Weitao Yang | Scholars@Duke

Weitao Yang
Philip Handler Distinguished Professor of Chemistry

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 Distinguished Professor of Chemistry, 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
- Computer Simulations of Enzymes awarded by National Institutes of Health 2000 - 2023
- Development and Applications of Density Functional Methods for Large Systems awarded by National Science Foundation 2019 - 2022
- Molecular Mechanisms of Spontaneous and Hsp70-assisted Renaturation of Misfolded Proteins awarded by National Science Foundation 2018 - 2021
- Center for Complex Materials from First Principles (CCM) awarded by Temple University 2018 - 2020
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2020
- Localized Orbital Scaling Correction for Periodic Systems 2018 - 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 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
External Relationships
- GAVIL¿N BIODESIGN, INC
- South China Normal University
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Su, Neil Qiang, Aaron Mahler, and Weitao Yang. “Preserving Symmetry and Degeneracy in the Localized Orbital Scaling Correction Approach.” The Journal of Physical Chemistry Letters 11, no. 4 (February 10, 2020): 1528–35. https://doi.org/10.1021/acs.jpclett.9b03888.
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  - Yao, Y., W. Yang, Q. Lin, H. Li, L. Wang, F. Gu, and D. Yang. “1,3-Dipolar cycloaddition of nitrones to oxa(aza)bicyclic alkenes.” Organic Chemistry Frontiers 6, no. 19 (October 7, 2019): 3360–64. https://doi.org/10.1039/c9qo00660e.
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  - Mei, Yuncai, and Weitao Yang. “Excited-State Potential Energy Surfaces, Conical Intersections, and Analytical Gradients from Ground-State Density Functional Theory.” The Journal of Physical Chemistry Letters 10, no. 10 (May 6, 2019): 2538–45. https://doi.org/10.1021/acs.jpclett.9b00712.
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  - Jin, Ye, and Weitao Yang. “Excitation Energies from the Single-Particle Green's Function with the GW Approximation.” The Journal of Physical Chemistry. A 123, no. 14 (April 2019): 3199–3204. https://doi.org/10.1021/acs.jpca.9b02379.
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  - Mei, Yuncai, and Weitao Yang. “Charge transfer excitation energies from ground state density functional theory calculations.” The Journal of Chemical Physics 150, no. 14 (April 2019): 144109. https://doi.org/10.1063/1.5087883.
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  - Yao, Y., W. Yang, C. Wang, F. Gu, and D. Yang. “Radical Addition of Thiols to Oxa(aza)bicyclic Alkenes in Water.” Asian Journal of Organic Chemistry 8, no. 4 (April 1, 2019): 506–13. https://doi.org/10.1002/ajoc.201900033.
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  - Jin, Ye, Neil Qiang Su, and Weitao Yang. “Renormalized Singles Green's Function for Quasi-Particle Calculations beyond the G0 W0 Approximation.” The Journal of Physical Chemistry Letters 10, no. 3 (February 2019): 447–52. https://doi.org/10.1021/acs.jpclett.8b03337.
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  - Wang, Hao, and Weitao Yang. “Toward Building Protein Force Fields by Residue-Based Systematic Molecular Fragmentation and Neural Network.” Journal of Chemical Theory and Computation 15, no. 2 (February 2019): 1409–17. https://doi.org/10.1021/acs.jctc.8b00895.
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  - Zhang, Pan, Lin Shen, and Weitao Yang. “Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models.” The Journal of Physical Chemistry. B 123, no. 4 (January 15, 2019): 901–8. https://doi.org/10.1021/acs.jpcb.8b11905.
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  - Mei, Yuncai, Chen Li, Neil Qiang Su, and Weitao Yang. “Approximating Quasiparticle and Excitation Energies from Ground State Generalized Kohn-Sham Calculations.” The Journal of Physical Chemistry. A 123, no. 3 (January 10, 2019): 666–73. https://doi.org/10.1021/acs.jpca.8b10380.
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  - Mondal, Manas, Ying Yang, Lijiang Yang, Weitao Yang, and Yi Qin Gao. “Role of Conformational Fluctuations of Protein toward Methylation in DNA by Cytosine-5-methyltransferase.” Journal of Chemical Theory and Computation 14, no. 12 (December 2018): 6679–89. https://doi.org/10.1021/acs.jctc.8b00732.
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  - Pinter, B., R. Al-Saadon, Z. Chen, and W. Yang. “Spin-state energetics of iron(II) porphyrin from the particle-particle random phase approximation.” European Physical Journal B 91, no. 11 (November 1, 2018). https://doi.org/10.1140/epjb/e2018-90169-6.
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  - Su, Neil Qiang, Chen Li, and Weitao Yang. “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): 9678–83. https://doi.org/10.1073/pnas.1807095115.
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  - Shen, Lin, Xiancheng Zeng, Hao Hu, Xiangqian Hu, and Weitao Yang. “Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants.” Journal of Chemical Theory and Computation 14, no. 9 (September 2018): 4948–57. https://doi.org/10.1021/acs.jctc.8b00403.
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  - Sutton, Christopher, Yang Yang, Du Zhang, and Weitao Yang. “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): 4029–36. https://doi.org/10.1021/acs.jpclett.8b01366.
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  - Wang, Hao, and Weitao Yang. “Force Field for Water Based on Neural Network.” The Journal of Physical Chemistry Letters 9, no. 12 (June 4, 2018): 3232–40. https://doi.org/10.1021/acs.jpclett.8b01131.
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  - Al-Saadon, Rachael, Christopher Sutton, and Weitao Yang. “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. https://doi.org/10.1021/acs.jctc.8b00153.
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  - Zhang, D. D., X. Yang, X. Zheng, and W. Yang. “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): 927–34. https://doi.org/10.1080/00268976.2017.1382738.
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  - Contreras-García, Julia, and Weitao Yang. “Perspective: Chemical Information Encoded in Electron Density.” Wu Li Hua Xue Xue Bao = Acta Physico Chimica Sinica 34, no. 6 (March 2018): 567–80. https://doi.org/10.3866/PKU.WHXB201801261.
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  - Li, C., X. Zheng, N. Q. Su, and W. Yang. “Localized orbital scaling correction for systematic elimination of delocalization error in density functional approximations.” National Science Review 5, no. 2 (March 1, 2018): 203–15. https://doi.org/10.1093/nsr/nwx111.
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  - Shen, Lin, and Weitao Yang. “Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.” Journal of Chemical Theory and Computation 14, no. 3 (March 2018): 1442–55. https://doi.org/10.1021/acs.jctc.7b01195.
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  - Zhang, Xiao, Xueqian Li, Matthew E. Reish, Du Zhang, Neil Qiang Su, Yael Gutiérrez, Fernando Moreno, Weitao Yang, Henry O. Everitt, and Jie Liu. “Plasmon-Enhanced Catalysis: Distinguishing Thermal and Nonthermal Effects.” Nano Letters 18, no. 3 (March 2018): 1714–23. https://doi.org/10.1021/acs.nanolett.7b04776.
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  - Hu, L., C. Xu, L. Peng, F. L. Gu, and W. Yang. “Photocatalytic activity and the radiative lifetimes of excitons via an ab initio approach.” Journal of Materials Chemistry A 6, no. 31 (January 1, 2018): 15027–32. https://doi.org/10.1039/c8ta04140g.
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  - Wang, W., W. Yang, and Z. Li. “Field Electron Emission Images Far Away from a Semi-Infinitely Long Emitter: A Multiscale Simulation.” Journal of Physical Chemistry C, January 1, 2018. https://doi.org/10.1021/acs.jpcc.8b08910.
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  - Li, Guoqing, Du Zhang, Yifei Yu, Shengyang Huang, Weitao Yang, and Linyou Cao. “Activating MoS2 for pH-Universal Hydrogen Evolution Catalysis.” Journal of the American Chemical Society 139, no. 45 (November 2, 2017): 16194–200. https://doi.org/10.1021/jacs.7b07450.
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  - Jin, Ye, Du Zhang, Zehua Chen, Neil Qiang Su, and Weitao Yang. “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): 4746–51. https://doi.org/10.1021/acs.jpclett.7b02165.
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  - Jin, Ye, Yang Yang, Du Zhang, Degao Peng, and Weitao Yang. “Excitation energies from particle-particle random phase approximation with accurate optimized effective potentials.” The Journal of Chemical Physics 147, no. 13 (October 2017): 134105. https://doi.org/10.1063/1.4994827.
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  - Wu, Jingheng, Lin Shen, and Weitao Yang. “Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.” The Journal of Chemical Physics 147, no. 16 (October 2017): 161732. https://doi.org/10.1063/1.5006882.
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  - Chen, Zehua, Du Zhang, Ye Jin, Yang Yang, Neil Qiang Su, and Weitao Yang. “Multireference Density Functional Theory with Generalized Auxiliary Systems for Ground and Excited States.” The Journal of Physical Chemistry Letters 8, no. 18 (September 6, 2017): 4479–85. https://doi.org/10.1021/acs.jpclett.7b01864.
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  - Peng, Daoling, Shaopeng Li, Liang Peng, Feng Long Gu, and Weitao Yang. “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): 4101–12. https://doi.org/10.1021/acs.jctc.7b00321.
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  - Ayers, Paul, and Weitao Yang. “Robert G. Parr (1921-2017).” Angewandte Chemie (International Ed. in English) 56, no. 36 (August 4, 2017): 10639. https://doi.org/10.1002/anie.201705477.
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  - Zhang, Du, Neil Qiang Su, and Weitao Yang. “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 3, 2017): 3223–27. https://doi.org/10.1021/acs.jpclett.7b01275.
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  - Li, Chen, Jianfeng Lu, and Weitao Yang. “On extending Kohn-Sham density functionals to systems with fractional number of electrons.” The Journal of Chemical Physics 146, no. 21 (June 2017): 214109. https://doi.org/10.1063/1.4982951.
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  - Scholl, Zackary N., Weitao Yang, and Piotr E. Marszalek. “Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase.” Biophysical Journal 112, no. 9 (May 2017): 1829–40. https://doi.org/10.1016/j.bpj.2017.03.028.
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  - Lewis, Charles A., Lin Shen, Weitao Yang, and Richard Wolfenden. “Three Pyrimidine Decarboxylations in the Absence of a Catalyst.” Biochemistry 56, no. 10 (March 6, 2017): 1498–1503. https://doi.org/10.1021/acs.biochem.7b00055.
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  - Perdew, John P., Weitao Yang, Kieron Burke, Zenghui Yang, Eberhard K. U. Gross, Matthias Scheffler, Gustavo E. Scuseria, et al. “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): 2801–6. https://doi.org/10.1073/pnas.1621352114.
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  - Yang, Yang, Adriel Dominguez, Du Zhang, Vitalij Lutsker, Thomas A. Niehaus, Thomas Frauenheim, and Weitao Yang. “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. https://doi.org/10.1063/1.4977928.
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  - Zhang, Xiao, Xueqian Li, Du Zhang, Neil Qiang Su, Weitao Yang, Henry O. Everitt, and Jie Liu. “Product selectivity in plasmonic photocatalysis for carbon dioxide hydrogenation.” Nature Communications 8 (February 23, 2017): 14542. https://doi.org/10.1038/ncomms14542.
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  - Li, Chen, and Weitao Yang. “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. https://doi.org/10.1063/1.4974988.
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  - Li, Guoqing, Du Zhang, Qiao Qiao, Yifei Yu, David Peterson, Abdullah Zafar, Raj Kumar, et al. “All The Catalytic Active Sites of MoS2 for Hydrogen Evolution.” Journal of the American Chemical Society 138, no. 51 (December 15, 2016): 16632–38. https://doi.org/10.1021/jacs.6b05940.
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  - Shen, Lin, Jingheng Wu, and Weitao Yang. “Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.” Journal of Chemical Theory and Computation 12, no. 10 (October 2016): 4934–46. https://doi.org/10.1021/acs.jctc.6b00663.
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  - Zhang, Du, and Weitao Yang. “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. https://doi.org/10.1063/1.4964501.
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  - Yang, Yang, Ernest R. Davidson, and Weitao Yang. “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): E5098–5107. https://doi.org/10.1073/pnas.1606021113.
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  - Scholl, Zackary N., Qing Li, Weitao Yang, and Piotr E. Marszalek. “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): 18263–75. https://doi.org/10.1074/jbc.M116.729525.
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  - Yang, Yang, Lin Shen, Du Zhang, and Weitao Yang. “Conical Intersections from Particle-Particle Random Phase and Tamm-Dancoff Approximations.” The Journal of Physical Chemistry Letters 7, no. 13 (July 2016): 2407–11. https://doi.org/10.1021/acs.jpclett.6b00936.
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  - Wang, Hao, and Weitao Yang. “Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory.” The Journal of Chemical Physics 144, no. 22 (June 2016): 224107. https://doi.org/10.1063/1.4953558.
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  - Yang, Y., K. Burke, and W. Yang. “Accurate atomic quantum defects from particle-particle random phase approximation.” Molecular Physics 114, no. 7–8 (April 17, 2016): 1189–98. https://doi.org/10.1080/00268976.2015.1123316.
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  - Rupakheti, Chetan, Rachael Al-Saadon, Yuqi Zhang, Aaron M. Virshup, Peng Zhang, Weitao Yang, and David N. Beratan. “Diverse Optimal Molecular Libraries for Organic Light-Emitting Diodes.” Journal of Chemical Theory and Computation 12, no. 4 (April 2016): 1942–52. https://doi.org/10.1021/acs.jctc.5b00829.
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  - Shen, Lin, and Weitao Yang. “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): 2017–27. https://doi.org/10.1021/acs.jctc.5b01107.
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  - Li, Chen, Jianfeng Lu, and Weitao Yang. “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. https://doi.org/10.1063/1.4936411.
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  - Zheng, X., C. Li, D. Zhang, and W. Yang. “Scaling correction approaches for reducing delocalization error in density functional approximations.” Science China Chemistry 58, no. 12 (December 1, 2015): 1825–44. https://doi.org/10.1007/s11426-015-5501-z.
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  - Yang, Yang, Degao Peng, Ernest R. Davidson, and Weitao Yang. “Singlet-triplet energy gaps for diradicals from particle-particle random phase approximation.” The Journal of Physical Chemistry. A 119, no. 20 (May 2015): 4923–32. https://doi.org/10.1021/jp512727a.
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  - Zhang, DaDi, Xiao Zheng, Chen Li, and Weitao Yang. “Orbital relaxation effects on Kohn-Sham frontier orbital energies in density functional theory.” The Journal of Chemical Physics 142, no. 15 (April 2015): 154113. https://doi.org/10.1063/1.4918347.
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  - Li, Shaopeng, Linping Hu, Liang Peng, Weitao Yang, and Feng Long Gu. “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): 923–31. https://doi.org/10.1021/ct500889k.
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  - Rupakheti, Chetan, Aaron Virshup, Weitao Yang, and David N. Beratan. “Strategy to discover diverse optimal molecules in the small molecule universe.” Journal of Chemical Information and Modeling 55, no. 3 (March 2015): 529–37. https://doi.org/10.1021/ci500749q.
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  - Scholl, Zackary N., Weitao Yang, and Piotr E. Marszalek. “Direct observation of multimer stabilization in the mechanical unfolding pathway of a protein undergoing oligomerization.” Acs Nano 9, no. 2 (February 10, 2015): 1189–97. https://doi.org/10.1021/nn504686f.
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  - Li, Chen, Xiao Zheng, Aron J. Cohen, Paula Mori-Sánchez, and Weitao Yang. “Local scaling correction for reducing delocalization error in density functional approximations.” Physical Review Letters 114, no. 5 (February 4, 2015): 053001. https://doi.org/10.1103/physrevlett.114.053001.
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  - Scholl, Z. N., W. Yang, and P. E. Marszalek. “Erratum: Chaperones rescue luciferase folding by separating its domains (Journal of Biological Chemistry (2014) 289 (28607-28618) DOI: 10.1074/jbc.A114.582049).” Journal of Biological Chemistry 290, no. 2 (January 9, 2015): 883. https://doi.org/10.1074/jbc.A114.582049.
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  - Zhang, Du, Degao Peng, Peng Zhang, and Weitao Yang. “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): 1025–38. https://doi.org/10.1039/c4cp04109g.
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  - Guo, Hua, Daiqian Xie, and Weitao Yang. “A tribute to Guosen Yan.” Theoretical Chemistry Accounts 133, no. 12 (December 2014). https://doi.org/10.1007/s00214-014-1581-7.
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  - Peng, Degao, Yang Yang, Peng Zhang, and Weitao Yang. “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. https://doi.org/10.1063/1.4901716.
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  - Scholl, Zackary N., Weitao Yang, and Piotr E. Marszalek. “Chaperones rescue luciferase folding by separating its domains.” The Journal of Biological Chemistry 289, no. 41 (October 2014): 28607–18. https://doi.org/10.1074/jbc.M114.582049.
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  - Su, Neil Qiang, Weitao Yang, Paula Mori-Sánchez, and Xin Xu. “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): 9201–11. https://doi.org/10.1021/jp5029992.
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  - Yang, Yang, Degao Peng, Jianfeng Lu, and Weitao Yang. “Excitation energies from particle-particle random phase approximation: Davidson algorithm and benchmark studies.” The Journal of Chemical Physics 141, no. 12 (September 28, 2014): 124104–124104. https://doi.org/10.1063/1.4895792.
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  - Li, Y., A. Nese, X. Hu, N. V. Lebedeva, T. W. Lajoie, J. Burdynska, M. C. Stefan, et al. “Shifting electronic structure by inherent tension in molecular bottlebrushes with polythiophene backbones.” Acs Macro Letters 3, no. 8 (August 19, 2014): 738–42. https://doi.org/10.1021/mz5003323.
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  - Shenvi, Neil, Helen van Aggelen, Yang Yang, and Weitao Yang. “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. https://doi.org/10.1063/1.4886584.
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  - Aggelen, Helen van, Yang Yang, and Weitao Yang. “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. https://doi.org/10.1063/1.4865816.
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  - Chaudret, Robin, Julia Contreras-Garcia, Mickaël Delcey, Olivier Parisel, Weitao Yang, and Jean-Philip Piquemal. “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. https://doi.org/10.1021/ct4006135.
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  - Peng, Degao, Helen van Aggelen, Yang Yang, and Weitao Yang. “Linear-response time-dependent density-functional theory with pairing fields.” The Journal of Chemical Physics 140, no. 18 (May 2014): 18A522. https://doi.org/10.1063/1.4867540.
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  - Yang, Weitao. “Preface: Special topic on advances in density functional theory.” The Journal of Chemical Physics 140, no. 18 (May 2014): 18A101. https://doi.org/10.1063/1.4872309.
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  - Yu, Y., S. Y. Huang, Y. Li, S. N. Steinmann, W. Yang, and L. Cao. “Layer-dependent electrocatalysis of MoS2 for hydrogen evolution.” Nano Letters 14, no. 2 (February 12, 2014): 553–58. https://doi.org/10.1021/nl403620g.
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  - Franks, Andrew T., Degao Peng, Weitao Yang, and Katherine J. Franz. “Characterization of a photoswitching chelator with light-modulated geometric, electronic, and metal-binding properties.” Inorganic Chemistry 53, no. 3 (February 2014): 1397–1405. https://doi.org/10.1021/ic402221x.
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  - Yang, Yang, Helen van Aggelen, and Weitao Yang. “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. https://doi.org/10.1063/1.4834875.
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  - Yang, Yang, Helen van Aggelen, Stephan N. Steinmann, Degao Peng, and Weitao Yang. “Benchmark tests and spin adaptation for the particle-particle random phase approximation.” The Journal of Chemical Physics 139, no. 17 (November 2013): 174110. https://doi.org/10.1063/1.4828728.
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  - Jin, Yingdi, Erin R. Johnson, Xiangqian Hu, Weitao Yang, and Hao Hu. “Contributions of Pauli repulsions to the energetics and physical properties computed in QM/MM methods.” Journal of Computational Chemistry 34, no. 27 (October 2013): 2380–88. https://doi.org/10.1002/jcc.23401.
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  - Peng, Liang, Feng Long Gu, and Weitao Yang. “Effective preconditioning for ab initio ground state energy minimization with non-orthogonal localized molecular orbitals.” Physical Chemistry Chemical Physics : Pccp 15, no. 37 (October 2013): 15518–27. https://doi.org/10.1039/c3cp52989d.
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  - Zhang, Du, Stephan N. Steinmann, and Weitao Yang. “Dynamical second-order Bethe-Salpeter equation kernel: a method for electronic excitation beyond the adiabatic approximation.” The Journal of Chemical Physics 139, no. 15 (October 2013): 154109. https://doi.org/10.1063/1.4824907.
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  - Van Aggelen, H., Y. Yang, and W. Yang. “Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random-phase approximation.” Physical Review a Atomic, Molecular, and Optical Physics 88, no. 3 (September 24, 2013). https://doi.org/10.1103/PhysRevA.88.030501.
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  - Peng, Degao, Stephan N. Steinmann, Helen van Aggelen, and Weitao Yang. “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. https://doi.org/10.1063/1.4820556.
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  - Yang, Weitao, Paula Mori-Sánchez, and Aron J. Cohen. “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. https://doi.org/10.1063/1.4817183.
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  - Wang, Jun, and Weitao Yang. “Concerted proton transfer mechanism of Clostridium thermocellum ribose-5-phosphate isomerase.” The Journal of Physical Chemistry. B 117, no. 32 (August 2, 2013): 9354–61. https://doi.org/10.1021/jp404948c.
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  - Shenvi, Neil, Helen van Aggelen, Yang Yang, Weitao Yang, Christine Schwerdtfeger, and David Mazziotti. “The tensor hypercontracted parametric reduced density matrix algorithm: coupled-cluster accuracy with O(r(4)) scaling.” The Journal of Chemical Physics 139, no. 5 (August 2013): 054110. https://doi.org/10.1063/1.4817184.
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  - Steinmann, Stephan N., and Weitao Yang. “Wave function methods for fractional electrons.” The Journal of Chemical Physics 139, no. 7 (August 2013): 074107. https://doi.org/10.1063/1.4817849.
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  - Virshup, Aaron M., Julia Contreras-García, Peter Wipf, Weitao Yang, and David N. Beratan. “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. https://doi.org/10.1021/ja401184g.
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  - Peng, Degao, and Weitao Yang. “Fukui function and response function for nonlocal and fractional systems.” The Journal of Chemical Physics 138, no. 18 (May 2013): 184108. https://doi.org/10.1063/1.4803101.
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  - Wu, Pan, Robin Chaudret, Xiangqian Hu, and Weitao Yang. “Noncovalent Interaction Analysis in Fluctuating Environments.” Journal of Chemical Theory and Computation 9, no. 5 (May 2013): 2226–34. https://doi.org/10.1021/ct4001087.
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  - Zheng, Xiao, Ting Zhou, and Weitao Yang. “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. https://doi.org/10.1063/1.4801922.
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  - De Vleeschouwer, Freija, Artiom Chankisjijev, Weitao Yang, Paul Geerlings, and Frank De Proft. “Pushing the boundaries of intrinsically stable radicals: inverse design using the thiadiazinyl radical as a template.” The Journal of Organic Chemistry 78, no. 7 (April 2013): 3151–58. https://doi.org/10.1021/jo400101d.
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  - Chaudret, Robin, Jerry M. Parks, and Weitao Yang. “Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs.” The Journal of Chemical Physics 138, no. 4 (January 2013): 045102. https://doi.org/10.1063/1.4772182.
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  - De Vleeschouwer, Freija, Weitao Yang, David N. Beratan, Paul Geerlings, and Frank De Proft. “Inverse design of molecules with optimal reactivity properties: acidity of 2-naphthol derivatives.” Physical Chemistry Chemical Physics : Pccp 14, no. 46 (December 2012): 16002–13. https://doi.org/10.1039/c2cp42623d.
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  - Shenvi, Neil, and Weitao Yang. “Achieving partial decoherence in surface hopping through phase correction.” The Journal of Chemical Physics 137, no. 22 (December 2012): 22A528. https://doi.org/10.1063/1.4746407.
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  - Zeng, Xiancheng, Xiangqian Hu, and Weitao Yang. “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): 4960–67. https://doi.org/10.1021/ct300758v.
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  - Zheng, Xiao, Min Liu, Erin R. Johnson, Julia Contreras-García, and Weitao Yang. “Delocalization error of density-functional approximations: a distinct manifestation in hydrogen molecular chains.” The Journal of Chemical Physics 137, no. 21 (December 2012): 214106. https://doi.org/10.1063/1.4768673.
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  - Gillet, Natacha, Robin Chaudret, Julia Contreras-Garcίa, Weitao Yang, Bernard Silvi, and Jean-Philip Piquemal. “Coupling quantum interpretative techniques: another look at chemical mechanisms in organic reactions.” Journal of Chemical Theory and Computation 8, no. 11 (November 2012): 3993–97. https://doi.org/10.1021/ct300234g.
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  - Lin, Xiangsong, Xiangqian Hu, Javier J. Concepcion, Zuofeng Chen, Shubin Liu, Thomas J. Meyer, and Weitao Yang. “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): 15669–72. https://doi.org/10.1073/pnas.1118344109.
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  - Peng, Degao, Xiangqian Hu, Deepa Devarajan, Daniel H. Ess, Erin R. Johnson, and Weitao Yang. “Variational fractional-spin density-functional theory for diradicals.” The Journal of Chemical Physics 137, no. 11 (September 2012): 114112. https://doi.org/10.1063/1.4749242.
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  - Xu, Yuehua, Bao-Ji Wang, San-Huang Ke, Weitao Yang, and A. Z. Alzahrani. “Highly tunable spin-dependent electron transport through carbon atomic chains connecting two zigzag graphene nanoribbons.” The Journal of Chemical Physics 137, no. 10 (September 2012): 104107. https://doi.org/10.1063/1.4752197.
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  - Johnson, Erin R., Julia Contreras-García, and Weitao Yang. “Density-Functional Errors in Alkanes: A Real-Space Perspective.” Journal of Chemical Theory and Computation 8, no. 8 (August 2, 2012): 2676–81. https://doi.org/10.1021/ct300412g.
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  - Hu, Xiangqian, Yingdi Jin, Xiancheng Zeng, Hao Hu, and Weitao Yang. “Liquid water simulations with the density fragment interaction approach.” Physical Chemistry Chemical Physics : Pccp 14, no. 21 (June 2012): 7700–7709. https://doi.org/10.1039/c2cp23714h.
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  - Wu, Pan, G Andrés Cisneros, Hao Hu, Robin Chaudret, Xiangqian Hu, and Weitao Yang. “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): 6889–97. https://doi.org/10.1021/jp212643j.
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  - Peng, D., B. Zhao, A. J. Cohen, X. Hu, and W. Yang. “Optimized effective potential for calculations with orbital-free potential functionals.” Molecular Physics 110, no. 9–10 (May 10, 2012): 925–34. https://doi.org/10.1080/00268976.2012.681310.
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  - Jiang, N., G. Zuber, S. Keinan, A. Nayak, W. Yang, M. J. Therien, and D. N. Beratan. “Design of coupled porphyrin chromophores with unusually large hyperpolarizabilities.” Journal of Physical Chemistry C 116, no. 17 (May 3, 2012): 9724–33. https://doi.org/10.1021/jp2115065.
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  - Yang, Weitao, Aron J. Cohen, and Paula Mori-Sánchez. “Derivative discontinuity, bandgap and lowest unoccupied molecular orbital in density functional theory.” The Journal of Chemical Physics 136, no. 20 (May 2012): 204111. https://doi.org/10.1063/1.3702391.
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  - Mori-Sánchez, P., A. J. Cohen, and W. Yang. “Failure of the random-phase-approximation correlation energy.” Physical Review a Atomic, Molecular, and Optical Physics 85, no. 4 (April 5, 2012). https://doi.org/10.1103/PhysRevA.85.042507.
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  - Yang, Weitao, Aron J. Cohen, Frank De Proft, and Paul Geerlings. “Analytical evaluation of Fukui functions and real-space linear response function.” The Journal of Chemical Physics 136, no. 14 (April 2012): 144110. https://doi.org/10.1063/1.3701562.
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  - Lee, Whasil, Xiancheng Zeng, Kristina Rotolo, Ming Yang, Christopher J. Schofield, Vann Bennett, Weitao Yang, and Piotr E. Marszalek. “Mechanical anisotropy of ankyrin repeats.” Biophys J 102, no. 5 (March 7, 2012): 1118–26. https://doi.org/10.1016/j.bpj.2012.01.046.
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  - Sun, Zhigang, Weitao Yang, and Dong H. Zhang. “Higher-order split operator schemes for solving the Schrödinger equation in the time-dependent wave packet method: applications to triatomic reactive scattering calculations.” Physical Chemistry Chemical Physics : Pccp 14, no. 6 (February 2012): 1827–45. https://doi.org/10.1039/c1cp22790d.
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  - Cho, J., Q. Lin, S. Yang, J. G. S. Jr, Y. Cheng, E. Lin, J. Yang, et al. “Sulfur-doped zinc oxide (ZnO) Nanostars: Synthesis and simulation of growth mechanism.” Nano Research 5, no. 1 (2012): 20–26. https://doi.org/10.1007/s12274-011-0180-3.
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  - Cohen, A. J., P. Mori-Sánchez, and W. Yang. “Challenges for density functional theory.” Chemical Reviews 112, no. 1 (2012): 289–320. https://doi.org/10.1021/cr200107z.
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  - Yang, W., P. Mori-Sanchez, and A. J. Cohen. “Insight and progress in density functional theory.” Aip Conference Proceedings 1504 (January 1, 2012): 605–6. https://doi.org/10.1063/1.4771769.
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  - Zhang, J., W. Yang, J. P. Piquemal, and P. Ren. “Modeling structural coordination and ligand binding in zinc proteins with a polarizable potential.” Journal of Chemical Theory and Computation 8, no. 4 (2012): 1314–24. https://doi.org/10.1021/ct200812y.
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  - Shenvi, Neil, and Weitao Yang. “An algebraic operator approach to electronic structure.” The Journal of Chemical Physics 135, no. 24 (December 2011): 244111. https://doi.org/10.1063/1.3671388.
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  - Contreras-García, Julia, Weitao Yang, and Erin R. Johnson. “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): 12983–90. https://doi.org/10.1021/jp204278k.
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  - Wu, Pan, Xiangqian Hu, and Weitao Yang. “λ-Meta Dynamics Approach To Compute Absolute Solvation Free Energy.” The Journal of Physical Chemistry Letters 2, no. 17 (September 2011): 2099–2103. https://doi.org/10.1021/jz200808x.
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  - Lin, X., X. Hu, J. J. Concepcion, Z. Chen, S. Liu, T. J. Meyer, and W. Yang. “Catalytic mechanism for single-site water oxidation process: A theoretical study.” Acs National Meeting Book of Abstracts, August 25, 2011.
  - Zheng, Xiao, Aron J. Cohen, Paula Mori-Sánchez, Xiangqian Hu, and Weitao Yang. “Improving band gap prediction in density functional theory from molecules to solids.” Physical Review Letters 107, no. 2 (July 7, 2011): 026403. https://doi.org/10.1103/physrevlett.107.026403.
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  - Shenvi, Neil, Joseph E. Subotnik, and Weitao Yang. “Phase-corrected surface hopping: correcting the phase evolution of the electronic wavefunction.” The Journal of Chemical Physics 135, no. 2 (July 2011): 024101. https://doi.org/10.1063/1.3603447.
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  - Tam, Eugenia S., Joshua J. Parks, William W. Shum, Yu-Wu Zhong, Mitk’El B. Santiago-Berríos, Xiao Zheng, Weitao Yang, Garnet K-L Chan, Héctor D. Abruña, and Daniel C. Ralph. “Single-molecule conductance of pyridine-terminated dithienylethene switch molecules.” Acs Nano 5, no. 6 (June 2011): 5115–23. https://doi.org/10.1021/nn201199b.
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  - Cui, Ganglong, and Weitao Yang. “Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method.” The Journal of Chemical Physics 134, no. 20 (May 2011): 204115. https://doi.org/10.1063/1.3593390.
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  - Shenvi, Neil, Joseph E. Subotnik, and Weitao Yang. “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. https://doi.org/10.1063/1.3575588.
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  - Lee, W., X. Zeng, H. X. Zhou, V. Bennett, W. Yang, and P. E. Marszalek. “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. https://doi.org/10.1074/jbc.A110.179697.
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  - Contreras-García, Julia, Erin R. Johnson, Shahar Keinan, Robin Chaudret, Jean-Philip Piquemal, David N. Beratan, and Weitao Yang. “NCIPLOT: a program for plotting non-covalent interaction regions.” Journal of Chemical Theory and Computation 7, no. 3 (March 2011): 625–32. https://doi.org/10.1021/ct100641a.
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  - Ess, Daniel H., Erin R. Johnson, Xiangqian Hu, and Weitao Yang. “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. https://doi.org/10.1021/jp109280y.
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  - Hu, Xiangqian, Hao Hu, Jeffrey A. Melvin, Kathleen W. Clancy, Dewey G. McCafferty, and Weitao Yang. “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): 478–85. https://doi.org/10.1021/ja107513t.
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  - Sun, Zhigang, and Weitao Yang. “Communication: An exact short-time solver for the time-dependent Schrödinger equation.” The Journal of Chemical Physics 134, no. 4 (January 2011): 041101. https://doi.org/10.1063/1.3549570.
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  - Lee, Whasil, Xiancheng Zeng, Huan-Xiang Zhou, Vann Bennett, Weitao Yang, and Piotr E. Marszalek. “Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations.” J Biol Chem 285, no. 49 (December 3, 2010): 38167–72. https://doi.org/10.1074/jbc.M110.179697.
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  - Cui, G., and W. Yang. “Challenges with range-separated exchange-correlation functionals in time-dependent density functional theory calculations.” Molecular Physics 108, no. 19–20 (October 10, 2010): 2745–50. https://doi.org/10.1080/00268976.2010.523442.
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  - Johnson, Erin R., Weitao Yang, and Ernest R. Davidson. “Spin-state splittings, highest-occupied-molecular-orbital and lowest-unoccupied-molecular-orbital energies, and chemical hardness.” The Journal of Chemical Physics 133, no. 16 (October 2010): 164107. https://doi.org/10.1063/1.3497190.
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  - Cui, Ganglong, Weihai Fang, and Weitao Yang. “Efficient construction of nonorthogonal localized molecular orbitals in large systems.” The Journal of Physical Chemistry. A 114, no. 33 (August 2010): 8878–83. https://doi.org/10.1021/jp1027838.
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  - Hu, Xiangqian, Hao Hu, David N. Beratan, and Weitao Yang. “A gradient-directed Monte Carlo approach for protein design.” Journal of Computational Chemistry 31, no. 11 (August 2010): 2164–68. https://doi.org/10.1002/jcc.21506.
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  - Heaton-Burgess, Tim, and Weitao Yang. “Structural manifestation of the delocalization error of density functional approximations: C(4N+2) rings and C(20) bowl, cage, and ring isomers.” The Journal of Chemical Physics 132, no. 23 (June 2010): 234113. https://doi.org/10.1063/1.3445266.
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  - Ke, San-Huang, Rui Liu, Weitao Yang, and Harold U. Baranger. “Time-dependent transport through molecular junctions.” The Journal of Chemical Physics 132, no. 23 (June 2010): 234105. https://doi.org/10.1063/1.3435351.
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  - Johnson, Erin R., Shahar Keinan, Paula Mori-Sánchez, Julia Contreras-García, Aron J. Cohen, and Weitao Yang. “Revealing noncovalent interactions.” Journal of the American Chemical Society 132, no. 18 (May 2010): 6498–6506. https://doi.org/10.1021/ja100936w.
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  - Chen, Zuofeng, Javier J. Concepcion, Xiangqian Hu, Weitao Yang, Paul G. Hoertz, and Thomas J. Meyer. “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): 7225–29. https://doi.org/10.1073/pnas.1001132107.
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  - Hammill, Jared T., Julia Contreras-García, Aaron M. Virshup, David Beratan, Weitao Yang, and Peter Wipf. “Synthesis and chemical diversity analysis of bicyclo[3.3.1]non-3-en-2-ones.” Tetrahedron 66, no. 31 (March 2010): 5852–62. https://doi.org/10.1016/j.tet.2010.04.112.
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  - Hu, Hao, and Weitao Yang. “Elucidating solvent contributions to solution reactions with ab initio QM/MM methods.” The Journal of Physical Chemistry. B 114, no. 8 (March 2010): 2755–59. https://doi.org/10.1021/jp905886q.
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  - Zheng, Xiao, San-Huang Ke, and Weitao Yang. “Conductive junctions with parallel graphene sheets.” The Journal of Chemical Physics 132, no. 11 (March 2010): 114703. https://doi.org/10.1063/1.3357416.
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  - Hu, X., D. Xiao, S. Keinan, I. Asselberghs, M. J. Therien, K. Clays, W. Yang, and D. N. Beratan. “Predicting the frequency dispersion of electronic hyperpolarizabilities on the basis of absorption data and thomas-kuhn sum rules.” Journal of Physical Chemistry C 114, no. 5 (February 11, 2010): 2349–59. https://doi.org/10.1021/jp911556x.
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  - Hu, Xiangqian, and Weitao Yang. “Accelerating self-consistent field convergence with the augmented Roothaan-Hall energy function.” The Journal of Chemical Physics 132, no. 5 (February 2010): 054109. https://doi.org/10.1063/1.3304922.
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  - Zeng, Xiancheng, Hao Hu, Huan-Xiang Zhou, Piotr E. Marszalek, and Weitao Yang. “Equilibrium sampling for biomolecules under mechanical tension.” Biophysical Journal 98, no. 4 (February 2010): 733–40. https://doi.org/10.1016/j.bpj.2009.11.004.
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  - Cui, Ganglong, Weihai Fang, and Weitao Yang. “Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals.” Physical Chemistry Chemical Physics : Pccp 12, no. 2 (January 2010): 416–21. https://doi.org/10.1039/b916688b.
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  - Rinderspacher, B Christopher, Jan Andzelm, Adam Rawlett, Joseph Dougherty, David N. Beratan, and Weitao Yang. “Discrete Optimization of Electronic Hyperpolarizabilities in a Chemical Subspace.” Journal of Chemical Theory and Computation 5, no. 12 (December 2009): 3321–29. https://doi.org/10.1021/ct900325p.
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  - Hu, X., D. N. Beratan, and W. Yang. “Emergent strategies for inverse molecular design.” Science in China, Series B: Chemistry 52, no. 11 (November 1, 2009): 1769–76. https://doi.org/10.1007/s11426-009-0260-3.
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  - Hu, Xiangqian, David N. Beratan, and Weitao Yang. “A gradient-directed Monte Carlo method for global optimization in a discrete space: application to protein sequence design and folding.” The Journal of Chemical Physics 131, no. 15 (October 2009): 154117. https://doi.org/10.1063/1.3236834.
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  - Balabin, Ilya A., Weitao Yang, and David N. Beratan. “Modeling allosteric regulation in GPCRs: Toward rational structure-based drug design.” Abstracts of Papers of the American Chemical Society 238 (August 16, 2009).
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  - Yang, Weitao. “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).
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  - Balabin, Ilya A., Weitao Yang, and David N. Beratan. “Coarse-grained modeling of allosteric regulation in protein receptors.” Proceedings of the National Academy of Sciences of the United States of America 106, no. 34 (August 12, 2009): 14253–58. https://doi.org/10.1073/pnas.0901811106.
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  - Kasper, Amanda C., Eui Jung Moon, Xiangqian Hu, Yongho Park, Ceshea M. Wooten, Hyoungsu Kim, Weitao Yang, Mark W. Dewhirst, and Jiyong Hong. “Analysis of HIF-1 inhibition by manassantin A and analogues with modified tetrahydrofuran configurations.” Bioorg Med Chem Lett 19, no. 14 (July 15, 2009): 3783–86. https://doi.org/10.1016/j.bmcl.2009.04.071.
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  - Li, Z., C. Y. Wang, S. H. Ke, and W. Yang. “First-principles study for transport properties of defective carbon nanotubes with oxygen adsorption.” European Physical Journal B 69, no. 3 (June 1, 2009): 375–82. https://doi.org/10.1140/epjb/e2009-00179-2.
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  - Bulat, Felipe A., Luise Couchman, and Weitao Yang. “Contact geometry and conductance of crossed nanotube junctions under pressure.” Nano Letters 9, no. 5 (May 2009): 1759–63. https://doi.org/10.1021/nl803388m.
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  - Cohen, Aron J., Paula Mori-Sánchez, and Weitao Yang. “Second-Order Perturbation Theory with Fractional Charges and Fractional Spins.” Journal of Chemical Theory and Computation 5, no. 4 (April 2009): 786–92. https://doi.org/10.1021/ct8005419.
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  - Parks, Jerry M., Hao Hu, Johannes Rudolph, and Weitao Yang. “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): 5217–24. https://doi.org/10.1021/jp805137x.
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  - Zeng, Xiancheng, Hao Hu, Xiangqian Hu, and Weitao Yang. “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. https://doi.org/10.1063/1.3120605.
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  - Hu, Hao, and Weitao Yang. “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. https://doi.org/10.1016/j.theochem.2008.12.025.
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  - Ke, San-Huang, Weitao Yang, Stefano Curtarolo, and Harold U. Baranger. “Thermopower of molecular junctions: an ab initio study.” Nano Letters 9, no. 3 (March 2009): 1011–14. https://doi.org/10.1021/nl8031229.
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  - Mori-Sánchez, Paula, Aron J. Cohen, and Weitao Yang. “Discontinuous nature of the exchange-correlation functional in strongly correlated systems.” Physical Review Letters 102, no. 6 (February 13, 2009): 066403. https://doi.org/10.1103/physrevlett.102.066403.
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  - Cohen, A. J., P. Mori Sanchez, and W. T. Yang. “Second-order perturbation theory with fractional charges and fractional spins.” Journal of Chemical Theory and Computation 5, no. 5 (2009): 786–92.
  - Balamurugan, D., Weitao Yang, and David N. Beratan. “Exploring chemical space with discrete, gradient, and hybrid optimization methods.” The Journal of Chemical Physics 129, no. 17 (November 2008): 174105. https://doi.org/10.1063/1.2987711.
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  - Heaton Burgess, T., and W. T. Yang. “Optimized eﬀective potentials from arbitrary basis sets.” Journal of Chemical Physics 129 (November 2008).
  - Heaton-Burgess, Tim, and Weitao Yang. “Optimized effective potentials from arbitrary basis sets.” The Journal of Chemical Physics 129, no. 19 (November 2008): 194102. https://doi.org/10.1063/1.2982799.
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  - Hu, Hao, Amy Boone, and Weitao Yang. “Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase.” Journal of the American Chemical Society 130, no. 44 (November 2008): 14493–503. https://doi.org/10.1021/ja801202j.
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  - Johnson, Erin R., Paula Mori-Sánchez, Aron J. Cohen, and Weitao Yang. “Delocalization errors in density functionals and implications for main-group thermochemistry.” The Journal of Chemical Physics 129, no. 20 (November 2008): 204112. https://doi.org/10.1063/1.3021474.
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  - Keinan, Shahar, Michael J. Therien, David N. Beratan, and Weitao Yang. “Molecular design of porphyrin-based nonlinear optical materials.” The Journal of Physical Chemistry. A 112, no. 47 (November 2008): 12203–7. https://doi.org/10.1021/jp806351d.
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  - Ke, San-Huang, Weitao Yang, and Harold U. Baranger. “Quantum-interference-controlled molecular electronics.” Nano Letters 8, no. 10 (October 2008): 3257–61. https://doi.org/10.1021/nl8016175.
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  - Parks, Jerry M., Hao Hu, Aron J. Cohen, and Weitao Yang. “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. https://doi.org/10.1063/1.2994288.
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  - Cohen, Aron J., Paula Mori-Sánchez, and Weitao Yang. “Fractional spins and static correlation error in density functional theory.” The Journal of Chemical Physics 129, no. 12 (September 2008): 121104. https://doi.org/10.1063/1.2987202.
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  - Keinan, Shahar, William D. Paquette, John J. Skoko, David N. Beratan, Weitao Yang, Sunita Shinde, Paul A. Johnston, John S. Lazo, and Peter Wipf. “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): 3256–63. https://doi.org/10.1039/b806712k.
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  - Xiao, Dequan, Felipe A. Bulat, Weitao Yang, and David N. Beratan. “A donor-nanotube paradigm for nonlinear optical materials.” Nano Letters 8, no. 9 (September 2008): 2814–18. https://doi.org/10.1021/nl801388z.
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  - Li, Z., C. Y. Wang, X. Zhang, S. H. Ke, and W. Yang. “Transport properties of an armchair carbon nanotube with a double vacancy under stretching.” Journal of Physics Condensed Matter 20, no. 34 (August 27, 2008). https://doi.org/10.1088/0953-8984/20/34/345225.
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  - Cohen, Aron J., Paula Mori-Sánchez, and Weitao Yang. “Insights into current limitations of density functional theory.” Science (New York, N.Y.) 321, no. 5890 (August 2008): 792–94. https://doi.org/10.1126/science.1158722.
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  - Fujimoto, Kazuhiro, and Weitao Yang. “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. https://doi.org/10.1063/1.2958257.
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  - Hu, Xiangqian, David N. Beratan, and Weitao Yang. “A gradient-directed Monte Carlo approach to molecular design.” The Journal of Chemical Physics 129, no. 6 (August 2008): 064102. https://doi.org/10.1063/1.2958255.
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  - Burger, Steven K., and Weitao Yang. “Linear-scaling quantum calculations using non-orthogonal localized molecular orbitals.” Journal of Physics. Condensed Matter : An Institute of Physics Journal 20, no. 29 (July 2008): 294209. https://doi.org/10.1088/0953-8984/20/29/294209.
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  - Xiao, Dequan, Weitao Yang, and David N. Beratan. “Inverse molecular design in a tight-binding framework.” The Journal of Chemical Physics 129, no. 4 (July 2008): 044106. https://doi.org/10.1063/1.2955756.
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  - Li, Z., C. Y. Wang, X. Zhang, S. H. Ke, and W. Yang. “First-principles study for transport properties of armchair carbon nanotubes with a double vacancy under strain.” Journal of Applied Physics 103, no. 11 (June 20, 2008). https://doi.org/10.1063/1.2939279.
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  - Mori-Sánchez, Paula, Aron J. Cohen, and Weitao Yang. “Localization and delocalization errors in density functional theory and implications for band-gap prediction.” Physical Review Letters 100, no. 14 (April 7, 2008): 146401. https://doi.org/10.1103/physrevlett.100.146401.
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  - Bulat, F. A., S. H. Ke, W. Yang, and L. Couchman. “Lead-molecule coupling effects on the distortion-dependent conductance of carbon nanotubes.” Physical Review B Condensed Matter and Materials Physics 77, no. 15 (April 1, 2008). https://doi.org/10.1103/PhysRevB.77.153401.
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  - Cohen, A. J., P. Mori-Sánchez, and W. Yang. “Fractional charge perspective on the band gap in density-functional theory.” Physical Review B Condensed Matter and Materials Physics 77, no. 11 (March 18, 2008). https://doi.org/10.1103/PhysRevB.77.115123.
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  - Heaton-Burgess, Tim, Aron J. Cohen, Weitao Yang, and Ernest R. Davidson. “Size extensivity of the direct optimized effective potential method.” The Journal of Chemical Physics 128, no. 11 (March 2008): 114702. https://doi.org/10.1063/1.2877129.
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  - Parks, Jerry M., Rama K. Kondru, Hao Hu, David N. Beratan, and Weitao Yang. “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): 3168–76. https://doi.org/10.1021/jp076885j.
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  - Zeng, Xiancheng, Hao Hu, Xiangqian Hu, Aron J. Cohen, and Weitao Yang. “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. https://doi.org/10.1063/1.2832946.
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  - Hu, Hao, Zhenyu Lu, Jerry M. Parks, Steven K. Burger, and Weitao Yang. “Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.” The Journal of Chemical Physics 128, no. 3 (January 2008): 034105. https://doi.org/10.1063/1.2816557.
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  - Hu, Hao, and Weitao Yang. “Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.” Annual Review of Physical Chemistry 59 (January 2008): 573–601. https://doi.org/10.1146/annurev.physchem.59.032607.093618.
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  - Lee, Hyunjoo, Kwan Woo Kim, Janghyun Park, Hyoungsu Kim, Sanghee Kim, Deukjoon Kim, Xiangqian Hu, Weitao Yang, and Jiyong Hong. “A general strategy for construction of both 2,6-cis- and 2,6-trans-disubstituted tetrahydropyrans: substrate-controlled asymmetric total synthesis of (+)-scanlonenyne.” Angewandte Chemie (International Ed. in English) 47, no. 22 (January 2008): 4200–4203. https://doi.org/10.1002/anie.200705663.
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  - Bulat, Felipe A., Tim Heaton-Burgess, Aron J. Cohen, and Weitao Yang. “Optimized effective potentials from electron densities in finite basis sets.” The Journal of Chemical Physics 127, no. 17 (November 2007): 174101. https://doi.org/10.1063/1.2800021.
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  - Wang, Wei, Juan Qiao, Liduo Wang, Lian Duan, Deqiang Zhang, Weitao Yang, and Yong Qiu. “Synthesis, structures, and optical properties of cadmium iodide/phenethylamine hybrid materials with controlled structures and emissions.” Inorganic Chemistry 46, no. 24 (November 2007): 10252–60. https://doi.org/10.1021/ic7007304.
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  - Ke, San-Huang, Harold U. Baranger, and Weitao Yang. “Contact transparency of nanotube-molecule-nanotube junctions.” Physical Review Letters 99, no. 14 (October 2, 2007): 146802. https://doi.org/10.1103/physrevlett.99.146802.
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  - Burger, Steven K., and Weitao Yang. “Sequential quadratic programming method for determining the minimum energy path.” The Journal of Chemical Physics 127, no. 16 (October 2007): 164107. https://doi.org/10.1063/1.2780147.
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  - Ke, San-Huang, Harold U. Baranger, and Weitao Yang. “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. https://doi.org/10.1063/1.2770718.
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  - Liu, Rui, San-Huang Ke, Weitao Yang, and Harold U. Baranger. “Cobaltocene as a spin filter.” The Journal of Chemical Physics 127, no. 14 (October 2007): 141104. https://doi.org/10.1063/1.2796151.
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  - Hu, Hao, and Weitao Yang. “PHYS 301-Free energies of chemical reactions in enzyme and in solution.” Abstracts of Papers of the American Chemical Society 234 (August 19, 2007).
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  - Parks, Jerry M., Hao Hu, Rama Kondru, and Weitao Yang. “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).
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  - Zeng, Xiancheng, Hao Hu, and Weitao Yang. “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).
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  - Cohen, Aron J., Paula Mori-Sánchez, and Weitao Yang. “Assessment and formal properties of exchange-correlation functionals constructed from the adiabatic connection.” The Journal of Chemical Physics 127, no. 3 (July 2007): 034101. https://doi.org/10.1063/1.2749510.
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  - Hu, Hao, Zhenyu Lu, Marcus Elstner, Jan Hermans, and Weitao Yang. “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): 5685–91. https://doi.org/10.1021/jp070308d.
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  - Heaton-Burgess, Tim, Felipe A. Bulat, and Weitao Yang. “Optimized effective potentials in finite basis sets.” Physical Review Letters 98, no. 25 (June 20, 2007): 256401. https://doi.org/10.1103/physrevlett.98.256401.
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  - Cohen, Aron J., Paula Mori-Sánchez, and Weitao Yang. “Development of exchange-correlation functionals with minimal many-electron self-interaction error.” The Journal of Chemical Physics 126, no. 19 (May 2007): 191109. https://doi.org/10.1063/1.2741248.
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  - Hu, Hao, Zhenyu Lu, and Weitao Yang. “Fitting Molecular Electrostatic Potentials from Quantum Mechanical Calculations.” Journal of Chemical Theory and Computation 3, no. 3 (May 2007): 1004–13. https://doi.org/10.1021/ct600295n.
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  - Ke, San-Huang, Harold U. Baranger, and Weitao Yang. “Role of the exchange-correlation potential in ab initio electron transport calculations.” The Journal of Chemical Physics 126, no. 20 (May 2007): 201102. https://doi.org/10.1063/1.2743004.
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  - Hu, Hao, Zhenyu Lu, and Weitao Yang. “QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.” Journal of Chemical Theory and Computation 3, no. 2 (March 2007): 390–406. https://doi.org/10.1021/ct600240y.
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  - Heaton-Burgess, Tim, Paul Ayers, and Weitao Yang. “Spin-potential functional formalism for current-carrying noncollinear magnetic systems.” Physical Review Letters 98, no. 3 (January 18, 2007): 036403. https://doi.org/10.1103/physrevlett.98.036403.
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  - Hori, Takumi, Hideaki Takahashi, Shin-Ichi Furukawa, Masayoshi Nakano, and Weitao Yang. “Computational study on the relative acidity of acetic acid by the QM/MM method combined with the theory of energy representation.” The Journal of Physical Chemistry. B 111, no. 3 (January 2007): 581–88. https://doi.org/10.1021/jp066334d.
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  - Ke, S. H., H. U. Baranger, and W. Yang. “Role of the exchange-correlation potential in ab initio electron transport calculations.” Journal of Chemical Physics 126 (2007): 201102/1-201102/4.
  - Keinan, Shahar, Xiangqian Hu, David N. Beratan, and Weitao Yang. “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): 176–81. https://doi.org/10.1021/jp0646168.
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  - Ke, S. H., H. U. Baranger, and W. Yang. “Development of ab initio calculation for electron transport and the effects of lead and contact structures in molecular electronics.” Journal of Computational and Theoretical Nanoscience 3, no. 5 (December 29, 2006): 819–23. https://doi.org/10.1166/jctn.2006.022.
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  - Burger, Steven K., and Weitao Yang. “Automatic integration of the reaction path using diagonally implicit Runge-Kutta methods.” The Journal of Chemical Physics 125, no. 24 (December 2006): 244108. https://doi.org/10.1063/1.2402166.
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  - Ping, L., W. Yang, L. C. Pedersen, M. Negishi, and L. G. Pedersen. “Searching for the minimum energy path in the sulfuryl transfer reaction catalyzed by human estrogen sulfotransferase: Role of enzyme dynamics.” International Journal of Quantum Chemistry 106, no. 14 (November 15, 2006): 2981–98. https://doi.org/10.1002/qua.21123.
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  - Champagne, Benoît, Felipe A. Bulat, Weitao Yang, Sean Bonness, and Bernard Kirtman. “Density functional theory investigation of the polarizability and second hyperpolarizability of polydiacetylene and polybutatriene chains: treatment of exact exchange and role of correlation.” The Journal of Chemical Physics 125, no. 19 (November 2006): 194114. https://doi.org/10.1063/1.2388262.
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  - Mori-Sánchez, Paula, Aron J. Cohen, and Weitao Yang. “Many-electron self-interaction error in approximate density functionals.” The Journal of Chemical Physics 125, no. 20 (November 2006): 201102. https://doi.org/10.1063/1.2403848.
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  - Lu, Zhenyu, Hao Hu, Weitao Yang, and Piotr E. Marszalek. “Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method.” Biophysical Journal 91, no. 6 (September 2006): L57–59. https://doi.org/10.1529/biophysj.106.090324.
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  - Zhang, Qingmin, Zhenyu Lu, Hao Hu, Weitao Yang, and Piotr E. Marszalek. “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): 9387–93. https://doi.org/10.1021/ja057693+.
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  - Burger, Steven K., and Weitao Yang. “A combined explicit-implicit method for high accuracy reaction path integration.” Journal of Chemical Physics 124, no. 22 (June 14, 2006). https://doi.org/10.1063/1.2202830.
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  - Ayers, Paul W., and Weitao Yang. “Legendre-transform functionals for spin-density-functional theory.” The Journal of Chemical Physics 124, no. 22 (June 2006): 224108. https://doi.org/10.1063/1.2200884.
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  - Burger, Steven K., and Weitao Yang. “A combined explicit-implicit method for high accuracy reaction path integration.” The Journal of Chemical Physics 124, no. 22 (June 2006): 224102. https://doi.org/10.1063/1.2202830.
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  - Ke, San-Huang, Weitao Yang, and Harold U. Baranger. “Nanotube-metal junctions: 2- and 3-terminal electrical transport.” The Journal of Chemical Physics 124, no. 18 (May 2006): 181102. https://doi.org/10.1063/1.2200356.
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  - Liu, Rui, San-Huang Ke, Harold U. Baranger, and Weitao Yang. “Negative differential resistance and hysteresis through an organometallic molecule from molecular-level crossing.” Journal of the American Chemical Society 128, no. 19 (May 2006): 6274–75. https://doi.org/10.1021/ja057054z.
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  - Mori-Sánchez, Paula, Aron J. Cohen, and Weitao Yang. “Self-interaction-free exchange-correlation functional for thermochemistry and kinetics.” The Journal of Chemical Physics 124, no. 9 (March 2006): 91102. https://doi.org/10.1063/1.2179072.
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  - Wang, Mingliang, Xiangqian Hu, David N. Beratan, and Weitao Yang. “Designing molecules by optimizing potentials.” Journal of the American Chemical Society 128, no. 10 (March 2006): 3228–32. https://doi.org/10.1021/ja0572046.
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  - Wang, Mingliang, Zhenyu Lu, and Weitao Yang. “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. https://doi.org/10.1063/1.2181145.
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  - Hori, T., H. Takahashi, M. Nakano, T. Nitta, and W. Yang. “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 15, 2006): 240–44. https://doi.org/10.1016/j.cplett.2005.11.096.
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  - Burger, Steven K., and Weitao Yang. “Quadratic string method for determining the minimum-energy path based on multiobjective optimization.” The Journal of Chemical Physics 124, no. 5 (February 2006): 054109. https://doi.org/10.1063/1.2163875.
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  - Cisneros, G Andrés, Min Wang, Peter Silinski, Michael C. Fitzgerald, and Weitao Yang. “Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase.” The Journal of Physical Chemistry. A 110, no. 2 (January 2006): 700–708. https://doi.org/10.1021/jp0543328.
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  - Liu, Rui, San-Huang Ke, Weitao Yang, and Harold U. Baranger. “Organometallic molecular rectification.” The Journal of Chemical Physics 124, no. 2 (January 2006): 024718. https://doi.org/10.1063/1.2141955.
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  - Sohn, Jungsan, Jerry M. Parks, Gregory Buhrman, Paul Brown, Kolbrun Kristjánsdóttir, Alexias Safi, Herbert Edelsbrunner, Weitao Yang, and Johannes Rudolph. “Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate.” Biochemistry 44, no. 50 (December 2005): 16563–73. https://doi.org/10.1021/bi0516879.
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  - Liu, Rui, San-Huang Ke, Harold U. Baranger, and Weitao Yang. “Organometallic spintronics: dicobaltocene switch.” Nano Letters 5, no. 10 (October 2005): 1959–62. https://doi.org/10.1021/nl0513380.
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  - Wu, Qin, Aron J. Cohen, and Weitao Yang. “Analytic energy gradients of the optimized effective potential method.” The Journal of Chemical Physics 123, no. 13 (October 2005): 134111. https://doi.org/10.1063/1.1989310.
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  - Ke, San-Huang, Harold U. Baranger, and Weitao Yang. “Models of electrodes and contacts in molecular electronics.” The Journal of Chemical Physics 123, no. 11 (September 2005): 114701. https://doi.org/10.1063/1.1993558.
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  - Mori-Sánchez, P., Q. Wu, and W. Yang. “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 8, 2005): 62204.
  - Mori-Sánchez, Paula, Qin Wu, and Weitao Yang. “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. https://doi.org/10.1063/1.1904584.
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  - Bulat, Felipe A., Alejandro Toro-Labbé, Benoît Champagne, Bernard Kirtman, and Weitao Yang. “Density-functional theory (hyper)polarizabilities of push-pull pi-conjugated systems: treatment of exact exchange and role of correlation.” The Journal of Chemical Physics 123, no. 1 (July 2005): 014319. https://doi.org/10.1063/1.1926275.
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  - Hu, Hao, and Weitao Yang. “Dual-topology/dual-coordinate free-energy simulation using QM/MM force field.” The Journal of Chemical Physics 123, no. 4 (July 2005): 041102. https://doi.org/10.1063/1.1990113.
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  - Getty, S. A., C. Engtrakul, L. Wang, R. Liu, S. H. Ke, H. U. Baranger, W. Yang, M. S. Fuhrer, and L. R. Sita. “Near-perfect conduction through a ferrocene-based molecular wire.” Physical Review B Condensed Matter and Materials Physics 71, no. 24 (June 15, 2005). https://doi.org/10.1103/PhysRevB.71.241401.
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  - Wu, Q., A. J. Cohen, and W. Yang. “Excitation energies from time-dependent density functional theory with accurate exchange-correlation potentials.” Molecular Physics 103, no. 6–8 (March 20, 2005): 711–17. https://doi.org/10.1080/0026897051234267.
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  - Ke, S. H., H. U. Baranger, and W. Yang. “Electron transport through molecules: Gate-induced polarization and potential shift.” Physical Review B Condensed Matter and Materials Physics 71, no. 11 (March 15, 2005). https://doi.org/10.1103/PhysRevB.71.113401.
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  - Cisneros, G Andrés, 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.” The Journal of Chemical Physics 122, no. 11 (March 2005): 114502. https://doi.org/10.1063/1.1860560.
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  - Jiang, H., D. Ullmo, W. Yang, and H. U. Baranger. “Scrambling and gate-induced fluctuations in realistic quantum dots.” Physical Review B Condensed Matter and Materials Physics 71, no. 8 (February 1, 2005). https://doi.org/10.1103/PhysRevB.71.085313.
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  - Ke, San-Huang, Harold U. Baranger, and Weitao Yang. “Contact atomic structure and electron transport through molecules.” The Journal of Chemical Physics 122, no. 7 (February 2005): 074704. https://doi.org/10.1063/1.1851496.
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  - Bulat, Felipe A., Alejandro Toro-Labbe, Benoit Champagne, Bernard Kirtman, and Weitao Yang. “Dft (hyper)polarizabilities of push-pull pi-conjugated systems, treatment of exact exchange and role correlation.” J. Chem. Phys. 123 (2005): 014319/1-014319/7.
  - Ke, San-Huang, Harold Baranger, and Weitao Yang. “"Contact Atomic Structure and Electron Transport Through Molecules".” J. Chem. Phys. 122 (2005): 114502/1-114502/7.
  - Liu, Rui, San-Huang Ke, Harold U. Baranger, and Weitao Yang. “Intermolecular effect in molecular electronics.” The Journal of Chemical Physics 122, no. 4 (January 2005): 44703. https://doi.org/10.1063/1.1825377.
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  - Ullmo, D., H. Jiang, W. Yang, and H. U. Baranger. “Interactions and broken time-reversal symmetry in chaotic quantum dots.” Physical Review B Condensed Matter and Materials Physics 71, no. 20 (January 1, 2005). https://doi.org/10.1103/PhysRevB.71.201310.
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  - Ulmo, Dennis, Hong Jiang, Weitao Yang, and Harold Baranger. “"Landau Fermi Liquid Picture of Spin Density Functional Theory: Strutinsky Approach to Quantum Dots".” Phys. Rev. B., Rapid Communication 71 (2005): 201310/1-201310/4.
  - Wu, Qin, Aron J. Cohen, and Weitao Yang. “Analytic energy gradients of the optimized effective potential method.” J. Chem. Phys. 123, no. 134111/1-134111/10 (2005).
  - Ke, San-Huang, Harold U. Baranger, and Weitao Yang. “Molecular conductance: chemical trends of anchoring groups.” Journal of the American Chemical Society 126, no. 48 (December 2004): 15897–904. https://doi.org/10.1021/ja047367e.
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  - Cohen, A. J., Q. Wu, and W. Yang. “Calculation of nuclear magnetic resonance shielding constants using potential-based methods.” Chemical Physics Letters 399, no. 1–3 (November 21, 2004): 84–88. https://doi.org/10.1016/j.cplett.2004.09.112.
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  - Ullmo, D., H. Jiang, W. Yang, and H. U. Baranger. “Landau Fermi-liquid picture of spin density functional theory: Strutinsky approach to quantum dots.” Physical Review B Condensed Matter and Materials Physics 70, no. 20 (November 1, 2004). https://doi.org/10.1103/PhysRevB.70.205309.
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  - Goj, L. A., G. A. Cisneros, W. Yang, and R. A. Widenhoefer. “Erratum: "Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization" (Journal of Organometallic Chemistry (2003) vol. 687 (498-507) 10.1016/j.jorganchem.2003.09.046).” Journal of Organometallic Chemistry 689, no. 17 (September 1, 2004): 2845. https://doi.org/10.1016/j.jorganchem.2004.06.001.
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  - Jiang, Hong, and Weitao Yang. “Conjugate-gradient optimization method for orbital-free density functional calculations.” The Journal of Chemical Physics 121, no. 5 (August 2004): 2030–36. https://doi.org/10.1063/1.1768163.
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  - Ke, S. H., H. U. Baranger, and W. Yang. “Electron transport through molecules: Self-consistent and non-self-consistent approaches.” Physical Review B Condensed Matter and Materials Physics 70, no. 8 (August 1, 2004). https://doi.org/10.1103/PhysRevB.70.085410.
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  - Liu, Haiyan, Zhenyu Lu, G Andres Cisneros, and Weitao Yang. “Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.” The Journal of Chemical Physics 121, no. 2 (July 2004): 697–706. https://doi.org/10.1063/1.1759318.
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  - Lu, Zhenyu, Wieslaw Nowak, Gwangrog Lee, Piotr E. Marszalek, and Weitao Yang. “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): 9033–41. https://doi.org/10.1021/ja031940x.
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  - Lu, Zhenyu, and Weitao Yang. “Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.” The Journal of Chemical Physics 121, no. 1 (July 2004): 89–100. https://doi.org/10.1063/1.1757436.
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  - Wang, Mingliang, Zhenyu Lu, and Weitao Yang. “Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method.” The Journal of Chemical Physics 121, no. 1 (July 2004): 101–7. https://doi.org/10.1063/1.1757437.
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  - Cisneros, G Andrés, 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, no. 22 (June 2004): 6885–92. https://doi.org/10.1021/bi049943p.
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  - Jiang, H., D. Ullmo, W. Yang, and H. U. Baranger. “Electron-electron interactions in isolated and realistic quantum dots: A density functional theory study.” Physical Review B Condensed Matter and Materials Physics 69, no. 23 (June 1, 2004). https://doi.org/10.1103/PhysRevB.69.235326.
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  - Feng, Huasheng, Jiang Bian, Lemin Li, and Weitao Yang. “An efficient method for constructing nonorthogonal localized molecular orbitals.” The Journal of Chemical Physics 120, no. 20 (May 2004): 9458–66. https://doi.org/10.1063/1.1691396.
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  - Xie, Li, Haiyan Liu, and Weitao Yang. “Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes.” The Journal of Chemical Physics 120, no. 17 (May 2004): 8039–52. https://doi.org/10.1063/1.1691404.
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  - Yang, Weitao, Paul W. Ayers, and Qin Wu. “Potential functionals: dual to density functionals and solution to the v-representability problem.” Physical Review Letters 92, no. 14 (April 9, 2004): 146404. https://doi.org/10.1103/physrevlett.92.146404.
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  - Lu, Zhenyu, Wieslaw Nowak, Gwangrog Lee, Piotr Marszalek, and Wietao Yang. “"Elastic Properties of Single Amylose Chains in Water".” J. Am. Chem. Soc. 126 (2004): 9033–41.
  - Lu, Zhenyu, and Weitao Yang. “"Reaction Path Potential for Complex Systems Derived From ab initioqm/mm Calculations".” J. Chem. Phys. 121 (2004): 89–100.
  - Wang, Mingliang, 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 (2004): 101–7.
  - Goj, L. A., G. A. Cisneros, W. Yang, and R. A. Widenhoefer. “Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization.” Journal of Organometallic Chemistry 687, no. 2 (December 7, 2003): 498–507. https://doi.org/10.1016/j.jorganchem.2003.09.046.
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  - Mori-Sánchez, P., Q. Wu, and W. Yang. “Accurate polymer polarizabilities with exact exchange density-functional theory.” Journal of Chemical Physics 119, no. 21 (December 1, 2003): 11001–4. https://doi.org/10.1063/1.1630011.
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  - WU, Q. I. N., and W. E. I. T. A. O. YANG. “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): 627–38. https://doi.org/10.1142/s0219633603000690.
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  - Jiang, H., H. Baranger, and W. Yang. “Density-functional theory simulation of large quantum dots.” Physical Review B Condensed Matter and Materials Physics 68, no. 16 (October 24, 2003). https://doi.org/10.1103/PhysRevB.68.165337.
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  - Ke, San-Huang, Harold U. Baranger, and Weitao Yang. “Addition energies of fullerenes and carbon nanotubes as quantum dots: the role of symmetry.” Physical Review Letters 91, no. 11 (September 12, 2003): 116803. https://doi.org/10.1103/physrevlett.91.116803.
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  - Wu, Q., P. W. Ayers, and W. Yang. “Density-functional theory calculations with correct long-range potentials.” Journal of Chemical Physics 119, no. 6 (August 8, 2003): 2978–90. https://doi.org/10.1063/1.1590631.
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  - Cisneros, G Andrés, Haiyan Liu, Yingkai Zhang, and Weitao Yang. “Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase.” Journal of the American Chemical Society 125, no. 34 (August 2003): 10384–93. https://doi.org/10.1021/ja029672a.
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  - Wu, Q., and W. Yang. “A direct optimization method for calculating density functionals and exchange-correlation potentials from electron densities.” Journal of Chemical Physics 118, no. 6 (February 8, 2003): 2498–2509. https://doi.org/10.1063/1.1535422.
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  - Hasegawa, J. Y., M. Ishida, H. Nakatsuji, Z. Lu, H. Liu, and W. Yang. “Energetics of the electron transfer from bacteriopheophytin to ubiquinone in the photosynthetic reaction center for Rhodopseudomonas viridis: Theoretical study.” Journal of Physical Chemistry B 107, no. 3 (January 23, 2003): 838–47. https://doi.org/10.1021/jp022334b.
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  - Jiang, Hong, Harold U. Baranger, and Weitao Yang. “Spin and conductance-peak-spacing distributions in large quantum dots: a density-functional theory study.” Physical Review Letters 90, no. 2 (January 17, 2003): 026806. https://doi.org/10.1103/physrevlett.90.026806.
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  - Jiang, H., H. U. Baranger, and W. Yang. “Density-functional theory simulation of large quantum dots.” Physical Review B Condensed Matter and Materials Physics 68, no. 16 (2003): 1653371–79.
  - Jiang, Hong, Harold U. Baranger, and Weitao Yang. “Desnity functional theory simulation of large quantum dots.” Phys. Rev. B. 68 (2003).
  - Yang, Weitao, and Qin Wu. “Direct method for optimized effective potentials in density-functional theory.” Physical Review Letters 89, no. 14 (September 16, 2002): 143002. https://doi.org/10.1103/physrevlett.89.143002.
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  - Yang, Wei, Hsiau-Wei Lee, Homme Hellinga, and Jenny J. Yang. “Structural analysis, identification, and design of calcium-binding sites in proteins.” Proteins 47, no. 3 (May 15, 2002): 344–56. https://doi.org/10.1002/prot.10093.
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  - Cisneros, G. A., H. Y. Liu, Y. K. Zhang, and W. T. Yang. “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.
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  - Lu, Z. Y., H. Y. Liu, and W. T. Yang. “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.
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  - Yang, W. T., Y. K. Zhang, and H. Y. Liu. “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.
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  - Wu, Q., and W. Yang. “Empirical correction to density functional theory for van der Waals interactions.” Journal of Chemical Physics 116, no. 2 (January 8, 2002): 515–24. https://doi.org/10.1063/1.1424928.
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  - Liu, H., M. Elstner, E. Kaxiras, T. Frauenheim, J. Hermans, and W. Yang. “Quantum mechanics simulation of protein dynamics on long timescale.” Proteins 44, no. 4 (September 2001): 484–89. https://doi.org/10.1002/prot.1114.
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  - Baik, M. H., J. S. Silverman, I. V. Yang, P. A. Ropp, V. A. Szalai, W. Yang, and H. H. Thorp. “Using density functional theory to design DNA base analogues with low oxidation potentials.” Journal of Physical Chemistry B 105, no. 27 (July 12, 2001): 6437–44. https://doi.org/10.1021/jp010643g.
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  - Enkvist, C., Y. Zhang, and W. Yang. “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 (September 1, 2000): 325–29. https://doi.org/10.1002/1097-461X(2000)79:5<325::AID-QUA6>3.0.CO;2-B.
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  - Liu, H., Y. Zhang, and W. Yang. “How is the active site of enolase organized to catalyze two different reaction steps?” Journal of the American Chemical Society 122, no. 28 (July 19, 2000): 6560–70. https://doi.org/10.1021/ja9936619.
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  - Yang, W., Y. Zhang, and P. W. Ayers. “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): 5172–75. https://doi.org/10.1103/physrevlett.84.5172.
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  - Zhang, Y., H. Liu, and W. 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.” Journal of Chemical Physics 112, no. 8 (February 22, 2000): 3483–92. https://doi.org/10.1063/1.480503.
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  - Liu, S., J. M. Pérez-Jordâ, and W. Yang. “Nonorthogonal localized molecular orbitals in electronic structure theory.” Journal of Chemical Physics 112, no. 4 (January 22, 2000): 1634–44. https://doi.org/10.1063/1.480730.
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  - Enkvist, Christer, Yingkai Zhang, and Weitao Yang. “Density Functional Study of A Weakly Hydrogen Bonded System: the Benzene-Ammonia Complex.” The International Journal of Quantum Chemistry 79 (2000): 325–29.
  - Liu, Haiyan, 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 (2000).
  - Zhang, Y., and W. Yang. “Perspective on "Density-functional theory for fractional particle number: Derivative discontinuities of the energy".” Theoretical Chemistry Accounts 103, no. 3–4 (January 1, 2000): 346–48. https://doi.org/10.1007/s002149900021.
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  - Little, S. B., J. R. Rabinowitz, P. Wei, and W. Yang. “A comparison of calculated and experimental geometries for crowded polycyclic aromatic hydrocarbons and their metabolites.” Polycyclic Aromatic Compounds 1999, no. 14–15 (December 1, 1999): 53–61.
  - Zhang, Y., T. S. Lee, and W. Yang. “A pseudobond approach to combining quantum mechanical and molecular mechanical methods.” Journal of Chemical Physics 110, no. 1 (December 1, 1999): 46–54. https://doi.org/10.1063/1.478083.
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  - Lewis, J. P., S. Liu, T. S. Lee, and W. Yang. “A Linear-Scaling Quantum Mechanical Investigation of Cytidine Deaminase.” Journal of Computational Physics 151, no. 1 (May 1, 1999): 242–63. https://doi.org/10.1006/jcph.1999.6219.
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  - Zhang, Yingkai, Taisung Lee, and Weitao Yang. “A psuedo-bond approach to combining quantum mechanical and molecular mechanical methods.” J. Chem. Phys. 110 (1999): 46–54.
  - Yang, W. “Generalized adiabatic connection in density functional theory.” Journal of Chemical Physics 109, no. 23 (December 1, 1998): 10107–10. https://doi.org/10.1063/1.477701.
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  - Zhang, Y., and W. Yang. “A challenge for density functionals: Self-interaction error increases for systems with a noninteger number of electrons.” Journal of Chemical Physics 109, no. 7 (December 1, 1998): 2604–8. https://doi.org/10.1063/1.476859.
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  - Yang, W. T., M. Levy, and S. Trickey. “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.
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  - Pan, W., T. S. Lee, and W. Yang. “Parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations.” Journal of Computational Chemistry 19, no. 9 (July 15, 1998): 1101–9. https://doi.org/10.1002/(SICI)1096-987X(19980715)19:9<1101::AID-JCC10>3.0.CO;2-8.
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  - Lewis, J. P., C. W. Carter, J. Hermans, W. Pan, T. S. Lee, and W. Yang. “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 10, 1998): 5407–10. https://doi.org/10.1021/ja973522w.
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  - Acker, J. C., L. B. Marks, D. P. Spencer, W. Yang, M. A. Avery, R. K. Dodge, G. L. Rosner, and M. W. Dewhirst. “Serial in vivo observations of cerebral vasculature after treatment with a large single fraction of radiation.” Radiation Research 149, no. 4 (April 1998): 350–59. https://doi.org/10.2307/3579697.
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  - Lewis, J. P., C. W. Carter, J. Hermans, W. Pan, T. S. Lee, and W. T. Yang. “Quantum mechanical methods for large biomolecular systems: Applications in the study of the cytidine deaminase enzyme.” Biophysical Journal 74, no. 2 (February 1, 1998): A132–A132.
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  - Pérez-Jordá, J. M., and W. Yang. “On the scaling of multipole methods for particle-particle interactions.” Chemical Physics Letters 282, no. 1 (January 2, 1998): 71–78. https://doi.org/10.1016/S0009-2614(97)01153-6.
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  - Lee, T. S., J. P. Lewis, and W. Yang. “Linear-scaling quantum mechanical calculations of biological molecules: The divide-and-conquer approach.” Computational Materials Science 12, no. 3 (January 1, 1998): 259–77. https://doi.org/10.1016/S0927-0256(98)00029-9.
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  - Lee, T. S., and W. Yang. “Frozen density matrix approach for electronic structure calculations.” International Journal of Quantum Chemistry 69, no. 3 (January 1, 1998): 397–404. https://doi.org/10.1002/(sici)1097-461x(1998)69:3<397::aid-qua17>3.0.co;2-%23.
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  - Yang, Weitao, Mel Levy, and S. Trickey. “Symposium on density functional and applications (part 1 of ii) - introduction.” Int. J. Quantum Chem. 69 (1998).
  - York, D. M., T. S. Lee, and W. Yang. “Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods.” Physical Review Letters 80, no. 22 (January 1, 1998): 5011–14. https://doi.org/10.1103/PhysRevLett.80.5011.
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  - Zhang, Y., and W. Yang. “Comment on “generalized gradient approximation made simple”.” Physical Review Letters 80, no. 4 (January 1, 1998): 890. https://doi.org/10.1103/PhysRevLett.80.890.
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  - Zhang, Y., W. Pan, and W. Yang. “Describing van der Waals interaction in diatomic molecules with generalized gradient approximations: The role of the exchange functional.” Journal of Chemical Physics 107, no. 19 (November 15, 1997): 7921–25. https://doi.org/10.1063/1.475105.
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  - Pan, W., T. Zhu, and W. Yang. “First-principles study of the structural and electronic properties of ethylene adsorption on Si(100)-(2×1) surface.” Journal of Chemical Physics 107, no. 10 (September 8, 1997): 3981–85. https://doi.org/10.1063/1.474753.
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  - Pérez-Jordá, J. M., and W. Yang. “Fast evaluation of the Coulomb energy for electron densities.” Journal of Chemical Physics 107, no. 4 (July 22, 1997): 1218–26. https://doi.org/10.1063/1.474466.
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  - Zhu, Tianhai, Wei Pan, and Weitao Yang. “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. https://doi.org/10.1007/s002140050195.
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  - Yang, W. “Absolute-energy-minimum principles for linear-scaling electronic-structure calculations.” Physical Review B Condensed Matter and Materials Physics 56, no. 15 (January 1, 1997): 9294–97. https://doi.org/10.1103/PhysRevB.56.9294.
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  - York, D. M., T. S. Lee, and W. Yang. “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 6, 1996): 297–304. https://doi.org/10.1016/S0009-2614(96)01198-0.
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  - York, D. M., T. S. Lee, and W. Yang. “Quantum mechanical study of aqueous polarization effects on biological macromolecules.” Journal of the American Chemical Society 118, no. 44 (November 6, 1996): 10940–41. https://doi.org/10.1021/ja961937w.
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  - Lee, T. S., D. M. York, and W. Yang. “Linear-scaling semiempirical quantum calculations for macromolecules.” Journal of Chemical Physics 105, no. 7 (August 15, 1996): 2744–50. https://doi.org/10.1063/1.472136.
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  - Ni, H., D. M. York, L. Bartolotti, R. L. Wells, and W. Yang. “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 (June 19, 1996): 5732–36. https://doi.org/10.1021/ja951706+.
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  - Pérez-Jordá, J. M., and W. Yang. “A concise redefinition of the solid spherical harmonics and its use in fast multipole methods.” Journal of Chemical Physics 104, no. 20 (May 22, 1996): 8003–6. https://doi.org/10.1063/1.471517.
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  - Zhu, T., W. Pan, and W. Yang. “Structure of solid-state systems from embedded-cluster calculations: A divide-and-conquer approach.” Physical Review. B, Condensed Matter 53, no. 19 (May 1996): 12713–24. https://doi.org/10.1103/physrevb.53.12713.
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  - York, D. M., and W. Yang. “A chemical potential equalization method for molecular simulations.” Journal of Chemical Physics 104, no. 1 (January 1, 1996): 159–72. https://doi.org/10.1063/1.470886.
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  - Pérez-Jordá, J. M., and W. Yang. “A simple O(N log N) algorithm for the rapid evaluation of particle-particle interactions.” Chemical Physics Letters 247, no. 4–6 (December 29, 1995): 484–90. https://doi.org/10.1016/S0009-2614(95)01235-4.
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  - Pérez-Jorda, J. M., and W. Yang. “An algorithm for 3D numerical integration that scales linearly with the size of the molecule.” Chemical Physics Letters 241, no. 4 (July 28, 1995): 469–76. https://doi.org/10.1016/0009-2614(95)00665-Q.
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  - Wei, P., and W. Yang. “Structure and stability of molybdenum carbide clusters (MoC4)n (n=1 to 4) and their anions.” Physical Review. B, Condensed Matter 51, no. 11 (March 1995): 7224–30. https://doi.org/10.1103/physrevb.51.7224.
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  - Lee, T. S., D. M. York, and W. Yang. “A new definition of atomic charges based on a variational principle for the electrostatic potential energy.” The Journal of Chemical Physics 102, no. 19 (January 1, 1995): 7549–56. https://doi.org/10.1063/1.469086.
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  - Parr, R. G., and W. Yang. “Density-functional theory of the electronic structure of molecules.” Annual Review of Physical Chemistry 46 (January 1995): 701–28. https://doi.org/10.1146/annurev.pc.46.100195.003413.
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  - Yang, W., and T. S. Lee. “A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules.” The Journal of Chemical Physics 103, no. 13 (January 1, 1995): 5674–78. https://doi.org/10.1063/1.470549.
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  - York, D. M., W. Yang, H. Lee, T. Darden, and L. G. Pedersen. “Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics.” Journal of the American Chemical Society 117, no. 17 (January 1, 1995): 5001–2. https://doi.org/10.1021/ja00122a034.
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  - Zhao, Q., and W. Yang. “Analytical energy gradients and geometry optimization in the divide-and-conquer method for large molecules.” The Journal of Chemical Physics 102, no. 24 (January 1, 1995): 9598–9603. https://doi.org/10.1063/1.468776.
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  - Lu, J. P., and W. Yang. “Shape of large single- and multiple-shell fullerenes.” Physical Review. B, Condensed Matter 49, no. 16 (April 1994): 11421–24. https://doi.org/10.1103/physrevb.49.11421.
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  - York, D., J. P. Lu, and W. Yang. “Density-functional calculations of the structure and stability of C240.” Physical Review. B, Condensed Matter 49, no. 12 (March 1994): 8526–28. https://doi.org/10.1103/physrevb.49.8526.
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  - York, D., and W. Yang. “The fast Fourier Poisson method for calculating Ewald sums.” The Journal of Chemical Physics 101, no. 4 (January 1, 1994): 3298–3300. https://doi.org/10.1063/1.467576.
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  - Zhu, T., and W. Yang. “Structure of the ammonia dimer studied by density functional theory.” International Journal of Quantum Chemistry 49, no. 5 (January 1, 1994): 613–23. https://doi.org/10.1002/qua.560490507.
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  - Bemish, R. J., P. A. Block, L. G. Pedersen, Weitao Yang, and R. E. Miller. “The ar-c2h2 inter-molecular potential from high resolution spectroscopy and ab initio theory: A case for multi-center interactions.” J. Chem. Phys. 99 (1993): 8593–98.
  - Bemish, R. J., P. A. Block, L. G. Pedersen, Y. Weitao, and R. E. Miller. “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): 8585–98.
  - Bemish, R. J., P. A. Block, L. G. Pedersen, Y. Weitao, and R. E. Miller. “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 (January 1, 1993): 8585–98. https://doi.org/10.1063/1.465582.
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  - Lee, C., G. Fitzgerald, and W. Yang. “Nonlocal density functional calculations: Comparison of two implementation schemes.” Journal of Chemical Physics 98, no. 4 (January 1, 1993): 2971–74. https://doi.org/10.1063/1.464125.
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  - Zhu, T., C. Lee, and W. Yang. “Examination of several exchange-correlation energy functionals by accurate self-consistent atomic calculations.” The Journal of Chemical Physics 98, no. 6 (January 1, 1993): 4814–21. https://doi.org/10.1063/1.464985.
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  - Zhu, T., C. Lee, and W. Yang. “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). https://doi.org/10.1063/1.466236.
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  - Crawford, T. D., and W. Yang. “The Hartley basis functions and transform: alternatives to plane waves and the Fourier transform.” Chemical Physics Letters 192, no. 1 (April 24, 1992): 45–48. https://doi.org/10.1016/0009-2614(92)85425-A.
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  - 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, no. C (March 24, 1992): 461–79. https://doi.org/10.1016/0166-1280(92)85024-F.
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  - Lee, C., and W. Yang. “The divideâandâconquer densityâfunctional approach: Molecular internal rotation and density of states.” Journal of Chemical Physics 96, no. 3 (February 1, 1992): 2408–11. https://doi.org/10.1063/1.462039.
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  - Yang, W. “Direct calculation of electron density in density-functional theory: Implementation for benzene and a tetrapeptide.” Physical Review. A, Atomic, Molecular, and Optical Physics 44, no. 11 (December 1991): 7823–26. https://doi.org/10.1103/physreva.44.7823.
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  - 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 1, 1991): 1208–14. https://doi.org/10.1063/1.460028.
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  - Yang, W. “Direct calculation of electron density in density-functional theory.” Physical Review Letters 66, no. 11 (January 1, 1991): 1438–41. https://doi.org/10.1103/PhysRevLett.66.1438.
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  - Morrison, R. C., W. Yang, R. G. Parr, and C. Lee. “Approximate density matrices and wigner distribution functions from density, kinetic energy density, and idempotency constraints.” International Journal of Quantum Chemistry 38, no. 6 (January 1, 1990): 819–30. https://doi.org/10.1002/qua.560380605.
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  - Yang, W. “Integral Formulation of Density-Functional Theory.” Advances in Quantum Chemistry 21, no. C (January 1, 1990): 293–302. https://doi.org/10.1016/S0065-3276(08)60601-2.
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  - Yang, W., and A. C. Peet. “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 1, 1990): 522–26. https://doi.org/10.1063/1.458454.
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  - Peet, A. C., and W. Yang. “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 1, 1989): 6598–6612.
  - Peet, A. C., and W. Yang. “The collocation method for calculating vibrational bound states of molecular systems - with application to Ar-HCl.” The Journal of Chemical Physics 90, no. 3 (January 1, 1989): 1746–51. https://doi.org/10.1063/1.456068.
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  - Yang, W., A. C. Peet, and W. H. Miller. “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 (January 1, 1989): 7537–42. https://doi.org/10.1063/1.457277.
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  - Yang, W., and W. H. Miller. “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 (January 1, 1989): 3504–8. https://doi.org/10.1063/1.456880.
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  - Yang, W., and A. C. Peet. “The collocation method for bound solutions of the Schrödinger equation.” Chemical Physics Letters 153, no. 1 (December 2, 1988): 98–104. https://doi.org/10.1016/0009-2614(88)80139-8.
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  - Yang, W. “Ab initio approach for many-electron systems without invoking orbitals: An integral formulation of density-functional theory.” Physical Review. A, General Physics 38, no. 11 (December 1988): 5494–5503. https://doi.org/10.1103/physreva.38.5494.
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  - Yang, W. “Thermal properties of many-electron systems: An integral formulation of density-functional theory.” Physical Review. A, General Physics 38, no. 11 (December 1988): 5504–11. https://doi.org/10.1103/physreva.38.5504.
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  - Yang, W. “Dynamic linear response of many-electron systems: An integral formulation of density-functional theory.” Physical Review. A, General Physics 38, no. 11 (December 1988): 5512–19. https://doi.org/10.1103/physreva.38.5512.
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  - Lee, C., W. Yang, and R. G. Parr. “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.” Physical Review. B, Condensed Matter 37, no. 2 (January 1988): 785–89. https://doi.org/10.1103/physrevb.37.785.
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  - Lee, C., W. Yang, and R. G. Parr. “Local softness and chemical reactivity in the molecules CO, SCN^- and H2CO.” Journal of Molecular Structure: Theochem 163, no. C (January 1, 1988): 305–13. https://doi.org/10.1016/0166-1280(88)80397-X.
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  - Yang, W., R. G. Parr, and L. Uytterhoeven. “New relation between hardness and compressibility of minerals.” Physics and Chemistry of Minerals 15, no. 2 (December 1, 1987): 191–95. https://doi.org/10.1007/BF00308783.
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  - Xie, Wenhui, 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, no. 3 (January 1, 1987): 258–64. https://doi.org/10.3866/PKU.WHXB19870308.
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  - Yang, W. “Ab initio approach for many-electron systems without invoking orbitals: An integral formulation of density-functional theory.” Physical Review Letters 59, no. 14 (January 1, 1987): 1569–72. https://doi.org/10.1103/PhysRevLett.59.1569.
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  - Yang, W. “Gradient correction in Thomas-Fermi theory.” Physical Review. A, General Physics 34, no. 6 (December 1986): 4575–85. https://doi.org/10.1103/physreva.34.4575.
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  - Yang, W., R. G. Parr, and C. Lee. “Various functionals for the kinetic energy density of an atom or molecule.” Physical Review. A, General Physics 34, no. 6 (December 1986): 4586–90. https://doi.org/10.1103/physreva.34.4586.
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  - Yang, W., and W. J. Mortier. “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): 5708–11. https://doi.org/10.1021/ja00279a008.
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  - Yang, W., and J. E. Harriman. “Analysis of the kinetic energy functional in density functional theory.” The Journal of Chemical Physics 84, no. 6 (January 1, 1986): 3320–23. https://doi.org/10.1063/1.450265.
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  - Yang, W., and R. G. Parr. “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): 6723–26. https://doi.org/10.1073/pnas.82.20.6723.
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  - Levy, M., W. Yang, and R. G. Parr. “A new functional with homogeneous coordinate scaling in density functional theory: F[ρ, λ].” The Journal of Chemical Physics 83, no. 5 (January 1, 1985): 2334–36. https://doi.org/10.1063/1.449326.
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  - Yang, W., C. Lee, and S. K. Ghosh. “Molecular softness as the average of atomic softnesses: Companion principle to the geometric mean principle for electronegativity equalization.” Journal of Physical Chemistry 89, no. 25 (January 1, 1985): 5412–14. https://doi.org/10.1021/j100271a019.
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  - Parr, R. G., and W. Yang. “Density Functional Approach to the Frontier-Electron Theory of Chemical Reactivity.” Journal of the American Chemical Society 106, no. 14 (January 1, 1984): 4049–50. https://doi.org/10.1021/ja00326a036.
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  - Yang, W., R. G. Parr, and R. Pucci. “Electron density, Kohn-Sham frontier orbitals, and Fukui functions.” The Journal of Chemical Physics 81, no. 6 (January 1, 1984): 2862–63. https://doi.org/10.1063/1.447964.
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- Book Sections
  - Andrés Cisneros, G., and W. Yang. “Comparison of reaction barriers in energy and free energy for enzyme catalysis.” In Challenges and Advances in Computational Chemistry and Physics, 7:57–78, 2009. https://doi.org/10.1007/978-1-4020-9956-4_3.
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- Conference Papers
  - Scholl, Zackary N., Qing Li, Weitao Yang, and Piotr Marszalek. “Single-Molecule Force-Spectroscopy Reveals the Calcium Dependency of Folding Intermediates in the Multidomain Protein S.” In Biophysical Journal, 110:393a-393a. Elsevier BV, 2016. https://doi.org/10.1016/j.bpj.2015.11.2122.
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  - Scholl, Zackary N., Weitao Yang, and Piotr Marszalek. “Direct Observation of Multimer Stabilization in the Mechanical Unfolding Pathway of a Protein Undergoing Oligomerization.” In Biophysical Journal, 110:392a-393a. Elsevier BV, 2016. https://doi.org/10.1016/j.bpj.2015.11.2121.
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  - Wang, W., Z. Li, and W. Yang. “Angular momentum dependent field emission energy distribution.” In Ivnc 2015 Technical Digest: 28th International Vacuum Nanoelectronics Conference, 30–31, 2015. https://doi.org/10.1109/IVNC.2015.7225519.
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  - Scholl, Zackary N., Weitao Yang, and Piotr Marszalek. “N-terminal Domain Of Luciferase Controls Misfolding Avoidance.” In Protein Science, 23:249–249. WILEY-BLACKWELL, 2014.
    Link to Item
  - Yang, Weitao. “Mechanism of catalytic reactions and redox processes for solar fuel with multiscale QM/MM simulation.” In Abstracts of Papers of the American Chemical Society, Vol. 246. AMER CHEMICAL SOC, 2013.
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  - Scholl, Zackary N., Weitao Yang, and Piotr E. Marszalek. “Improving Single Molecule Force Spectroscopy through Automated Real-Time Data Collection and Quantification of Experimental Conditions.” In Biophysical Journal, 104:512a-512a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.2827.
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  - Yang, Weitao. “Progress in exchange-correlation energy functionals.” In Abstracts of Papers of the American Chemical Society, Vol. 242. AMER CHEMICAL SOC, 2011.
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  - Rinderspacher, B Christopher, David N. Beratan, and Weitao Yang. “CINF 71-Inverse design of host-guest complexes in competitive binding problems.” In Abstracts of Papers of the American Chemical Society, Vol. 236. AMER CHEMICAL SOC, 2008.
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  - Cohen, Aron J., Paula Mori-Sanchez, Tim Heaton-Burgess, Felipe A. Bulat, and Weitao Yang. “COMP 436-Accurate density functionals addressing the self-interaction error and potential functional formalism.” In Abstracts of Papers of the American Chemical Society, Vol. 234. AMER CHEMICAL SOC, 2007.
    Link to Item
  - Yang, W. T., Z. Y. Lu, and M. L. Wang. “Reaction path potential for simulation of chemical reactions in enzymes derived from ab initio QM/MM calculations.” In Abstracts of Papers of the American Chemical Society, 228:U247–U247. AMER CHEMICAL SOC, 2004.
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Teaching & Mentoring
Recent Courses
- CHEM 310: Physical Chemistry I 2020
- CHEM 393: Research Independent Study 2020
- CHEM 394: Research Independent Study 2020
- CHEM 493: Research Independent Study 2020
- CHEM 494: Research Independent Study 2020
- CHEM 542: Quantum Mechanics 2020
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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