1
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Kroes GJ. Computational approaches to dissociative chemisorption on metals: towards chemical accuracy. Phys Chem Chem Phys 2021; 23:8962-9048. [PMID: 33885053 DOI: 10.1039/d1cp00044f] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the state-of-the-art in the theory of dissociative chemisorption (DC) of small gas phase molecules on metal surfaces, which is important to modeling heterogeneous catalysis for practical reasons, and for achieving an understanding of the wealth of experimental information that exists for this topic, for fundamental reasons. We first give a quick overview of the experimental state of the field. Turning to the theory, we address the challenge that barrier heights (Eb, which are not observables) for DC on metals cannot yet be calculated with chemical accuracy, although embedded correlated wave function theory and diffusion Monte-Carlo are moving in this direction. For benchmarking, at present chemically accurate Eb can only be derived from dynamics calculations based on a semi-empirically derived density functional (DF), by computing a sticking curve and demonstrating that it is shifted from the curve measured in a supersonic beam experiment by no more than 1 kcal mol-1. The approach capable of delivering this accuracy is called the specific reaction parameter (SRP) approach to density functional theory (DFT). SRP-DFT relies on DFT and on dynamics calculations, which are most efficiently performed if a potential energy surface (PES) is available. We therefore present a brief review of the DFs that now exist, also considering their performance on databases for Eb for gas phase reactions and DC on metals, and for adsorption to metals. We also consider expressions for SRP-DFs and briefly discuss other electronic structure methods that have addressed the interaction of molecules with metal surfaces. An overview is presented of dynamical models, which make a distinction as to whether or not, and which dissipative channels are modeled, the dissipative channels being surface phonons and electronically non-adiabatic channels such as electron-hole pair excitation. We also discuss the dynamical methods that have been used, such as the quasi-classical trajectory method and quantum dynamical methods like the time-dependent wave packet method and the reaction path Hamiltonian method. Limits on the accuracy of these methods are discussed for DC of diatomic and polyatomic molecules on metal surfaces, paying particular attention to reduced dimensionality approximations that still have to be invoked in wave packet calculations on polyatomic molecules like CH4. We also address the accuracy of fitting methods, such as recent machine learning methods (like neural network methods) and the corrugation reducing procedure. In discussing the calculation of observables we emphasize the importance of modeling the properties of the supersonic beams in simulating the sticking probability curves measured in the associated experiments. We show that chemically accurate barrier heights have now been extracted for DC in 11 molecule-metal surface systems, some of which form the most accurate core of the only existing database of Eb for DC reactions on metal surfaces (SBH10). The SRP-DFs (or candidate SRP-DFs) that have been derived show transferability in many cases, i.e., they have been shown also to yield chemically accurate Eb for chemically related systems. This can in principle be exploited in simulating rates of catalyzed reactions on nano-particles containing facets and edges, as SRP-DFs may be transferable among systems in which a molecule dissociates on low index and stepped surfaces of the same metal. In many instances SRP-DFs have allowed important conclusions regarding the mechanisms underlying observed experimental trends. An important recent observation is that SRP-DFT based on semi-local exchange DFs has so far only been successful for systems for which the difference of the metal work function and the molecule's electron affinity exceeds 7 eV. A main challenge to SRP-DFT is to extend its applicability to the other systems, which involve a range of important DC reactions of e.g. O2, H2O, NH3, CO2, and CH3OH. Recent calculations employing a PES based on a screened hybrid exchange functional suggest that the road to success may be based on using exchange functionals of this category.
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Affiliation(s)
- Geert-Jan Kroes
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
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2
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Zhou S, Wang Y, Gao J. Solvation Induction of Free Energy Barriers of Decarboxylation Reactions in Aqueous Solution from Dual-Level QM/MM Simulations. JACS AU 2021; 1:233-244. [PMID: 34467287 PMCID: PMC8395672 DOI: 10.1021/jacsau.0c00110] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Indexed: 06/13/2023]
Abstract
Carbon dioxide capture, corresponding to the recombination process of decarboxylation reactions of organic acids, is typically barrierless in the gas phase and has a relatively low barrier in aprotic solvents. However, these processes often encounter significant solvent-reorganization-induced barriers in aqueous solution if the decarboxylation product is not immediately protonated. Both the intrinsic stereoelectronic effects and solute-solvent interactions play critical roles in determining the overall decarboxylation equilibrium and free energy barrier. An understanding of the interplay of these factors is important for designing novel materials applied to greenhouse gas capture and storage as well as for unraveling the catalytic mechanisms of a range of carboxy lyases in biological CO2 production. A range of decarboxylation reactions of organic acids with rates spanning nearly 30 orders of magnitude have been examined through dual-level combined quantum mechanical and molecular mechanical simulations to help elucidate the origin of solvation-induced free energy barriers for decarboxylation and the reverse carboxylation reactions in water.
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Affiliation(s)
- Shaoyuan Zhou
- Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, China
- Institute
of Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen 518055, China
| | - Yingjie Wang
- Institute
of Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen 518055, China
| | - Jiali Gao
- Institute
of Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen 518055, China
- Beijing
University Shenzhen Graduate School, Shenzhen 518055, China
- Department
of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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3
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Laloo JZA, Rhyman L, Larrañaga O, Ramasami P, Bickelhaupt FM, de Cózar A. Ion-Pair S N 2 Reaction of OH - and CH 3 Cl: Activation Strain Analyses of Counterion and Solvent Effects. Chem Asian J 2018; 13:1138-1147. [PMID: 29437289 DOI: 10.1002/asia.201800082] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/12/2018] [Indexed: 11/10/2022]
Abstract
We have theoretically studied the non-identity SN 2 reactions of Mn OH(n-1) +CH3 Cl (M+ =Li+ , Na+ , K+ , and MgCl+ ; n=0, 1) in the gas phase and in THF solution at the OLYP/6-31++G(d,p) level using polarizable continuum model (PCM) implicit solvation. We want to explore and understand the effect of the metal counterion M+ and solvation on the reaction profile and the stereoselectivity of these processes. To this end, we have explored the potential energy surfaces of the backside (SN 2-b) and frontside (SN 2-f) pathways. To explain the computed trends, we have carried out analyses with an extended activation strain model (ASM) of chemical reactivity that includes the treatment of solvation effects.
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Affiliation(s)
- Jalal Z A Laloo
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, 80837, Mauritius
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, 80837, Mauritius.,Department of Applied Chemistry, University of Johannesburg, Doornfontein Campus, Johannesburg, 2028, South Africa
| | - Olatz Larrañaga
- Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco (UPV/EHU) and Donostia International Physics Center (DIPC), P. K. 1072, 20018, San Sebastián-Donostia, Spain
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, 80837, Mauritius.,Department of Applied Chemistry, University of Johannesburg, Doornfontein Campus, Johannesburg, 2028, South Africa
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands.,Institute of Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Abel de Cózar
- Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco (UPV/EHU) and Donostia International Physics Center (DIPC), P. K. 1072, 20018, San Sebastián-Donostia, Spain.,Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands.,IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain
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4
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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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5
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Ojeda-May P, Nam K. Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations. J Chem Theory Comput 2017. [PMID: 28628742 DOI: 10.1021/acs.jctc.7b00322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The strategy and implementation of scalable and efficient semiempirical (SE) QM/MM methods in CHARMM are described. The serial version of the code was first profiled to identify routines that required parallelization. Afterward, the code was parallelized and accelerated with three approaches. The first approach was the parallelization of the entire QM/MM routines, including the Fock matrix diagonalization routines, using the CHARMM message passage interface (MPI) machinery. In the second approach, two different self-consistent field (SCF) energy convergence accelerators were implemented using density and Fock matrices as targets for their extrapolations in the SCF procedure. In the third approach, the entire QM/MM and MM energy routines were accelerated by implementing the hybrid MPI/open multiprocessing (OpenMP) model in which both the task- and loop-level parallelization strategies were adopted to balance loads between different OpenMP threads. The present implementation was tested on two solvated enzyme systems (including <100 QM atoms) and an SN2 symmetric reaction in water. The MPI version exceeded existing SE QM methods in CHARMM, which include the SCC-DFTB and SQUANTUM methods, by at least 4-fold. The use of SCF convergence accelerators further accelerated the code by ∼12-35% depending on the size of the QM region and the number of CPU cores used. Although the MPI version displayed good scalability, the performance was diminished for large numbers of MPI processes due to the overhead associated with MPI communications between nodes. This issue was partially overcome by the hybrid MPI/OpenMP approach which displayed a better scalability for a larger number of CPU cores (up to 64 CPUs in the tested systems).
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Affiliation(s)
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington , Arlington, Texas 76019-0065, United States
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6
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Saez DA, Vogt-Geisse S, Inostroza-Rivera R, Kubař T, Elstner M, Toro-Labbé A, Vöhringer-Martinez E. The effect of the environment on the methyl transfer reaction mechanism between trimethylsulfonium and phenolate. Phys Chem Chem Phys 2016; 18:24033-42. [DOI: 10.1039/c6cp02821g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The methyl transfer reaction mechanism in different molecular environments were studied by electronic structure methods and QM/MM molecular dynamics simulations.
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Affiliation(s)
- David Adrian Saez
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
| | - Stefan Vogt-Geisse
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
| | | | - Tomáš Kubař
- Center for Functional Nanomaterials
- Karlsruhe Institute of Technology
- Germany
- Institute for Physical Chemistry
- Karlsruhe Institute of Technology
| | - Marcus Elstner
- Institute for Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Alejandro Toro-Labbé
- QTC
- Facultad de Química
- Pontificia Universidad Católica de Chile
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
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7
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Wang S, MacKay L, Lamoureux G. Development of Semiempirical Models for Proton Transfer Reactions in Water. J Chem Theory Comput 2015; 10:2881-90. [PMID: 26588263 DOI: 10.1021/ct500164h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This letter presents a method for the parametrization of semiempirical models for proton transfer reactions in water clusters. Two new models are developed: AM1-W, which is a reparameterization of the classic AM1 model, and AM1PG-W, which is a modified AM1-like model including a pairwise correction to the core repulsion function. Both models show good performance on hydrogen-bonding energies and on proton transfer energy profiles, which are of great importance for proton transfer reactions in large water clusters and in proteins. The parametrization method introduced is general and can be used to develop any other system-specific semiempirical models.
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Affiliation(s)
- Shihao Wang
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM) and ‡Department of Physics, Concordia University , Montréal, Canada
| | - Laurent MacKay
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM) and ‡Department of Physics, Concordia University , Montréal, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM) and ‡Department of Physics, Concordia University , Montréal, Canada
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8
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Wu X, Liu R, Sathyamoorthy B, Yamato K, Liang G, Shen L, Ma S, Sukumaran DK, Szyperski T, Fang W, He L, Chen X, Gong B. Discrete Stacking of Aromatic Oligoamide Macrocycles. J Am Chem Soc 2015; 137:5879-82. [DOI: 10.1021/jacs.5b02552] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiangxiang Wu
- Key
Laboratory of Theoretical and Computational Photochemistry of the
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Rui Liu
- Key
Laboratory of Theoretical and Computational Photochemistry of the
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Department
of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Bharathwaj Sathyamoorthy
- Department
of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Kazuhiro Yamato
- Department
of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Guoxing Liang
- Department
of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Lin Shen
- Department
of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Sufang Ma
- Key
Laboratory of Theoretical and Computational Photochemistry of the
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Dinesh K. Sukumaran
- Department
of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Thomas Szyperski
- Department
of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Weihai Fang
- Key
Laboratory of Theoretical and Computational Photochemistry of the
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lan He
- National Institute for Food and Drug Control, Beijing 100050, China
| | - Xuebo Chen
- Key
Laboratory of Theoretical and Computational Photochemistry of the
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Bing Gong
- Key
Laboratory of Theoretical and Computational Photochemistry of the
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Department
of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
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9
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Ren X, Song Y, Liu A, Zhang J, Yang P, Zhang J, An M. Experimental and theoretical studies of DMH as a complexing agent for a cyanide-free gold electroplating electrolyte. RSC Adv 2015. [DOI: 10.1039/c5ra13140e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Golden bright gold electrodeposit with a smooth and compact surface can be obtained from the introduced cyanide-free gold electroplating electrolyte.
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Affiliation(s)
- Xuefeng Ren
- State Key Laboratory of Urban Water Resource and Environment
- School of Chemical Engineering and Technology
- Harbin Institute of Technology
- Harbin
- China
| | - Ying Song
- State Key Laboratory of Urban Water Resource and Environment
- School of Chemical Engineering and Technology
- Harbin Institute of Technology
- Harbin
- China
| | - Anmin Liu
- State Key Laboratory of Urban Water Resource and Environment
- School of Chemical Engineering and Technology
- Harbin Institute of Technology
- Harbin
- China
| | - Jie Zhang
- State Key Laboratory of Urban Water Resource and Environment
- School of Chemical Engineering and Technology
- Harbin Institute of Technology
- Harbin
- China
| | - Peixia Yang
- State Key Laboratory of Urban Water Resource and Environment
- School of Chemical Engineering and Technology
- Harbin Institute of Technology
- Harbin
- China
| | - Jinqiu Zhang
- State Key Laboratory of Urban Water Resource and Environment
- School of Chemical Engineering and Technology
- Harbin Institute of Technology
- Harbin
- China
| | - Maozhong An
- State Key Laboratory of Urban Water Resource and Environment
- School of Chemical Engineering and Technology
- Harbin Institute of Technology
- Harbin
- China
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10
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Kuechler ER, York DM. Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl. J Chem Phys 2014; 140:054109. [PMID: 24511924 PMCID: PMC3977776 DOI: 10.1063/1.4863344] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/13/2014] [Indexed: 11/15/2022] Open
Abstract
The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.
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Affiliation(s)
- Erich R Kuechler
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
| | - Darrin M York
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
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