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Issue 10, 2020
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Vibrations of the guanine–cytosine pair in chloroform: an anharmonic computational study

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Abstract

We compute at the anharmonic level the vibrational spectra of the Watson–Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500–1700 cm−1) and in the N–H stretching region (2800–3600 cm−1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N–H amido streching mode of G falls at ∼2900 cm−1, while the N–H amino of G and C falls at ∼3100 cm−1 when hydrogen-bonded, or ∼3500 cm−1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm−1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute–solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.

Graphical abstract: Vibrations of the guanine–cytosine pair in chloroform: an anharmonic computational study

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Supplementary files

Article information


Submitted
25 Nov 2019
Accepted
30 Jan 2020
First published
31 Jan 2020

This article is Open Access

Phys. Chem. Chem. Phys., 2020,22, 5509-5522
Article type
Paper

Vibrations of the guanine–cytosine pair in chloroform: an anharmonic computational study

J. A. Green and R. Improta, Phys. Chem. Chem. Phys., 2020, 22, 5509
DOI: 10.1039/C9CP06373K

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