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

Abstract

The conformational equilibrium of thymidine and deuterothymidine molecules in low-temperature Ar matrices has been studied using low-temperature matrix-isolation Fourier IR spectroscopy and quantum-chemical calculations by the DFT/B3LYP and MP2 methods. It has been found that two anti-conformers ta2_0 and ta3_0 with different structures of the sugar ring, C2 0 -endo and C3 0 -endo, predominate in low-temperature matrices. In isolated state, each of these conformers has a few low-barrier satellites that can fully pass into more stable structures when a molecule enters the matrix. The main syn conformer ts2_0 is stabilized by an intramolecular hydrogen bond between the O5 0 H group of the sugar and the C2O group of the base (O5 0 H⋅⋅⋅O2), while C2 0 -endo is the predominant conformation of the deoxyribose ring. The considerably lower population of ts2_0 compared to the anti-conformers ta2_0, ta3_0 can be explained by the smaller population of satellite conformations. It has been shown that the absorption band of νN3D stretching vibration is split by the Fermi resonance.

Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields

“… Same as Figure 3 , for the 1350–1950 cm –1 frequency region of thymidine. The experimental results come from ref ( 52 ). …”

“…The potential energy surface of the investigated nucleosides is characterized by many low-energy conformers in addition to the global minimum one. 52 We have presented semiclassical simulations based on a short-time dynamics (less than 1 ps long) initiated at the global minimum. Adoption of a much longer dynamics is not a viable route in semiclassical calculations not only because of computational costs but also because the semiclassical propagator loses rather quickly its unitarity and ability to reproduce quantum effects.…”

“…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.…”

Spectral and structural features of bio-composite films of graphene oxide and molybdenum disulphide with molecules of 5-bromouracyl and 5-bromo-2’-deoxyuridine

“…Для 5BrU мы рассматривали только дикето-форму, как доминирующую структуру для изолированного состояния молекулы [21]. Расчеты показали, что относительные энергии и заселенность конформационных изомеров 5BrdU достаточно близки к параметрам аналогичных изомеров, рассмотренных нами для 2'-дезокси-уридина и тимидина [13,14,22]. Наиболее характерные представители син-и анти-подмножеств конформационных изомеров 5BrdU показаны на Рис.…”

Quantum Vibrational Spectroscopy of Explicitly Solvated Thymidine in Semiclassical Approximation

“…In particular, we could analyze the C4O and C5C6 stretchings (see Figure 1 for the atom numbering employed) that are also detected by the gas phase experiment. 51 …”