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Studies of molecular structures and spectral characteristics of biopolymer components – nucleic acid bases,
nucleosides and amino acids as well as nanodimensional components on their base, isolated in low temperature matrices of inert gases,
by IR Fourier and UV spectroscopy and by quantum-chemical calculations
Scientists elaborating the theme:
Stepanian S.G., Senior researcher, Candidate in Physics and Mathematics;
Ivanov A.Yu., Senior researcher, Candidate in Physics and Mathematics;
Plokhotnichenko A.M., Research worker, Candidate in Physics and Mathematics
The main scientific directions:
- Studies on molecular structures of isolated DNA fragments (pyrimidine and purine bases of nucleic acids, nucleosides), of proteins (amino acids) and various biologically active molecules (monosaccharides, drugs)
- Determination of spectral and structural characteristics of complexes formed by biopolymer fragments and by bioactive molecules and atoms
- The advancement of experimental methods for obtaining isolated biomolecules and their spectral studying as well as methods of forming nanosized complexes at low temperatures.
The most important (substantial) scientific results obtained by group scientists:
- For the first time, spectral and structural parameters have been revealed for some nucleosides, ribose and deoxyribose and neutral forms of aliphatic amino acids.
- Information has been obtained on the concurrence between two types of intermolecular interactions – hydrogen binding and stacking – upon the formation of dimmers of nucleic acid bases.
- By ab initio quantum chemical methods, spatial structures of the above biopolymer components and the conformational constitution of the biopolymer components have been determined.
Equipment and methods
- 1. Vacuum (up to 0.1 Torr) single-beam IR Fourier spectrometer (0.1 cm-1 apodized resolution) equipped
with the cryogenic vacuum device (Fig. 1), based on the small-sized liquid helium cryostat P118 (B.I. Verkin ILTPE production).
This equipment is used in studies on high-resolution vibrational spectra of bioorganic molecules and their complexes in inert gas matrices
at wide temperature (5-40 K) and frequency range ( 10000-10 cm-1). To control the intensity of molecular beams and the matrix composition,
the low temperature block is equipped with low temperature differential quartz microbalances.
The cryovacuum chamber construction permits to mount optical devices for UV irradiation of low temperature matrices (Fig. 1)
and an additional chamber for simultaneous evaporation of metals and biomolecules (Fig. 2).
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- IR and UV-spectrometers for studying absorption spectra of solutions and gases in the frequency range 50000-400 cm-1
- The setup on the base of VUP-5Ì post (10-7 Torr vacuum) is applied for obtaining films by the methods of
- thermal evaporation (up to 3000îÑ),
- cathode beam evaporation,
- magnetron sputtering
To control the film thickness upon its growth, the setup is equipped with quartz microbalances.
It is possible to irradiate the film upon its growth by ultraviolet lamp light or by laser.
- Scientists of the group calculate structural and thermodynamic parameters of biomolecules and their intermolecular complexes
by nonempirical methods (HF, MP2, MP4, QCISD, CC) and vibrational spectra to harmonic and inharmonic approximations.
- The works are carried out in close cooperation with scientists of Laboratory of Theoretical Computational Chemistry, Arizona University (Tucson, USA) (The head is Pr. L. Adamowich).
The main latest publications are the following:
- Blagoi Yu.P., Sheina G.G., Ivanov A.Y., Radchenko E.D., Kosevich M.V., Shelkovsky V.S., Boryak O.A., Rubin Yu.V.
Low-temperature experimental studies in molecular biophysics: a review
Low Temperature Physics. - 1999. - 25, N 10. - P. 747-459.
- F.Huisken and O.Werhahn, A.Yu. Ivanov and S.A. Krasnokutski
The O-H stretching vibrations of glycine trapped in rare gas matrices and helium clusters.
J. Chem. Phys. 111, 7 (1999), p. 2978-2984
- Reva I.D., Stepanian S.G., Adamowicz L., Fausto R.
Combined FTIR matrix isolation and ab initio studies of pyruvic acid: proof for existence of the second conformer
J. Phys. Chem. A. – 2001. – V. 105A. – P. 4773-4780
- Stepanian S.G., Reva I.D., Radchenko E.D., Adamowicz L.
Conformers of non-ionized proline. Matrix-isolation infrared and post-Hartree-Fock ab-initio study
J. Phys. Chem. A. – 2001. – V. 105A. – P. 10664-10672.
- Reva I.D., Stepanian S.G., Adamowicz L., Fausto R.
Missing Conformers. Comparative Study of Conformational Cooling in Cyanoacetic Acid and Methyl Cyanoacetate Isolated in Low Temperature
Inert Gas Matrixes
Chem. Phys. Lett. – 2003. – V.374. – P. 631-638.
- Reva I.D., Stepanian S.G., Adamowicz L., Fausto R.
Conformational behavior of cyanoacetic acid: a combined matrix isolation Fourier transform infrared spectroscopy and theoretical sstudy
J. Phys. Chem. A – 2003. – V. 107A. – P. 6351-6359.
- A.Yu. Ivanov, S.A. Krasnokutski, G.Sheina, Yu.P.Blagoi
Conformational structures and vibrational spectra of isolated pyrimidine nucleosides: Fourier transform infrared matrix isolation
study of 2-deoxyuridine.
Spectrochimica Acta Part A 59 ,(2003), 1959-1973.
- A.Yu.Ivanov, S.A.Krasnokutski, G.G.Sheina
Molecular structures of thymidine isomers isolated in the low temperature inert matrices.
Fizika Nizkih Themperatyr (FNT), V29, ¹ 9-10, sept./oct. 2003, p.1065-1070.
- A.Yu.Ivanov, V.A.Karachevtsev
FTIR spectra and conformations of 2’-deoxyuridine in Kr matrices
Fizika Nizkih Themperatyr (FNT),. -2007. –V.33, ¹6/7. - p.772-777.
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