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Teng C, Huang D, Donahue E, Bao JL. Exploring torsional conformer space with physical prior mean function-driven meta-Gaussian processes. J Chem Phys 2023; 159:214111. [PMID: 38051097 DOI: 10.1063/5.0176709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/12/2023] [Indexed: 12/07/2023] Open
Abstract
We present a novel approach for systematically exploring the conformational space of small molecules with multiple internal torsions. Identifying unique conformers through a systematic conformational search is important for obtaining accurate thermodynamic functions (e.g., free energy), encompassing contributions from the ensemble of all local minima. Traditional geometry optimizers focus on one structure at a time, lacking transferability from the local potential-energy surface (PES) around a specific minimum to optimize other conformers. In this work, we introduce a physics-driven meta-Gaussian processes (meta-GPs) method that not only enables efficient exploration of target PES for locating local minima but, critically, incorporates physical surrogates that can be applied universally across the optimization of all conformers of the same molecule. Meta-GPs construct surrogate PESs based on the optimization history of prior conformers, dynamically selecting the most suitable prior mean function (representing prior knowledge in Bayesian learning) as a function of the optimization progress. We systematically benchmarked the performance of multiple GP variants for brute-force conformational search of amino acids. Our findings highlight the superior performance of meta-GPs in terms of efficiency, comprehensiveness of conformer discovery, and the distribution of conformers compared to conventional non-surrogate optimizers and other non-meta-GPs. Furthermore, we demonstrate that by concurrently optimizing, training GPs on the fly, and learning PESs, meta-GPs exhibit the capacity to generate high-quality PESs in the torsional space without extensive training data. This represents a promising avenue for physics-based transfer learning via meta-GPs with adaptive priors in exploring torsional conformer space.
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Affiliation(s)
- Chong Teng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Daniel Huang
- Department of Computer Science, San Francisco State University, San Francisco, California 94132, USA
| | - Elizabeth Donahue
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Junwei Lucas Bao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
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Chen W, Zhang P, Truhlar DG, Zheng J, Xu X. Identification of Torsional Modes in Complex Molecules Using Redundant Internal Coordinates: The Multistructural Method with Torsional Anharmonicity with a Coupled Torsional Potential and Delocalized Torsions. J Chem Theory Comput 2022; 18:7671-7682. [PMID: 36441527 DOI: 10.1021/acs.jctc.2c00952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of internal-rotation modes in the normal-mode analysis of complex molecules is important for accurately describing the thermodynamic properties and kinetics of complex molecules when it is necessary to treat the anharmonicity of torsions and the multiconformer anharmonicity caused by the internal rotations. However, identifying and distinguishing torsional modes are very challenging because they are coupled to one another. In this work, we present a new strategy to automatically identify torsional vibrations and separate them from the other vibrational modes. By combining a redundant-internal-coordinate auto-generation procedure with torsional projection techniques, we automate the procedure of identifying and separating the coupled torsions, and we show that we can obtain robust and consistent results with various reasonable definitions of redundant-internal-coordinate sets. This model has been implemented in a new development version of the MSTor program to reduce the user input needed for multistructural and torsional anharmonicity (MS-T) calculations. The new method is called multistructural and torsional anharmonicity with a coupled torsional potential and delocalized torsions ([MS-T(CD)]. As example applications, we consider MS-T(CD) calculations on three molecules (2-hexyl radical, n-propylbenzene, and 5-hydroperoxy-6-oxohexanoylperoxy radical) that have multiple rotors and that provide challenges to choosing good sets of nonredundant-internal coordinates, and we compare the performance of the new strategy to five other torsion identification methods. The new strategy is demonstrated to be efficient in separating the torsional and nontorsional elements in the Hessian matrix, as well as in providing reasonable projected nontorsional frequencies to be used for calculations of partition function and thermochemistry.
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Affiliation(s)
- Wenqi Chen
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing100084, China
| | - Pengchao Zhang
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing100084, China
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MinnesotaMN55455-0431, United States
| | - Jingjing Zheng
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut06492, United States
| | - Xuefei Xu
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing100084, China
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3
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Sumiya Y, Maeda S. Rate Constant Matrix Contraction Method for Systematic Analysis of Reaction Path Networks. CHEM LETT 2020. [DOI: 10.1246/cl.200092] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yosuke Sumiya
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- National Institute for Materials Science (NIMS), Research and Services Division of Materials Data and Integrated System (MaDIS), Tsukuba, Ibaraki 305-0044, Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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4
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Bao JL, Zhang X, Truhlar DG. Predicting pressure-dependent unimolecular rate constants using variational transition state theory with multidimensional tunneling combined with system-specific quantum RRK theory: a definitive test for fluoroform dissociation. Phys Chem Chem Phys 2018; 18:16659-70. [PMID: 27273734 DOI: 10.1039/c6cp02765b] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Understanding the falloff in rate constants of gas-phase unimolecular reaction rate constants as the pressure is lowered is a fundamental problem in chemical kinetics, with practical importance for combustion, atmospheric chemistry, and essentially all gas-phase reaction mechanisms. In the present work, we use our recently developed system-specific quantum RRK theory, calibrated by canonical variational transition state theory with small-curvature tunneling, combined with the Lindemann-Hinshelwood mechanism, to model the dissociation reaction of fluoroform (CHF3), which provides a definitive test for falloff modeling. Our predicted pressure-dependent thermal rate constants are in excellent agreement with experimental values over a wide range of pressures and temperatures. The present validation of our methodology, which is able to include variational transition state effects, multidimensional tunneling based on the directly calculated potential energy surface along the tunneling path, and torsional and other vibrational anharmonicity, together with state-of-the-art reaction-path-based direct dynamics calculations, is important because the method is less empirical than models routinely used for generating full mechanisms, while also being simpler in key respects than full master equation treatments and the full reduced falloff curve and modified strong collision methods of Troe.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA.
| | - Xin Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing, 100029, P. R. China. and Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA.
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA.
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5
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Nasiri R, Luo KH. Specificity Switching Pathways in Thermal and Mass Evaporation of Multicomponent Hydrocarbon Droplets: A Mesoscopic Observation. Sci Rep 2017; 7:5001. [PMID: 28694476 PMCID: PMC5504037 DOI: 10.1038/s41598-017-05160-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/07/2017] [Indexed: 11/21/2022] Open
Abstract
For well over one century, the Hertz-Knudsen equation has established the relationship between thermal - mass transfer coefficients through a liquid - vapour interface and evaporation rate. These coefficients, however, have been often separately estimated for one-component equilibrium systems and their simultaneous influences on evaporation rate of fuel droplets in multicomponent systems have yet to be investigated at the atomic level. Here we first apply atomistic simulation techniques and quantum/statistical mechanics methods to understand how thermal and mass evaporation effects are controlled kinetically/thermodynamically. We then present a new development of a hybrid method of quantum transition state theory/improved kinetic gas theory, for multicomponent hydrocarbon systems to investigate how concerted-distinct conformational changes of hydrocarbons at the interface affect the evaporation rate. The results of this work provide an important physical concept in fundamental understanding of atomistic pathways in topological interface transitions of chain molecules, resolving an open problem in kinetics of fuel droplets evaporation.
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Affiliation(s)
- Rasoul Nasiri
- Department of Mechanical Engineering, University College London, Torrington Place, London, WC1E 7JE, UK.
| | - Kai H Luo
- Department of Mechanical Engineering, University College London, Torrington Place, London, WC1E 7JE, UK.
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Bao JL, Xing L, Truhlar DG. Dual-Level Method for Estimating Multistructural Partition Functions with Torsional Anharmonicity. J Chem Theory Comput 2017; 13:2511-2522. [DOI: 10.1021/acs.jctc.7b00232] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry, Chemical Theory
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Lili Xing
- Department of Chemistry, Chemical Theory
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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Bao JL, Truhlar DG. Variational transition state theory: theoretical framework and recent developments. Chem Soc Rev 2017; 46:7548-7596. [DOI: 10.1039/c7cs00602k] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
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Sumiya Y, Nagahata Y, Komatsuzaki T, Taketsugu T, Maeda S. Kinetic Analysis for the Multistep Profiles of Organic Reactions: Significance of the Conformational Entropy on the Rate Constants of the Claisen Rearrangement. J Phys Chem A 2015; 119:11641-9. [DOI: 10.1021/acs.jpca.5b09447] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yosuke Sumiya
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Yutaka Nagahata
- Graduate
School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Tamiki Komatsuzaki
- Graduate
School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Molecule
and Life Nonlinear Sciences Laboratory, Research Institute for Electronic
Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
| | - Tetsuya Taketsugu
- Department
of Chemistry, Faculty of Science, Hokkaido University, Kita 10,
Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Satoshi Maeda
- Department
of Chemistry, Faculty of Science, Hokkaido University, Kita 10,
Nishi 8, Kita-ku, Sapporo 060-0810, Japan
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Bao JL, Seal P, Truhlar DG. Nanodusty plasma chemistry: a mechanistic and variational transition state theory study of the initial steps of silyl anion–silane and silylene anion–silane polymerization reactions. Phys Chem Chem Phys 2015; 17:15928-35. [DOI: 10.1039/c5cp01979f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The aim of the present work is to understand the detailed reaction mechanisms in the growth of nanodusty particles, which is critical in plasma chemistry, physics and engineering.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry
- Chemical Theory Center
- and Supercomputing Institute
- University of Minnesota
- Minneapolis
| | - Prasenjit Seal
- Department of Chemistry
- Chemical Theory Center
- and Supercomputing Institute
- University of Minnesota
- Minneapolis
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center
- and Supercomputing Institute
- University of Minnesota
- Minneapolis
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