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Effect of the Enhanced Cyan Fluorescent Protein framework on the UV/visible absorption spectra of some chromophores. Interdiscip Sci 2010; 2:38-47. [DOI: 10.1007/s12539-010-0084-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 11/09/2009] [Accepted: 11/10/2009] [Indexed: 10/19/2022]
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2
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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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Shiratori K, Nobusada K. Development of a Finite-Temperature Density Functional Approach to Electrochemical Reactions. J Phys Chem A 2008; 112:10681-8. [DOI: 10.1021/jp803923f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Kazuya Shiratori
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan, and Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan
| | - Katsuyuki Nobusada
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan, and Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan
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RUIZ-LÓPEZ MANUELF. The multipole moment expansion solvent continuum model: a brief review. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2008. [DOI: 10.1007/978-1-4020-8270-2_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Ardura D, López R, Sordo TL. Relative Gibbs Energies in Solution through Continuum Models: Effect of the Loss of Translational Degrees of Freedom in Bimolecular Reactions on Gibbs Energy Barriers. J Phys Chem B 2005; 109:23618-23. [PMID: 16375339 DOI: 10.1021/jp0540499] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present here a cell model for evaluating Gibbs energy barriers corresponding to bimolecular reactions (or processes of larger molecularity) in which a loss of translational degrees of freedom takes place along the reaction coordinate. With this model, we have studied the Walden inversion processes: Xa- + H3CXb --> XaCH3 + Xb- (X = F, Cl, Br, and I). In these processes, our model yields an increase of about 2.3-3.4 kcal/mol in Gibbs energy in solution corresponding to the loss of the translational degrees of freedom when passing from separate reactants to the TS in good agreement with experimental data. The corresponding value in the gas phase is about 6.7-7.1 kcal/mol. When the difference between these two figures is used to correct the results obtained by the standard UAHF implementation of the continuum model, the theoretical results are brought significantly closer to the experimental ones. This seems to indicate that for these reactions the parametrization used does not adequately introduce the increase in Gibbs energy corresponding to the constriction of the translational motion of the species along the reaction coordinate when passing from the gas phase to solution. Therefore, we believe that continuum models could perform much better if we released the parametrization process from the task of taking into account the constriction in translation motion in solution, which could be more adequately evaluated using the cell model proposed here, thus allowing it to focus on better reproducing all the remaining solvation effects.
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Affiliation(s)
- Diego Ardura
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, C/Julián Clavería, 8, 33006 Oviedo, Spain
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Sato H, Sakaki S. Comparison of Electronic Structure Theories for Solvated Molecules: RISM-SCF versus PCM. J Phys Chem A 2004. [DOI: 10.1021/jp0374758] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Yoshida, Kyoto 606-8501, Japan
| | - Shigeyoshi Sakaki
- Department of Molecular Engineering, Kyoto University, Yoshida, Kyoto 606-8501, Japan
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Nielsen CB, Sauer SPA, Mikkelsen KV. Response theory in the multipole reaction field model for equilibrium and nonequilibrium solvation: Exact theory and the second order polarization propagator approximation. J Chem Phys 2003. [DOI: 10.1063/1.1587131] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Schenter GK, Garrett BC, Truhlar DG. The Role of Collective Solvent Coordinates and Nonequilibrium Solvation in Charge-Transfer Reactions. J Phys Chem B 2001. [DOI: 10.1021/jp011981k] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gregory K. Schenter
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, and Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Bruce C. Garrett
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, and Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, and Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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Chuang YY, Truhlar DG. Nonequilibrium Solvation Effects for a Polyatomic Reaction in Solution. J Am Chem Soc 1999. [DOI: 10.1021/ja991809i] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yao-Yuan Chuang
- Contribution from the Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Contribution from the Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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Cramer CJ, Truhlar DG. Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. Chem Rev 1999; 99:2161-2200. [PMID: 11849023 DOI: 10.1021/cr960149m] [Citation(s) in RCA: 1727] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Cramer
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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Spencer S, Gagliardi L, Handy NC, Ioannou AG, Skylaris CK, Willetts A, Simper AM. Hydration of UO22+ and PuO22+. J Phys Chem A 1999. [DOI: 10.1021/jp983543s] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steven Spencer
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 lEW, U.K
| | - Laura Gagliardi
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 lEW, U.K
| | - Nicholas C. Handy
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 lEW, U.K
| | - Andrew G. Ioannou
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 lEW, U.K
| | | | - Andrew Willetts
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 lEW, U.K
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Ruiz-López MF, Oliva A, Tuñón I, Bertrán J. Self-Consistent Reaction Field Calculations of Nonequilibrium Solvent Effects on Proton Transfer Processes through Low-Barrier Hydrogen Bonds. J Phys Chem A 1998. [DOI: 10.1021/jp983288b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. F. Ruiz-López
- Laboratoire de Chimie Théorique, UMR CNRS-UHP 7565, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Unitat de Química Física, Universitat Autónoma de Barcelona, 08193 Bellaterra (Barcelona), Spain, and Departamento de Química Física, Universidad de Valencia, 46100 Burjasot, Spain
| | - A. Oliva
- Laboratoire de Chimie Théorique, UMR CNRS-UHP 7565, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Unitat de Química Física, Universitat Autónoma de Barcelona, 08193 Bellaterra (Barcelona), Spain, and Departamento de Química Física, Universidad de Valencia, 46100 Burjasot, Spain
| | - I. Tuñón
- Laboratoire de Chimie Théorique, UMR CNRS-UHP 7565, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Unitat de Química Física, Universitat Autónoma de Barcelona, 08193 Bellaterra (Barcelona), Spain, and Departamento de Química Física, Universidad de Valencia, 46100 Burjasot, Spain
| | - J. Bertrán
- Laboratoire de Chimie Théorique, UMR CNRS-UHP 7565, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Unitat de Química Física, Universitat Autónoma de Barcelona, 08193 Bellaterra (Barcelona), Spain, and Departamento de Química Física, Universidad de Valencia, 46100 Burjasot, Spain
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Li GS, Maigret B, Rinaldi D, Ruiz-L�pez MF. Influence of environment on proton-transfer mechanisms in model triads from theoretical calculations. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(19981130)19:15<1675::aid-jcc1>3.0.co;2-k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Basilevsky MV, Parsons DF, Vener MV. An advanced dielectric continuum approach for treating solvation effects: Time correlation functions. I. Local treatment. J Chem Phys 1998. [DOI: 10.1063/1.475472] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Basilevsky M, Vener M. Collective medium coordinates and their application in the theory of chemical reactions. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0166-1280(96)04973-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Tuñón I, Martins-Costa MTC, Millot C, Ruiz-López MF. Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. I. Proton transfer in strongly H-bonded complexes. J Chem Phys 1997. [DOI: 10.1063/1.473457] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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17
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Strnad M, Martins-Costa MTC, Millot C, Tuñón I, Ruiz-López MF, Rivail JL. Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. II. Charge separation processes. J Chem Phys 1997. [DOI: 10.1063/1.473458] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Equilibrium and non-equilibrium solvent effects in electrophilic halogenation of ethylenic compounds. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0166-1280(96)04530-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Okuno Y. Microscopic description of nonadiabatic, nonequilibrium, and equilibrium solvations for solvated cluster reactions: (H2O)nCl−+CH3Cl→ClCH3+Cl−(H2O)n. J Chem Phys 1996. [DOI: 10.1063/1.472424] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Truhlar DG, Garrett BC, Klippenstein SJ. Current Status of Transition-State Theory. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp953748q] [Citation(s) in RCA: 1585] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donald G. Truhlar
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Bruce C. Garrett
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, MS K1-96, Richland, Washington 99352
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