Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

Mateusz Z Brela; Marek Boczar; Leszek M Malec; Marek J Wójcik; Takahito Nakajima

doi:10.1016/j.saa.2018.01.050

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

Spectrochim Acta A Mol Biomol Spectrosc. 2018 May 15:197:194-201. doi: 10.1016/j.saa.2018.01.050. Epub 2018 Jan 31.

Authors

Mateusz Z Brela¹, Marek Boczar¹, Leszek M Malec¹, Marek J Wójcik², Takahito Nakajima³

Affiliations

¹ Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
² Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan. Electronic address: wojcik@chemia.uj.edu.pl.
³ RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.

PMID: 29395929
DOI: 10.1016/j.saa.2018.01.050

Abstract

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

Keywords: 1-Methyluracil and 1-Methyl-4-thiouracil; Ab initio molecular dynamics; Hydrogen bond; Uracil.