Vasilii I. Avdeev

Effect of cisplatin binding on guanine in nucleic acid: an ab initio study

Abstract To investigate the molecular mechanism of the antitumour activity of cisplatin, ab initio Hartree-Fock pseudo potential calculations have been performed for some Pt(II) complexes with the guanine nucleic base. We propose that cisplatin binding to guanine in DNA leads to a point mutation as the latter is the only change that the nucleic acid could “remember” after replication. Two ways of producing the point mutation are examined. The first is shifting the keto-enol tautomerization of guanine towards the enol form (rare in DNA) in the presence of cisplatin. The second is the action of cisplatin on the guaninecytosine pairing in DNA through binding to the O6 site of guanine which is involved in one of three hydrogen bonds between these nucleic bases. For this purpose the complex of cis-Pt(NH3)32+ and the hydrogen-bonded formamide-formamide pair has been calculated. The results obtained suggest, first, that the keto-enol tautomerization is not subject to crucial change in the presence of cisplatin. Second, it is found that the oxygen of the formamide coordinated by Pt(II) is no longer available for hydrogen bonding with the corresponding part of the complementary molecule. Hence, one can predict that binding of cisplatin to the O6 site of guanine breaks the corresponding hydrogen bond between guanine and cytosine which, in turn, can cause the point mutation.

Quasimolecular stable forms of oxygen on silver surface. Theoretical analysis by the density functional theory method

Abstract A quantum chemical investigation of possible associative oxygen forms on defective silver surface has been performed with the use of gradient-corrected density functional theory (DFT) in the cluster approximation. A surface defect was simulated by a cation vacancy (V). Cluster models (M1: Ag12 and M2: O3Ag12) of an active adsorption site (AS) with a vacancy were chosen on the basis of the structure of high-temperature layered silver oxide. The adsorbed layer on the defective surface was simulated by three oxygen atoms. For the atomic and associative (molecular) forms, the computations gave two stable structures of the adsorbed layer with C 3V and C 2V symmetry. The quasimolecular C 2V structure –Ag–O–O ep –O–Ag– resembling metal ozonides is by 44 kcal/mol more stable than the atomic C 3V structure. The C 2V structure is singlet and has an electrophilic epoxidizing oxygen atom O ep . A theoretical estimation of the density of states (DOS) in the quasimolecular oxygen form revealed a complex structure below the 4d band. Additional DOS peaks in this region are due to associative O–O bonds.

Autocatalytic gas-phase dehydrogenation of ethane

Homogeneous gas-phase pyrolysis of ethane by continuous CO2 laser irradiation was used in our experiments for bulk heating of the reaction mixture. Laser energy was absorbed by ethylene, the main product of ethane dehydrogenation, and transferred to the reaction medium via collisional relaxation. A mechanism of ethane dehydrogenation is suggested to describe the pyrolysis process. The mechanism is autocatalytic in respect of ethylene and includes ethane–ethylene interaction with the formation of methyl and propyl radicals. Rate constants of elementary reactions, selectivity, and yields of pyrolysis products were determined. The composition of ethane dehydrogenation products determined in the experiments was substantially different from the calculated thermodynamic equilibrium composition.

Mechanism of direct oxidation of cyclohexene to cyclohexanone with nitrous oxide. Theoretical analysis by DFT method

New very effective results on the liquid-phase oxidation of cyclohexene to cyclohexanone by nitrous oxide are analyzed using the B3LYP/6-31G* approximation to predict a two-step reaction mechanism correlated with the experimental data.

Models of finely dispersed MgO and V2O5 on silica. Theoretical analysis of optical properties using TDDFT

The results of Density Functional Theory (DFT) calculations on optical properties of vanadium complexes VOCl3, VOCl4-, VOCl52-, as well as the VO43- ion, are presented. The spectra of excited states in the range 25000-60000 cm-1 have been analyzed using the time-dependent DFT method (TDDFT). Spectroscopic features of structural defects (low-coordinated (LC) oxygen ions), as well as surface point defects (F+ and F sites) in MgO, have been studied within the cluster approach. The charge-transfer spectra and frequencies of normal vibrations for a number of active site models of finely dispersed oxides MgO and V2O5 on silica have been calculated. Comparison of the obtained results with experimental electronic diffuse reflectance spectra and fundamental frequencies confirms a hypothesis about the structure of active centers of finely dispersed oxide V2O5 on silica as monomeric forms, (O=V-On).

Theoretical analysis of thermally stable adsorption forms of oxygen on silver

Theoretical analysis of the properties of oxygen in the surface layer of silver is performed in a cluster approximation. The oxygen molecule is placed in an octahedral cavity of the Ag14 cubic cluster. The O2/Ag14 system is optimized and structural parameters determined by the ab initio Hartree- Fock method. The energies are estimated by methods taking into account electron correlation in the Möller- Plesset and density functional theory approximations. For the three nonequivalent positions of O2 in the Ag14 cluster,it is shown that the molecular forms of oxygen may be stabilized. The calculations showed that the ground state of the O2/Ag14 system is a triplet but the spin density is delocalized over the silver atoms. Spin polarization leads to splitting of the 3Σg- level. The oxygen molecule has intermediate parameters between the superoxide O21− and peroxide O22− with the bond length R(O- O) 1.41 å.

Low-temperature catalytic decomposition of hydrogen sulfide on metal catalysts under layer of solvent

When hydrogen sulfide decomposition {2 H2S ↔ 2 H2 + S2(gas)} is carried out in the flow regime at room temperature on metal catalysts placed in a liquid capable of dissolving H2S and sulfur, the reaction equilibrium can be significantly (up to 100%) shifted to the right yielding the desired product – hydrogen. The process efficiency was demonstrated using aqueous solutions of monoethanolamine (MEA), sodium carbonate, which is widely used in industry for H2S absorption from tail gases, and aqueous hydrazine as examples. IR and Raman spectroscopy data demonstrated that sulfur obtained in the solutions is in the form of diatomic molecules. DFT calculations showed that diatomic sulfur forms weakly bound coordinative complexes with solvent molecules. Some problems related to sulfur accumulation and recovery from the solvents are discussed. GRAPHICAL ABSTRACT

Properties of Adsorbed Oxygen Forms on a Defective Ag(111) Surface. DFT Analysis

A cluster model of an Ag12–3O (ASV) adsorption center using layered silver oxide as a prototype is proposed. The model includes a cation vacancy V on the Ag(111) surface and oxide type subsurface oxygen atoms Oox. Density functional theory (DFT) (B3LYP/LANL1MB approximation) is used to analyze the electronic structure of ASV and oxygen adsorption on this center, ASV+O → AS–O. As shown by the calculations, the adsorbed oxygen is associated with the subsurface oxygen atoms Oss to form structures similar to metal ozonides — Ag–Oss–Oep–Oss–Ag–Oox–Ag, containing electrophilic oxygen Oep along with the oxide oxygen Oox. The optical spectra of the ASV and AS–O centers were calculated by the configuration interaction method with single excitations (CIS). For ASV, the most intense absorption bands were obtained in the region 500-700 nm. Oxygen association is accompanied by a sharp decrease in spectrum intensity in the range 600-700 nm and an increase in the intensity of the peak at 500 nm. Vibration frequencies and (IR) intensities were determined for the ASV and AS–O centers. The ASV center exhibits a characteristic spectrum in the region 350-500 cm–1, which corresponds to the frequency spectrum of the surface oxide Ag2O. For associated oxygen forms (AS–O center), the calculations predict additional peaks around 980, 640 and 230 cm–1. These peaks are due to the vibrations of the Oss–Oep–Oss structural unit, stabilized at the cation vacancy.

Atomic and molecular forms of oxygen on Ag(331). Theoretical analysis using the DFT method

Oxygen adsorption on Ag(331) is analyzed in a cluster approximation using the density functional theory (DFT) method. Adsorption centers (AC) for the bridge (S2) and three-center (S3) coordinations of oxygen are identified on the stepwise face Ag(331) and the Ag-O bond energies at these centers are calculated. For atomic adsorption, the Ag-O bond strength varies from 50 to 65 kcal/mole, depending on AC. The heat of molecular adsorption DH = 5 kcal/mole for S2(L1-L2) type AC. The molecule is oriented parallel to Ag(110) between the terraces with R(O-O) = 1.34 å Calculations showed that the ground state of the O2Ag20(331) system is a triplet, but a part of spin density is delocalized on silver atoms, so that the spin density on oxygen ρs(O) = 0.46 (ρs = 1.0 for the free O2 molecule). The energy of the singlet state is 9 kcal/mole greater than that of the ground state.

Adducts of hydrogen and methane with Os(II) and Os(IV) complexes: Theoretical analysis of (η2-H2)OsCl2(PH3)2 and (η-CH4)OsCl2(PH3)2 molecular complexes by RHF, MP2 and DFT methods

Abstract A theoretical study of model OsCl2(PH3)2 complex and its adducts with hydrogen and methane is reported. Geometry of two isomers of OsCl2(PH3)2 complex and structures of possible σ complexes (η2-H2)OsCl2(PH3)2, (η2-CH4)OsCl2(PH3)2 have been calculated using density functional theory and MP2-method. It was shown that some isomers of weakly bonded hydrogen σ-complex OsH2Cl2(PH3)2 can form stable methane adducts followed by reductive elimination of hydrogen. Calculations of the reaction pathways for methane oxidative addition to isomers of 14-electron intermediate OsCl2(PH3)2 have been performed. For the isomer active in this reaction, structures of the transition state and methylhydride product were calculated. Frequencies of vibrations of stable σ-complex (η2-CH4)OsCl2(PH3)2 along with its deuterated form (η2-CD4)OsCl2(PH3)2 have been computed in the MP2/LAN1DZ approximation.