics 102, no. 24 (June 22, 1995): 9598-9603. Full Text
  - Lee, TS, York, DM, and Yang, W. "A new definition of atomic charges based on a variational principle for the electrostatic potential energy." The Journal of Chemical Physics 102, no. 19 (May 15, 1995): 7549-7556. Full Text
  - York, DM, Yang, W, Lee, H, Darden, T, and Pedersen, LG. "Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics." Journal of the American Chemical Society 117, no. 17 (May 1995): 5001-5002. Full Text
  - Parr, RG, and Yang, W. "Density-functional theory of the electronic structure of molecules." Annual Review of Physical Chemistry 46 (January 1995): 701-728. Full Text
  - York, D, and Yang, W. "The fast Fourier Poisson method for calculating Ewald sums." The Journal of Chemical Physics 101, no. 4 (August 15, 1994): 3298-3300. Full Text
  - Zhu, T, and Yang, W. "Structure of the ammonia dimer studied by density functional theory." International Journal of Quantum Chemistry 49, no. 5 (February 15, 1994): 613-623. Full Text
  - Bemish, RJ, Block, PA, Pedersen, LG, Yang, W, and 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 99, no. 11 (December 1993): 8585-8598. Full Text
  - Zhu, T, Lee, C, and Yang, W. "Erratum: Examination of several exchange‐correlation energy functionals by accurate self‐consistent atomic calculations [J. Chem. Phys. 98, 4814 (1993)]." The Journal of Chemical Physics 99, no. 5 (September 1993): 4239-4239. Full Text
  - Zhu, T, Lee, C, and Yang, W. "Examination of several exchange‐correlation energy functionals by accurate self‐consistent atomic calculations." The Journal of Chemical Physics 98, no. 6 (March 15, 1993): 4814-4821. Full Text
  - Lee, C, Fitzgerald, G, and Yang, W. "Nonlocal density functional calculations: Comparison of two implementation schemes." The Journal of Chemical Physics 98, no. 4 (February 15, 1993): 2971-2974. Full Text
  - "Erratum: Examination of several exchange-correlation energy functionals by accurate self-consistent atomic calculations (Journal of Chemical Physics (1993) 98 (4814))." The Journal of Chemical Physics 99, no. 5 (January 1, 1993): 4239-null. Full Text
  - Bemish, RJ, Block, PA, Pedersen, LG, Weitao, Y, and 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 99, no. 11 (1993): 8585-8598.
  - Bemish, RJ, Block, PA, Pedersen, LG, Yang, W, and Miller, RE. "The ar-c2h2 inter-molecular potential from high resolution spectroscopy and ab initio theory: A case for multi-center interactions." J. Chem. Phys. 99 (1993): 8593-8598. (Academic Article)
  - Crawford, TD, and Yang, W. "The Hartley basis functions and transform: alternatives to plane waves and the Fourier transform." Chemical Physics Letters 192, no. 1 (April 1992): 45-48. Full Text
  - Yang, W. "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 (March 1992): 461-479. Full Text
  - Lee, C, and Yang, W. "The divide‐and‐conquer density‐functional approach: Molecular internal rotation and density of states." The Journal of Chemical Physics 96, no. 3 (February 1992): 2408-2411. Full Text
  - Yang, W. "A local projection method for the linear combination of atomic orbital implementation of density‐functional theory." The Journal of Chemical Physics 94, no. 2 (January 15, 1991): 1208-1214. Full Text
  - Morrison, RC, Yang, W, Parr, RG, and Lee, C. "Approximate density matrices and wigner distribution functions from density, kinetic energy density, and idempotency constraints." International Journal of Quantum Chemistry 38, no. 6 (December 1990): 819-830. Full Text
  - Yang, W, and Peet, AC. "A method for calculating vibrational bound states: Iterative solution of the collocation equations constructed from localized basis sets." The Journal of Chemical Physics 92, no. 1 (January 1990): 522-526. Full Text
  - Yang, W. "Integral Formulation of Density-Functional Theory." (1990): 293-302. Full Text
  - Yang, W, Peet, AC, and Miller, WH. "A collocation approach for quantum scattering based on the S‐matrix version of the Kohn variational principle." The Journal of Chemical Physics 91, no. 12 (December 15, 1989): 7537-7542. Full Text
  - Peet, AC, and Yang, W. "An adapted form of the collocation method for calculating energy levels of rotating atom–diatom complexes." The Journal of Chemical Physics 91, no. 11 (December 1989): 6598-6603. Full Text
  - Yang, W, and Miller, WH. "Block Lanczos approach combined with matrix continued fraction for the S‐matrix Kohn variational principle in quantum scattering." The Journal of Chemical Physics 91, no. 6 (September 15, 1989): 3504-3508. Full Text
  - Peet, AC, and Yang, W. "The collocation method for calculating vibrational bound states of molecular systems—with application to Ar–HCl." The Journal of Chemical Physics 90, no. 3 (February 1989): 1746-1751. Full Text
  - Yang, W, and Peet, AC. "The collocation method for bound solutions of the Schrödinger equation." Chemical Physics Letters 153, no. 1 (December 1988): 98-104. Full Text
  - Lee, C, Yang, W, and Parr, RG. "Local softness and chemical reactivity in the molecules CO, SCN− and H2CO." Journal of Molecular Structure: Theochem 163 (January 1988): 305-313. Full Text
  - Yang, W, Parr, RG, and Uytterhoeven, L. "New relation between hardness and compressibility of minerals." Physics and Chemistry of Minerals 15, no. 2 (December 1987): 191-195. Full Text
  - Xue, W, and Yang, W. "Application of a scaled particle theory to polar solute system and calculation of the salt effect constant." Acta Physica-Chimica Sinica 3 (1987): 258-. (Academic Article)
  - Yang, W, and Mortier, WJ. "The use of global and local molecular parameters for the analysis of the gas-phase basicity of amines." Journal of the American Chemical Society 108, no. 19 (September 1986): 5708-5711. Full Text
  - Yang, W, and Harriman, JE. "Analysis of the kinetic energy functional in density functional theory." The Journal of Chemical Physics 84, no. 6 (March 15, 1986): 3320-3323. Full Text
  - Yang, W, Lee, C, and Ghosh, SK. "Molecular softness as the average of atomic softnesses: companion principle to the geometric mean principle for electronegativity equalization." The Journal of Physical Chemistry 89, no. 25 (December 1985): 5412-5414. Full Text
  - Yang, W, and Parr, RG. "Hardness, softness, and the fukui function in the electronic theory of metals and catalysis." Proceedings of the National Academy of Sciences of the United States of America 82, no. 20 (October 1985): 6723-6726. Full Text
  - Levy, M, Yang, W, and Parr, RG. "A new functional with homogeneous coordinate scaling in density functional theory: F [ ρ,λ]." The Journal of Chemical Physics 83, no. 5 (September 1985): 2334-2336. Full Text
  - Yang, W, Parr, RG, and Pucci, R. "Electron density, Kohn–Sham frontier orbitals, and Fukui functions." The Journal of Chemical Physics 81, no. 6 (September 15, 1984): 2862-2863. Full Text
  - Parr, RG, and Yang, W. "Density functional approach to the frontier-electron theory of chemical reactivity." Journal of the American Chemical Society 106, no. 14 (July 1984): 4049-4050. Full Text
  - Bulat, FA, Ke, S-H, Yang, W, and Couchman, L. "Lead-molecule coupling effects on the distortion-dependent conductance of carbon nanotubes(Published online)." Physical Review B 77, no. 15. Full Text
  - Cohen, AJ, Mori-Sánchez, P, and Yang, W. "Fractional charge perspective on the band gap in density-functional theory(Published online)." Physical Review B 77, no. 11. Full Text
  - Getty, SA, Engtrakul, C, Wang, L, Liu, R, Ke, S-H, Baranger, HU, Yang, W, Fuhrer, MS, and Sita, LR. "Near-perfect conduction through a ferrocene-based molecular wire(Published online)." Physical Review B 71, no. 24. Full Text
  - Hu, L, Xu, C, Peng, L, Gu, FL, and Yang, W. "Photocatalytic activity and the radiative lifetimes of excitons via an ab initio approach(Published online)." Journal of Materials Chemistry A 6, no. 31: 15027-15032. Full Text
  - Jiang, H, Baranger, HU, and Yang, W. "Density-functional theory simulation of large quantum dots(Published online)." Physical Review B 68, no. 16. Full Text
  - Jiang, H, Ullmo, D, Yang, W, and Baranger, HU. "Electron-electron interactions in isolated and realistic quantum dots: A density functional theory study(Published online)." Physical Review B 69, no. 23. Full Text
  - Jiang, H, Ullmo, D, Yang, W, and Baranger, HU. "Scrambling and gate-induced fluctuations in realistic quantum dots(Published online)." Physical Review B 71, no. 8. Full Text
  - Ke, S-H, Baranger, HU, and Yang, W. "Electron transport through molecules: Gate-induced polarization and potential shift(Published online)." Physical Review B 71, no. 11. Full Text
  - Ke, S-H, Baranger, HU, and Yang, W. "Electron transport through molecules: Self-consistent and non-self-consistent approaches(Published online)." Physical Review B 70, no. 8. Full Text
  - Lee, C, Yang, W, and Parr, RG. "Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density(Published online)." Physical Review B 37, no. 2: 785-789. Full Text
  - Liu, S, Pérez-Jordá, JM, and Yang, W. "Nonorthogonal localized molecular orbitals in electronic structure theory." The Journal of Chemical Physics 112, no. 4 (January 22, 2000): 1634-1644. Full Text
  - Lu, JP, and Yang, W. "Shape of large single- and multiple-shell fullerenes(Published online)." Physical Review B 49, no. 16: 11421-11424. Full Text
  - Mori-Sánchez, P, Cohen, AJ, and Yang, W. "Failure of the random-phase-approximation correlation energy(Published online)." Physical Review A 85, no. 4. Full Text
  - Ullmo, D, Jiang, H, Yang, W, and Baranger, H. "Landau Fermi-liquid picture of spin density functional theory: Strutinsky approach to quantum dots(Published online)." Physical Review B 70, no. 20. Full Text
  - Ullmo, D, Jiang, H, Yang, W, and Baranger, HU. "Interactions and broken time-reversal symmetry in chaotic quantum dots(Published online)." Physical Review B 71, no. 20. Full Text
  - Wei, P, and Yang, W. "Structure and stability of molybdenum carbide clusters (MoC4)n(n=1 to 4) and their anions(Published online)." Physical Review B 51, no. 11: 7224-7230. Full Text
  - Yang, W, Parr, RG, and Lee, C. "Various functionals for the kinetic energy density of an atom or molecule(Published online)." Physical Review A 34, no. 6: 4586-4590. Full Text
  - Yang, W. "Gradient correction in Thomas-Fermi theory(Published online)." Physical Review A 34, no. 6: 4575-4585. Full Text
  - Yang, W. "Ab initioapproach for many-electron systems without invoking orbitals: An integral formulation of density-functional theory(Published online)." Physical Review Letters 59, no. 14: 1569-1572. Full Text
  - Yang, W. "Ab initioapproach for many-electron systems without invoking orbitals: An integral formulation of density-functional theory(Published online)." Physical Review A 38, no. 11: 5494-5503. Full Text
  - Yang, W. "Thermal properties of many-electron systems: An integral formulation of density-functional theory(Published online)." Physical Review A 38, no. 11: 5504-5511. Full Text
  - Yang, W. "Dynamic linear response of many-electron systems: An integral formulation of density-functional theory(Published online)." Physical Review A 38, no. 11: 5512-5519. Full Text
  - Yang, W. "Direct calculation of electron density in density-functional theory(Published online)." Physical Review Letters 66, no. 11: 1438-1441. Full Text
  - Yang, W. "Direct calculation of electron density in density-functional theory: Implementation for benzene and a tetrapeptide(Published online)." Physical Review A 44, no. 11: 7823-7826. Full Text
  - Yang, W. "Absolute-energy-minimum principles for linear-scaling electronic-structure calculations(Published online)." Physical Review B 56, no. 15: 9294-9297. Full Text
  - York, D, Lu, JP, and Yang, W. "Density-functional calculations of the structure and stability ofC240(Published online)." Physical Review B 49, no. 12: 8526-8528. Full Text
  - York, DM, Lee, T-S, and Yang, W. "Quantum Mechanical Treatment of Biological Macromolecules in Solution Using Linear-Scaling Electronic Structure Methods(Published online)." Physical Review Letters 80, no. 22: 5011-5014. Full Text
  - Zhang, Y, and Yang, W. "Comment on “Generalized Gradient Approximation Made Simple”(Published online)." Physical Review Letters 80, no. 4: 890-890. Full Text
  - Zhang, Y, and Yang, W. "Perspective on "Density-functional theory for fractional particle number: derivative discontinuities of the energy"." Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) 103, no. 3-4 (February 9, 2000): 346-348. Full Text
  - Zhu, T, Pan, W, and Yang, W. "Structure of solid-state systems from embedded-cluster calculations: A divide-and-conquer approach(Published online)." Physical Review B 53, no. 19: 12713-12724. Full Text
  - van Aggelen, H, Yang, Y, and Yang, W. "Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random-phase approximation(Published online)." Physical Review A 88, no. 3. Full Text
- Conference Papers
  - Scholl, ZN, Li, Q, Yang, W, and Marszalek, P. "Single-Molecule Force-Spectroscopy Reveals the Calcium Dependency of Folding Intermediates in the Multidomain Protein S." February 2016. Full Text
  - Scholl, ZN, Yang, W, and Marszalek, P. "Direct Observation of Multimer Stabilization in the Mechanical Unfolding Pathway of a Protein Undergoing Oligomerization." February 2016. Full Text
  - Wang, W, Li, Z, and Weitao Yang, . "Angular momentum dependent field emission energy distribution." 2015 28th International Vacuum Nanoelectronics Conference (IVNC). July 13, 2015 - July 17, 2015.: IEEE, July 2015. Full Text
  - Scholl, ZN, Yang, W, and Marszalek, P. "N-terminal Domain Of Luciferase Controls Misfolding Avoidance." July 2014. Link to Item
  - Yang, W. "Mechanism of catalytic reactions and redox processes for solar fuel with multiscale QM/MM simulation." September 8, 2013. Link to Item
  - Scholl, ZN, Yang, W, and Marszalek, PE. "Improving Single Molecule Force Spectroscopy through Automated Real-Time Data Collection and Quantification of Experimental Conditions." January 29, 2013. Full Text Link to Item
  - Yang, W. "Progress in exchange-correlation energy functionals." August 28, 2011. Link to Item
  - Rinderspacher, BC, Beratan, DN, and Yang, W. "CINF 71-Inverse design of host-guest complexes in competitive binding problems." August 17, 2008. Link to Item
  - Cohen, AJ, Mori-Sanchez, P, Heaton-Burgess, T, Bulat, FA, and Yang, W. "COMP 436-Accurate density functionals addressing the self-interaction error and potential functional formalism." August 19, 2007. Link to Item
  - Yang, WT, Lu, ZY, and Wang, ML. "Reaction path potential for simulation of chemical reactions in enzymes derived from ab initio QM/MM calculations." August 22, 2004. Link to Item
Teaching & Mentoring
Recent Courses
- CHEM 393: Research Independent Study 2019
- CHEM 394: Research Independent Study 2019
- CHEM 493: Research Independent Study 2019
- CHEM 494: Research Independent Study 2019
- CHEM 310: Physical Chemistry I 2018
- CHEM 542: Quantum Mechanics 2018
Scholarly, Clinical, & Service Activities
Presentations & Appearances
Service to the Profession
- Editorial Board, Journal of Physical Chemistry. 2011 - 2015 2011 - 2015
- International Advisory Committee, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, China. 2009 - 2013 2009 - 2013

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