Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems

Suzuki, Kenkichi; Morokuma, Keiji; Maeda, Satoshi

doi:10.1002/jcc.24857

Cited by 7 publications

(17 citation statements)

References 40 publications

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“…Recently, an extended technique called multistructural microiteration (MSM) was proposed 68 . The MSM describes the entire molecule by a single QM structure and a weighted sum of multiple MM structures as schematically illustrated in Figure 7(a).…”

Section: Application Examplesmentioning

confidence: 99%

Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force

Maeda

Harabuchi

2021

WIREs Comput Mol Sci

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This article provides an overview on an automated reaction path search method called artificial force induced reaction (AFIR). The AFIR method induces various chemical transformations by applying force between pairs of fragments in a system. By pushing fragments from their various mutual orientations or by applying force between various fragment pairs using the AFIR method, many reaction paths can be explored systematically. In this article, the basic ideas and several different implementations are introduced first. Then, its thoroughness in the automated reaction path search is discussed with its applications to two small molecules. In the later part, its versatility is shown with discussing some previous application examples to organic reaction, organometallic catalysis, photoreaction, surface reaction, phase transition, and enzyme reaction. In addition, an attempt of predicting an idea of new synthesis method from scratch on the basis of the concept quantum chemistry‐aided retrosynthetic analysis (QCaRA) is presented, where the AFIR method was used as a reaction path search engine in QCaRA. Finally, future outlook and a comment on the GRRM program in which the AFIR method is available are given. This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics

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Section: Application Examplesmentioning

confidence: 99%

Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force

Maeda

Harabuchi

2021

WIREs Comput Mol Sci

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“…4(a). 27 The weight of each MM structure is determined by a Boltzmann distribution and varies according to the QM structure� Recently, by combining the MSM and AFIR methods, a reaction path was calculated in which L-lactate dehydrogenase (LDH) in rabbit muscle catalyzes the transformation of pyruvate to L-lactate. termed as surrounding structural TS (SSTS) in Fig.…”

Section: Lactate Dehydrogenasementioning

confidence: 99%

Reactivity prediction through quantum chemical calculations

Maeda¹,

Harabuchi²,

Hasegawa³

et al. 2021

ACM

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The main challenge in chemistry is understanding and controlling the movement of atoms, which play a leading role in chemical reactions. In principle, one could predict the movement of atoms by solving the Schrödinger equation, however, which for many-particle systems is too complicated to solve with high accuracy. Thanks to advances in quantum chemical calculation methods, the Schrödinger equation for the motion of electrons is solvable with reasonable accuracy under various approximations.1 Among the approximation algorithms, the density functional theory (DFT) based on the Kohn-Sham equation is routinely used in calculations of the potential energy surface (PES) for a system of several hundred atoms.

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“…The weight ω i is given aswhere β = 1/ k B T MSM , in which k B is the Boltzmann constant and T MSM is a model temperature parameter (see Computational Details section). 30 During geometry optimization, all the N structures in the real system were optimized one-by-one with the atoms fixed in the model system (reaction-center region) before changing the positions of atoms in the model system. In other words, the optimization of the model system was performed in the geometrical subspace in which the gradient of the region not involved in the reaction (part of the real system excluding the model system) was zero.…”

Section: Theoretical Backgroundmentioning

confidence: 99%

“…47 The MEP calculations were performed by the MSM method using the GRRM program combined with the Gaussian 09 program. 30,48,49 The initial path of the mixed calculation was obtained by the AFIR method with the model collision energy parameter of the AFIR method set to γ = 150 kJ/mol and the model temperature parameter of the MSM method set to T MSM = 50 000 K; these settings are discussed in our previous papers. 30,36 The artificial force was applied to two atom pairs: between the shifting proton and acceptor oxygen and between the shifting hydride and acceptor carbon.…”

Section: Computational Detailsmentioning

confidence: 99%

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Roles of Closed- and Open-Loop Conformations in Large-Scale Structural Transitions of l-Lactate Dehydrogenase

2019

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The mechanism of l -lactate generation from pyruvate by l -lactate dehydrogenase (LDH) from the rabbit muscle was studied theoretically by the multistructural microiteration (MSM) method combined with the quantum mechanics/molecular mechanics (QM/MM)–ONIOM method, where the MSM method describes the MM environment as a weighted average of multiple different structures that are fully relaxed during geometry optimization or a reaction path calculation for the QM part. The results showed that the substrate binding and product states were stabilized only in the open-loop conformation of LDH and the reaction occurred in the closed-loop conformation. In other words, before and after the chemical reaction, a large-scale structural transition from the open-loop conformation to the closed-loop conformation and vice versa occurred. The closed-loop conformation stabilized the transition state of the reaction. In contrast, the open-loop conformation stabilized the substrate binding and final states. In other words, the closed- to open-loop transition at the substrate binding state urges capture of the substrate molecule, the subsequent open- to closed-loop transition promotes the product generation, and the final closed- to open-loop transition at the final state prevents the reverse reaction going back to the substrate binding state. It is thus suggested that the exchange of stability between the closed- and open-loop conformations at different states promotes the catalytic cycle.

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Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems

Cited by 7 publications

References 40 publications

Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force

Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force

Reactivity prediction through quantum chemical calculations

Roles of Closed- and Open-Loop Conformations in Large-Scale Structural Transitions of l-Lactate Dehydrogenase

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