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

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.