Yu. P. Blagoi

IR spectra of guanine and hypoxanthine isolated molecules

High resolution spectra of guanine, hypoxanthine, isocytosine, 2-aminopyrimidine and their deutero- and methyl derivatives obtained in Ar matrices by the low temperature IR spectroscopy method are reported. Normal modes of enol tautomers of guanine, 9-CH3-guanine, hypoxanthine and 2-aminopurine are calculated. Force fields are the same as for purine. Results calculated are used to interpret the experimental spectra. Keto—enol tautomerism is shown to exist in guanine and hypoxanthine, the proportions of enol tautomer being 50 and 5%, respectively. Possible biological applications of the results obtained are discussed.

Theoretical and experimental studies of adenine, purine and pyrimidine isolated molecule structure

Abstract High-resolution spectra of adenine isolated molecules and its deutero- and methyl- derivatives, and of purine were obtained using low-temperature IR spectroscopy in inert gas matrices. Normal modes of adenine and purine tautomers were calculated by the valence-force field method to interpret data obtained. Force constants of model compounds —imidazole and pyrimidice—were used in calculations as zero parameters or adenine and purine. Results obtained lead to the conclusion that the imidazole ring tautomerization influences IR spectra band splitting.

Experimental and theoretical studies of molecular structure features of cytosine

Abstract High-resolution vibrational spectra of the heterocyclic nitrogen compounds cytosine, its deutero analogue and pyrimidine, have been obtained by IR spectroscopy in an Ar matrix. On the basis of calculation results, the normal vibrations of isolated molecules are assigned and the forces constants found. It is shown that an isolated molecule of cytosine exists mainly in the enol form, which agrees with theoretical predictions.

FTIR spectroscopic study of the UV-induced rotamerization of glycine in the low temperature matrices (Kr, Ar, Ne)

Using UV irradiation, the spectral bands of three glycine conformers in the FTIR matrix spectra were separated in the range 4000–180 cm−1. The absolute infrared intensities of the spectral bands of these conformers were measured. The spectral manifestations of the weak intramolecular H-bonds NH2---O in conformers I, III and the strong H-bond N---H-O-C in conformer II were found. The influence of the matrix cage on the efficiency of UV isomerization was demonstrated. The thermodynamic parameters of glycine conformers at T=358 K were established as: KI–II=0.13(±0.025), ΔHI–II=1000 (±600) J mol−1, ΔSI–II=−14.2(±2) J mol−1 K−1; and KI–III=0.16(±0.02), ΔHI–III=5800(±600) J mol−1, ΔSI–III=1(±2) J mol−1 K−1.

Infrared matrix isolation studies of amino acids. Molecular structure of proline

Abstract IR spectra of proline and deuteroproline isolated in low temperature Ar matrixes have been obtained. It is shown that in the isolated state proline exists in the molecular form. The spectra are interpreted using normal coordinate analysis. It is found that band splitting in the spectra is caused by the occurrence of two proline conformations. The structures of these conformation differ in the position of the COOH group with respect to pyrrolidine ring. The conformations are found to be stabilized by the intramolecular hydrogen bond. It has been shown that conformational equilibrium results in the splitting of most bands in the IR spectra of proline and deuteroproline. This splitting is maximal for CO stretching bands (23 cm −1 ). The structure and relative energies of the conformations are determined by the AM1 quantum chemical method.

FTIR spectroscopy of uracil derivatives isolated in Kr, Ar and Ne matrices: matrix effect and Fermi resonance

Abstract The vibrational spectra of uracil (2,4-dioxopyrimidine), 1,3-dideuterouracil and 5-methyluracil (thymine) in low temperature Kr, Ar and Ne matrices have been studied by Fourier-transform infrared (FTIR) spectroscopy. The absolute infrared intensities and frequencies of the absorption bands in the infrared (IR) spectra of uracil have been measured. The hypotheses of non-planar conformations of uracil and 5-methyluracil has been tested experimentally. It is shown that the increasing number of spectral bands can be attributed to the Fermi resonance and the matrix splitting. The matrix (Kr, Ar, Ne) effect on fine structure of the absorption bands and Fermi resonance in the IR spectra of uracil, 1,3-dideuterouracil, 5-methyluracil has been studied experimentally.

Study of Ca2+, Mn2+ and Cu2+ binding to DNA in solution by means of IR spectroscopy

The interaction of Cu2+, Mn2+ and Ca2+ ions with the DNA macromolecule was studied in aqueous solutions at different metal ion concentrations. All these ions interact with both the bases and the phosphate groups of DNA. Cu2+ ions alter the DNA B-conformation at [Cu2+] > 2 × 10−2M. Metal ions binding to DNA induce DNA compactisation. The highly positive cooperativity of this process was shown. The binding constants and parameters of cooperativity of the metal ions binding to DNA were estimated.

The IR spectrum of formic acid in an argon matrix

Abstract A new method of preparation of matrix-isolated molecules of formic acid at low temperatures has been developed. A set of experimental frequencies and intensities of the IR spectrum of monomer molecules of formic acid isolated in a low temperature argon matrix has been obtained. It is shown on the basis of analysis of the IR spectrum that the new method eliminates association and decomposition of molecules of the acid during preparation of the sample.

FTIR investigation of the effect of matrices (Kr, Ar, Ne) on the UV-induced isomerization of the monomeric links of biopolymers

Abstract UV-induced isomerization of monomeric glycine and 2-hydroxypyrimidine in Kr, Ar and Ne matrices was investigated using Fourier transform infrared (FTIR) spectroscopy. The spectral bands of the three conformers of glycine and two tautomers of 2-hydroxypyrimidine were detected unambiguously. UV irradiation caused the partial conversion of the hydroxy form of 2-hydroxypyrimidine into the oxo form. The efficiency of the isomerization of glycine and 2-hydroxypyrimidine was reduced in the Ne matrix in comparison with the Ar and Kr matrices.

Poly(rA) • Poly(rU) with Ni2+ Ions at Different Temperatures: Infrared Absorption and Vibrational Circular Dichroism Spectroscopy

Abstract Phase transitions were studied of the sodium salt of poly(rA) •poly(rU) induced by elevated temperature without Ni2+ and with Ni2+ in 0.07 M concentration in D2O (∼0.4 [Ni]/[P]). The temperature was varied from 20° C to 90° C. The double-stranded conformation of poly(rA)•poly(rU) was observed at room temperature (20° C—23° C) with and without Ni2+ ions. In the absence of Ni2+ ions, partial double- to triple-strand transition of poly(rA) •poly(rU) occurred at 58° C, whereas only single-stranded molecules existed at 70° C. While poly(rU) did not display significant helical structure, poly(rA) still maintained some helicity at this temperature. Ni2+ ions significantly stabilized the triple-helical structure. The temperature range of the stable triple-helix was between 45° C and 70° C with maximum stability around 53° C. Triple-to single-stranded transition of poly(rA) •poly(rU) occurred around 72° C with loss of base stacking in single-stranded molecules. Stacked or aggregated structures of poly(rA) formed around 86° C. Hysteresis took place in the presence of Ni2+ during the reverse transition from the triple-stranded to the double-stranded form upon cooling. Reverse Hoogsteen type of hydrogen-bonding of the third strand in the triplex was suggested to be the most probable model for the triple-helical structure. VCD spectroscopy demonstrated significant advantages over infrared absorption or the related electronic CD spectroscopy.