A. Yu. Ivanov

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.

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.

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.

A low-temperature quartz microbalance

The design of a low-temperature quartz microbalance based on standard radio engineering quartz resonators is described. The sensitivity of the balance on PK88CP, PK104-5M, and PΓ-07 resonators at a 5-K temperature is determined. Special features of the practical use of the microbalance in the FTIR matrix insulation spectroscopy are considered. It is shown that, for films of solidified inert gases, one may ignore the dependence of the sensitivity on the frequency shift below 0.5–1.0% of the initial frequency of the resonator.

FTIR spectra and conformations of 2′-deoxyuridine in Kr matrices

The Fourier transform infrared spectra in the range 4000–200cm−1 of pyrimidine nucleoside 2′-deoxyuridine (dU) are obtained in low-temperature inert Kr matrices. For the first time, instead of a usual flat mirror, a low-temperature, one-coordinate retroreflector is used as the matrix substrate. Owing to this, the matrix setup is insensitive to dip angle vibrations of the cryostat and is favorable to work with thinner matrix layers. Of two syn-conformers with dU_s1 and dU_s2 (stabilized by the intramolecular hydrogen bond O5′H…O2), only the dT_s2 conformer with C2′-endo structure of the ribose ring is uniquely quenched. The height of the interconversion barrier of the minor syn-conformer dU_s1 was estimated to be below 0.7kcal∕mole. It is shown that the energy relaxation of impurities in Kr is slower than in Ar matrices.

Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil

Low-temperature matrix isolation Fourier-transform infrared spectroscopy and quantum-chemical calculations with DFT/B3LYP and MP2 methods were used for investigation of isolated 5-bromouracil (BrU) molecules. Only one tautomeric form of BrU was dominated in the low-temperature Ne, Ar, and Kr matrices. It was revealed that population of minor hydroxy-tautomers did not exceed 0.2%. Appearance of additional absorption bands in the region of stretching vibrations νCO (about 1710 cm−1) as well as of deformation ones (1297, 1093, 901 cm−1) was explained by Fermi resonance. In Ne matrices the peak intensities of absorption bands assigned to the out-of-plane vibrations of the ring and exocyclic atoms were decreased sharply. For the first time, least square method with the using of polynomial was proposed for the corrective scaling of calculated frequencies of vibrations. It is shown that the correction of calculated frequencies with the polynomial of degree two permits to decrease the root-mean-square discrepancy...

Vibrational spectra of adenine molecules in Kr, Ar, and Ne matrices

IR Fourier spectra of adenine molecules isolated in low-temperature Kr, Ar, and Ne matrices are obtained over the frequency range of 3800–450 cm−1 with a resolution of 0.25 cm−1. MP2 and DFT/BeLYP quantum-mechanical calculations are used to determine the populations of the main structural isomers of adenine for different evaporation temperatures. It is found that the populations of the minor isomers of adenine do not exceed the observation threshold of 0.2% at an evaporation temperature of 450 K. The effect of the matrices reduces to splitting most of the absorption bands of the main isomer A_9H. Splitting of a number of deformation vibration bands owing to Fermi resonances is observed in the 1700–450 cm−1 range. DFT/B3LYP calculations with a polynomial correction for the frequencies of the vibrational spectra are used to determine the spectral ranges within which it is best to search for the most intense vibrations of the rare isomers: 3440–3310, 1710–1680, and 1580–1540 cm−1. It is found that a triple F...

Features of the conformational structures of 2′-deoxyuridine, matrix isolated in Ar and Kr

The conformational equilibrium of molecules of the nucleoside 2′-deoxyuridine (dU) in Ar and Kr low-temperature matrices is investigated with the aid of low-temperature matrix-isolation FTIR spectroscopy and quantum calculations by the DFT and MP2 methods. It is found that in the low-temperature matrices the dominant forms are two anti-conformers of dU with different structures of the sugar ring: C2′-endo and C3′-endo. The main syn-confomer is stabilized by intramolecular hydrogen bond O5′H—O2, while C2′-endo is the dominant conformation of its deoxyribose ring in Ar and Kr low-temperature matrices. The possibility that minor syn-conformers without the intramolecular hydrogen bond O5′H—O2 are present in the matrix samples is also demonstrated. An influence of the matrix on the orientation of the hydroxyl group O3′H of the sugar ring of the main syn-conformer is found.

Conformational equilibrium of 2-deoxyadenosine molecules isolated in inert Ar matrices

The FTIR spectra of 2-deoxyadenosine (dA) molecules isolated in low-temperature Ar matrices were obtained in the range of 3800−180 cm−1 with a resolution of 0.3 cm−1. The population analysis of the major structural isomers of dA was carried out by MP2 and DFT quantum-mechanical calculation methods. It was established that dA can sustain prolonged evaporation at 440 K without undergoing thermal decomposition. For the first time, it was shown that the populations of dA syn-conformers with the intramolecular hydrogen bond O5′H–N3 is close to (76 ± 5)% in the gas phase and matrix. Upon freezing in the matrix the syn-conformers with the intramolecular hydrogen bond O5′H–N3 and C3′-endo structure of the deoxyribose ring were fully transformed into the subset of syn-conformers with the C2′-endo structure of the deoxyribose ring. Only two structures from this subset with different rotation angles of the O3′H-group can be stabilized in the matrix. Unlike pyrimidine nucleosides, the dA conformers with the intramole...

Manifestation of Fermi resonance in the vibrational spectra of 5-ioduracil, and its deutero-derivatives isolated in low-temperature Ar matrices

The FTIR spectra of isolated 5-ioduracil (5IU) molecules, and its deutero-derivatives, were obtained in low-temperature (T = 8 K) argon matrices in the frequency range of 3800–200 cm−1, with a resolution of 0.3 cm−1. The tautomer population is estimated at the evaporation temperature 395 K, using DFT (functionals B3LYP and B2PLYP) and MP2 quantum-mechanical methods. It is found that the main keto tautomer population in 5IU is above 99.8%. 5IU vibrational spectra are calculated using the DFT/B3LYP method and 6-311++G(df,pd) basis, and the calculated frequencies are corrected using a second order polynomial. It is found that in the region of vCO stretching vibrations of 5IU molecules, a triple Fermi resonance is manifested between the fundamental vC4O mode, and the combinational vibrations with frequencies 1745.3 and 1722.5 cm−1. Six combination modes in the region of ring stretching vibrations, and in-plane deformational vibrations, of 5IU are found. This classification of the vibrational spectrum bands of...