1
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γ-ray radiolysis of dihydroxyurea in nitric acid and its radiolytic products. J Radioanal Nucl Chem 2022. [DOI: 10.1007/s10967-022-08388-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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2
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Fukutani T, Miyazawa K, Iwata S, Satoh H. G-RMSD: Root Mean Square Deviation Based Method for Three-Dimensional Molecular Similarity Determination. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Tomonori Fukutani
- Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kohei Miyazawa
- Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Satoru Iwata
- Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroko Satoh
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Research Organization of Information and Systems (ROIS), 4-3-13 Toranomon, Minato-ku, Tokyo 105-0001, Japan
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3
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Ohno K, Kishimoto N, Iwamoto T, Satoh H, Watanabe H. High performance global exploration of isomers and isomerization channels on quantum chemical potential energy surface of H 5 C 2 NO 2. J Comput Chem 2021; 42:192-204. [PMID: 33146910 DOI: 10.1002/jcc.26446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 11/07/2022]
Abstract
High performance global exploration of isomers and isomerization channels on the quantum chemical potential energy surface (PES) is performed for H5 C2 NO2 by using the scaled hypersphere search-anharmonic downward distortion following (SHS-ADDF) method. A multi-node operation, NeoGRRM, has achieved high performance exploration calculations for the large system by submitting SHS-ADDF sub-jobs into many cores in parallel and unifying the results of sub-jobs into the total lists of the main-job. Global exploration of equilibrium (EQ) and transition-state structures at the level of B3LYP/6-31G(d) gave 3210 EQs and 23278 TSs. Nine compounds were found in the low energy regions of 0-100 kJ/mol; the lowest energy compound is N-methylcarbamic acid, the second is methyl carbamate, and the third is glycine (the most fundamental amino acid). Interconversion pathways between the conformers of each of the low energy compounds were surveyed. Isomerization channels around glycine were explored in detail. The lowest energy barriers around some of the EQs turned to be negative after zero-point energy corrections. This indicates that those structures cannot exist as independent structures because they spontaneously collapse into more stable structures. The global PES search showed various interesting dissociating channels which indicate synthon reaction pathways in the reverse directions.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Tokyo, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Naoki Kishimoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Hiroko Satoh
- Institute for Quantum Chemical Exploration, Tokyo, Japan.,Department of Chemistry, University of Zurich, Zurich, Switzerland.,Research Organization of Information and Systems (ROIS), Tokyo, Japan
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4
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Quantum chemical exploration of polymerized forms of polycyclic aromatic hydrocarbons: D6h tetramer and polymer of coronene. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Ohno K, Oki T, Yamakado H. Quantum Chemical Exploration of Intermolecular Reactions of Acetylene. J Comput Chem 2020; 41:687-697. [PMID: 31793029 DOI: 10.1002/jcc.26120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 11/09/2022]
Abstract
Quantum chemical explorations of potential energy surfaces showed that acetylene produces various products starting from molecular arrays in short distances of 1.3-2.5 Å. Arrays of (C2 H2 )2 gave cyclobutadiene, tetrahedrane, and acetylene dimers. Arrays of (C2 H2 )3 gave benzene, prismane, benzvalene, Dewar benzene, and acetylene trimers. Arrays of (C2 H2 )4 gave cubane, cyclooctatetranene, and acetylene tetramers. Different forms of initial arrays yielded different sets of products; a parallel array of two monomers gave cyclobutadiene, whereas a cross array gave tetrahedrane. Initial molecular arrays with unusually close contacts were estimated to require local forces of 1-9 × 10-8 N. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Konan 1-9-36, Minato-ku, Tokyo, 108-0075, Japan.,Tohoku University, Graduate School of Science, Aramaki Aza-Aoba 6-3, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Takuto Oki
- Faculty of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
| | - Hideo Yamakado
- Faculty of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
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6
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Lee K, Woo Kim J, Youn Kim W. Efficient Construction of a Chemical Reaction Network Guided By a Monte Carlo Tree Search. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.201900057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Kyunghoon Lee
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro, Yuseong-gu Daejeon 305-701 Korea
| | - Jin Woo Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro, Yuseong-gu Daejeon 305-701 Korea
| | - Woo Youn Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro, Yuseong-gu Daejeon 305-701 Korea
- KI for Artificial IntelligenceKorea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro, Yuseong-gu Daejeon 305-701 Korea
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7
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Ohno K, Satoh H, Iwamoto T. Quantum chemical exploration of new π-electron systems: Capsule-formed dimers of polycyclic aromatic hydrocarbons. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.04.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Ohno K, Satoh H, Iwamoto T. Quantum chemical exploration of dimeric forms of polycyclic aromatic hydrocarbons, naphthalene, perylene, and coronene. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.12.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Kodaya Y, Yamakado H, Ohno K. Limited Search Characteristics of the Scaled Hypersphere Search Method: A Systematic Case Study for Isomers of BCNOS. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yoshitomo Kodaya
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Hideo Yamakado
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Koichi Ohno
- Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Institute for Quantum Chemical Exploration, LOOP-X, 3-9-15 Kaigan, Minato-ku, Tokyo 108-0022, Japan
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10
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Ohno K, Kodaya Y, Yamakado H. Quantum chemical exploration of formaldehyde clusters (H 2 CO) n (n = 2-4). J Comput Chem 2018; 39:1498-1507. [PMID: 29607516 DOI: 10.1002/jcc.25220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/13/2018] [Accepted: 03/17/2018] [Indexed: 01/25/2023]
Abstract
Global exploration of equilibrium structures and interconversion pathways on the quantum chemical potential energy surface (PES) is performed for (H2 CO)n (n = 2-4) by using the Scaled Hypersphere Search-Anharmonic Downward Distortion Following (SHS-ADDF) method. Density functional theoretical (DFT) calculations with empirical dispersion corrections (D3) yielded comparable results for formaldehyde dimer in comparison with recent detailed studies at CCSD(T) levels. Based on DFT-D3 calculations, trimer and tetramer structures and their stabilities were studied. For tetramer, a highly symmetrical S4 structure was found as the most stable form in good accordance with experimentally determined tetramer unit in the formaldehyde crystal. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Kaigan 3-9-15, Minato-ku, Tokyo, 108-0022, Japan.,Department of Chemistry Graduate School of Science, Tohoku University, Aramaki Aza-Aoba 6-3, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Yoshitomo Kodaya
- Graduate School of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
| | - Hideo Yamakado
- Faculty of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
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11
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Kim Y, Kim JW, Kim Z, Kim WY. Efficient prediction of reaction paths through molecular graph and reaction network analysis. Chem Sci 2018; 9:825-835. [PMID: 29675146 PMCID: PMC5887236 DOI: 10.1039/c7sc03628k] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/11/2017] [Indexed: 12/29/2022] Open
Abstract
Despite remarkable advances in computational chemistry, prediction of reaction mechanisms is still challenging, because investigating all possible reaction pathways is computationally prohibitive due to the high complexity of chemical space. A feasible strategy for efficient prediction is to utilize chemical heuristics. Here, we propose a novel approach to rapidly search reaction paths in a fully automated fashion by combining chemical theory and heuristics. A key idea of our method is to extract a minimal reaction network composed of only favorable reaction pathways from the complex chemical space through molecular graph and reaction network analysis. This can be done very efficiently by exploring the routes connecting reactants and products with minimum dissociation and formation of bonds. Finally, the resulting minimal network is subjected to quantum chemical calculations to determine kinetically the most favorable reaction path at the predictable accuracy. As example studies, our method was able to successfully find the accepted mechanisms of Claisen ester condensation and cobalt-catalyzed hydroformylation reactions.
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Affiliation(s)
- Yeonjoon Kim
- Department of Chemistry , KAIST , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Korea .
| | - Jin Woo Kim
- Department of Chemistry , KAIST , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Korea .
| | - Zeehyo Kim
- Department of Chemistry , KAIST , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Korea .
| | - Woo Youn Kim
- Department of Chemistry , KAIST , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Korea .
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12
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Simm GN, Reiher M. Context-Driven Exploration of Complex Chemical Reaction Networks. J Chem Theory Comput 2017; 13:6108-6119. [DOI: 10.1021/acs.jctc.7b00945] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Gregor N. Simm
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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13
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Kishimoto N, Waizumi H. An automated and efficient conformation search of l-cysteine and l,l-cystine using the scaled hypersphere search method. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.07.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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