Home – Home – Jornals – Journal of Structural Chemistry 2017 number 2

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.

Electronic, vibrational, and electronic vibrational spectra of the 7-azaindole dimer, the 7-azaindole complex with a water molecule, and their tautomers are calculated. Transition states are considered based on the analysis of frequencies and shapes of low-frequency vibrations and the Mulliken charge redistribution. The performed quantum chemical calculation of chemical reactions enabled the determination of the structure of transition states and proton transfer conditions. It is shown that in the 7-AzI dimer the proton transfer has a consistent character with the formation of a zwitterionic form. The structure of excited states is calculated and the fluorescence spectra of the first electronic transitions that can be used as a criterion of the formation of 7-AzI tautomers as a result of chemical reactions proceeding through a proton transfer in the 7-azaindole dimer and the 7-azaindole complex with a water molecule are interpreted.

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 an enantiomer. Conformers differ from each other in the relative orientation of fragments of the -SO₂NHNH₂ group, energies of frontier orbitals, the direction and value of 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. A change in the structure of benzenesulfonic acid hydrazide in 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 Felbamate is a novel anticonvulsant and neuropathic pain drug that can exist as three possible tautomers. Herein, employing density functional theory (DFT) and handling the solvent effects with the PCM model, the structural parameters, energy behavior, natural bond orbital analysis (NBO), as well as the tautomerism of Felbamate are investigated. F1 is the kinetically and thermodynamically most stable tautomer of Felbamate, which contains the amide group in each of the carbamate moieties. The calculated NMR chemical shifts and IR vibrational frequencies are in good agreement with the experimental values, confirming the suitability of the optimized geometry for Felbamate. The tautomerization reaction of F1 to each of the other tautomers occurs via an intramolecular proton transfer. This reaction affects considerably the structural parameters and atomic charges of the Felbamate molecule. A large HOMO-LUMO energy gap implies a high stability of the F1 tautomer.

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.

Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the most frequently prescribed drugs and have multiple therapeutic uses. These drugs are predominantly used for the treatment of musculoskeletal diseases because of their analgesic, antipyretic, and antiplatelet activities. Oxicams constitute an interesting class of organic compounds and have been investigated in the search for new analgesic and anti-inflammatory drugs. In the present work, a theoretical investigation of the molecular structure and spectroscopic properties of a series of five oxicams in different solvents was performed using density functional theory (DFT) methods. The geometric optimizations of the oxicams were carried out using the M06 density functional and the CBSB7 basis set. The infrared data were all obtained at the same theoretical level. The UV-Vis absorption and NMR data of some oxicams were calculated using the DFT and CBSB3 basis sets. The analysis of structural parameters, particularly the bond length and spectroscopic data, indicated that interactions occurred between the hydrogen bond types for 4-meloxicam, isoxicam, and normeloxicam. Stereoelectronic interactions caused by the substitution of alkyl groups caused the bond lengths to elongate. Similarly, the substitution of heteroatoms, such as nitrogen, sulfur, or oxygen, increased the bond lengths and angular stresses.

There are experimental evidences that in the methanol solution of glycyrrhizic acid (GA) and cholesterol in methanol, 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, on the contrary to aqueous solutions, GA in methanol does not form small stable clusters, including 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.

A geometric optimization is performed for the neutral, zwitterionic, and protonated forms of pyridoxine in vacuum and in water with a solvent within the polarizable continuum model (PCM). The structural parameters are optimized for pyridoxine complexes in the neutral and zwitterionic forms with 4-10 water molecules. An analysis is performed of how the number of molecules of the solvent set by the model affects the agreement between the calculated and experimental NMR spectra.

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. Molecules of the compounds studied have three chiral centers, but out of four possible diastereomeric pairs for each of compounds, the crystals of only one diastereomer are obtained, moreover, four of them crystallize as true racemates, two as racemic conglomerates. Crystals of five compounds are solvates with molecules of different nature (water, acetonitrile, dimethylformamide, dimethylsulfoxide). Crystals of the compounds studied are stabilized by both classical hydrogen bonds of N-H⋯O and O-H⋯O types and interactions of the С-H⋯O type.

The X-ray diffraction study of an indoline alkaloid of pseudokopsinine extracted from the plant Vinca erecta and its mono- and double salts is performed. The experimentally determined positions of Н atoms suggest the sp ³ hybridization of the indoline nitrogen atom in the base and salts. The pseudokopsinine base and double salt have an intramolecular Н bond between the NH group proton and the ether oxygen atom of the methoxycarbonyl group, which is absent in the monosalt and the related indolines. The intermolecular Н bonds and/or the packing efficiency cause a conformational change in F and Е heterocycles in the indoline hetero framework of pseudokopsinine salts in comparison with that observed in the base.

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.

A hydrogen bonded chloride hydrate assembly {[(H₂O)Cl]}^-¥ is ion-countered by organic molecular [C₂₃H₂₈NO₄]⁺ cations and the crystal structure of {3-[2-(1,3-benzodioxol-5-yl)-7-methoxy-1-benzofuran-5-yl] propyl} diethylamine [C₂₃H₂₈NO₄]⁺×[H₂OCl]^- is synthesized. Its structure is studied using X-ray crystallography. The molecular geometrical parameters, frontier molecular orbital energies (HOMO, LUMO), their energy gap (D E ), molecular electrostatic potential analysis of the compound are calculated by DFT/B3LYP at the 6-311G( d , p ) level. Benzofuran and benzodioxo ring systems of the title compound, except the diethylamine group, are essentially planar and a dihedral angle between the ring systems is 7.38(14)°. The complex compound crystallizes in the monoclinic space group P 21/ c , with a = 15.230(4) Å, b = 11.418(2) Å, c = 12.880(3) Å, b = 94.56(3)°, V = 2232.8(9) ų, D _calc = 1.297g/cm³, Z = 4. The hydrogen bonded chloride hydrate is self-assembled to form a supramolecular array of strong N-H…Cl and O-H…Cl bifurcated hydrogen bonds making tetramers which consist of a fused four-membered ring with a graph-set descriptor and a pseudo cyclic centrosymmetric (8) ring motif. The hybrid dihalide-dihydrate clusters of [Cl₂(H₂O)₂]^- are observed in the compound, too. The supramolecular crystal packing is consolidated by these bifurcated hydrogen bonds and the stacking of the sheet through strong p…p interactions. Moreover, the chain hydrogen bonds form intermolecular and intramolecular C-H…O hydrogen bonds and the 1D supramolecular array is organized by C-H…p interactions. The intercontacts in the crystal structure are analyzed using the Hirshfeld surfaces computational method. The calculated geometrical parameters are in good agreement with the observed single crystal XRD data.

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.

Quantitative structure-activity relationship (QSAR) models can be applied as a powerful tool for predicting the response in biological and chemical systems. D₂ receptor subtypes as dopamine receptors assist dopaminergic neurotransmission in brain. In this work, binding affinities of synthesized agonists with D₂-like receptors in binding assays using rat brain were related to the structural properties of these agonists. The structural descriptors of these compounds are calculated. A stepwise variable selection is applied for PLS modeling. The walk and path counts, 2D autocorrelations, 3D atom pairs, RDF, 3D-MoRSE, WHIM, GETAWAY blocks are among the selected descriptors. The PLS model is built with 5 latent variables. The predictive ability of the model is evaluated on a set of 5 ligands, which are not used in modeling steps and the acceptable results are obtained.

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.

A new dinitrosyl iron complex of the composition [Fe(SC(NHCH₃)₂)₂(NO)₂]Cl (I) is obtained by direct nitrosylation of ferrous sulfate and a hydrochloric acid solution of 1,3-dimethylthiourea. The characteristic features of the molecular and crystal structure of complex I is determined by single crystal X-ray diffraction analysis.

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

The crystal and molecular structure of a copper(II) complex based on 2-methyl-3-{[3-methyl-5-oxo-1-phenylpyrazole-4-ylidene-methyl]amino}-quinazoline-4-one is studied by single crystal X-ray diffraction. The chelate core is demonstrated to have a pyramidal structure.

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.

A novel Schiff base is synthesized by condensation of 4-methylphenylsulfonyl-2-benzaldehyde and N-aminoquinazoline-4-one. The molecular and crystal structure of the produced compound is determined by the XRD method. It is found that the crystal contains two independent molecules between which a p-stacking interaction occurs.

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 a,w-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.

To explore the role of the evolutionary conservative interhelical hydrogen bond (IHB) Ser74-Trp158 in maintaining the conformational stability of the β₂-adrenergic receptor, this work employs the molecular dynamics technique to study the conformational behavior of the receptor in the presence and absence of IHB. It is found that the Ser74-Trp158 IHB cleavage can cause further conformational transformations (helix shifts, change in the conformation of some amino acid residues). The S74A mutation in the receptor, which makes the IHB formation impossible, also leads to conformational changes: in the presence of cholesterol the mutated receptor takes a conformation close to the active form.

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

A study is presented of caffeine effects on the complexation of the DNA molecule with Cu²⁺ and Mg²⁺ ions in solution. DNA binding with cations and caffeine is captured from changes in DNA circular dichroism and UV absorption spectra. The complexation of caffeine with M²⁺ ions is studied by IR spectroscopy. Caffeine is found to form complexes of different structure with Mg²⁺ and Cu²⁺ ions in solution. In the presence of caffeine, DNA solutions with MCl₂ show signs of formation of intricate complexes involving nitrogenous bases. In DNA solutions with CuCl₂, the presence of caffeine causes additional destabilization of the secondary DNA structure. In DNA solutions with MgCl₂, the presence of caffeine leads to the formation of new complexes with the participation of Mg²⁺, caffeine, and bases without disrupting the secondary DNA structure.

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)₂NO₃ 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 work the properties of high-molecular DNA complexes with a photosensitive cationic azobenzene-containing surfactant capable of UV light induced trans-cis isomerization are studied. DNA compaction caused by its binding with surfactant cis- and trans-isomers is compared, the effect of the low-molecular NaCl salt concentration on the interaction process of the components is considered, and the effect of different surfactant concentrations on the volume and optical anisotropy of the DNA molecule is analyzed. The phase separation in solutions is examined.

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.