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Simulation of the Resonance Raman Spectra for 5-Halogenated (F, Cl, and Br) Uracils

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Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
*E-mail: [email protected]. Phone: +01 (780) 492-1854. Fax: +01 (780) 492-8231.
Cite this: J. Phys. Chem. A 2015, 119, 17, 3961–3971
Publication Date (Web):April 9, 2015
https://doi.org/10.1021/acs.jpca.5b01052
Copyright © 2015 American Chemical Society

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    Abstract

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    The resonance Raman spectra of the 5-halogenated (F, Cl, and Br) uracils are simulated via the Herzberg–Teller (HT) short-time dynamics formalism. The gradient of the S1 excited state is computed at the CAMB3LYP/aug-cc-pVTZ level of theory in the conductor-like polarizable continuum model for water (C-PCM, H2O), based on the equilibrium geometry determined using PBE0/aug-cc-pVTZ in H2O (C-PCM). The simulated resonance Raman spectra show good agreement with the experimental spectra in terms of both peak positions and intensities. The differences between the resonance Raman spectra of the three 5-halogenated uracils, caused by the effect of halogen substitution, are examined in terms of ground-state normal-mode eigenvectors and excited-state Cartesian gradients, according to the HT formalism. The differences in the normal-mode eigenvectors and excited-state Cartesian gradients between 5-fluorouracil and 5-chlorouracil are used to interpret the dissimilarity between their resonance Raman spectra. Meanwhile, the similarity between the spectra of 5-chlorouracil and 5-bromouracil is explained by the correspondence between their normal modes and excited-state gradients.

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    The optimized geometries of the 5-halogenated uracils; the vibrational frequencies, PED analysis, and corresponding normal-mode displacements of modes 8–27 of the 5-halogenated uracils; and the cosine similarity for the corresponding normal modes, resonance Raman spectra for different excitation energies, and resonance Raman spectrum for the experimental displacements. This material is available free of charge via the Internet at http://pubs.acs.org.

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    Cited By

    This article is cited by 9 publications.

    1. Sayan Mondal, Chandrabhas Narayana. Role of Explicit Solvation in the Simulation of Resonance Raman Spectra within Short-Time Dynamics Approximation. The Journal of Physical Chemistry B 2019, 123 (41) , 8800-8813. https://doi.org/10.1021/acs.jpcb.9b07471
    2. Mónica B. Mamián-López, Marcia L. A. Temperini. On the Cooperativity Effect in Watson and Crick and Wobble Pairs for a Halouracil Series and Its Potential Quantitative Application Studied through Surface-Enhanced Raman Spectroscopy. Analytical Chemistry 2018, 90 (24) , 14165-14172. https://doi.org/10.1021/acs.analchem.8b02188
    3. Sayan Mondal and Mrinalini Puranik . Ultrafast Nuclear Dynamics of Photoexcited Guanosine-5′-Monophosphate in Three Singlet States. The Journal of Physical Chemistry B 2017, 121 (29) , 7095-7107. https://doi.org/10.1021/acs.jpcb.7b05735
    4. Mozhdeh Mohammadpour and Zahra Jamshidi . Effect of Chemical Nature of the Surface on the Mechanism and Selection Rules of Charge-Transfer Surface-Enhanced Raman Scattering. The Journal of Physical Chemistry C 2017, 121 (5) , 2858-2871. https://doi.org/10.1021/acs.jpcc.6b12069
    5. Fenghua Chen, Jie Fan, Xiuzhi Chen, Yanping Li, Chengfeng Liang, Shizhao Ren, Rongrong Xue. Polymorph control of 5-fluorouracil during a ball milling process. CrystEngComm 2021, 23 (46) , 8027-8032. https://doi.org/10.1039/D1CE01211H
    6. E. Akalin, S. Celik, S. Akyuz. Molecular Modeling, Dimer Calculations, Vibrational Spectra, and Molecular Docking Studies of 5-Chlorouracil. Journal of Applied Spectroscopy 2020, 86 (6) , 975-985. https://doi.org/10.1007/s10812-020-00926-2
    7. Shuai Sun, Alex Brown. Effects of hydrogen bonding with H2O on the resonance Raman spectra of uracil and thymine. Computational and Theoretical Chemistry 2017, 1100 , 70-82. https://doi.org/10.1016/j.comptc.2016.12.014
    8. Mozhdeh Mohammadpour, Zahra Jamshidi. Comparative assessment of density functional methods for evaluating essential parameters to simulate SERS spectra within the excited state energy gradient approximation. The Journal of Chemical Physics 2016, 144 (19) https://doi.org/10.1063/1.4948813
    9. Sayan Mondal, Mrinalini Puranik. Sub-50 fs excited state dynamics of 6-chloroguanine upon deep ultraviolet excitation. Physical Chemistry Chemical Physics 2016, 18 (20) , 13874-13887. https://doi.org/10.1039/C6CP01746K

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