A combined computational and NMR-spectroscopic approach for tautomer elucidation under extreme conditions towards investigating the robustness of genetic codes

Abstract

The goal of this work was to establish a combined computational and experimental workflow for the prediction of tautomeric ratios of small molecules in solution under various environmental conditions. Quantum chemical (QC) calculations using the embedded cluster reference interaction site model (EC-RISM), which takes into account the solvent structure and the mutual polarization of solute and solvent and is able to incorporate environmental effects via appropriate correction terms, form the computational part of this workflow, NMR experiments the experimental part. Benchmarking of EC-RISM for the prediction of tautomeric ratios was performed using the SAMPL2 dataset and histamine, for which the workflow was extensively tested at ambient conditions and used to identify the nuclei most sensitive to tautomerism. This system was also used to develop an EC-RISM based force field (FF) reparametrization workflow. A temperature-dependent correction term for EC-RISM was developed, benchmarked, and used in conjunction with a pressure-dependent correction term to calculate NMR chemical shifts. Various computational NMR referencing methods were developed using reference shielding constants of trimethylsilylpropanesulfonate (DSS) and ammonia and their performance was tested on N-methyl-acetamide (NMA) and trimethylamine-N-oxide (TMAO). The tautomeric ratios of nucleobases were calculated at different pressures and temperatures for the natural species and the hachimoji expanded genetic alphabet. Initial steps were also taken towards the prediction of the tautomeric ratios of larger nucleic acid building blocks such as nucleotides.