Laboratory of Structure and Mechanism of Reactions in Solutions

Head of Laboratory: Prof. Yu.I. Naberukhin, Dr. Sci.
Researchers: N.N. Medvedev, Dr. Sci.
N.L. Lavrik, Dr. Sci.
Yu. Ya. Efimov, Cand. Sci.
V.P. Voloshin, Cand. Sci.
V.A. Luchnikov, Cand. Sci.
(Group of Investigation of Disordered System Structure)
G.I. Skubnevskaya, Cand. Sci.
S.N. Dubtsov, Cand. Sci.
G.G. Dultseva, Cand. Sci.
(Group of Atmospheric Chemistry)
V.V. Khramtsov, Dr. Sci.
I.A.Slepneva, Cand.Sci.
S.I. Dikalov, Cand. Sci.
M.Yu. Balakirev, Cand. Sci.
Yu.I. Glazachev
(Group of Biophysics)

Investigation of the structure and dynamics of disordered systems (liquids including water, amorphous solids, porous and granular substances) by means of computer simulations, vibrational spectroscopy and X-ray diffraction (Group of Investigation of Disordered System Structure).

Studies of the kinetics of photolysis and photonucleation of organic compounds in the gas phase. Physicochemical aspects of smog formation. Mathematical and laboratory modelling in atmospheric chemistry with respect to the conditions existing in Siberia (Group of Atmospheric Chemistry).

Investigation of the mechanisms of free radical processes in biological systems, the role of oxygen-centred radicals and nitrogen oxide (Group of Biophysics).

Development and application of the Voronoi-Delaunay tessellation of space for analysis of the structure of computer-simulated models of disordered substances. A set of programs for the construction of the Voronoi polyhedra, Delaunay simplexes, Voronoi and Delaunay networks for any disordered systems have been created. The methods of analysis of the structure of computer models have been developed on the basis of these geometrical objects using the ideas of percolation theory. Interesting regularities in the structure of monatomic systems like liquid or amorphous argon were revealed with the help of these methods. At present, computer models of liquid and amorphous water are under investigation.

Computer porometry. The above-mentioned methods of geometrical analysis are applied to the studies of the void structure in the models of granular porous materials. Similar to the method of mercury porometry, it becomes possible to build intrusion curves that indicate the fraction of volume occupied by accessible pores; that allows one to study spatial pore distribution, to calculate different percolation characteristics of the models of porous materials (ceramics, catalyst supports). The quantitative analysis of the structure of interatomic space opens the possibilities to study the mechanisms of diffusion and solubility of impurities in liquids and glasses.

Development of the theory describing the shapes of bands in vibrational spectra of aqueous systems on the basis of the fluctuation concept of hydrogen bond. The procedures have been developed to calculate temperature invariants allowing to calculate the contours of stretching bands of HOD, H₂O, and D₂O molecules within temperature range from amorphous state to 200^oC in good agreement with experiment, as well as contributions of hydrogen bonds to thermodynamic functions of water.

Development of experimental methods of investigation and numerical simulations of photonucleation kinetics. An original approach is being worked out that provides the combined investigation of the kinetics of photolysis and initial stages of aerosol formation. This approach involves numerical modelling on the basis of the measured characteristics of processes occurring in submicron aerosols (particle concentrations and size distributions). This allows to calculate quantum yields of aerosol formation, rate constants of the slow stages of reactions that limit gas-to-particle conversion, and the size of the nuclei of the new phase.

Investigations of chemical processes in the atmosphere under the conditions existing in Siberia. The concentrations of major pollutants are monitored under anthropogenic load and under background conditions. The chemical block of a 3D-model of transport and transformation of pollutants is developed. This provides a basis for studying ecological problems of Siberia, including scientifically reasonable ecological examination.

Investigations of the mechanisms of free-radical processes in biological and chemical systems. Development of new methods to study stable and short-lived radicals using ESR and NMR spectroscopy.

1. Application of pH-sensitive spin probe allows one to measure local pH within the range 0 – 14. This method is used to study proton diffusion in aqueous solutions and glass matrices, proton transport through biological membranes, to measure acidity in micropores of polyelectrolytes, zeolites, kaolin, as well as in the in vivo systems (see review by Khramtsov, 1988, 1998).

2. A principally new method has been developed to determine SH groups using biradical disulphide probes and ESR spectroscopy. The sensitivity of this method is 0.1 m M. This method has won wide application, in particular for the analysis of intracellular glutathione and for the studies of oxidative rupture of thiols (see the review by Khramtsov and Wolodarsky, 1998).

3. In collaboration with the Novosibirsk Institute of Organic Chemistry, a series of new spin traps has been proposed based on 2H-imidazoles, as well as hydroxylamine derivatives, for the detection of O-, C-, and S-centred radicals. The use of cyclic hydroxylamines and ESR spectroscopy allows to determine superoxide radical in biological systems in vitro and in vivo (see Alexis Biochemicals Catalogue, issue 2, 1998, section “New traps”).

4. The mechanisms of nitrogen oxide evolution and capture by a series of new NO-donors and acceptors are investigated with the help of the developed ESR technique of nitrogen oxide determination in aqueous solutions using 2-imidazoline probes.

5. Spin exchange in nitroxide radicals is used to measure oxygen concentrations (ESR oxymetry technique). The use of modern magnetic resonance methods (ESR, NMR), as well as optical and fluorescent ones (including a set-up created for the first time in the USSR, namely, FRAP – Fluorescence Recovery After Photodecolourisation) helps obtain unique information concerning the structural and functional organisation of membrane-associated enzymatic monoxygenase system (see the review by Weiner, 1986).

6. In collaboration with the University of Columbus (USA) a new method to study free radicals is being developed, i.e. NMR of spin traps.

International collaboration
1. Dortmund University, Germany (Prof. A. Geiger, Prof. B. Lippert).

7. Centre for Biological Chemistry, University of Frankfurt, Germany (Prof. G. Zimmer).

9. Institute of Physiology and Balneology, Freiburg, Germany (Prof. E. Bassonge).

10. National Institute of Health and Environment, North Carolina, USA (Prof. R. Mason).

11. Department of Biomedical Physics, University of Aberdeen, Scotland, UK (Prof. M. Foster).

12. University of Nimegen, the Netherlands (Dr. E. Rayers, Head of the Group of Molecular Spectroscopy).

1. N.N. Medvedev, V.P. Voloshin, Yu.I. Naberukhin. Structure of simple liquids as a percolation problem on the Voronoi network. J.Phys.A: Math.Gen., 21, L247-L252 (1988).

2. Yu.I.Naberukhin, V.P. Voloshin, and N.N. Medvedev. Geometrical analysis of the structure of simple liquids: percolation approach. Molecular Physics, 73, 917-936 (1991).

3. Yu.Ya.Efimov, Yu.I.Naberukhin. Fluctuation Theory of hydrogen bonding in liquids. Structure, spectral bandshapes and temperature dependence. // Faraday Discuss. Chem. Soc., N 85, p.117-123 (1988).

4. Dultseva G.G., Skubnevskaya G.I., Tikhonov A.Ya. et al. Derivatives of dihydropyrazine-1,4-dioxide, 3-imidazoline 3 - oxide, and a-phenyl nitrones with functional groups as new spin traps in solution and in the gas phase. (1996) J.Phys.Chem., 100, p.17523.

5. Dubtsov S.N., Koutzenogii K. P., Levykin A.I. and Skubnevskaya G. I. Photochemical aerosol formation of haloidbenzenes - comparison between theory and experiment. J.Aerosol Sci.(1995), 26, 705.

6. V.V. Penenko, G.I. Skubnevskaya. Numerical modelling for the problems of atmospheric chemistry. Uspekhi Khimii (Advances in Chemistry), 59, 1757 (1990) (in Russian).

7. Khramtsov,V.V. and Weiner,L.M. 1988. Proton exchange in stable nitroxyl radicals: pH-sensitive spin probes. In: Imidazoline Nitroxides (ed. Volodarsky, L.B.) V.2, pp.37-80, CRC Press, Boca Raton.

8. Khramtsov V.V., Weiner L.M. Proton transport in free radicals. Spin pH probes. Uspekhi khimii (Advances in Chemistry), 57, N 9, 1440-1466 (1988) (in Russian).

9. Dikalov S., V. Khramtsov, and G. Zimmer, 1997, Reaction of lipoate and its derivatives with reactive oxygen species. In: Lipoic Acid in Health and Disease (Eds J. Fuchs, L.Packer, and G.Zimmer), Marcel Dekker Inc., New York, pp.47-66.

10. Khramtsov, V.V. and Volodarsky, L.B., 1998, Use of imidazoline nitroxides in studies of chemical reactions: ESR measurements of concentration and reactivity of protons, thiols and nitric oxide, in:Biological Magnetic Resonance, Volume 14: Spin Labeling: The Next Millennium (L.J.Berliner, Ed.), pp.109-180, Plenum Press, New York.