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Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine.

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Title: Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine.
Authors: Katsyuba, Sergey A.1 (AUTHOR) skatsyuba@yahoo.com, Burganov, Timur I.1 (AUTHOR)
Source: Spectrochimica Acta Part A: Molecular & Biomolecular Spectroscopy. Mar2024, Vol. 309, pN.PAG-N.PAG. 1p.
Subjects: Thymine, Nucleic acids, Raman spectroscopy, Vibrational spectra, Spectrometry, Hydrogen bonding
Abstract: [Display omitted] • A cluster model of a solute surrounded by 30 water molecules allows reproducing experimental Raman spectra of aqueous thymine. • B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ computations are sufficient for the above purpose. • The strong effect of water on vibrational spectra of thymine is mainly a result of hydrogen bonding with 6 nearest water molecules. As in the case of cytosine [Phys. Chem. Chem. Phys. 2023 , 25 , 24121–24128], Raman and infrared (IR) spectra of aqueous thymine and its N-deuterated derivative, thymine-d 2 have been computationally reproduced and interpreted with the use of the recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions [ J. Phys. Chem. B , 2020 , 124 , 6664–6670]. A cluster model of a solute surrounded by 30 water molecules is shown to be sufficient to reproduce experimental vibrational frequencies and relative Raman intensities with the use of B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ simulations. Analogous PBE-D3 computations provided a less good, but still reasonably accurate, modeling of Raman spectra. It is shown that strong changes of frequencies and relative intensities of the Raman bands of thymine, caused by its hydration, can be interpreted mainly as a result of hydrogen bonding with 6 nearest water molecules. Non-negligible improvement of the quality of simulations for larger clusters comprising water molecules that do not have direct contacts with the solute, suggests that spectroscopic effects of hydration should be ascribed to the joined action of solute–solvent and solvent–solvent interactions. Nevertheless, the moderate number of water molecules required for successful simulations of the Raman spectra of aqueous thymine, suggests that the vibrational modes and derivatives of the polarizability of the solute are mainly locally influenced, while the effect of bulk water is rather modest. [ABSTRACT FROM AUTHOR]
Copyright of Spectrochimica Acta Part A: Molecular & Biomolecular Spectroscopy is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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DbLabel: Engineering Source
An: 174951389
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  Data: Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine.
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  Data: <searchLink fieldCode="AR" term="%22Katsyuba%2C+Sergey+A%2E%22">Katsyuba, Sergey A.</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> skatsyuba@yahoo.com</i><br /><searchLink fieldCode="AR" term="%22Burganov%2C+Timur+I%2E%22">Burganov, Timur I.</searchLink><relatesTo>1</relatesTo> (AUTHOR)
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  Data: <searchLink fieldCode="JN" term="%22Spectrochimica+Acta+Part+A%3A+Molecular+%26+Biomolecular+Spectroscopy%22">Spectrochimica Acta Part A: Molecular & Biomolecular Spectroscopy</searchLink>. Mar2024, Vol. 309, pN.PAG-N.PAG. 1p.
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  Data: <searchLink fieldCode="DE" term="%22Thymine%22">Thymine</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleic+acids%22">Nucleic acids</searchLink><br /><searchLink fieldCode="DE" term="%22Raman+spectroscopy%22">Raman spectroscopy</searchLink><br /><searchLink fieldCode="DE" term="%22Vibrational+spectra%22">Vibrational spectra</searchLink><br /><searchLink fieldCode="DE" term="%22Spectrometry%22">Spectrometry</searchLink><br /><searchLink fieldCode="DE" term="%22Hydrogen+bonding%22">Hydrogen bonding</searchLink>
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  Data: [Display omitted] • A cluster model of a solute surrounded by 30 water molecules allows reproducing experimental Raman spectra of aqueous thymine. • B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ computations are sufficient for the above purpose. • The strong effect of water on vibrational spectra of thymine is mainly a result of hydrogen bonding with 6 nearest water molecules. As in the case of cytosine [Phys. Chem. Chem. Phys. 2023 , 25 , 24121–24128], Raman and infrared (IR) spectra of aqueous thymine and its N-deuterated derivative, thymine-d 2 have been computationally reproduced and interpreted with the use of the recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions [ J. Phys. Chem. B , 2020 , 124 , 6664–6670]. A cluster model of a solute surrounded by 30 water molecules is shown to be sufficient to reproduce experimental vibrational frequencies and relative Raman intensities with the use of B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ simulations. Analogous PBE-D3 computations provided a less good, but still reasonably accurate, modeling of Raman spectra. It is shown that strong changes of frequencies and relative intensities of the Raman bands of thymine, caused by its hydration, can be interpreted mainly as a result of hydrogen bonding with 6 nearest water molecules. Non-negligible improvement of the quality of simulations for larger clusters comprising water molecules that do not have direct contacts with the solute, suggests that spectroscopic effects of hydration should be ascribed to the joined action of solute–solvent and solvent–solvent interactions. Nevertheless, the moderate number of water molecules required for successful simulations of the Raman spectra of aqueous thymine, suggests that the vibrational modes and derivatives of the polarizability of the solute are mainly locally influenced, while the effect of bulk water is rather modest. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Spectrochimica Acta Part A: Molecular & Biomolecular Spectroscopy is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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RecordInfo BibRecord:
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      – Type: doi
        Value: 10.1016/j.saa.2023.123832
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      – Code: eng
        Text: English
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        PageCount: 1
        StartPage: N.PAG
    Subjects:
      – SubjectFull: Thymine
        Type: general
      – SubjectFull: Nucleic acids
        Type: general
      – SubjectFull: Raman spectroscopy
        Type: general
      – SubjectFull: Vibrational spectra
        Type: general
      – SubjectFull: Spectrometry
        Type: general
      – SubjectFull: Hydrogen bonding
        Type: general
    Titles:
      – TitleFull: Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine.
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            NameFull: Katsyuba, Sergey A.
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            NameFull: Burganov, Timur I.
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            – D: 15
              M: 03
              Text: Mar2024
              Type: published
              Y: 2024
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