Stepan G. Stepanian

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.

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.

Raman Spectroscopy Study and First-Principles Calculations of the Interaction between Nucleic Acid Bases and Carbon Nanotubes

In this work, we have used Raman spectroscopy and quantum chemical methods (MP2 and DFT) to study the interactions between nucleic acid bases (NABs) and single-walled carbon nanotubes (SWCNT). We found that the appearance of the interaction between the nanotubes and the NABs is accompanied by a spectral shift of the high-frequency component of the SWCNT G band in the Raman spectrum to a lower frequency region. The value of this shift varies from 0.7 to 1.3 cm(-1) for the metallic nanotubes and from 2.1 to 3.2 cm(-1) for the semiconducting nanotubes. Calculations of the interaction energies between the NABs and a fragment of the zigzag(10,0) carbon nanotube performed at the MP2/6-31++G(d,p)[NABs atoms]|6-31G(d)[nanotube atoms] level of theory while accounting for the basis set superposition error during geometry optimization allowed us to order the NABs according to the increasing interaction energy value. The order is: guanine (-67.1 kJ mol(-1)) > adenine (-59.0 kJ mol(-1)) > cytosine (-50.3 kJ mol(-1)) approximately = thymine (-50.2 kJ mol(-1)) > uracil (-44.2 kJ mol(-1)). The MP2 equilibrium structures and the interaction energies were used as reference points in the evaluation of the ability of various functionals in the DFT method to predict those structures and energies. We showed that the M05, MPWB1K, and MPW1B95 density functionals are capable of correctly predicting the SWCNT-NAB geometries but not the interaction energies, while the M05-2X functional is capable of correctly predicting both the geometries and the interaction energies.

An infrared study on matrix-isolated benzoic acid

Abstract The infrared spectra of benzoic acid and deuterobenzoic acid embedded in Ar matrices were obtained. The only benzoic acid conformer with syn position of O-H and CO groups was found to fix in the matrices. We have demonstrated that both a raise of benzoic acid concentration and a matrix annealing lead to formation of H-bonded benzoic acid dimers. The results of semiempirical AM1 calculations allowed us to determine probable structures of the dimers observed. The interpretation of the experimental IR spectra was carried out by normal-coordinate analysis for benzoic acid monomer and dimer.

Interaction of fragmented double-stranded DNA with carbon nanotubes in aqueous solution

Aqueous suspensions of ultrasonically fragmented double-stranded (fds-) DNA and single-walled carbon nanotubes (SWNTs) have been investigated by UV- and IR-absorption, NIR-emission and Raman spectroscopy. According to gel-electrophoresis, the lengths of the polymer fragments were 100–500 base pairs. Analysis of IR and UV data indicates the presence of both double-stranded (ds) and single-stranded (ss)-regions in the fragments. SWNT complex with DNA was revealed by NIR-emission and Raman spectroscopy. It turned out that fds-DNA is less efficient in holding nanotubes in the aqueous solution than ss-DNA. From the UV-data, the character of the helix-coil transition is seen to be like that for fds-DNA off and on nanotube, however, DNA thermostability increased in this latter case. The effective charge density on the DNA sugar-phosphate backbone of the fds-DNA:SWNT hybrid was less than that of DNA alone. Spectroscopic data can be explained by a model in which the formation of hybrids starts due to the interaction between untwisted ss-regions of DNA and the nanotube: the strands wrap on the tube and thus create an ‘anchor’ for the whole polymer. The ds-part of the polymer is located close to the nanotube.

Combined Raman scattering and ab initio investigation of the interaction between pyrene and carbon SWNT

Raman spectra of HiPco SWNT and SWNT-pyrene films were measured in the 160–1800 cm−1 range. Due to the non-covalent interaction between SWNT and pyrene the most intensive component of the SWNT G mode (1590 cm−1) is downshifted by 2 cm−1 and becomes narrower. Also the intensity of the low-frequency component of the G mode (1550 cm−1) decreases by about 30%. Structures and interaction energies in the complexes of pyrene and zigzag (n, 0) SWNTs [6 ≤ n ≤ 20] were determined at the MP2 level of theory. The BSSE-free geometry optimization of the pyrene-zigzag (12,0) SWNT complex converged to a structure with a 1/2staggered conformation and with an intermolecular distance of 3.5 Å. The BSSE-free interaction energy in the complex is −30.8 kj mol−1. Increasing of the nanotube diameter leads to a higher interaction energy. This energy becomes equal to −37.2 kJ mol−1 in the case of a planar carbon surface.