Comparison of the Hydrogen Bond Interaction Dynamics in the Guanine and Cytosine Crystals: Ab Initio Molecular Dynamics and Spectroscopic Study

Mateusz Z Brela; Oskar Klimas; Ewa Surmiak; Marek Boczar; Takahito Nakajima; Marek J Wójcik

doi:10.1021/acs.jpca.9b09655

Comparison of the Hydrogen Bond Interaction Dynamics in the Guanine and Cytosine Crystals: Ab Initio Molecular Dynamics and Spectroscopic Study

J Phys Chem A. 2019 Dec 19;123(50):10757-10763. doi: 10.1021/acs.jpca.9b09655. Epub 2019 Dec 5.

Authors

Mateusz Z Brela¹, Oskar Klimas¹, Ewa Surmiak¹, Marek Boczar¹, Takahito Nakajima², Marek J Wójcik^{1

2}

Affiliations

¹ Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Kraków , Poland.
² RIKEN, Advanced Institute for Computational Science , 7-1-26, Minatojima-minami-machi , Chuo-ku, Kobe , Hyogo 650-0047 , Japan.

PMID: 31735026
DOI: 10.1021/acs.jpca.9b09655

Abstract

In this work, we present the comparison study of guanine and cytosine crystals based on the hydrogen bond (HB) dynamics. The ab initio molecular dynamics gave us a base for detailed analysis. The analysis of the trajectories by power spectrum generation, as well as the fluctuation of the interaction energies, showed large differences between HB networks in the considered crystals. The charge flow is present in the guanine molecule which forms the flat surfaces in the crystals. In the cytosine zigzag structure, the charge flow is blocked. The interaction energy is significantly less stabilizing in the cytosine structure than in the guanine. Finally, the possible influence of charge transfer on the melting temperature has been discussed.