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Publications
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, 2017, 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

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