Welcome to Pengfei (Jimmy) Li's website!
Welcome to Pengfei (Jimmy) Li's Webpage
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Here is the link to my google scholar citation page.
Here is the link to my ORCID.
Metal Ion Force Field Development
[1] The Extended Zinc AMBER Force Field (EZAFF) Based on an Empirical Approach
Z. Yu,
P. Li
and K. M. Merz, Jr.
J. Chem. Theory Comput.
Accepted
[2] Metal Ion Modeling Using Classical Mechanics
P. Li
and K. M. Merz, Jr.
Chem. Rev.,
2017
,
117
, 1564-1686
(Journal Impact Factor: 47.928, Open Access with ACS AuthorChoice, 123 pages, 200 equations, 1040 references)
[3] Advances in Metal Ion Modeling
P. Li
PhD Thesis, Michigan State University,
2016
[4] Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model
P. Li
, L. F. Song and K. M. Merz, Jr.
J. Chem. Theory Comput.
2015
, 11,
1645-1657
[5] Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water
P. Li
,
L. F. Song and K. M. Merz, Jr.
J. Phys. Chem. B
2015
, 119,
883-895
[6] Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions
P. Li
and
K. M. Merz, Jr.
J. Chem. Theory Comput.
2014
10
, 289-297
[7] Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent
P. Li
, B. P. Roberts, D. K. Chakravorty and K. M. Merz, Jr.
J. Chem. Theory Comput.
2013
,
9
, 2733-2748.
Molecular Dynamics Simulations
[1] Metal Capture Mechanism of a Copper Metallochaperone
D. K. Chakravorty,
P. Li
,
T. T. Tran, C. A. Bayse, K. M. Merz, Jr.
Biochemistry
,
2016
,
55
, 501-509
QM/MM Studies of Enzymes
[1] Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations
P. Li
, A. V. Soudackov, and S. Hammes-Schiffer
J. Am. Chem. Soc.
2018
,
140
, 3068-3076.
(Journal Impact Factor: 13.858)
[2] QM/MM studies into the H2O2-dependent activity of lytic polysaccharide monooxygenases: evidence for the formation of a caged hydroxyl radical intermediate
B. Wang, E. M. Johnston,
P. Li
, S. Shaik, G. J. Davies, P. H. Walton, and C. Rovira
ACS Catal.
,
2018
,
8
, 1346-1351
(Journal Impact Factor: 10.614)
Software Development
[1] D.A. Case, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, J. Smith, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2018), AMBER 2018, University of California, San Francisco.
[2] D.A. Case, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, D. Greene, N. Homeyer, S. Izadi, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D. Mermelstein, K.M. Merz, G. Monard, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, C.L. Simmerling, W.M. Botello-Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2017), AMBER 2017, University of California, San Francisco.
[3] D.A. Case, R.M. Betz, W. Botello-Smith, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand,
P. Li
, C. Lin, T. Luchko, R. Luo, B. Madej, D. Mermelstein, K.M. Merz, G. Monard, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, C. Sagui, C.L. Simmerling, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, L. Xiao, and P.A. Kollman (2016), AMBER 2016, University of California, San Francisco.
[4] MCPB.py: A Python Based Metal Center Parameter Builder
P. Li
and K. M. Merz, Jr.
J. Chem. Inf. Model.
2016
,
56
, 599-604
[5] D.A. Case, J.T. Berryman, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand,
P. Li
, T. Luchko, R. Luo, B. Madej, K.M. Merz, G. Monard, P. Needham, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, R. Salomon-Ferrer, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, D.M. York and P.A. Kollman (2015), AMBER 2015, University of California, San Francisco.
QM Studies
[1]
Effects of Structural Modification on the Ground State of Metallabenzenes: Singlet versus Triplet State
M. Lin,
P. Li
and Z.
Cao
J. Theor. Comput. Chem.
2011
,
10
, 861-874
[2] Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy
Y. Tan, N. Zhao, J. Liu,
P. Li
, C. N. Stedwell, L. Yu, N. C. Polfer,
J. Am. Soc. Mass Spectrom.
2017,
28
, 539-550.
NMR Chemical Shift Perturbation Prediction
[1]
Using Ligand Induced Protein Chemical Shift Perturbations to Determine Protein-ligand Structures
Z. Yu,
P. Li
and K. M. Merz, Jr.,
Biochemistry
,
2
017
,
56
, 3249-2362.
Movable Type Method
[1] KECSA-Movable Type Implicit Solvation Model (KMTISM)
Z. Zheng, T. Wang,
P. Li
and K. M. Merz, Jr.
J. Chem. Theory Comput.
2015
,
11
, 667-682
