The conformational structure of adenosine molecules, isolated in low-temperature Ar matrices

Abstract

FTIR spectra of adenosine (Ado) molecules, isolated in low-temperature matrices, are obtained in the infrared range of 3800–400 cm−1, with a resolution of 0.3. MP2 and DT/B3LYP quantum-mechanical methods are used to calculate the population of major structural Ado isomers. It is shown that Ado can withstand prolonged evaporation at a temperature of 465 K without thermal decomposition. The structure five major conformers that are fixed in Ar matrices at 6 K, are established. Ado anti-conformers with intramolecular hydrogen bonds O2′H-N3, are found. The population of these anti-conformers is more than one and a half times less than the syn-conformer population having the intramolecular hydrogen bond O5′H-N3. In low-temperature matrices, the majority of the dominant conformers are fixed with a C2′-endo ribose ring structure. Similar to 2′-deoxyadenosine (dA), Ado conformers with intramolecular hydrogen bonds O3′H-O5 or O5′H-O3 were not found.

Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields

“…The global minima adopted in this work are the ones described in the papers by Ivanov. This is true for all molecules with the exception of deoxyguanosine, which is reported in one paper by Saigusa. − In Figure the minimum geometries predicted by DFT B3LYP/6-31G* ab initio calculations are reported. For brevity, we report here only the DFT minimum structures while the AMBER and AMOEBA ones can be found in the SI.…”

“…The necessity to sample a larger portion of the phase space is certainly more compelling when experiments are performed at room temperature. For the investigated nucleosides the benchmark experimental values have been obtained at very low temperature (6–12 K) − and, even if we cannot rule out that several low-energy conformers might have been populated in the experiment, supported by results we deem that our semiclassical estimates derived from trajectories started at the global minimum provide accurate comparisons to the experiments.…”

“…All these systems have been experimentally studied in the gas phase in recent years. Specifically, thymidine, uridine, and adenosine have been investigated in argon matrices by the Ivanov group, while a comprehensive study of deoxyguanosine isolated and in mono- and dihydrated clusters has been performed by the Saigusa group. − The presence of such experimental data gives us a precise benchmark for our calculations, since an exact quantum theoretical estimation is out of reach for molecular systems of this size.…”

Nucleoside conformers in low-temperature argon matrices: Fourier transform IR spectroscopy of isolated thymidine and deuterothymidine molecules and quantum-mechanical calculations

“…Using this scenario, we studied a number of pyrimidine and purine nucleosides (2 0 -deoxyuridine, 15-17 uridine 18 2 0 -deoxyadenosine, 19 and adenosine. 20 In this work, special attention was paid to the analysis of individual fragments of the potential energy surface and calculation of the height of barriers between the main thymidine conformers using the DFT/B3LYP and MP2 methods. To reach a more accurate interpretation of experimental infrared absorption spectra, the spectra of O5 0 -,O3 0 -, N3-deuterothymidine molecules isolated in Ar matrices were also measured.…”

Role of the Hydrogen Bond on the Internal Conversion of Photoexcited Adenosine

“…Adenosine in the gas phase has multiple conformers. 24 We worked on two of them: a syn conformer with a hydrogen bond and an anti conformer without it. We do not expect these two conformers to be particularly relevant for DNA.…”