Aqueous Contact Ion Pairs of Phosphate Groups with Na$^+$, Ca$^{2+}$ and Mg$^{2+}$ -- Structural Discrimination by Femtosecond Infrared Spectroscopy and Molecular Dynamics Simulations

Abstract

The extent of contact and solvent shared ion pairs of phosphate groups with Na$^+$, Ca$^{2+}$ and Mg$^{2+}$ ions in aqueous environment and their relevance for the stability of polyanionic DNA and RNA structures is highly debated. Employing the asymmetric phosphate stretching vibration of dimethyl phosphate (DMP), a model system of the sugar-phosphate backbone of DNA and RNA, we present linear infrared, femtosecond infrared pump-probe and absorptive 2D-IR spectra that report on contact ion pair formation via the presence of blue shifted spectral signatures. Compared to the linear infrared spectra, the nonlinear spectra reveal contact ion pairs with increased sensitivity because the spectra accentuate differences in peak frequency, transition dipole moment strength, and excited state lifetime. The experimental results are corroborated by long time scale MD simulations, benchmarked by density functional simulations on phosphate-ion-water clusters. The microscopic interpretation reveals subtle structural differences of ion pairs formed by the phosphate group and the ions Na$^+$, Ca$^{2+}$ and Mg$^{2+}$. Intricate properties of the solvation shell around the phosphate group and the ion are essential to explain the experimental observations. The present work addresses a challenging to probe topic with the help of a model system and establishes new experimental data of contact ion pair formation, thereby underlining the potential of nonlinear 2D-IR spectroscopy as an analytical probe of phosphate-ion interactions in complex biological systems.