Journal of Computational Chemistry
Journal of Computational Chemistry
4 years ago

Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study

Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study
Rahul Chakraborty, Samik Bose, Debashree Ghosh
Ionization of nucleobases is affected by their biological environment, which includes both the effect of adjacent nucleotides as well as the presence of water around it. Guanine and its nucleotide have the lowest ionization potentials among the various DNA bases. Therefore, the threshold of ionization is dependent on that of guanine and its characterization is crucial to the prediction of interaction of light with DNA. We investigate the effect of solvation on the vertical ionization energies (VIEs) of guanine and its nucleotide. In this work, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) approach with effective fragment potential as the MM method of choice and equation-of-motion coupled-cluster for ionization potential with singles and doubles (EOM-IP-CCSD) as the QM method. The performance of the hybrid scheme with respect to the full QM method shows an accuracy of ≤ 0.02–0.04 eV. The lowest few ionizations of the nucleotide are found to be from different parts of the moiety, that is, the nucleic acid base, phosphate, or sugar, and these ionization energies are very closely spaced giving rise to a very complicated spectrum. Furthermore, microsolvation has large effects on these ionizations and can lead to red or blue shift depending on the position of the water molecule. Even a single water molecule can change the order of ionized states in the nucleotide. The VIEs of the bulk solvated chromophores are predicted and compared to existing experimental spectra. The predominant role of polarization in the solvatochromic shift is noticed. © 2017 Wiley Periodicals, Inc. The ionization energies and their places of origin in gas phase are studied for guanine and its nucleotide. We discuss how they change with solvation. It is found that even one water can change the origin of ionization accentuating the role of short range interactions. We also show the necessity of a hybrid QM/MM approach in estimating the effect of solvation on VIE. We highlight the effect of polarization on these ionizations in solvation.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/jcc.24913

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