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Takenaka N, Kitamura Y, Nagaoka M. Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution. J Phys Chem B 2016; 120:2001-11. [PMID: 26794718 DOI: 10.1021/acs.jpcb.5b10061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface (FES) which is analogous to a Born-Oppenheimer potential energy surface. To survey the FES, an efficient computational research protocol is proposed within the QM/MM framework; (i) we first obtain some stable states (or transition states) involved by optimizing their structures on the FES, in a stepwise fashion, finally using the free energy gradient (FEG) method, and then (ii) we directly obtain the FE differences among any arbitrary states on the FES, efficiently by employing the QM/MM method with energy representation (ER), i.e., the QM/MM-ER method. To validate the calculation accuracy and efficiency, we applied the above FEG-ER methodology to a typical isomerization reaction of glycine in aqueous solution, and reproduced quite satisfactorily the experimental value of the reaction FE. Further, it was found that the structural relaxation of the solute in the QM/MM force field is not negligible to estimate correctly the FES. We believe that the present research protocol should become prevailing as one computational strategy and will play promising and important roles in solution chemistry toward solution reaction ergodography.
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Affiliation(s)
- Norio Takenaka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,ESICB, Kyoto University , Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520, Japan
| | - Yukichi Kitamura
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
| | - Masataka Nagaoka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,ESICB, Kyoto University , Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
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Kitamura Y, Takenaka N, Koyano Y, Nagaoka M. Dual Approach to Vibrational Spectra in Solution: Microscopic Influence of Hydrogen Bonding to the State of Motion of Glycine in Water. J Chem Theory Comput 2014; 10:3369-79. [PMID: 26588305 DOI: 10.1021/ct500235a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have proposed a new theoretical methodology to clarify the microscopic nature of the vibrational properties in solution, which consists of a combination of the vibrational frequency analyses (VFAs) with two kinds of Hessian matrices, that is, the effective Hessian on the free energy surface (free energy Hessian: "FE-Hessian") and the instantaneous one (instantaneous normal mode Hessian: "INM-Hessian") within QM/MM framework. In these VFAs, the Hessians were obtained by the analytical approach, having the advantages from the aspect of both the computational efficiency and accuracy in comparison to those obtained by the numerical one. In the present study, we have applied them to the glycine aqueous solution. First, by using the VFA with the FE-Hessian (VFA-FEH), we estimated the vibrational frequency shifts induced by solvent water molecules. The calculated values were quantitatively in agreement with experimental ones. It was clearly demonstrated that such vibrational shifts are attributed to not only the structural relaxation but also the explicit solute-solvent interactions (i.e., interatomic interactions). Second, by using the VFA with the INM-Hessian (VFA-INMH), the vibrational spectra in solution were investigated through the vibrational INM densities of states (DOS). By the comparison between the spectroscopic features and the microscopic solvation structure around glycine molecule, it was found that the frequency shifts and bandwidths in IR spectra are closely correlated with the hydrogen bonding (HB) network formations. In particular, the instantaneous changes of vibrational states of the hydroxyl group and carbonyl one, showing apparently inverse tendency on the strength of the HB interaction, can be explained very well on the basis of two different mechanisms, that is, the direct change of electron density in the bonding orbitals and the indirect one due to hyperconjugation between the lone electron pair and the antibonding orbitals, respectively. In conclusion, the present dual VFA approach is a quite useful strategy to interpret the microscopic origin of the experimental vibrational spectra.
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Affiliation(s)
- Yukichi Kitamura
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Japan Society for the Promotion of Science (JSPS), Tokyo 102-0083, Japan
| | - Norio Takenaka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University Katsura , Kyoto 615-8520, Japan
| | - Yoshiyuki Koyano
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masataka Nagaoka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University Katsura , Kyoto 615-8520, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
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Miyamoto H, Aida M. Helmholtz Energy Change between Neutral and Zwitterionic Forms of Glycine in Aqueous Solution Using Ab Initio Expanded QM/MM-MC with QM Solvent. CHEM LETT 2013. [DOI: 10.1246/cl.130412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hidenori Miyamoto
- Center for Quantum Life Sciences (QuLiS), Hiroshima University
- Department of Chemistry, Graduate School of Science, Hiroshima University
| | - Misako Aida
- Center for Quantum Life Sciences (QuLiS), Hiroshima University
- Department of Chemistry, Graduate School of Science, Hiroshima University
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