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Lee-Ping Wang, Ph.D - Publications

Affiliations: 
2015- Chemistry University of California, Davis, Davis, CA 
Website:
http://www.lpwchem.org/
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57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang LP, Cole DJ, Gilson MK, et al. Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of Chemical Theory and Computation. PMID 37167319 DOI: 10.1021/acs.jctc.3c00039  0.72
2022 Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. Journal of Chemical Theory and Computation. PMID 35533269 DOI: 10.1021/acs.jctc.1c01268  0.719
2022 Boothroyd S, Wang LP, Mobley DL, Chodera JD, Shirts MR. Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. Journal of Chemical Theory and Computation. PMID 35507313 DOI: 10.1021/acs.jctc.1c01111  0.73
2021 Smith DGA, Lolinco AT, Glick ZL, Lee J, Alenaizan A, Barnes TA, Borca CH, Di Remigio R, Dotson DL, Ehlert S, Heide AG, Herbst MF, Hermann J, Hicks CB, Horton JT, ... ... Wang LP, et al. Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. The Journal of Chemical Physics. 155: 204801. PMID 34852489 DOI: 10.1063/5.0059356  0.756
2021 Caceres-Delpiano J, Wang LP, Essex JW. The automated optimisation of a coarse-grained force field using free energy data. Physical Chemistry Chemical Physics : Pccp. PMID 34723311 DOI: 10.1039/d0cp05041e  0.324
2021 Stoppelman JP, Ng TT, Nerenberg PS, Wang LP. Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids. The Journal of Physical Chemistry. B. PMID 34668708 DOI: 10.1021/acs.jpcb.1c07547  0.307
2021 Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, ... ... Wang LP, et al. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. Journal of Chemical Theory and Computation. PMID 34551262 DOI: 10.1021/acs.jctc.1c00571  0.724
2020 Qiu Y, Smith DGA, Stern CD, Feng M, Jang H, Wang LP. Driving torsion scans with wavefront propagation. The Journal of Chemical Physics. 152: 244116. PMID 32610969 DOI: 10.1063/5.0009232  0.43
2020 Liou SH, Chuo SW, Qiu Y, Wang LP, Goodin DB. Linkage Between Proximal and Distal Movements of P450cam Induced by Putidaredoxin. Biochemistry. PMID 32369344 DOI: 10.1021/Acs.Biochem.0C00294  0.323
2020 Hutchings M, Liu J, Qiu Y, Song C, Wang LP. Bond order time series analysis for detecting reaction events in ab initio molecular dynamics simulations. Journal of Chemical Theory and Computation. PMID 32003992 DOI: 10.1021/Acs.Jctc.9B01039  0.389
2020 Kantonen SM, Muddana HS, Schauperl M, Henriksen NM, Wang LP, Gilson MK. Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters. Journal of Chemical Theory and Computation. PMID 31917572 DOI: 10.1021/Acs.Jctc.9B00713  0.403
2020 Seritan S, Bannwarth C, Fales BS, Hohenstein EG, Isborn CM, Kokkila‐Schumacher SIL, Li X, Liu F, Luehr N, Snyder JW, Song C, Titov AV, Ufimtsev IS, Wang L, Martínez TJ. TeraChem : A graphical processing unit ‐accelerated electronic structure package for large‐scale ab initio molecular dynamics Wires Computational Molecular Science. 11. DOI: 10.1002/wcms.1494  0.743
2019 Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson M. Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. Journal of Chemical Theory and Computation. PMID 31603667 DOI: 10.1021/Acs.Jctc.9B00748  0.631
2019 Wang LP, Song C. Car-Parrinello Monitor for more robust Born-Oppenheimer molecular dynamics. Journal of Chemical Theory and Computation. PMID 31318557 DOI: 10.1021/Acs.Jctc.9B00439  0.42
2019 Qiu Y, Nerenberg PS, Head-Gordon T, Wang LP. Systematic Optimization of Water Models Using Liquid/Vapor Surface Tension Data. The Journal of Physical Chemistry. B. PMID 31314516 DOI: 10.1021/Acs.Jpcb.9B05455  0.362
2019 Chuo SW, Wang LP, Britt RD, Goodin DB. An Intermediate Conformational State of Cytochrome P450cam-CN in Complex with Putidaredoxin. Biochemistry. PMID 30994334 DOI: 10.1021/Acs.Biochem.9B00192  0.304
2019 Xu Z, Luo N, Federman SR, Jackson WM, Ng C, Wang L, Crabtree KN. Ab Initio Study of Ground-state CS Photodissociation via Highly Excited Electronic States The Astrophysical Journal. 882: 86. DOI: 10.3847/1538-4357/Ab35Ea  0.325
2018 Wade AD, Wang LP, Huggins DJ. Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties. Journal of Chemical Information and Modeling. PMID 30113842 DOI: 10.1021/Acs.Jcim.8B00166  0.41
2018 Qiu Y, Schwegler BR, Wang LP. Polarizable Molecular Simulations Reveal How Silicon-containing Functional Groups Govern the Desalination Mechanism in Nanoporous Graphene. Journal of Chemical Theory and Computation. PMID 29894622 DOI: 10.1021/Acs.Jctc.8B00226  0.356
2018 Jang H, Qiu Y, Hutchings ME, Nguyen M, Berben LA, Wang LP. Quantum chemical studies of redox properties and conformational changes of a four-center iron CO reduction electrocatalyst. Chemical Science. 9: 2645-2654. PMID 29732050 DOI: 10.1039/C7Sc04342B  0.378
2017 Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. Plos Computational Biology. 13: e1005659. PMID 28746339 DOI: 10.1371/Journal.Pcbi.1005659  0.691
2017 Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. The Journal of Physical Chemistry. B. PMID 28306259 DOI: 10.1021/Acs.Jpcb.7B02320  0.686
2017 Huang J, Mei Y, Koenig G, Simmonett AC, Pickard FC, Wu Q, Wang LP, MacKerell AD, Brooks BR, Shao Y. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical (QM/MM) Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. Journal of Chemical Theory and Computation. PMID 28081366 DOI: 10.1021/Acs.Jctc.6B01125  0.417
2017 Demerdash O, Wang L, Head‐Gordon T. Advanced models for water simulations Wires Computational Molecular Science. 8. DOI: 10.1002/Wcms.1355  0.458
2016 McKiernan KA, Wang LP, Pande VS. Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field. Journal of Chemical Theory and Computation. PMID 27786477 DOI: 10.1021/Acs.Jctc.6B00801  0.528
2016 Wang LP, Song C. Geometry optimization made simple with translation and rotation coordinates. The Journal of Chemical Physics. 144: 214108. PMID 27276946 DOI: 10.1063/1.4952956  0.373
2015 Wang LP, McGibbon RT, Pande VS, Martínez TJ. Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways. Journal of Chemical Theory and Computation. PMID 26683346 DOI: 10.1021/Acs.Jctc.5B00830  0.657
2015 Song C, Wang LP, Martínez TJ. Automated Code Engine for Graphical Processing Units: Application to the Effective Core Potential Integrals and Gradients. Journal of Chemical Theory and Computation. PMID 26586267 DOI: 10.1021/Acs.Jctc.5B00790  0.473
2015 Kokkila Schumacher SI, Hohenstein EG, Parrish RM, Wang LP, Martínez TJ. Tensor Hypercontraction Second-Order Møller-Plesset Perturbation Theory: Grid Optimization and Reaction Energies. Journal of Chemical Theory and Computation. 11: 3042-3052. PMID 26575741 DOI: 10.1021/Acs.Jctc.5B00272  0.522
2015 McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, Pande VS. MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical Journal. 109: 1528-32. PMID 26488642 DOI: 10.1016/J.Bpj.2015.08.015  0.685
2015 Qi R, Wang LP, Wang Q, Pande VS, Ren P. United polarizable multipole water model for molecular mechanics simulation. The Journal of Chemical Physics. 143: 014504. PMID 26156485 DOI: 10.1063/1.4923338  0.537
2015 Song C, Wang LP, Sachse T, Preiß J, Presselt M, Martínez TJ. Efficient implementation of effective core potential integrals and gradients on graphical processing units. The Journal of Chemical Physics. 143: 014114. PMID 26156472 DOI: 10.1063/1.4922844  0.552
2015 Welborn M, Chen J, Wang LP, Van Voorhis T. Why many semiempirical molecular orbital theories fail for liquid water and how to fix them. Journal of Computational Chemistry. 36: 934-9. PMID 25766721 DOI: 10.1002/Jcc.23887  0.734
2015 Laury ML, Wang LP, Pande VS, Head-Gordon T, Ponder JW. Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model. The Journal of Physical Chemistry. B. 119: 9423-37. PMID 25683601 DOI: 10.1021/Jp510896N  0.542
2014 Wang LP, Martinez TJ, Pande VS. Building Force Fields: An Automatic, Systematic, and Reproducible Approach. The Journal of Physical Chemistry Letters. 5: 1885-91. PMID 26273869 DOI: 10.1021/Jz500737M  0.683
2014 Wang LP, Titov A, McGibbon R, Liu F, Pande VS, Martínez TJ. Discovering chemistry with an ab initio nanoreactor. Nature Chemistry. 6: 1044-8. PMID 25411881 DOI: 10.1038/Nchem.2099  0.72
2014 Mavros MG, Tsuchimochi T, Kowalczyk T, McIsaac A, Wang LP, Voorhis TV. What can density functional theory tell us about artificial catalytic water splitting? Inorganic Chemistry. 53: 6386-97. PMID 24694041 DOI: 10.1021/Ic5002557  0.71
2014 Wang L, Titov A, McGibbon R, Liu F, Pande VS, Martínez TJ. Erratum: Corrigendum: Discovering chemistry with an ab initio nanoreactor Nature Chemistry. 7: 87-87. DOI: 10.1038/Nchem.2139  0.569
2014 Wang LP, Martinez TJ, Pande VS. Building force fields: An automatic, systematic, and reproducible approach Journal of Physical Chemistry Letters. 5: 1885-1891. DOI: 10.1021/jz500737m  0.583
2014 Wang L, Head-Gordon T, Ponder J, Ren P, Chodera J, Eastman P, Martinez TJ, Pande VS. Systematic Improvement on the Classical Molecular Model of Water Biophysical Journal. 106: 403a. DOI: 10.1016/J.Bpj.2013.11.2273  0.728
2014 Fried SD, Wang L, Boxer SG, Pande VS. Calculations of the Electric Field in Solutions and Proteins with Polarizable Force Fields Biophysical Journal. 106: 403a. DOI: 10.1016/J.Bpj.2013.11.2271  0.582
2013 Wang LP, Chen J, Van Voorhis T. Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data. Journal of Chemical Theory and Computation. 9: 452-60. PMID 26589047 DOI: 10.1021/Ct300826T  0.724
2013 Fried SD, Wang LP, Boxer SG, Ren P, Pande VS. Calculations of the electric fields in liquid solutions. The Journal of Physical Chemistry. B. 117: 16236-48. PMID 24304155 DOI: 10.1021/Jp410720Y  0.531
2013 Wang LP, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martinez TJ, Pande VS. Systematic improvement of a classical molecular model of water. The Journal of Physical Chemistry. B. 117: 9956-72. PMID 23750713 DOI: 10.1021/Jp403802C  0.72
2013 Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, et al. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. Journal of Chemical Theory and Computation. 9: 461-469. PMID 23316124 DOI: 10.1021/Ct300857J  0.772
2013 Wang LP, Tofan D, Chen J, Van Voorhis T, Cummins CC. A pathway to diphosphorus from the dissociation of photoexcited tetraphosphorus Rsc Advances. 3: 23166-23171. DOI: 10.1039/C3Ra43940B  0.531
2013 Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, et al. OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation Journal of Chemical Theory and Computation. 9: 461-469. DOI: 10.1021/ct300857j  0.767
2012 Wang LP, Van Voorhis T. A Polarizable QM/MM Explicit Solvent Model for Computational Electrochemistry in Water. Journal of Chemical Theory and Computation. 8: 610-7. PMID 26596609 DOI: 10.1021/Ct200340X  0.641
2011 Kowalczyk T, Wang LP, Van Voorhis T. Simulation of solution phase electron transfer in a compact donor-acceptor dyad. The Journal of Physical Chemistry. B. 115: 12135-44. PMID 21961889 DOI: 10.1021/Jp204962K  0.776
2011 Wang L, Voorhis TV. Direct-Coupling O2 Bond Forming a Pathway in Cobalt Oxide Water Oxidation Catalysts Journal of Physical Chemistry Letters. 2: 2200-2204. DOI: 10.1021/Jz201021N  0.335
2011 Yost SR, Wang L, Voorhis TV. Molecular Insight Into the Energy Levels at the Organic Donor/Acceptor Interface: A Quantum Mechanics/Molecular Mechanics Study Journal of Physical Chemistry C. 115: 14431-14436. DOI: 10.1021/Jp203387M  0.346
2010 Wang LP, Van Voorhis T. Communication: Hybrid ensembles for improved force matching. The Journal of Chemical Physics. 133: 231101. PMID 21186847 DOI: 10.1063/1.3519043  0.597
2010 Difley S, Wang LP, Yeganeh S, Yost SR, Van Voorhis T. Electronic properties of disordered organic semiconductors via QM/MM simulations. Accounts of Chemical Research. 43: 995-1004. PMID 20443554 DOI: 10.1021/Ar900246S  0.762
2010 Wang LP, Wu Q, Van Voorhis T. Acid-base mechanism for ruthenium water oxidation catalysts. Inorganic Chemistry. 49: 4543-53. PMID 20394383 DOI: 10.1021/Ic100075K  0.59
2010 Van Voorhis T, Kowalczyk T, Kaduk B, Wang LP, Cheng CL, Wu Q. The diabatic picture of electron transfer, reaction barriers, and molecular dynamics. Annual Review of Physical Chemistry. 61: 149-70. PMID 20055670 DOI: 10.1146/Annurev.Physchem.012809.103324  0.774
2007 Khine M, Ionescu-Zanetti C, Blatz A, Wang LP, Lee LP. Single-cell electroporation arrays with real-time monitoring and feedback control. Lab On a Chip. 7: 457-62. PMID 17389961 DOI: 10.1039/B614356C  0.441
2005 Ionescu-Zanetti C, Wang LP, Di Carlo D, Hung P, Di Blas A, Hughey R, Lee LP. Alkaline hemolysis fragility is dependent on cell shape: results from a morphology tracker. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. 65: 116-23. PMID 15849725 DOI: 10.1002/Cyto.A.20135  0.423
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