Research Highlight:

Our paper, "Quantum chemical studies of redox properties and conformational changes of a four-center iron CO2 reduction electrocatalyst", is featured on the front cover of Chemical Science!

Papers published since start of research program at UC Davis:

* LPW corresponding author

40. Qiu Y, Schwegler BR & Wang L-P.* (2018) “Polarizable molecular simulations reveal how silicon-containing functional groups govern the desalination mechanism in nanoporous graphene”, J. Chem. Theory Comput., accepted manuscript. (DOI)

39. Jang H, Qiu Y, Hutchings ME, Nguyen M, Berben LA & Wang L-P.* (2018) “Quantum chemical studies of redox properties and conformational changes of a four-center iron CO2 reduction electrocatalyst”, Chem. Sci. 9, 2645-2654. (DOI, PDF)

38. Demerdash O, Wang L-P & Head-Gordon T. (2017) “Advanced models for water simulations”, WIRES Comput. Mol. Sci. 8, e1355. (DOI, PDF)

37. Eastman P, Swails J, Chodera JD, Mcgibbon RT, Zhao Y, Beauchamp KA, Wang L-P, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR & Pande VS. (2017) “OpenMM 7: Rapid development of high performance algorithms for molecular dynamics”, PLOS Comput. Biol. 13, e1005659. (DOI, PDF)

36. Huang J, Mei Y, König G, Simmonett AC, Pickard FC, Wu Q, Wang L-P, Mackerell AD, Brooks BR & Shao Y. (2017) “An estimation of hybrid quantum mechanical molecular mechanical polarization energies for small molecules using polarizable force-field approaches”, J. Chem. Theory Comput. 13, 679-695. (DOI, PDF)

35. Wang L-P, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ & Pande VS. (2017) “Building a more predictive protein force field: A systematic and reproducible route to AMBER-FB15”, J. Phys. Chem. B 121, 4023-4039. (DOI, PDF)

34. Khedri Z, Xiao A, Yu H, Landig CS, Li W, Diaz S, Wasik BR, Parrish CR, Wang L-P, Varki A & Chen X. (2017) “A chemical biology solution to problems with studying biologically important but unstable 9-o-acetyl sialic acids”, ACS Chem. Biol. 12, 214-224. (DOI, PDF)

33. McKiernan KA, Wang L-P & Pande VS. (2016) “Training and validation of a liquid-crystalline phospholipid bilayer force field”, J. Chem. Theory Comput. 12, 5960-5967. (DOI, PDF)

32. Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao YZ, Margul DT, Swails J, Zeng Q, Case DA, Eastman P, Wang L-P, Essex JW, Head-Gordon M, Pande VS, Ponder JW, Shao YH, Skylaris CK, Todorov IT, Tuckerman ME & Head-Gordon T. (2016) “Advanced potential energy surfaces for molecular simulation”, J. Phys. Chem. B 120, 9811-9832. (DOI, PDF)

31. Wang C-Y, Liao X, Wang L-P, Wang C-H & Manga M. (2016) “Large earthquakes create vertical permeability by breaching aquitards”, Water Resour. Res. 52, 5923-5937. (DOI, PDF)

30. Wang L-P* & Song CC. (2016) “Geometry optimization made simple with translation and rotation coordinates”, J. Chem. Phys. 144, 214108. (DOI, PDF)

29. Song CC, Wang L-P & Martínez TJ. (2016) “Automated code engine for graphical processing units: Application to the effective core potential integrals and gradients”, J. Chem. Theory Comput. 12, 92-106. (DOI, PDF)

28. Wang L-P, McGibbon RT, Pande VS & Martínez TJ. (2016) “Automated discovery and refinement of reactive molecular dynamics pathways”, J. Chem. Theory Comput. 12, 638-649. (DOI, PDF)

27. McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernandez CX, Schwantes CR, Wang L-P, Lane TJ & Pande VS. (2015) “MDTraj: A modern open library for the analysis of molecular dynamics trajectories”, Biophys. J. 109, 1528-1532. (DOI, PDF)

26. Song CC, Wang L-P, Sachse T, Preiss J, Presselt M & Martínez TJ. (2015) “Efficient implementation of effective core potential integrals and gradients on graphical processing units”, J. Chem. Phys. 143, 014114. (DOIPDF)

25. Qi R†, Wang L-P†, Wang QT, Pande VS & Ren PY. (2015) “United polarizable multipole water model for molecular mechanics simulation”, J. Chem. Phys. 143, 014504. (DOI, PDF
†Equal contributions.

Papers published prior to start of research program at UC Davis:

24. Kokkila Schumacher SIL, Hohenstein EG, Parrish RM, Wang L-P & Martínez TJ. (2015) “Tensor hypercontraction second-order Moller-Plesset perturbation theory: Grid optimization and reaction energies”, J. Chem. Theory Comput. 11, 3042-3052. (DOI, PDF)

23. Welborn M, Chen JH, Wang L-P & Van Voorhis T. (2015) “Why many semiempirical molecular orbital theories fail for liquid water and how to fix them”, J. Comput. Chem. 36, 934-939. (DOI, PDF)

22. Laury ML†, Wang L-P†, Pande VS, Head-Gordon T & Ponder JW. (2015) “Revised parameters for the AMOEBA polarizable atomic multipole water model”, J. Phys. Chem. B 119, 9423-9437. (DOI, PDF)
† Equal contributions.       

21. Wang L-P, Titov A, Mcgibbon R, Liu F, Pande VS & Martínez TJ. (2014) “Discovering chemistry with an ab initio nanoreactor”, Nat. Chem. 6, 1044-1048. (DOI, PDF
Highlighted in Nov. 10, 2014 issue of Chemical & Engineering News.

20. Wang L-P, Martínez TJ & Pande VS. (2014) “Building force fields: An automatic, systematic, and reproducible approach”, J. Phys. Chem. Lett. 5, 1885-1891. (DOI, PDF)

19. Mavros MG, Tsuchimochi T, Kowalczyk T, Mcisaac A, Wang L-P & Van Voorhis T. (2014) “What can density functional theory tell us about artificial catalytic water splitting?”, Inorg. Chem. 53, 6386-6397. (DOI, PDF)

18. Mu XJ, Wang QT, Wang L-P, Fried SD, Piquemal JP, Dalby KN & Ren PY. (2014) “Modeling organochlorine compounds and the sigma-hole effect using a polarizable multipole force field”, J. Phys. Chem. B 118, 6456-6465. (DOI, PDF)

17.  Fried SD, Wang L-P, Boxer SG, Ren PY & Pande VS. (2013) “Calculations of the electric fields in liquid solutions”, J. Phys. Chem. B 117, 16236-16248. (DOI, PDF)

16.  Wang L-P, Tofan D, Chen JH, Van Voorhis T & Cummins CC. (2013) “A pathway to diphosphorus from the dissociation of photoexcited tetraphosphorus”, RSC Advances 3, 23166-23171. (DOI, PDF)

15.  Wang L-P, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martínez TJ & Pande VS. (2013) “Systematic improvement of a classical molecular model of water”, J. Phys. Chem. B 117, 9956-9972. (DOI, PDF)

14.  Wang C-Y, Wang L-P, Manga M, Wang CH & Chen CH. (2013) “Basin-scale transport of heat and fluid induced by earthquakes”, Geophys. Res. Lett. 40, 3893-3897. (DOI, PDF)

13.  Wang C-Y, Chen WP & Wang L-P. (2013) “Temperature beneath tibet”, Earth Planet. Sci. Lett. 375, 326-337. (DOI, PDF)

12.  Wang L-P, Chen JH & Van Voorhis T. (2013) “Systematic parametrization of polarizable force fields from quantum chemistry data”, J. Chem. Theory Comput. 9, 452-460. (DOI, PDF)

11. Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang L-P, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR & Pande VS. (2013) “OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation”, J. Chem. Theory Comput. 9, 461-469. (DOI, PDF)

10.  Wang L-P & Van Voorhis T. (2012) “A polarizable QM/MM explicit solvent model for computational electrochemistry in water”, J. Chem. Theory Comput. 8, 610-617. (DOI, PDF)

9.    Kowalczyk T, Wang L-P & Van Voorhis T. (2011) “Simulation of solution phase electron transfer in a compact donor-acceptor dyad”, J. Phys. Chem. B 115, 12135-12144. (DOI, PDF)

8.    Wang L-P & Van Voorhis T. (2011) “Direct-coupling O2 bond forming a pathway in cobalt oxide water oxidation catalysts”, J. Phys. Chem. Lett. 2, 2200-2204. (DOI, PDF)

7.    Yost SR, Wang L-P & Van Voorhis T. (2011) “Molecular insight into the energy levels at the organic donor/acceptor interface: A quantum mechanics/molecular mechanics study”, J. Phys. Chem. C 115, 14431-14436. (DOI, PDF)

6.    Wang L-P, Wu Q & Van Voorhis T. (2010) “Acid-base mechanism for ruthenium water oxidation catalysts”, Inorg. Chem. 49, 4543-4553. (DOI, PDF)

5.    Wang L-P & Van Voorhis T. (2010) “Communication: Hybrid ensembles for improved force matching”, J. Chem. Phys. 133, 231101. (DOI, PDF)

4.    Difley S, Wang L-P, Yeganeh S, Yost SR & Van Voorhis T. (2010) “Electronic properties of disordered organic semiconductors via QM/MM simulations”, Accounts Chem. Res. 43, 995-1004 and front cover. (DOI, PDF)

3.    Van Voorhis T, Kowalczyk T, Kaduk B, Wang L-P, Cheng CL & Wu Q. (2010) “The diabatic picture of electron transfer, reaction barriers, and molecular dynamics”, Ann. Rev. Phys. Chem. 61 (eds S. R. Leone et al.), 149-170. (DOI, PDF)

2.    Khine M, Ionescu-Zanetti C, Blatz A, Wang L-P & Lee LP. (2007) “Single-cell electroporation arrays with real-time monitoring and feedback control”, Lab on a Chip 7, 457-462. (DOI, PDF)

1.    Ionescu-Zanetti C, Wang L-P, Di Carlo D, Hung P, Di Blas A, Hughey R & Lee LP. (2005) “Alkaline hemolysis fragility is dependent on cell shape: Results from a morphology tracker”, Cytom. Part A 65, 116-123. (DOI, PDF)