1
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Pelaez RP, Simeon G, Galvelis R, Mirarchi A, Eastman P, Doerr S, Thölke P, Markland TE, De Fabritiis G. TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations. J Chem Theory Comput 2024. [PMID: 38743033 DOI: 10.1021/acs.jctc.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Achieving a balance between computational speed, prediction accuracy, and universal applicability in molecular simulations has been a persistent challenge. This paper presents substantial advancements in TorchMD-Net software, a pivotal step forward in the shift from conventional force fields to neural network-based potentials. The evolution of TorchMD-Net into a more comprehensive and versatile framework is highlighted, incorporating cutting-edge architectures such as TensorNet. This transformation is achieved through a modular design approach, encouraging customized applications within the scientific community. The most notable enhancement is a significant improvement in computational efficiency, achieving a very remarkable acceleration in the computation of energy and forces for TensorNet models, with performance gains ranging from 2× to 10× over previous, nonoptimized, iterations. Other enhancements include highly optimized neighbor search algorithms that support periodic boundary conditions and smooth integration with existing molecular dynamics frameworks. Additionally, the updated version introduces the capability to integrate physical priors, further enriching its application spectrum and utility in research. The software is available at https://github.com/torchmd/torchmd-net.
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Affiliation(s)
- Raul P Pelaez
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guillem Simeon
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Raimondas Galvelis
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain
- Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain
| | - Antonio Mirarchi
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Peter Eastman
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stefan Doerr
- Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain
| | | | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Gianni De Fabritiis
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain
- Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
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2
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Pelaez RP, Simeon G, Galvelis R, Mirarchi A, Eastman P, Doerr S, Thölke P, Markland TE, Fabritiis GD. TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations. ArXiv 2024:arXiv:2402.17660v2. [PMID: 38463504 PMCID: PMC10925388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Achieving a balance between computational speed, prediction accuracy, and universal applicability in molecular simulations has been a persistent challenge. This paper presents substantial advancements in the TorchMD-Net software, a pivotal step forward in the shift from conventional force fields to neural network-based potentials. The evolution of TorchMD-Net into a more comprehensive and versatile framework is highlighted, incorporating cutting-edge architectures such as TensorNet. This transformation is achieved through a modular design approach, encouraging customized applications within the scientific community. The most notable enhancement is a significant improvement in computational efficiency, achieving a very remarkable acceleration in the computation of energy and forces for TensorNet models, with performance gains ranging from 2-fold to 10-fold over previous iterations. Other enhancements include highly optimized neighbor search algorithms that support periodic boundary conditions and the smooth integration with existing molecular dynamics frameworks. Additionally, the updated version introduces the capability to integrate physical priors, further enriching its application spectrum and utility in research. The software is available at https://github.com/torchmd/torchmd-net.
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3
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Sabanés Zariquiey F, Galvelis R, Gallicchio E, Chodera JD, Markland TE, De Fabritiis G. Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. J Chem Inf Model 2024; 64:1481-1485. [PMID: 38376463 DOI: 10.1021/acs.jcim.3c02031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechanics methodology (NNP/MM). We compute relative binding free energies with the Alchemical Transfer Method and validate its performance against established benchmarks and find significant enhancements compared with conventional MM force fields like GAFF2.
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Affiliation(s)
- Francesc Sabanés Zariquiey
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain
- Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain
| | - Raimondas Galvelis
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain
- Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain
| | - Emilio Gallicchio
- Department of Chemistry, Graduate Center, Brooklyn College, City University of New York, New York, New York 11210, United States
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, California 94305, United States
| | - Gianni De Fabritiis
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain
- Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
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4
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Zariquiey FS, Galvelis R, Gallicchio E, Chodera JD, Markland TE, de Fabritiis G. Enhancing Protein-Ligand Binding Affinity Predictions using Neural Network Potentials. ArXiv 2024:arXiv:2401.16062v2. [PMID: 38351937 PMCID: PMC10862936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechanics methodology (NNP/MM). We compute relative binding free energies (RBFE) with the Alchemical Transfer Method (ATM) and validate its performance against established benchmarks and find significant enhancements compared to conventional MM force fields like GAFF2.
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5
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Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JPGLM, Rodriguez-Guerra J, Simmonett AC, Singh S, Swails J, Turner P, Wang Y, Zhang I, Chodera JD, De Fabritiis G, Markland TE. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. J Phys Chem B 2024; 128:109-116. [PMID: 38154096 PMCID: PMC10846090 DOI: 10.1021/acs.jpcb.3c06662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features in simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations with only a modest increase in cost.
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Affiliation(s)
- Peter Eastman
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Raimondas Galvelis
- Acellera Labs, C Dr Trueta 183, 08005, Barcelona, Spain
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Raúl P. Peláez
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Charlles R. A. Abreu
- Chemical Engineering Department, School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 68542, Brazil
- Redesign Science Inc., 180 Varick St., New York, NY 10014, USA
| | - Stephen E. Farr
- EaStCHEM School of Chemistry, University of Edinburgh, EH9 3FJ, United Kingdom
| | - Emilio Gallicchio
- Department of Chemistry and Biochemistry, Brooklyn College of the City University of New York, NY, USA
- Ph.D. Program in Chemistry and Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Anton Gorenko
- Stream HPC, Koningin Wilhelminaplein 1 - 40601, 1062 HG Amsterdam, Netherlands
| | - Michael M. Henry
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York NY 10065, USA
| | - Frank Hu
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Andreas Krämer
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany
| | - Julien Michel
- EaStCHEM School of Chemistry, University of Edinburgh, EH9 3FJ, United Kingdom
| | - Joshua A. Mitchell
- The Open Force Field Initiative, Open Molecular Software Foundation, Davis, CA 95616, USA
| | - Vijay S. Pande
- Andreessen Horowitz, 2865 Sand Hill Rd, Menlo Park, CA 94025, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - João PGLM Rodrigues
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Jaime Rodriguez-Guerra
- Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics, Virchowweg 6, 10117 Berlin, Germany
| | - Andrew C. Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sukrit Singh
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York NY 10065, USA
| | - Jason Swails
- Entos Inc., 9310 Athena Circle, La Jolla, CA 92037, USA
| | - Philip Turner
- College of Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Yuanqing Wang
- Simons Center for Computational Physical Chemistry and Center for Data Science, New York University, 24 Waverly Place, New York, NY 10004, USA
| | - Ivy Zhang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York NY 10065, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York NY 10065, USA
| | - Gianni De Fabritiis
- Acellera Labs, C Dr Trueta 183, 08005, Barcelona, Spain
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003, Barcelona, Spain
- ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain
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6
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Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, Rodriguez-Guerra J, Simmonett AC, Singh S, Swails J, Turner P, Wang Y, Zhang I, Chodera JD, Fabritiis GD, Markland TE. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. ArXiv 2023:arXiv:2310.03121v2. [PMID: 37986730 PMCID: PMC10659447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost.
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7
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Galvelis R, Varela-Rial A, Doerr S, Fino R, Eastman P, Markland TE, Chodera JD, De Fabritiis G. NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics. J Chem Inf Model 2023; 63:5701-5708. [PMID: 37694852 PMCID: PMC10577237 DOI: 10.1021/acs.jcim.3c00773] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared with traditional molecular mechanics. To tackle this issue, we introduce an optimized implementation of the hybrid method (NNP/MM), which combines a neural network potential (NNP) and molecular mechanics (MM). This approach models a portion of the system, such as a small molecule, using NNP while employing MM for the remaining system to boost efficiency. By conducting molecular dynamics (MD) simulations on various protein-ligand complexes and metadynamics (MTD) simulations on a ligand, we showcase the capabilities of our implementation of NNP/MM. It has enabled us to increase the simulation speed by ∼5 times and achieve a combined sampling of 1 μs for each complex, marking the longest simulations ever reported for this class of simulations.
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Affiliation(s)
- Raimondas Galvelis
- Acellera Labs, C/Doctor Trueta 183, Barcelona 08005, Spain
- Computational Science Laboratory, Universitat Pompeu Fabra, PRBB, C/Doctor Aiguader 88, Barcelona 08003, Spain
| | - Alejandro Varela-Rial
- Acellera Ltd, Devonshire House 582 Honeypot Lane, Stanmore Middlesex, HA7 1JS, United Kingdom
| | - Stefan Doerr
- Acellera Ltd, Devonshire House 582 Honeypot Lane, Stanmore Middlesex, HA7 1JS, United Kingdom
| | - Roberto Fino
- Acellera Labs, C/Doctor Trueta 183, Barcelona 08005, Spain
| | - Peter Eastman
- Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, California 94305, United States
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Gianni De Fabritiis
- Computational Science Laboratory, Universitat Pompeu Fabra, PRBB, C/Doctor Aiguader 88, Barcelona 08003, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, Barcelona 08010, Spain
- Acellera Ltd, Devonshire House 582 Honeypot Lane, Stanmore Middlesex, HA7 1JS, United Kingdom
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8
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Atsango AO, Morawietz T, Marsalek O, Markland TE. Developing machine-learned potentials to simultaneously capture the dynamics of excess protons and hydroxide ions in classical and path integral simulations. J Chem Phys 2023; 159:074101. [PMID: 37581418 DOI: 10.1063/5.0162066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanisms ideally requires utilizing ab initio molecular dynamics simulations to model the bond breaking and formation involved in proton transfer and path-integral simulations to model the nuclear quantum effects relevant to light hydrogen atoms. These requirements result in a prohibitive computational cost, especially at the time and length scales needed to converge proton transport properties. Here, we present machine-learned potentials (MLPs) that can model both excess protons and hydroxide ions at the generalized gradient approximation and hybrid density functional theory levels of accuracy and use them to perform multiple nanoseconds of both classical and path-integral proton defect simulations at a fraction of the cost of the corresponding ab initio simulations. We show that the MLPs are able to reproduce ab initio trends and converge properties such as the diffusion coefficients of both excess protons and hydroxide ions. We use our multi-nanosecond simulations, which allow us to monitor large numbers of proton transfer events, to analyze the role of hypercoordination in the transport mechanism of the hydroxide ion and provide further evidence for the asymmetry in diffusion between excess protons and hydroxide ions.
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Affiliation(s)
- Austin O Atsango
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Ondrej Marsalek
- Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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9
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Chen MS, Mao Y, Snider A, Gupta P, Montoya-Castillo A, Zuehlsdorff TJ, Isborn CM, Markland TE. Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure. J Phys Chem Lett 2023; 14:6610-6619. [PMID: 37459252 DOI: 10.1021/acs.jpclett.3c01444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical spectra. For chromophores in the condensed phase, the large number of atoms needed to simulate the environment has traditionally prohibited the use of high-level excited-state electronic structure methods. By leveraging transfer learning, we show how to construct machine-learned models to accurately predict the high-level excitation energies of a chromophore in solution from only 400 high-level calculations. We show that when the electronic excitations of the green fluorescent protein chromophore in water are treated using EOM-CCSD embedded in a DFT description of the solvent the optical spectrum is correctly captured and that this improvement arises from correctly treating the coupling of the electronic transition to electric fields, which leads to a larger response upon hydrogen bonding between the chromophore and water.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Andrew Snider
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Prachi Gupta
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Andrés Montoya-Castillo
- Department of Chemistry, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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10
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Chen MS, Lee J, Ye HZ, Berkelbach TC, Reichman DR, Markland TE. Data-Efficient Machine Learning Potentials from Transfer Learning of Periodic Correlated Electronic Structure Methods: Liquid Water at AFQMC, CCSD, and CCSD(T) Accuracy. J Chem Theory Comput 2023; 19:4510-4519. [PMID: 36730728 DOI: 10.1021/acs.jctc.2c01203] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Obtaining the atomistic structure and dynamics of disordered condensed-phase systems from first-principles remains one of the forefront challenges of chemical theory. Here we exploit recent advances in periodic electronic structure and provide a data-efficient approach to obtain machine-learned condensed-phase potential energy surfaces using AFQMC, CCSD, and CCSD(T) from a very small number (≤200) of energies by leveraging a transfer learning scheme starting from lower-tier electronic structure methods. We demonstrate the effectiveness of this approach for liquid water by performing both classical and path integral molecular dynamics simulations on these machine-learned potential energy surfaces. By doing this, we uncover the interplay of dynamical electron correlation and nuclear quantum effects across the entire liquid range of water while providing a general strategy for efficiently utilizing periodic correlated electronic structure methods to explore disordered condensed-phase systems.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California94305, United States
| | - Joonho Lee
- Department of Chemistry, Columbia University, New York, New York10027, United States
| | - Hong-Zhou Ye
- Department of Chemistry, Columbia University, New York, New York10027, United States
| | - Timothy C Berkelbach
- Department of Chemistry, Columbia University, New York, New York10027, United States
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York10010, United States
| | - David R Reichman
- Department of Chemistry, Columbia University, New York, New York10027, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California94305, United States
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11
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Jung KA, Kelly J, Markland TE. Electron transfer at electrode interfaces via a straightforward quasiclassical fermionic mapping approach. J Chem Phys 2023; 159:014109. [PMID: 37409707 DOI: 10.1063/5.0156136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
Electron transfer at electrode interfaces to molecules in solution or at the electrode surface plays a vital role in numerous technological processes. However, treating these processes requires a unified and accurate treatment of the fermionic states of the electrode and their coupling to the molecule being oxidized or reduced in the electrochemical processes and, in turn, the way the molecular energy levels are modulated by the bosonic nuclear modes of the molecule and solvent. Here we present a physically transparent quasiclassical scheme to treat these electrochemical electron transfer processes in the presence of molecular vibrations by using an appropriately chosen mapping of the fermionic variables. We demonstrate that this approach, which is exact in the limit of non-interacting fermions in the absence of coupling to vibrations, is able to accurately capture the electron transfer dynamics from the electrode even when the process is coupled to vibrational motions in the regimes of weak coupling. This approach, thus, provides a scalable strategy to explicitly treat electron transfer from electrode interfaces in condensed-phase molecular systems.
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Affiliation(s)
- Kenneth A Jung
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Joseph Kelly
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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12
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Dominic AJ, Sayer T, Cao S, Markland TE, Huang X, Montoya-Castillo A. Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations. Proc Natl Acad Sci U S A 2023; 120:e2221048120. [PMID: 36920924 PMCID: PMC10041170 DOI: 10.1073/pnas.2221048120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
The ability to predict and understand complex molecular motions occurring over diverse timescales ranging from picoseconds to seconds and even hours in biological systems remains one of the largest challenges to chemical theory. Markov state models (MSMs), which provide a memoryless description of the transitions between different states of a biochemical system, have provided numerous important physically transparent insights into biological function. However, constructing these models often necessitates performing extremely long molecular simulations to converge the rates. Here, we show that by incorporating memory via the time-convolutionless generalized master equation (TCL-GME) one can build a theoretically transparent and physically intuitive memory-enriched model of biochemical processes with up to a three order of magnitude reduction in the simulation data required while also providing a higher temporal resolution. We derive the conditions under which the TCL-GME provides a more efficient means to capture slow dynamics than MSMs and rigorously prove when the two provide equally valid and efficient descriptions of the slow configurational dynamics. We further introduce a simple averaging procedure that enables our TCL-GME approach to quickly converge and accurately predict long-time dynamics even when parameterized with noisy reference data arising from short trajectories. We illustrate the advantages of the TCL-GME using alanine dipeptide, the human argonaute complex, and FiP35 WW domain.
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Affiliation(s)
| | - Thomas Sayer
- Department of Chemistry, University of Colorado, Boulder, CO80309
| | - Siqin Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | | | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
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13
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Montoya-Castillo A, Markland TE. A derivation of the conditions under which bosonic operators exactly capture fermionic structure and dynamics. J Chem Phys 2023; 158:094112. [PMID: 36889969 DOI: 10.1063/5.0138664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The dynamics of many-body fermionic systems are important in problems ranging from catalytic reactions at electrochemical surfaces to transport through nanojunctions and offer a prime target for quantum computing applications. Here, we derive the set of conditions under which fermionic operators can be exactly replaced by bosonic operators that render the problem amenable to a large toolbox of dynamical methods while still capturing the correct dynamics of n-body operators. Importantly, our analysis offers a simple guide on how one can exploit these simple maps to calculate nonequilibrium and equilibrium single- and multi-time correlation functions essential in describing transport and spectroscopy. We use this to rigorously analyze and delineate the applicability of simple yet effective Cartesian maps that have been shown to correctly capture the correct fermionic dynamics in select models of nanoscopic transport. We illustrate our analytical results with exact simulations of the resonant level model. Our work provides new insights as to when one can leverage the simplicity of bosonic maps to simulate the dynamics of many-electron systems, especially those where an atomistic representation of nuclear interactions becomes essential.
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Affiliation(s)
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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14
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Atsango AO, Montoya-Castillo A, Markland TE. An accurate and efficient Ehrenfest dynamics approach for calculating linear and nonlinear electronic spectra. J Chem Phys 2023; 158:074107. [PMID: 36813724 DOI: 10.1063/5.0138671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Linear and nonlinear electronic spectra provide an important tool to probe the absorption and transfer of electronic energy. Here, we introduce a pure state Ehrenfest approach to obtain accurate linear and nonlinear spectra that is applicable to systems with large numbers of excited states and complex chemical environments. We achieve this by representing the initial conditions as sums of pure states and unfolding multi-time correlation functions into the Schrödinger picture. By doing this, we show that one can obtain significant improvements in accuracy over the previously used projected Ehrenfest approach and that these benefits are particularly pronounced in cases where the initial condition is a coherence between excited states. While such initial conditions do not arise when calculating linear electronic spectra, they play a vital role in capturing multidimensional spectroscopies. We demonstrate the performance of our method by showing that it is able to quantitatively capture the exact linear, 2D electronic spectroscopy, and pump-probe spectra for a Frenkel exciton model in slow bath regimes and is even able to reproduce the main spectral features in fast bath regimes.
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Affiliation(s)
- Austin O Atsango
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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15
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Fried SDE, Kirsh JM, Zheng C, Mao Y, Markland TE, Boxer SG. Carbon-deuterium bonds as reporters of electric fields in solvent and protein environments. Biophys J 2023; 122:481a. [PMID: 36784478 DOI: 10.1016/j.bpj.2022.11.2574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | - Jacob M Kirsh
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Chu Zheng
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA, USA
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16
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Eastman P, Behara PK, Dotson DL, Galvelis R, Herr JE, Horton JT, Mao Y, Chodera JD, Pritchard BP, Wang Y, De Fabritiis G, Markland TE. SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 2023; 10:11. [PMID: 36599873 PMCID: PMC9813265 DOI: 10.1038/s41597-022-01882-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023] Open
Abstract
Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, along with other useful quantities such as multipole moments and bond orders. We train a set of machine learning potentials on it and demonstrate that they can achieve chemical accuracy across a broad region of chemical space. It can serve as a valuable resource for the creation of transferable, ready to use potential functions for use in molecular simulations.
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Affiliation(s)
- Peter Eastman
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
| | - Pavan Kumar Behara
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - David L Dotson
- The Open Force Field Initiative, Open Molecular Software Foundation, Davis, CA, 95616, USA
| | | | - John E Herr
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Josh T Horton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Benjamin P Pritchard
- Molecular Sciences Software Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24060, USA
| | - Yuanqing Wang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Gianni De Fabritiis
- Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain and ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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17
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Fried SDE, Zheng C, Mao Y, Markland TE, Boxer SG. Solvent Organization and Electrostatics Tuned by Solute Electronic Structure: Amide versus Non-Amide Carbonyls. J Phys Chem B 2022; 126:5876-5886. [PMID: 35901512 PMCID: PMC10081530 DOI: 10.1021/acs.jpcb.2c03095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to exploit carbonyl groups to measure electric fields in enzymes and other complex reactive environments by using the vibrational Stark effect has inspired growing interest in how these fields can be measured, tuned, and ultimately designed. Previous studies have concentrated on the role of the solvent in tuning the fields exerted on the solute. Here, we explore instead the role of the solute electronic structure in modifying the local solvent organization and electric field exerted on the solute. By measuring the infrared absorption spectra of amide-containing molecules, as prototypical peptides, and contrasting them with non-amide carbonyls in a wide range of solvents, we show that these solutes experience notable differences in their frequency shifts in polar solvents. Using vibrational Stark spectroscopy and molecular dynamics simulations, we demonstrate that while some of these differences can be rationalized by using the distinct intrinsic Stark tuning rates of the solutes, the larger frequency shifts for amides and dimethylurea primarily result from the larger solvent electric fields experienced by their carbonyl groups. These larger fields arise due to their stronger p-π conjugation, which results in larger C═O bond dipole moments that further induce substantial solvent organization. Using electronic structure calculations, we decompose the electric fields into contributions from solvent molecules that are in the first solvation shell and those from the bulk and show that both of these contributions are significant and become larger with enhanced conjugation in solutes. These results show that structural modifications of a solute can be used to tune both the solvent organization and electrostatic environment, indicating the importance of a solute-centric paradigm in modulating and designing the electrostatic environment in condensed-phase chemical processes.
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Affiliation(s)
- Steven D E Fried
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Chu Zheng
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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18
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Montoya-Castillo A, Chen MS, Raj SL, Jung KA, Kjaer KS, Morawietz T, Gaffney KJ, van Driel TB, Markland TE. Optically Induced Anisotropy in Time-Resolved Scattering: Imaging Molecular-Scale Structure and Dynamics in Disordered Media with Experiment and Theory. Phys Rev Lett 2022; 129:056001. [PMID: 35960558 DOI: 10.1103/physrevlett.129.056001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Time-resolved scattering experiments enable imaging of materials at the molecular scale with femtosecond time resolution. However, in disordered media they provide access to just one radial dimension thus limiting the study of orientational structure and dynamics. Here we introduce a rigorous and practical theoretical framework for predicting and interpreting experiments combining optically induced anisotropy and time-resolved scattering. Using impulsive nuclear Raman and ultrafast x-ray scattering experiments of chloroform and simulations, we demonstrate that this framework can accurately predict and elucidate both the spatial and temporal features of these experiments.
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Affiliation(s)
| | - Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Sumana L Raj
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Kenneth A Jung
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Kasper S Kjaer
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Kelly J Gaffney
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Tim B van Driel
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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19
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Fried SD, Zheng C, Mao Y, Markland TE, Boxer SG. Tuning solvent electrostatic environment of amide carbonyls as prototypical peptide backbones. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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20
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Huang Z, Chen MS, Woroch CP, Markland TE, Kanan MW. A framework for automated structure elucidation from routine NMR spectra. Chem Sci 2021; 12:15329-15338. [PMID: 34976353 PMCID: PMC8635205 DOI: 10.1039/d1sc04105c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022] Open
Abstract
Methods to automate structure elucidation that can be applied broadly across chemical structure space have the potential to greatly accelerate chemical discovery. NMR spectroscopy is the most widely used and arguably the most powerful method for elucidating structures of organic molecules. Here we introduce a machine learning (ML) framework that provides a quantitative probabilistic ranking of the most likely structural connectivity of an unknown compound when given routine, experimental one dimensional 1H and/or 13C NMR spectra. In particular, our ML-based algorithm takes input NMR spectra and (i) predicts the presence of specific substructures out of hundreds of substructures it has learned to identify; (ii) annotates the spectrum to label peaks with predicted substructures; and (iii) uses the substructures to construct candidate constitutional isomers and assign to them a probabilistic ranking. Using experimental spectra and molecular formulae for molecules containing up to 10 non-hydrogen atoms, the correct constitutional isomer was the highest-ranking prediction made by our model in 67.4% of the cases and one of the top-ten predictions in 95.8% of the cases. This advance will aid in solving the structure of unknown compounds, and thus further the development of automated structure elucidation tools that could enable the creation of fully autonomous reaction discovery platforms. A machine learning model and graph generator were able to accurately predict for the presence of nearly 1000 substructures and the connectivity of small organic molecules from experimental 1D NMR data.![]()
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Affiliation(s)
- Zhaorui Huang
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | - Michael S Chen
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | | | | | - Matthew W Kanan
- Department of Chemistry, Stanford University Stanford CA 94305 USA
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21
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Atsango AO, Tuckerman ME, Markland TE. Characterizing and Contrasting Structural Proton Transport Mechanisms in Azole Hydrogen Bond Networks Using Ab Initio Molecular Dynamics. J Phys Chem Lett 2021; 12:8749-8756. [PMID: 34478302 DOI: 10.1021/acs.jpclett.1c02266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Imidazole and 1,2,3-triazole are promising hydrogen-bonded heterocycles that conduct protons via a structural mechanism and whose derivatives are present in systems ranging from biological proton channels to proton exchange membrane fuel cells. Here, we leverage multiple time-stepping to perform ab initio molecular dynamics of imidazole and 1,2,3-triazole at the nanosecond time scale. We show that despite the close structural similarities of these compounds, their proton diffusion constants vary by over an order of magnitude. Our simulations reveal the reasons for these differences in diffusion constants, which range from the degree of hydrogen-bonded chain linearity to the effect of the central nitrogen atom in 1,2,3-triazole on proton transport. In particular, we uncover evidence of two "blocking" mechanisms in 1,2,3-triazole, where covalent and hydrogen bonds formed by the central nitrogen atom limit the mobility of protons. Our simulations thus provide insights into the origins of the experimentally observed 10-fold difference in proton conductivity.
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Affiliation(s)
- Austin O Atsango
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mark E Tuckerman
- Department of Chemistry, New York University, New York, New York 10003, United States
- Courant Institute of Mathematical Science, New York University, New York, New York 10012, United States
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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22
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Chen MS, Morawietz T, Mori H, Markland TE, Artrith N. AENET-LAMMPS and AENET-TINKER: Interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials. J Chem Phys 2021; 155:074801. [PMID: 34418919 DOI: 10.1063/5.0063880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Machine-learning potentials (MLPs) trained on data from quantum-mechanics based first-principles methods can approach the accuracy of the reference method at a fraction of the computational cost. To facilitate efficient MLP-based molecular dynamics and Monte Carlo simulations, an integration of the MLPs with sampling software is needed. Here, we develop two interfaces that link the atomic energy network (ænet) MLP package with the popular sampling packages TINKER and LAMMPS. The three packages, ænet, TINKER, and LAMMPS, are free and open-source software that enable, in combination, accurate simulations of large and complex systems with low computational cost that scales linearly with the number of atoms. Scaling tests show that the parallel efficiency of the ænet-TINKER interface is nearly optimal but is limited to shared-memory systems. The ænet-LAMMPS interface achieves excellent parallel efficiency on highly parallel distributed-memory systems and benefits from the highly optimized neighbor list implemented in LAMMPS. We demonstrate the utility of the two MLP interfaces for two relevant example applications: the investigation of diffusion phenomena in liquid water and the equilibration of nanostructured amorphous battery materials.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Hideki Mori
- Department of Mechanical Engineering, College of Industrial Technology, 1-27-1 Nishikoya, Amagasaki, Hyogo 661-0047, Japan
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Nongnuch Artrith
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
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23
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Hu Y, Ounkham P, Marsalek O, Markland TE, Krishmoorthy B, Clark AE. Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics. Front Chem 2021; 9:624937. [PMID: 33748074 PMCID: PMC7973227 DOI: 10.3389/fchem.2021.624937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022] Open
Abstract
Nuclear quantum effects (NQEs) are known to impact a number of features associated with chemical reactivity and physicochemical properties, particularly for light atoms and at low temperatures. In the imaginary time path integral formalism, each atom is mapped onto a "ring polymer" whose spread is related to the quantum mechanical uncertainty in the particle's position, i.e., its thermal wavelength. A number of metrics have previously been used to investigate and characterize this spread and explain effects arising from quantum delocalization, zero-point energy, and tunneling. Many of these shape metrics consider just the instantaneous structure of the ring polymers. However, given the significant interest in methods such as centroid molecular dynamics and ring polymer molecular dynamics that link the molecular dynamics of these ring polymers to real time properties, there exists significant opportunity to exploit metrics that also allow for the study of the fluctuations of the atom delocalization in time. Here we consider the ring polymer delocalization from the perspective of computational topology, specifically persistent homology, which describes the 3-dimensional arrangement of point cloud data, (i.e. atomic positions). We employ the Betti sequence probability distribution to define the ensemble of shapes adopted by the ring polymer. The Wasserstein distances of Betti sequences adjacent in time are used to characterize fluctuations in shape, where the Fourier transform and associated principal components provides added information differentiating atoms with different NQEs based on their dynamic properties. We demonstrate this methodology on two representative systems, a glassy system consisting of two atom types with dramatically different de Broglie thermal wavelengths, and ab initio molecular dynamics simulation of an aqueous 4 M HCl solution where the H-atoms are differentiated based on their participation in proton transfer reactions.
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Affiliation(s)
- Yunfeng Hu
- Department of Mathematics and Statistics, Washington State University, Pullman, WA, United States
| | - Phonemany Ounkham
- Department of Chemistry, Washington State University, Pullman, WA, United States
| | - Ondrej Marsalek
- Faculty of Mathematics and Physics, Charles University, Prague, Czech
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, CA, United States
| | - Bala Krishmoorthy
- Department of Mathematics and Statistics, Washington State University, Vancouver, WA, United States
| | - Aurora E Clark
- Department of Chemistry, Washington State University, Pullman, WA, United States
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24
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Cao S, Montoya-Castillo A, Wang W, Markland TE, Huang X. On the advantages of exploiting memory in Markov state models for biomolecular dynamics. J Chem Phys 2021; 153:014105. [PMID: 32640825 DOI: 10.1063/5.0010787] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Biomolecular dynamics play an important role in numerous biological processes. Markov State Models (MSMs) provide a powerful approach to study these dynamic processes by predicting long time scale dynamics based on many short molecular dynamics (MD) simulations. In an MSM, protein dynamics are modeled as a kinetic process consisting of a series of Markovian transitions between different conformational states at discrete time intervals (called "lag time"). To achieve this, a master equation must be constructed with a sufficiently long lag time to allow interstate transitions to become truly Markovian. This imposes a major challenge for MSM studies of proteins since the lag time is bound by the length of relatively short MD simulations available to estimate the frequency of transitions. Here, we show how one can employ the generalized master equation formalism to obtain an exact description of protein conformational dynamics both at short and long time scales without the time resolution restrictions imposed by the MSM lag time. Using a simple kinetic model, alanine dipeptide, and WW domain, we demonstrate that it is possible to construct these quasi-Markov State Models (qMSMs) using MD simulations that are 5-10 times shorter than those required by MSMs. These qMSMs only contain a handful of metastable states and, thus, can greatly facilitate the interpretation of mechanisms associated with protein dynamics. A qMSM opens the door to the study of conformational changes of complex biomolecules where a Markovian model with a few states is often difficult to construct due to the limited length of available MD simulations.
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Affiliation(s)
- Siqin Cao
- Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | | | - Wei Wang
- Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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25
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Mao Y, Montoya-Castillo A, Markland TE. Excited state diabatization on the cheap using DFT: Photoinduced electron and hole transfer. J Chem Phys 2020; 153:244111. [PMID: 33380087 DOI: 10.1063/5.0035593] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Excited state electron and hole transfer underpin fundamental steps in processes such as exciton dissociation at photovoltaic heterojunctions, photoinduced charge transfer at electrodes, and electron transfer in photosynthetic reaction centers. Diabatic states corresponding to charge or excitation localized species, such as locally excited and charge transfer states, provide a physically intuitive framework to simulate and understand these processes. However, obtaining accurate diabatic states and their couplings from adiabatic electronic states generally leads to inaccurate results when combined with low-tier electronic structure methods, such as time-dependent density functional theory, and exorbitant computational cost when combined with high-level wavefunction-based methods. Here, we introduce a density functional theory (DFT)-based diabatization scheme that directly constructs the diabatic states using absolutely localized molecular orbitals (ALMOs), which we denote as Δ-ALMO(MSDFT2). We demonstrate that our method, which combines ALMO calculations with the ΔSCF technique to construct electronically excited diabatic states and obtains their couplings with charge-transfer states using our MSDFT2 scheme, gives accurate results for excited state electron and hole transfer in both charged and uncharged systems that underlie DNA repair, charge separation in donor-acceptor dyads, chromophore-to-solvent electron transfer, and singlet fission. This framework for the accurate and efficient construction of excited state diabats and evaluation of their couplings directly from DFT thus offers a route to simulate and elucidate photoinduced electron and hole transfer in large disordered systems, such as those encountered in the condensed phase.
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Affiliation(s)
- Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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26
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Chen MS, Zuehlsdorff TJ, Morawietz T, Isborn CM, Markland TE. Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments. J Phys Chem Lett 2020; 11:7559-7568. [PMID: 32808797 DOI: 10.1021/acs.jpclett.0c02168] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The excited-state dynamics of chromophores in complex environments determine a range of vital biological and energy capture processes. Time-resolved, multidimensional optical spectroscopies provide a key tool to investigate these processes. Although theory has the potential to decode these spectra in terms of the electronic and atomistic dynamics, the need for large numbers of excited-state electronic structure calculations severely limits first-principles predictions of multidimensional optical spectra for chromophores in the condensed phase. Here, we leverage the locality of chromophore excitations to develop machine learning models to predict the excited-state energy gap of chromophores in complex environments for efficiently constructing linear and multidimensional optical spectra. By analyzing the performance of these models, which span a hierarchy of physical approximations, across a range of chromophore-environment interaction strengths, we provide strategies for the construction of machine learning models that greatly accelerate the calculation of multidimensional optical spectra from first principles.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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27
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Long Z, Atsango AO, Napoli JA, Markland TE, Tuckerman ME. Elucidating the Proton Transport Pathways in Liquid Imidazole with First-Principles Molecular Dynamics. J Phys Chem Lett 2020; 11:6156-6163. [PMID: 32633523 DOI: 10.1021/acs.jpclett.0c01744] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Imidazole is a promising anhydrous proton conductor with a high conductivity comparable to that of water at a similar temperature relative to its melting point. Previous theoretical studies of the mechanism of proton transport in imidazole have relied either on empirical models or on ab initio trajectories that have been too short to draw significant conclusions. Here, we present the results of multiple time-step ab initio molecular dynamics simulations of an excess proton in liquid imidazole reaching 1 ns in total simulation time. We find that the proton transport is dominated by structural diffusion, with the diffusion constant of the proton defect being ∼8 times higher than that of self-diffusion of the imidazole molecules. By using correlation function analysis, we decompose the mechanism for proton transport into a series of first-order processes and show that the proton transport mechanism occurs over three distinct time and length scales. Although the mechanism at intermediate times is dominated by hopping along pseudo-one-dimensional chains, at longer times the overall rate of diffusion is limited by the re-formation of these chains. These results provide a more complete picture of the traditional idealized Grotthuss structural diffusion mechanism.
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Affiliation(s)
- Zhuoran Long
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Austin O Atsango
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Joseph A Napoli
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mark E Tuckerman
- Department of Chemistry, New York University, New York, New York 10003, United States
- Courant Institute of Mathematical Science, New York University, New York, New York 10012, United States
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
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28
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Roy S, Schenter GK, Napoli JA, Baer MD, Markland TE, Mundy CJ. Resolving Heterogeneous Dynamics of Excess Protons in Aqueous Solution with Rate Theory. J Phys Chem B 2020; 124:5665-5675. [DOI: 10.1021/acs.jpcb.0c02649] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Gregory K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, Washington 99352, United States
| | - Joseph A. Napoli
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305, United States
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, Washington 99352, United States
| | - Thomas E. Markland
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305, United States
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, Washington 99352, United States
- Affiliate Professor, Department of Chemical Engineering, University of Washington, Seattle, United States
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29
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Abstract
At room temperature, the quantum contribution to the kinetic energy of a water molecule exceeds the classical contribution by an order of magnitude. The quantum kinetic energy (QKE) of a water molecule is modulated by its local chemical environment and leads to uneven partitioning of isotopes between different phases in thermal equilibrium, which would not occur if the nuclei behaved classically. In this work, we use ab initio path integral simulations to show that QKEs of the water molecules and the equilibrium isotope fractionation ratios of the oxygen and hydrogen isotopes are sensitive probes of the hydrogen bonding structures in aqueous ionic solutions. In particular, we demonstrate how the QKE of water molecules in path integral simulations can be decomposed into translational, rotational and vibrational degrees of freedom, and use them to determine the impact of solvation on different molecular motions. By analyzing the QKEs and isotope fractionation ratios, we show how the addition of the Na+, Cl- and HPO42- ions perturbs the competition between quantum effects in liquid water and impacts their local solvation structures.
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Affiliation(s)
- Lu Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
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30
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Mao Y, Montoya-Castillo A, Markland TE. Accurate and efficient DFT-based diabatization for hole and electron transfer using absolutely localized molecular orbitals. J Chem Phys 2019; 151:164114. [DOI: 10.1063/1.5125275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Thomas E. Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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31
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Morawietz T, Urbina AS, Wise PK, Wu X, Lu W, Ben-Amotz D, Markland TE. Hiding in the Crowd: Spectral Signatures of Overcoordinated Hydrogen-Bond Environments. J Phys Chem Lett 2019; 10:6067-6073. [PMID: 31549833 DOI: 10.1021/acs.jpclett.9b01781] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecules with an excess number of hydrogen-bonding partners play a crucial role in fundamental chemical processes, ranging from anomalous diffusion in supercooled water to transport of aqueous proton defects and ordering of water around hydrophobic solutes. Here we show that overcoordinated hydrogen-bond environments can be identified in both the ambient and supercooled regimes of liquid water by combining experimental Raman multivariate curve resolution measurements and machine learning accelerated quantum simulations. In particular, we find that OH groups appearing in spectral regions usually associated with non-hydrogen-bonded species actually correspond to hydrogen bonds formed in overcoordinated environments. We further show that only these species exhibit a turnover in population as a function of temperature, which is robust and persists under both constant pressure and density conditions. This work thus provides a new tool to identify, interpret, and elucidate the spectral signatures of crowded hydrogen-bond networks.
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Affiliation(s)
- Tobias Morawietz
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Andres S Urbina
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Patrick K Wise
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Xiangen Wu
- College of Marine Science and Technology , China University of Geosciences , Wuhan 430074 , China
| | - Wanjun Lu
- College of Marine Science and Technology , China University of Geosciences , Wuhan 430074 , China
| | - Dor Ben-Amotz
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Thomas E Markland
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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32
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Zuehlsdorff TJ, Montoya-Castillo A, Napoli JA, Markland TE, Isborn CM. Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches. J Chem Phys 2019; 151:074111. [PMID: 31438704 DOI: 10.1063/1.5114818] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. Here, we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic time scale separation; the Franck-Condon method, which includes dynamical effects but generally only at the harmonic level; and the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap fluctuations and test the ability to approximate the requisite time correlation functions using classical dynamics with quantum correction factors. These results provide insights as to when these methods are applicable and able to capture the features of condensed phase spectra qualitatively and, in some cases, quantitatively across a range of regimes.
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Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | | | - Joseph A Napoli
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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33
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Yuan R, Napoli JA, Yan C, Marsalek O, Markland TE, Fayer MD. Tracking Aqueous Proton Transfer by Two-Dimensional Infrared Spectroscopy and ab Initio Molecular Dynamics Simulations. ACS Cent Sci 2019; 5:1269-1277. [PMID: 31403075 PMCID: PMC6661862 DOI: 10.1021/acscentsci.9b00447] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Indexed: 05/26/2023]
Abstract
Proton transfer in water is ubiquitous and a critical elementary event that, via proton hopping between water molecules, enables protons to diffuse much faster than other ions. The problem of the anomalous nature of proton transport in water was first identified by Grotthuss over 200 years ago. In spite of a vast amount of modern research effort, there are still many unanswered questions about proton transport in water. An experimental determination of the proton hopping time has remained elusive due to its ultrafast nature and the lack of direct experimental observables. Here, we use two-dimensional infrared spectroscopy to extract the chemical exchange rates between hydronium and water in acid solutions using a vibrational probe, methyl thiocyanate. Ab initio molecular dynamics (AIMD) simulations demonstrate that the chemical exchange is dominated by proton hopping. The observed experimental and simulated acid concentration dependence then allow us to extrapolate the measured single step proton hopping time to the dilute limit, which, within error, gives the same value as inferred from measurements of the proton mobility and NMR line width analysis. In addition to obtaining the proton hopping time in the dilute limit from direct measurements and AIMD simulations, the results indicate that proton hopping in dilute acid solutions is induced by the concerted multi-water molecule hydrogen bond rearrangement that occurs in pure water. This proposition on the dynamics that drive proton hopping is confirmed by a combination of experimental results from the literature.
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Affiliation(s)
- Rongfeng Yuan
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Joseph A. Napoli
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Chang Yan
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ondrej Marsalek
- Charles
University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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34
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Pfalzgraff WC, Montoya-Castillo A, Kelly A, Markland TE. Efficient construction of generalized master equation memory kernels for multi-state systems from nonadiabatic quantum-classical dynamics. J Chem Phys 2019; 150:244109. [DOI: 10.1063/1.5095715] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- William C. Pfalzgraff
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Department of Chemistry, Chatham University, Pittsburgh, Pennsylvania 15232, USA
| | | | - Aaron Kelly
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Thomas E. Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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35
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Boyer MA, Marsalek O, Heindel JP, Markland TE, McCoy AB, Xantheas SS. Beyond Badger's Rule: The Origins and Generality of the Structure-Spectra Relationship of Aqueous Hydrogen Bonds. J Phys Chem Lett 2019; 10:918-924. [PMID: 30735052 DOI: 10.1021/acs.jpclett.8b03790] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The structure of hydrogen bonded networks is intimately intertwined with their dynamics. Despite the incredibly wide range of hydrogen bond strengths encountered in water clusters, ion-water clusters, and liquid water, we demonstrate that the previously reported correlation between the change in the equilibrium bond length of the hydrogen bonded OH covalent bond and the corresponding shift in its harmonic frequency in water clusters is much more broadly applicable. Surprisingly, this correlation describes the ratios for both the equilibrium OH bond length/harmonic frequency and the vibrationally averaged bond length/anharmonic frequency in water, hydronium water, and halide water clusters. Consideration of harmonic and anaharmonic data leads to a correlation of -19 ± 1 cm-1/0.001 Å. The fundamental nature of this correlation is further confirmed through the analysis of ab initio Molecular Dynamics (AIMD) trajectories for liquid water. We demonstrate that this simple correlation for both harmonic and anharmonic systems can be modeled by the response of an OH bond to an external field. Treating the OH bond as a Morse oscillator, we develop analytic expressions, which relate the ratio of the shift in the vibrational frequency of the hydrogen-bonded OH bond to the shift in OH bond length, to parameters in the Morse potential and the ratio of the first and second derivatives of the field-dependent projection of the dipole moment of water onto the hydrogen-bonded OH bond. Based on our analysis, we develop a protocol for reconstructing the AIMD spectra of liquid water from the sampled distribution of the OH bond lengths. Our findings elucidate the origins of the relationship between the molecular structure of the fleeting hydrogen-bonded network and the ensuing dynamics, which can be probed by vibrational spectroscopy.
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Affiliation(s)
- Mark A Boyer
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Ondrej Marsalek
- Charles University , Faculty of Mathematics and Physics , Ke Karlovu 3 , 121 16 Prague 2, Czech Republic
| | - Joseph P Heindel
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Thomas E Markland
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Anne B McCoy
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Sotiris S Xantheas
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
- Advanced Computing, Mathematics and Data Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , P.O. Box 999, MS K1-83, Richland , Washington 99352 , United States
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36
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Schran C, Marsalek O, Markland TE. Corrigendum to “Unravelling the influence of quantum proton delocalization on electronic charge transfer through the hydrogen bond” [Chem. Phys. Lett. 678 (2017) 289–295]. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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37
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Abstract
Developing accurate ab initio molecular dynamics (AIMD) models that capture both electronic reorganization and nuclear quantum effects associated with hydrogen bonding is key to quantitative understanding of bulk water and its anomalies as well as its role as a universal solvent. For condensed phase simulations, AIMD has typically relied on the generalized gradient approximation (GGA) of density functional theory (DFT) as the underlying model chemistry for the potential energy surface, with nuclear quantum effects (NQEs) sometimes modeled by performing classical molecular dynamics simulations at elevated temperatures. Here we show that the properties of liquid water obtained from the meta-GGA B97M-rV functional, when evaluated using accelerated path integral molecular dynamics simulations, display accuracy comparable to a computationally expensive dispersion-corrected hybrid functional, revPBE0-D3. We show that the meta-GGA DFT functional reproduces bulk water properties including radial distribution functions, self-diffusion coefficients, and infrared spectra with comparable accuracy of a much more expensive hybrid functional. This work demonstrates that the underlying quality of a good DFT functional requires evaluation with quantum nuclei and that high-temperature simulations are a poor proxy for properly treating NQEs.
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Affiliation(s)
| | - Ondrej Marsalek
- Charles University , Faculty of Mathematics and Physics , Ke Karlovu 3 , 121 16 Prague 2 , Czech Republic
| | - Thomas E Markland
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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38
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Abstract
We derive a rigorous, quantum mechanical map of fermionic creation and annihilation operators to continuous Cartesian variables that exactly reproduces the matrix structure of the many-fermion problem. We show how our scheme can be used to map a general many-fermion Hamiltonian and then consider two specific models that encode the fundamental physics of many fermionic systems, the Anderson impurity and Hubbard models. We use these models to demonstrate how efficient mappings of these Hamiltonians can be constructed using a judicious choice of index ordering of the fermions. This development provides an alternative exact route to calculate the static and dynamical properties of fermionic systems and sets the stage to exploit the quantum-classical and semiclassical hierarchies to systematically derive methods offering a range of accuracies, thus enabling the study of problems where the fermionic degrees of freedom are coupled to complex anharmonic nuclear motion and spins which lie beyond the reach of most currently available methods.
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Affiliation(s)
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California, 94305, USA.
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39
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Zuehlsdorff TJ, Napoli JA, Milanese JM, Markland TE, Isborn CM. Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water. J Chem Phys 2018; 149:024107. [PMID: 30007372 DOI: 10.1063/1.5025517] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.
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Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Joseph A Napoli
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Joel M Milanese
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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40
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Abstract
Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, disentangling the transient structural motifs of proton defects in the water hydrogen bond network and the mechanisms for their interconversion remains a formidable challenge. Here, we use simulations treating the quantum nature of both the electrons and nuclei to show how the experimentally observed spectroscopic features and relaxation time scales can be elucidated using a physically transparent coordinate that encodes the overall asymmetry of the solvation environment of the proton defect. We demonstrate that this coordinate can be used both to discriminate the extremities of the features observed in the linear vibrational spectrum and to explain the molecular motions that give rise to the interconversion time scales observed in recent nonlinear experiments. This analysis provides a unified condensed-phase picture of the proton structure and dynamics that, at its extrema, encompasses proton sharing and spectroscopic features resembling the limiting Eigen [H3O(H2O)3]+ and Zundel [H(H2O)2]+ gas-phase structures, while also describing the rich variety of interconverting environments in the liquid phase.
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Affiliation(s)
- Joseph A Napoli
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Ondrej Marsalek
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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41
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42
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Morawietz T, Marsalek O, Pattenaude SR, Streacker LM, Ben-Amotz D, Markland TE. The Interplay of Structure and Dynamics in the Raman Spectrum of Liquid Water over the Full Frequency and Temperature Range. J Phys Chem Lett 2018; 9:851-857. [PMID: 29394069 DOI: 10.1021/acs.jpclett.8b00133] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
While many vibrational Raman spectroscopy studies of liquid water have investigated the temperature dependence of the high-frequency O-H stretching region, few have analyzed the changes in the Raman spectrum as a function of temperature over the entire spectral range. Here, we obtain the Raman spectra of water from its melting to boiling point, both experimentally and from simulations using an ab initio-trained machine learning potential. We use these to assign the Raman bands and show that the entire spectrum can be well described as a combination of two temperature-independent spectra. We then assess which spectral regions exhibit strong dependence on the local tetrahedral order in the liquid. Further, this work demonstrates that changes in this structural parameter can be used to elucidate the temperature dependence of the Raman spectrum of liquid water and provides a guide to the Raman features that signal water ordering in more complex aqueous systems.
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Affiliation(s)
- Tobias Morawietz
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Ondrej Marsalek
- Charles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Shannon R Pattenaude
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Louis M Streacker
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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43
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Wang L, Fried SD, Markland TE. Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site. J Phys Chem B 2017; 121:9807-9815. [DOI: 10.1021/acs.jpcb.7b06985] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lu Wang
- Department
of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Stephen D. Fried
- Medical Research
Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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44
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Marsalek O, Markland TE. Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects. J Phys Chem Lett 2017; 8:1545-1551. [PMID: 28296422 DOI: 10.1021/acs.jpclett.7b00391] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the reactivity and spectroscopy of aqueous solutions at the atomistic level is crucial for the elucidation and design of chemical processes. However, the simulation of these systems requires addressing the formidable challenges of treating the quantum nature of both the electrons and nuclei. Exploiting our recently developed methods that provide acceleration by up to 2 orders of magnitude, we combine path integral simulations with on-the-fly evaluation of the electronic structure at the hybrid density functional theory level to capture the interplay between nuclear quantum effects and the electronic surface. Here we show that this combination provides accurate structure and dynamics, including the full infrared and Raman spectra of liquid water. This allows us to demonstrate and explain the failings of lower-level density functionals for dynamics and vibrational spectroscopy when the nuclei are treated quantum mechanically. These insights thus provide a foundation for the reliable investigation of spectroscopy and reactivity in aqueous environments.
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Affiliation(s)
- Ondrej Marsalek
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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45
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Abstract
Competing pathways in catalytic reactions often involve transition states with very different charge distributions, but this difference is rarely exploited to control selectivity. The proximity of a counterion to a charged catalyst in an ion paired complex gives rise to strong electrostatic interactions that could be used to energetically differentiate transition states. Here we investigate the effects of ion pairing on the regioselectivity of the hydroarylation of 3-substituted phenyl propargyl ethers catalyzed by cationic Au(I) complexes, which forms a mixture of 5- and 7-substituted 2H-chromenes. We show that changing the solvent dielectric to enforce ion pairing to a SbF6- counterion changes the regioselectivity by up to a factor of 12 depending on the substrate structure. Density functional theory (DFT) is used to calculate the energy difference between the putative product-determining isomeric transition states (ΔΔE‡) in both the presence and absence of the counterion. The change in ΔΔE‡ upon switching from the unpaired transition states in high solvent dielectric to ion paired transition states in low solvent dielectric (Δ(ΔΔE‡)) was found to be in good agreement with the experimentally observed selectivity changes across several substrates. Our calculations indicate that the origin of Δ(ΔΔE‡) lies in the preferential electrostatic stabilization of the transition state with greater charge separation by the counterion in the ion paired case. By performing calculations at multiple different values of the solvent dielectric, we show that the role of the solvent in changing selectivity is not solely to enforce ion pairing, but rather that interactions between the ion paired complex and the solvent also contribute to Δ(ΔΔE‡). Our results provide a foundation for exploiting electrostatic control of selectivity in other ion paired systems.
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Affiliation(s)
- Vivian M Lau
- Department of Chemistry, Stanford University , 337 Campus Drive, Stanford, California 94305, United States
| | - William C Pfalzgraff
- Department of Chemistry, Stanford University , 337 Campus Drive, Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University , 337 Campus Drive, Stanford, California 94305, United States
| | - Matthew W Kanan
- Department of Chemistry, Stanford University , 337 Campus Drive, Stanford, California 94305, United States
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46
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Kelly A, Montoya-Castillo A, Wang L, Markland TE. Generalized quantum master equations in and out of equilibrium: When can one win? J Chem Phys 2016; 144:184105. [DOI: 10.1063/1.4948612] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Aaron Kelly
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Lu Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Thomas E. Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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47
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Ceriotti M, Fang W, Kusalik PG, McKenzie RH, Michaelides A, Morales MA, Markland TE. Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges. Chem Rev 2016; 116:7529-50. [DOI: 10.1021/acs.chemrev.5b00674] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Michele Ceriotti
- Laboratory
of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Wei Fang
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Peter G. Kusalik
- Department
of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Ross H. McKenzie
- School
of Mathematics and Physics, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Angelos Michaelides
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Miguel A. Morales
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305, United States
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48
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Marsalek O, Markland TE. Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory. J Chem Phys 2016; 144:054112. [DOI: 10.1063/1.4941093] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ondrej Marsalek
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Thomas E. Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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49
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Pfalzgraff WC, Kelly A, Markland TE. Nonadiabatic Dynamics in Atomistic Environments: Harnessing Quantum-Classical Theory with Generalized Quantum Master Equations. J Phys Chem Lett 2015; 6:4743-4748. [PMID: 26563917 DOI: 10.1021/acs.jpclett.5b02131] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The development of methods that can efficiently and accurately treat nonadiabatic dynamics in quantum systems coupled to arbitrary atomistic environments remains a significant challenge in problems ranging from exciton transport in photovoltaic materials to electron and proton transfer in catalysis. Here we show that our recently introduced MF-GQME approach, which combines Ehrenfest mean field theory with the generalized quantum master equation framework, is able to yield quantitative accuracy over a wide range of charge-transfer regimes in fully atomistic environments. This is accompanied by computational speed-ups of up to 3 orders of magnitude over a direct application of Ehrenfest theory. This development offers the opportunity to efficiently investigate the atomistic details of nonadiabatic quantum relaxation processes in regimes where obtaining accurate results has previously been elusive.
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Affiliation(s)
- William C Pfalzgraff
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Aaron Kelly
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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Kelly A, Brackbill N, Markland TE. Accurate nonadiabatic quantum dynamics on the cheap: Making the most of mean field theory with master equations. J Chem Phys 2015; 142:094110. [DOI: 10.1063/1.4913686] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Aaron Kelly
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Nora Brackbill
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Thomas E. Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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