51
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Hirose J, Wakikawa T, Satake S, Kojima M, Hatano M, Ishihara K, Yoshino T, Matsunaga S. Cp*Rh III/Chiral Disulfonate/CuOAc Catalyst System for the Enantioselective Intramolecular Oxyamination of Alkenes. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jumpei Hirose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Takumi Wakikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Shun Satake
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Masahiro Kojima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Manabu Hatano
- Graduate School of Pharmaceutical Sciences, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Kazuaki Ishihara
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Tatsuhiko Yoshino
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan
| | - Shigeki Matsunaga
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan
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52
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Ishigaki Y, Tadokoro T, Harabuchi Y, Hayashi Y, Maeda S, Suzuki T. Anthraquinodimethane Ring-flip in Sterically Congested Alkenes: Isolation of Isomer and Elucidation of Intermediate through Experimental and Theoretical Approach. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yusuke Ishigaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomoki Tadokoro
- 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
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| | - Yuki Hayashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Satoshi Maeda
- 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
| | - Takanori Suzuki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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53
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Sugiyama K, Saita K, Maeda S. A reaction route network for methanol decomposition on a Pt(111) surface. J Comput Chem 2021; 42:2163-2169. [PMID: 34432314 DOI: 10.1002/jcc.26746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/17/2021] [Accepted: 08/02/2021] [Indexed: 11/10/2022]
Abstract
A reaction route network for the decomposition reaction of methanol on a Pt(111) surface was constructed by using the artificial force-induced reaction (AFIR) method, which can search for reaction paths automatically and systematically. Then, the network was kinetically analyzed by applying the rate constant matrix contraction (RCMC) method. Specifically, the time hierarchy of the network, the time evolution of the population initially given to CH3 OH to the other species on the network, and the most favorable route from CH3 OH to major and minor products were investigated by the RCMC method. Consistently to previous studies, the major product on the network was CO+4H, and the most favorable route proceeded through the following steps: CH3 OH → CH2 OH+H → HCOH+2H → HCO+3H → CO+4H. Furthermore, paths to byproducts found on the network and their kinetic importance were discussed. The present procedure combining AFIR and RCMC was thus successful in explaining the title reaction without using any information on its product or the reaction mechanism.
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Affiliation(s)
- Kanami Sugiyama
- 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.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.,Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba, Japan.,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Hokkaido University, Sapporo, Japan
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54
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Hasebe M, Tsutsumi T, Taketsugu T, Tsuneda T. One-to-One Correspondence between Reaction Pathways and Reactive Orbitals. J Chem Theory Comput 2021; 17:6901-6909. [PMID: 34694803 DOI: 10.1021/acs.jctc.1c00693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The one-to-one correspondence between reaction pathways in the potential energy theory and reactive orbitals in the electronic theory for reactions is presented. In this study, the reactive orbital energy method is applied to the intrinsic reaction coordinates of the global reaction route map generated by an automated reaction path search method. The reactive orbital energy method specifies the pairs of occupied and unoccupied reactive orbitals driving chemical reactions and determines whether the reactions are electron transfer-driven or dynamics-driven. Surprisingly, it is found that the reactive orbital pairs are determined one by one for the electron transfer-driven reaction pathways from an identical molecule. The reactive orbital energy method is also found to provide the sophisticated interpretations of reactions for the electronic motions. This one-to-one correspondence is expected to trigger the unification of the potential energy theory and the electronic theory for reactions that have been independently developed.
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Affiliation(s)
- Masatoshi Hasebe
- 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
| | - 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
| | - Takao Tsuneda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Graduate School of Science Technology and Innovation, Kobe University, Nada-ku, Kobe, Hyogo 657-8501, Japan
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55
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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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56
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Li YK, Babin MC, Debnath S, Iwasa T, Kumar S, Taketsugu T, Asmis KR, Lyalin A, Neumark DM. Structural Characterization of Nickel-Doped Aluminum Oxide Cations by Cryogenic Ion Trap Vibrational Spectroscopy. J Phys Chem A 2021; 125:9527-9535. [PMID: 34693712 DOI: 10.1021/acs.jpca.1c07156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isolated nickel-doped aluminum oxide cations (NiOm)(Al2O3)n(AlO)+ with m = 1-2 and n = 1-3 are investigated by infrared photodissociation (IRPD) spectroscopy in combination with density functional theory and the single-component artificial force-induced reaction method. IRPD spectra of the corresponding He-tagged cations are reported in the 400-1200 cm-1 spectral range and assigned based on a comparison to calculated harmonic IR spectra of low-energy isomers. Simulated spectra of the lowest energy structures generally match the experimental spectra, but multiple isomers may contribute to the spectra of the m = 2 series. The identified structures of the oxides (m = 1) correspond to inserting a Ni-O moiety into an Al-O bond of the corresponding (Al2O3)1-3(AlO)+ cluster, yielding either a doubly or triply coordinated Ni2+ center. The m = 2 clusters prefer similar structures in which the additional O atom either is incorporated into a peroxide unit, leaving the oxidation state of the Ni2+ atom unchanged, or forms a biradical comprising a terminal oxygen radical anion Al-O•- and a Ni3+ species. These clusters represent model systems for under-coordinated Ni sites in alumina-supported Ni catalysts and should prove helpful in disentangling the mechanism of selective oxidative dehydrogenation of alkanes by Ni-doped catalysts.
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Affiliation(s)
- Ya-Ke Li
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, 04103 Leipzig, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Mark C Babin
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Sreekanta Debnath
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, 04103 Leipzig, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Takeshi Iwasa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Sonu Kumar
- 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
| | - Knut R Asmis
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, 04103 Leipzig, Germany
| | - Andrey Lyalin
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan.,Center for Green Research on Energy and Environmental Materials, National Institute for Material Science (NIMS), Tsukuba 305-0044, Japan
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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57
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Kise K, Ooi S, Saito H, Yorimitsu H, Osuka A, Tanaka T. Five-Fold Symmetric Pentaindolo- and Pentakis(benzoindolo)Corannulenes: Unique Structural Dynamics Derived from the Combination of Helical and Bowl Inversions. Angew Chem Int Ed Engl 2021; 61:e202112589. [PMID: 34738305 DOI: 10.1002/anie.202112589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 01/13/2023]
Abstract
Peripherally π-extended corannulenes bearing quintuple azahelicene units, 10 and 11, were prepared and their dynamic behaviors were studied experimentally and theoretically. The fused corannulenes were synthesized from sym-pentabromocorannulene in three steps. X-Ray diffraction analysis for 10 displayed a conformer possessing a P(M) bowl chirality and a PPMPM (PMPMM) helical chirality, which was found to be the most stable conformer(s). Variable-temperature NMR measurements of 10 and 11 revealed that their structural isomers can be interconvertible in solution, depending on the steric congestion around the helical scaffolds. Automated search for conformers in the equilibrium and transition states by Artificial Force Induced Reaction (AFIR) method revealed their interconversion networks, including bowl-inversion and helical-inversion. This analysis indicated that the co-existing corannulene and azahelicene moieties influence the conformational dynamics, which leads to mitigation of the activation energy barriers for isomerization.
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Affiliation(s)
- Koki Kise
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shota Ooi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hayate Saito
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hideki Yorimitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Atsuhiro Osuka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takayuki Tanaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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58
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Automated Construction and Optimization Combined with Machine Learning to Generate Pt(II) Methane C–H Activation Transition States. Top Catal 2021. [DOI: 10.1007/s11244-021-01506-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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59
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Martínez-Núñez E, Barnes GL, Glowacki DR, Kopec S, Peláez D, Rodríguez A, Rodríguez-Fernández R, Shannon RJ, Stewart JJP, Tahoces PG, Vazquez SA. AutoMeKin2021: An open-source program for automated reaction discovery. J Comput Chem 2021; 42:2036-2048. [PMID: 34387374 DOI: 10.1002/jcc.26734] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023]
Abstract
AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.
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Affiliation(s)
- Emilio Martínez-Núñez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York, USA
| | - David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Sabine Kopec
- Institut de Sciences Moléculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, Orsay, France
| | - Daniel Peláez
- Institut de Sciences Moléculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, Orsay, France
| | - Aurelio Rodríguez
- Galicia Supercomputing Center (CESGA), Santiago de Compostela, Spain
| | | | - Robin J Shannon
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | | | - Pablo G Tahoces
- Department of Electronics and Computer Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Saulo A Vazquez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela, Spain
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60
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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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61
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Ohmura T, Morimasa Y, Ichino T, Miyake Y, Murata Y, Suginome M, Tajima K, Taketsugu T, Maeda S. Mechanism of 2,6-Dichloro-4,4′-bipyridine-Catalyzed Diboration of Pyrazines Involving a Bipyridine-Stabilized Boryl Radical. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshimichi Ohmura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yohei Morimasa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomoya Ichino
- Department of Chemistry, Faculty of Science, Hokkaido University, N10-W8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Yusuke Miyake
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yasujiro Murata
- Division of Synthetic Chemistry, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Michinori Suginome
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kunihiko Tajima
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, N10-W8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, N21-W10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, N10-W8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, N21-W10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
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62
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Saito H, Shimokawa J, Yorimitsu H. The dioxasilepanyl group as a versatile organometallic unit: studies on stability, reactivity, and utility. Chem Sci 2021; 12:9546-9555. [PMID: 34349929 PMCID: PMC8278973 DOI: 10.1039/d1sc02083h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/05/2021] [Indexed: 12/15/2022] Open
Abstract
Organic synthesis is performed based on precise choices of functional groups and reactions employed. In a multistep synthesis, an ideal functional group should be compatible with various reaction conditions and unaltered until it is subjected to a selective conversion. The current study was set out to search for a silicon functionality that meets these criteria. Here we have established a new silicon-based synthetic methodology centred on a bulky 7-membered dialkoxysilyl group (2,4,4,7,7-pentamethyl-1,3,2-dioxasilepan-2-yl) that uniquely has both stability and on-demand reactivity. The exceptional stability of this functional group was corroborated by both experimental and computational studies which demonstrated that key factors for its stability were a 7-membered structure and steric hindrance. In turn, the dioxasilepanyl group was found to become reactive and to be easily transformed in the presence of appropriate activators. Combined with the development of easy and robust methods to introduce the dioxasilepanyl group onto aryl rings, these findings have allowed a shorter and more efficient synthesis of a bioactive molecule, thus demonstrating the potential utility of the easily accessible dioxasilepanyl group in organic synthesis.
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Affiliation(s)
- Hayate Saito
- Department of Chemistry, Graduate School of Science, Kyoto University Sakyo-ku Kyoto 606-8502 Japan
| | - Jun Shimokawa
- Department of Chemistry, Graduate School of Science, Kyoto University Sakyo-ku Kyoto 606-8502 Japan
| | - Hideki Yorimitsu
- Department of Chemistry, Graduate School of Science, Kyoto University Sakyo-ku Kyoto 606-8502 Japan
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63
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Odajima M, Tajima K, Fukui N, Shinokubo H. Non-Planar Perylene Bisimide Analogues with Inserted Carbonyl and Methylene Subunits. Angew Chem Int Ed Engl 2021; 60:15838-15843. [PMID: 33928728 DOI: 10.1002/anie.202104882] [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: 04/09/2021] [Indexed: 01/04/2023]
Abstract
The synthesis and properties of dinaphthotropone bisimide (DNTrBI) and dinaphthocycloheptatriene bisimide (DNCHepBI) are described. Their molecular design is conceptually based on the insertion of a carbon atom into a perylene bisimide (PBI) core. These molecules adopt non-planar structures due to the presence of a seven-membered ring. The PBI derivative into which a carbonyl group was inserted (DNTrBI) immediately underwent nonradiative decay and/or intersystem crossing in its excited state. The PBI derivative into which a methylene group was inserted (DNCHepBI) was susceptible to deprotonation on account of the two electron-withdrawing naphthalene monoimide units. Subsequent aerobic oxidation resulted in the formation of a C-C bond at the central methylene unit, thus affording a σ-dimer. The formation of this C-C bond is dynamically redox-active, i.e., electron injection into the σ-dimer almost quantitatively regenerated the deprotonated DNCHepBI.
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Affiliation(s)
- Mai Odajima
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Keita Tajima
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Norihito Fukui
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroshi Shinokubo
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
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64
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Odajima M, Tajima K, Fukui N, Shinokubo H. Non‐Planar Perylene Bisimide Analogues with Inserted Carbonyl and Methylene Subunits. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mai Odajima
- Department of Molecular and Macromolecular Chemistry Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Keita Tajima
- Department of Molecular and Macromolecular Chemistry Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Norihito Fukui
- Department of Molecular and Macromolecular Chemistry Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroshi Shinokubo
- Department of Molecular and Macromolecular Chemistry Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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65
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Hayashi H, Takano H, Katsuyama H, Harabuchi Y, Maeda S, Mita T. Synthesis of Difluoroglycine Derivatives from Amines, Difluorocarbene, and CO 2 : Computational Design, Scope, and Applications. Chemistry 2021; 27:10040-10047. [PMID: 33929060 DOI: 10.1002/chem.202100812] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 12/24/2022]
Abstract
A three-component reaction (3CR) for the synthesis of difluoroglycine derivatives has been achieved by using amines, difluorocarbene (generated in situ), and the abundant, inexpensive, and nontoxic C1 source CO2 . Various tert-amines and pyridine, (iso)quinoline, imidazole, thiazole, and pyrazole derivatives were incorporated, and the corresponding products were isolated in solid form without purification by column chromatography on silica gel. Detailed reaction profiles of the 3CR were obtained from computational analysis using DFT calculations, and the results critically suggest that simple ammonia is not applicable to this reaction. In addition, as strongly supported by computational predictions, a new reagent that can generate difluorocarbene at 0 °C without any additives was discovered. Finally, radical substitution reactions of the obtained difluoroglycine derivatives under photoredox conditions, as well as a synthetic application as an N-heterocyclic carbene ligand are shown.
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Affiliation(s)
- Hiroki Hayashi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido, 0010021, Japan.,JST, ERATO Maeda Artificial Intelligence in Chemical Reaction, Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 0600810, Japan
| | - Hideaki Takano
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido, 0010021, Japan.,JST, ERATO Maeda Artificial Intelligence in Chemical Reaction, Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 0600810, Japan
| | - Hitomi Katsuyama
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido, 0010021, Japan.,JST, ERATO Maeda Artificial Intelligence in Chemical Reaction, Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 0600810, Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido, 0010021, Japan.,JST, ERATO Maeda Artificial Intelligence in Chemical Reaction, Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 0600810, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 0600810, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido, 0010021, Japan.,JST, ERATO Maeda Artificial Intelligence in Chemical Reaction, Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 0600810, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 0600810, Japan.,Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki, 3050044, Japan
| | - Tsuyoshi Mita
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido, 0010021, Japan.,JST, ERATO Maeda Artificial Intelligence in Chemical Reaction, Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 0600810, Japan
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66
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Murata Y, Matsunagi K, Kashida J, Shoji Y, Özen C, Maeda S, Fukushima T. Observation of Borane–Olefin Proximity Interaction Governing the Structure and Reactivity of Boron‐Containing Macrocycles. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yukihiro Murata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
- Department of Chemical Science and Engineering School of Materials and Chemical Technology Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8502 Japan
| | - Kenta Matsunagi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
- Department of Chemical Science and Engineering School of Materials and Chemical Technology Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8502 Japan
| | - Junki Kashida
- Laboratory for Chemistry and Life Science, Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
- Department of Chemical Science and Engineering School of Materials and Chemical Technology Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8502 Japan
| | - Yoshiaki Shoji
- Laboratory for Chemistry and Life Science, Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
- Department of Chemical Science and Engineering School of Materials and Chemical Technology Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8502 Japan
| | - Cihan Özen
- Institute for Chemical Reaction Design and Discovery, (WPI-ICReDD) Hokkaido University Sapporo 060-8510 Japan
- Department of Chemistry Hokkaido University Sapporo 060-8510 Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery, (WPI-ICReDD) Hokkaido University Sapporo 060-8510 Japan
- Department of Chemistry Hokkaido University Sapporo 060-8510 Japan
| | - Takanori Fukushima
- Laboratory for Chemistry and Life Science, Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
- Department of Chemical Science and Engineering School of Materials and Chemical Technology Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8502 Japan
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67
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Murata Y, Matsunagi K, Kashida J, Shoji Y, Özen C, Maeda S, Fukushima T. Observation of Borane-Olefin Proximity Interaction Governing the Structure and Reactivity of Boron-Containing Macrocycles. Angew Chem Int Ed Engl 2021; 60:14630-14635. [PMID: 33860607 DOI: 10.1002/anie.202103512] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 11/06/2022]
Abstract
While attractive interactions between borane and olefin have been postulated to trigger various boron-mediated organic transformations, proximity structures of these functional groups, other than the formation of weak van der Waals complexes, have never been directly observed. Here we show that a close intramolecular borane-olefin interaction operates in macrocyclic systems containing borane and olefinic groups obtained by multi-step 1,2-carboboration between a strained alkyne and 9-borafluorene derivatives. Depending on Lewis acidity of the borane moiety and the size of the macrocycles, the magnitude of interaction changes, resulting in different reaction modes. The whole picture of the multi-step reactions has been revealed experimentally with theoretical supports. The present finding may not only provide a deeper understanding of the fundamental boron-mediated interaction but also lead to the development of new organic transformations involving molecular activation by boranes.
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Affiliation(s)
- Yukihiro Murata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.,Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8502, Japan
| | - Kenta Matsunagi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.,Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8502, Japan
| | - Junki Kashida
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.,Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8502, Japan
| | - Yoshiaki Shoji
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.,Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8502, Japan
| | - Cihan Özen
- Institute for Chemical Reaction Design and Discovery, (WPI-ICReDD), Hokkaido University, Sapporo, 060-8510, Japan.,Department of Chemistry, Hokkaido University, Sapporo, 060-8510, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery, (WPI-ICReDD), Hokkaido University, Sapporo, 060-8510, Japan.,Department of Chemistry, Hokkaido University, Sapporo, 060-8510, Japan
| | - Takanori Fukushima
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.,Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8502, Japan
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68
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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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69
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Takayanagi T. Application of Reaction Path Search Calculations to Potential Energy Surface Fits. J Phys Chem A 2021; 125:3994-4002. [PMID: 33915053 DOI: 10.1021/acs.jpca.1c01512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There has been significant progress in recent years in the use of machine learning techniques to model high-dimensional reactive potential energy surfaces using large-scale data obtained from ab initio electronic structure calculations. In these methods, the strategy used to gather data becomes a key issue as the molecular size increases. In this work, we examine the applicability of the reaction path search algorithm implemented in the Global Reaction Route Mapping (GRRM) code as a data-gathering approach. The electronic energies and gradients sampled by using the GRRM calculation are directly used in potential energy surface fitting to a permutationally invariant polynomial function. This simple approach was applied to the HNS and HCNO reaction systems, and we found that the fitted potential energy surfaces reasonably reproduce the features of the electronic structure calculations used in the GRRM calculations. This suggests that the GRRM sampling scheme can be used to construct an initial potential energy surface.
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Affiliation(s)
- Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Saitama City, Saitama 338-8570, Japan
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70
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Yamashita Y, Noguchi A, Fushimi S, Hatanaka M, Kobayashi S. Chiral Metal Salts as Ligands for Catalytic Asymmetric Mannich Reactions with Simple Amides. J Am Chem Soc 2021; 143:5598-5604. [PMID: 33821631 DOI: 10.1021/jacs.0c13317] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Catalytic asymmetric Mannich reactions of imines with weakly acidic simple amides were developed using a chiral potassium hexamethyldisilazide (KHMDS)-bis(oxazoline) potassium salt (K-Box) catalyst system. The desired reactions proceeded to afford the target compounds in high yields with high diastereo- and enantioselectivities. It was suggested that a K enolate interacted with K-Box to form a chiral K enolate that reacted with imines efficiently. In this system, K-Box (potassium salt of Box) worked as a chiral ligand of the active potassium species.
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Affiliation(s)
- Yasuhiro Yamashita
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Aika Noguchi
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Seiya Fushimi
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Miho Hatanaka
- Department of Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Shu Kobayashi
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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71
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Tanaka Y, Tajima K, Fukui N, Shinokubo H. Dinaphtho[1,8‐
bc
:1′,8′‐
fg
][1,5]dithiocine Bisimide. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202000722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuki Tanaka
- Department of Molecular and Macromolecular Chemistry Graduate School of Engineering Nagoya University Furo-chi, Chikusa-ku 464-8603 Nagoya Japan
| | - Keita Tajima
- Department of Molecular and Macromolecular Chemistry Graduate School of Engineering Nagoya University Furo-chi, Chikusa-ku 464-8603 Nagoya Japan
| | - Norihito Fukui
- Department of Molecular and Macromolecular Chemistry Graduate School of Engineering Nagoya University Furo-chi, Chikusa-ku 464-8603 Nagoya Japan
| | - Hiroshi Shinokubo
- Department of Molecular and Macromolecular Chemistry Graduate School of Engineering Nagoya University Furo-chi, Chikusa-ku 464-8603 Nagoya Japan
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72
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Gimadiev T, Nugmanov R, Batyrshin D, Madzhidov T, Maeda S, Sidorov P, Varnek A. Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data. J Chem Inf Model 2021; 61:554-559. [PMID: 33502186 DOI: 10.1021/acs.jcim.0c01280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Presently, quantum chemical calculations are widely used to generate extensive data sets for machine learning applications; however, generally, these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surfaces provides important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulting from quantum chemical calculations. Our tool allows one to store, assemble, and analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for pathway analysis by graph algorithms. Original condensed graph of reaction technology is used to store any chemical reaction as a single graph.
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Affiliation(s)
- Timur Gimadiev
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan
| | - Ramil Nugmanov
- Laboratory of Chemoinformatics and Molecular Modeling, Butlerov Institute of Chemistry, Kazan Federal University, 18, Kremlyovskaya str., 420008 Kazan, Russia
| | - Dinar Batyrshin
- Laboratory of Chemoinformatics and Molecular Modeling, Butlerov Institute of Chemistry, Kazan Federal University, 18, Kremlyovskaya str., 420008 Kazan, Russia
| | - Timur Madzhidov
- Laboratory of Chemoinformatics and Molecular Modeling, Butlerov Institute of Chemistry, Kazan Federal University, 18, Kremlyovskaya str., 420008 Kazan, Russia
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan
| | - Pavel Sidorov
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan
| | - Alexandre Varnek
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan.,Laboratory of Chemoinformatics, UMR 7140 CNRS, University of Strasbourg, 4, Blaise Pascal str., 67081 Strasbourg, France
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73
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Kinoshita SN, Harabuchi Y, Inokuchi Y, Maeda S, Ehara M, Yamazaki K, Ebata T. Substitution effect on the nonradiative decay and trans → cis photoisomerization route: a guideline to develop efficient cinnamate-based sunscreens. Phys Chem Chem Phys 2021; 23:834-845. [PMID: 33284297 DOI: 10.1039/d0cp04402d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cinnamate derivatives are very useful as UV protectors in nature and as sunscreen reagents in daily life. They convert harmful UV energy to thermal energy through effective nonradiative decay (NRD) including trans → cis photoisomerization. However, the mechanism is not simple because different photoisomeirzation routes have been observed for different substituted cinnamates. Here, we theoretically examined the substitution effects at the phenyl ring of methylcinnamate (MC), a non-substituted cinnamate, on the electronic structure and the NRD route involving trans → cis isomerization based on time-dependent density functional theory. A systematic reaction pathway search using the single-component artificial force-induced reaction method shows that the very efficient photoisomerization route of MC can be essentially described as "1ππ* (trans) → 1nπ* → T1 (3ππ*) → S0 (trans or cis)". We found that for efficient 1ππ* (trans) → 1nπ* internal conversion (IC), MC should have the substituent at the appropriate position of the phenyl ring to stabilize the highest occupied π orbital. Substitution at the para position of MC slightly lowers the 1ππ* state energy and photoisomerization occurs via a slightly less efficient "1ππ* (trans) → 3nπ* → T1 (3ππ*) → S0 (trans or cis)" pathway. Substitution at the meta or ortho positions of MC significantly lowers the 1ππ* state energy so that the energy barrier of IC (1ππ* → 1nπ*) becomes very high. This substitution leads to a much longer 1ππ* state lifetime than that of MC and para-substituted MC, and a change in the dominant photoisomerization route to "1ππ* (trans) → C[double bond, length as m-dash]C bond twisting on 1ππ* → S0 (trans or cis)". As a whole, the "1ππ* → 1nπ*" IC observed in MC is the most important initial step for the rapid change of UV energy to thermal energy. We also found that the stabilization of the π orbital (i) minimizes the energy gap between 1ππ* and 1nπ* at the 1ππ* minimum and (ii) makes the 0-0 level of 1ππ* higher than 1nπ* as observed in MC. These MC-like relationships between the 1ππ* and 1nπ* energies should be ideal to maximize the "1ππ* → 1nπ*" IC rate constant according to Marcus theory.
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Affiliation(s)
- Shin-Nosuke Kinoshita
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan and Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| | - Yoshiya Inokuchi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan and Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| | - Masahiro Ehara
- SOKENDAI, the Graduate University for Advanced Studies, Myodaiji, Okazaki 444-8585, Japan and Institute for Molecular Science and Research Center for Computational Science, 38, Myodaiji, Okazaki 444-8585, Japan
| | - Kaoru Yamazaki
- Institute for Materials Research, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
| | - Takayuki Ebata
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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74
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Shibata T, Shiozawa N, Nishibe S, Takano H, Maeda S. Pt( ii)-Chiral diene-catalyzed enantioselective formal [4 + 2] cycloaddition initiated by C–C bond cleavage and elucidation of a Pt( ii)/( iv) cycle by DFT calculations. Org Chem Front 2021. [DOI: 10.1039/d1qo01467f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A Pt(ii)-chiral diene complex demonstrates a high catalytic activity in the enantioselective formal [4 + 2] cycloaddition along with C–C bond cleavage of biphenylene at room temp. DFT calculations elucidated that the present catalysis involves a rare Pt(ii)/Pt(iv) cycle.
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Affiliation(s)
- Takanori Shibata
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo 169-8555, Japan
| | - Natsumi Shiozawa
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo 169-8555, Japan
| | - Shun Nishibe
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo 169-8555, Japan
| | - Hideaki Takano
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo 169-8555, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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75
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Takahashi K, Satoshi M. Mining hydroformylation in complex reaction network via graph theory. RSC Adv 2021; 11:23235-23240. [PMID: 35479801 PMCID: PMC9036754 DOI: 10.1039/d1ra03395f] [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] [Received: 04/30/2021] [Accepted: 06/16/2021] [Indexed: 11/21/2022] Open
Abstract
Data science is introduced to identify the reactant, product, and reaction path in the chemical reaction network. Cobalt catalyzed hydroformylation is investigated where the reaction network is built via first principles calculations. The closeness centrality and high frequency node are found to be the reactant cobalt tetracarbonyl hydride. In addition, betweenness centrality uncovers three reaction paths which have the products of aldehyde, CH2O, and CO2, respectively. The energy profile determines that the reaction path leading to aldehyde is energetically favored; thus, the reaction path for cobalt catalyzed hydroformylation is identified without kinetics. Hence, the proposed approach can act as a first step towards understanding the complex chemical reaction network and towards further kinetic understanding of the chemical reaction. Data science is introduced to identify the reactant, product, and reaction path in the chemical reaction network.![]()
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Affiliation(s)
| | - Maeda Satoshi
- Department of Chemistry
- Hokkaido University
- Sapporo 060-8510
- Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD)
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76
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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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77
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Thakkar A, Johansson S, Jorner K, Buttar D, Reymond JL, Engkvist O. Artificial intelligence and automation in computer aided synthesis planning. REACT CHEM ENG 2021. [DOI: 10.1039/d0re00340a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this perspective we deal with questions pertaining to the development of synthesis planning technologies over the course of recent years.
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Affiliation(s)
- Amol Thakkar
- Hit Discovery
- Discovery Sciences
- R&D
- AstraZeneca
- Gothenburg
| | | | - Kjell Jorner
- Early Chemical Development
- Pharmaceutical Sciences
- R&D
- AstraZeneca
- Macclesfield
| | - David Buttar
- Early Chemical Development
- Pharmaceutical Sciences
- R&D
- AstraZeneca
- Macclesfield
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern
- Switzerland
| | - Ola Engkvist
- Hit Discovery
- Discovery Sciences
- R&D
- AstraZeneca
- Gothenburg
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78
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Murase H, Nagata Y, Akahori S, Shinokubo H, Miyake Y. Aggregation-Induced Emission in Tetrathia[8]circulene Octaoxides via Restriction of the Dynamic Motion of their Negatively Curved π-Frameworks. Chem Asian J 2020; 15:3873-3877. [PMID: 32975006 DOI: 10.1002/asia.202001129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Indexed: 11/05/2022]
Abstract
Curved polycyclic aromatic hydrocarbons exhibit intriguing properties, but their flexible and dynamic nature is often considered to be unfavorable for achieving excellent emission properties. In this study, we prepared tetrathia[8]circulene octaoxides that adopt a negatively curved conformation. We found that these molecules exhibit aggregation-induced emission (AIE) that originates from the restriction of the dynamic motion of their saddle-shaped π-frameworks in the solid and aggregated states.
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Affiliation(s)
- Hiroyasu Murase
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yuya Nagata
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Shuhei Akahori
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroshi Shinokubo
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yoshihiro Miyake
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
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79
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Borysenko IO, Sviatenko LK, Okovytyy SI, Leszczynski J. Efficient approach for exploring the multiple-channel bimolecular interactions of conformationally flexible reagents. Epoxide ring opening reaction. Struct Chem 2020. [DOI: 10.1007/s11224-020-01663-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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80
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Kinetic prediction of reverse intersystem crossing in organic donor-acceptor molecules. Nat Commun 2020; 11:3909. [PMID: 32764588 PMCID: PMC7411052 DOI: 10.1038/s41467-020-17777-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/17/2020] [Indexed: 11/13/2022] Open
Abstract
Reverse intersystem crossing (RISC), the uphill spin-flip process from a triplet to a singlet excited state, plays a key role in a wide range of photochemical applications. Understanding and predicting the kinetics of such processes in vastly different molecular structures would facilitate the rational material design. Here, we demonstrate a theoretical expression that successfully reproduces experimental RISC rate constants ranging over five orders of magnitude in twenty different molecules. We show that the spin flip occurs across the singlet–triplet crossing seam involving a higher-lying triplet excited state where the semi-classical Marcus parabola is no longer valid. The present model explains the counterintuitive substitution effects of bromine on the RISC rate constants of previously unknown molecules, providing a predictive tool for material design. Understanding and predicting the kinetics of reverse intersystem crossing (RISC) facilitates the design of materials. Here, the authors demonstrate a theoretical expression that reproduces experimental RISC rate constants ranging over five orders of magnitude in selected molecules.
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81
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as-Indaceno[3,2,1,8,7,6-ghijklm]terrylene as a near-infrared absorbing C 70-fragment. Nat Commun 2020; 11:3873. [PMID: 32747710 PMCID: PMC7400669 DOI: 10.1038/s41467-020-17684-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/13/2020] [Indexed: 12/27/2022] Open
Abstract
Carbon and hydrogen are fundamental components of organic molecules and a fascinating plethora of functions can be generated using these two elements. Yet, realizing attractive electronic structures only by using carbon and hydrogen remains challenging. Herein, we report the synthesis and properties of the C70 fragment as-indaceno[3,2,1,8,7,6-ghijklm]terrylene, which exhibits near-infrared (NIR) absorption (up to ca. 1300 nm), even though this molecule consists of only 34 carbon and 14 hydrogen atoms. A remarkably small highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap is confirmed by electrochemical measurement and theoretical calculations. Furthermore, as-indacenoterrylene is stable despite the absence of peripheral substituents, which contrasts with the cases of other NIR-absorbing hydrocarbons such as diradicaloids and antiaromatic molecules. The results of this study thus offer fundamental insights into the design of hydrocarbons with a small band gap.
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82
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Watanabe K, Kawashima Y, Mukai C, Takagi T, Suwa Y, Tian YS, Kawashita N. A Comparison between the Cycloadditions of Allenyl- and Vinyl-Cyclopentanes Using Density Functional Theory and GRRM Program. Chem Pharm Bull (Tokyo) 2020; 68:737-741. [DOI: 10.1248/cpb.c20-00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kazuki Watanabe
- Graduate School of Pharmaceutical Sciences, Osaka University
| | | | - Chisato Mukai
- Organization of Frontier Science and Innovation, Kanazawa University
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Yukinori Suwa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Yu-Shi Tian
- Graduate School of Pharmaceutical Sciences, Osaka University
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83
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Ozen C, Satoh T, Maeda S. A theoretical study on the alkali metal carboxylate‐promoted
L‐Lactide
polymerization. J Comput Chem 2020. [DOI: 10.1002/jcc.26386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cihan Ozen
- Institute for Chemical Reaction Design and Discovery (WPI‐ICReDD) Hokkaido University Sapporo Japan
| | - Toshifumi Satoh
- Division of Applied Chemistry, Faculty of Engineering Hokkaido University Sapporo Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI‐ICReDD) Hokkaido University Sapporo Japan
- Department of Chemistry, Faculty of Science Hokkaido University Sapporo Japan
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84
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Takagi M, Maeda S. Global Search for Crystal Structures of Carbon under High Pressure. ACS OMEGA 2020; 5:18142-18147. [PMID: 32743188 PMCID: PMC7391844 DOI: 10.1021/acsomega.0c01709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
In this study, a systematic search for structures of carbon crystals under high pressure was performed by using the artificial force induced reaction method including periodic boundary conditions. To perform a search under an arbitrary pressure, an algorithm to take account of the pressure was implemented in the GRRM program. At 100 GPa, the search generated 710 unique structures automatically. These structures were compared with 982 structures obtained by the search under zero pressure. The structures at 100 GPa were much denser than those under zero pressure. Besides, new structures that were denser than diamond were obtained at 100 GPa.
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Affiliation(s)
- Makito Takagi
- Department
of Chemistry, Faculty of Science, Hokkaido
University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Satoshi Maeda
- Department
of Chemistry, Faculty of Science, Hokkaido
University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Institute
for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- Research
and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0044, Japan
- JST,
ERATO Maeda Artificial Intelligence for Chemical Reaction Design and
Discovery Project, Kita
10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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85
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Saito H, Yamamoto K, Sumiya Y, Liu L, Nogi K, Maeda S, Yorimitsu H. Palladium‐Catalyzed C−H Iodination of Arenes by Means of Sulfinyl Directing Groups. Chem Asian J 2020; 15:2442-2446. [DOI: 10.1002/asia.202000591] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/16/2020] [Indexed: 01/15/2023]
Affiliation(s)
- Hayate Saito
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto 606-8502 Japan
| | - Keita Yamamoto
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto 606-8502 Japan
| | - Yosuke Sumiya
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Ling‐Jun Liu
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto 606-8502 Japan
- Institute of Organic and Polymeric Materials National Taipei University of Technology Taipei 10608 Taiwan
| | - Keisuke Nogi
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto 606-8502 Japan
| | - Satoshi Maeda
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD) Hokkaido University Kita 21 Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
| | - Hideki Yorimitsu
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto 606-8502 Japan
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86
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Ineffective OH Pinning of the Flipping Dynamics of a Spherical Guest within a Tight‐Fitting Tube. Angew Chem Int Ed Engl 2020; 59:14570-14576. [DOI: 10.1002/anie.202005538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/29/2020] [Indexed: 01/27/2023]
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87
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Matsuno T, Someya M, Sato S, Maeda S, Isobe H. Ineffective OH Pinning of the Flipping Dynamics of a Spherical Guest within a Tight‐Fitting Tube. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Taisuke Matsuno
- Department of Chemistry The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Maki Someya
- Department of Chemistry The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Sota Sato
- Department of Chemistry The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Satoshi Maeda
- Department of Chemistry and Institute for Chemical Reaction Design and Discovery (WPI-ICReDD) Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo 060-0810 Japan
| | - Hiroyuki Isobe
- Department of Chemistry The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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88
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Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review. Catalysts 2020. [DOI: 10.3390/catal10060691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.
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89
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Mita T, Harabuchi Y, Maeda S. Discovery of a synthesis method for a difluoroglycine derivative based on a path generated by quantum chemical calculations. Chem Sci 2020; 11:7569-7577. [PMID: 34094133 PMCID: PMC8159455 DOI: 10.1039/d0sc02089c] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced 'quantum chemistry aided retrosynthetic analysis' (QCaRA), which uses quantum chemical calculations to search systematically for the decomposition paths of a target product and proposes a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the most promising path chosen by an organic chemist among the predicted paths led to the discovery of a synthesis method for a difluoroglycine derivative. We emphasize that the purpose of this study is not to propose a fully automated workflow. Therefore, the extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes.
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Affiliation(s)
- Tsuyoshi Mita
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21 Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan .,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project Kita 10 Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21 Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan .,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project Kita 10 Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan.,Department of Chemistry, Faculty of Science, Hokkaido University Kita 10 Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan.,JST, PRESTO 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21 Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan .,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project Kita 10 Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan.,Department of Chemistry, Faculty of Science, Hokkaido University Kita 10 Nishi 8, Kita-ku 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
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90
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Sumiya Y, Maeda S. Rate Constant Matrix Contraction Method for Systematic Analysis of Reaction Path Networks. CHEM LETT 2020. [DOI: 10.1246/cl.200092] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yosuke Sumiya
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- National Institute for Materials Science (NIMS), Research and Services Division of Materials Data and Integrated System (MaDIS), Tsukuba, Ibaraki 305-0044, Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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91
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Abstract
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various algorithmic advances have shown that such structural screenings must and can be automated and routinely carried out. This will replace the standard approach of manually studying a selected and restricted number of molecular structures for a chemical mechanism. The complexity of the task has led to many different approaches. However, all of them address the same general target, namely to produce a complete atomistic picture of the kinetics of a chemical process. It is the purpose of this overview to categorize the problems that should be targeted and to identify the principal components and challenges of automated exploration machines so that the various existing approaches and future developments can be compared based on well-defined conceptual principles.
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Affiliation(s)
- Jan P. Unsleber
- Laboratory for Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory for Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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92
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Zhang J, Zhang Q, Zhu Z, Wang B. Theoretical investigation on the palladium-catalyzed selective formation of spirocyclenes from dienallenes. J Organomet Chem 2020. [DOI: 10.1016/j.jorganchem.2020.121173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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93
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Quapp W, Bofill JM. Some Mathematical Reasoning on the Artificial Force Induced Reaction Method. J Comput Chem 2020; 41:629-634. [PMID: 31792984 DOI: 10.1002/jcc.26115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 11/07/2022]
Abstract
There are works of the Maeda-Morokuma group, which propose the artificial force induced reaction (AFIR) method (Maeda et al., J. Comput. Chem. 2014, 35, 166 and 2018, 39, 233). We study this important method from a theoretical point of view. The understanding of the proposers does not use the barrier breakdown point of the AFIR parameter, which usually is half of the reaction path between the minimum and the transition state which is searched for. Based on a comparison with the theory of Newton trajectories, we could better understand the method. It allows us to follow along some reaction pathways from minimum to saddle point, or vice versa. We discuss some well-known two-dimensional test surfaces where we calculate full AFIR pathways. If one has special AFIR curves at hand, one can also study the behavior of the ansatz. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Wolfgang Quapp
- Leipzig University, Mathematisches Institut, Universität Leipzig, PF 100920, D-04009, Leipzig, Germany
| | - Josep Maria Bofill
- Universitat de Barcelona, Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, and Institut de Química Teòrica i Computacional, Universitat de Barcelona, (IQTCUB), Martí i Franquès, 1, 08028, Barcelona, Spain
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94
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Mechanism and kinetics of astrophysically relevant gas-phase stereoinversion in glutamic acid: A computational study. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.molap.2019.100061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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95
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Shoji Y, Kashida J, Fukushima T. Organic Transformations Using Electron-Deficient Boron Compounds. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yoshiaki Shoji
- Laboratory for Chemistry and Life Science (CLS), Institute of Innovative Research, Tokyo Institute of Technology
| | | | - Takanori Fukushima
- Laboratory for Chemistry and Life Science (CLS), Institute of Innovative Research, Tokyo Institute of Technology
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96
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Domon K, Puripat M, Fujiyoshi K, Hatanaka M, Kawashima SA, Yamatsugu K, Kanai M. Catalytic Chemoselective O-Phosphorylation of Alcohols. ACS CENTRAL SCIENCE 2020; 6:283-292. [PMID: 32123747 PMCID: PMC7047436 DOI: 10.1021/acscentsci.9b01272] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Indexed: 05/16/2023]
Abstract
Phosphorylation of alcohols is a fundamentally important reaction in both life science and physical science. Product phosphate monoesters play key roles in living organisms, natural products, pharmaceuticals, and organic materials. Most of the chemical methods to date for synthesizing phosphate monoesters, however, require multistep sequences or are limited to specific types of substrates possibly due to harsh conditions. An alternative way to enable the simple production of phosphate monoesters from highly functionalized precursor alcohols is, thus, highly desired. We report herein a catalytic phosphorylation of alcohols with high functional group tolerance using tetrabutylammonium hydrogen sulfate (TBAHS) and phosphoenolpyruvic acid monopotassium salt (PEP-K) as the catalyst and phosphoryl donor, respectively. This method enables the direct introduction of a nonprotected phosphate group to the hydroxy group of a diverse menu of alcohol substrates, including functionalized small molecules, carbohydrates, and unprotected peptides. Nuclear magnetic resonance, mass spectrometric, and density functional theory analyses suggest that an unprecedented mixed anhydride species, generated from PEP-K and TBAHS, acts as an active phosphoryl donor in this reaction. This operationally simple and chemoselective catalytic phosphorylation allows for the efficient production of densely functionalized O-phosphorylated compounds, which are useful in diverse fields including biology and medicine.
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Affiliation(s)
- K. Domon
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Puripat
- Institute
for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - K. Fujiyoshi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Hatanaka
- Institute
for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
- Graduate
School of Science and Technology, Data Science Center, NAIST, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - S. A. Kawashima
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - K. Yamatsugu
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Kanai
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
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97
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Quapp W, Bofill JM. Comment on "Exploring Potential Energy Surface with External Forces". J Chem Theory Comput 2020; 16:811-815. [PMID: 31725299 DOI: 10.1021/acs.jctc.9b00736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, a work (Wolinski, K., J. Chem. Theory Comput. 2018, 14, 6306, 10.1021/acs.jctc.8b00885 ) was published in which the SEGO method (standard and enforced geometry optimization) was proposed to find new minimums on potential energy surfaces. We study this important method from a theoretical point of view. Up to now, the understanding of the proposer does not take into account the barrier breakdown point on a SEGO path being usually half of the path, which is searched for. However, a better understanding of the method allows us to follow along the reaction pathway from a minimum to a saddle point or vice versa. We discuss the well-known two-dimensional MB test surface where we calculate full SEGO pathways. If one has special SEGO curves at hand, one can also detect some weaknesses of the ansatz.
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Affiliation(s)
- Wolfgang Quapp
- Mathematisches Institut , Universität Leipzig , PF 100920, D-04009 Leipzig , Germany
| | - Josep Maria Bofill
- Departament de Química Inorgánica i Orgánica, Institut de Química Teòrica i Computacional (IQTCUB) , Universitat de Barcelona , Martí i Franquès, 1, 08028 Barcelona , Spain
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98
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Ito T, Harabuchi Y, Maeda S. AFIR explorations of transition states of extended unsaturated systems: automatic location of ambimodal transition states. Phys Chem Chem Phys 2020; 22:13942-13950. [DOI: 10.1039/d0cp02379e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on the artificial force induced reaction (AFIR) method, we proposed a procedure to systematically explore ambimodal transition states (TSs) that cause the dynamical bifurcation.
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Affiliation(s)
- Takuma Ito
- Graduate School of Chemical Sciences and Engineering
- Hokkaido University
- Sapporo 060-8628
- Japan
| | - Yu Harabuchi
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
| | - Satoshi Maeda
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
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99
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Nabata H, Takagi M, Saita K, Maeda S. Computational searches for crystal structures of dioxides of group 14 elements (CO 2, SiO 2, GeO 2) under ultrahigh pressure. RSC Adv 2020; 10:22156-22163. [PMID: 35516614 PMCID: PMC9054535 DOI: 10.1039/d0ra03359f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/03/2020] [Indexed: 01/20/2023] Open
Abstract
In this study, we focused on the effect of pressure on the crystal structures of dioxides of group 14 elements, i.e. SiO2, GeO2, and CO2.
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Affiliation(s)
- Hitoshi Nabata
- Graduate School of Chemical Sciences and Engineering
- Hokkaido University
- Sapporo 060-8628
- Japan
| | - Makito Takagi
- Graduate School of Nanobioscience
- Yokohama City University
- Yokohama
- Japan
| | - Kenichiro Saita
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
| | - Satoshi Maeda
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
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100
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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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