The using of the polynomial correction of calculated frequencies for the analysis of the vibrational spectra of uracil and 2-deoxyuridine molecules isolated in the low temperature argon matrices
Keywords:
Nucleosides, FTIR spectroscopy, matrix isolation, Fermi resonance
Abstract
The FT-IR spectra of uracil and 2-deoxyuridine (dU) molecules isolated in low temperature Ar matrices
were obtained in the range of 2400-400 cm-1 with resolution 0.3 cm-1. The vibrational spectra of the main
conformers of these molecules were calculated by quantum-mechanical method DFT/B3LYP. It was
shown that the basis set 6-311++G (df, pd) to give the best agreement of the calculated spectrum with
experiment. The polynomial with least square optimization for uracil have been proposed for the
correction of the frequencies of vibrational spectra of dU. It was established that unlike of the uracil
spectra in the νCО region the splitting of νCО absorption bands of dU are related to the conformers
superposition rather than Fermi resonance.
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References
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4. Iizumi S. First observation of infrared and UV–visible absorption spectra of adenine radical in low-temperature argon matrices / S. Iizumi, S. Ninomiya, M. Sekine, M. Nakata // J. Mol. Struct. – 2012.–V. 1025.– P.43-47.
5. Stepanian S. G. Conformational composition of neutral leucine. Matrix isolation infrared and ab initio study / S. G. Stepanian, A. Yu. Ivanov, L. Adamowicz // Chemical Physics-2013.-V.423- P.20-29.
6. Ivanov, A.Yu. Conformational structures and vibrational spectra of isolated pyrimidine nucleosides: Fourier transform infrared matrix isolation study od 2’-deoxyuridine / A. Yu. Ivanov, S. A. Krasnokutski, G. Sheina, Yu. P. Blagoi // Spectrochimica Acta A. – 2003. – V. 59. – P.1959-1973.
7. Ivanov A. Yu. FTIR spectra and conformations of 2′-deoxyuridine in Kr matrices / A. Yu. Ivanov, V. A. Karachevtsev // Low Temp. Phys. – 2007. – V.33. – P.590-594.
8. Ivanov A. Yu. The peculiarities of conformational structures of 2-deoxyuridine isolated in the low-temperature matrices of Ar and Kr / A. Yu. Ivanov // Low Temp. Phys. – 2008. – V.34. – P.762-769.
9. Жураківський, Р.О. Вичерпний конфірмаційний аналіз 2’-дезоксиуридину квантово-хімчним методом функціоналу густини / Р. О. Жураківський, Д. М. Говорун // Біополімери і клітина. – 2006. – Т. 22. – С.384-389. /Zhurakivs'kyj, R.O. Vycherpnyj konfirmacijnyj analiz 2’-dezoksyurydynu kvantovo-himchnym metodom funkcionalu gustyny / R. O. Zhurakivs'kyj, D. M. Govorun // Biopolimery i klityna. – 2006. – T. 22. – S.384-389./
10. Ivanov A. Yu. FTIR spectroscopy of uracil derivatives isolated in Kr, Ar and Ne matrices: matrix effect and Fermi resonance / A.Yu. Ivanov, A.M. Plokhotnichenko, E.D. Radchenko [et al.] // J. Mol. Struct.-1995.-V.372.-P.91-100.
11. Kovacs A. Vibrational analysis of α-D-glucose trapped in Ar matrix / A. Kovacs, A. Yu. Ivanov // J. Phys. Chem. B. – 2009. – V.113 – P. 2151-2159.
12. Ivanov A. Yu. A low-temperature quartz microbalance / A. Yu. Ivanov, A. M. Plokhotnichenko // Instr. Experim. Techn. – 2009. – V. 52. – P. 308-311.
13. Granovsky A. A. Firefly, version 7.1G / A. A. Granovsky - http://classic.-chem.msu.su/ gran/firefly/ index.html, 2009.
14. General atomic and molecular electronic structure system / M. W. Schmidt, K. K. Baldridge, J. A. Boatz, [et al.] // J. Comput. Chem. – 1993. – V.14. – P. 1347-1363.
15. Saenger W. Principles of nucleic acids structure / W. Saenger - Springer-Verlag, New York, 1984.- 584 p.
16. Irikura, K. Program SYNSPEC / K. Irikura -National Institute of Standards and Technology, Gaithersburg, MD 20899, USA, 1995.
17. Ivanov, A. Yu. Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil / A. Yu Ivanov, Yu. V.Rubin , S. A. Egupov, L. F. Belous, V. A. Karachevtsev // Физика Низких Температур – 2013. – Т. 39. – С. 704-711.
18. Ivanov A. Yu. Tautomeric transitions of isocytosine isolated in argon and neon matrices induced by UV irradiation / A. Yu. Ivanov, S. G. Stepanian, L. Adamowicz // J. Mol. Struct. – 2012 – V. 1025 – P. 92-104.
Cited
How to Cite
Ivanov, A. Y. (1). The using of the polynomial correction of calculated frequencies for the analysis of the vibrational spectra of uracil and 2-deoxyuridine molecules isolated in the low temperature argon matrices. Biophysical Bulletin, 1(29). Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/2324
Section
Molecular biophysics
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