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Akazawa D, Sasaki T, Nagasaka M, Shiga M. X-ray absorption spectra of aqueous cellobiose: Experiment and theory. J Chem Phys 2022; 156:044202. [DOI: 10.1063/5.0078963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daisuke Akazawa
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8561, Japan
| | - Takehiko Sasaki
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8561, Japan
| | | | - Motoyuki Shiga
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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Kondo T, Sasaki T, Shiga M. The mechanism of sorbitol dehydration in hot acidic solutions. J Comput Chem 2021; 42:1783-1791. [PMID: 34245044 DOI: 10.1002/jcc.26710] [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: 03/31/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/23/2022]
Abstract
Sugar alcohol dehydration in hot water is an important reaction that allows for environmentally friendly biomass conversion without the use of organic solvents. Here, we report a free-energy analysis by metadynamics (MTD) simulations based on ab initio density functional theory and semiempirical density-functional tight-binding method to understand the mechanism of dehydration reactions of d-sorbitol (SBT) in hot acidic water. Comparing the results of ab initio and semiempirical MTD, it was found that the latter gives a reliable free energy surface of SBT dehydration reaction, although the results vary upon the inclusion of dispersion correction. It was found that the reaction proceeds consistently via an SN 2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected by the acidic species. This mechanism was further verified by real-time trajectories started from the transition state using ab initio molecular dynamics simulations. The free energy barriers of the reaction pathways leading to five-membered ether products are lower than those leading to six-membered ether products, in agreement with experiment. This outcome can be ascribed, in part, to our finding that the reaction barrier of the pathway is correlated to the stability of the SBT confined conformation at the initial stage of the reaction.
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Affiliation(s)
- Tomomi Kondo
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, Chiba, Japan
| | - Takehiko Sasaki
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Motoyuki Shiga
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, Chiba, Japan
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Kondo T, Sasaki T, Ruiz-Barragan S, Ribas-Ariño J, Shiga M. Refined metadynamics through canonical sampling using time-invariant bias potential: A study of polyalcohol dehydration in hot acidic solutions. J Comput Chem 2020; 42:156-165. [PMID: 33124054 DOI: 10.1002/jcc.26443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 12/17/2022]
Abstract
We propose a canonical sampling method to refine metadynamics simulations a posteriori, where the hills obtained from metadynamics are used as a time-invariant bias potential. In this way, the statistical error in the computed reaction barriers is reduced by an efficient sampling of the collective variable space at the free energy level of interest. This simple approach could be useful particularly when two or more free energy barriers are to be compared among chemical reactions in different or competing conditions. The method was then applied to study the acid dependence of polyalcohol dehydration reactions in high-temperature aqueous solutions. It was found that the reaction proceeds consistently via an SN 2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected significantly by the acidic species. Although demonstration is shown for a specific problem, the computational method suggested herein could be generally used for simulations of complex reactions in the condensed phase.
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Affiliation(s)
- Tomomi Kondo
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.,Center for Computational Science and e-Systems, Japan Atomic Energy Agency, Chiba, Japan
| | - Takehiko Sasaki
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Sergi Ruiz-Barragan
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, Chiba, Japan
| | - Jordi Ribas-Ariño
- Departament de Ciència dels Materials i Química Física and IQTCUB, Universitat de Barcelona, Barcelona, Spain
| | - Motoyuki Shiga
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, Chiba, Japan
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Kunnikuruvan S, Nair NN. Mechanistic Insights into the Brønsted Acid-Catalyzed Dehydration of β-d-Glucose to 5-Hydroxymethylfurfural under Ambient and Subcritical Conditions. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00678] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sooraj Kunnikuruvan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
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Chang YL, Sasaki T, Ribas-Ariño J, Machida M, Shiga M. Understanding Competition of Polyalcohol Dehydration Reactions in Hot Water. J Phys Chem B 2019; 123:1662-1671. [DOI: 10.1021/acs.jpcb.8b11615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yong Lik Chang
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8561, Japan
| | - Takehiko Sasaki
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8561, Japan
| | - Jordi Ribas-Ariño
- Departament de Química-Física i CERQT, Universitat de Barcelona, Diagonal, 645, 08028 Barcelona, Spain
| | - Masahiko Machida
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Motoyuki Shiga
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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Nanao H, Sasaki H, Sato O, Yamaguchi A, Shirai M. Benzyl methyl ether production from benzyl alcohol and methanol in carbonic water. Catal Today 2018. [DOI: 10.1016/j.cattod.2017.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Kim YJ, Rakshit S, Jin GY, Ghosh P, Lee YM, Park WW, Kim YS, Kwon OH. Synergistic Configuration of Diols as Brønsted Bases. Chemistry 2017; 23:17179-17185. [PMID: 28924983 DOI: 10.1002/chem.201703668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 02/03/2023]
Abstract
As viscous hydroxylic organic compounds, diols are of interest for their functional molecular conformation, which is based on inter- and intramolecular hydrogen (H)-bonds. By utilising steady-state electronic and vibrational spectroscopy, time-resolved fluorescence spectroscopy, and computational analyses, we report the association of the hydroxyl groups of diols via intra- or intermolecular H-bonds to enhance their reactivity as a base. Whereas the formation of an intermolecularly H-bonded dimer is requisite for diols of weak intramolecular H-bond to extract a proton from a model strong photoacid, a well-configured single diol molecule with an optimised intramolecular H-bond is revealed to serve as an effective Brønsted base with increased basicity. This observation highlights the collective role of H-bonding in acid-base reactions, and provides mechanistic backgrounds to understand the reactivity of polyols in the acid-catalysed dehydration for the synthesis of cyclic ethers at the molecular level.
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Affiliation(s)
- Ye-Jin Kim
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.,Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Surajit Rakshit
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Current address: Department of Chemistry, Vijaygarh Jotish Roy College, 8/2, Bejoygarh, Jadavpur, Kolkata, West Bengal, 700032, India
| | - Geun Young Jin
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Prasun Ghosh
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Current address: Geological Survey of India, Southern Region, Bandlaguda Road, Hyderabad, 5000068, India
| | - Young Min Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Won-Woo Park
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yung Sam Kim
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Oh-Hoon Kwon
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.,Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
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