Home – Home – Jornals – 2009 number 5

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(С=С) are most conformation sensitive. The calculated value of I(С=С) for vinyl phenyl ether more than twice exceeds the corresponding value for vinyl methyl ether. The calculated and experimental values of I(С=С) 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,р,π-interaction.

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.

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.

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 (T_g) values of polyacrylates. Three quantum chemical descriptors (the molecular average polarizability α, the entropy S, and the lowest unoccupied molecular orbital E_LUMO) 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.

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 C_s symmetry is present in the gas phase. The following experimental values of structural parameters are obtained: r_h1(C-H)_av = 1.086(6) Å, r_h1(C-C)_av = 1.395(3) Å, r_h1(C1-S) = 1.773(4) Å, r_h1(S=O) = 1.423(3) Å, r_h1(S-Cl) = 2.048(4) Å, r_h1(N-O) = 1.224(3) Å, r_h1(N-C4) = 1.477(3) Å, ∠(С1-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.

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.

Monte Carlo simulation of caffeine aqueous solutions containing a superhelical В-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.

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.

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 VO_n 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.

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.

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.

The title complexes, K₂[Eu^III(dtpa)(H₂O)]·5H₂O (H₅dtpa = diethylenetriamine-N,N,N′,N″,N″-pentaacetic acid), Na₂[Tb^III(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[Eu^III(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) ų, Z = 2, R = 0.0325 and wR = 0.1013 for 4407 observed reflections with I ≥ 2σ(I). The [Eu^III(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[Tb^III(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) ų, Z = 4, R = 0.0309 and wR = 0.0704 for 5429 observed reflections with I ≥ ≥ 2σ(I). In the [Tb^III(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.

By the ¹Н 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 ¹Н NMR chemical shift value is δ^ket = 0.8 ppm, and enolic CH₃C(OН)=CH₂, for which δ^en(ОН) = 11 ppm, δ^en(CH₂) = 8.9 ppm, and δ^en(CH₃) = 1.6 ppm are found, the average value over three proton sites being 〈δ^en〉 = 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.

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 (СН₃)₃С → СН₃ 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.

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.

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, g_xx = 1.987, g_yy = 1.987, g_zz = 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, g_xx = 1.984, g_yy = 1.984, g_zz = 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.

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.

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.

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 ОН-group is established based on the spectral and single crystal XRD data. The presence of an intramolecular N-Н…О=C hydrogen bond is noted.

The dielectric spectra of polypropyleneglycols H-(C₃H₆O)_Nр-OH (PPGs), where N_р = 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 n_DH. 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 m_DH. The relaxation time τ_DH at 303 K and 423 K and the parameters n_DH and m_DH 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_р = 7), and PPG-2025 (N_р = 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_р were studied.

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.

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.

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, PolyА, BSA, and RNase А) 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 А 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.

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).

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 М 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 (V_sp) of DNA on the radiation dose changed at different contents of alcohol. There is a critical concentration (С_cr) at which the structure of the mixed solvent is rearranged. The V_sp of DNA decreased as the radiation dose increased at С_alc = 12 wt.% < С_cr and increased at С_alc = 23 wt.% > С_cr. In both cases, the largest V_sp of DNA was observed in water−ethanol solutions. The secondary structure of the macromolecule in the systems corresponds to the В form. It was shown that the observed conformational changes in irradiated DNA at С_alc < С_cr and С_alc > С_cr could not be explained only by the ability of alcohols to intercept the ОН radicals formed in radiolysis of water.

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.

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.

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 зdepends only on the spacer length.

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.

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 а) 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.