Molecular structure and vibrational spectra of isolated nucleosides at low temperatures (Review article)

Abstract

The application of various action spectroscopy and absorption spectroscopy methods for studying the structure of biological molecules and their constituent fragments in an isolated state is considered. The main attention is paid to the results achieved in the study of the nucleosides which are the structural units of DNA and RNA. It has been demonstrated that modern low-temperature spectroscopy methods allow registration the vibrational spectra of isolated nucleosides in neutral or ionized form. It was shown that most of the nucleosides can be converted into the gas phase by prolonged evaporation from the Knudsen cell without thermal decomposition. Cooling molecules to cryogenic temperatures plays an important role in these studies. The conformational equilibrium of the gas phase between syn and anti subsets of nucleosides is maintained due to fast cooling when frozen in inert matrices. Within these subsets, interconversion processes between conformers can occur during cooling if the conformers are separated by low energy barriers. In inert gas matrices at 6 K, subsets of the syn-conformers of deoxyribonucleosides are mainly frozen with the C2′-endo structure of the deoxyribose ring. The structures of molecular ions of nucleosides are very different from their neutral forms. In particular protonation leads to the domination of the enol forms of thymidine, as well as syn-conformations of adenosine, stabilized by the intramolecular hydrogen bond N3H+•••O5.

Infrared Spectroscopy of RNA Nucleosides in a Wide Range of Temperatures

“…There are several works on the infrared spectroscopy on the purine nucleosides adenosine (Ado) and guanosine (Guo) (see Scheme 1 for the chemical structures) mainly made with the purpose of bands assignment, base pairing, hydrogen bonding, and as a key step toward the understanding of the infrared spectra of the nucleotides, polynucleotides, and RNA. Without aiming to be comprehensive, we mention a selection of papers dealing with the spectroscopy of purine nucleosides [21][22][23][24][25][26][27][28][29]. The primary objective of this study is to provide the astrophysics and astrochemistry/astrobiology community with the midinfrared spectra of purine nucleosides (Figures 1 and 2, Tables 1 and 2) as a means of potentially identifying these compounds in condensed form in space.…”

Matrix-formation dynamics dictate methyl nitrite conformer abundance

“…42,[46][47][48] For molecules with higher interconversion barriers similar to that seen in CH3ONO, there are typically no significant changes in the conformer abundance between the gas and matrix phases. 15,19,[49][50][51] The complex dynamics of the matrix-formation process and subsequent diffusion of molecules on the surface of a growing matrix are rarely discussed as contributing factors in possible differing conformer abundances between the gas and matrix phases. Theoretical and experimental work focusing on the sticking dynamics, energy transfer, and angle dependence of deposition are typically confined to atoms and molecules sticking to a metal surface or molecular ices, not on inert matrices.…”