Gas-phase structures of protonated arabino nucleosides

Abstract

Nucleoside modification plays an important role in the native function of DNA and RNA and is also an important synthetic tool for pharmaceuticals. The gas-phase structures of several protonated arabino nucleosides, an important family of modified nucleoside pharmaceuticals, are examined in this work. Infrared multiple photon dissociation action spectra are collected for the protonated forms of the adenine, cytosine, guanine, and uracil arabinosides ([araAdo+H]+, [araCyd+H]+, [araGuo+H]+, and [araUrd+H]+) in the IR fingerprint and hydrogen-stretching regions. Electronic structure calculations are performed to determine low-energy conformers of [araAdo+H]+, [araCyd+H]+, [araGuo+H]+, and [araUrd+H]+, and generate predicted IR spectra for comparison to experiments. Conformers displaying a unique O2′H⋯O5′ hydrogen-bonding interaction are populated in each of these systems. Conformers exhibiting hydrogen-bonding interactions between the nucleobase and O5′ are also found to display good agreement with the measured spectra. Competition between sugar–sugar, and nucleobase–sugar hydrogen bonding reveals a preference for [araCyd+H]+, [araGuo+H]+, and [araUrd+H]+ to stabilize the sugar ring pucker over the nucleobase rotation. N3 protonation of [araAdo+H]+ provides a very strong N3H+⋯O5′ hydrogen-bonding interaction, such that nucleobase–sugar hydrogen-bonding takes energetic preference over stabilization of the sugar puckering. However, conformers exhibiting each mode of hydrogen bonding contribute to the measured spectrum of [araAdo+H]+.