Igor Reva

Infrared spectra of benzoic acid monomers and dimers in argon matrix

Abstract The infrared spectra of benzoic and deuterobenzoic acids isolated in Ar matrices were measured using the matrix-to-sample ( M / S ) ratios 750 and 250. The spectra were interpreted both by AMl semiempirical and variational methods. The calculation of the potential energy surface of benzoic acid monomer shows that only the syn conformer of benzoic acid must be present in the matrix, which is in complete agreement with experimental data obtained previously. Matrix annealing mainly favours the formation of cyclic symmetrical dimers with two intermolecular H-bonds. The frequency shifts of some vibrations of the COOH group on association are measured. More complex aggregates were revealed in the matrix isolation measurements.

The rotamerization of conformers of glycine isolated in inert gas matrices. An infrared spectroscopic study

Abstract The infrared spectra of glycine isolated in Ne, Ar and Kr matrices have been measured. The matrix-isolated glycine is shown to be in the molecular form. The spectral manifestations, both conformational and site splitting, are separated. Three different conformers of glycine have been identified experimentally for the first time. It is shown that during the deposition of the samples the substrate temperature must be lowered to 13 K — this is a decisive factor permitting fixation of a complete set of glycine conformers in an inert matrix. The relative energies of the three glycine conformers are estimated to be 0, 1.3–1.6 and 0.9–1.5 kcal/mol.

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.

Missing conformers. Comparative study of conformational cooling in cyanoacetic acid and methyl cyanoacetate isolated in low temperature inert gas matrixes

Abstract A comparative conformational study of two related systems, methyl cyanoacetate (MCA) and cyanoacetic acid (CAA), is presented. Ab initio calculations predicted that both systems have two nearly isoenergetic conformers separated by similar low energy barriers (about 3 kJ mol −1 ). In xenon matrixes deposited at temperatures above 40 K for MCA and above 20 K for CAA only one conformer was observed for each of the two systems. However, below those temperatures two MCA and two CAA conformers were trapped into the matrixes. Conformational cooling was found responsible for this behavior. Factors contributing to this effect are discussed.

Structure of isolated 1,4-butanediol: combination of MP2 calculations, NBO analysis, and matrix-isolation infrared spectroscopy.

Theoretical calculations at the MP2 level, NBO and AIM analysis, and matrix-isolation infrared spectroscopy have been used to investigate the structure of the isolated molecule of 1,4-butanediol (1,4-BDO). Sixty-five structures were found to be minima on the potential energy surface, and the three most stable forms are characterized by a folded backbone conformation leading to the formation of an intramolecular H-bond. To better characterize the intramolecular interactions and particularly the hydrogen bonds, natural bond orbital analysis (NBO) was performed for the four most stable conformers, and was further complemented with an atoms-in-molecules (AIM) topological analysis. Infrared spectra of 1,4-BDO isolated in low-temperature argon and xenon matrixes show a good agreement with a population-weighted mean theoretical spectrum, and the spectral features of the conformers expected to be trapped in the matrixes were observed experimentally. Annealing the xenon matrix from 20 to 60 K resulted in significant spectral changes, which were interpreted based on the barriers to intramolecular rotation. An estimation of the intramolecular hydrogen bond energy was carried out following three different methodologies.

A correlation between the proton stretching vibration red shift and the hydrogen bond length in polycrystalline amino acids and peptides.

The FTIR spectra of pure and isotopically diluted (H/D and D/H) polycrystalline L-glutamine, L-hystidine, L-tyrosine, DL-serine, L-threonine, di-, tri-glycine and di-glycine x HCl x H2O salt were measured in the range 4000-2000 cm(-1) at temperatures from 300 to 10 K. The frequencies of decoupled proton stretching mode bands upsilon1, which can be observed only at low temperature, were used for estimation of the of upsilon1-bands red shift, which occurs upon formation of H-bonds involving ionized NH3+ and/or peptide HN-CO groups. The empirical correlation between the red shift and H-bond length, which was found previously for binary gas phase H-bonded complexes, carbohydrates and nucleosides [M. Rozenberg, A. Loewenschuss and Y. Marcus, Phys. Chem. Chem. Phys., 2000, 2, 2699-2702; M. Rozenberg, C. Jung and G. Shoham, Phys. Chem. Chem. Phys., 2003, 5, 1533-1535], was now extended to H-bonded networks in polycrystalline amino acids and peptides. The energies of the different H-bonds present in the crystalline structures could also be successfully estimated from the well-established empirical correlation [A. V. Iogansen, Spectrochim. Acta, 1999, A55, 1585-1612] between this property and the red shifts of the corresponding upsilon1 mode bands.

Conformational Cooling Dynamics in Matrix-Isolated 1,3-Butanediol

The complete conformational space of monomeric 1,3-butanediol has been characterized theoretically, and 73 unique stable conformers were found at the MP2/6-311++G(d,p) level. These were classified into nine families whose members share the same heavy atom backbone configurations and differ in the hydrogen atom orientations. The first and third most populated backbone families are governed by the formation of an intramolecular hydrogen bond; however, the second precludes this type of interaction and was frequently overlooked in previous studies. Its stability is determined by the relatively high entropy of its main conformers. The hydrogen bonding of four of the most important conformers was characterized by means of atoms in molecules (AIM, also known as QTAIM) and natural bond orbital (NBO) analyses. Using appropriate isodesmic reactions, hydrogen bonding energy stabilizations of 12-14 kJ mol(-1) have been found. Experimentally, monomeric molecules of 1,3-butanediol were isolated in low-temperature inert matrixes, and their infrared spectra were analyzed from the viewpoint of the conformational distribution. All the relevant transition states for the conformational interconversion reaction paths were characterized at the same level of theory to interpret the conformational cooling dynamics observed in the low-temperature matrixes. The energy barriers for rotation of the OH groups were calculated to be very low (<3 kJ mol(-1)). These barriers were overcome in the experiments at 10 K (Ar matrix), in the process of matrix deposition, and population within each family was reduced to the most stable conformers. Further increase in the substrate temperature (up to 40 K, Xe matrix) resulted in conformational cooling where the medium-height barriers (approximately 13 kJ mol(-1)) could be surmounted and all conformational population converted to the ground conformational state. Remarkably, this state turned to consist of two forms of the most stable hydrogen bonded family, which were predicted by calculations to be accidentally degenerated and were found in the annealed matrix in equal amounts. All of these experimentally observed conformational cooling processes were analyzed and supported by full agreement with the theoretical calculations.

Vibrational spectrum and molecular structure of triphenylamine monomer: A combined matrix-isolation FTIR and theoretical study

Theoretical optimization of triphenylamine geometry, carried out at DFT(B3LYP) level using 6-31G** and aug-cc-pVDZ basis sets, predicted a propeller-like structure of the compound with D3 overall symmetry. In this structure, the central NCCC atoms are coplanar and the phenyl rings are symmetrically twisted from this plane by 41.5° (6-31G**) or 41.6° (aug-cc-pVDZ). The experimental FTIR spectrum of triphenylamine monomers isolated in an argon matrix was measured and interpreted by comparison with theoretical spectra calculated at the DFT(B3LYP) level with 6-31G** or aug-cc-pVDZ basis sets. The good agreement between the experimental and theoretical spectra allowed a positive assignment of the observed infrared absorption bands. Conformational flexibility of triphenylamine was investigated by carrying out a series of theoretical scans of the potential energy hypersurface of the system. Special attention was granted to the minimal energy pathway between the left-hand rotating and right-hand rotating symmetry identical structures of the compound. A route conserving a C2 symmetry axis was identified as implying an energy barrier of 20 kJ mol−1 only, whereas the calculated barrier for the concerted twist of all the phenyl rings (the route with conservation of the C3 symmetry axis) was as high as 54 kJ mol−1.

The Pyrolysis of Isoxazole Revisited: A New Primary Product and the Pivotal Role of the Vinylnitrene. A Low-Temperature Matrix Isolation and Computational Study

This paper describes the pyrolysis of parent isoxazole and of its 5-methyl and 3,5-dimethyl derivatives by the high-pressure pulsed pyrolysis method, where activation of the precursor molecules occurs predominantly by collisions with the host gas (Ar in our case), rather than with the walls of the pyrolysis tube, where catalyzed processes may occur. The products were trapped at 15 K in Ar matrices and were characterized by vibrational spectroscopy. Thereby, hitherto unobserved primary products of pyrolysis of isoxazole and of its 5-methyl derivative, 3-hydroxypropenenitrile or 3-hydroxybutenenitrile, respectively, were observed. E-Z photoisomerization could be induced in the above hydroxynitriles. On pyrolysis of isoxazole, ketenimine and CO were observed as decomposition products, but this process did not occur when the 5-methyl derivative was pyrolyzed. Instead, the corresponding ketonitrile was formed. In the case of 3,5-dimethylisoxazole, 2-acetyl-3-methyl-2H-azirine was detected at moderate pyrolysis temperatures, whereas at higher temperatures, 2,5-dimethyloxazole was the only observed rearrangement product (next to products of dissociation). These findings are rationalized on the basis of quantum chemical calculations. Thereby it becomes evident that carbonyl-vinylnitrenes play a pivotal role in the observed rearrangements, a role that had not been recognized in previous theoretical studies because it had been assumed that vinylnitrenes are closed-shell singlet species, whereas they are in fact open-shell singlet biradicaloids. Thus, the primary processes had to be modeled by the multiconfigurational CASSCF method, followed by single-point MR-CISD calculations. The picture that emerges from these calculations is in excellent accord with the experimental findings; that is, they explain why some possible products are observed while others are not.

Conformational Switching Induced by Near-Infrared Laser Irradiation

This work describes a molecular system where it is possible to effectively control the interconversion between two different stable conformational states, using selective narrow-band near-infrared irradiation. Monomers of hydroxyacetone (HA) isolated in low temperature argon matrices at 15 K exist exclusively in the conformational ground state Cc. Narrow-band near-infrared vibrational excitation of the first OH stretching overtone of the Cc form resulted in conformational isomerization. The photoproduct was identified as the higher energy Tt conformer of HA, and it was found to be stable at 15 K. The reverse isomerization, converting Tt into Cc, could also be induced by laser excitation of the first OH stretching overtone of the Tt form. The interpretation of the experimental observations was supported by anharmonic and harmonic calculations of the vibrational spectra and barriers to intramolecular rotation.