Том 58, № 2 (2017)

A computer simulation of complexes of (6,6) open carbon nanotubes (CNTs) with neutral molecules, zwitterions and glycine, alanine, and phenylalanine amino acid anions is performed. In starting structures amino acids are arranged in three types: on the external side face, the open end, and inside CNT. The structure is optimized within the density functional theory with regard to the GD3 dispersion correction with and without taking into account solvation effects. It is found that the greatest CNT–amino acid interaction occurs in the neutral aqueous medium at dissociative chemisorption of the zwitterion (adsorption energy 80-90 kcal/mol) and in the basic medium at anion chemisorption (energy ~48-50 kcal/mol) on the open CNT end.

Conformational properties of a benzenesulfonic acid hydrazide molecule and its para-nitro and para-methyl derivatives, which have found wide application as porofors and biologically active compounds, are studied. It is found that the benzenesulfonic acid hydrazide molecule has six conformers with relative energies of 0//0 kcal/mol, 0.34//0.98 kcal/mol, 2.51//2.25 kcal/mol, 2.54//2.56 kcal/mol, 2.90//3.28 kcal/mol, 6.64//6.43 kcal/mol (MP2//DFT(B3LYP) with the cc-pVTZ basis set), each conformer has enantiomer. The conformers differ from each other in the relative orientation of the fragments of the–SO2NHNH2 group, the energies of the frontier orbitals, the direction and value of the dipole moments. It is shown that the introduction of a nitro or methyl group into the para-position practically does not affect the conformational properties of the sulfonyl hydrazide group. Change in the structure of benzenesulfonic acid hydrazide during the crystal–gas transition is considered and it is revealed that in the crystal the conformation similar in structure to one of the high-energy conformers of the free molecule is stabilized. The NBO analysis of the electron density distribution is performed and it is shown that the occurrence of the gauche effect in all conformers of the molecules under study can be interpreted by the manifestation of the total action of strong anomeric effects between the lone pairs of nitrogen atoms and antibonding orbitals of S=O, N–H, C–S, and N–S bonds.

The structural and optical properties of 3-substitutedphenyl-1,5-diphenylformazans are studied by quantum chemical methods. The density functional theory (DFT) is employed to optimize the ground state geometries of formazans substituted with different electron donating and withdrawing groups in both gas and solvent phases. The absorption spectra of formazan derivatives are calculated using time dependent density functional theory (TD-DFT). The polarizable continuum model (PCM) calculations of 3-substitutedphenyl-1,5-diphenylformazans are performed for bulk solvent effects. The geometrical parameters, vibrational frequencies, and relative stabilities of isomers of 3-substitutedphenyl-1,5-diphenylformazans are studied. The results obtained by TD-DFT calculations reveal that the substitution of electron withdrawing and donating substituents affects the absorption spectra of 3-substitutedphenyl-1,5-diphenylformazans. The calculated maximum absorption wavelengths (λ_max) are highly consistent with the experimental values as found from UV-vis spectra.

There are experimental evidences that in the methanol solution of glycyrrhizic acid (GA) and cholesterol, the cholesterol molecules have two different types of the environment. One corresponds to free molecules and another corresponds to the molecules associated with GA. However, the nature of these associates remains unclear. The all-atom molecular dynamics simulation of GA solutions in methanol is performed. It is shown that, contrary to aqueous solutions, GA in methanol does not form small stable clusters, even in the presence of cholesterol. The arising associates do not have distinct structures and exist for no longer than dozens of nanoseconds. The concentrations of these clusters and their stability constants are estimated. It is necessary to assume the existence of larger-scale associates to explain the experimental data.

Six new derivatives of perhydropyrimidine-2-ones obtained in a three-component system of urea, aromatic aldehydes, and dichloromethylacetylbenzoylmethanes are studied by single crystal X-ray diffraction. The molecules have three chiral centers, but out of four possible diastereomeric pairs for each of the compounds, crystals of only one diastereomer are obtained. Moreover, four of them crystallize as true racemates, and two as racemic conglomerates. Crystals of five compounds are solvates with solvents of different nature (water, acetonitrile, dimethylformamide, dimethylsulfoxide). Crystals of the compounds are stabilized by both classical hydrogen bonds of N–H⋯O and O–H⋯O types and interactions of the С–H⋯O type.

Schiff bases and their metal complexes have a number of biological activities such as antidepressant, analgesic, antimicrobial, antiviral, and antitumor. In the present studies, the 1-((E)-(pentylimino)methyl)naphthalen-2-ol ligand is prepared by the reaction of 2-hydroxynaphthaldehyde with n-amyl amine. The ligand results in CoL₃, NiL₂ and CuL₂ complexes when reacted with the cobalt acetate, nickel acetate, and copper acetate salts respectively. The complexes along with their ligand are fully characterized by X-ray diffraction studies and biologically screened. The ligand structure reveals that it is a zwitterion species where the iminic nitrogen atom is protonated and the C–O bond shows a high double bond character. The cobalt complex has an octahedral geometry around the metal center and each nitrogen atom is in the trans position to the oxygen donor site. On the other hand, the copper complex shows a centrosymmetric square planar coordination, and in this case, the nitrogen sites are trans to each other. The complexes and the ligand are found to be more potent than the standard drugs used against some microbes in their preliminary biological studies.

The review is devoted to measurement methods of bond rupture forces in complex biological molecules, namely, the unwinding forces of a DNA double helix. Mechanical methods not affecting electromagnetically a system under study, which is especially significant for biological systems, are considered. We describe two main methods: atomic force microscopy and rupture event scanning. The latter is a new method also based on the mechanical action but it has a much simpler instrumental implementation. The capabilities of both methods are compared and they are shown to be promising to investigate chemical bond rupture forces in biological systems. The application of these methods to study the strength of chemical bonds is associated with overcoming numerous technical difficulties in both performance of measurements themselves and chemical modification of conjugated surfaces. We demonstrate the applicability of these methods not only for fundamental studies of the strength of chemical bonds determining the stability and the related possibility of functioning of three-dimensional biomolecular complexes, but also for the design of biosensors based on the mechanical effect (quartz crystal microbalance, QCM), e.g., with an opportunity of rapid analysis of DNA.

Molecular orbital populations of an ab initio wave function of the tetra-heme cytochrome с 1M1P are analyzed to show mutual polarization of amino acids, as predicted by the effect of the mutual polarization of amino acids in biomolecules, which has previously been described by the author.

Spin-forbidden CO binding to the iron–sulfur cluster-free hydrogenase (Hmd) is studied by the DFT calculation. The result shows that the surface of the triplet causes a PHmd–CO minimum and that ^3,5MECP is the lowest energy path to PHmd–CO. It is found that this CO binding involves a low barrier of 0.931 kcal/mol because of the need to change from a bound triplet state to the Hmd quintet ground state.

By interaction of AgClO₄ with 2-amino-5-allylthio-1,3,4-thiadiazole (Aаtd) in the ethanol solution, a new [Ag(Aаtd)(ClO₄)] π complex is obtained. It is studied by single crystal X-ray diffraction.

A single crystal X-ray diffraction analysis of 4-dichloromethylene-5-benzoyl-6-phenyl-perhydropyrimidin-2-one and its functionally substituted analogue with a methylcarbonyl substituent at the N(1) atom in the heterocycle is performed. The molecules of both compounds have two chiral centers. Only rel(S,R)-diastereomers are found in the crystals (the crystals are centrosymmetric). In the 4-dichloromethylene-5-benzoyl-6-phenyl-perhydropyrimidin-2-one molecule the heterocycle is in the С(6)-sofa conformation, whereas the molecule of the substituted analogue has a distorted boat conformation. Due to classical hydrogen bonds there are 1D and 0D supramolecular structures in the crystals of the studied compounds. Interactions of the С–H⋯O type, which only stabilize the structure of already formed associates rather than link the chains or dimers with each other, are also noted.

The asymmetric unit of the title compound C₁₄H₁₂BrN (systematic name (E)-N-(4-bromophenyl)-1-(p-tolyl)methanimine) contains one half-molecule: a crystallographic center of inversion is located at the midpoint of the bridging N=C bond. The central HC=N unit makes dihedral angles of 15.7(3)° and 15.2(4)° with bromobenzene and methylbenzene ring systems, respectively. The C and N atoms of the HC=N central unit are disordered over two sites in a 50:50 ratio. The Br atom of the 4-bromoaniline ring and the methyl atom of the 4-methylbenzilidene ring systems are also 50% disordered. In the crystal, molecules are linked by C–H⋯π interactions forming slabs parallel to the bc plane. The atomic coordinates are not available for the previously reported crystal structure of the title compound: CSD refcode MBZCLE. The reported R factor of 0.103 for the analysis in the space group P2₁/a is much higher than in the present analysis, which gives 0.033 in the space group P2₁/c.

Based on the information from the Cambridge Structural Database, 28 crystalline homomolecular structures of α,ω-diols are analyzed (five of them at two temperature). Two variants of violation of the A. I. Kitaigorodsky “centrosymmetric rule” are found: 1) approximately centrosymmetric molecules do not take positions in the centers of inversion, which are present in space groups; 2) the compound forms two polymorphs, one of which obeys the rule and in another the molecules have a substantially non-centrosymmetric conformation. It is shown that the molecular coordination number found from the calculation of distances combines the molecules whose interactions with the central molecule often have strongly different contributions to the crystal energy. The idea of the energy coordination number of molecules is introduced. It is found that in compounds with similar structures this parameter can have diverse values that are not an unambiguous consequence of the number of hydrogen bonds formed by molecules or the number of molecules thus bonded to the central one.

Electrospray ionization mass spectrometry is used to study thymidine solutions in the presence of copper ions and EDTA. The results show formation of thymidine–EDTA complexes in the absence of CuCl₂, and the existence of thymidine–EDTA–CuCl₂ complexes in a CuCl₂ and EDTA containing thymidine solution. The stoichiometry of the complexes is determined.

The work considers DNA complexes with silver ions and a silver coordination compound containing phenanthroline ligands. The formation conditions of luminescent silver nanoclusters and nanoparticles having a plasmon resonance are analyzed. It is shown that nanoclusters form on reducing silver ions after the formation of their coordination bonds with nitrogenous bases of the macromolecule. The [Ag(Phen)₂]NO₃ compound cannot form such a bond and interacts with DNA by intercalating one of the phenanthroline ligands into a double helix. The preliminary binding of cis-DDP with DNA hinders the formation of silver nanoclusters.

In the cell culture experiments, the AEDL peptide proved to be an efficient agent stimulating the cell renewal processes and the enhancement of the functional activity of bronchial epithelial cells. A presumed target of the peptide action is a DNA molecule. The work studies the peptide binding with high-molecular DNA in solutions with different ionic strengths. The spectral (UV spectophotometery and circular dichroism) and hydrodynamic (viscosimetry) methods show that, under the experimental conditions, the AEDL peptide forms a complex with DNA and that nitrogen bases are involved in the binding. The character of spectral changes in DNA suggests a possible interaction of the AEDL peptide with DNA in the major furrow at the guanine N7 site without a visible distortion of the double helix structure.