Publications

Yihan's Google Scholar Profile

[Preprints]

• Titouan Duston, Zhen Tao, Xuezhi Bian, Mansi Bhati, Jonathan Rawlinson, Robert G Littlejohn, Zheng Pei, Yihan Shao, Joseph E Subotnik*, A Phase Space Approach to Vibrational Circular Dichroism. 

• Bidhan Ghosh, Prakash Kafle, Rishav Mukherjee, Randall Welles, Deacon Herndon, Kenneth Nicholas, Yihan Shao, Indrajeet Sharma*, "Sulfenylnitrene-Mediated Nitrogen-Atom Insertion into Pyrroles, Indoles, and Imidazoles".

[2024]

• 153. Zachary J. Ingram,  Chance W. Lander, Madeleine C. Oliver, Nazmiye Gökçe Altınçekiç, Liangliang Huang, Yihan Shao, and Hyunho Noh*, "Hydrogen-Atom Binding Energy of Structurally Well-defined Cerium Oxide Nodes at the Metal−Organic Framework-Liquid Interfaces", Accepted by the Journal of Physical Chemistry C. 

• 152. Kwangho Nam,* Yihan Shao, Dan-Thomas Major, Magnus Wolf Watz, "Perspectives on computational enzyme modeling: From mechanisms to design and drug development", ACS Omega, 9, 7393 (2024). 

• 151. Zhen Chen, Jiahui Chen, Wakana Mori, Yongjia Yi, Jian Rong, Yinlong Li, Erick R. Calderon Leon, Tuo Shao, Zhendong Song, Tomoteru Yamasaki, Hideki Ishii, Yiding Zhang, Tomomi Kokufuta, Kuan Hu, Lin Xie, Lee Josephson, Richard Van, Yihan Shao, Stewart Factor, Ming-Rong Zhang*, and Steven H. Liang*, "Preclinical Evaluation of Novel Positron Emission Tomography (PET) Probes for Imaging Leucine-Rich Repeat Kinase 2 (LRRK2)", Journal of Medicinal Chemistry, 67, 2559 (2024).

• 150. Bidhan Ghosh, Adam Alber, Chance W. Lander, Yihan Shao, Kenneth M. Nicholas, Indrajeet Sharma,* "Catalytic Stereoselective 1,2-cis-Furanosylations Enabled by Enynal-Derived Copper Carbenes", ACS Catalysis, 14, 1037 (2024).   

• 149. William M. MacCuaig,Carly Wickizer, Richard S. Van, Megan R. Lerner, William E. Grizzle, Yihan Shao, Maged Henary,* and Lacey R. McNally,* "Influence of structural moieties in squaraine dyes on optoacoustic signal shape and intensity", Chem, 10, 713 (2024).

• 148. Xiaoliang Pan,* Ryan Snyder,* Jia-Ning Wang, Chance Lander, Carly Wickizer, Richard Van, Andrew Chesney, Yuanfei Xue, Yuezhi Mao,* Ye Mei,* Jingzhi Pu,* Yihan Shao,* "Training Machine Learning Potentials for Reactive Systems: A Colab Tutorial on Basic Models", Journal of Computational Chemistry, 45, 638 (2024). 

[2023]

• 147. Jing Zhang, Carly Wickizer, Weihua Ding, Richard Van, Liuyue Yang, Biyue Zhu, Jun Yang, Can Martin Zhang, Shiqian Shen, Yihan Shao, Chongzhao Ran, "In Vivo Three-dimensional Brain Imaging with Chemiluminescence Probes in Alzheimers Disease Models",  Proceedings of National Academy of Sciences, 120, e2310131120 (2023).

• 146. Xiaoliang Pan,* Richard Van , Jingzhi Pu ,* Kwangho Nam ,* Yuezhi Mao ,* Yihan Shao,* "Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions", Journal of Chemical Theory and Computation, 19, 8234 (2023). 

• 145. Maximilian Menger, Qi Ou, Yihan Shao, Shirin Faraji, Joseph E Subotnik,* Dale Cofer-Shabica,* "Nature of Hops, Coordinates, and Detailed Balance for Nonadiabatic Simulations in the Condensed Phase", J. Phys. Chem. A, 127, 8427 (2023). 

• 144. Ryan Snyder, Bryant Kim, Xiaoliang Pan, Yihan Shao,* Jingzhi Pu,* "Bridging Semiempirical and Ab Initio QM/MM Potentials by Gaussian Process Regression and Its Sparse Variants for Free Energy Simulation", Journal of Chemical Physics, 159, 054107 (2023).  

• 143. Jennifer Londoño-Salazar, Megan Ayala, Douglas R Powell, Yihan Shao,* George B Richter-Addo,* "Interactions of arylhydroxylamines and alkylaldoximes with a rhodium porphyrin", Journal of Inorganic Biochemistry, 247, 112337 (2023). 

• 142. Jia-Ning Wang, Yuanfei Xue, Pengfei Li, Xiaoliang Pan, Meiting Wang, Yihan Shao,* Yan Mo,* Ye Mei,* "Perspective: Reference-Potential Methods for the Study of Thermodynamic Properties in Chemical Processes: Theory, Applications, and Pitfalls", Journal of Physical Chemistry Letters, 14, 4866 (2023). 

• 141. Songyuan Yao, Richard Van, Xiaoliang Pan, Ji Hwan Park, Yuezhi Mao,* Jingzhi Pu,* Ye Mei* and Yihan Shao*, "Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations", RSC Advances, 13, 4565 (2023). 

• 140. Chance Lander, Vardhan Satalkar, Junjie Yang, Xiaoliang Pan, Zheng Pei, Aayushi Catterji, Chungen Liu, Kenneth M. Nicholas, Robert H. Cichewicz, Zhibo Yang,* and Yihan Shao,* "Visualization of Electron Density Changes Along Chemical Reaction Pathways", Molecular Physics, 120, e2113566 (2023).

​[2022]

• 139. Vishikh Athavale,* Hung-Hsuan Teh, Yihan Shao, Joseph E Subotnik,* "Analytical gradients and derivative couplings for the TDDFT-1D method", Journal of Chemical Physics, 157, 244110 (2022).  

• 138. Ahmed Haider, Chunyu Zhao, Lu Wang, Zhiwei Xiao, Jian Rong, Xiaotian Xia, Zhen Chen, Stefanie K. Pfister, Natalia Mast, Eylan Yutuc, Jiahui Chen, Yinlong Li, Tuo Shao, Geoffrey I. Warnock, Alyaa Dawoud, Theresa R. Connors, Derek H. Oakley, Huiyi Wei, Jinghao Wang, Zhihua Zheng, Hao Xu, April T. Davenport, James B. Daunais, Richard S. Van, Yihan Shao, Yuqin Wang, Ming-Rong Zhang, Catherine Gebhard, Irina Pikuleva, Allan I. Levey, William J. Griffiths, Steven H. Liang*, "Assessment of cholesterol homeostasis in the living human brain", Science Translational Medicine, 14, eadc9967 (2022). 

• 137. Zheng Pei, Yuezhi Mao,* Yihan Shao,* Wanzhen Liang,* "Analytic High-Order Energy Derivatives for Metal Nanoparticle-Mediated Infrared and Raman Scattering Spectra within the Framework of Quantum Mechanics/Molecular Mechanics Model with Induced Charges and Dipoles", Journal of Chemical Physics, 157, 164110 (2022). 

• 136. Ryan Snyder, Bryant Kim, Xiaoliang Pan, Yihan Shao,* and Jingzhi Pu*, "Facilitating Ab Initio QM/MM Free Energy Simulations by Gaussian Process Regression with Derivative Observations", Physical Chemistry Chemical Physics, 24, 25134 (2022).  2022 HOT PCCP article

• 135. Kenneth M. Nicholas,* Chance Lander, and Yihan Shao, "Computational Evaluation of Potential Molecular Catalysts for Nitrous Oxide Decomposition",  Inorganic Chemistry, 61, 14591 (2022). 

• 134. Biyue Zhu, Jing Yang,  Richard Van,   Fan Yang,   Yue Yu,   Astra Yu,   Kathleen Ran,   Keyi Yin,   Yingxia Liang,   Xunuo Shen,   Wei Yin,   Se Hoon Choi,   Ying Lu,  Changning Wang,  Yihan Shao,  Liang Shi, Rudolph E. Tanzi,   Can Zhang,*   Yan Cheng,*   Zhirong Zhang,  and  Chongzhao Ran,* "Epitope alteration by small molecules and applications in drug discovery", Chemical Science, 13, 8104 (2022).   

• 133. D. Vale Cofer-Shabica,* Maximilian F.S.J. Menger, Qi Ou, Yihan Shao, Joseph E. Subotnik, and Shirin Faraji,* "INAQS, a generic interface for non-adiabatic QM/MM dynamics: Design, implementation, and validation for GROMACS/Q-CHEM simulations", Journal of Chemical Theory and Computation, 18, 4801 (2022). 

• ​132. Ran Cheng, Masayuki Fujinaga, Jing Yang, Jian Rong, Ahmed Haider, Daisuke Ogasawara, Richard S. Van, Tuo Shao, Zhen Chen, Xiaofei Zhang, Erick R. Calderon Leon, Yiding Zhang, Wakana Mori, Katsushi Kumata, Tomoteru Yamasaki, Lin Xie, Shaofa Sun, Lu Wang, Chongzhao Ran, Yihan Shao, Benjamin Cravatt, Lee Josephson, Ming-Rong Zhang,* and Steven H. Liang,* "A novel monoacylglycerol lipase-targeted 18F-labeled probe for positron emission tomography imaging of brown adipose tissue in the energy network", Acta Pharmacologica Sinica, 43, 3002 (2022). 

• 131. Xiaoliang Pan, Richard Van, Evgeny Epifanovsky, Jian Liu, Jingzhi Pu,* Kwangho Nam,* Yihan Shao,*, "Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semi-empirical QM/MM Hamiltonian", Journal of Physical Chemistry B, 126, 4226 (2022). 

• 130. WanZhen Liang* (main corresponding author), Zheng Pei, Yuezhi Mao*, and Yihan Shao*, "Evaluation of Molecular Photophysical and Photochemical Properties Using Linear Response Time-Dependent Density Functional Theory with Classical Embedding: Successes and Challenges", Journal of Chemical Physics, 156, 210901 (2022). 

• 129. Vardhan Satalkar, Enrico Benassi,* Yuezhi Mao,* Xiaoliang Pan, Chongzhao Ran, Xiaoyuan Chen, Yihan Shao,* "Computational Investigation of Substituent Effects on the Fluorescence Wavelengths of Oxyluciferin Analog", Journal of Photochemistry and Photobiology A, 431, 114018 (2022). 

• 128. Junjie Yang, Zheng Pei, Erick Calderon Leon, Carly Wickizer, Binbin Weng, Yuezhi Mao, Qi Ou,* and Yihan Shao,* "Cavity quantum-electrodynamical time-dependent density functional theory within Gaussian atomic basis. II. Analytic energy gradient", Journal of Chemical Physics, 156, 124104 (2022). 

• 127. Ye Guan, Jennifer Londoño-Salazar, ZhengPei, Douglas R. Powell, Yihan Shao*, George B. Richter-Addo,*  "Interactions of N-hydroxyamphetamine with an iron porphyrin: A unique intramolecular H-bond probed by DFT calculations", Journal of Inorganic Biochemistry, 231, 111779 (2022).

[2021]

• 126. Yuanfei Xue, Jia-Ning Wang, Wenxin Hu, Jun Zheng, Yongle Li, Xiaoliang Pan, Yan Mo*, Yihan Shao, Lu Wang*, and Ye Mei*, "Affordable Ab Initio Path Integral for Thermodynamic Properties via Molecular Dynamics Simulations Using Semiempirical Reference Potential", Journal of Physical Chemistry A, 125, 10667 (2021). 

• 125. Bryant Kim, Yihan Shao*, Jingzhi Pu*, "Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability", Journal of Chemical Theory and Computation, 17, 7682 (2021). 

• 124. Xiaoyun Deng, Fernando Salgado-Polo, Tuo Shao, Zhiwei Xiao, Richard Van, Jiahui Chen, Jian Rong, Ahmed Haider, Yihan Shao, Lee Josephson, Anastassis Perrakis*, and Steven H. Liang*, "Imaging Autotaxin In Vivo with 18F-Labeled Positron Emission Tomography Ligands", Journal of Medicinal Chemistry, 64, 15053 (2021). 

• 123. Qi Ou, Yihan Shao, and Zhigang Shuai,* "Enhanced Reverse Intersystem Crossing Promoted by Triplet Exciton–Photon Coupling", Journal of the American Chemical Society, 143, 17786 (2021). 

• 122. Jian Rong, Wakana Mori, Xiaotian Xia, Michael A Schafroth, Chunyu Zhao, Richard S Van, Tomoteru Yamasaki, Jiahui Chen, Zhiwei Xiao, Ahmed Haider, Daisuke Ogasawara, Atsuto Hiraishi, Tuo Shao, Yiding Zhang, Zhen Chen, Fuwen Pang, Kuan Hu, Lin Xie, Masayuki Fujinaga, Katsushi Kumata, Yuancheng Gou, Yang Fang, Shuyin Gu, Huiyi Wei, Liang Bao, Hao Xu, Thomas L Collier, Yihan Shao, Richard E Carson, Benjamin F Cravatt, Lu Wang,* Ming-Rong Zhang,* Steven H Liang.* "Novel Reversible-Binding PET Ligands for Imaging Monoacylglycerol Lipase Based on the Piperazinyl Azetidine Scaffold", Journal of Medicinal Chemistry, 64, 14283 (2021).

• 121. Ahmed Haider, Zhiwei Xiao, Xiaotian Xia, Jiahui Chen, Richard S. Van, Shi Kuang, Chunyu Zhao, Jian Rong, Tuo Shao, Perla Ramesh, Appu Aravind, Yihan Shao, Chongzhao Ran, Larry  J.Young, Steven H. Liang,* "Development of a triazolobenzodiazepine-based PET probe for subtype-selective vasopressin 1A receptor imaging", Pharmacological Research, 173, 105886 (2021).

• 120.  Evgeny Epifanovsky, Andrew T. B. Gilbert, Xintian Feng, Joonho Lee, Yuezhi Mao, Narbe Mardirossian, Pavel Pokhilko, Alec F. White, Marc P. Coons, Adrian L. Dempwolff, Zhengting Gan, Diptarka Hait, Paul R. Horn, Leif D. Jacobson, Ilya Kaliman, Jörg Kussmann, Adrian W. Lange, Ka Un Lao, Daniel S. Levine, Jie Liu, Simon C. McKenzie, Adrian F. Morrison, Kaushik D. Nanda, Felix Plasser, Dirk R. Rehn, Marta L. Vidal, Zhi-Qiang You, Ying Zhu, Bushra Alam, Benjamin J. Albrecht, Abdulrahman Aldossary, Ethan Alguire, Josefine H. Andersen, Vishikh Athavale, Dennis Barton, Khadiza Begam, Andrew Behn, Nicole Bellonzi, Yves A. Bernard, Eric J. Berquist, Hugh G. A. Burton, Abel Carreras, Kevin Carter-Fenk, Romit Chakraborty, Alan D. Chien, Kristina D. Closser, Vale Cofer-Shabica, Saswata Dasgupta, Marc de Wergifosse, Jia Deng, Michael Diedenhofen, Hainam Do, Sebastian Ehlert, Po-Tung Fang, Shervin Fatehi, Qingguo Feng, Triet Friedhoff, James Gayvert, Qinghui Ge, Gergely Gidofalvi, Matthew Goldey, Joe Gomes, Cristina E. González-Espinoza, Sahil Gulania, Anastasia O. Gunina, Magnus W. D. Hanson-Heine, Phillip H. P. Harbach, Andreas Hauser, Michael F. Herbst, Mario Hernández Vera, Manuel Hodecker, Zachary C. Holden, Shannon Houck, Xunkun Huang, Kerwin Hui, Bang C. Huynh, Maxim Ivanov, Ádám Jász, Hyunjun Ji, Hanjie Jiang, Benjamin Kaduk, Sven Kähler, Kirill Khistyaev, Jaehoon Kim, Gergely Kis, Phil Klunzinger, Zsuzsanna Koczor-Benda, Joong Hoon Koh, Dimitri Kosenkov, Laura Koulias, Tim Kowalczyk, Caroline M. Krauter, Karl Kue, Alexander Kunitsa, Thomas Kus, István Ladjánszki, Arie Landau, Keith V. Lawler, Daniel Lefrancois, Susi Lehtola, Run R. Li, Yi-Pei Li, Jiashu Liang, Marcus Liebenthal, Hung-Hsuan Lin, You-Sheng Lin, Fenglai Liu, Kuan-Yu Liu, Matthias Loipersberger, Arne Luenser, Aaditya Manjanath, Prashant Manohar, Erum Mansoor, Sam F. Manzer, Shan-Ping Mao, Aleksandr V. Marenich, Thomas Markovich, Stephen Mason, Simon A. Maurer, Peter F. McLaughlin, Maximilian F. S. J. Menger, Jan-Michael Mewes, Stefanie A. Mewes, Pierpaolo Morgante, J. Wayne Mullinax, Katherine J. Oosterbaan, Garrette Paran, Alexander C. Paul, Suranjan K. Paul, Fabijan Pavošević, Zheng Pei, Stefan Prager, Emil I. Proynov, Ádám Rák, Eloy Ramos-Cordoba, Bhaskar Rana, Alan E. Rask, Adam Rettig, Ryan M. Richard, Fazle Rob, Elliot Rossomme, Tarek Scheele, Maximilian Scheurer, Matthias Schneider, Nickolai Sergueev, Shaama M. Sharada, Wojciech Skomorowski, David W. Small, Christopher J. Stein, Yu-Chuan Su, Eric J. Sundstrom, Zhen Tao, Jonathan Thirman, Gábor J. Tornai, Takashi Tsuchimochi, Norm M. Tubman, Srimukh Prasad Veccham, Oleg Vydrov, Jan Wenzel, Jon Witte, Atsushi Yamada, Kun Yao, Sina Yeganeh, Shane R. Yost, Alexander Zech, Igor Ying Zhang, Xing Zhang, Yu Zhang, Dmitry Zuev, Alán Aspuru-Guzik, Alexis T. Bell, Nicholas A. Besley, Ksenia B. Bravaya, Bernard R. Brooks, David Casanova, Jeng-Da Chai, Sonia Coriani, Christopher J. Cramer, György Cserey, A. Eugene DePrince III, Robert A. DiStasio Jr., Andreas Dreuw, Barry D. Dunietz, Thomas R. Furlani, William A. Goddard III, Sharon Hammes-Schiffer, Teresa Head-Gordon, Warren J. Hehre, Chao-Ping Hsu, Thomas-C. Jagau, Yousung Jung, Andreas Klamt, Jing Kong, Daniel S. Lambrecht, WanZhen Liang, Nicholas J. Mayhall, C. William McCurdy, Jeffrey B. Neaton, Christian Ochsenfeld, John A. Parkhill, Roberto Peverati, Vitaly A. Rassolov, Yihan Shao, Lyudmila V. Slipchenko, Tim Stauch, Ryan P. Steele, Joseph E. Subotnik, Alex J. W. Thom, Alexandre Tkatchenko, Donald G. Truhlar, Troy Van Voorhis, Tomasz A. Wesolowski, K. Birgitta Whaley, H. Lee Woodcock III, Paul M. Zimmerman, Shirin Faraji, Peter M. W. Gill, Martin Head-Gordon,* John M. Herbert,* and Anna I. Krylov,* "Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package", Journal of Chemical Physics, 155, 084801 (2021). 

• 119. Xiaoliang Pan, Junjie Yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang, Jingzhi Pu,* Ye Mei,* Kwangho Nam,* Yihan Shao,* "Machine Learning Assisted Free Energy Simulation of Solution–Phase and Enzyme Reactions", Journal of Chemical Theory and Computation, 17, 5745 (2021). 

• 118. Junbo Chen, Jin Kato, Jason B. Harper, Yihan Shao, and Junming Ho*, "On the Accuracy of QM/MM Models: A Systematic Study of Intramolecular Proton Transfer Reactions of Amino Acids in Water", Journal of Physical Chemistry B, 125, 9304 (2021).

• 117. Bryant Kim, Ryan Snyder, Mulpuri Nagaraju, Yan Zhou, Pedro Ojeda-May, Seth Keeton, Mellisa Hege, Yihan Shao*, and Jingzhi Pu*, "Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force", Journal of Chemical Theory and Computation, 17, 4961 (2021).

• 116.  Junjie Yang, Qi Ou,* Zheng Pei, Hua Wang, Binbin Weng, Zhigang Shuai,* Kieran Mullen,* and Yihan Shao*, "Quantum-Electrodynamical Time-Dependent Density Functional Theory Within Gaussian Atomic Basis", Journal of Chemical Physics, 155, 064107 (2021). 

• 115. Simon L Dürr, Dénes Berat, Olga Bohuszewicz, Pablo G Jambrina, Reynier Suardiaz,  Christine Peter, Yihan Shao, Edina Rosta*, "The role of conserved residues in the DEDDh motif: the proton transfer mechanism of HIV-1 RNase H", ACS Catalysis, 11, 7915 (2021). 

• 114. Zhen Chen, Wakana Mori, Jian Rong, Michael A. Schafroth, Tuo Shao, Richard S. Van, Daisuke Ogasawara, Tomoteru Yamasaki, Atsuto Hiraishi, Akiko Hatori, Jiahui Chen, Yiding Zhang, Kuan Hu, Masayuki Fujinaga, Jiyun Sun, Qingzhen Yu, Thomas L. Collier, Yihan Shao, Benjamin F. Cravatt, Lee Josephson, Ming-Rong Zhang,* Steven H. Liang,* "Development of a highly-specific18F-labeledirreversible positron emission tomographytracer for monoacylglycerol lipase mapping", Acta Pharmaceutica Sinica B, 11, 1686 (2021). 

• 113. Zheng Pei, Qi Ou,* Yuezhi Mao,* Junjie Yang, Aurelien de la Lande, Felix Plasser,* Wanzhen Liang,* Zhigang Shuai,* and Yihan Shao,* "Elucidating the Electronic Structure of a Delayed Fluorescence Emitter via Orbital Interactions, Excitation Energy Components, Charge-Transfer Numbers, and Vibrational Reorganization Energies", Journal of Physical Chemistry Letters, 12, 2712 (2021). 

• 112. Tien Le , Yihan Shao, and Bin Wang,* "Plasmon-Induced CO2 Conversion on Al@Cu2O: A DFT Study", Journal of Physical Chemistry C, 125, 6108 (2021).  

• 111. Jia-Ning Wang, Wei Liu,  Pengfei Li, Yan Mo,* Wenxin Hu,  Jun Zheng, Xiaoliang Pan, Yihan Shao, and Ye Mei,* "Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM", Journal of Chemical Theory of Computation, 17, 1318 (2021). 

• 110. Ji-yun Sun, Katsushi Kumata, Zhen Chen, Yi-ding Zhang, Jia-hui Chen, Akiko Hatori, Hua-long Fu, Jian Ron, Xiao-yun Deng, Tomoteru Yamasaki, Lin Xie, Kuan Hu, Masayuki Fujinaga, Qing-zhen Yu, Tuo Shao, Thomas Lee Collier, Lee Josephson, Yihan Shao, Yun-fei Du, Lu Wang, Hao Xu,* Ming-rong Zhang,* and Steven H. Liang,* "Synthesis and preliminary evaluation of novel 11C-labeled GluN2B-selective NMDA receptor negative allosteric modulators", Acta Pharmacologica Sinica 42, 491 (2021).​

• 109. Xiaoliang Pan, Kwangho Nam, Evgeny Epifanovsky, Andrew C. Simmonett, Edina Rosta, and Yihan Shao*, "A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations", Journal of Chemical Physics, 154, 024115 (2021).

[2020]

• 108. Xiaofei Zhang, Yiding Zhang, Zhen Chen, Tuo Shao, Richard Van, Katsushi Kumata, Xiaoyun Deng, Hualong Fu, Tomoteru Yamasaki, Jian Rong, Kuan Hu, Akiko Hatori, Lin Xie, Qingzhen Yu, Weijian Ye, Hao Xu, Douglas J Sheffler, Nicholas D P Cosford, Yihan Shao, Pingping Tang, Lu Wang,* Ming-Rong Zhang,* Steven H Liang,* "Synthesis and preliminary studies of 11C-labeled tetrahydro-1,7-naphthyridine-2-carboxamides for PET imaging of metabotropic glutamate receptor 2", Theranostics, 10, 11178 (2020). 

• 107. Zheng Pei, Junjie Yang, Jingheng Deng, Yuezhi Mao, Qin Wu, Zhibo Yang, Bin Wang, Christine M. Aikens, Wanzhen Liang,* Yihan Shao,* "Analysis and Visualization of  Energy Densities? II. Insights from Linear-Response Time-Dependent Density Functional Theory Calculations", Physical Chemistry Chemical Physics, 22, 26852 (2020).

• 106. Junjie Yang, Zheng Pei, Jingheng Deng, Yuezhi Mao, Qin Wu,  Zhibo Yang, Bin Wang, Christine M. Aikens, Wanzhen Liang,* and Yihan Shao,* "Analysis and Visualization of the Energy Densities. I. Insights from Real-Time Time-Dependent Density Functional Theory Simulations", Physical Chemistry Chemical Physics, 22, 26838 (2020) .

• 105.Wenxin Hu, Pengfei Li,* Jia-Ning Wang, Yuanfei Xu, Yan Mo,* Jun Zheng, Xiaoliang Pan, Yihan Shao, and Ye Mei,* "Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 3. Gaussian Smoothing on Density-of-States", Journal  of Chemical Theory and Computation, 16, 6814 (2020). 

• 104. Yamasaki, T.; Zhang, X.; Kumata, K.; Zhang, Y.; Deng, X.; Fujinaga, M.; Chen, Z.; Mori, W.; Hu, K; Wakizaka, H; Hatori, A.; Xie, L.; Ogawa, M.; Nengaki, N.; Van, R.; Shao, Y.; Sheffler, D. J.; Cosford, N. D. P.; Liang, S. H.  and Zhang, M.-R. "Identification and Development of A New Positron Emission Tomography Ligand 4-(2-Fluoro-4-[11C]methoxyphenyl)-5-((1-methyl-1H-pyrazol-3-yl)methoxy)picolinamide for Imaging of Metabotropic Glutamate Receptor Subtype 2 (mGlu2)", Journal of Medicinal Chemistry, 63, 11469 (2020).

• 103. Jing Yang, Wei Yin, Richard Van, Keyi Yin, Peng Wang, Chao Zheng, Biyue Zhu, Kathleen Ran, Can Zhang, Mohanraja Kumar, Yihan Shao & Chongzhao Ran,* "Turn-on chemiluminescence probes and dualamplification of signal for detection of amyloid beta species in vivo," Nature Communications 11, 4052 (2020).

• 102.  Xiaoyun Deng, Yiding Zhang, Jian Rong, Katsushi Kumata, Tuo Shao, Gangqiang Wang, Akiko Hatori, Wakana Mori, Qingzhen Yu, Kuan Hu, Masayuki Fujinaga, Yihan Shao, Lee Josephson, Shaofa Sun,* Ming-Rong Zhang,*, Steven Liang,*  "Synthesis and preliminary evaluation of 18F-labeled 1-(6,7-dimethyl-4-(methylamino)-1,3-dihydro-2H-pyrrolo[3,4-c]pyridin-2-yl)-2-(trans-2-(6-fluoropyridin-3-yl)cyclopropyl)ethan-1-one for imaging muscarinic acetylcholine receptor subtype 4", Tetrahedron Letters, 61, 152060 (2020).

• 101. Xiaoyun Deng, Yiding Zhang, Zhen Chen, Katsushi Kumata, Richard Van, Jian Rong, Tuo Shao, Akiko Hatori, Wakana Mori, Qingzhen Yu, Kuan Hu, Masayuki Fujinaga, Hsiao-Ying Wey, Yihan Shao, Lee Josephson, Giulia Murtas, Loredano Pollegioni, Ming-Rong Zhang,* Steven Liang*, "Synthesis and preliminary evaluation of 4-hydroxy-6-(3-[11C] methoxyphenethyl)pyridazin-3(2H)-one, a 11C-labeled D-amino acid oxidase (DAAO) inhibitor for PET imaging",  Bioorganic & Medicinal Chemistry Letters, 30, 127326 (2020).

• 100. Zhen Chen, Jiahui Chen, Natalia Mast, Jian Rong, Xiaoyun Deng, Tuo Shao, Hualong Fu, Qingzhen Yu, Jiyun Sun, Yihan Shao, Lee Josephson, Thomas Lee Collier, Irina Pikuleva, Steven H. Liang,⁎ "Synthesis and pharmacokinetic study of a 11C-labeled cholesterol 24-hydroxylase inhibitor using ‘in-loop’ [11C]CO2 fixation method", Bioorganic & Medicinal Chemistry Letters, 30, 127068 (2020).

• 99. Junbo Chen,  Bun Chan*,   Yihan Shao,  Junming Ho*, "How accurate are approximate quantum chemical methods at modelling solute–solvent interactions in solvated clusters?", Physical Chemistry Chemical Physics, 22, 3855 (2020).

• 98. Nicole Bellonzi*, Ethan Alguire, Shervin Fatehi, Yihan Shao, and Joseph E. Subotnik, "TD-DFT spin-adiabats with analytic nonadiabatic derivative coupling", Journal of Chemical Physics, 152, 044112 (2020).

• 97. Yihan Shao,* Ye Mei, Dage Sundholm,* Ville R. I. Kaila,* "Benchmarking the performance of time-dependent density functional theory methods on biochromophores", Journal of Chemical Theory and Computation, 16, 587 (2020). 

• 96. Mingjie Liu, Yihan Shao, and Qin Wu*, "Charge Reduction of Ions in the Ionic Liquid 1-ethy-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide on the Au (111) Surface", Theoretical Chemistry Accounts, 139, Article 24 (2020).

• 95. Yunwen Tao, Zheng Pei, Nicole Bellonzi, Yuezhi Mao*, Zhu Zou, Wanzhen Liang, Zhibo Yang, Yihan Shao*, "Constructing Spin-Adiabatic States for the Modeling of Spin-Crossing Reactions I. A Shared-Orbital Implementation", International Journal of Quantum Chemistry, 120, e26213 (2020).

​

​[2019]

• 94. Zhen Chen, Wakana Mori, Hualong Fu, Michael Andreas Schafroth, Akiko Hatori, Tuo Shao, Genwei Zhang, Richard S. Van, Yiding Zhang, Kuan Hu, Masayuki Fujinaga, Lu Wang, Vasily Belov, Daisuke Ogasawara, Pilar Giffenig, Xiaoyun Deng, Jian Rong, Qingzhen Yu, Xiaofei Zhang, Mikhail I Papisov, Yihan Shao, Thomas Lee Collier, Jun-An Ma, Benjamin F. Cravatt, Lee Josephson, Ming-Rong Zhang*, and Steven H Liang*, "Design, Synthesis and Evaluation of 18F-labeled Monoacylglycerol Lipase Inhibitors as Novel Positron Emission Tomography Probes", Journal of Medicinal Chemistry, 62, 8866 (2019). 

• 93. Zhen Chen, Tuo Shao, Wei Gao, Hualong Fu, Thomas Lee Collier, Jian Rong, Xiaoyun Deng, Qingzhen Yu, Xiaofei Zhang, April T. Davenport, James B. Daunais, Hsiao-Ying Wey, Yihan Shao, Lee Josephson, Wen-Wei Qiu,* and Steven Liang*, "Synthesis and Preliminary Evaluation of [11C]GNE-1023 as a Potent PET Probe for Imaging Leucine-Rich Repeat Kinase 2 (LRRK2) in Parkinson’s Disease", ChemMedChem, 14, 1580 (2019).

• ​92. Hari R. Khatri, Changho Han, Erica Luong, Xiaoliang Pan,Amna T. Adam, Maali D. Alshammari, Yihan Shao, and David A. Colby*, "Controlling the Cleavage of Carbon–Carbon Bonds to Generate α,α-Difluorobenzyl Carbanions for the Construction of Difluoromethylbenzenes", Journal of Organic Chemistry, 84, 11665 (2019).

• ​91. Xiaoliang Pan, Pengfei Li, Junming Ho, Jingzhi Pu*, Ye Mei*, Yihan Shao*, "Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. II. Recalibrating Semi-Empirical Parameters with Force Matching", Physical Chemistry Chemical Physics, 21, 20595 (2019).

• 90. Junbo Chen, Yihan Shao, Junming Ho*, "Are Explicit Solvent Models More Accurate than Implicit Solvent Models? A Case Study on the Menschutkin Reaction", Journal of Physical Chemistry A, 123, 5580 (2019). 

• 89. Pengfei Li, Fengjiao Liu, Yihan Shao, Ye Mei*, "Computational Insights into Endo/Exo Selectivity of Diels--Alder Reaction in Explicit Solvent at ab Initio Quantum Mechanical/Molecular Mechanical Level", Journal of Physical Chemistry B, 123, 5131 (2019).

• 88. Hualong Fu, Weiting Tang, Zhen Chen, Vasily V. Belov, Genwei Zhang, Tuo Shao, Xiaofei Zhang, Qingzhen Yu, Jian Rong, Xiaoyun Deng, Wei Han, Scott J. Myers, Pilar Giffenig, Lu Wang, Lee Josephson, Yihan Shao, April T. Davenport, James B. Daunais, Mikhail Papisov, Hongjie Yuan, Zijing Li*, Stephen F. Traynelis*, and Steven H. Liang*, "Synthesis and Preliminary Evaluations of a Triazole-Cored Antagonist as a PET Imaging Probe ([18F]N2B-0518) for GluN2B Subunit in the Brain", ACS Chemical Neuroscience, 5, 2263 (2019).

• 87. Xiaoyun Deng, Akiko Hatori, Zhen Chen, Katsushi Kumata, Tuo Shao, Xiaofei Zhang, Tomoteru Yamasaki, Kuan Hu, Qingzhen Yu, Longle Ma, Gangqiang Wang, Lu Wang, Yihan Shao, Lee Josephson, Shaofa Sun*, Ming‐Rong Zhang*, Steven Liang*, "Synthesis and Preliminary Evaluation of 11C‐Labeled VU0467485/AZ13713945 and Its Analogues for Imaging Muscarinic Acetylcholine Receptor Subtype 4", ChemMedChem, 14, 303 (2019). 

• 86. Zhen Chen, Wakana Mori, Xiaoyun Deng, Ran Cheng, Daisuke Ogasawara, Genwei Zhang, Michael A. Schafroth, Kenneth Dahl, Hualong Fu, Akiko Hatori, Tuo Shao, Yiding Zhang, Tomoteru Yamasaki,  Xiaofei Zhang, Jian Rong, Qingzhen Yu, Kuan Hu, Masayuki Fujinaga, Lin Xie, Katsushi Kumata, Yuancheng Gou, Jingjin Chen, Shuyin Gu, Liang Bao, Lu Wang, Thomas Lee Collier, Neil Vasdev , Yihan Shao, Jun-An Ma, Benjamin F. Cravatt, Christopher Fowler, Lee Josephson, Ming-Rong Zhang*, and Steven H. Liang*,  "Design, Synthesis and Evaluation of Reversible and Irreversible Monoacylglycerol Lipase Positron Emission Tomography (PET) Tracers Using a ‘Tail Switching’ Strategy on a Piperazinyl Azetidine Skeleton",  Journal of Medicinal Chemistry, 62, 3336 (2019).

• 85. Vardhan Satalkar, Theo A. Rushmore, Elizabeth Phillips, Xiaoliang Pan, Enrico Benassi, Qin Wu, Chongzhao Ran*, Yihan Shao*, Computational modeling of curcumin‑based fluorescent probe molecules, Theoretical Chemistry Accounts, 138, 29 (2019). ​

[2018]

• 84. Pengfei Li, Xiangyu Jia, Xiaoliang Pan, Yihan Shao, and Ye Mei*, "Accelerated Computation of Free Energy Profile at ab initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. I. Weighted Thermodynamics Perturbation", Journal of Chemical Theory and Computation, 14, 5583 (2018).

• 83. Xiaoliang Pan, Edina Rosta, Yihan Shao*, "Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations", Molecules, 23, 2500 (2018).

• 82. Pengfei Li, Fengjiao Liu, Xiangyu Jia, Yihan Shao, Wenxin Hu*, Jun Zheng, Ye Mei*,   "Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level", Molecules, 23, 2487 (2018).

• 81. Junming Ho*, Yihan Shao, Jin Kato,  "Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters", Molecules, 23, 2466 (2018).

• 80. Yuezhi Mao, Martin Head-Gordon, Yihan Shao*, "Unraveling Substituent Effects on Frontier Orbitals of Conjugated Molecules Using an Absolutely Localized Molecular Orbital Based Analysis", Chemical Science, 9, 8598 (2018). 

• 79.  Zhen Chen, Wakana Mori, Xiaofei Zhang, Tomoteru Yamasaki, Patrick J. Dunn, Genwei Zhang, Hualong Fu, Tuo Shao, Yiding Zhang, Akiko Hatori, Longle Ma, Masayuki Fujinaga, Lin Xie, Xiaoyun Deng, Hua Li, Qingzhen Yu, Jian Rong, Lee Josephson, Jun-An Ma, Yihan Shao, Susumu Tomita, Ming-Rong Zhang,* Steven H. Liang*, "Synthesis, pharmacology and preclinical evaluation of 11C-labeled 1,3-dihydro-2H-benzo[d]imidazole-2-ones for imaging γ8-dependent transmembrane AMPA receptor regulatory protein", European Journal of Medicinal Chemistry, 157, 898 (2018). 

• 78.  Xiang Tian, Genwei Zhang, Yihan Shao*, Zhibo Yang*, "Towards Enhanced Metabolomic Data Analysis of Mass Spectrometry Image: Multivariate Curve Resolution and Machine Learning", Analytica Chimica Acta, 1037, 211 (2018).

[2017]

• 77. Jian Yang, Xueli Zhang, Peng Yuan, Jing Yang, Yungen Xu, Jaime Grutzendler, Yihan Shao, Anna Moore, and Chongzhao Ran*, "Oxalate-curcumin based probe for micro- and macro-imaging of reactive oxygen species in Alzheimers disease", Proc. Nat. Acad. Sci. 114, 12384 (2017). 

• 76. Meiting Wang, Pengfei Li, Xiangyu Jia, Wei Liu, Yihan Shao, Wenxin Hu, Jun Zheng, Bernard R. Brooks, and Ye Mei*, "Efficient Strategy for the Calculation of Salvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level", J. Chem. Inf. Model. 57, 2476 (2017). 

• 75. Yuezhi Mao, Yihan Shao*, Jacek Dziedzic, Chris-Kriton Skylarks, Teresa Head-Gordon, and Martin Head-Gordon*, "Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis", J. Chem. Theory Comput., 13, 1963 (2017). 

• 74. Jing Huang, Ye Mei, Gerhard Koenig, Andrew C. Simmonett, Frank C Pickard, Qin Wu, Lee-Ping Wang, Alexander D. MacKerell, Bernard R. Brooks, and Yihan Shao*, "An Estimation of Hybrid Quantum Mechanical Molecular Mechanical (QM/MM) Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches", J. Chem. Theory Comput., 13, 679 (2017).  

[2016] 

• 73. Frank C. Pickard, Gerhard König, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder, Bernard R. Brooks, "Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pKa corrections",  J. Comput.-Aided Mol. Design, 30, 1087 (2016).

• 72. Frank C. Pickard, Gerhard König, Andrew C. Simmonett, Yihan Shao, Bernard R. Brooks, "An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations", Bioorganic & Medicinal Chemistry, 24, 4988 (2016). 

--- Yihan Joined the University of Oklahoma ---

• 71. Gerhard König, Frank C. Pickard IV, Jing Huang, Andrew C. Simmonett, Florentina Tofoleanu, Juyong Lee, Pavlo O. Dral, Samarjeet Prasad, Michael Jones, Yihan Shao, Walter Thiel, Bernard R. Brooks, "Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge", J. Comput.-Aided Mol. Design, 30, 989 (2016). 

• 70. Jacek Dziedzic, Yuezhi Mao, Yihan Shao, Jay Ponder, Teresa Head-Gordon, Martin Head-Gordon and Chris-Kriton Skylaris, "TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field", J. Chem. Phys. 145, 124106 (2016).

• 69.Alex Albaugh, Henry A. Boateng, Richard T Bradshaw, Omar N. Demerdash, Jacek Dziedzic, Yuezhi Mao, Daniel Toby Margul, Jason M Swails, Qiao Zeng, David A. Case, Peter Kenneth Eastman, Jonathan W. Essex, Martin Head-Gordon, Vijay S. Pande, Jay William Ponder, Yihan Shao, Chris-Kriton Skylaris, Ilian T. Todorov, Mark Edward Tuckerman, and Teresa Head-Gordon, "Advanced Potential Energy Surfaces for Molecular Simulation", J. Phys. Chem. B, 120, 9811 (2016).

• 68. Pradeep Kumar Gurunathan, Atanu Acharya, Debashree Ghosh, Dmytro Kosenkov, Ilya Kaliman, Yihan Shao, Anna I. Krylov, and Lyudmila V. Slipchenko, "Extension of the Effective Fragment Potential Method to Macromolecules", J. Phys. Chem. B, 120, 6562 (2016). 

• 67. Xiangyu Jia, Meiting Wang, Yihan Shao, Gerhard Koenig, Bernard R. Brooks, John Z. H. Zhang, and Ye Mei,"Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics", J. Chem. Theory Comput., 12, 499 (2016). 

• 66. Gerhard König,Ye Mei,Frank C. Pickard IV, Andrew C. Simmonett, Benjamin T. Miller, John M. Herbert, H. Lee Woodcock, Bernard R. Brooks and Yihan Shao, "Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical / Molecular Mechanical Method", J. Chem. Theory Comput., 12, 332 (2016).

[2015]

• 65. Zhibo Liu, Haojun Chen, Kai Chen, Yihan Shao, Dale O. Kiesewetter, Gang Niu, and Xiaoyuan Chen, "Boramino acid as a marker for amino acid transporters", Sci. Adv., 1:e1500694 (2015).

• 64. Kristina Closser, Qinghui Ge, Yuezhi Mao, Yihan Shao and Martin Head-Gordon, "Superposition of Fragment Excitations for Excited States of Large Clusters with Application to Helium Clusters", J. Chem. Theory Comput., 11, 5791 (2015).

• 63. Andrew C. Simmonett, Frank C. Pickard IV, Yihan Shao, Thomas E. Cheatham III and Bernard R. Brooks, "Efficient treatment of induced dipoles", J. Chem. Phys. 143, 074115 (2015).

• 62. Ye Mei, Andrew C. Simmonett, Frank C. Pickard, IV, Robert A. DiStasio, Jr., Bernard R. Brooks, and Yihan Shao,"Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions", J. Phys. Chem. A 119, 5865 (2015).

• 61. Alexander J. Sodt, Ye Mei, Gerhard König, Peng Tao, Ryan P. Steele, Bernard R. Brooks, and Yihan Shao, "Multiple Environment Single System Quantum Mechanical/molecular Mechanical (MESS-QM/MM) Calculations. I. Estimation of Polarization Energies", J. Phys. Chem. A 119, 1511 (2015).

• 60. Yihan Shao, Zhengting Gan, Evgeny Epifanovsky, Andrew T.B. Gilbert, Michael Wormit, Joerg Kussmann, Adrian W. Lange, Andrew Behn, Jia Deng, Xintian Feng, Debashree Ghosh, Matthew Goldey, Paul R. Horn, Leif D. Jacobson, Ilya Kaliman, Rustam Z. Khaliullin, Tomasz Kus, Arie Landau, Jie Liu, Emil I. Proynov, Young Min Rhee, Ryan M. Richard, Mary A. Rohrdanz, Ryan P. Steele, Eric J. Sundstrom, H. Lee Woodcock III, Paul M. Zimmerman, Dmitry Zuev, Ben Albrecht, Ethan Alguire, Brian Austin, Gregory J. O. Beran, Yves A. Bernard, Eric Berquist, Kai Brandhorst, Ksenia B. Bravaya, Shawn T. Brown, David Casanova, Chun-Min Chang, Yunqing Chen, Siu Hung Chien, Kristina D. Closser, Deborah L. Crittenden, Michael Diedenhofen, Robert A. DiStasio Jr., Hainam Do, Anthony D. Dutoi, Richard G. Edgar, Shervin Fatehi, Laszlo Fusti-Molnar, An Ghysels, Anna Golubeva-Zadorozhnaya, Joseph Gomes, Magnus W.D. Hanson-Heine, Philipp H.P. Harbach, Andreas W. Hauser, Edward G. Hohenstein, Zachary C. Holden, Thomas-C. Jagau, Hyunjun Ji, Ben Kaduk, Kirill Khistyaev, Jaehoon Kim, Jihan Kim, Rollin A. King, Phil Klunzinger, Dmytro Kosenkov, Tim Kowalczyk, Caroline M. Krauter, Ka Un Lao, Adele Laurent, Keith V. Lawler, Sergey V. Levchenko, Ching Yeh Lin, Fenglai Liu, Ester Livshits, Rohini C. Lochan, Arne Luenser, Prashant Manohar, Samuel F. Manzer, Shan-Ping Mao, Narbe Mardirossian, Aleksandr V. Marenich, Simon A. Maurer, Nicholas J. Mayhall, Eric Neuscamman, C. Melania Oana, Roberto Olivares-Amaya, Darragh P. O'Neill, John A. Parkhill, Trilisa M. Perrine, Roberto Peverati, Alexander Prociuk, Dirk R. Rehn, Edina Rosta, Nicholas J. Russ, Shaama M. Sharada, Sandeep Sharma, David W. Small, Alexander Sodt, Tamar Stein, David Stuck, Yu-Chuan Su, Alex J.W. Thom, Takashi Tsuchimochi, Vitalii Vanovschi, Leslie Vogt, Oleg Vydrov, Tao Wang, Mark A. Watson, Jan Wenzel, Alec White, Christopher F. Williams, Jun Yang, Sina Yeganeh, Shane R. Yost, Zhi-Qiang You, Igor Ying Zhang, Xing Zhang, Yan Zhao, Bernard R. Brooks, Garnet K.L. Chan, Daniel M. Chipman, Christopher J. Cramer, William A. Goddard III, Mark S. Gordon, Warren J. Hehre, Andreas Klamt, Henry F. Schaefer III, Michael W. Schmidt, C. David Sherrill, Donald G. Truhlar, Arieh Warshel, Xin Xu, Alan Aspuru-Guzik, Roi Baer, Alexis T. Bell, Nicholas A. Besley, Jeng-Da Chai, Andreas Dreuw, Barry D. Dunietz, Thomas R. Furlani, Steven R. Gwaltney, Chao-Ping Hsu, Yousung Jung, Jing Kong, Daniel S. Lambrecht, WanZhen Liang, Christian Ochsenfeld, Vitaly A. Rassolov, Lyudmila V. Slipchenko, Joseph E. Subotnik, Troy Van Voorhis, John M. Herbert, Anna I. Krylov, Peter M.W. Gill and Martin Head-Gordon, "Advances in molecular quantum chemistry contained in the Q-Chem 4 program package", Mol. Phy. 113, 184 (2015).

[2014]

• 59. Peng Tao, Alexander J. Sodt, Yihan Shao, Gerhard Koenig, and Bernard R. Brooks, "Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics", J. Chem. Theory Comput. 10, 41983 (2014).

• 58. Qi Ou, Shervin Fatehi, Ethan Alguire, Yihan Shao and Joseph E. Subotnik, "Derivative couplings between TDDFT excited states obtained by direct differentiation in the Tamm-Dancoff approximation", J. Chem. Phys. 141, 024114 (2014).

• 57. Dmitry Zuev, Thomas-C. Jagau, Ksenia B. Bravaya, Evgeny Epifanovsky, Yihan Shao, Eric Sundstrom, Martin Head-Gordon, and Anna I. Krylov, "Complex absorbing potentials within EOM-CC family of methods: Theory, implementation, and benchmarks", J. Chem. Phys. 141, 024102 (2014).  Erratum

• 56. Ethan C. Alguire, Shervin Fatehi, Yihan Shao, and Joseph E. Subotnik, "Analysis of Localized Diabatic States beyond the Condon Approximation for Excitation Energy Transfer Processes", J. Phys. Chem. A 118, 11891 (2014).

• 55. Matthew Goldey, Robert A. DiStasio, Jr., Yihan Shao, and Martin Head-Gordon, "Shared memory multiprocessing implementation of resolution-of-the-identity second-order Moller-Plesset perturbation theory with attenuated and unattenuated results for intermolecular interactions between large molecules", Mol. Phys. 112, 836 (2014).

[2013]

• 54. Evgeny Epifanovsky, Dmitry Zuev, Xintian Feng, Kirill Khistyaev, Yihan Shao, and Anna I. Krylov, General implementation of the resolution-of-the-identity and Cholesky representations of electron repulsion integrals within coupled-cluster and equation-of-motion methods: Theory and benchmarks", J. Chem. Phys. 139, 134105 (2013).

• 53. Yuanhang Huang, Yihan Shao, and Gregory J. O. Beran, "Accelerating MP2C dispersion corrections for dimers and molecular crystals", J. Chem. Phys. 138, 224112 (2013).

• 52. Seoin Back, Johan A. Schmidt, Hyunjun Ji, Jiyoung Heo, Yihan Shao, and Yousung Jung, "On the structure of Si(100) surface: Importance of higher order correlations for buckled dimer", J. Chem. Phys. 138, 204709 (2013).

• 51. Hyunjun Ji, Yihan Shao, William A. Goddard, and Yousung Jung, "Analytic Derivatives of Quartic-Scaling Doubly Hybrid XYGJ-OS Functional: Theory, Implementation, and Benchmark Comparison with M06-2X and MP2 Geometries for Nonbonded Complexes", J. Chem. Theory Comput. 9, 1971 (2013).

• 50. Debashree Ghosh, Dmytro Kosenkov, Vitalii Vanovschi, Joanna Flick, Ilya Kaliman, Yihan Shao, Andrew T.B. Gilbert, Anna I. Krylov, and Lyudmila V. Slipchenko, "Effective fragment potential method in Q-CHEM: A guide for users and developers", J. Comput. Chem. 34, 1060 (2013).

[2012]

• 49. Peng Tao, Milan Hodoscek, Joseph D. Larkin, Yihan Shao, and Bernard R. Brooks, "Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints", J. Chem. Theory Comput. 8, 5035 (2012).

• 48. Shushu Zhang, Zexing Qu, Peng Tao, Bernard Brooks, Yihan Shao, Xiaoyuan Chen, and Chungen Liu, "Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes", J. Phys. Chem. C, 116, 12434 (2012).

• 47. Yves A. Bernard, Yihan Shao, and Anna I. Krylov, "General formulation of spin-flip time-dependent density functional theory using non-collinear kernels: Theory, implementation, and benchmarks", J. Chem. Phys. 136, 204103 (2012). 

• 46. Xinle Liu, Shervin Fatehi, Yihan Shao, Brad S. Veldkamp, and Joseph E. Subotnik, "Adjusting charge transfer state energies for configuration interaction singles: Withoua any parameterization and with minimal cost", J. Chem. Phys. 136, 161101 (2012). 

• 45. Chun-Min Chang, Yihan Shao, and Jing Kong, "Ewald mesh method for quantum mechanical calculations" , J. Chem. Phys. 136, 114112 (2012).

• 44. Emil Proynov, Fenglai Liu, Yihan Shao and Jing Kong, "Improved self-consistent and resolution-of-identity approximated Becke'05 density functional model of nondynamic electron correlation" , J. Chem. Phys. 136, 034102 (2012). 

[2011]

• 43. Shervin Fatehi, Ethan Alguire, Yihan Shao and Joseph E. Subotnik, "Analytic derivative couplings between configuration-interaction-singles states with built-in electron-translation factors for translational invariance", J. Chem. Phys. 135, 234105 (2011).

• 42. An Ghysels, H. Lee Woodcock III, Joseph D. Larkin, Benjamin T. Miller, Yihan Shao, Jing Kong, Dimitri Van Neck, Veronique Van Speybroeck, Michel Waroquier and Bernard R. Brooks, "Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian", J. Chem. Theory Comput. 7, 496 (2011).

[2010] 

• 41. Fenglai Liu, Zhengting Gan, Yihan Shao, Chao-Ping Hsu, Andreas Dreuw, Martin Head-Gordon, Benjamin T. Miller, Bernard R. Brooks, Jian-Guo Yu, Thomas R. Furlani and Jing Kong, "A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm-Dancoff approximation", Mol. Phys. 108, 2791 (2010).

• 40. Emil Proynov, Yihan Shao and Jing Kong, "Efficient self-consistent DFT calculation of nondynamic correlation based on the B05 method", Chem. Phys. Lett. 493, 381 (2010).

• 39. Roberto Olivares-Amaya, Mark A. Watson, Richard G. Edgar, Leslie Vogt, Yihan Shao and Alan Aspuru-Guzik,"Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library", J. Chem. Theory Comput. 6, 135 (2010).

[2008] 

• 38. H. Lee Woodcock, Wenjun Zheng, An Ghysels, Yihan Shao, Jing Kong and Bernard R. Brooks, "Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit", J. Chem. Phys. 129, 214109 (2008).

• 37. Leslie Vogt, Roberto Olivares-Amaya, Sean Kermes, Yihan Shao, Carlos Amador-Bedolla and Alan Aspuru-Guzik,"Accelerating Resolution-of-the-Identity Second-Order Moller-Plesset Quantum Chemistry Calculations with Graphical Processing Unit", J. Phys. Chem. A, 112, 2049 (2008).

• 36. Marek Freindorf, Yihan Shao, Jing Kong, Thomas R. Furlani, "Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin", J. Inorg. Chem. 102, 427 (2008).

[2007] 

• 35. Yousung Jung, Yihan Shao and Martin Head-Gordon, "Fast evaluation of scaled opposite spin second-order Moller-Plesset correlation energies using auxiliary basis expansions and exploiting sparsity", J. Comput. Chem. 28, 1953 (2007).

• 34. Rohini C. Lochan, Yihan Shao and Martin Head-Gordon, "Quartic-Scaling Analytical Energy Gradient of Scaled Opposite-Spin Second-Order Moller-Plesset Perturbation Theory", J. Chem. Theory Comput. 3, 988 (2007).

• 33. Yihan Shao and Jing Kong, "YinYang Atom: A Simple Combined ab Initio Quantum Mechanical Molecular Mechanical Model",  J. Phys. Chem. A, 111, 3661 (2007).

• 32. Robert A. Distasio Jr., Ryan P. Steele, Young Min Rhee, Yihan Shao and Martin Head-Gordon, "An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Moller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis", J. Comput. Chem. 28, 839 (2007).

[2006]

• 31. Ryan P. Steele, Yihan Shao, Robert A. DiStasio Jr. and Martin Head-Gordon, "Dual-Basis Analytic Gradients. 1. Self-Consistent Field Theory", J. Phys. Chem. A, 110, 13915 (2006).

• 30. Ryan P. Steele, Robert A. DiStasio, Yihan Shao, Jing Kong and Martin Head-Gordon, "Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations", J. Chem. Phys. 125, 074108 (2006).

• 29. Yihan Shao, Laszlo Fusti Molnar, Yousung Jung, Joerg Kussmann, Christian Ochsenfeld, Shawn T. Brown, Andrew T.B. Gilbert, Lyudmila V. Slipchenko, Sergey V. Levchenko, Darragh P. O’Neill, Robert A. DiStasio Jr, Rohini C. Lochan, Tao Wang, Gregory J.O. Beran, Nicholas A. Besley, John M. Herbert, Ching Yeh Lin, Troy Van Voorhis, Siu Hung Chien, Alex Sodt, Ryan P. Steele, Vitaly A. Rassolov, Paul E. Maslen, Prakashan P. Korambath, Ross D. Adamson, Brian Austin, Jon Baker, Edward F. C. Byrd, Holger Dachsel, Robert J. Doerksen, Andreas Dreuw, Barry D. Dunietz, Anthony D. Dutoi, Thomas R. Furlani, Steven R. Gwaltney, Andreas Heyden, So Hirata, Chao-Ping Hsu, Gary Kedziora, Rustam Z. Khalliulin, Phil Klunzinger, Aaron M. Lee, Michael S. Lee, WanZhen Liang, Itay Lotan, Nikhil Nair, Baron Peters, Emil I. Proynov, Piotr A. Pieniazek, Young Min Rhee, Jim Ritchie, Edina Rosta, C. David Sherrill, Andrew C. Simmonett, Joseph E. Subotnik, H. Lee Woodcock III, Weimin Zhang, Alexis T. Bell, Arup K. Chakraborty, Daniel M. Chipman, Frerich J. Keil, Arieh Warshel, Warren J. Hehre, Henry F. Schaefer III, Jing Kong, Anna I. Krylov, Peter M. W. Gill and Martin Head-Gordon, “Advances in methods and algorithms in a modern quantum chemistry program package", Phys. Chem. Chem. Phys. 8, 3172 (2006).

• 28. Marek Freindorf , Yihan Shao, Shawn T. Brown, Jing Kong, Thomas R. Furlani, “A combined density functional theory and molecular mechanics (QM/MM) study of FeCO vibrations in carbonmonoxy myoglobin", Chem. Phys. Lett. 419, 563 (2006).

[2005]

• 27. Marek Freindorf , Yihan Shao, Thomas R. Furlani and Jing Kong, “Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential", J. Comput. Chem. 26, 1270 (2005).

• 26. Paul E. Maslen, Anthony D. Dutoi, Michael S. Lee, Yihan Shao and Martin Head-Gordon, “Accurate local approximations to the triples correlation energy: formulation, implementation and tests of 5th-order scaling models", Mol. Phys. 103, 425 (2005).

[2004]

• 25. Zhi-Qiang You, Yihan Shao and Chao-Ping Hsu , “Calculating electron transfer couplings by the Spin-Flip approach: energy splitting and dynamical correlation effects", Chem. Phys. Lett. 390, 116 (2004).

• 24. Ana-Maria C. Cristian, Yihan Shao and Anna I. Krylov , “Bonding Patterns in Benzene Triradicals from Structural, Spectroscopic, and Thermochemical Perspectives", J. Phys. Chem. A, 108, 6581 (2004).

• 23. Joseph E. Subotnik, Yihan Shao, WanZhen Liang and Martin Head-Gordon , “An efficient method for calculating maxima of homogeneous functions of orthogonal matrices: Applications to localized occupied orbitals", J. Chem. Phys. 121, 9220 (2004).

• 22. WanZhen Liang, Roi Baer, Chandra Saravanana, Yihan Shao, Alexis T Bell and Martin Head-Gordon , “Fast methods for resumming matrix polynomials and Chebyshev matrix polynomials", J. Comput. Phys. 194, 575 (2004).

[2003]

• 21. Yousung Jung, Yihan Shao, Mark S. Gordon, Douglas J. Doren and Martin Head-Gordon, “Are both symmetric and buckled dimers on Si(100) minima? Density functional and multireference perturbation theory calculations", J. Chem. Phys. 119, 10917 (2003).

• 20. Yihan Shao, Chandra Saravanan, Martin Head-Gordon  and Christopher A. White, “Curvy steps for density matrix-based energy minimization: Application to large-scale selfconsistent-field calculations", J. Chem. Phys. 118, 6144 (2003).

• 19. Martin Head-Gordon , Yihan Shao, Chandra Saravanan and Christopher A. White, “Curvy steps for density matrix based energy minimization: tensor formulation and toy applications", Mol. Phys. 101, 37 (2003).

• 18. Chandra Saravanan, Yihan Shao, Roi Baer, Philip N. Ross, Martin Head-Gordon, “Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks", J. Comput. Chem. 24, 618 (2003).

• 17. Yihan Shao, Martin Head-Gordon and Anna I. Krylov , “The spin-flip approach within time-dependent density functional theory: Theory and applications to diradicals", J. Chem. Phys. 118, 4807 (2003).

• 16. WanZhen Liang, Chandra Saravanan, Yihan Shao, Roi Baer, Alexis T. Bell and Martin Head-Gordon , “Improved Fermi operator expansion methods for fast electronic structure calculations", J. Chem. Phys. 119, 4117 (2003).

[2002]

• 15. WanZhen Liang, Yihan Shao, Christian Ochsenfeld, Alexis T. Bell and Martin Head-Gordon , “Fast evaluation of a linear number of local exchange matrices", Chem. Phys. Lett. 358, 43 (2002).

[2001]

• 14. Yihan Shao, Christopher A. White and Martin Head-Gordon , “Efficient evaluation of the Coulomb force in density-functional theory calculations", J. Chem. Phys. 114, 6572 (2001).

[2000]

• 13. Yihan Shao and Martin Head-Gordon , “An improved J matrix engine for density functional theory calculations", Chem. Phys. Lett. 323, 425 (2000).

• 12. Jing Kong, Christopher A. White, Anna I. Krylov, David Sherrill, Ross D. Adamson, Thomas R. Furlani, Michael S. Lee, Aaron M. Lee, Steven R. Gwaltney, Terry R. Adams, Christian Ochsenfeld, Andrew T. B. Gilbert, Gary S. Kedziora, Vitaly A. Rassolov, David R. Maurice, Nikhil Nair, Yihan Shao, Nicholas A. Besley, Paul E. Maslen, Jeremy P. Dombroski, Holger Daschel, Weimin Zhang, Prakashan P. Korambath, Jon Baker, Edward F. C. Byrd, Troy Van Voorhis, Manabu Oumi, So Hirata, Chao-Ping Hsu, Naoto Ishikawa, Jan Florian, Arieh Warshel, Benny G. Johnson, Peter M. W. Gill, Martin Head-Gordon  and John A. Pople, “Q-Chem 2.0: a high-performance ab initio electronic structure program package", J. Comput. Chem. 21, 1532 (2000).

[1996]

• 11. Yihan Shao, Jian Wu and Yuansheng Jiang , “Enumeration and Symmetry of Substitution Isomers", J. Phys. Chem. 100, 15064 (1996).

• 10. Yihan Shao and Yuansheng Jiang , “Enumeration of B24-mNm Cages", J. Phys. Chem. 100, 1554 (1996).

• 9. Yihan Shao, Jian Wu and Yuansheng Jiang , “Isomer counting and isomer permutation representation", Chem. Phys. Lett. 248, 366 (1996).

• 8. Chungen Liu, Yihan Shao and Yuansheng Jiang , “Factorization of the Hueckel Hamiltonian matrix for highly symmetrical molecules", Croat. Chem. Acta, 69, 201 (1996).

[1995]

• 7. Yihan Shao and Yuansheng Jiang , “Symmetry of hydrogenated C60", Chem. Phys. Lett. 242, 191 (1995).

• 6. Yuansheng Jiang , Xiaoliang Qian and Yihan Shao, “The evaluation of moments for benzenoid hydrocarbons", Theoret. Chim. Acta, 90, 135 (1995).

• 5. Yuansheng Jiang , Chungen Liu and Yihan Shao, “Analyitcal solution of graph spectra for fullerenes", Prog. in Phys. (in Chinese), 15, 307 (1995).

[1994]

• 4. Chungen Liu, Yihan Shao and Yuansheng Jiang , “Analytical solution of graph spectra for fullerenes", Chem. Phys. Lett. 228, 131 (1994).

• 3. Chungen Liu, Miaomiao Wang, Yihan Shao and Yuansheng Jiang , “Factorization of the Hueckel Hamiltonian matrix for C540", Phys. Lett. A, 196, 120 (1994).

• 2. Yuansheng Jiang , Yihan Shao and Edward C. Kirby, “Topology and Stability of Trivalent Polyhedral Clusters", Fullerene Sci. Tech. 2, 481 (1994).

• 1. Jun Liu, Yihan Shao and Yuansheng Jiang , “Exact solution of graph spectrum of C60", Chem. Phys. Lett. 210, 149 (1993).