Miroslav M. Ristić

Electron-Vibrational Coupling and Fluorescence Spectra of Tetra-, Penta-, and Hexacoordinated Chlorophylls c1 and c2.

Chlorophylls (Chls) are a group of pigments related to light absorption, excitation energy, and electron transfer in photosynthetic complexes. Given the importance of intramolecular nuclear motion for these electronic processes, many experimental studies were performed in order to relate its coupling to electronic coordinates of these pigments, but a detailed analysis is still lacking for isolated Chls c1 and c2. To gain insight into the intramolecular motion and fluoroscence spectra of these two pigments in tetra-, penta-, and hexacoodinated states, we performed a quantum chemical study based on density functional theory and multimode harmonic approximation with displaced, distorted, and rotated normal modes. In order to benchmark the employed methods, we simulated the high-resolution fluorescence spectra of tetracoodinated Chls a, b, and d and compared them with available experimental spectra obtained with fluorescence line-narrowing techniques. Although the experimental spectra were obtained for ligand coordinated Chls, qualitatively good agreement was found between the simulated and experimental spectra. Almost all resonances were reproduced in the spectroscopically interesting region from 200 to 1700 cm(-1). The significance of mode distortion and rotation for the simulated spectra is discussed. The fluorescence spectra of Chls c1 and c2 consist of a group of peaks in the 200-450 cm(-1) spectral range, a group of weak peaks from 700 to 1000 cm(-1), and a large group of strong peaks from 1100 to 1600 cm(-1). Ligand effects are also addressed, and a mode is identified as a sensitive probe for the coordination state of Chls c1 and c2.

Ionization of N2 in radio-frequent electric field

Rate coefficients for the electron impact ionization of the N2 molecule are calculated in non-equilibrium conditions in the presence of time-dependent electric field. A Monte Carlo simulation has been developed in order to determine non-equilibrium electron energy distribution functions within one period of the radio-frequent (RF) electric field. By using these distribution functions, rate coefficients for ionization of the N2 molecule have been obtained time resolved within one period in the frequency range from 13.56 up to 500 MHz, at effective reduced electric field values up to 700 Td. This work presents an insight into the temporal characteristics of ionizing process and provides the ionization rate coefficients that can be of great use for correct implementation in modeling RF plasma discharges. A behavior of rate coefficients under the influence of magnitude and frequency of the fields was studied separately revealing some interesting features in time dependence.

Electron energy transfer rate coefficients of carbon dioxide.

An extensive set of integral cross sections (ICSs) for electron impact vibrational excitation of the CO(2) molecule has been used to calculate electron energy transfer rate coefficients. The ICSs for electron impact symmetric stretch vibrational excitation are measured by using a high resolution double trochoidal electron spectrometer, while ICSs for the bending and asymmetric vibrations have been adopted from previous publications. Calculations of the energy transfer rate coefficients are performed for the equilibrium conditions in the mean electron energy range from 0 to 11 eV. By use of extended Monte Carlo simulations, electron energy distribution functions (EEDFs) and electron energy transfer rate coefficients are determined in the nonequilibrium conditions, for low and moderate values of the electric field over gas number density ratios, E/N, up to 150 Td. Contributions of higher vibrational levels are emphasized. The results are compared with the data available in the literature.

Ionization of CO in radio-frequency electric field

The rate coefficients for the electron impact ionization of the CO molecule have been calculated in the presence of the radio-frequency (RF) electric field. The non-equilibrium electron energy distribution functions, used for the rate coefficient calculations, were generated by using a Monte Carlo simulation. The rate coefficients were obtained, time resolved within one period, in the frequency range from 13.56 up to 500 MHz, at effective reduced electric field values up to 700 Td. A temporal behavior of the rate coefficients under the influence of magnitude and frequency of the fields has been studied. The total ionization rate coefficients and the rate coefficients for the production of different ion fragments have been period averaged and presented in the order to be of use for practical implementation in the RF discharges in CO. Also, the temporal characteristics of the electron energy distribution functions and the diffusion coefficients have been studied separately revealing some interesting feature...

Investigation of structure and vibrational properties of cyclobutane pirimidine dimer

We performed a theoretical analysis of the structure and vibrational properties of cyclobutane pyrimidine dimer, which is the main product in a photochemical reaction involving two molecules of 1-methylthymine. Thymine is a pyrimidine base that has the highest yield of the dimerization photoproducts. Methylation in position one was chosen because in this position thymine is linked to sugar in DNA. The calculations were performed at the B3LYP/cc-pVTZ level with a Gaussian program package. All molecular geometries were optimized without symmetry constraints in vacuum and D2O. Vibrational frequencies were calculated in the harmonic approximation. It was shown that there are two stable isomers, CPD(cis-syn) and CPD(trans-syn). CPD(trans-syn) is more stable both in vacuum and in D2O. By dissolving these molecules in D2O, both structures become more stable, although the stabilization of the less stable isomer is more pronounced due to its larger dipole moment. Thus, the difference in stability of the two isomers in D2O is almost two times lower than in vacuum. Because of the similarity of the two isomers’ structures, the difference in their vibrational spectra is not pronounced. Within the harmonic approximation, there is only a slight difference in the C=O and C-H stretching region. The difference in the N-H stretching region is more pronounced; in the CPD(cis-syn) molecule the two bonds vibrate separately, whereas in the CPD(trans-syn) the two modes couple, and this coupling results in symmetric and asymmetric N-H stretching. The observation shows that a slight difference in geometry can be reflected in the shape of the infrared spectra. A more detailed analysis of the vibrational properties would involve computation of anharmonic coupling terms, which would enable a more precise determination of the peak positions.

Resonant vibrational excitation and de-excitation of N2(v) by low-energy electrons.

We have calculated cross sections and rate coefficients for low-energy electron impact excitation of the nitrogen molecule from vibrationally excited levels N2(v) 1-8. Calculations are performed in the 2Pig shape resonance energy region, from 0 to 5 eV. The cross sections are determined by using our recent integral cross section measurements of the ground level vibrational excitation and the most recent cross sections for elastic electron scattering, applying the principle of detailed balance. The rate coefficient calculations are performed for the Maxwellian electron energy distribution. By using extended Monte Carlo simulations, the electron energy distribution functions (EEDF) and the rate coefficients are also determined for the nonequilibrium conditions, in the presence of the homogeneous external electric field for the typical, moderate values of the electric field over gas number density ratios, E/N.