Quantum chemical profiling of the electronic structure and hydrolytic stability of modified ribonucleosides

Abstract

Chemical modifications to RNA play essential roles in regulating structure, stability, and biological function, yet a unifying physicochemical framework for understanding how these structural modifications perturb the underlying electronic landscape and influence intrinsic reactivity remains lacking. Here, we apply density functional theory to compute electronic-structure descriptors for a comprehensive set of naturally occurring modified ribonucleosides. By analyzing HOMO–LUMO gaps as measures of global electronic softness and Wiberg bond indices as local descriptors of glycosidic bond strength, we establish systematic relationships linking stereoelectronic substitution patterns and nucleobase π-conjugation to molecular reactivity and hydrolytic stability. We find that sulfur and selenium incorporation and major-groove substitutions tend to narrow HOMO–LUMO gaps and weaken glycosidic bonds, whereas C-glycosides (as in pseudouridines) confer electronic stabilization. These results reveal physical principles governing the intrinsic reactivity of modified RNA building blocks and provide a predictive framework for anticipating modification-dependent behavior relevant to RNA stability, degradation, and next-generation sequencing technologies used to characterize the epitranscriptome.