Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory

Li, Chenghan; Voth, Gregory A.

doi:10.1021/acs.jpcb.1c05992

Title: Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory

Journal Article · 13 September 2021 · Journal of Physical Chemistry. B

DOI: https://doi.org/10.1021/acs.jpcb.1c05992 · OSTI ID:1819982

Li, Chenghan ^[1];

^[1]

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States

Not Available

View Journal Article

Cite

Export

Save

Research Organization:: Univ. of Chicago, IL (United States); University of Chicago, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0018648

OSTI ID:: 1819982

Journal Information:: Journal of Physical Chemistry. B, Journal Name: Journal of Physical Chemistry. B Journal Issue: 37 Vol. 125; ISSN 1520-6106

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (54)

LINCS: A linear constraint solver for molecular simulations Hess, Berk; Bekker, Henk; Berendsen, Herman J. C. Journal of Computational Chemistry, Vol. 18, Issue 12 https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H	journal	September 1997
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method Kumar, Shankar; Rosenberg, John M.; Bouzida, Djamal Journal of Computational Chemistry, Vol. 13, Issue 8 https://doi.org/10.1002/jcc.540130812	journal	October 1992
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Bonded-atom fragments for describing molecular charge densities Hirshfeld, F. L. Theoretica Chimica Acta, Vol. 44, Issue 2 https://doi.org/10.1007/BF00549096	journal	January 1977
Protons and how they are transported by proton pumps Buch-Pedersen, M. J.; Pedersen, B. P.; Veierskov, B. Pflügers Archiv - European Journal of Physiology, Vol. 457, Issue 3 https://doi.org/10.1007/s00424-008-0503-8	journal	May 2008
Implementing the Nelder-Mead simplex algorithm with adaptive parameters Gao, Fuchang; Han, Lixing Computational Optimization and Applications, Vol. 51, Issue 1 https://doi.org/10.1007/s10589-010-9329-3	journal	May 2010
Experimental pKa Values of Buried Residues: Analysis with Continuum Methods and Role of Water Penetration Fitch, Carolyn A.; Karp, Daniel A.; Lee, Kelly K. Biophysical Journal, Vol. 82, Issue 6 https://doi.org/10.1016/S0006-3495(02)75670-1	journal	June 2002
ATP synthesis driven by proton transport in F ₁ F ₀ -ATP synthase Weber, Joachim; Senior, Alan E. FEBS Letters, Vol. 545, Issue 1 https://doi.org/10.1016/S0014-5793(03)00394-6	journal	April 2003
Experimental measurement of the effective dielectric in the hydrophobic core of a protein García-Moreno, Bertrand E.; Dwyer, John J.; Gittis, Apostolos G. Biophysical Chemistry, Vol. 64, Issue 1-3 https://doi.org/10.1016/S0301-4622(96)02238-7	journal	February 1997
Et tu, Grotthuss! and other unfinished stories Cukierman, Samuel Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1757, Issue 8 https://doi.org/10.1016/j.bbabio.2005.12.001	journal	August 2006
Chance and design—Proton transfer in water, channels and bioenergetic proteins Wraight, Colin A. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1757, Issue 8 https://doi.org/10.1016/j.bbabio.2006.06.017	journal	August 2006
The NRAMP family of metal-ion transporters Nevo, Yaniv; Nelson, Nathan Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1763, Issue 7 https://doi.org/10.1016/j.bbamcr.2006.05.007	journal	July 2006
The Coupled Proton Transport in the ClC-ec1 Cl−/H+ Antiporter Zhang, Yong; Voth, Gregory A. Biophysical Journal, Vol. 101, Issue 10 https://doi.org/10.1016/j.bpj.2011.10.021	journal	November 2011
Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter Lee, Sangyun; Swanson, Jessica M. J.; Voth, Gregory A. Biophysical Journal, Vol. 110, Issue 6 https://doi.org/10.1016/j.bpj.2016.02.014	journal	March 2016
Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale Li, Chenghan; Yue, Zhi; Espinoza-Fonseca, L. Michel Biophysical Journal, Vol. 119, Issue 5 https://doi.org/10.1016/j.bpj.2020.07.027	journal	September 2020
PLUMED 2: New feathers for an old bird Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide Computer Physics Communications, Vol. 185, Issue 2 https://doi.org/10.1016/j.cpc.2013.09.018	journal	February 2014
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
Recent developments in libxc — A comprehensive library of functionals for density functional theory Lehtola, Susi; Steigemann, Conrad; Oliveira, Micael J. T. SoftwareX, Vol. 7 https://doi.org/10.1016/j.softx.2017.11.002	journal	January 2018
Ab Initio Molecular Dynamics Marx, Dominik; Hutter, Jurg https://doi.org/10.1017/CBO9780511609633	book	January 2009
Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins Lee, Sangyun; Liang, Ruibin; Voth, Gregory A. Journal of Chemical Theory and Computation, Vol. 12, Issue 2 https://doi.org/10.1021/acs.jctc.5b01109	journal	January 2016
Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport Biswas, Rajib; Tse, Ying-Lung Steve; Tokmakoff, Andrei The Journal of Physical Chemistry B, Vol. 120, Issue 8 https://doi.org/10.1021/acs.jpcb.5b09466	journal	November 2015
Multistate Density Functional Theory for Effective Diabatic Electronic Coupling Ren, Haisheng; Provorse, Makenzie R.; Bao, Peng The Journal of Physical Chemistry Letters, Vol. 7, Issue 12 https://doi.org/10.1021/acs.jpclett.6b00915	journal	May 2016
Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects Marsalek, Ondrej; Markland, Thomas E. The Journal of Physical Chemistry Letters, Vol. 8, Issue 7 https://doi.org/10.1021/acs.jpclett.7b00391	journal	March 2017
Conformational Consequences of Ionization of Lys, Asp, and Glu Buried at Position 66 in Staphylococcal Nuclease Karp, Daniel A.; Stahley, Mary R.; García-Moreno E., Bertrand Biochemistry, Vol. 49, Issue 19 https://doi.org/10.1021/bi902114m	journal	April 2010
Constrained Density Functional Theory Kaduk, Benjamin; Kowalczyk, Tim; Van Voorhis, Troy Chemical Reviews, Vol. 112, Issue 1 https://doi.org/10.1021/cr200148b	journal	November 2011
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ ₁ and χ ₂ Dihedral Angles Best, Robert B.; Zhu, Xiao; Shim, Jihyun Journal of Chemical Theory and Computation, Vol. 8, Issue 9 https://doi.org/10.1021/ct300400x	journal	August 2012
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics Yamashita, Takefumi; Peng, Yuxing; Knight, Chris Journal of Chemical Theory and Computation, Vol. 8, Issue 12 https://doi.org/10.1021/ct3006437	journal	September 2012
Multiscale Reactive Molecular Dynamics for Absolute p K _a Predictions and Amino Acid Deprotonation Nelson, J. Gard; Peng, Yuxing; Silverstein, Daniel W. Journal of Chemical Theory and Computation, Vol. 10, Issue 7 https://doi.org/10.1021/ct500250f	journal	May 2014
Block-Localized Density Functional Theory (BLDFT), Diabatic Coupling, and Their Use in Valence Bond Theory for Representing Reactive Potential Energy Surfaces Cembran, Alessandro; Song, Lingchun; Mo, Yirong Journal of Chemical Theory and Computation, Vol. 5, Issue 10 https://doi.org/10.1021/ct9002898	journal	August 2009
The Origin of Coupled Chloride and Proton Transport in a Cl ^– /H ⁺ Antiporter Lee, Sangyun; Mayes, Heather B.; Swanson, Jessica M. J. Journal of the American Chemical Society, Vol. 138, Issue 45 https://doi.org/10.1021/jacs.6b06683	journal	November 2016
Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux Wang, Zhi; Swanson, Jessica M. J.; Voth, Gregory A. Journal of the American Chemical Society, Vol. 140, Issue 48 https://doi.org/10.1021/jacs.8b07614	journal	November 2018
A Multi-State Empirical Valence Bond Model for Weak Acid Dissociation in Aqueous Solution Čuma, Martin; Schmitt, Udo W.; Voth, Gregory A. The Journal of Physical Chemistry A, Vol. 105, Issue 12 https://doi.org/10.1021/jp0038207	journal	February 2001
A Multistate Empirical Valence Bond Description of Protonatable Amino Acids ^† Maupin, C. Mark; Wong, Kim F.; Soudackov, Alexander V. The Journal of Physical Chemistry A, Vol. 110, Issue 2 https://doi.org/10.1021/jp053596r	journal	January 2006
Hydrated Excess Protons Can Create Their Own Water Wires Peng, Yuxing; Swanson, Jessica M. J.; Kang, Seung-gu The Journal of Physical Chemistry B, Vol. 119, Issue 29 https://doi.org/10.1021/jp5095118	journal	September 2014
Electronic Population Analysis on LCAO–MO Molecular Wave Functions. II. Overlap Populations, Bond Orders, and Covalent Bond Energies Mulliken, R. S. The Journal of Chemical Physics, Vol. 23, Issue 10 https://doi.org/10.1063/1.1740589	journal	October 1955
Systematic optimization of long-range corrected hybrid density functionals Chai, Jeng-Da; Head-Gordon, Martin The Journal of Chemical Physics, Vol. 128, Issue 8 https://doi.org/10.1063/1.2834918	journal	February 2008
Comment on “Free energy simulations of single and double ion occupancy in gramicidin A” [J. Chem. Phys. 126, 105103 (2007)] Roux, Benoît; Andersen, Olaf S.; Allen, Toby W. The Journal of Chemical Physics, Vol. 128, Issue 22 https://doi.org/10.1063/1.2931568	journal	June 2008
Polymorphic transitions in single crystals: A new molecular dynamics method Parrinello, M.; Rahman, A. Journal of Applied Physics, Vol. 52, Issue 12 https://doi.org/10.1063/1.328693	journal	December 1981
A multicenter numerical integration scheme for polyatomic molecules Becke, A. D. The Journal of Chemical Physics, Vol. 88, Issue 4 https://doi.org/10.1063/1.454033	journal	February 1988
Nosé–Hoover chains: The canonical ensemble via continuous dynamics Martyna, Glenn J.; Klein, Michael L.; Tuckerman, Mark The Journal of Chemical Physics, Vol. 97, Issue 4 https://doi.org/10.1063/1.463940	journal	August 1992
Multiscale reactive molecular dynamics Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A. The Journal of Chemical Physics, Vol. 137, Issue 22 https://doi.org/10.1063/1.4743958	journal	December 2012
Perspective: How good is DFT for water? Gillan, Michael J.; Alfè, Dario; Michaelides, Angelos The Journal of Chemical Physics, Vol. 144, Issue 13 https://doi.org/10.1063/1.4944633	journal	April 2016
CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations Kühne, Thomas D.; Iannuzzi, Marcella; Del Ben, Mauro The Journal of Chemical Physics, Vol. 152, Issue 19 https://doi.org/10.1063/5.0007045	journal	May 2020
Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase Liang, Ruibin; Swanson, Jessica M. J.; Peng, Yuxing Proceedings of the National Academy of Sciences, Vol. 113, Issue 27 https://doi.org/10.1073/pnas.1601982113	journal	June 2016
Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase Liang, Ruibin; Swanson, Jessica M. J.; Wikström, Mårten Proceedings of the National Academy of Sciences, Vol. 114, Issue 23 https://doi.org/10.1073/pnas.1703654114	journal	May 2017
Proton movement and coupling in the POT family of peptide transporters Parker, Joanne L.; Li, Chenghan; Brinth, Allete Proceedings of the National Academy of Sciences, Vol. 114, Issue 50 https://doi.org/10.1073/pnas.1710727114	journal	November 2017
The M2 Proton Channels of Influenza A and B Viruses Pinto, Lawrence H.; Lamb, Robert A. Journal of Biological Chemistry, Vol. 281, Issue 14 https://doi.org/10.1074/jbc.R500020200	journal	April 2006
H+/ATP ratio of proton transport-coupled ATP synthesis and hydrolysis catalysed by CF0F1-liposomes Turina, P. The EMBO Journal, Vol. 22, Issue 3 https://doi.org/10.1093/emboj/cdg073	journal	February 2003
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method Barducci, Alessandro; Bussi, Giovanni; Parrinello, Michele Physical Review Letters, Vol. 100, Issue 2 https://doi.org/10.1103/PhysRevLett.100.020603	journal	January 2008
Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics Zhang, Linfeng; Han, Jiequn; Wang, Han Physical Review Letters, Vol. 120, Issue 14 https://doi.org/10.1103/PhysRevLett.120.143001	journal	April 2018
Proton-Coupled Sugar and Amino Acid Transporters in Plants Bush, D. R. Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 44, Issue 1 https://doi.org/10.1146/annurev.pp.44.060193.002501	journal	June 1993
Voltage-Gated Proton Channels and Other Proton Transfer Pathways Decoursey, Thomas E. Physiological Reviews, Vol. 83, Issue 2 https://doi.org/10.1152/physrev.00028.2002	journal	April 2003
CRC Handbook of Chemistry and Physics Haynes, William M. CRC Press https://doi.org/10.1201/b17118	book	June 2014
Stabilization of Internal Charges in a Protein: Water Penetration or Conformational Change? Denisov, Vladimir P.; Schlessman, Jamie L.; García-Moreno E., Bertrand Biophysical Journal, Vol. 87, Issue 6 https://doi.org/10.1529/biophysj.104.048454	journal	December 2004

Similar Records

Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface

Journal Article · 2021 · Journal of Chemical Theory and Computation · OSTI ID:1818157

Li, Chenghan; Voth, Gregory A.

Constrained density functional theory calculation with iterative optimization

Journal Article · 2018 · Physical Review B · OSTI ID:1463044

Kidd, Daniel; Umar, A. S.; Varga, Kálmán

Charge constrained density functional molecular dynamics for simulation of condensed phase electron transfer reactions

Journal Article · 2009 · Journal of Chemical Physics · OSTI ID:21559764

Oberhofer, Harald; Blumberger, Jochen

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Chemical reactions
Free energy
Monomers
Peptides and proteins
Reaction mechanisms

Title: Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory

Citation Formats

References (54)

Similar Records

Related Subjects