On the Prebiotic Selection of Nucleotide Anomers: Computational Data

The data generated for this article are obtained from computational quantum chemistry. The data consist of raw total molecular energies, zero-point energy-corrected molecular energies, and Gibbs energies, all obtained from the Density Functional Theory (DFT) calculations with the commonly used DFT functional B3LYP and the Pople-style basis set 6-31G(d,p). The calculated data include two sets obtained in parallel and contrasted: A vacuum (gas) phase set and corresponding calculations performed with implicit aqueous solvation implemented through the self-consistent reaction field (SCRF) polarizable continuum model (PCM) using the integral equation formalism variant (IEFPCM) as implemented in the Gaussian 16 suite of programmes. The calculations give the energy differences between the α-anomers and the corresponding β-anomers of the canonical nucleosides and nucleotides as well as compares different hypothetical reaction paths that lead to the present-day nucleosides/nucleotides assembled from their three building blocks, namely, the sugar, the phosphate, and the nitrogenous base. A comparison is also given for the relative energies of the uracil (U) and thymine (T) nucleosides/nucleotides in their canonical forms contrasted with their form that is not generally observed in biological systems, that is, where T is linked to a ribose sugar and U to a deoxyribose sugar. This data can form the nucleus for a much larger database that includes non-canonical bases, sugars, and even linkers (different sugars, or linkers other than sugars e.g. peptide links) in an effort to pin-down the thermodynamics that led to the observed present day selection of the particular forms of these nucleic acid building blocks. Machine learning may be used in the future on such an enlarged dataset to estimate the relative stabilities of synthetic nucleoside/nucleotides that could perhaps be used in molecular medicine applications.