A.M. Plokhotnichenko

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.

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.

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.

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.

The rotamerization of conformers of glycine isolated in inert gas matrices. An infrared spectroscopic study (Chem. Phys. Letters 232 (1995) 141)

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 ofglycine 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.

Adsorption of biopolymers on SWCNT: ordered poly(rC) and disordered poly(rI).

Polymer adsorption onto single-walled carbon nanotubes (SWCNTs) depends on its rigidity/flexibility. The adsorption properties of two related homopolynucleotides poly(rI) and poly(rC) but of different rigidities were compared, employing absorption spectroscopy and molecular dynamics simulation. It was shown that adsorption of the poor base stacked poly(rI) onto the nanotube is less effective than that of the strong base stacked poly(rC), the chain of which is of higher rigidity. Analysis of UV absorption spectra of polymer:nanotube suspension at heating until 90 °C, which leads to partial nanotube aggregation because of the weakly bound polymer sliding from the tube surface, revealed that the percent of precipitated nanotubes in suspension with poly(rI) is larger than that in suspension with poly(rC) (16% vs 7%). This fact indicates the higher stability of SWCNT:poly(rC) hybrid in comparison with SWCNT:poly(rI). Less effective adsorption of poly(rI) is confirmed with a weaker hypochromic effect of nanotubes covered with poly(rI) than with poly(rC), which originates from π-π stacking of nitrogen bases with the nanotube surface. Spontaneous adsorption of oligomers on the nanotube simulated by the molecular dynamics showed that oligomer r(I)25 has a weaker energy of binding to the carbon nanotube surface than r(C)25. The oligomer with ordered bases has a tendency to form the stretched conformation along the nanotube, which provides a higher binding energy, while more flexible r(I)25 forms the stable loop spaced away from the nanotube surface, the stability of which is strengthened with H-bonding between bases.

Unusual aggregation of poly(rC)-wrapped carbon nanotubes in aqueous suspension induced by cationic porphyrin

Unusual aggregation of biopolymer-wrapped single-walled carbon nanotubes (SWCNTs) induced by cationic porphyrin meso-tetrakis(4-N-methyl-pyridyl)porphine (TMPyP4) in aqueous suspension has been studied by absorption spectroscopy and molecular dynamics simulation. After the addition of a small dose of TMPyP4 (10−6 M) into a poly(rC)–SWCNTs suspension, the absorption intensity of the nanotubes decreases, SWCNT bands demonstrate a red-shift and visible aggregation of SWCNTs is observed at concentrations above 10−5 M. However, formed aggregates are stable in suspension without precipitation for a few days. The Soret band of TMPyP4 in the absorption spectra exhibits hypochromism which is indicative of the π–π stacking interaction of the porphyrin core with π-systems of the biopolymer–SWCNT hybrid. The aggregation process of poly(rC)–SWCNT affects the spectral position of the Soret band, which is red-shifted. The spectral shift depends on TMPyP4 concentration: 18 nm at low porphyrin concentrations (10−7–10−6 M) and 14 nm at concentrations higher than 10−6 M. Such behavior of the Soret band is interpreted in terms of different types of porphyrin binding with poly(rC)–SWCNT resulting in effective nanotube aggregation. The molecular dynamics simulation is in good agreement with the experiment and demonstrates that the most stable complex, consisting of two nanotubes, can be formed when TMPyP4 molecules bind nanotubes, both owing to π–π stacking of the porphyrin core with the surface of one nanotube and with the oligonucleotide adsorbed onto another nanotube. The electrostatic interaction between porphyrin positively charged groups and the negative phosphate backbone of the oligonucleotide increases the stability of this complex as well.

Luminescence and Raman scattering of nonpolymerized and photopolymerized fullerene films at 297 and 5K

Luminescence and Raman scattering spectroscopy are used to study nonpolymerized and photopolymerized (with 45% and 85% polymerization) fullerene films (0.5μm thick on a Si substrate) at 5 and 297K. The films were polymerized while they were being deposited and irradiated with UV light. The wide-band emission observed at room temperature from a nonpolymerized fullerene film becomes structured at 5K. A short-wavelength band peaking at 695nm appears in the emission. The intensity of this band decreases with polymerization. Analysis of the low-temperature luminescence spectra of fullerene shows that polymerization is accompanied by a shift of the luminescence bands into the red region. Low-temperature investigations revealed lines in the Raman scattering spectrum of an 85% polymerized film which peak at the frequencies 1466 and 1461cm−1. These lines are due to the vibrations of fullerene dimers and a polymerized chain, respectively. Dimers predominate in a film with 45% polymerization in the polymerized phase...