Literature DB >> 23389653

Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods.

Satoshi Maeda1, Koichi Ohno, Keiji Morokuma.   

Abstract

Global reaction route mapping (GRRM), a fully-automated search for all important reaction pathways relevant to a given purpose, on the basis of quantum chemical calculations enables systematic elucidation of complex chemical reaction mechanisms. However, GRRM had previously been limited to very simple systems. This is mainly because such calculations are highly demanding even in small systems when a brute-force sampling is considered. Hence, we have developed two independent but complementary methods: anharmonic downward distortion following (ADDF) and artificial force induced reaction (AFIR) methods. ADDF can follow reaction pathways starting from local minima on the potential energy surface (PES) toward transition structures (TSs) and dissociation channels. AFIR can find pathways starting from two or more reactants toward TSs for their associative reactions. In other words, ADDF searches for A → X type isomerization and A → X + Y type dissociation pathways, whereas AFIR finds A + B → X (+ Y) type associative pathways. Both follow special paths called the ADDF path and the AFIR path, and these tend to pass through near TSs of corresponding reaction pathways, giving approximate TSs. Such approximate TSs can easily be re-optimized to corresponding true TSs by standard geometry optimizations. On the basis of these two methods, we have proposed practical strategies of GRRM. The GRRM strategies have been applied to a variety of chemical systems ranging from thermal- and photochemical-reactions in small systems to organometallic- and enzyme-catalysis, on the basis of quantum chemical calculations. In this perspective, we present an overview of the GRRM strategies and some results of applications. Their practical usage for systematic prediction is also discussed.

Year:  2013        PMID: 23389653     DOI: 10.1039/c3cp44063j

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  29 in total

1.  Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin.

Authors:  Xiya Lu; Victor Ovchinnikov; Darren Demapan; Daniel Roston; Qiang Cui
Journal:  Biochemistry       Date:  2017-03-01       Impact factor: 3.162

2.  Quantum Chemical Calculations to Trace Back Reaction Paths for the Prediction of Reactants.

Authors:  Yosuke Sumiya; Yu Harabuchi; Yuuya Nagata; Satoshi Maeda
Journal:  JACS Au       Date:  2022-04-22

3.  QM/MM free energy simulations: recent progress and challenges.

Authors:  Xiya Lu; Dong Fang; Shingo Ito; Yuko Okamoto; Victor Ovchinnikov; Qiang Cui
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

4.  Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

Authors:  Qiang Cui; Tanmoy Pal; Luke Xie
Journal:  J Phys Chem B       Date:  2021-01-06       Impact factor: 2.991

5.  Implementation and performance of the artificial force induced reaction method in the GRRM17 program.

Authors:  Satoshi Maeda; Yu Harabuchi; Makito Takagi; Kenichiro Saita; Kimichi Suzuki; Tomoya Ichino; Yosuke Sumiya; Kanami Sugiyama; Yuriko Ono
Journal:  J Comput Chem       Date:  2017-11-14       Impact factor: 3.376

6.  Fast exploration of an optimal path on the multidimensional free energy surface.

Authors:  Changjun Chen
Journal:  PLoS One       Date:  2017-05-18       Impact factor: 3.240

7.  Organic linkers control the thermosensitivity of the emission intensities from Tb(iii) and Eu(iii) in a chameleon polymer.

Authors:  Miho Hatanaka; Yuichi Hirai; Yuichi Kitagawa; Takayuki Nakanishi; Yasuchika Hasegawa; Keiji Morokuma
Journal:  Chem Sci       Date:  2016-08-25       Impact factor: 9.825

8.  Discovery of a synthesis method for a difluoroglycine derivative based on a path generated by quantum chemical calculations.

Authors:  Tsuyoshi Mita; Yu Harabuchi; Satoshi Maeda
Journal:  Chem Sci       Date:  2020-05-22       Impact factor: 9.825

9.  The dioxasilepanyl group as a versatile organometallic unit: studies on stability, reactivity, and utility.

Authors:  Hayate Saito; Jun Shimokawa; Hideki Yorimitsu
Journal:  Chem Sci       Date:  2021-06-08       Impact factor: 9.825

10.  Stille coupling via C-N bond cleavage.

Authors:  Dong-Yu Wang; Masatoshi Kawahata; Ze-Kun Yang; Kazunori Miyamoto; Shinsuke Komagawa; Kentaro Yamaguchi; Chao Wang; Masanobu Uchiyama
Journal:  Nat Commun       Date:  2016-09-30       Impact factor: 14.919

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