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arXiv · 2108.11379

Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions

Thomas Elsaesser·Jakob Schauss·Achintya Kundu·Benjamin P. Fingerhut
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Abstract

Electric interactions have a strong impact on the structure and dynamics of biomolecules in their native water environment. Given the variety of water arrangements in hydration shells and the femto- to subnanosecond time range of structural fluctuations, there is a strong quest for sensitive noninvasive probes of local electric fields. The stretching vibrations of phosphate groups, in particular the asymmetric (PO2)- stretching vibration νAS(PO2)-, allow for a quantitative mapping of dynamic electric fields in aqueous environments via a field-induced redshift of their transition frequencies and concomitant changes of vibrational line shapes. We present a systematic study of νAS(PO2)- excitations in molecular systems of increasing complexity, including dimethyl phosphate (DMP), short DNA and RNA duplex structures, and transfer RNA (tRNA) in water. A combination of linear infrared absorption, two-dimensional infrared (2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives quantitative insight in electric-field tuning rates of vibrational frequencies, electric field and fluctuation amplitudes, and molecular interaction geometries. Beyond neat water environments, the formation of contact ion pairs of phosphate groups with Mg2+ ions is demonstrated via frequency upshifts of the νAS(PO2)- vibration, resulting in a distinct vibrational band. The frequency positions of contact geometries are determined by an interplay of attractive electric and repulsive exchange interactions.

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Thomas Elsaesser, Jakob Schauss, Achintya Kundu, Benjamin P. Fingerhut. 2021-08-25. Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions. https://doi.org/10.1021/acs.jpcb.1c01502

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