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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Zhang D, Kishimoto N. Quantum Chemical Investigation into the Structural Analysis and Calculated Raman Spectra of Amylose Modeled with Linked Glucose Molecules. Molecules 2024; 29:2842. [PMID: 38930907 PMCID: PMC11206574 DOI: 10.3390/molecules29122842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
This study presents a quantum chemical investigation into the structural analysis and calculated Raman spectra of modeled amylose with varying units of linked glucose molecules. We systematically examined the rotation of hydroxymethyl groups and intramolecular hydrogen bonds within these amylose models. Our study found that as the number of linked glucose units increases, the linear structure becomes more complex, resulting in curled, cyclic, or helical structures facilitated by establishing various intramolecular interactions. The hydroxymethyl groups were confirmed to form interactions with oxygen atoms and with hydroxymethyl and hydroxyl groups from adjacent rings in the molecular structures. We identified distinct peaks and selected specific bands applicable in various analytical contexts by comparing their calculated Raman spectra. Representative vibrational modes within selected regions were identified across the different lengths of amylose models, serving as characteristic signatures for linear and more coiled structural conformations. Our findings contribute to a deeper understanding of amylose structures and spectroscopic signatures, with implications for theoretical studies and potential applications. This work provides valuable reference points for the detailed assignment of Raman peaks of amylose structure, facilitating their application in broader research on carbohydrate structures and their associated spectroscopic properties.
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Affiliation(s)
| | - 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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3
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Nakao A, Harabuchi Y, Maeda S, Tsuda K. Exploring the Quantum Chemical Energy Landscape with GNN-Guided Artificial Force. J Chem Theory Comput 2023; 19:713-717. [PMID: 36689311 PMCID: PMC9933424 DOI: 10.1021/acs.jctc.2c01061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Artificial force has been proven useful to get over energy barriers and quickly search a large portion of the energy landscape. This work proposes a method based on graph neural networks to optimize the choice of transformation patterns to examine and accelerate energy landscape exploration. In open search from glutathione, the search efficiency was largely improved in comparison to random selection. We also applied transfer learning from glutathione to tuftsin, resulting in further efficiency gains.
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Affiliation(s)
- Atsuyuki Nakao
- Graduate
School of Frontier Sciences, The University
of Tokyo, Kashiwa277-8561, Japan
| | - Yu Harabuchi
- Institute
for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo001-0021, Japan,JST
ERATO Maeda Artificial Intelligence for Chemical Reaction Design and
Discovery Project, Sapporo060-0810, Japan,Department
of Chemistry, Faculty of Science, Hokkaido
University, Sapporo060-0810, Japan
| | - Satoshi Maeda
- Institute
for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo001-0021, Japan,JST
ERATO Maeda Artificial Intelligence for Chemical Reaction Design and
Discovery Project, Sapporo060-0810, Japan,Department
of Chemistry, Faculty of Science, Hokkaido
University, Sapporo060-0810, Japan
| | - Koji Tsuda
- Graduate
School of Frontier Sciences, The University
of Tokyo, Kashiwa277-8561, Japan,RIKEN
Center for Advanced Intelligence Project, Tokyo103-0027, Japan,Research
and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba305-0047, Japan,
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4
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Oda K, Tsutsumi T, Keshavamurthy S, Furuya K, Armentrout PB, Taketsugu T. Dynamically Hidden Reaction Paths in the Reaction of CF 3+ + CO. ACS PHYSICAL CHEMISTRY AU 2022; 2:388-398. [PMID: 36193292 PMCID: PMC9524575 DOI: 10.1021/acsphyschemau.2c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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Reaction paths on
a potential energy surface are widely used in
quantum chemical studies of chemical reactions. The recently developed
global reaction route mapping (GRRM) strategy automatically constructs
a reaction route map, which provides a complete picture of the reaction.
Here, we thoroughly investigate the correspondence between the reaction
route map and the actual chemical reaction dynamics for the CF3+ + CO reaction studied by guided ion beam tandem
mass spectrometry (GIBMS). In our experiments, FCO+, CF2+, and CF+ product ions were observed,
whereas if the collision partner is N2, only CF2+ is observed. Interestingly, for reaction with CO, GRRM-predicted
reaction paths leading to the CF+ + F2CO product
channel are found at a barrier height of about 2.5 eV, whereas the
experimentally obtained threshold for CF+ formation was
7.48 ± 0.15 eV. In other words, the ion was not obviously observed
in the GIBMS experiment, unless a much higher collision energy than
the requisite energy threshold was provided. On-the-fly molecular
dynamics simulations revealed a mechanism that hides these reaction
paths, in which a non-statistical energy distribution at the first
collisionally reached transition state prevents the reaction from
proceeding along some reaction paths. Our results highlight the existence
of dynamically hidden reaction paths that may be inaccessible in experiments
at specific energies and hence the importance of reaction dynamics
in controlling the destinations of chemical reactions.
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Affiliation(s)
- Kohei Oda
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Srihari Keshavamurthy
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India
| | - Kenji Furuya
- Faculty of Arts and Science, Kyushu University, Motooka, Fukuoka 819-0395, Japan
- Department of Molecular and Material Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
- Department of Chemistry, University of Utah, Salt Lake City 84112, United States
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, Salt Lake City 84112, United States
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
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5
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Miwa Y, Hasegawa K, Udagawa T, Shinke Y, Kutsumizu S. Effect of alkali metal cations on network rearrangement in polyisoprene ionomers. Phys Chem Chem Phys 2022; 24:17042-17049. [PMID: 35796495 DOI: 10.1039/d2cp01159j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effects of cations, Li+, Na+, and Cs+, on the structure of ionic aggregates and network rearrangement in carboxylated polyisoprene (PI) ionomers were studied. We found that network rearrangement via interaggregate hopping of metal carboxylates is improved with a decrease in cation size, even though density functional theory (DFT) calculation indicated the increase in the attractive interaction between metal carboxylates. At the same time, we also found that as the size of the cation decreases, the inclusion of the PI segment in the ionic aggregate increases. The DFT calculation suggested the cation-π interaction between the cation and double bonds in the PI segment as the cause for the inclusion. The inclusion of the PI segment with a low glass transition temperature (Tg) plasticizes the ionic aggregate and would sterically hinder the attractive interaction between metal carboxylates. In fact, the electron spin resonance measurement revealed a decrease in the Tg of the ionic aggregate with a decrease in cation size. Based on our findings, we proposed that the inclusion of PI segments in the ionic aggregate is the possible cause for the enhancement of network rearrangement in the carboxylated PI ionomers with a decrease in the cation size.
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Affiliation(s)
- Yohei Miwa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan. .,PRESTO, Japan Science and Technology Agency, Japan
| | - Koki Hasegawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan.
| | - Taro Udagawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan.
| | - Yu Shinke
- The Yokohama Rubber Co., Ltd, Hiratsuka, 254-8601, Japan
| | - Shoichi Kutsumizu
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan.
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6
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Tsutsumi T, Ono Y, Taketsugu T. Reaction Space Projector (ReSPer) for Visualizing Dynamic Reaction Routes Based on Reduced-Dimension Space. Top Curr Chem (Cham) 2022; 380:19. [PMID: 35266073 DOI: 10.1007/s41061-022-00377-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/21/2022] [Indexed: 11/26/2022]
Abstract
To analyze chemical reaction dynamics based on a reaction path network, we have developed the "Reaction Space Projector" (ReSPer) method with the aid of the dimensionality reduction method. This program has two functions: the construction of a reduced-dimensionality reaction space from a molecular structure dataset, and the projection of dynamic trajectories into the low-dimensional reaction space. In this paper, we apply ReSPer to isomerization and bifurcation reactions of the Au5 cluster and succeed in analyzing dynamic reaction routes involved in multiple elementary reaction processes, constructing complicated networks (called "closed islands") of nuclear permutation-inversion (NPI) isomerization reactions, and elucidating dynamic behaviors in bifurcation reactions with reference to bundles of trajectories. Interestingly, in the second application, we find a correspondence between the contribution ratios in the ability to visualize and the symmetry of the morphology of closed islands. In addition, the third application suggests the existence of boundaries that determine the selectivity in bifurcation reactions, which was discussed in the phase space. The ReSPer program is a versatile and robust tool to clarify dynamic reaction mechanisms based on the reduced-dimensionality reaction space without prior knowledge of target reactions.
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Affiliation(s)
- Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuriko Ono
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.
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7
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Kawajiri A, Udagawa T, Minoura M, Murai T. Stereoselective Transesterification of P-Chirogenic Hydroxybinaphthyl Phosphinates. Chemistry 2022; 11:e202100294. [PMID: 35261188 PMCID: PMC9630046 DOI: 10.1002/open.202100294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/21/2022] [Indexed: 01/31/2023]
Abstract
The substitution reaction of phosphinates with a binaphthyloxy group at the phosphorus atom with lithium alkoxides proceeded with good to high efficiencies to give P-chirogenic phosphinates with a high enantiomeric ratio. As alcohols, primary, secondary, and tertiary alcohols could be used, and the use of tert-butyl alcohol yielded the products with a higher enantiomeric ratio. A substrate with two different alkyl groups on the phosphorus atom could also participate in the substitution reaction to give the corresponding products in good yields with excellent selectivity. The molecular structures of one of the substrates and the corresponding products, determined by X-ray analyses, proved that the substitution reaction at the phosphorus atom proceeded with inversion of the absolute configuration. The usefulness of the reaction was demonstrated by using it to prepare a drug candidate for Duchenne muscular dystrophy. Finally, thionation of the resulting phosphinates was carried out to form P-chirogenic phosphinothioates.
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Affiliation(s)
- Akari Kawajiri
- Department of Chemistry and Biomolecular Science Faculty of EngineeringGifu University YanagidoGifu501-1193Japan
| | - Taro Udagawa
- Department of Chemistry and Biomolecular Science Faculty of EngineeringGifu University YanagidoGifu501-1193Japan
| | - Mao Minoura
- Department of Chemistry College of ScienceRikkyo University Nishi-ikebukuro, Toshima-kuTokyo171-8501Japan
| | - Toshiaki Murai
- Department of Chemistry and Biomolecular Science Faculty of EngineeringGifu University YanagidoGifu501-1193Japan
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8
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Tsutsumi T, Ono Y, Taketsugu T. Visualization of reaction route map and dynamical trajectory in reduced dimension. Chem Commun (Camb) 2021; 57:11734-11750. [PMID: 34642706 DOI: 10.1039/d1cc04667e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the quantum chemical approach, chemical reaction mechanisms are investigated based on a potential energy surface (PES). Automated reaction path search methods enable us to construct a global reaction route map containing multiple reaction paths corresponding to a series of elementary reaction processes. The on-the-fly molecular dynamics (MD) method provides a classical trajectory exploring the full-dimensional PES based on electronic structure calculations. We have developed two reaction analysis methods, the on-the-fly trajectory mapping method and the reaction space projector (ReSPer) method, by introducing a structural similarity to a pair of geometric structures and revealed dynamic aspects affecting chemical reaction mechanisms. In this review, we will present the details of these analysis methods and discuss the dynamics effects of reaction path curvature and reaction path bifurcation with applications to the CH3OH + OH- collision reaction and the Au5 cluster branching and isomerization reactions.
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Affiliation(s)
- Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
| | - Yuriko Ono
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan. .,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
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9
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Udagawa T, Murphy RB, Darwish TA, Tachikawa M, Mori S. H/D Isotope Effects in Keto-Enol Tautomerism of β-Dicarbonyl Compounds —Importance of Nuclear Quantum Effects of Hydrogen Nuclei—. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Taro Udagawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Rhys B. Murphy
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights NSW 2234, Australia
| | - Tamim A. Darwish
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights NSW 2234, Australia
| | - Masanori Tachikawa
- Graduate School of NanobioScience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | - Seiji Mori
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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10
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Maeda S, Harabuchi Y. Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1538] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI‐ICReDD), Hokkaido University Sapporo Hokkaido Japan
- Department of Chemistry, Faculty of Science Hokkaido University Sapporo Hokkaido Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project Sapporo Hokkaido Japan
- National Institute for Materials Science (NIMS) Research and Services Division of Materials Data and Integrated System (MaDIS) Tsukuba Ibaraki Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI‐ICReDD), Hokkaido University Sapporo Hokkaido Japan
- Department of Chemistry, Faculty of Science Hokkaido University Sapporo Hokkaido Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project Sapporo Hokkaido Japan
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11
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Ebisawa S, Tsutsumi T, Taketsugu T. Geometric analysis of anharmonic downward distortion following paths. J Comput Chem 2021; 42:27-39. [PMID: 33098122 DOI: 10.1002/jcc.26430] [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: 06/20/2020] [Revised: 09/16/2020] [Accepted: 09/27/2020] [Indexed: 11/07/2022]
Abstract
A mathematical aspect of the anharmonic downward distortion following (ADDF) path is discussed. The ADDF method is utilized as an automated reaction path search method, which can explore transition state geometries on a potential energy surface from a potential minimum. We show that the maximum number of the ADD stationary paths intersecting the potential minimum is 2f + 1 - 2, where f denotes the degree of freedom of the system. We also show that the bifurcation of the ADD stationary path is essential to detect all the transition states connected from a given minimum. The ADDF computation is demonstrated for a H2 O molecule in which pitchfork bifurcation is observed.
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Affiliation(s)
- Shuichi Ebisawa
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Takuro Tsutsumi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
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12
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Hatanaka M, Yoshimura T, Puripat M, Parasuk V. Stereoselectivity of the Biginelli Reaction Catalyzed by Chiral Primary Amine: A Computational Study. HETEROCYCLES 2021. [DOI: 10.3987/com-20-s(k)55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Artificial Force-Induced Reaction Method for Systematic Elucidation of Mechanism and Selectivity in Organometallic Reactions. TOP ORGANOMETAL CHEM 2020. [DOI: 10.1007/3418_2020_51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Muramatsu S, Tsukuda T. Reductive Activation of Small Molecules by Anionic Coinage Metal Atoms and Clusters in the Gas Phase. Chem Asian J 2019; 14:3763-3772. [PMID: 31553821 DOI: 10.1002/asia.201901156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Indexed: 11/08/2022]
Abstract
Metal atoms and clusters exhibit chemical properties that are significantly different or totally absent in comparison to their bulk counterparts. Such peculiarity makes them potential building units for the generation of novel catalysts. Investigations of the gas-phase reactions between size- and charge-selected atoms/clusters and small molecules have provided fundamental insights into their intrinsic reactivity, thus leading to a guiding principle for the rational design of the single-atom and cluster-based catalysts. Especially, recent gas-phase studies have elucidated that small molecules such as O2 , CO2 , and CH3 I can be catalytically activated by negatively-charged atoms/clusters via donation of a partial electronic charge. This Minireview showcases typical examples of such "reductive activation" processes promoted by anions of metal atoms and clusters. Here, we focus on anionic atoms/clusters of coinage metals (Cu, Ag, and Au) owing to the simplicity of their electronic structures. The determination of a correlation between their activation modes and the electronic structures might be helpful for the future development of innovative coinage metal catalysts.
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Affiliation(s)
- Satoru Muramatsu
- Department of Chemistry, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima-shi, Hiroshima, 739-8526, Japan
| | - Tatsuya Tsukuda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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15
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Özen C, Shoji Y, Fukushima T, Maeda S. A Theoretical Study on the Mechanism of the Oxidative Deborylation/C-C Coupling Reaction of Borepin Derivatives. J Org Chem 2019; 84:1941-1950. [PMID: 30676027 DOI: 10.1021/acs.joc.8b02917] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One-electron oxidation of borepin derivatives that consists of a boron-containing seven-membered ring has been reported to cause deborylation/C-C coupling, yielding aromatic compounds. The reaction can be achieved not only by transition metal compounds but also by oxidants without transition metal such as O2 and other organic compounds. Despite numerous experimental attempts, the mechanism of this peculiar reaction as well as the fate of the BCl part eliminated from borepin remain unclear to date. Based on theoretical approaches using the artificial force induced reaction method, here we address the mechanism of the unusual boron-mediated C-C coupling. For this purpose, two borepin derivatives (1 and 35), bearing ethyl and phenyl groups, respectively, were used as reactants, and FeCl3/MeNO2 and O2 were chosen as oxidants. The calculations revealed reaction pathways that provided an overall picture of the mechanism of the target reaction, which features four key steps, namely, (i) quaternization of the boron atom by the coordination of oxidant, (ii) intersystem crossing, (iii) skeletal rearrangement to form a six-membered ring, and (iv) elimination of a boron moiety. The intrinsic nature of boron, i.e., a strong tendency to accept a coordination ligand even under oxidative conditions, is responsible for the oxidative deborylation/C-C coupling of borepin.
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Affiliation(s)
- Cihan Özen
- Department of Chemistry , Hokkaido University , Sapporo 060-8510 , Japan
| | - Yoshiaki Shoji
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , Yokohama 226-8503 , Japan
| | - Takanori Fukushima
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , Yokohama 226-8503 , Japan
| | - Satoshi Maeda
- Department of Chemistry , Hokkaido University , Sapporo 060-8510 , Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD) , Hokkaido University , Sapporo 001-0021 , Japan.,Research and Services Division of Materials Data and Integrated System (MaDIS) , National Institute for Materials Science (NIMS) , Tsukuba 305-0044 , Japan
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16
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Sugiyama K, Sumiya Y, Takagi M, Saita K, Maeda S. Understanding CO oxidation on the Pt(111) surface based on a reaction route network. Phys Chem Chem Phys 2019; 21:14366-14375. [DOI: 10.1039/c8cp06856a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kinetic analysis by the rate constant matrix contraction on the reaction route network of CO oxidation on the Pt(111) surface obtained by the artificial force induced reaction reveals the impact of entropic contributions arising from a variety of local minima and transition states.
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Affiliation(s)
- Kanami Sugiyama
- Graduate School of Chemical Sciences and Engineering
- Hokkaido University
- Sapporo
- Japan
| | - Yosuke Sumiya
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo
- Japan
| | - Makito Takagi
- Graduate School of Chemical Sciences and Engineering
- Hokkaido University
- Sapporo
- Japan
| | - Kenichiro Saita
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo
- Japan
| | - Satoshi Maeda
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo
- Japan
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17
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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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18
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Maeda S, Sugiyama K, Sumiya Y, Takagi M, Saita K. Global Reaction Route Mapping for Surface Adsorbed Molecules: A Case Study for H2O on Cu(111) Surface. CHEM LETT 2018. [DOI: 10.1246/cl.171194] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0044, Japan
| | - Kanami Sugiyama
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Yosuke Sumiya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Makito Takagi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Kenichiro Saita
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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19
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Tsutsumi T, Harabuchi Y, Ono Y, Maeda S, Taketsugu T. Analyses of trajectory on-the-fly based on the global reaction route map. Phys Chem Chem Phys 2018; 20:1364-1372. [PMID: 29260170 DOI: 10.1039/c7cp06528k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A methodology to analyze a trajectory on-the-fly (TOF) based on a global reaction route map consisting of intrinsic reaction coordinate (IRC) pathways is proposed. By using the distance functions in the configurational space, the location of each point on the trajectories is detected, providing a dynamical picture that the molecular system goes over several minima and transition states in the reaction path network. In its application to structural transformations of an Au5 cluster, a variety of reaction routes are obtained, and the hopping from one IRC to another IRC (IRC-jump) is analyzed. The branching of trajectories over many minima on the potential energy surface via valley-ridge transition points is also discussed.
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Affiliation(s)
- Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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20
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Maeda S, Harabuchi Y, Takagi M, Saita K, Suzuki K, Ichino T, Sumiya Y, Sugiyama K, Ono Y. Implementation and performance of the artificial force induced reaction method in the GRRM17 program. J Comput Chem 2017; 39:233-251. [PMID: 29135034 PMCID: PMC5765425 DOI: 10.1002/jcc.25106] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 12/20/2022]
Abstract
This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC-AFIR), single-component algorithm (SC-AFIR), and double-sphere algorithm (DS-AFIR), are available, where the MC-AFIR was the only algorithm which has been available in the previous 2014 version. The MC-AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC-AFIR performs automated generation of global or semiglobal reaction path network. The DS-AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
| | - Makito Takagi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Kenichiro Saita
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kimichi Suzuki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | - Tomoya Ichino
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yosuke Sumiya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Kanami Sugiyama
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Yuriko Ono
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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21
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From nitrogen inversion in amines to stereoinversion in aminium salts: role of a single water molecule. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2090-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Vong KKH, Maeda S, Tanaka K. Propargyl-Assisted Selective Amidation Applied in C-terminal Glycine Peptide Conjugation. Chemistry 2016; 22:18865-18872. [PMID: 27731535 DOI: 10.1002/chem.201604247] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Indexed: 11/08/2022]
Abstract
Alkyl esters, such as propargyl esters, typically lack the electron-withdrawing inductive effects needed to participate in nucleophilic acyl substitution reactions. Herein, we report an unusual observation in which glycine propargyl ester derivatives displayed selective, base-independent reactivity towards linear alkylamines under mild, metal-free conditions. Through global reaction route mapping (GRRM) modeling calculations, it is predicted that these observations may be governed by factors related to hydrogen-bonding and intermolecular interactions, rather than electron-withdrawing inductive effects. Based on this concept of propargyl-assisted selective amidation, a direct application was made to develop a novel site-specific C-terminal glycine peptide bioconjugation technique as a proof-of-concept, which relies upon the selective reactivity of glycine propargyl esters over that of aspartate and glutamate side-chain-linked propargyl esters.
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Affiliation(s)
- Kenward King Ho Vong
- Biofunctional Synthetic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Katsunori Tanaka
- Biofunctional Synthetic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan.,Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlyovskaya Street, Kazan, 420008, Russia.,JST, PRESTO, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
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23
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Global reaction route mapping of water-catalysed gas phase oxidation of glyoxylic acid with hydroxyl radical. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2019-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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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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25
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Harabuchi Y, Taketsugu T, Maeda S. Nonadiabatic Pathways of Furan and Dibenzofuran: What Makes Dibenzofuran Fluorescent? CHEM LETT 2016. [DOI: 10.1246/cl.160398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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26
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Maeda S, Harabuchi Y, Takagi M, Taketsugu T, Morokuma K. Artificial Force Induced Reaction (AFIR) Method for Exploring Quantum Chemical Potential Energy Surfaces. CHEM REC 2016; 16:2232-2248. [DOI: 10.1002/tcr.201600043] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry, Faculty of Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Makito Takagi
- Graduate School of Chemical Sciences and Engineering; Hokkaido University; Sapporo 060-8628 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
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27
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Kaur R, Vikas V. Exploring the role of a single water molecule in the tropospheric reaction of glycolaldehyde with an OH radical: a mechanistic and kinetics study. RSC Adv 2016. [DOI: 10.1039/c6ra01299j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This work reveals that though a single-water molecule decelerates the atmospheric reaction between the glycolaldehyde and OH radical, however, it facilitates the cis–trans interconversion along the hydrogen-abstraction pathways.
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Affiliation(s)
- Ramanpreet Kaur
- Quantum Chemistry Group
- Department of Chemistry & Centre of Advanced Studies in Chemistry
- Panjab University
- Chandigarh-160014
- India
| | - Vikas Vikas
- Quantum Chemistry Group
- Department of Chemistry & Centre of Advanced Studies in Chemistry
- Panjab University
- Chandigarh-160014
- India
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28
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Kawano J, Maeda S, Nagai T. The effect of Mg2+ incorporation on the structure of calcium carbonate clusters: investigation by the anharmonic downward distortion following method. Phys Chem Chem Phys 2016; 18:2690-8. [DOI: 10.1039/c5cp05139h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A structure similar to calcite appears when only four CaCO3 units aggregate into the cluster, and the addition of Mg changes its structure.
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Affiliation(s)
- Jun Kawano
- Creative Research Institution (CRIS)
- Hokkaido University
- Sapporo
- 001-0021 Japan
- Department of Earth and Planetary Sciences
| | - Satoshi Maeda
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo
- 060-0810 Japan
| | - Takaya Nagai
- Department of Earth and Planetary Sciences
- Faculty of Science
- Hokkaido University
- Sapporo
- 060-0810 Japan
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29
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Harabuchi Y, Ono Y, Maeda S, Taketsugu T. Analyses of bifurcation of reaction pathways on a global reaction route map: A case study of gold cluster Au5. J Chem Phys 2015; 143:014301. [DOI: 10.1063/1.4923163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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30
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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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31
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Kaur G, Vikas. Exploring the mechanism of isomerisation and water-migration in the water-complexes of amino-acid l-proline: electrostatic potential and vibrational analysis. RSC Adv 2015. [DOI: 10.1039/c5ra06088e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This work reveals interesting pathways for water-migration and neutral ↔ zwitterionic isomerisation in the water complexes of l-proline.
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Affiliation(s)
- Gurpreet Kaur
- Quantum Chemistry Group
- Department of Chemistry & Centre of Advanced Studies in Chemistry
- Panjab University
- Chandigarh – 160014
- India
| | - Vikas
- Quantum Chemistry Group
- Department of Chemistry & Centre of Advanced Studies in Chemistry
- Panjab University
- Chandigarh – 160014
- India
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