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Bac S, Quiton SJ, Kron KJ, Chae J, Mitra U, Mallikarjun Sharada S. A matrix completion algorithm for efficient calculation of quantum and variational effects in chemical reactions. J Chem Phys 2022; 156:184119. [PMID: 35568565 DOI: 10.1063/5.0091155] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
This work examines the viability of matrix completion methods as cost-effective alternatives to full nuclear Hessians for calculating quantum and variational effects in chemical reactions. The harmonic variety-based matrix completion (HVMC) algorithm, developed in a previous study [S. J. Quiton et al., J. Chem. Phys. 153, 054122 (2020)], exploits the low-rank character of the polynomial expansion of potential energy to recover vibrational frequencies (square roots of eigenvalues of nuclear Hessians) constituting the reaction path using a small sample of its entities. These frequencies are essential for calculating rate coefficients using variational transition state theory with multidimensional tunneling (VTST-MT). HVMC performance is examined for four SN2 reactions and five hydrogen transfer reactions, with each H-transfer reaction consisting of at least one vibrational mode strongly coupled to the reaction coordinate. HVMC is robust and captures zero-point energies, vibrational free energies, zero-curvature tunneling, and adiabatic ground state and free energy barriers as well as their positions on the reaction coordinate. For medium to large reactions involving H-transfer, with the sole exception of the most complex Ir catalysis system, less than 35% of total eigenvalue information is necessary for accurate recovery of key VTST-MT observables.
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Affiliation(s)
- Selin Bac
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA
| | - Stephen Jon Quiton
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA
| | - Kareesa J Kron
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA
| | - Jeongmin Chae
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - Urbashi Mitra
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - Shaama Mallikarjun Sharada
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA
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Rosales AR, Quinn TR, Wahlers J, Tomberg A, Zhang X, Helquist P, Wiest O, Norrby PO. Application of Q2MM to predictions in stereoselective synthesis. Chem Commun (Camb) 2018; 54:8294-8311. [PMID: 29971313 DOI: 10.1039/c8cc03695k] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Quantum-Guided Molecular Mechanics (Q2MM) can be used to derive transition state force fields (TSFFs) that allow the fast and accurate predictions of stereoselectivity for a wide range of catalytic enantioselective reactions. The basic ideas behind the derivation of TSFFs using Q2MM are discussed and the steps involved in obtaining a TSFF using the Q2MM code, publically available at github.com/q2mm, are shown. The applicability for a range of reactions, including several non-standard applications of Q2MM, is demonstrated. Future developments of the method are also discussed.
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Affiliation(s)
- Anthony R Rosales
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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Okumura H, Higashi M, Yoshida Y, Sato H, Akiyama R. Theoretical approaches for dynamical ordering of biomolecular systems. Biochim Biophys Acta Gen Subj 2017; 1862:212-228. [PMID: 28988931 DOI: 10.1016/j.bbagen.2017.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/30/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. SCOPE OF REVIEW We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. MAJOR CONCLUSIONS The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. GENERAL SIGNIFICANCE These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan.
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Yuichiro Yoshida
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
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Higashi M, Truhlar DG. Combined Electrostatically Embedded Multiconfiguration Molecular Mechanics and Molecular Mechanical Method: Application to Molecular Dynamics Simulation of a Chemical Reaction in Aqueous Solution with Hybrid Density Functional Theory. J Chem Theory Comput 2015; 4:1032-9. [PMID: 26636356 DOI: 10.1021/ct8000816] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We here combine the electrostatically embedded multiconfiguration molecular mechanics (EE-MCMM) method for generating global potential energy surfaces in the presence of an electrostatic potential with molecular mechanics (MM). The resulting EE-MCMM/MM method is illustrated by applying it to carry out a molecular dynamics simulation for the symmetric bimolecular reaction Cl(-) + CH3Cl' → ClCH3 + Cl'(-) in aqueous solution with hybrid density functional theory as the quantum mechanical level. The potential of mean force is calculated, and the free energy barrier is found to be 25.3 kcal/mol, which is in good agreement with previous work. The advantage of the combined EE-MCMM and MM method is that the number of quantum mechanical calculations required for the active subsystem is very small compared to straight direct dynamics.
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Affiliation(s)
- Masahiro Higashi
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
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Ghysels A, Van Speybroeck V, Verstraelen T, Van Neck D, Waroquier M. Calculating Reaction Rates with Partial Hessians: Validation of the Mobile Block Hessian Approach. J Chem Theory Comput 2015; 4:614-25. [PMID: 26620936 DOI: 10.1021/ct7002836] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In an earlier paper, the authors have developed a new method, the mobile block Hessian (MBH), to accurately calculate vibrational modes for partially optimized molecular structures [J. Chem. Phys. 2007, 126 (22), 224102]. The proposed procedure remedies the artifact of imaginary frequencies, occurring in standard frequency calculations, when parts of the molecular system are optimized at different levels of theory. Frequencies are an essential ingredient in predicting reaction rate coefficients due to their input in the vibrational partition functions. The question arises whether the MBH method is able to describe the chemical reaction kinetics in an accurate way in large molecular systems where a full quantum chemical treatment at a reasonably high level of theory is unfeasible due to computational constraints. In this work, such a validation is tested in depth. The MBH method opens a lot of perspectives in predicting accurate kinetic parameters in chemical reactions where the standard full Hessian procedure fails.
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Affiliation(s)
- A Ghysels
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
| | - V Van Speybroeck
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
| | - T Verstraelen
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
| | - D Van Neck
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
| | - M Waroquier
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
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Nance J, Jakubikova E, Kelley CT. Reaction Path Following with Sparse Interpolation. J Chem Theory Comput 2014; 10:2942-9. [PMID: 26588269 DOI: 10.1021/ct5004669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computing the potential energy of an N-atom molecule is an expensive optimization process of 3N - 6 molecular coordinates, so following reaction pathways as a function of all 3N - 6 coordinates is unfeasible for large molecules. In this paper, we present a method that isolates d < 3N - 6 molecular coordinates and continuously follows reaction paths on d-dimensional potential energy surfaces approximated by a Smolyak's sparse grid interpolation algorithm.1 Compared to dense grids, sparse grids efficiently improve the ratio of invested storage and computing time to approximation accuracy and thus allow one to increase the number of coordinates d in molecular reaction path following simulations. Furthermore, evaluation of the interpolant is much less expensive than the evaluation of the actual energy function, so our technique offers a computationally efficient way to simulate reaction paths on ground and excited state potential energy surfaces. To demonstrate the capabilities of our method, we present simulation results for the isomerization of 2-butene with two, three, and six degrees of freedom.
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Affiliation(s)
- James Nance
- Department of Mathematics and ‡Department of Chemsitry, North Carolina State University , Raleigh, North Carolina, United States
| | - Elena Jakubikova
- Department of Mathematics and ‡Department of Chemsitry, North Carolina State University , Raleigh, North Carolina, United States
| | - C T Kelley
- Department of Mathematics and ‡Department of Chemsitry, North Carolina State University , Raleigh, North Carolina, United States
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Bender JD, Doraiswamy S, Truhlar DG, Candler GV. Potential energy surface fitting by a statistically localized, permutationally invariant, local interpolating moving least squares method for the many-body potential: Method and application to N4. J Chem Phys 2014; 140:054302. [DOI: 10.1063/1.4862157] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Zheng J, Seal P, Truhlar DG. Role of conformational structures and torsional anharmonicity in controlling chemical reaction rates and relative yields: butanal + HO2reactions. Chem Sci 2013. [DOI: 10.1039/c2sc21090h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Bellucci MA, Coker DF. Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach. J Chem Phys 2011; 135:044115. [PMID: 21806098 DOI: 10.1063/1.3610907] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We describe a new method for constructing empirical valence bond potential energy surfaces using a parallel multilevel genetic program (PMLGP). Genetic programs can be used to perform an efficient search through function space and parameter space to find the best functions and sets of parameters that fit energies obtained by ab initio electronic structure calculations. Building on the traditional genetic program approach, the PMLGP utilizes a hierarchy of genetic programming on two different levels. The lower level genetic programs are used to optimize coevolving populations in parallel while the higher level genetic program (HLGP) is used to optimize the genetic operator probabilities of the lower level genetic programs. The HLGP allows the algorithm to dynamically learn the mutation or combination of mutations that most effectively increase the fitness of the populations, causing a significant increase in the algorithm's accuracy and efficiency. The algorithm's accuracy and efficiency is tested against a standard parallel genetic program with a variety of one-dimensional test cases. Subsequently, the PMLGP is utilized to obtain an accurate empirical valence bond model for proton transfer in 3-hydroxy-gamma-pyrone in gas phase and protic solvent.
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Affiliation(s)
- Michael A Bellucci
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
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Yu T, Zheng J, Truhlar DG. Multi-structural variational transition state theory. Kinetics of the 1,4-hydrogen shift isomerization of the pentyl radical with torsional anharmonicity. Chem Sci 2011. [DOI: 10.1039/c1sc00225b] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Sonnenberg JL, Schlegel HB. Empirical valence bond models for reactive potential energy surfaces. II. Intramolecular proton transfer in pyridone and the Claisen reaction of allyl vinyl ether. Mol Phys 2010. [DOI: 10.1080/00268970701622277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Wong KF, Sonnenberg JL, Paesani F, Yamamoto T, Vaníček J, Zhang W, Schlegel HB, Case DA, Cheatham TE, Miller WH, Voth GA. Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology. J Chem Theory Comput 2010; 6:2566-2580. [PMID: 21116485 DOI: 10.1021/ct900579k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The rates of intramolecular proton transfer are calculated on a full-dimensional reactive electronic potential energy surface that incorporates high level ab initio calculations along the reaction path and by using classical Transition State theory, Path-Integral Quantum Transition State Theory, and the Quantum Instanton approach. The specific example problem studied is malonaldehyde. Estimates of the kinetic isotope effect using the latter two methods are found to be in reasonable agreement with each other. Improvements and extensions of this practical, yet chemically accurate framework for the calculations of quantized, reactive dynamics are also discussed.
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Affiliation(s)
- Kim F Wong
- Center for Biophysical Modeling & Simulations and Department of Chemistry, University of Utah, Salt Lake City, Utah, 84112
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Tishchenko O, Truhlar DG. Gradient-based multiconfiguration Shepard interpolation for generating potential energy surfaces for polyatomic reactions. J Chem Phys 2010; 132:084109. [PMID: 20192292 DOI: 10.1063/1.3310296] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper describes and illustrates a way to construct multidimensional representations of reactive potential energy surfaces (PESs) by a multiconfiguration Shepard interpolation (MCSI) method based only on gradient information, that is, without using any Hessian information from electronic structure calculations. MCSI, which is called multiconfiguration molecular mechanics (MCMM) in previous articles, is a semiautomated method designed for constructing full-dimensional PESs for subsequent dynamics calculations (classical trajectories, full quantum dynamics, or variational transition state theory with multidimensional tunneling). The MCSI method is based on Shepard interpolation of Taylor series expansions of the coupling term of a 2 x 2 electronically diabatic Hamiltonian matrix with the diagonal elements representing nonreactive analytical PESs for reactants and products. In contrast to the previously developed method, these expansions are truncated in the present version at the first order, and, therefore, no input of electronic structure Hessians is required. The accuracy of the interpolated energies is evaluated for two test reactions, namely, the reaction OH+H(2)-->H(2)O+H and the hydrogen atom abstraction from a model of alpha-tocopherol by methyl radical. The latter reaction involves 38 atoms and a 108-dimensional PES. The mean unsigned errors averaged over a wide range of representative nuclear configurations (corresponding to an energy range of 19.5 kcal/mol in the former case and 32 kcal/mol in the latter) are found to be within 1 kcal/mol for both reactions, based on 13 gradients in one case and 11 in the other. The gradient-based MCMM method can be applied for efficient representations of multidimensional PESs in cases where analytical electronic structure Hessians are too expensive or unavailable, and it provides new opportunities to employ high-level electronic structure calculations for dynamics at an affordable cost.
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Affiliation(s)
- Oksana Tishchenko
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA.
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14
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Zhang Y, Lin H. Quantum tunneling in testosterone 6beta-hydroxylation by cytochrome P450: reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces. J Phys Chem A 2010; 113:11501-8. [PMID: 19480428 DOI: 10.1021/jp901850c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6beta-hydrogen abstraction and the 6beta-d(1)-testosterone 6beta-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.
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Affiliation(s)
- Yan Zhang
- Chemistry Department, University of Colorado Denver, Denver, Colorado 80217-3364, USA
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15
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Higashi M, Truhlar DG. Efficient Approach to Reactive Molecular Dynamics with Accurate Forces. J Chem Theory Comput 2009; 5:2925-9. [DOI: 10.1021/ct900301d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Masahiro Higashi
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
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16
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Tishchenko O, Truhlar DG. Non-Hermitian Multiconfiguration Molecular Mechanics. J Chem Theory Comput 2009; 5:1454-61. [DOI: 10.1021/ct900077g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Oksana Tishchenko
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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17
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Sonnenberg JL, Wong KF, Voth GA, Schlegel HB. Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations. J Chem Theory Comput 2009; 5:949-61. [DOI: 10.1021/ct800477y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jason L. Sonnenberg
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Kim F. Wong
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Gregory A. Voth
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - H. Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
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18
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Tishchenko O, Truhlar DG. Efficient global representations of potential energy functions: Trajectory calculations of bimolecular gas-phase reactions by multiconfiguration molecular mechanics. J Chem Phys 2009; 130:024105. [DOI: 10.1063/1.3042145] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Zhang Y, Morisetti P, Kim J, Smith L, Lin H. Regioselectivity preference of testosterone hydroxylation by cytochrome P450 3A4. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0480-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Higashi M, Truhlar DG. Electrostatically Embedded Multiconfiguration Molecular Mechanics Based on the Combined Density Functional and Molecular Mechanical Method. J Chem Theory Comput 2008; 4:790-803. [DOI: 10.1021/ct800004y] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Masahiro Higashi
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
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21
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Albu TV, Espinosa-García J, Truhlar DG. Computational Chemistry of Polyatomic Reaction Kinetics and Dynamics: The Quest for an Accurate CH5 Potential Energy Surface. Chem Rev 2007; 107:5101-32. [DOI: 10.1021/cr078026x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Titus V. Albu
- Department of Chemistry, Box 5055, Tennessee Technological University, Cookeville, Tennessee 38505
| | | | - Donald G. Truhlar
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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22
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Albu TV, Swaminathan S. Hybrid density functional theory with a specific reaction parameter: hydrogen abstraction reaction of difluoromethane by the hydroxyl radical. J Mol Model 2007; 13:1109-21. [PMID: 17704956 DOI: 10.1007/s00894-007-0235-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 07/18/2007] [Indexed: 10/22/2022]
Abstract
Accurate potential energy surfaces for the OH + CH2F2 --> H2O + CHF2 reaction are constructed using hybrid and hybrid meta density functional theory methods (mPW1PW91, B1B95, and mPW1B95) with specific reaction parameters in conjunction with the 6-31 + G(d,p) basis set. The accuracy of a surface is examined by comparing the calculated rate constants with the experimental ones. The rate constants are calculated over the temperature range 200-1,500 K using variational transition state theory with multidimensional tunneling contributions. The hybrid density functional theory methods with specific-reaction-parameter Hartree-Fock exchange contributions (39.2-41.0% for mPW1PW91, 41.0-42.2% for B1B95, and 44.9-46.3% for mPW1B95, respectively) provide accurate rate constants over an extended temperature range. The classical barrier height for the hydrogen abstraction reaction on these potential energy surfaces is determined to be 5.0-5.3 kcal mol(-1), and the best estimate value is 5.14 kcal mol(-1).
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Affiliation(s)
- Titus V Albu
- Department of Chemistry, Tennessee Technological University, Box 5055, Cookeville, TN 38505, USA.
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Ghysels A, Van Neck D, Van Speybroeck V, Verstraelen T, Waroquier M. Vibrational modes in partially optimized molecular systems. J Chem Phys 2007; 126:224102. [PMID: 17581039 DOI: 10.1063/1.2737444] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this paper the authors develop a method to accurately calculate localized vibrational modes for partially optimized molecular structures or for structures containing link atoms. The method avoids artificially introduced imaginary frequencies and keeps track of the invariance under global translations and rotations. Only a subblock of the Hessian matrix has to be constructed and diagonalized, leading to a serious reduction of the computational time for the frequency analysis. The mobile block Hessian approach (MBH) proposed in this work can be regarded as an extension of the partial Hessian vibrational analysis approach proposed by Head [Int. J. Quantum Chem. 65, 827 (1997)]. Instead of giving the nonoptimized region of the system an infinite mass, it is allowed to move as a rigid body with respect to the optimized region of the system. The MBH approach is then extended to the case where several parts of the molecule can move as independent multiple rigid blocks in combination with single atoms. The merits of both models are extensively tested on ethanol and di-n-octyl-ether.
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Affiliation(s)
- A Ghysels
- Center for Molecular Modeling, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
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Tishchenko O, Truhlar DG. Global Potential Energy Surfaces with Correct Permutation Symmetry by Multiconfiguration Molecular Mechanics. J Chem Theory Comput 2007; 3:938-48. [DOI: 10.1021/ct600315h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Oksana Tishchenko
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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Fernandez-Ramos A, Miller JA, Klippenstein SJ, Truhlar DG. Modeling the kinetics of bimolecular reactions. Chem Rev 2007; 106:4518-84. [PMID: 17091928 DOI: 10.1021/cr050205w] [Citation(s) in RCA: 474] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Antonio Fernandez-Ramos
- Departamento de Quimica Fisica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Tishchenko O, Truhlar DG. Optimizing the Performance of the Multiconfiguration Molecular Mechanics Method. J Phys Chem A 2006; 110:13530-6. [PMID: 17165880 DOI: 10.1021/jp0640833] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Multiconfiguration molecular mechanics (MCMM) is a general algorithm for constructing potential energy surfaces for reactive systems (Kim, Y.; Corchado, J. C.; Villà, J.; Xing, J.; Truhlar, D. G. J. Chem. Phys. 2000, 112, 2718). This paper illustrates how the performance of the MCMM method can be improved by adopting improved molecular mechanics parameters. We carry out calculations of reaction rate constants using variational transition state theory with optimized multidimensional tunneling on the MCMM PESs for three hydrogen transfer reactions, and we compare the results to direct dynamics. We find that the MCMM method with as little as one electronic structure Hessian can describe the dynamically important regions of the ground-electronic state PES, including the corner-cutting-tunneling region of the reaction swath, with practical accuracy.
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Affiliation(s)
- Oksana Tishchenko
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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Lin H, Zhao Y, Tishchenko O, Truhlar DG. Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations. J Chem Theory Comput 2006; 2:1237-54. [DOI: 10.1021/ct600171u] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hai Lin
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
| | - Yan Zhao
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
| | - Oksana Tishchenko
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
| | - Donald G. Truhlar
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
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Abstract
This essay provides a perspective on several issues in valence bond theory: the physical significance of semilocal bonding orbitals, the capability of valence bond concepts to explain systems with multireferences character, the use of valence bond theory to provide analytical representations of potential energy surfaces for chemical dynamics by the method of semiempirical valence bond potential energy surfaces (an early example of specific reaction parameters), by multiconfiguration molecular mechanics, by the combined valence bond-molecular mechanics method, and by the use of valence bond states as coupled diabatic states for describing electronically nonadiabatic processes (photochemistry). The essay includes both ab initio and semiempirical approaches.
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Affiliation(s)
- Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431, USA.
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Kim Y, Kim Y. Dynamics of the Concerted Triple Proton Transfer in Cyclic Water Trimer Using the Multiconfiguration Molecular Mechanics Algorithm. J Phys Chem A 2005; 110:600-8. [PMID: 16405332 DOI: 10.1021/jp0530193] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cyclic water clusters are important molecular species to understand the nature of hydrogen bonded networks. Theoretical studies for the dynamics of triple proton transfer in the cyclic water trimer were performed. The potential energy surface (PES) of triple proton transfer is generated by the multiconfiguration molecular mechanics (MCMM) algorithm. We have used the MP2/6-31G(d,p) level for high-level ab initio data (energies, gradients, and Hessians), which are used in the Shepard interpolation. Eight high-level reference points were added step by step, including two points for the critical configurations of the large curvature tunneling paths. The more high-level points are used, the better the potential energy surfaces become. The rate constant and kinetic isotope effect (KIE) for the triple proton transfer at 300 K, which have been calculated by the canonical variational transition-state theory with microcanonical optimized multidimensional semiclassical tunneling approximation, are 1.6 x 10(-3) s(-1) and 230, respectively. Tunneling is very important not only for the triple proton transfer but also for the triple deuterium transfer. The MCMM results show good agreement with those from the direct ab initio dynamics calculations.
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Affiliation(s)
- Yangsoo Kim
- Department of Chemistry, Kyung Hee University, Yong-In City, Kyunggi-Do, 449-701, Korea
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