1
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Magrino T, Huet L, Saitta AM, Pietrucci F. Critical Assessment of Data-Driven versus Heuristic Reaction Coordinates in Solution Chemistry. J Phys Chem A 2022; 126:8887-8900. [DOI: 10.1021/acs.jpca.2c07640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Théo Magrino
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, CNRS UMR 7590, Paris 75005, France
| | - Léon Huet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, CNRS UMR 7590, Paris 75005, France
| | - A. Marco Saitta
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, CNRS UMR 7590, Paris 75005, France
| | - Fabio Pietrucci
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, CNRS UMR 7590, Paris 75005, France
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2
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Stuyver T, Shaik S. Promotion Energy Analysis Predicts Reaction Modes: Nucleophilic and Electrophilic Aromatic Substitution Reactions. J Am Chem Soc 2021; 143:4367-4378. [PMID: 33689334 DOI: 10.1021/jacs.1c00307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To develop an approach to pre-emptively predict the existence of major reaction modes associated with a chemical system, based on exclusive consideration of reactant properties, we build herein on the valence bond perspective of chemical reactivity. In this perspective, elementary chemical reactions are conceptualized as crossovers between individual diabatic/semilocalized states. As demonstrated, the spacings between the main diabatic states in the reactant geometries-the so-called promotion energies-contain predictive information about which types of crossings are likely to occur on a potential energy surface, facilitating the identification of potential transition states and products. As an added bonus, promotion energy analysis provides direct insight into the impact of environmental effects, e.g., the presence of (polar) solvents and/or (local) electric fields, on a mechanistic landscape. We illustrate the usefulness of our approach by focusing on model nucleophilic and electrophilic aromatic substitution reactions. Overall, we envision our analysis to be useful not only as a tool for conceptualizing individual mechanistic landscapes but also as a facilitator of systematic reaction-network exploration efforts. Because the emerging VB descriptors are computationally inexpensive (and can alternatively be inferred through machine learning), they could be evaluated on-the-fly as part of an exploration algorithm. The so-predicted reaction modes could subsequently be examined in detail through computationally more-demanding methods.
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Affiliation(s)
- Thijs Stuyver
- Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel
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3
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Shaik S. Stories of My Journeys Through Valence Bond Theory, DFT, MD and their Applications to Complex Objects. Isr J Chem 2020. [DOI: 10.1002/ijch.202000090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sason Shaik
- Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram 91904 Jerusalem Israel
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4
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Vermeeren P, Hansen T, Jansen P, Swart M, Hamlin TA, Bickelhaupt FM. A Unified Framework for Understanding Nucleophilicity and Protophilicity in the S N 2/E2 Competition. Chemistry 2020; 26:15538-15548. [PMID: 32866336 PMCID: PMC7756690 DOI: 10.1002/chem.202003831] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Indexed: 11/11/2022]
Abstract
The concepts of nucleophilicity and protophilicity are fundamental and ubiquitous in chemistry. A case in point is bimolecular nucleophilic substitution (SN 2) and base-induced elimination (E2). A Lewis base acting as a strong nucleophile is needed for SN 2 reactions, whereas a Lewis base acting as a strong protophile (i.e., base) is required for E2 reactions. A complicating factor is, however, the fact that a good nucleophile is often a strong protophile. Nevertheless, a sound, physical model that explains, in a transparent manner, when an electron-rich Lewis base acts as a protophile or a nucleophile, which is not just phenomenological, is currently lacking in the literature. To address this fundamental question, the potential energy surfaces of the SN 2 and E2 reactions of X- +C2 H5 Y model systems with X, Y = F, Cl, Br, I, and At, are explored by using relativistic density functional theory at ZORA-OLYP/TZ2P. These explorations have yielded a consistent overview of reactivity trends over a wide range in reactivity and pathways. Activation strain analyses of these reactions reveal the factors that determine the shape of the potential energy surfaces and hence govern the propensity of the Lewis base to act as a nucleophile or protophile. The concepts of "characteristic distortivity" and "transition state acidity" of a reaction are introduced, which have the potential to enable chemists to better understand and design reactions for synthesis.
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Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical ChemistryAmsterdam Institute of, Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale, Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
| | - Thomas Hansen
- Department of Theoretical ChemistryAmsterdam Institute of, Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale, Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, 2333CCLeidenThe Netherlands
| | - Paul Jansen
- Department of Theoretical ChemistryAmsterdam Institute of, Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale, Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Laboratory of Physical ChemistryETH ZurichVladimir-Prelog-Weg 28093ZurichSwitzerland
| | - Marcel Swart
- ICREAPg. Lluís Companys 2308010BarcelonaSpain
- IQCC & Dept. QuímicaUniversitat de GironaCampus Montilivi (Ciències)17003GironaSpain
| | - Trevor A. Hamlin
- Department of Theoretical ChemistryAmsterdam Institute of, Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale, Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical ChemistryAmsterdam Institute of, Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale, Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525AJNijmegenThe Netherlands
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5
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Jiao Y, Weinhold F. NBO/NRT Two-State Theory of Bond-Shift Spectral Excitation. Molecules 2020; 25:E4052. [PMID: 32899858 PMCID: PMC7571041 DOI: 10.3390/molecules25184052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/04/2022] Open
Abstract
We show that natural bond orbital (NBO) and natural resonance theory (NRT) analysis methods provide both optimized Lewis-structural bonding descriptors for ground-state electronic properties as well as suitable building blocks for idealized "diabatic" two-state models of the associated spectroscopic excitations. Specifically, in the framework of single-determinant Hartree-Fock or density functional methods for a resonance-stabilized molecule or supramolecular complex, we employ NBO/NRT descriptors of the ground-state determinant to develop a qualitative picture of the associated charge-transfer excitation that dominates the valence region of the electronic spectrum. We illustrate the procedure for the elementary bond shifts of SN2-type halide exchange reaction as well as the more complex bond shifts in a series of conjugated cyanine dyes. In each case, we show how NBO-based descriptors of resonance-type 3-center, 4-electron (3c/4e) interactions provide simple estimates of spectroscopic excitation energy, bond orders, and other vibronic details of the excited-state PES that anticipate important features of the full multi-configuration description. The deep 3c/4e connections to measurable spectral properties also provide evidence for NBO-based estimates of ground-state donor-acceptor stabilization energies (sometimes criticized as "too large" compared to alternative analysis methods) that are also found to be of proper magnitude to provide useful estimates of excitation energies and structure-dependent spectral shifts.
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Affiliation(s)
- Yinchun Jiao
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China;
| | - Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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6
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Xin X, Niu X, Liu W, Wang D. Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy. Chemphyschem 2020; 21:762-769. [PMID: 32154979 DOI: 10.1002/cphc.202000039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/15/2020] [Indexed: 02/03/2023]
Abstract
We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.
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Affiliation(s)
- Xin Xin
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Xiao Niu
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Wanqi Liu
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
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7
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Rincon L, Torres FJ, Mora JR, Zambrano CH, Rodriguez V. A valence bond perspective of the reaction force formalism. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2538-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Pan X, Li P, Ho J, Pu J, Mei Y, Shao Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching. Phys Chem Chem Phys 2019; 21:20595-20605. [PMID: 31508625 PMCID: PMC6761017 DOI: 10.1039/c9cp02593f] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire an AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced QM/MM free energy profiles at the B3LYP/6-31G* level of theory all within 1 kcal mol-1 with a 20 to 45 fold reduction in the computer time.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019, USA.
| | - Pengfei Li
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China.
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, LD326, Indianapolis, IN 46202, USA.
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China. and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019, USA.
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9
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Tirado-Rives J, Jorgensen WL. QM/MM Calculations for the Cl - + CH 3Cl S N2 Reaction in Water Using CM5 Charges and Density Functional Theory. J Phys Chem A 2019; 123:5713-5717. [PMID: 31246023 DOI: 10.1021/acs.jpca.9b04121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The prototypical SN2 reaction of chloride ion with methyl chloride has been reinvestigated in aqueous solution using QM/MM methodology featuring MO6-2X/6-31+G(d) calculations with the TIP4P water model, and partial charges were computed with the CM5 method. Though the DFT method yields excellent gas-phase energetics for the reaction, the QM/MM approach is found to yield overestimation of the activation barrier by ca. 12 kcal/mol. The discrepancy is traced to underestimate of the magnitude of the partial charges on the chlorine atoms in the transition structure. When CM1 or CM3 charges based on semiempirical wave functions are used instead, the agreement with experiment is much improved. The findings emphasize the sensitivity of the results of QM/MM calculations to the choice of QM method, the MM force field, and implementation of the QM/MM interface.
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Affiliation(s)
- Julian Tirado-Rives
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , United States
| | - William L Jorgensen
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , United States
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10
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Liu P, Wang D, Xu Y. A new, double-inversion mechanism of the F - + CH 3Cl S N2 reaction in aqueous solution. Phys Chem Chem Phys 2018; 18:31895-31903. [PMID: 27844085 DOI: 10.1039/c6cp06195h] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry. As a novel, double-inversion mechanism has just been found for the F- + CH3Cl SN2 reaction in the gas phase [Nat. Commun., 2015, 6, 5972], here, using multi-level quantum mechanics methods combined with the molecular mechanics method, we discovered a new, double-inversion mechanism for this reaction in aqueous solution. However, the structures of the stationary points along the reaction path show significant differences from those in the gas phase due to the strong influence of solvent and solute interactions, especially due to the hydrogen bonds formed between the solute and the solvent. More importantly, the relationship between the two double-inversion transition states is not clear in the gas phase, but, here we revealed a novel intermediate complex serving as a "connecting link" between the two transition states of the abstraction-induced inversion and the Walden-inversion mechanisms. A detailed reaction path was constructed to show the atomic-level evolution of this novel double reaction mechanism in aqueous solution. The potentials of mean force were calculated and the obtained Walden-inversion barrier height agrees well with the available experimental value.
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Affiliation(s)
- Peng Liu
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Yulong Xu
- School of Science, Qilu University of Technology, Jinan, 250353, China
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11
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Liu P, Li C, Wang D. Multilevel Quantum Mechanics Theories and Molecular Mechanics Calculations of the Cl - + CH 3I Reaction in Water. J Phys Chem A 2017; 121:8012-8016. [PMID: 28945365 DOI: 10.1021/acs.jpca.7b08103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Cl- + CH3I → CH3Cl + I- reaction in water was studied using combined multilevel quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculated with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 and 19.0 kcal/mol, respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.
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Affiliation(s)
- Peng Liu
- College of Physics and Electronics, Shandong Normal University , Jinan 250014, China
| | - Chen Li
- College of Physics and Electronics, Shandong Normal University , Jinan 250014, China
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University , Jinan 250014, China
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12
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Elementary S N 2 reaction revisited. Effects of solvent and alkyl chain length on kinetics of halogen exchange in haloalkanes elucidated by Empirical Valence Bond simulation. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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14
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Liu P, Zhang J, Wang D. Multi-level quantum mechanics theories and molecular mechanics study of the double-inversion mechanism of the F - + CH 3I reaction in aqueous solution. Phys Chem Chem Phys 2017; 19:14358-14365. [PMID: 28540950 DOI: 10.1039/c7cp02313h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A double-inversion mechanism of the F- + CH3I reaction was discovered in aqueous solution using combined multi-level quantum mechanics theories and molecular mechanics. The stationary points along the reaction path show very different structures to the ones in the gas phase due to the interactions between the solvent and solute, especially strong hydrogen bonds. An intermediate complex, a minimum on the potential of mean force, was found to serve as a connecting-link between the abstraction-induced inversion transition state and the Walden-inversion transition state. The potentials of mean force were calculated with both the DFT/MM and CCSD(T)/MM levels of theory. Our calculated free energy barrier of the abstraction-induced inversion is 69.5 kcal mol-1 at the CCSD(T)/MM level of theory, which agrees with the one at 72.9 kcal mol-1 calculated using the Born solvation model and gas-phase data; and our calculated free energy barrier of the Walden inversion is 24.2 kcal mol-1, which agrees very well with the experimental value at 25.2 kcal mol-1 in aqueous solution. The calculations show that the aqueous solution makes significant contributions to the potentials of mean force and exerts a big impact on the molecular-level evolution along the reaction pathway.
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Affiliation(s)
- Peng Liu
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
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15
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Proenza YG, de Souza MAF, Longo RL. Dynamical Bifurcation in Gas-Phase XH - + CH 3 Y S N 2 Reactions: The Role of Energy Flow and Redistribution in Avoiding the Minimum Energy Path. Chemistry 2016; 22:16220-16229. [PMID: 27651104 DOI: 10.1002/chem.201602976] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Indexed: 11/10/2022]
Abstract
The gas-phase reactions of XH- (X=O, S) + CH3 Y (Y=F, Cl, Br) span nearly the whole range of SN 2 pathways, and show an intrinsic reaction coordinate (IRC) (minimum energy path) with a deep well owing to the CH3 XH⋅⋅⋅Y- (or CH3 S- ⋅⋅⋅HF) hydrogen-bonded postreaction complex. MP2 quasiclassical-type direct dynamics starting at the [HX⋅⋅⋅CH3 ⋅⋅⋅Y]- transition-state (TS) structure reveal distinct mechanistic behaviors. Trajectories that yield the separated CH3 XH+Y- (or CH3 S- +HF) products directly are non-IRC, whereas those that sample the CH3 XH⋅⋅⋅Y- (or CH3 S- ⋅⋅⋅HF) complex are IRC. The IRCIRC/non-IRC ratios of 90:10, 40:60, 25:75, 2:98, 0:100, and 0:100 are obtained for (X, Y)=(S, F), (O, F), (S, Cl), (S, Br), (O, Cl), and (O, Br), respectively. The properties of the energy profiles after the TS cannot provide a rationalization of these results. Analysis of the energy flow in dynamics shows that the trajectories cross a dynamical bifurcation, and that the inability to follow the minimum energy path arises from long vibration periods of the X-C⋅⋅⋅Y bending mode. The partition of the available energy to the products into vibrational, rotational, and translational energies reveals that if the vibrational contribution is more than 80 %, non-IRC behavior dominates, unless the relative fraction of the rotational and translational components is similar, in which case a richer dynamical mechanism is shown, with an IRC/non-IRC ratio that correlates to this relative fraction.
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Affiliation(s)
- Yaicel G Proenza
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, 50.740-560, Recife, PE, Brazil
| | - Miguel A F de Souza
- Instituto de Química, CCET, Universidade Federal do Rio Grande do Norte, 59.072-970, Natal, RN, Brazil
| | - Ricardo L Longo
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, 50.740-560, Recife, PE, Brazil.
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16
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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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17
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Sharir-Ivry A, Varatharaj R, Shurki A. Valence bond and enzyme catalysis: a time to break down and a time to build up. Chemistry 2015; 21:7159-69. [PMID: 25808731 DOI: 10.1002/chem.201406236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 11/12/2022]
Abstract
Understanding enzyme catalysis and developing ability to control of it are two great challenges in biochemistry. A few successful examples of computational-based enzyme design have proved the fantastic potential of computational approaches in this field, however, relatively modest rate enhancements have been reported and the further development of complementary methods is still required. Herein we propose a conceptually simple scheme to identify the specific role that each residue plays in catalysis. The scheme is based on a breakdown of the total catalytic effect into contributions of individual protein residues, which are further decomposed into chemically interpretable components by using valence bond theory. The scheme is shown to shed light on the origin of catalysis in wild-type haloalkane dehalogenase (wt-DhlA) and its mutants. Furthermore, the understanding gained through our scheme is shown to have great potential in facilitating the selection of non-optimal sites for catalysis and suggesting effective mutations to enhance the enzymatic rate.
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Affiliation(s)
- Avital Sharir-Ivry
- Institute for Drug Design, School of Pharmacy, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120 (Israel), Fax: (+972) 2-675-7076
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18
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Shurki A, Derat E, Barrozo A, Kamerlin SCL. How valence bond theory can help you understand your (bio)chemical reaction. Chem Soc Rev 2015; 44:1037-52. [DOI: 10.1039/c4cs00241e] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This Tutorial Review describes modern VB theory, using a didactic example of an SN2 reaction to illustrate its immediate applications.
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Affiliation(s)
- Avital Shurki
- Institute for Drug Research
- School of Pharmacy
- The Hebrew University of Jerusalem
- Jerusalem
- Israel
| | - Etienne Derat
- Institut Parisien de Chimie Moléculaire
- UMR 8232
- Paris
- France
| | - Alexandre Barrozo
- Science for Life Laboratory
- Department of Cell and Molecular Biology
- Uppsala University
- Uppsala
- Sweden
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19
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Sharir-Ivry A, Varatharaj R, Shurki A. Challenges within the Linear Response Approximation When Studying Enzyme Catalysis and Effects of Mutations. J Chem Theory Comput 2014; 11:293-302. [DOI: 10.1021/ct500751f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Avital Sharir-Ivry
- Institute for Drug Design,
School of Pharmacy, The Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Rajapandian Varatharaj
- Institute for Drug Design,
School of Pharmacy, The Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Avital Shurki
- Institute for Drug Design,
School of Pharmacy, The Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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20
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Shurki A, Sharir-Ivry A. Valence Bond-Based Hybrid Quantum Mechanics Molecular Mechanics Approaches and Proper Inclusion of the Effect of the Surroundings. Isr J Chem 2014. [DOI: 10.1002/ijch.201400038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Usharani D, Lai W, Li C, Chen H, Danovich D, Shaik S. A tutorial for understanding chemical reactivity through the valence bond approach. Chem Soc Rev 2014; 43:4968-88. [PMID: 24710199 DOI: 10.1039/c4cs00043a] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This is a tutorial on the usage of valence bond (VB) diagrams for understanding chemical reactivity in general, and hydrogen atom transfer (HAT) reactivity in particular. The tutorial instructs the reader how to construct the VB diagrams and how to estimate HAT barriers from raw data, starting with the simplest reaction H + H2 and going all the way to HAT in the enzyme cytochrome P450. Other reactions are treated as well, and some unifying principles are outlined. The tutorial projects the unity of reactivity treatments, following Coulson's dictum "give me insight, not numbers", albeit with its modern twist: giving numbers and insight.
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Affiliation(s)
- Dandamudi Usharani
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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22
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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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Zhang J, Xu Y, Chen J, Wang D. A multilayered-representation, quantum mechanical/molecular mechanics study of the CH3Cl + F− reaction in aqueous solution: the reaction mechanism, solvent effects and potential of mean force. Phys Chem Chem Phys 2014; 16:7611-7. [DOI: 10.1039/c3cp55401e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multi-layered representation, hybrid quantum mechanical and molecular mechanics method study of the CH3Cl + F− → CH3F + Cl− reaction in water.
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Affiliation(s)
- Jingxue Zhang
- College of Physics and Electronics
- Shandong Normal University
- Jinan, 250014 China
| | - Yulong Xu
- College of Physics and Electronics
- Shandong Normal University
- Jinan, 250014 China
- School of Science
- Qilu University of Technology
| | - Jie Chen
- College of Physics and Electronics
- Shandong Normal University
- Jinan, 250014 China
| | - Dunyou Wang
- College of Physics and Electronics
- Shandong Normal University
- Jinan, 250014 China
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24
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Jiang L, Orimoto Y, Aoki Y. Substituent Effects on Menshutkin-Type Reactions in the Gas Phase and Solutions: Theoretical Approach from the Orbital Interaction View. J Chem Theory Comput 2013; 9:4035-45. [DOI: 10.1021/ct4006163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lizhi Jiang
- Department of Molecular
and Material Sciences, Interdisciplinary Graduate School of Engineering
Sciences, Kyushu University, Kasuga Fukuoka
816-8580, Japan
| | - Yuuichi Orimoto
- Department
of Material Sciences, Faculty of Engineering Sciences, Kyushu University, Kasuga Fukuoka 816-8580, Japan
| | - Yuriko Aoki
- Department
of Material Sciences, Faculty of Engineering Sciences, Kyushu University, Kasuga Fukuoka 816-8580, Japan
- Group, CREST, Japan Science and Technology Agency (JST), Kawaguchi Center
Building, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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25
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Olsen S, McKenzie RH. A two-state model of twisted intramolecular charge-transfer in monomethine dyes. J Chem Phys 2012; 137:164319. [DOI: 10.1063/1.4762561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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26
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Fernández I, Bickelhaupt FM, Cossío FP. Type-I dyotropic reactions: understanding trends in barriers. Chemistry 2012; 18:12395-403. [PMID: 22915249 DOI: 10.1002/chem.201200897] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Indexed: 11/10/2022]
Abstract
To understand the factors that control the activation barrier of type-I 1,2-dyotropic reactions (X-EH(2)-CH(2)-X*→X*-EH(2)-CH(2)-X, with E=C and Si, X=H, CH(3), SiH(3), F to I) and trends therein as a function of the migrating groups X, we have explored ten archetypal model reactions of this class using relativistic density functional theory (DFT) at ZORA-OLYP/TZ2P. The main trends in reactivity are rationalized using the activation strain model of chemical reactivity, which had to be extended from bimolecular to unimolecular reactions. Thus, the above type-I dyotropic reactions can be conceived as a relative rotation of the CH(2)CH(2) and [X···X] fragments in X-CH(2)-CH(2)-X. The picture that emerges from these analyses is that reduced C-X bonding in the transition state is the origin of the reaction barrier. Also the trends in reactivity on variation of X can be understood in terms of how sensitive the C-X interaction is towards adopting the transition-state geometry. A valence bond analysis complements the analyses and confirms the picture emerging from the activation strain model.
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Affiliation(s)
- Israel Fernández
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain.
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27
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Wu W, Su P, Shaik S, Hiberty PC. Classical Valence Bond Approach by Modern Methods. Chem Rev 2011; 111:7557-93. [DOI: 10.1021/cr100228r] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Sason Shaik
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University, Jerusalem 91904, Israel
| | - Philippe C. Hiberty
- Laboratoire de Chimie Physique, Groupe de Chimie Théorique, CNRS UMR 8000, Université de Paris-Sud, 91405 Orsay Cédex, France
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28
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Hirao H. Correlation diagram approach as a tool for interpreting chemistry: an introductory overview. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Shaik S, Hiberty PC. A primer on qualitative valence bond theory – a theory coming of age. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sason Shaik
- Institute of Chemistry and the Lise Meitner‐Minerva Center for Computational Quantum Chemisty, The Edmond J. Safra Campus‐Givat Ram, The Hebrew University, Jerusalem, Israel
| | - Philippe C. Hiberty
- Laboratoire de Chimie Physique, CNRS UMR 8000, Bat 349, Université de Paris‐Sud, 19405 Orsay, France
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30
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Shaik S, Lai W, Chen H, Wang Y. The valence bond way: reactivity patterns of cytochrome P450 enzymes and synthetic analogs. Acc Chem Res 2010; 43:1154-65. [PMID: 20527755 DOI: 10.1021/ar100038u] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The preceding decade has witnessed an immense surge of activity in the bioinorganic chemistry of transition metal enzymes and synthetic analogs that model their operation. The wide range of research covers both experimental and theoretical investigations of structure and reactivity patterns. Theory, and especially density functional theory (DFT), has become a very useful tool, an important partner of experiment in resolving structural and mechanistic issues. This flare of activity has generated a great deal of knowledge on intermediates, transition states, barriers, rate constants, rate-equilibrium relationships, stereoselectivity, and so forth. This abundance of acquired knowledge has created the need for establishing order, namely, the outlining of broad generalizations, as well as the creation of a more-intuitive interface between experimental and theoretical data. The valence bond (VB) diagram model, originally developed for organic reactions, is such a theoretical framework that has the potential to guide the requisite generalizations in the field of bioinorganic chemical reactivity. In this Account, we briefly describe the principles of construction of VB diagrams for bioinorganic reactions, detailing applications in the booming research area of heme enzyme (specifically cytochrome P450) reactivity, and particularly two archetypal reactions of these enzymes, alkane hydroxylation and thioether sulfoxidation. For congruence with the lingua franca of bioinorganic chemistry, the VB model is formulated to create bridges to (i) the molecular orbital (MO) description, (ii) the oxidation state formulation of transition metal complexes, and (iii) widely used concepts such as the Bell-Evans-Polanyi (BEP) principle. The VB diagram model reveals the origins of the barrier, describes the formation of transition states and reaction intermediates, and allows the prediction of barrier heights and structure-reactivity relationships. Thus, from the VB diagram model, we can rationalize the mechanistic selection during alkane hydroxylation compared with thioether sulfoxidation, as well as the different behaviors of the spin states during the reactions with the active species of P450, the high-valent iron oxo species called compound I (Cpd I). Furthermore, the VB model leads to expressions that enable us to estimate barrier heights from easily accessible reactant properties, such as bond energies, ionization potential, and electron affinities. We further show that the model is not limited to these archetypal processes: its applicability is wider and more general. Accordingly, we outline the potential applications of these principles to other reactions of P450 (such as olefin epoxidation and arene hydroxylation) and to similar reactions of nonheme enzymes and synthetic models. The VB diagram model leads to a unified understanding of complex bioinorganic transformations, creates order in the data, and provides an important framework for making useful predictions.
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Affiliation(s)
- Sason Shaik
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Wenzhen Lai
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Hui Chen
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Yong Wang
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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31
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Sharir-Ivry A, Shnerb T, Štrajbl M, Shurki A. VB/MM Protein Landscapes: A Study of the SN2 Reaction in Haloalkane Dehalogenase. J Phys Chem B 2010; 114:2212-8. [DOI: 10.1021/jp905143d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Avital Sharir-Ivry
- Department of Medicinal Chemistry and Natural Product, The Institute of Drug Research, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Tamar Shnerb
- Department of Medicinal Chemistry and Natural Product, The Institute of Drug Research, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Marek Štrajbl
- Department of Medicinal Chemistry and Natural Product, The Institute of Drug Research, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Avital Shurki
- Department of Medicinal Chemistry and Natural Product, The Institute of Drug Research, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
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32
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Shaik S. Valence bond all the way: From the degenerate H-exchange to cytochrome P450. Phys Chem Chem Phys 2010; 12:8706-20. [DOI: 10.1039/c001372m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Valero R, Song L, Gao J, Truhlar DG. Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase S(N)2 Reaction of Acetate Ion with 1,2-Dichloroethane. J Chem Theory Comput 2009; 5:1-22. [PMID: 20047005 PMCID: PMC2658610 DOI: 10.1021/ct800318h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Diabatic models are widely employed for studying chemical reactivity in condensed phases and enzymes, but there has been little discussion of the pros and cons of various diabatic representations for this purpose. Here we discuss and contrast six different schemes for computing diabatic potentials for a charge rearrangement reaction. They include (i) the variational diabatic configurations (VDC) constructed by variationally optimizing individual valence bond structures and (ii) the consistent diabatic configurations (CDC) obtained by variationally optimizing the ground-state adiabatic energy, both in the nonorthogonal molecular orbital valence bond (MOVB) method, along with the orthogonalized (iii) VDC-MOVB and (iv) CDC-MOVB models. In addition, we consider (v) the fourfold way (based on diabatic molecular orbitals and configuration uniformity), and (vi) empirical valence bond (EVB) theory. To make the considerations concrete, we calculate diabatic electronic states and diabatic potential energies along the reaction path that connects the reactant and the product ion-molecule complexes of the gas-phase bimolecular nucleophilic substitution (S(N)2) reaction of 1,2-dichloethane (DCE) with acetate ion, which is a model reaction corresponding to the reaction catalyzed by haloalkane dehalogenase. We utilize ab initio block-localized molecular orbital theory to construct the MOVB diabatic states and ab initio multi-configuration quasidegenerate perturbation theory to construct the fourfold-way diabatic states; the latter are calculated at reaction path geometries obtained with the M06-2X density functional. The EVB diabatic states are computed with parameters taken from the literature. The MOVB and fourfold-way adiabatic and diabatic potential energy profiles along the reaction path are in qualitative but not quantitative agreement with each other. In order to validate that these wave-function-based diabatic states are qualitatively correct, we show that the reaction energy and barrier for the adiabatic ground state, obtained with these methods, agree reasonably well with the results of high-level calculations using the composite G3SX and G3SX(MP3) methods and the BMC-CCSD multi-coefficient correlation method. However, a comparison of the EVB gas-phase adiabatic ground-state reaction path with those obtained from MOVB and with the fourfold way reveals that the EVB reaction path geometries show a systematic shift towards the products region, and that the EVB lowest-energy path has a much lower barrier. The free energies of solvation and activation energy in water reported from dynamical calculations based on EVB also imply a low activation barrier in the gas phase. In addition, calculations of the free energy of solvation using the recently proposed SM8 continuum solvation model with CM4M partial atomic charges lead to an activation barrier in reasonable agreement with experiment only when the geometries and the gas-phase barrier are those obtained from electronic structure calculations, i.e., methods i-v. These comparisons show the danger of basing the diabatic states on molecular mechanics without the explicit calculation of electronic wave functions. Furthermore, comparison of schemes i-v with one another shows that significantly different quantitative results can be obtained by using different methods for extracting diabatic states from wave function calculations, and it is important for each user to justify the choice of diabatization method in the context of its intended use.
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Affiliation(s)
- Rosendo Valero
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431
| | - Lingchun Song
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431
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Song L, Mo Y, Gao J. An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane. J Chem Theory Comput 2009; 5:174-185. [PMID: 20047006 PMCID: PMC2658615 DOI: 10.1021/ct800421y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An effective Hamiltonian mixed molecular orbital and valence bond (EH-MOVB) method is described to obtain an accurate potential energy surface for chemical reactions. Building upon previous results on the construction of diabatic and adiabatic potential surfaces using ab initio MOVB theory, we introduce a diabatic-coupling scaling factor to uniformly scale the ab initio off-diagonal matrix element H(12) such that the computed energy of reaction from the EH-MOVB method is in agreement with the target value. The scaling factor is very close to unity, resulting in minimal alteration of the potential energy surface of the original MOVB model. Furthermore, the relative energy between the reactant and product diabatic states in the EH-MOVB method can be improved to match the experimental energy of reaction. A key ingredient in the EH-MOVB theory is that the off-diagonal matrix elements are functions of all degrees of freedom of the system and the overlap matrix is explicitly evaluated. The EH-MOVB method has been applied to the nucleophilic substitution reaction between hydrosulfide and chloromethane to illustrate the methodology and the results were matched to reproduce the results from ab initio valence bond self-consistent valence bond (VBSCF) calculations. The diabatic coupling (the off-diagonal matrix element in the generalized secular equation) has small variations along the minimum energy reaction path in the EH-MOVB model, whereas it shows a maximum value at the transition state and has nearly zero values in the regions of the ion-dipole complexes from VBSCF calculations. The difference in the diabatic coupling stabilization is attributed to the large overlap integral in the computationally efficient MOVB method.
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Affiliation(s)
- Lingchun Song
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
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35
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Song L, Gao J. On the construction of diabatic and adiabatic potential energy surfaces based on ab initio valence bond theory. J Phys Chem A 2008; 112:12925-35. [PMID: 18828577 PMCID: PMC2736346 DOI: 10.1021/jp803050e] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A theoretical model is presented for deriving effective diabatic states based on ab initio valence bond self-consistent field (VBSCF) theory by reducing the multiconfigurational VB Hamiltonian into an effective two-state model. We describe two computational approaches for the optimization of the effective diabatic configurations, resulting in two ways of interpreting such effective diabatic states. In the variational diabatic configuration (VDC) method, the energies of the diabatic states are variationally minimized. In the consistent diabatic configuration (CDC) method, both the configuration coefficients and orbital coefficients are simultaneously optimized to minimize the adiabatic ground-state energy in VBSCF calculations. In addition, we describe a mixed molecular orbital and valence bond (MOVB) approach to construct the CDC diabatic and adiabatic states for a chemical reaction. Note that the VDC-MOVB method has been described previously. Employing the symmetric S(N)2 reaction between NH(3) and CH(3)NH(3)(+) as a test system, we found that the results from ab initio VBSCF and from ab initio MOVB calculations using the same basis set are in good agreement, suggesting that the computationally efficient MOVB method is a reasonable model for VB simulations of condensed phase reactions. The results indicate that CDC and VDC diabatic states converge, respectively, to covalent and ionic states as the molecular geometries are distorted from the minimum of the respective diabatic state along the reaction coordinate. Furthermore, the resonance energy that stabilizes the energy of crossing between the two diabatic states, resulting in the transition state of the adiabatic ground-state reaction, has a strong dependence on the overlap integral between the two diabatic states and is a function of both the exchange integral and the total diabatic ground-state energy.
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Affiliation(s)
- Lingchun Song
- Department of Chemistry and the Minnesota Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Su P, Wu W, Kelly CP, Cramer CJ, Truhlar DG. VBSM: A Solvation Model Based on Valence Bond Theory. J Phys Chem A 2008; 112:12761-8. [DOI: 10.1021/jp711655k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peifeng Su
- Department of Chemistry, State Key Laboratory of Physical
Chemistry of Solid Surfaces, Centre for Theoretical Chemistry, Xiamen
University, Xiamen 36105, P. R. China, and Department of Chemistry
and Supercomputing Institute, University of Minnesota, 207 Pleasant
Street S.E., Minneapolis, Minnesota 55455-0431
| | - Wei Wu
- Department of Chemistry, State Key Laboratory of Physical
Chemistry of Solid Surfaces, Centre for Theoretical Chemistry, Xiamen
University, Xiamen 36105, P. R. China, and Department of Chemistry
and Supercomputing Institute, University of Minnesota, 207 Pleasant
Street S.E., Minneapolis, Minnesota 55455-0431
| | - Casey P. Kelly
- Department of Chemistry, State Key Laboratory of Physical
Chemistry of Solid Surfaces, Centre for Theoretical Chemistry, Xiamen
University, Xiamen 36105, P. R. China, and Department of Chemistry
and Supercomputing Institute, University of Minnesota, 207 Pleasant
Street S.E., Minneapolis, Minnesota 55455-0431
| | - Christopher J. Cramer
- Department of Chemistry, State Key Laboratory of Physical
Chemistry of Solid Surfaces, Centre for Theoretical Chemistry, Xiamen
University, Xiamen 36105, P. R. China, and Department of Chemistry
and Supercomputing Institute, University of Minnesota, 207 Pleasant
Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry, State Key Laboratory of Physical
Chemistry of Solid Surfaces, Centre for Theoretical Chemistry, Xiamen
University, Xiamen 36105, P. R. China, and Department of Chemistry
and Supercomputing Institute, University of Minnesota, 207 Pleasant
Street S.E., Minneapolis, Minnesota 55455-0431
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37
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Sharir-Ivry A, Shurki A. A VB/MM View of the Identity SN2 Valence-Bond State Correlation Diagram in Aqueous Solution. J Phys Chem A 2008; 112:13157-63. [DOI: 10.1021/jp801722e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Avital Sharir-Ivry
- Department of Medicinal Chemistry and Natural Products, School of Pharmacy, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Avital Shurki
- Department of Medicinal Chemistry and Natural Products, School of Pharmacy, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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38
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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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39
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Su P, Song L, Wu W, Shaik S, Hiberty PC. Heterolytic Bond Dissociation in Water: Why Is It So Easy for C4H9Cl But Not for C3H9SiCl? J Phys Chem A 2008; 112:2988-97. [DOI: 10.1021/jp8004647] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peifeng Su
- Department of Chemistry, College of Chemistry and Chemical Engineering, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China, Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University, Jerusalem 91904, Israel, and Laboratoire de Chimie Physique, Bât 490, Université de Paris-Sud, CNRS UMR 8000, 91405 Orsay, France
| | - Lingchun Song
- Department of Chemistry, College of Chemistry and Chemical Engineering, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China, Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University, Jerusalem 91904, Israel, and Laboratoire de Chimie Physique, Bât 490, Université de Paris-Sud, CNRS UMR 8000, 91405 Orsay, France
| | - Wei Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China, Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University, Jerusalem 91904, Israel, and Laboratoire de Chimie Physique, Bât 490, Université de Paris-Sud, CNRS UMR 8000, 91405 Orsay, France
| | - Sason Shaik
- Department of Chemistry, College of Chemistry and Chemical Engineering, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China, Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University, Jerusalem 91904, Israel, and Laboratoire de Chimie Physique, Bât 490, Université de Paris-Sud, CNRS UMR 8000, 91405 Orsay, France
| | - Philippe C. Hiberty
- Department of Chemistry, College of Chemistry and Chemical Engineering, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China, Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University, Jerusalem 91904, Israel, and Laboratoire de Chimie Physique, Bât 490, Université de Paris-Sud, CNRS UMR 8000, 91405 Orsay, France
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40
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An electron localization function and catastrophe theory analysis on the molecular mechanism of gas-phase identity SN2 reactions. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0427-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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41
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Bucko T. Ab initio calculations of free-energy reaction barriers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2008; 20:064211. [PMID: 21693873 DOI: 10.1088/0953-8984/20/6/064211] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction-the nucleophilic substitution of methyl chloride by a chlorine anion.
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Affiliation(s)
- T Bucko
- Fakultät für Physik and Center for Computational Materials Science, Universität Wien, Sensengasse, Wien 1090, Austria
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van Bochove MA, Bickelhaupt FM. Nucleophilic Substitution at C, Si and P: How Solvation Affects the Shape of Reaction Profiles. European J Org Chem 2008. [DOI: 10.1002/ejoc.200700953] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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Su P, Ying F, Wu W, Hiberty PC, Shaik S. The Menshutkin Reaction in the Gas Phase and in Aqueous Solution: A Valence Bond Study. Chemphyschem 2007; 8:2603-14. [DOI: 10.1002/cphc.200700626] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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44
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Arnaut LG, Formosinho SJ. The rates of S(N)2 reactions and their relation to molecular and solvent properties. Chemistry 2007; 13:8018-28. [PMID: 17616960 DOI: 10.1002/chem.200700276] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The energy barriers of symmetrical methyl exchanges in the gas phase have been calculated with the reaction path of the intersecting/interacting-state model (ISM). Reactive bond lengths increase down a column of the Periodic Table and compensate for the decrease in the force constants, which explains the near constancy of the intrinsic barriers in the following series of nucleophiles: F(-) approximately Cl(-) approximately Br(-) approximately I(-). This compensation is absent along the rows of the Periodic Table and the trend in the reactivity is dominated by the increase in the electrophilicity index of the nucleophile in the series C<N<O<F. Solvent effects have been quantitatively incorporated into the ISM model through a correlation between electrophilicity and the solvent acceptor number. This correlation is transferable between nucleophiles and solvents and allows the methyl transfer rate constants in solution to be calculated with remarkable simplicity and accuracy. The relationship between the S(N)2 and electron-transfer mechanisms is clarified and it is shown that smaller solvent static effects should be expected for electron transfer in the absence of a thermodynamic driving force.
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Affiliation(s)
- Luis G Arnaut
- Chemistry Department, University of Coimbra, P-3049 Coimbra Codex, Portugal.
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