Ab Initio Comprehensive Conformational Analysis of 2‘-Deoxyuridine, the Biologically Significant DNA Minor Nucleoside, and Reconstruction of Its Low-Temperature Matrix Infrared Spectrum
| ISSN: | 1520-5207 1520-6106 |
|---|---|
| Přístupová URL adresa: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4a1fa2448080938d6125827917a94a35 https://doi.org/10.1021/jp074747o |
| Přírůstkové číslo: | edsair.doi.dedup.....4a1fa2448080938d6125827917a94a35 |
| Autor: | Roman O. Zhurakivsky, Dmytro M. Hovorun, Yevgen P. Yurenko, Mahmoud Ghomi, S. P. Samijlenko |
| Rok vydání: | 2007 |
| Předmět: |
Models
Molecular Spectrophotometry Infrared Stereochemistry Population Molecular Conformation Ab initio Infrared spectroscopy Crystallography X-Ray Vibration Ab initio quantum chemistry methods Materials Chemistry Physical and Theoretical Chemistry education Conformational isomerism education.field_of_study Hydrogen bond Chemistry Temperature Computational Biology Water Hydrogen Bonding DNA Deoxyuridine Surfaces Coatings and Films Oxygen Crystallography Intramolecular force Valence bond theory |
| Zdroj: | The Journal of Physical Chemistry B. 112:1240-1250 |
| ISSN: | 1520-5207 1520-6106 |
| Popis: | A comprehensive conformational analysis of isolated 2'-deoxyuridine (dU), a minor DNA nucleoside, has been performed by means of ab initio calculations at the MP2/6-311++G (d,p)//DFT B3LYP/6-31G (d,p) level of theory. At 298.15 and 420 K, all 94 allowed conformers of dU are within 8.96 and 7.91 kcal/mol Gibbs energy ranges, respectively. Syn orientation for the base and South (S) conformers for the sugar dominate at 298.15 K: syn/anti=62.3%:37.7% and S/N=77.2%:22.8%. At 420 K in the majority of conformers, the base is anti oriented and the population of North (N) sugars increases: syn/anti=39.3%:60.7% and S/N=63.0%:37.0%. Values of all conformational parameters and correlations between them, as well as their correlations with valence bonds, and also correlations between valence bonds and angles were estimated. In general, 14 types of intramolecular H-bonds were detected (1-3 H-bonds per conformer, the total number 175), namely, C1'H...O2 (16 H-bonds), C2'H1...O5' (9), C2'H2...O2 (21), C3'H...O2 (21), C5'H1...O2 (14), C5'H2...O2 (11), C6H...O4' (37), C6H...O5' (22), C3'H...HC6 (4), O5'H...HC6 (2), O3'H...O5' (5), O5'H...O4' (1), O5'H...O3' (4), and O5'H...O2 (8). Geometric, vibrational, structural-topological, and energetic features of the OH...O intramolecular H-bonds in dU conformers were determined. The close similarity between energetic and geometric characteristics of dU and thymidine DNA-like conformers in anti and relevant syn conformations and their transition states of the anti-->syn interconversion implies that mismatch DNA glycosylase discriminates between the two nucleosides, mainly because of the difference in the shapes of their bases. Convolution of calculated IR spectra of all the dU conformers within the limits 3400-3700 cm(-1) appears to be consistent with its low-temperature matrix IR spectrum (Ivanov et al. Spectrochim. Acta, Part A 2003, 59, 1959), wavenumber discrepancy not exceeding 1%. It was concluded that, for a reliable reproduction of the experimental spectrum, the whole set of conformers should be taken into consideration. The suggested method makes reconstruction of the isolated nucleoside IR spectrum at a physiological interval of temperature reasonably possible. |
| Databáze: | OpenAIRE |
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