1
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Zhang D, Kishimoto N. Theoretical Analysis of Coordination Geometries in Transition Metal-Histidine Complexes Using Quantum Chemical Calculations. Molecules 2024; 29:3003. [PMID: 38998956 PMCID: PMC11243457 DOI: 10.3390/molecules29133003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/13/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024] Open
Abstract
A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+). Conformational exploration of the His ligand was initially performed to assess its stability upon coordination. Both 1:1 and 1:2 of metal-to-ligand complexes were scrutinized to elucidate their structural features and the relative stability of the complexes. This study examined the ability of His to act as a bidentate or tridentate coordinating ligand, along with the differences in coordination geometry when solvent effects were incorporated. The reduced density gradient (RDG) analysis and local electron attachment energy (LEAE) analysis were employed to elucidate the interaction planes and the nucleophilic and electrophilic properties. The electronic properties were analyzed through electrostatic potential (ESP) maps and natural population analysis (NPA) of atomic charge distributions. This computational study provides valuable insights into the diverse coordination modes of His and its interactions with divalent transition metal ions, contributing to a better understanding of the role of this amino acid ligand in the formation of transition metal complexes. The findings can aid in the design and construction of self-assembled structures involving His-metal coordination.
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Affiliation(s)
- Dapeng Zhang
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Naoki Kishimoto
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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2
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Uchida K, Ishida S, Iwamoto T. Dearomative Cycloaddition of an Isolable Dialkylsilylene with Diaryl Ketones. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kenya Uchida
- Tohoku University: Tohoku Daigaku Chemistry 6-3 Aramakiazaaoba, Aoba-ku 9808578 Sendai JAPAN
| | - Shintaro Ishida
- Tohoku University: Tohoku Daigaku Chemistry 6-3 Aramakiazaaoba, Aoba-ku 9808578 Sendai JAPAN
| | - Takeaki Iwamoto
- Tohoku University Department of Chemistry, Graduate School of Science 6-3 Aramaki-aza-aoba, Aoba-ku 980-8578 Sendai JAPAN
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3
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Zhao Y, Kikugawa G, Kawagoe Y, Shirasu K, Kishimoto N, Xi Y, Okabe T. Uncovering the Mechanism of Size Effect on the Thermomechanical Properties of Highly Cross-Linked Epoxy Resins. J Phys Chem B 2022; 126:2593-2607. [PMID: 35325528 DOI: 10.1021/acs.jpcb.1c10827] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Epoxy resins are widely used as matrix resins, especially for carbon-fiber-reinforced plastic, due to their outstanding physical and mechanical properties. To date, most research into cross-linking processes using simulation has considered only a distance-based criterion to judge the probability of reaction. In this work, a new algorithm was developed for use with the large-scale atomic/molecular massively parallel simulator (LAMMPS) simulation package to study the cross-linking process; this new approach combines both a distance-based criterion and several kinetic criteria to identify whether the reaction has occurred. Using this simulation framework, we investigated the effect of model size on predicted thermomechanical properties of three different structural systems: diglycidyl ether of bisphenol A (DGEBA)/4,4'-diaminodiphenyl sulfone (4,4'-DDS), DGEBA/diethylenetriamine (DETA), and tetraglycidyl diaminodiphenylmethane (TGDDM)/4,4'-DDS. Derived values of gel point, volume shrinkage, and cross-linked resin density were found to be insensitive to model size in these three systems. Other thermomechanical properties, i.e., glass-transition temperature, Young's modulus, and yield stress, were found to reach stable values for systems larger than ∼40 000 atoms for both DGEBA/4,4'-DDS and DGEBA/DETA. However, these same properties modeled for TGDDM/4,4'-DDS did not stabilize until the system size reached 50 000 atoms. Our results provide general guidelines for simulation system size and procedures to more accurately predict the thermomechanical properties of epoxy resins.
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Affiliation(s)
- Yinbo Zhao
- Department of Aerospace Engineering, Tohoku University, 6-6-01, Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan.,Institute of Fluid Science, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Gota Kikugawa
- Institute of Fluid Science, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yoshiaki Kawagoe
- Department of Aerospace Engineering, Tohoku University, 6-6-01, Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Keiichi Shirasu
- Department of Aerospace Engineering, Tohoku University, 6-6-01, Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Naoki Kishimoto
- Department of Chemistry, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Yingxiao Xi
- Department of Chemistry, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Tomonaga Okabe
- Department of Aerospace Engineering, Tohoku University, 6-6-01, Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan.,Department of Materials Science and Engineering, University of Washington, Box 352120, Seattle, Washington 98195, United States.,Research Center for Structural Materials, Polymer Matrix Hybrid Composite Materials Group, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
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4
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Anderson HL, Patrick CW, Scriven LM, Woltering SL. A Short History of Cyclocarbons. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200345] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Harry L. Anderson
- Department of Chemistry, Oxford University, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Connor W. Patrick
- Department of Chemistry, Oxford University, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Lorel M. Scriven
- Department of Chemistry, Oxford University, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Steffen L. Woltering
- Department of Chemistry, Oxford University, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
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5
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Oya Y, Nakazawa M, Shirasu K, Hino Y, Inuyama K, Kikugawa G, Li J, Kuwahara R, Kishimoto N, Waizumi H, Nishikawa M, Waas A, Odagiri N, Koyanagi A, Salviato M, Okabe T. Molecular dynamics simulation of cross-linking processes and material properties for epoxy resins using first-principle calculation combined with global reaction route mapping algorithms. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Uchida M, Shimizu T, Shibutani R, Matsumoto Y, Ishikawa H. A comprehensive infrared spectroscopic and theoretical study on phenol-ethyldimethylsilane dihydrogen-bonded clusters in the S 0 and S 1 states. J Chem Phys 2020; 153:104305. [PMID: 32933300 DOI: 10.1063/5.0019755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To investigate microscopic characters of Si-H⋯H-O type dihydrogen bonds, we observed OH and SiH stretch bands in both the S0 and S1 states of phenol-ethyldimethylsilane (PhOH-EDMS) clusters by infrared (IR)-ultraviolet (UV) and UV-IR double resonance spectroscopies. Density functional theory (DFT) calculations and energy decomposition analysis were also performed. Structures of two isomers identified were unambiguously determined through the analysis of IR spectra and DFT calculations. To discuss the strength of dihydrogen bond in various systems, we performed theoretical calculations on clusters of EDMS with several acidic molecules in addition to PhOH. It was revealed that charge-transfer interaction energies from a bonding σ orbital of SiH bond to an anti-bonding σ* orbital of OH bond well reflect strengths of dihydrogen bonds. Additionally, it was found that the red shift of SiH stretch frequencies can be used as a crude measure of the strength of dihydrogen bonds. Relationship between the red shifts of OH/SiH stretch frequencies and various electrostatic components of the interaction energy was examined. In the S1 state, large increases in red shifts were observed for both the OH and SiH stretch frequencies. Since the EDMS moiety is not associated with the electronic excitation in a cluster, the strength of dihydrogen bonds in the S1 and S0 states was able to be directly compared based on the red shifts of the SiH stretch bands. A significant increase in the red shift of SiH stretch frequency indicates a strengthening of the dihydrogen bonds during the electronic excitation of the PhOH moiety.
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Affiliation(s)
- Masaaki Uchida
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Takutoshi Shimizu
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Ryo Shibutani
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Yoshiteru Matsumoto
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Haruki Ishikawa
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
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7
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Uchida M, Shimizu T, Matsumoto Y, Ishikawa H. An effective Hamiltonian analysis of a Franck-Condon-like pattern in the IR spectra of phenol-alkylsilane dihydrogen-bonded clusters in the S 1 state. J Chem Phys 2020; 152:194306. [PMID: 33687225 DOI: 10.1063/5.0005259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Infrared (IR) spectra in a region of the OH stretch band of phenol (PhOH)-ethyldimethylsilane (EDMS), phenol (PhOH)-triethylsilane (TES), and phenol (PhOH)-t-butyldimethylsilane (BDMS) dihydrogen-bonded clusters in the S1 state were observed. All of the species exhibited unconventional band patterns in which many combination bands appeared with comparable intensities to those of allowed bands. Such a behavior is sometimes called a Franck-Condon-like pattern. In the case of the PhOH-BDMS, one intermolecular vibrational mode is involved in this behavior. The observed IR spectra were well reproduced based on the concept of the Franck-Condon-like behavior. As an alternative treatment, we analyzed the band patterns on the concept of intensity borrowing due to the vibrational anharmonic interaction. The analysis was based on an effective Hamiltonian involving an anharmonic interaction between the OH stretch and intermolecular vibrational modes. Two treatments provided the same results. Thus, it was confirmed that the Franck-Condon-like behavior originates from vibrational anharmonic interactions. In the cases of the PhOH-EDMS and PhOH-TES, we carried out a two-dimensional Franck-Condon and an effective Hamiltonian analysis to interpret the Franck-Condon-like patterns. We examined vibrational wave functions obtained by the latter analysis. Shapes of the wave functions suggest that a recombination of the intermolecular vibrational modes occurs during the excitation of OH stretch mode in these clusters, which is a similar behavior to the Duschinsky effect in the electronic transition.
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Affiliation(s)
- Masaaki Uchida
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Takutoshi Shimizu
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Yoshiteru Matsumoto
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Haruki Ishikawa
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
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8
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Ishida S, Uchida K, Mori M, Iwamoto T. Structures and Properties of Phenylene-Bridged 1,3-Diaza-2-silole and Related 2H
-Azasilirenes Obtained by the Reactions of a Dialkylsilylene with Arylnitriles. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shintaro Ishida
- Department of Chemistry; Graduate School of Science; Tohoku University; 980-8578 Aoba-ku Sendai Japan
| | - Kenya Uchida
- Department of Chemistry; Graduate School of Science; Tohoku University; 980-8578 Aoba-ku Sendai Japan
| | - Maiko Mori
- Department of Chemistry; Graduate School of Science; Tohoku University; 980-8578 Aoba-ku Sendai Japan
| | - Takeaki Iwamoto
- Department of Chemistry; Graduate School of Science; Tohoku University; 980-8578 Aoba-ku Sendai Japan
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9
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Ohno K. Quantum chemical exploration of conversion pathways and isomeric structures of C16 molecules. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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10
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Yokouchi Y, Ishida S, Iwamoto T. Facile Skeletal Rearrangement of Polycyclic Disilenes with Bicyclo[1.1.1]pentasilanyl Groups. Chemistry 2018; 24:11393-11401. [DOI: 10.1002/chem.201801517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/19/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Yuki Yokouchi
- Department of Chemistry, Graduate School of Science; Tohoku University; Aoba-ku Sendai 980-8578 Japan
| | - Shintaro Ishida
- Department of Chemistry, Graduate School of Science; Tohoku University; Aoba-ku Sendai 980-8578 Japan
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science; Tohoku University; Aoba-ku Sendai 980-8578 Japan
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11
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Kida M, Shimoyama D, Ikeda T, Sekiya R, Haino T, Ebata T, Jouvet C, Inokuchi Y. Pseudorotaxanes in the gas phase: structure and energetics of protonated dibenzylamine–crown ether complexes. Phys Chem Chem Phys 2018; 20:18678-18687. [DOI: 10.1039/c8cp02707b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Barrier in the “slippage” process with 24C8 and dBAMH+ is lower than the dissociation threshold in the gas phase.
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Affiliation(s)
- Motoki Kida
- Department of Chemistry
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Daisuke Shimoyama
- Department of Chemistry
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Toshiaki Ikeda
- Department of Chemistry
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Ryo Sekiya
- Department of Chemistry
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Takeharu Haino
- Department of Chemistry
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Takayuki Ebata
- Department of Chemistry
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Christophe Jouvet
- CNRS
- Aix-Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM)
- UMR-7345
- Marseille
| | - Yoshiya Inokuchi
- Department of Chemistry
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
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12
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Ohno K. Study of Potential Energy Surfaces towards Global Reaction Route Mapping. CHEM REC 2016; 16:2198-2218. [PMID: 27059804 DOI: 10.1002/tcr.201500284] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Indexed: 11/11/2022]
Abstract
The potential energy surface (PES) is just a theoretical construct based on the Born-Oppenheimer approximation, but it underlies various phenomena, including molecular vibrations, collisional ionizations, and chemical reactions. This account describes how a new idea for global reaction route mapping (GRRM), which had seemed to be impossible for chemical systems with more than three atoms, was born and has been developed during the course of the study of the PES. GRRM has pioneered new fields of chemistry. Furthermore, techniques for GRRM are still developing, and GRRM is further extending its application to various areas of chemistry and chemical physics.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Minato-ku, Tokyo, 108-0022, Japan.
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13
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Tokoyama H, Yamakado H, Maeda S, Ohno K. Isomers of Benzene on Its Global Network of Reaction Pathways. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20150088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | - Koichi Ohno
- Institute for Quantum Chemical Exploration
- Graduate School of Science, Tohoku University
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14
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Affiliation(s)
- Koichi Ohno
- Department of Chemistry, Graduate School of Science, Tohoku University
- National Institute for Informatics (NII)
- Institute for Quantum Chemical Exploration
| | - Hiroko Satoh
- National Institute for Informatics (NII)
- Department of Chemistry, University of Zurich
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science, Tohoku University
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15
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Maeda S, Taketsugu T, Ohno K, Morokuma K. From Roaming Atoms to Hopping Surfaces: Mapping Out Global Reaction Routes in Photochemistry. J Am Chem Soc 2015; 137:3433-45. [DOI: 10.1021/ja512394y] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Satoshi Maeda
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koichi Ohno
- Graduate
School of Science, Tohoku University, Sendai 980-8578, Japan
- Institute for Quantum Chemical Exploration, Tokyo 108-0022, Japan
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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16
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Maeda S, Taketsugu T, Morokuma K, Ohno K. Anharmonic Downward Distortion Following for Automated Exploration of Quantum Chemical Potential Energy Surfaces. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20140189] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University
| | | | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University
| | - Koichi Ohno
- Graduate School of Science, Tohoku University
- Institute for Quantum Chemical Exploration
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17
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Isegawa M, Liu F, Maeda S, Morokuma K. Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths. J Chem Phys 2014; 140:244310. [DOI: 10.1063/1.4883916] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Miho Isegawa
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Fengyi Liu
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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18
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Tokoyama H, Yamakado H, Maeda S, Ohno K. Exploration of Isomers of Benzene by GRRM/SCC-DFTB. CHEM LETT 2014. [DOI: 10.1246/cl.140024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | - Koichi Ohno
- Institute for Quantum Chemical Exploration
- Graduate School of Science, Tohoku University
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19
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Maeda S, Ohno K, Morokuma K. Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods. Phys Chem Chem Phys 2013; 15:3683-701. [DOI: 10.1039/c3cp44063j] [Citation(s) in RCA: 358] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Exploring Multiple Potential Energy Surfaces: Photochemistry of Small Carbonyl Compounds. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/268124] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In theoretical studies of chemical reactions involving multiple potential energy surfaces (PESs) such as photochemical reactions, seams of intersection among the PESs often complicate the analysis. In this paper, we review our recipe for exploring multiple PESs by using an automated reaction path search method which has previously been applied to single PESs. Although any such methods for single PESs can be employed in the recipe, the global reaction route mapping (GRRM) method was employed in this study. By combining GRRM with the proposed recipe, all critical regions, that is, transition states, conical intersections, intersection seams, and local minima, associated with multiple PESs, can be explored automatically. As illustrative examples, applications to photochemistry of formaldehyde and acetone are described. In these examples as well as in recent applications to other systems, the present approach led to discovery of many unexpected nonadiabatic pathways, by which some complicated experimental data have been explained very clearly.
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21
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Maeda S, Abe E, Hatanaka M, Taketsugu T, Morokuma K. Exploring Potential Energy Surfaces of Large Systems with Artificial Force Induced Reaction Method in Combination with ONIOM and Microiteration. J Chem Theory Comput 2012; 8:5058-63. [DOI: 10.1021/ct300633e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry,
Faculty
of Science, Hokkaido University, Sapporo
060-0810, Japan
| | - Erika Abe
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, Kyoto 606-8103,
Japan
| | - Miho Hatanaka
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, Kyoto 606-8103,
Japan
| | - Tetsuya Taketsugu
- Department of Chemistry,
Faculty
of Science, Hokkaido University, Sapporo
060-0810, Japan
| | - Keiji Morokuma
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, Kyoto 606-8103,
Japan
- Department of Chemistry
and Cherry
L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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22
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Ohshimo K, Inokuchi Y, Ebata T, Ohno K. Anionic Polymerization Mechanism of Acrylonitrile Trimer Anions: Key Branching Point between Cyclization and Chain Propagation. J Phys Chem A 2012; 116:7937-42. [DOI: 10.1021/jp305291r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Keijiro Ohshimo
- Chemical Dynamics Laboratory, RIKEN Advanced Science Institute , Wako, Saitama 351-0198, Japan
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23
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Nádasdi R, Zügner GL, Farkas M, Dóbé S, Maeda S, Morokuma K. Photochemistry of Methyl Ethyl Ketone: Quantum Yields and S
1
/S
0
‐Diradical Mechanism of Photodissociation. Chemphyschem 2010; 11:3883-95. [DOI: 10.1002/cphc.201000522] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rebeka Nádasdi
- Institute of Materials and Environmental Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59‐67, 1025 Budapest (Hungary), Fax: +36‐1‐438‐1147
| | - Gábor L. Zügner
- Institute of Materials and Environmental Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59‐67, 1025 Budapest (Hungary), Fax: +36‐1‐438‐1147
| | - Mária Farkas
- Institute of Materials and Environmental Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59‐67, 1025 Budapest (Hungary), Fax: +36‐1‐438‐1147
| | - Sándor Dóbé
- Institute of Materials and Environmental Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59‐67, 1025 Budapest (Hungary), Fax: +36‐1‐438‐1147
| | - Satoshi Maeda
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606‐8501 (Japan), Fax: +81‐75‐781‐4757
- The Hakubi Center, Kyoto University, Kyoto 606‐8501 (Japan)
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606‐8501 (Japan), Fax: +81‐75‐781‐4757
- Department of Chemistry and Cherry L. Emerson Centre for Scientific Computation, Emory University, Atlanta, GA 30322 (USA)
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24
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Maeda S, Ohno K, Morokuma K. An Automated and Systematic Transition Structure Explorer in Large Flexible Molecular Systems Based on Combined Global Reaction Route Mapping and Microiteration Methods. J Chem Theory Comput 2009; 5:2734-43. [DOI: 10.1021/ct9003383] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, Toyota Physical and Chemical Research Institute, Nagakute, Aichi 480-1192, Japan, and Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Koichi Ohno
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, Toyota Physical and Chemical Research Institute, Nagakute, Aichi 480-1192, Japan, and Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Keiji Morokuma
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, Toyota Physical and Chemical Research Institute, Nagakute, Aichi 480-1192, Japan, and Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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25
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Luo Y, Ohno K. Computational Study of Titanocene-Catalyzed Dehydrocoupling of the Adduct Me2NH·BH3: An Intramolecular, Stepwise Mechanism. Organometallics 2007. [DOI: 10.1021/om7003892] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yi Luo
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Koichi Ohno
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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