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Publications

(* represents corresponding authors)

Publication list via Google Scholar

Publications after joining Loyola

Journal Articles

  1. Z. Li, S. Bhowmik, L. Sagresti, G. Brancato, M. Smith, D. E. Benson, P. Li, and K. M. Merz Jr.,* “Simulating Metal-Imidazole Complexes”, Submitted, preprint available at ChemRxiv, DOI: 10.26434/chemrxiv-2024-l39zx

  2. M. Smith, R. Khatiwada, and P. Li,* “Exploring Ion Polarizabilities and Their Correlation with Van der Waals Radii: A Theoretical Investigation”, Submitted, preprint available at ChemRxiv, DOI: 10.26434/chemrxiv-2024-4jnjm

  3. Y. Wei, P. Li,* “Theoretical Insights into the Reduction of Azurin Metal Site with Unnatural Amino Acid Substitutions”, Resubmitted, preprint available at ChemRxiv, DOI: 10.26434/chemrxiv-2023-qpmzd-v2

  4. D. Fang, Z. Zhang, J. Zhai, B. Guo, P. Li, X. Liu, J. Song, S. Xie, R. Wu, Y. Zhao,* C. Wang,* “Enzymatic-related network of catalysis, polyamine, and tumors for acetylpolyamine oxidase: from calculation to experiment”, Chem. Sci., 2024, 15, 2867-2882.

  5. L. Landry, P. Li,* “Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins”, J. Chem. Inf. Model.,, 2024, 64, 812-824.

  6. D. Case, H. Aktulga, K. Belfon, D. Cerutti, G. Cisneros, V. Cruzeiro, N. Forouzesh, T. Giese, A. Götz, H. Gohlke, S. Izadi, K. Kasavajhala, M. Kaymak, E. King, T. Kurtzman, T. Lee, P. Li, J. Liu, T. Luchko, R. Luo, M. Machado, M. Manathunga, H. Nguyen, K. O'Hearn, A. Onufriev, F. PAN, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T. Cheatham, D. Roe, A. Roitberg, C. Simmerling, D. York, M. Nagan,* and K. Merz,* “AmberTools”, J. Chem. Inf. Model., 2023, 63, 6183-6191.

  7. X. Yang, S. Liu, Z. Yin, M. Chen, J. Song, P. Li, and L. Yang,* “New insight into the proton pumping mechanism of ba3 Cytochrome c Oxidase: the functions of key residues and waters”, Phys. Chem. Chem. Phys. 2023, 25, 25105-25115.

  8. A. Sharma, C. Whittington, M. Jabed, S. G. Hill, A. Kostenko, T. Yu, P. Li, P. E. Doan, B. M. Hoffman,* and A. R. Offenbacher,* “13C Electron Nuclear Double Resonance Spectroscopy-Guided Molecular Dynamics Computations Reveal the Structure of the Enzyme-Substrate Complex of an Active, N-linked Glycosylated Lipoxygenase”, Biochemistry, 2023, 62, 1531-1543.

  9. M. Smith, Z. Li, L. Landry, K. M. Merz, Jr.,* and P. Li,* “Consequences of Overfitting the van der Waals Radii of Ions”, J. Chem. Theory Comput, 2023, Article ASAP, DOI: 10.1021/acs.jctc.2c01255​

  10. W. Fang, S. Feng, Z. Jiang, W. Liang, P. Li,* and B. Wang,* “Understanding the Key Roles of pH Buffer in Accelerating the Lignin Degradation by Lignin Peroxidases”, JACS Au, 2023, 3, 536-549.

  11. T. Gerard, Y. Wei, E. Weerawardhana, A. Lugosan, M. Zeller, D. Dickie, P. Li,* and W. T. Lee,* “Novel Inorganic Fluorescent Chemosensor: Rational Design and Selective Mg2+ Detection”, ACS Omega, 2023, 8, 3835-3841.

  12. M. Smith and P. Li,* “Molecular Insights into the Calcium Binding in Troponin C Through a Molecular Dynamics Study”, J. Chem. Inf. Model., 2023, 63, 354-361.

  13. A. J. Veenis, P. Li, A. V. Soudackov, S. Hammes-Schiffer, and P. C. Bevilacqua,* “Investigation of the pKa of the Nucleophilic O2′ of the Hairpin Ribozyme”, J. Phys. Chem. B., 2021, 125, 11869.

  14. P. Li,* “Bridging the 12-6-4 Model and the Fluctuating Charge Model”, Front. Chem., 2021, 9:721960.

  15. Z. Li, L. F. Song, P. Li,* and K. M. Merz, Jr.,* “Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models”, J. Chem. Theory Comput., 2021, 17, 2342-2354.

  16. A. Sengupta, Z. Li, L. F. Song, P. Li,* and K. M. Merz. Jr.* “Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models”, J. Chem. Inf. Model.., 2021, 61, 869-880. (A correction published at J. Chem. Inf. Model., 2021, 61, 3734-3735.

Book Chapters

  1. ​Yang Wei and P. Li,* “Modeling Metal Ions in Enzyme Catalysis”, Compr. Comput. Chem. 2022, In print, DOI: 10.1016/B978-0-12-821978-2.00019-2

Software Packages (Dr. Li has been an AMBER developer since 2015)

  1. D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, N. Forouzesh, G. Giamba¸su, T. Giese, M.K. Gilson, H. Gohlke, A.W. Goetz, J. Harris, Z. Huang, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, A. Kovalenko, T. Kurtzman, T.S. Lee, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, X. Wu, Y. Wu, Y. Xiong, Y. Xue, D.M. York, C. Zhao, Q. Zhu, and P.A. Kollman (2024), Amber 2024, University of California, San Francisco.

  2. D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, N. Forouzesh, G. Giamba¸su, T. Giese, M.K. Gilson, H. Gohlke, A.W. Goetz, J. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, H. Wei, X. Wu, Y. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, Q. Zhu, and P.A. Kollman (2023), Amber 2023, University of California, San Francisco.

  3. D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022, University of California, San Francisco.

  4. D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, C. Jin, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2021), AMBER 2021, University of California, San Francisco.


Publications before joining Loyola

Journal Articles

  1. ​J. J. Goings, P. Li, Q. Zhu, and S. Hammes-Schiffer,* “Formation of an Unusual Glutamine Tautomer in a Blue-Light Using Flavin Photocycle Characterizes the Light-Adapted State”, Proc. Natl. Acad. Sci. U. S. A., 2020, 117, 26626-26632.

  2. P. Li, A. V. Soudackov, B. Koronkiewicz, J. M. Mayer, and S. Hammes-Schiffer,* “Theoretical Study of Shallow Distance Dependence of Proton-Coupled Electron Transfer in Oligoproline Peptides”, J. Am. Chem. Soc. 2020, 142, 13795-13804.

  3. C. R. Reinhardt, P. Li, G. Kang, J. Stubbe, C. L. Drennan, and S. Hammes-Schiffer,* “Conformational Motions and Water Networks at the 𝛼/𝛽 Interface in E. coli Ribonucleotide Reductase”, J. Am. Chem. Soc. 2020, 142, 13768-13778.

  4. Z. Li, L. F. Song, P. Li,* and K. M. Merz, Jr.,* “Systematic Parameterization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models”, J. Chem. Theory Comput., 2020, 16, 4429-4442.

  5. P. Li, A. Rangadurai, H. M. Al-Hashimi, and S. Hammes-Schiffer,* “Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations”, J. Am. Chem. Soc. 2020, 142, 11183-11191.

  6. P. Li and S. Hammes-Schiffer,* “Substrate-to-Product Conversion Facilitates Active Site Loop Opening in Yeast Enolase: A Molecular Dynamics Study”, ACS Catal. 2019, 9, 8985-8990.

  7. P. Li, A. V. Soudackov and S. Hammes-Schiffer,* “Impact of Mutations on the Binding Pocket of Soybean Lipoxygenase: Implications for Proton-Coupled Electron Transfer”, J. Phys. Chem. Lett. 2018, 9, 6444-6449.

  8. P. Li, A. V. Soudackov and S. Hammes-Schiffer,* “Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations”, J. Am. Chem. Soc. 2018, 140, 3068-3076.

  9. B. Wang, E. Johnston, P. Li, S. Shaik, G. Davies, P. H. Walton and C. Rovira,* “QM/MM Studies into the H2O2-Dependent Activity of Lytic Polysaccharide Monooxygenases: Evidence for the Formation of a Caged Hydroxyl Radical Intermediate”, ACS Catal. 2018, 8, 1346-1351.

  10. Y. Tan, N. Zhao, J. Liu, P. Li, C. N. Stedwell, L. Yu and N. C. Polfer,* “Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy”, J. Am. Soc. Mass Spectrom. 2017, 28, 539-550.

  11. Z. Yu, P. Li and K. M. Merz, Jr.,* “Extended Zinc AMBER Force Field (EZAFF)”, J. Chem. Theory Comput. 2018, 14, 242-254.

  12. Z. Yu, P. Li and K. M. Merz, Jr.,* “Using Ligand-Induced Protein Chemical Shift Perturbations to Determine Protein-Ligand Structures”, Biochemistry 2017, 56, 2349-2362.

  13. P. Li and K. M. Merz, Jr.,* “Metal Ion Modeling Using Classical Mechanics”, Chem. Rev. 2017, 117, 1564-1686.

  14. P. Li and K. M. Merz, Jr.,* “MCPB.py: A Python Based Metal Center Parameter Builder”, J. Chem. Inf. Model. 2016, 56, 599-604.

  15. D. K. Chakravorty,* P. Li, T. T. Tran, C. A. Bayse and K. M. Merz, Jr.,* “Metal Ion Capture Mechanism of a Copper Metallochaperone”, Biochemistry 2016, 55, 501-509.

  16. P. Li, L. F. Song and K. M. Merz, Jr.,* “Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model”, J. Chem. Theory Comput. 2015, 11, 1645-1657.

  17. Z. Zheng, T. Wang, P. Li and K. M. Merz, Jr.,* “KECSA-Movable Type Implicit Solvation Model (KMTISM)”, J. Chem. Theory Comput. 2015, 11, 667-682.

  18. P. Li, L. F. Song and K. M. Merz, Jr.,* “Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water”, J. Phys. Chem. B 2015, 119, 883-895.

  19. P. Li and K. M. Merz, Jr.,* “Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions”, J. Chem. Theory Comput. 2014, 10, 289-297.

  20. P. Li, B. P. Roberts, D. K. Chakravorty and K. M. Merz, Jr.,* “Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent”, J. Chem. Theory Comput. 2013, 9, 2733-2748.

  21. M. Lin, P. Li and Z. Cao,* “Effects of Structural Modification on the Ground State of Metallabenzenes: Singlet versus Triplet State”, J. Theor. Comput. Chem. 2011, 10, 861-874.

Book Chapters

  1. P. Li and K. M. Merz, Jr.,* “Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program”, Methods Mol. Biol. 2021, 2199, 257-275.

Software Packages (Dr. Li has been an AMBER developer since 2015)

  1. D. A. Case, K. Belfon, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, T. E. Cheatham, III, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, G. Giambasu, M. K. Gilson, H. Gohlke, A. W. Goetz, R Harris, S. Izadi, K. Kasavajhala, A. Kovalenko, R. Krasny, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K. M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F. Pan, S. Pantano, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, N. Skrynnikov, J. Smith, J. Swails, R. C. Walker, J. Wang, L. Wilson, R. M. Wolf, X. Wu, D. M. York and P. A. Kollman (2020), AMBER 2020, University of California, San Francisco.

  2. D. A. Case, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, T. E. Cheatham, III, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, D. Ghoreishi, G. Giambasu, T. Giese, M. K. Gilson, H. Gohlke, A. W. Goetz, D. Greene, R. Harris, N. Homeyer, Y. Huang, S. Izadi, A. Kovalenko, R. Krasny, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, D. J. Mermelstein, K. M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, 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, L. Wilson, R. M. Wolf, X. Wu, L. Xiao, Y. Xiong, D. M. York and P. A. Kollman (2019), AMBER 2019, University of California, San Francisco.

  3. 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.

  4. 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.

  5. 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.

  6. 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, Jr., G. Monard, P. Needham, H. 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.

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