Publishing House SB RAS:

Publishing House SB RAS:

Address of the Publishing House SB RAS:
Morskoy pr. 2, 630090 Novosibirsk, Russia



Advanced Search

Journal of Structural Chemistry

2009 year, number 5

1.
QUANTUM CHEMICAL ANALYSIS OF THE STRUCTURE AND SPECTROSCOPIC PROPERTIES OF ARYL VINYL ETHERS

Y. L. Frolov, A. V. Vashchenko
Keywords: DFT calculations, IR spectroscopy, Raman spectroscopy, aryl vinyl ethers, double bond vibration
Pages: 833-842

Abstract >>
A series of aromatic vinyl ethers and some compounds close to them in structure are studied by DFT (B3LYP/6-311+G(2d,p)) and MP2(full)/6-311+G(2d,p) methods. Measurements of Raman spectra are also used. The calculation of vibrational spectra of aryl vinyl ether (AVE) isomers shows that stretching vibrations ν(=) are most conformation sensitive. The calculated value of I(=) for vinyl phenyl ether more than twice exceeds the corresponding value for vinyl methyl ether. The calculated and experimental values of I(=) are consistent with the hypothesis about the presence of a common conjugated π-system in the molecules of substituted AVEs. Here the bridging oxygen atom provides the π,,π-interaction.
																								



2.
ELECTRONIC AND GEOMETRIC STRUCTURE OF ISOMERS OF NITRIC ACID. DFT QUANTUM CHEMICAL CALCULATIONS

I. I. Zakharov, O. I. Zakharova, A. B. Tselishchev, M. G. Loriya
Keywords: quantum chemical calculations, density functional (DFT) method, molecular structure, thermodynamic parameters, HNO3 isomers
Pages: 843-851

Abstract >>
Based on the B3LYP/6-311++G(3df,3pd) density functional method, quantum chemical calculations of the electronic structure, geometry, and thermodynamic parameters of eight isomers of nitric acid (three known isomers in the form of peroxynitrous acid ONOOH and five new isomers in the form of oxo-conformation OON(H)O) are presented in the work. The molecular structure of each isomer is characterized by a local minimum on the potential energy hypersurface of the HNO3 molecular system and corresponds to one of its stationary states. A theoretical study of the reactivity of nitric acid oxo-isomers characterized for the first time can provide adequate explanation for experiments on the autocatalytic use of nitric acid vapors in binding molecular nitrogen. The results obtained can be a direction for developing principally new methods to bind atmospheric nitrogen and activate methane, which are fundamental problems in chemical science and technology.
																								



3.
MODELING OF COMPLEXES BETWEEN CYTOCHROME P450 1A2 AND SUBSTRATES

A. A. Pogrebnoy, M. A. Grishina, V. A. Potemkin
Keywords: docking, modeling, complex, substrate, x-ray diffraction analysis, P450, 1A2, 2HI4
Pages: 852-858

Abstract >>
Based on the 2HI4 complex taken from the PDB database, molecular docking of 17 substrates in the cytochrome P450 1A2 cavity is performed using the 3D-QSAR algorithm CiS. The arrangement of substrate molecules in the 1A2 isoform cavity is considered, the orientation of the molecular reaction centers relative to heme is analyzed, and the character of interaction between substrates and active site aminoacid residues is investigated. The structures of the modeled complexes allow us to explain metabolic pathways in demethylation reactions and some reactions of hydroxylation, which enables an application of the CiS algorithm to predict metabolic pathways.
																								



4.
DFT-BASED QUANTUM THEORETIC QSPR STUDIES OF THE GLASS TRANSITION TEMPERATURES OF POLYACRYLATES

X.L. Yu, W.H. Yu, X.Y. Wang
Keywords: polyacrylates, density function theory, glass transition temperature, QSPR
Pages: 859-864

Abstract >>
A quantitative structure-property relationship (QSPR) model obtained by using multiple linear stepwise regression analysis, with correlation coefficient R of 0.979 for the training set and 0.951 for the validation set, was developed to predict the glass transition temperature (Tg) values of polyacrylates. Three quantum chemical descriptors (the molecular average polarizability α, the entropy S, and the lowest unoccupied molecular orbital ELUMO) obtained directly from polyacrylates monomer structure by density function theory (DFT) calculation, were used to produce the model. The result confirmed the role that quantum chemical descriptors play in studying QSPR of glass transition temperature for polymers.
																								



5.
GAS-PHASE ELECTRON DIFFRACTION AND QUANTUM CHEMICAL STUDY OF THE STRUCTURE OF THE 4-NITROBENZENE SULFONYL CHLORIDE MOLECULE

V. M. Petrov, V. N. Petrova, G. V. Girichev, N. I. Giricheva, H. Oberhammer, A. V. Bardina, S. N. Ivanov, A. V. Krasnov
Keywords: 4-nitrobenzene sulfonyl chloride, conformer, molecular structure, internal rotation, potential functions, gas-phase electron diffraction, quantum chemistry, mass-spectrometry
Pages: 865-872

Abstract >>
A combined gas-phase electron diffraction and quantum chemical (B3LYP/6-311+G**, B3LYP/cc-pVTZ, MP2/6-31G*, and MP2/cc-pVTZ) study of the structure of the 4-nitrobenzene sulfonyl chloride molecule is performed. It is found that at a temperature of 391(3) K only one conformer with Cs symmetry is present in the gas phase. The following experimental values of structural parameters are obtained: rh1(C-H)av = 1.086(6) Å, rh1(C-C)av = 1.395(3) Å, rh1(C1-S) = 1.773(4) Å, rh1(S=O) = 1.423(3) Å, rh1(S-Cl) = 2.048(4) Å, rh1(N-O) = 1.224(3) Å, rh1(N-C4) = 1.477(3) Å, ∠(1-S=O) = 109.0(4), ∠(Cl-S-O) = 106.7(2), ∠C1-S-Cl = 100.2(13), ∠O=S=O = 122.9(11), ∠O=N=O = 123.6(5). The C2-C1-S-Cl torsion angle that characterizes the position of the S-Cl bond relative to the benzene ring plane is 89(4). The NO2 group lies in the benzene ring plane. Internal rotation barriers calculated by B3LYP/6-311+G** and MP2/6-31G* methods are: V1 = 4.7 kcal/mol and 5.3 kcal/mol for the sulfonyl chloride group; V2 = 4.9 kcal/mol and 6.0 kcal/mol for the nitro group.
																								



6.
STRUCTURAL STUDIES OF L-seryl-L-HISTIDINE DIPEPTIDE BY MEANS OF MOLECULAR MODELING, DFT AND 1H NMR SPECTROSCOPY

Y. Liu, J.-B. Hou, X.-X. Liu, F.-M. Miao, Y.-F. Zhao
Keywords: Ser-His, dipeptide, molecular modeling, DFT, lowest energy structure
Pages: 873-877

Abstract >>
L-Seryl-L-histidine dipeptide is of scientific interest mainly because of its various biological activities. In this paper, the lowest energy structure of the dipeptide was determined by molecular modeling, and further validated by quantum chemistry calculations and 1H NMR spectroscopy.
																								



7.
STUDY OF CAFFEINE-DNA INTERACTION IN AQUEOUS SOLUTION BY PARALLEL MONTE CARLO SIMULATION

M. D. Kalugin, A. V. Teplukhin
Keywords: water, structure, caffeine, DNA, computer simulation, Monte Carlo, parallel computing
Pages: 878-889

Abstract >>
Monte Carlo simulation of caffeine aqueous solutions containing a superhelical -DNA fragment is performed using parallel computing. The binding sites of caffeine molecules with DNA were identified as well as the most probable structures of the resultant complexes. The degrees of caffeine molecule association in aqueous solutions with different concentrations were estimated and the main configuration types of molecular aggregates were revealed.
																								



8.
CHARACTERISTIC FEATURES OF CRYSTAL CHEMISTRY OF NATURAL MERCURY-CONTAINING SULFIDES AND SULFOSALTS

S. V. Borisov, S. A. Magarill, N. V. Pervukhina
Keywords: structure determining factors, cation and anion matrices, building blocks, structures of sulfides and sulfosalts, mercury-containing minerals
Pages: 890-897

Abstract >>
Many mercury-containing minerals belonging to the class of sulfides and sulfosalts are based on a highly symmetric sphalerite type structure (ZnS), where both components occupy sites with high point symmetry providing stable orientation of directed interatomic interactions. Some structures of natural compounds of this type are used to demonstrate that the geometric matrix of cations and anions tends to be preserved during variation of the chemical composition caused by migration of elements under natural conditions. The fundamental laws of crystal formation are confirmed: the governing role of the families of close packed (crystallographic) planes, the independence of ordering of different types of atoms, the tendency of sulfur atoms to mirror plane symmetry, and the trend to cluster formation in the development of crystal structures, as exemplified by [As4S12]12-, [(Cs,Tl)S12]23-, [Tl2S12]22- atomic groups.
																								



9.
STEREOCHEMISTRY OF VANADIUM IN OXYGEN-CONTAINING COMPOUNDS

V. N. Serezhkin, V. S. Urusov
Keywords: vanadium, oxygen-containing compounds, stereochemistry, crystal chemistry, Voronoi-Dirichlet polyhedra
Pages: 898-904

Abstract >>
Using Voronoi-Dirichlet (VD) polyhedra and the method of overlapping spheres, we analyze the coordination of 714 crystallographically different vanadium atoms in the structure of compounds containing VOn polyhedra. Vanadium atoms are found to be bonded to 4, 5, 6, or 7 oxygen atoms. The effect of the valence state and coordination number of vanadium atoms on the main parameters of their VD polyhedra is considered. A unified linear dependence between the solid angles of VD polyhedron faces corresponding to V-O bonds and the respective interatomic distances varying in a range of 1.55 Å to 2.79 Å is stated to exist. It is shown that the parameters of VD polyhedra can be used to determine the valence state of vanadium atoms.
																								



10.
ON METHODS TO DETERMINE THE SURFACE AREAS OF MOLECULES

M. A. Prokaeva, I. A. Baburin, V. N. Serezhkin
Keywords: surface area of molecules, Voronoi-Dirichlet polyhedra, Hirshfeld surface, van der Waals molecular models, intermolecular interactions
Pages: 905-910

Abstract >>
The known methods to determine the surface areas of molecules are discussed and a new method is proposed based on the molecule representation in the form of a molecular Voronoi-Dirichlet polyhedron. A linear correlation is found between the surface areas of molecules calculated using the molecular Voronoi-Dirichlet polyhedra and determined by the already known methods. The efficiency of the use of molecular Voronoi-Dirichlet polyhedra for the analysis of intermolecular interactions in crystal structures is demonstrated by concrete examples.
																								



11.
MOLECULAR AND CRYSTAL STRUCTURE OF TWO PHASES OF 1-FLUOROSILATRANE. SPECIFIC FEATURES OF THE ELECTRON DENSITY DISTRIBUTION

A. A. Korlyukov, M. Y. Antipin, M. I. Buzin, É. A. Zel'bst, Y. I. Bolgova, O. M. Trofimova, M. G. Voronkov
Keywords: 1-fluorosilatrane, molecular structure, X-ray diffraction, quantum chemical calculation
Pages: 911-916

Abstract >>
Using X-ray diffraction the presence of two phases of 1-fluorosilatrane (FSa) is stated and the specific features of their spatial structure are studied. Phase transition occurs at 156-158 K and is characterized by low energy. In the low-temperature phase, four crystallographically independent molecules are ordered, while in the high-temperature phase one of two independent molecules has disordered carbon β-atoms. A quantum chemical analysis of crystal packing in the low-temperature FSa phase is performed. The estimated value of the coordination N→Si bond strength in the crystal is 29.2 kcal/mol. The charge distribution indicates the localization of valence electron density around the O3SiF fragment.
																								



12.
SYNTHESES AND CRYSTAL STRUCTURES OF NINE-COORDINATE K2[EuIII(dtpa)(H2O)]5H2O AND Na2[TbIII(Httha)]6H2O COMPLEXES

B. Liu, Y.F. Wang, J. Wang, J. Gao, R. Xu, Y.M. Kong, L.Q. Zhang, X.D. Zhang
Keywords: Eu3+, Tb3+, Diethylenetriamine-N,N,N',N",N"-pentaacetic acid (H5dtpa), triethylenetetramine-N,N,N',N',N",N"-hexaacetic acid (H6ttha), complex
Pages: 917-923

Abstract >>
The title complexes, K2[EuIII(dtpa)(H2O)]5H2O (H5dtpa = diethylenetriamine-N,N,N′,N″,N″-pentaacetic acid), Na2[TbIII(Httha)]6H2O (H6ttha = triethylenetetramine-N,N,N′,N′,N″,N″-hexaacetic acid), were prepared, and their compositions and structures were determined by elemental analyses and single-crystal X-ray diffraction techniques. The crystal of K2[EuIII(dtpa)(H2O)]5H2O belongs to triclinic crystal system and P space group. The crystal data are as follows: a = 8.3540(17) Å, b = 10.147(2) Å, c = 15.059(3) Å, α = 84.63(3), β = 82.02(3), γ = 83.96(3), V = 1253.1(4) Å3, Z = 2, R = 0.0325 and wR = 0.1013 for 4407 observed reflections with I ≥ 2σ(I). The [EuIII(dtpa)(H2O)]2- has a nine-coordinate pseudo-monocapped square antiprismatic structure, in which the nine coordinate atoms, three N and six O are from one dtpa ligand and one water molecule. The crystal of the Na2[TbIII(Httha)]6H2O belongs to monoclinic system and P21/c space group. The crystal data are as follows: a = 10.3976(10) Å, b = 12.7908(13) Å, c = 23.199(2) Å, β = 90.914(2), V = = 3084.9(5) Å3, Z = 4, R = 0.0309 and wR = 0.0704 for 5429 observed reflections with I ≥ ≥ 2σ(I). In the [TbIII(Httha)]2-, the Tb3+ ion is nine-coordinated yielding a pseudo-monocapped square antiprismatic conformation, in which the ttha ligand coordinates to the central Tb3+ ion with four N atoms and five O atoms. There is a free non-coordinate carboxyl group (-CH2COOH) that can be modified by some biological molecules having target function.
																								



13.
SUPRAMOLECULAR INTERACTIONS AND STRUCTURAL TRANSFORMATIONS IN THE METAL-ORGANIC SORBENT-ACETONE NANOREACTOR SYSTEM

S. P. Gabuda, S. G. Kozlova, D. N. Dybtsev, V. P. Fedin
Keywords: metal-organic sorbent, Raman spectroscopy, 1H NMR, proton exchange, keto and enol forms of acetone
Pages: 924-930

Abstract >>
By the 1 NMR and Raman spectroscopy data it is shown that in the porous inclusion compound of Zn2(C8H4O4)2[(N2(CH2)6))]n(CH3)2CO (n ≈ 0-4.7) acetone molecules exist in two structural forms: ketonic (CH3)2CO, for which the 1 NMR chemical shift value is δket = 0.8 ppm, and enolic CH3C(O)=CH2, for which δen() = 11 ppm, δen(CH2) = 8.9 ppm, and δen(CH3) = 1.6 ppm are found, the average value over three proton sites being 〈δen〉 = 5.6 ppm. A sharp difference in chemical shift values for the keto and enol forms of acetone in the inclusion compounds can be assigned to the effect of structural chemical conditions in two types of adsorption centers.
																								



14.
CHROMATO-MASS-SPECTROMETRIC IDENTIFICATION OF COMPOUNDS WITH A BRANCHED CARBON SKELETON. CRITERIA FOR IDENTIFYING tert-BUTYL GROUPS IN THE STRUCTURE OF MOLECULES

I. G. Zenkevich
Keywords: organic compounds, structural analogues, tert-butyl group, mass spectrometry, gas chromatographic retention indices, identification
Pages: 931-945

Abstract >>
The previously proposed method of the integrated interpretation of mass-spectrometric and chromatographic data is applied to compounds with a branched carbon skeleton, namely, hydrocarbons containing tert-butyl groups. We estimate the increments of chromatographic retention indices for a hypothetical (3)33 transformation and determine the factors affecting their value. Several simple mass spectral characteristics are recommended to reveal tert-butyl groups in the structure of analyte molecules; however, one of the most informative criterion is to estimate the total number of carbon skeleton branches based on the homological increments of retention indices. The work shows high efficiency of the identification method proposed when the analytical and reference data are scarce.
																								



15.
PROJECTION INVERSIONS OF KNOTTED MOLECULAR STRUCTURES

L. I. Makarov
Keywords: knotted molecular structure, diagram graph representation, inversion
Pages: 946-950

Abstract >>
Some projection conversions of molecular structures containing a loop of elements with a topological model in the form of a knot are studied. We describe a graph representation of knot diagrams and inversion algorithms for points in the knot projection to obtain various projections.
																								



16.
EPR STUDY OF SOLID SOLUTIONS OF [Cr(NH3)5Cl]x[Rh(NH3)5Cl]1-x[PdCl4]nH2O AND [Cr(NH3)5Cl]x[Rh(NH3)5Cl]1-x[PtCl4] COMPOUNDS

V. A. Nadolinny, N. A. Nebogatikova, P. E. Plyusnin, S. V. Korenev
Keywords: EPR spectroscopy, chromium, rhodium, palladium, platinum, chloropentaammine complexes
Pages: 951-954

Abstract >>
In order to determine the features of the structure of double complex salts (DCSs) of [Cr(NH3)5Cl]×
[MCl4]nH2O, where M = Pd, Pt, n = 0, 1, the DCS solid solutions of palladium and platinum with isostructural DCSs containing the chloropentaammine rhodium cation, [Cr(NH3)5Cl]x[Rh(NH3)5Cl]1-x× [MCl4]nH2O, where x = 0.01-0.2, are synthesized and studied by the EPR method. DCSs with the isostructural chloropentaammine rhodium cation are used as a diluter for magneto concentrated systems. It is shown that DCS of platinum and anhydrous DCS of palladium have the identical environment of chromium ions. The EPR spectra of chromium ions for these compounds are described by the following spin Hamiltonian parameters: S = 3/2, gxx = 1.987, gyy = 1.987, gzz = 1.985, D = 1660 Gs, E = 235 Gs. For the palladium complex containing crystalline water, the EPR spectra of chromium ions are described by the parameters: S = 3/2, gxx = 1.984, gyy = 1.984, gzz = 1.984, D = 1060 Gs, E = 350 Gs. A decrease in the crystal field parameters for the aqueous palladium complex is caused by a redistribution of the electron density to the oxygen atom in the second sphere of the chromium ion environment.
																								



17.
STRUCTURE OF Ir-Al2O3 COATINGs OBTAINED BY CHEMICAL VAPOR DEPOSITION IN THE HYDROGEN ATMOSPHERE

N. V. Gelfond, N. B. Morozova, I. K. Igumenov, E. S. Filatov, S. A. Gromilov, R. I. Kvon
Keywords: Ir and Ir-Al2O3 composite coatings, chemical vapor deposition, iridium(III), aluminum(III), tris-acetylacetonates
Pages: 955-959

Abstract >>
Chemical vapor deposition is used to obtain Ir and Ir-Al2O3 coatings with a thickness of up to 5 μm and growth rate of 2.5 μm/h on steel substrates previously covered with an alumina layer. Tris-acetylacetonates of Ir(III) and Al(III) are used as precursors. The deposition process is carried out at the atmospheric pressure in the presence of hydrogen. The coatings obtained are studied by X-ray diffraction, X-ray photoelectron spectroscopy, and scanning electron microscopy. A dependence of the structure and composition of coatings on their preparation conditions is found.
																								



18.
PATHWAYS OF CONFORMATIONAL ISOMERIZATION of 4-PHENYL-1,3-DIOXANE

V. V. Kuznetsov, A. E. Kuramshina, S. A. Bochkor
Keywords: 4-phenyl-1,3-dioxane, conformer, minimum of the potential energy surface, twist-form, quantum chemistry
Pages: 960-962

Abstract >>
A study of the potential energy surface of 4-phenyl-1,3-dioxane by non-empirical quantum chemical RHF/STO-3G and 6-31G(d) approximations reveals six energetically inequivalent pathways of conformational isomerization of equatorial and axial chair forms.
																								



19.
MOLECULAR AND CRYSTAL STRUCTURE OF 2,4-DIETHOXYCARBONYL-5-HYDROXY- 5-METHYL-3-PHENYL-N-(3-CHLOROPHENYL)-1-CYCLOHEXENYLAMINE

A. P. Kriven'ko, É. A. Grigor'eva, A. V. Grigor'ev, V. V. Sorokin, S. F. Solodovnikov
Keywords: X-ray structural analysis, enaminoesters, cyclohexenes
Pages: 963-966

Abstract >>
Arylamination of 2,4-diethoxycarbonyl-5-hydroxy-5-methyl-3-phenylcyclohexanone affords 2,4-diethoxycarbonyl-5-hydroxy-5-methyl-3-phenyl-N-(3-chlorophenyl)-1-cyclohexenylamine. A distorted semi-chair conformation with psedoequatorial orientation of all substituents except the pseudoaxial -group is established based on the spectral and single crystal XRD data. The presence of an intramolecular N-ͅ=C hydrogen bond is noted.
																								



20.
ANALYSIS OF RELAXATION ON POLYPROPYLENEGLYCOLS ABOVE VITRIFICATION TEMPERATURE

T. M. Usacheva, N. V. Lifanova, V. I. Zhuravlev, V. K. Matveev
Keywords: polypropyleneglycols, dielectric spectra, dipole moments of clusters, dipole moments of molecules, intermolecular interactions
Pages: 967-979

Abstract >>
The dielectric spectra of polypropyleneglycols H-(C3H6O)N-OH (PPGs), where N = 1, 2, 3, 7, 12, 17, 20, 34, 69, were analyzed in terms of the Dissado−Hill (DH) cluster model above the vitrification temperatures. In PPGs, the structural clusters are associates formed by intra- and intermolecular hydrogen bonds. The activation processes of cleavage and formation of intermolecular hydrogen bonds in clusters, when the total number of intermolecular hydrogen bonds changes, are characterized by the parameter nDH. The fluctuation processes of simultaneous exchange of molecules between adjacent clusters correspond to redistributions of intermolecular hydrogen bonds between clusters, when only the position but not the total number of intermolecular hydrogen bonds changes, and are characterized by the parameter mDH. The relaxation time τDH at 303 K and 423 K and the parameters nDH and mDH of the dielectric spectra were calculated. The activation energies of relaxation in the range 210-323 K were determined. The mean statistic squares of the dipole moments of clusters and di-PG, PPG-425 (N = 7), and PPG-2025 (N = 34) molecules at 303 K and 423 K were calculated. The number of the units of the oxypropylene chains involved in relaxation was determined. The dependence of the parameters of the DH model, relaxation energies, , and on N were studied.
																								



21.
REACTIONS OF GUANIDINE POLYMETHACRYLATE WITH ZINC(II) TETRA-4-SULFOPHTHALOCYANINE SODIUM SALT IN AQUEOUS MEDIA

N. A. Pavlycheva, T. E. Popova, N. S. Lebedeva, S. Y. Khashirova, A. I. V'yugin
Keywords: immobilization of water-soluble metallophthalocyanines on polymers, zinc(II) tetra-4-sulfophthaloxyanine sodium salt, guanidine polymethacrylate, conformation, quantum-chemical calculations, viscosimetry, IR spectroscopy
Pages: 980-985

Abstract >>
The interaction of the zinc(II) tetra-4-sulfophthalocyanine sodium salt with guanidine polymethacrylate has been studied by electronic absorption (EAS) and IR spectroscopy and viscosimetry. It was found that the reaction between the macroheterocyclic compound and the polymer proceeds due to the binding of the sulfo groups of metallophthalocyanine and the guanidine cation of the polymer, which leads to an extension of the polymer knot and stabilization of its conformation.
																								



22.
COMPLEXES OF FERROMAGNETIC FLUIDS WITH PHOTODITAZIN AND THEIR PROMISING APPLICATIONS IN PHOTODYNAMIC THERAPY

Y. V. Kulvelis, V. A. Trunov, V. T. Lebedev, D. N. Orlova, D. Torok, M. L. Gelfond
Keywords: photodynamic therapy (PDT), photoditazin, magnetic fluids, neutron scattering
Pages: 986-990

Abstract >>
Nanosized complexes of ferroparticles with a sensitizer photoditazin (used in photodynamic therapy in oncology) have been synthesized and studied by small-angle neutron scattering. The structure of the complexes was determined, and the influence of the biocompatible polymer pluronic investigated. Clinical tests revealed increased efficiency of the complexes compared with the starting photoditazin. The complexes can be used as the first magnetically operated sensitizer for treatment of oncological diseases by photodynamic therapy.
																								



23.
CONFORMATION ANALYSIS OF NUCLEIC ACIDS AND PROTEINS ADSORBED ON SINGLE-SHELL CARBON NANOTUBES

G. I. Dovbeshko, O. M. Fesenko, E. D. Obraztsova, K. R. Allakhverdiev, A. E. Kaja
Keywords: carbon nanotubes, DNA, polyadenylic acid potassium salt (PolyA), rhibonuclease , bovine serum albumin
Pages: 991-998

Abstract >>
This paper presents a concise review of the experimental and calculated data reported in the literature on the noncovalent interactions of DNA and proteins with the nonfunctionalized carbon nanotubes. Our Raman scattering and electron microscopy data on carbon nanotubes and SEIRA spectral data on changes in the conformational state of the main biological polymers (DNA, Poly, BSA, and RNase ) in reactions with single-shell carbon nanotubes allowed us to define the character of noncovalent interactions in the tube−biomolecule system. An analysis of the data showed that reactions of DNA with nanotubes lead to the binding on the surface of the nanotube and form stable complexes with van der Waals interactions, in which π stacking plays the major role and which changes the hydrogen bonds in the biological molecule with structure rearrangements. Albumin and RNase are presumably adsorbed at the conventional binding sites of these proteins on the nanotube with participation of hydrophobic interaction and π stacking, as indicated by structure rearrangements in proteins.
																								



24.
LIGHT-INDUCED NONCOVALENT FIXATION OF DNA AND SYNTHETIC POLYIONS ON THE SURFACE OF SILICON SINGLE CRYSTALS

I. L. Volkov, N. V. Bazlov, A. S. Bondarenko, O. F. Vyvenko, N. A. Kas'yanenko
Keywords: DNA, polyions, silicon surface, noncovalent fixation, light, AFM
Pages: 999-1006

Abstract >>
The paper presents a simple method for fixing DNA and synthetic polyions on the surface of p and n type Si(100) single crystals. Different methods for preparing the surface for DNA fixation are compared. It is shown that the conformation of macromolecules fixed on a substrate depends on the presence of bivalent counterions in solution and the charge properties of the surface and polymer. The results of fixation were checked and analyzed by atomic force microscopy (AFM).
																								



25.
CONFORMATIONAL CHANGES OF DNA γ-IRRADIATED IN THE PRESENCE OF ALIPHATIC ALCOHOLS IN SOLUTION

S. V. Paston, V. V. Zamotin
Keywords: DNA conformation, quality of solvent, water?alcohol solutions, ? radiation, radicals
Pages: 1007-1013

Abstract >>
The conformational changes of DNA in aqueous solutions containing ethanol and iso- and n-propanol having concentrations of 0-23 wt.% and ionic strength μ = 0.003 NaCl and exposed to γ radiation at doses from 0 Gy to 30 Gy were studied by low-gradient viscosimetry and circular dichroism. The dependence of the specific volume (Vsp) of DNA on the radiation dose changed at different contents of alcohol. There is a critical concentration (cr) at which the structure of the mixed solvent is rearranged. The Vsp of DNA decreased as the radiation dose increased at alc = 12 wt.% < cr and increased at alc = 23 wt.% > cr. In both cases, the largest Vsp of DNA was observed in water−ethanol solutions. The secondary structure of the macromolecule in the systems corresponds to the form. It was shown that the observed conformational changes in irradiated DNA at alc < cr and alc > cr could not be explained only by the ability of alcohols to intercept the radicals formed in radiolysis of water.
																								



26.
CHANGES IN THE SECONDARY STRUCTURE OF HMGB1 PROTEIN BONDED TO DNA

. Y. Rodionova, . V. Chikhirzhina, V. I. Vorob'yov, A. ??. Polyanichko
Keywords: HMGB1, DNA, DNA?protein interactions, circular dichroism
Pages: 1014-1020

Abstract >>
The stage of noncooperative interaction of the chromosomal nonhistone protein HMGB1 with DNA has been studied by spectroscopic methods and gel retardation. It was found that complexation was accompanied by compaction of the DNA molecule over a wide range of protein/DNA ratios in the complex. A circular dichroism study showed that the binding with DNA changed the secondary structure of the HMGB1 protein. Changes in the structure of the protein start under the conditions of an excess of binding sites on DNA and end at a ratio of ~40-50 base pairs per protein molecule, the α-helicity of HMGB1 in the complex increasing by 20% compared with the free state. It is believed that the change in the secondary structure of HMGB1 during the binding with DNA underlies the mechanisms of the various functions of this protein in the cell.
																								



27.
THEORETICAL STUDIES OF THE ELECTRONIC AND STRUCTURAL FEATURES OF THE FRAGMENTS OF DIHYDROPHOLATE REDUCTASE INHIBITORS

E. S. Afonkina, E. S. Pereyaslavskaya, V. A. Potemkin, M. A. Grishina, G. L. Rusinov, O. V. Fedorova
Keywords: 3D- and 4D-QSAR, biological activity, dihydrofolate reductase, inhibitor, pharmacophore, multiconformation analysis
Pages: 1022-1026

Abstract >>
The effects of the structural characteristics of dihydrofolate reductase (DHFR) inhibitors on their tuberculostatic activity have been analyzed. It was shown that an increase in the electron density on bonds and atoms in the ring led to an increase in the biological activity of the compounds. A correlation was found between the biological activity and the characteristics of the critical points of electron density of bonds. The 3D- and 4D-QSAR studies with the CiS algorithm revealed the pharmacophore and antipharmacophore fragments of DHFR inhibitors, and regions of the receptor that are responsible for the biological action of dihydropyrimidines were found. Receptor−ligand complexes were modeled. For a series of drugs containing a podand chain, it was found that the chain performed only the transport membranotropic function because the increase in the size of molecules due to the podand chain gives rise to steric hindrances when the chain is built in the receptor cavity.
																								



28.
EFFECTS OF THE NATURE OF COUNTERIONS IN SOLUTION ON INTERACTIONS OF PHENOXAZONES, XANTHONES, AND CARBAZOLES CONTAINING BENZO-CROWN GROUPS WITH DNA

. B. Moroshkina, . . Bogdanov, . . Kolonistova, . B. Sedova, . . Urusova
Keywords: DNA, benzo-crown-containing phenoxazones, xanthones and carbazoles, spectrophotometry, circular dichroism, viscosimetry, optical anisotropy, interaction, intercalation
Pages: 1027-1033

Abstract >>
The interactions of DNA with phenoxazones, xanthones, and carbazoles containing the (benzo-18-crown-6)-4′-yl and (benzo-15-crown-5)-4′-yl radicals bonded to the chromophore via spacers of different lengths in the presence of Na+ and K+ ions were studied by spectrophotometry, circular dichroism, and dynamic birefringence. The thermodynamic parameters of the binding of the compounds with DNA and changes in the macromolecular parameters of the DNA molecule during complexation were determined. Based on the results of these studies, we suggested the models of bonding of these compounds to the double helix of DNA. It is shown that the mode of DNA binding with a phenoxazone derivative containing two (benzo-15-crown-5)-4′-yl radicals bonded via a fragment of glycine to chromophore depends on the type of the counterion in solution. In the presence of Na+, the chromophore is intercalated into the double helix of DNA; in the presence of K+, it is bound to DNA in the form of a dimer outside the double helix. The type of the counterion does not affect the mode of binding of other crown-containing compounds of actinocin with DNA. For compounds containing the (benzo-18-crown-6)-4′-yl radical, the mode of binding to DNA depends only on the spacer length.
																								



29.
EFFECTS OF PALLADIUM ACIDO COMPLEXES [Ln]m[PdX4] ON THE CONFORMATION OF DNA IN VITRO

N. A. Kas'yanenko, E. V. Levykina, O. S. Erofeeva, N. ??. Ivanova, I. A. Efimenko
Keywords: DNA, morphodone, palladium acido complexes, atomic force microscopy
Pages: 1034-1044

Abstract >>
The interactions of palladium cation−anion compounds (C4H10NO)2[PdCl4], K2[PdCl4], and K2[PdBr4] with DNA in 0.005 M NaCl and 0.15 M NaCl solutions were studied by spectrophotometry, circular dichroism, viscosimetry, dynamic birefringence, and atomic force microscopy. The interactions are primarily effected by coordination of the donor atoms of DNA bases by palladium. The end products of interactions with palladium acido complexes are independent of the macromolecule and the nature of halogen X in [PdX4]2-. The significant changes in the conformation of DNA in palladium complexes resulted from both intra- and intermolecular cross-linkings induced by palladium.
																								



30.
CHARACTERISTICS OF ULTRASONIC CLEAVAGE OF DNA

Y. D. Nechipurenko, M. V. Golovkin, D. Y. Nechipurenko, I. A. Il'icheva, L. A. Panchenko, R. V. Polozov, S. L. Grokhovskii
Keywords: ultrasonic cleavage of DNA, conformational heterogeneity of DNA, gel electrophoresis, site specificity, footprinting
Pages: 1045-1052

Abstract >>
The site effect (the dependence of the band intensity on the band position of gel) is the key factor that should be taken into account in quantitative analysis of the images of high-resolution electrophoretic gels containing many bands. We developed two procedures for taking this effect into account. The dependence of the relative frequencies of internucleotide bond cleavages on the type of nucleotide, obtained in the analysis of the splitting patterns of DNA fragments under the action of ultrasound or chemical factors, was evaluated by ) using the linearly sliding mean; b) describing the function of the site dependence as a third degree polynomial. The methods lead to similar results. An analysis of the splitting of different sequences, whose total length was more than 20,000 nucleotides, allowed us to determine the relative frequencies of bond cleavages in all 16 dinucleotides found in a DNA sequence. In ultrasonic treatment, the phosphodiester bond, lying between cytosine and guanine, undergoes cleavage more often than the corresponding bonds between other nucleotides in the sequence.