MS10-P01 Frequency and hydrogen bonding geometry of nucleobase homodimers in small molecule crystalsThe issue of various nucleobase pairs and their interactions occurring in RNA and DNA has been already studied from many different perspectives. In this survey, we wanted to approach the subject from more “chemical” point of view and see how nucleobases interact inside crystals. Our study is based on geometric data like bond lengths and bond angles taken from the Cambridge Structural Database (CSD), as well as types of protonation of investigated nucleobase, if the hydrogen positions were available.
We searched for nucleobase homodimers resembling those found in RNA and DNA, which means two nucleobases interacting through at least two hydrogen bonds formed in the molecule plane. The investigated compound were derivatives of adenine, guanine, hypoxanthine, thymine, uracil, and cytosine. We divided our findings into many categories including types of dimers, their protonation and if the N9 or N1 (for purines and pyrimidines respectively) is substituted with only hydrogen or larger substituent that may influence the way the nucleobase forms dimers. In our study, we analyze the various dependencies between the geometry of the molecule and what types of structures it prefers to form. We investigated not only neutral forms of nucleobases, but protonated too, and analyzed how protonation and charge influence the ability of a molecule to form homodimers.
Our study finds that for purines the most active edge is Hoogsten edge, taking part in the formation of dimers found in more than half of the investigated structures. Mixed interactions between the Hoogsteen edge and Watson-Crick edge are also very common, as they allow the molecules to align into infinite ribbons.
For pyrimidines, the situation is much different, as the various possible interactions between Watson-Crick edges of molecules dominate the charts. Only uracil behaves differently from thymine and cytosine, as it eagerly forms trans Watson-Crick - Hoogsten interaction, namely the Calcutta dimer.
For all nucleobases, there is a common trend of sugar edge interactions being more frequent if the molecule is substituted with hydrogen in N9 or N1.
Fig. 1. Examples of homodimers of adenine and cytosine, with the naming of the edges.References:
Keywords: nucleobases, hydrogen bonding