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Nagasaka M. Probing Isolated Water Molecules in Aqueous Acetonitrile Solutions Using Oxygen K-Edge X-ray Absorption Spectroscopy. J Phys Chem Lett 2024:5165-5170. [PMID: 38713030 DOI: 10.1021/acs.jpclett.4c01087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Oxygen K-edge X-ray absorption spectroscopy (XAS) of an aqueous acetonitrile solution exhibited a sharp peak at approximately 537 eV, which was similar to that of water vapor and was not observed in liquid water. The inner-shell spectra of isolated water molecules and water clusters of different sizes surrounded by acetonitrile molecules were obtained by extracting these water structures from the liquid structures of aqueous acetonitrile solutions, as calculated using molecular dynamics simulations. The sharp peak profiles of the O K-edge XAS spectra were derived not from water clusters but from isolated water molecules surrounded by acetonitrile molecules. The present study proposes that isolated water molecules are easily formed in aqueous acetonitrile solutions and that the electronic structures of the isolated water molecules can be analyzed using O K-edge XAS spectra, which separates the contributions of small water clusters.
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Affiliation(s)
- Masanari Nagasaka
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Myodaiji, Okazaki 444-8585, Japan
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Kudo Y, Kumaki F, Nagasaka M, Adachi JI, Noguchi Y, Koga N, Itabashi H, Hiyama M. Experimental and Theoretical Study for Core Excitation of Firefly Luciferin in Carbon K-Edge Spectra. J Phys Chem A 2024; 128:611-617. [PMID: 38227306 DOI: 10.1021/acs.jpca.3c07504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Carbon (C) K-edge X-ray absorption spectra for firefly luciferin were measured and assigned using time-dependent density functional theoretical calculations for luciferin anion and dianion to elucidate the effect of hydroxy-group deprotonation. It was found that the C K-edge spectra for luciferin had four characteristic peaks. The effect of deprotonation of the hydroxy group appears in the energy difference of the first and second peaks of these spectra. This energy difference is 1.0 eV at pH 7 and 2.3 eV at pH 10. The deprotonation of the hydroxy group can be distinguished based on the soft X-ray absorption spectra.
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Affiliation(s)
- Yuto Kudo
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Fumitoshi Kumaki
- Department of Materials Structure Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Masanari Nagasaka
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki 444-8585, Japan
| | - Jun-Ichi Adachi
- Department of Materials Structure Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Yoshifumi Noguchi
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Johoku 3-5-1, Hamamatsu, Shizuoka 432-8561, Japan
| | - Nobuaki Koga
- Graduate School of Informatics, Nagoya University, Nagoya 464-8601, Japan
| | - Hideyuki Itabashi
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
- Gunma University Center for Food Science and Wellness, Maebashi, Gunma 371-8510, Japan
| | - Miyabi Hiyama
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
- Gunma University Center for Food Science and Wellness, Maebashi, Gunma 371-8510, Japan
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Nagasaka M. Carbon K-edge x-ray absorption spectra of liquid alcohols from quantum chemical calculations of liquid structures obtained by molecular dynamics simulations. J Chem Phys 2023; 158:024501. [PMID: 36641387 DOI: 10.1063/5.0131017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
For reproducing the carbon K-edge x-ray absorption spectra of liquid alcohols, inner-shell quantum chemical calculations based on the Hartree-Fock method were performed with the snapshots of the liquid structures obtained by molecular dynamics simulations. The C K-edge inner-shell spectrum of liquid ethanol (EtOH) was obtained by the summation of one thousand calculated spectra of EtOH molecules including neighbor EtOH molecules within the CH2-CH2 distance of 6 Å. For the C K-edge inner-shell spectrum of liquid methanol (MeOH), we have calculated one thousand spectra of MeOH molecules including neighbor MeOH molecules within the CH3-CH3 distance of 6 Å. The calculated C K-edge inner-shell spectra of liquid alcohols well reproduced the spectral shapes of the experimentally obtained x-ray absorption spectra and the spectral changes from gas to liquid phases.
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Affiliation(s)
- Masanari Nagasaka
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan and SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki 444-8585, Japan
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