L-P. Wang Theoretical Chemistry Group

Papers published since start of research program at UC Davis:

* LPW corresponding author

74. Reeves HL & Wang L-P.* (2022) “The impact of conformational sampling on firstprinciples calculations of vicinal COCH J-couplings in carbohydrates.” Glycobiology, 33, 38-46. (DOI, PDF)

73. Yeo C, Nguyen M & Wang L-P.* (2022) “Benchmarking Density Functionals, Basis Sets, and Solvent Models in Predicting Thermodynamic Hydricities of Organic Hydrides.” J. Phys. Chem. A 126, 7566–7577. (DOI, PDF)

72. Nguyen QNN, Xia KT, Zhang Y, Chen N, Morimoto M, Pei X, Ha Y, Guo J, Yang W, Wang L-P, Bergman RG, Raymond KN, Toste FD & Tantillo DJ. (2022) “Source of Rate Acceleration for Carbocation Cyclization in Biomimetic Supramolecular Cages.” J. Am. Chem. Soc. 144, 14413–11424. (DOI, PDF)

71. Oh L, Varki A, Chen X & Wang L-P.* (2022) “SARS-CoV-2 and MERS-CoV Spike Protein Binding Studies Support Stable Mimic of Bound 9-O-Acetylated Sialic Acids.” Molecules 2022, 27, 5322. (DOI, PDF)

70. Oh L, Ji Y, Li W, Varki A, Chen X & Wang L-P.* (2022) “O‑Acetyl Migration within the Sialic Acid Side Chain: A Mechanistic Study Using the Ab Initio Nanoreactor.” Biochemistry 2022, 61, 2007–2013. (DOI, PDF)

69. Xu Z, Federman SR, Jackson WM, Ng CY, Wang L-P & Crabtree KN. (2022) “Multireference configuration interaction study of the predissociation of C2 via its F1Πu state.” J. Chem. Phys. 157, 024302. (DOI, PDF)

68. Lee J, Kind T, Tantillo DJ, Wang L-P & Fiehn O. (2022) “Evaluating the Accuracy of the QCEIMS Approach for Computational Prediction of Electron Ionization Mass Spectra of Purines and Pyrimidines”, Metabolites 12, 68. (DOI, PDF)

67. Rao G, Chen N, Marchiori DA, Wang L-P & Britt RD. (2022) “Accumulation and Pulse Electron Paramagnetic Resonance Spectroscopic Investigation of the 4‑Oxidobenzyl Radical Generated in the Radical S‑Adenosyl‑L‑methionine Enzyme HydG”. Biochemistry 61, 107–116. (DOI, PDF)

66. Britt RD, Tao L, Rao G, Chen N & Wang L-P. (2022) “Proposed Mechanism for the Biosynthesis of the [FeFe] Hydrogenase H-Cluster: Central Roles for the Radical SAM Enzymes HydG and HydE”, ACS Bio. Med. Chem. Au 2, 11–21. (DOI, PDF)

65. Boothroyd S, Madin OC, Mobley DL, Wang L-P, Chodera JD & Shirts MR. (2021) “Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties.” J. Chem. Theory Comput. 18, 3577–3592. (DOI, PDF)

64. Caceres-Delpiano J, Wang L-P* & Essex JW. (2021) “The automated optimisation of a coarse-grained force field using free energy data”, Phys. Chem. Chem. Phys. 23, 24842. (DOI, PDF)

63. Stoppelman JP, Ng TT, Nerenberg PS & Wang L-P.* (2021) “Development and Validation of AMBER-FB15-compatible Force Field Parameters for Phosphorylated Amino Acids”, J. Chem. Theory Comput. 125, 11927-11942. (DOI, PDF)

62. Chen N, Rao G, Britt RD & Wang L-P.* (2021) “Quantum Chemical Study of a Radical Relay Mechanism for the HydG-Catalyzed Synthesis of a Fe(II)(CO)2(CN) cysteine Precursor to the H-Cluster of [FeFe] Hydrogenase”, Biochemistry 60, 3016- 3026. (DOI, PDF)

61. 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, Gilson MK, Chodera JD, Bayly CI, Mobley DL & Wang L-P.* (2021) “Development and Benchmarking of Open Force Field v1.0.0 – the Parsley Small-Molecule Force Field”, J. Chem. Theory Comput. 17, 6262-6280. (DOI, PDF)

60. Das M, Chen N, LiWang A & Wang L-P.* (2021) “Identification and characterization of metamorphic proteins: Current and future perspectives”, Biopolymers 112, e23473. (DOI, PDF)

59. Borges RM, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang L-P, Wang S & Renslow RS. (2021) “Quantum Chemistry Calculations for Metabolomics”, Chem. Rev. 121, 5033–5670. (DOI, PDF)

58. Ji Y, Sasmal A, Li W, Oh L, Srivastava S, Hargett AA, Wasik BR, Yu H, Diaz S, Choudhury B, Parrish CR, Freedberg DI, Wang L-P, Varki A & Chen X. (2021) “Reversible O-Acetyl Migration within the Sialic Acid Side Chain and Its Influence on Protein Recognition”, ACS Chem. Biol. 16, 1951-1960. (DOI, PDF)

57. Schauperl M, Kantonen SM, Wang L-P & Gilson MK. (2020) “Data-driven analysis of the number of Lennard-Jones types needed in a force field”, Commun. Chem. 3, 173. (DOI, PDF)

56. Seritan S, Bannwarth C, Fales BS, Hohenstein EG, Isborn CM, Kokkila-Schumacher SIL, Li X, Liu F, Luehr N, Snyder JW, Song CC, Titov AV, Ufimtsev IS, Wang L-P & Martinez TJ. (2020) “TeraChem: A graphical processing unit-accelerated electronic structure package for large-scale ab initio molecular dynamics”, WIREs Comput. Mol. Sci. 10, e1494. (DOI, PDF)

55. Chen N, Das M, LiWang A & Wang L-P.* (2020) “Sequence-Based Prediction of Metamorphic Behavior in Proteins”, Biophys. J. 119, 1380–1390. (DOI, PDF)

54. Li W, Battistel MD, Reeves H, Oh L, Yu H, Chen X, Wang L-P* & Freedberg DI. (2020) “A combined NMR, MD and DFT conformational analysis of 9-O-acetyl sialic acidcontaining GM3 ganglioside glycan and its 9-N-acetyl mimic”, Glycobiology 30, 787– 801. (DOI, PDF)

53. Qiu Y, Smith DGA, Stern CD, Feng M, Jang H & Wang L-P.* (2020) “Driving torsion scans with wavefront propagation”, J. Chem. Phys. 152, 244116. (DOI, PDF)

52. Liou S-H, Chuo S-W, Qiu Y, Wang L-P & Goodin DB. (2020) “Linkage between Proximal and Distal Movements of P450cam Induced by Putidaredoxin”, Biochemistry 59, 2012–2021. (DOI, PDF)

51. Schauperl MS, Nerenberg PS, Jang H, Wang L-P, Bayly CI, Mobley DM & Gilson MK. (2020) “Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)”, Commun. Chem. 3, 44. (DOI, PDF)

50. Hutchings ME, Johnson L, Qiu Y, Song CC & Wang L-P.* (2020) “Bond-Order Time Series Analysis for Detecting Reaction Events in Ab Initio Molecular Dynamics Simulations”, J. Chem. Theory Comput. 16, 1606–1617. (DOI, PDF)

49. Kantonen SM, Muddana HS, Schauperl M, Henriksen NM, Wang L-P & Gilson MK. (2020) “Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters”, J. Chem. Theory Comput. 16, 1115–1127. (DOI, PDF)

48. Slochower DR, Henriksen NM, Wang L-P, Chodera JD, Mobley DL & Gilson MK. (2019) "Binding Thermodynamics of Host–Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative", J. Chem. Theory Comput. 15, 6225-6242. (DOI, PDF)

47. Xu Z, Luo N, Federman SR, Jackson WM, Ng C-Y, Wang L-P & Crabtree KN. (2019) "Ab Initio Study of Ground-state CS Photodissociation via Highly Excited Electronic States", Astrophys. J. 882:86. (DOI, PDF)

46. Chuo S-W, Liou S-H, Wang L-P, Britt RD, Poulos TL, Sevrioukova IR & Goodin DB. (2019) “Conformational Response of N-Terminally Truncated Cytochrome P450 3A4 to Ligand Binding in Solution”, Biochemistry 58, 3903–3910. (DOI, PDF)

45. Wang C-Y, Zhu A-Y, Liao X, Manga M & Wang L-P. (2019) “Capillary Effects on Groundwater Response to Earth Tides”, Water Resour. Res. 55, 6886–6895. (DOI, PDF)

44. Wang L-P* & Song CC. (2019) “Car–Parrinello Monitor for More Robust Born–Oppenheimer Molecular Dynamics”, J. Chem. Theory Comput. 15, 4454-4467. (DOI, PDF)

43. Qiu Y, Nerenberg PS, Head-Gordon T & Wang L-P.* (2019) “Systematic optimization of water models using liquid/vapor surface tension data”, J. Phys. Chem. B 123, 7061-7073. (DOI, PDF)

42. Chuo S-W, Wang L-P, Britt RD & Goodin DB. (2019) “An Intermediate Conformational State of Cytochrome P450cam-CN in Complex with Putidaredoxin”, Biochemistry 58, 2353-2361. (DOI, PDF)

41. Wade AD, Wang L-P* & Huggins DJ*. (2018) “Assimilating radial distribution functions to build water models with improved structural properties”, J. Chem. Inf. Model. 58, 1766-1778. (DOI, PDF)

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. 14, 4279-4290. (DOI, PDF)

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. (DOI, PDF)

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)