Hanna Rostkowska

Experimental matrix isolation and theoretical ab initio HF/6-31G(d, p) studies of infrared spectra of purine, adenine and 2-chloroadenine

Abstract The results of ab initio calculations at the Hartree—Fock level with the 6-31G( d , p ) basis set are reported for the harmonic vibrational infrared spectra of purine, adenine and 2-chloroadenine. These were compared with the experimental IR spectra of the compounds isolated in low-temperature matrices. The experimental spectra of 2-chloroadenine are reported for the first time. In the case of purine this comparison resulted in the complete assignment of the experimental IR spectrum. The proposed assignments of both the adenines studied are still incomplete.

Molecular structure and infrared spectra of 2-hydroxy-1,4- naphthoquinone; Experimental matrix isolation and theoretical Hartree–Fock and post Hartree–Fock study

Abstract The infrared spectra of 2-hydroxy-1,4-naphthoquinone (HNQ) isolated in low-temperature Ar and N 2 matrices are reported. The calculations of electronic energies for possible tautomers of HNQ (performed at RHF/6-31++G** and MP2/6-31++G** levels of theory) and the comparison of the experimental spectra with those theoretically calculated (at the RHF/6-31++G** and DFT(B3-LYP)/6-31++G** levels) show that the molecules of the compound isolated in low-temperature matrices exist in the form with intramolecular hydrogen bond. Theoretical results reproduce well the experimental infrared spectra of the matrix isolated HNQ. The assignment of the infrared absorption bands due to monomers of the compound isolated in Ar and N 2 matrices to the theoretically predicted normal modes is presented.

Infrared spectra of thiouracils: experimental matrix isolation and ab initio Hartree-Fock, post-Hartree-Fock and density functional theory studies

Abstract The experimental infrared absorption spectra of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil isolated in low-temperature argon matrices are compared with the spectra of these compounds computed by the density functional theory with the combined Becke3-LYP exchange-correlation energy functional (DFT(B3-LYP)) and conventional ab initio methods (Hartree-Fock (HF), MP2) using the standard 6-31G(d,p) basis set. The vibrational spectra computed at the DFT(B3-LYP)/6-31G(d,p) and HF/6-31G(d,p) levels of theory were found to reproduce well the experimental IR spectra. The results of MP2/6-31G(d,p) calculations predicted the normal modes due to out-of-plane vibrations somewhat less accurately. An assignment of the bands observed in the infrared spectra of the three thiouracils was performed, based on the comparison with the spectra calculated at the DFT(B3-LYP)/6-31G(d,p) level.

Infrared spectra of 2-thiocytosine and 5-fluoro-2-thiocytosine; experimental and ab initio studies

Abstract IR absorption spectra of 2-thiocytosine and 5-fluoro-2-thiocytosine isolated in low-temperature, inert gas matrices and in thin polycrystalline films are reported. The spectra of amino-thiol tautomeric forms of the compounds were studied for matrix isolated species, whereas the spectra of amino-thione tautomeric forms were observed for polycrystalline films. The experimental spectra were compared with the spectra predicted with the ab initio SCF/6-31G** method. The observed IR absorption bands in the spectra of monomers (amino-thiol forms) were assigned to the theoretically calculated normal modes.

Infrared experimental and ab initio quantum mechanical studies of 2-mercaptopyrimidine tautomers

Abstract Results are presented from ab initio SCF(3-21G*) calculations for the geometries and vibrational spectra (wavenumbers and absolute intensifies) of the thiol and thione tautomers of 2-mercaptopyrimidine. The results of calculations are compared with available experimental data, particularly with the reported vibrational spectra of the molecule isolated in inert gas matrices (Ar, N 2 ) and in crystalline state. The calculations of the normal modes predicted the experimental spectrum close enough to allow reliable assignment of most of the bands. The thiol⇌⇌thione tautomerism of the molecule is discussed. Matrix isolated monomers were observed in the thiol form only. That agrees with the results of ab initio calculations of internal energies of the tautomers [SCF(6-31Gu*) + MBPT(2)(6-31G*) + vib(0)(3-21G*); at the SCF(3-21G*) geometries] which predict the energy of thiol form to be ≈33 kJ mol −1 lower than that of thione form. In the crystalline state the hydrogen-bonded associations in the thione form dominate while in disordered amorphous layers, in matrices with a high guest-to-host ratio and in annealed matrices the associations both in thiol and thione form were observed.

The tautomeric equilibria of thioanalogues of nucleic acids: spectroscopic studies of 2-thiouracils in the vapour phase and in low temperature matrices

Abstract The IR absorption spectra in the NH, OH and SH stretching regions of 2-thiouracil and its N 1 -, N 3 -, O - and S -alkyl derivatives, isolated in the vapour phase and also isolated in inert low temperature matrices, and the UV absorption spectra of those compounds measured in the vapour phase are presented and discussed. These spectra establish unambiguously the tautomeric forms of these systems which are found for isolated molecules. 2-Thiouracil as well as its N 1 - and N 3 -methylated derivatives exists in the inert matrix and in the vapour phase only in the oxo-thione tautomeric form; this same form is found for these molecules in solutions and in the solid phase. In contrast, 2-methylthiouracil isolated in inert matrices and in the vapour adopts both the 4-oxo and the 4-hydroxy tautomeric forms, with an equilibrium constant K (oxo = hydroxy) of 1.2, while it exists only as the 4-oxo form in solutions and in the solid. The 4-neopentoxy derivative of 2-thiouracil, when isolated in an inert matrix, is found to be in the mercapto form only, while the thione form is dominant in the solid phase and in solution.

Near-Infrared Laser-Induced Generation of Three Rare Conformers of Glycolic Acid

Structural transformations were induced in conformers of glycolic acid by selective excitation with monochromatic tunable near-infrared laser light. For the compound isolated in Ar matrixes, near-IR excitation led to generation of two higher-energy conformers (GAC; AAT) differing from the most stable SSC form by 180° rotation around the C-C bond. A detailed investigation of this transformation revealed that one conformer (GAC) is produced directly from the near-IR-excited most stable conformer. The other higher-energy conformer (AAT) was effectively generated only upon excitation of the primary photoproduct (GAC) with another near-IR photon. Once these higher-energy conformers of glycolic acid were generated in an Ar matrix, they could be subsequently transformed into one another upon selective near-IR excitations. Interestingly, no repopulation of the initial most stable SSC conformer occurred upon near-IR excitation of the higher-energy forms of the compound isolated in solid Ar. A dramatically different picture of near-IR-induced conformational transformations was observed for glycolic acid isolated in N2 matrixes. In this case, upon near-IR excitation, the most stable SSC form converted solely into a new conformer (SST), where the acid OH group is rotated by 180°. This conformational transformation was found to be photoreversible. Moreover, SST conformer, photoproduced in the N2 matrix, spontaneously converted to the most stable SSC form of glycolic acid, when the matrix was kept at cryogenic temperature and in the dark.

Vibrational resonances in infrared spectra of uracils

Abstract Two regions in the i.r. spectra of uracils are analyzed: (a) the Nue5f8H stretching region in crystals, and (b) the Cue5fbO stretching region in matrix-isolated monomers. In these regions there is clear evidence of resonances leading to energy splittings and re-distributions of intensifies. These are: (a) a harmonic resonance between the Nue5f8H stretching in hydrogen-bonded groups and the Cue5f8H stretching, and (b) an anharmonic (Fermi) resonance between the Cue5fbO stretching and a combination band involving the N3ue5f8H and Cue5fbO bending vibrations. A theoretical interpretation of the resonances is presented.

Autoassociates and tautomerism of 2-oxo-5-halogenopyrimidines: theoretical and experimental investigations

Abstract Theoretical calculations (on a semi-empirical level) of energy and geometry of the autoassociates of two tautomeric forms of 2-oxo-5X-pyrimidines (X ue5fb H, Cl, Br) are presented. On the basis of the calculated energies of autoassociates it is possible to explain the enol—keto tautomeric transition between the gas phase and condensed phases. We propose a double-proton transfer reaction as a possible mechanism for the tautomeric transition. Infrared absorption spectra of 2-oxo-5X-pyrimidines in the v (NH …) and v (Cue5fbO) regions in solid phases and in low-temperature argon matrices are also presented and discussed. Comparison of IR spectra and results of the theoretical calculations with known crystallographic structures of 2-oxo-5X-pyrimidines (X ue5fb H, F, Cl) lead to the conclusion that the crystal structure of the 5-bromo derivative should be similar to that of the 5-chloro derivative.

Conformational transformation in squaric acid induced by near-IR laser light.

Two conformers of monomeric squaric acid (3,4-dihydroxy-3-cyclobutene-1,2-dione) were studied using the matrix-isolation method. Both forms of the compound, differing in rotation of one of the OH groups by 180°, were trapped from the gas phase into a low-temperature nitrogen matrix, whereas only the lowest-energy conformer was trapped in solid argon and in solid neon. Narrowband near-infrared laser light was used to induce transformation of the most stable form of squaric acid (having C2v symmetry) into the higher-energy conformer (Cs symmetry). Effective stabilization of the photogenerated species occurred only for the compound isolated in a nitrogen matrix. Moreover, the stabilization of the higher-energy Cs conformer of squaric acid by the solid nitrogen environment was found to strongly depend on the trapping site in the matrix. The spectroscopic characterization of the higher energy Cs conformer is reported here for the first time.