biostudies-literatureKolev SKMinistry of Education and ScienceEuropean Science FoundationEuropean Regional Development Fund23234-23244https://www.ebi.ac.uk/biostudies/studies/S-EPMC9280761biostudies-literatureUnknown7(27)The interactions between Na⁺ or Mg²⁺ ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg²⁺ ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na⁺ ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na⁺ ions and 5.5 oxygen atoms for solvated Na⁺ ions. In contrast, the inner solvation shell of Mg²⁺ ions was stable in both RNA-bonded and completely solvACS omegaSodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: <i>Ab Initio</i> Molecular Dynamics in Water Solution.PMC9280761D01-76/30.03.2021BG05M2OP001-1.001- 0004 C01Milenov TIKolev SKVayssilov GNSt Petkov PfalseSodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: <i>Ab Initio</i> Molecular Dynamics in Water Solution.The interactions between Na⁺ or Mg²⁺ ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg²⁺ ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na⁺ ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na⁺ ions and 5.5 oxygen atoms for solvated Na⁺ ions. In contrast, the inner solvation shell of Mg²⁺ ions was stable in both RNA-bonded and completely solv2022-01-01T00:00:00Z2022 Jul2026-05-09T18:09:17.407Z2022-07-19T09:20:55.139ZS-EPMC92807613584726210.1021/acsomega.2c01327