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. Display omitted •Spectroscopic features of uracil and methylated derivatives suggest different hydrogen bond networks in the crystal phase.•Power spectra obtained from molecular dynamics simulations reflect the strengths of hydrogen bonds.•Methylation of uracil ring creates the cyclic dimer structures.•Presence of sulfur atoms instead of oxygen atoms reflects the weakness of hydrogen bonds that form dimers.