STUDIA CHEMIA - Issue no.1 / 2016 - Table of contents

Professor Mircea Vasile Diudea was born on November 11, 1950. He graduated the Faculty of Chemistry of the University of Cluj in 1974 and received his PhD in 1979 under the supervision of Prof. I. Bodea in the field of organic chemical synthesis. He became full professor in 1996 at the Department of Organic Chemistry of the Babes-Bolyai University from Cluj.

In this paper, we investigate application of graph theory to some biological problems, specially reconstructing strings based on information about their substrings and sequence comparison by using overlap graphs and also weighted directed graph.

Keywords: Fragment assembly, Overlap graphs, sequence comparison, Alignment-free method, Weighted directed graph

Starting from 5-amino-2-mercapto-1,3,4-thiadiazole, 23 compounds, Schiff bases and S-mercapto-substituted derivatives, were synthesized. Their structural elucidation was based on elemental analysis, mass spectrometry and proton nuclear magnetic resonance spectroscopy (1H NMR). The screening of the antimicrobial activity of the title compounds was realized using the diffusimetric method against several strains of Gram-positive and Gram-negative bacteria and one fungal strain (Candida albicans). Some of the molecules showed moderate to good antibacterial activity against Gram-negative (S. typhimurium, E. coli) and better activity against Gram-positive (B. cereus, L. monocytogenes, S. aureus) bacterial strains. All compounds exhibited moderate to very good activity against C. albicans. Qualitative relationships (SAR) were also established between the chemical structures and the antimicrobial activity of these compounds.

Keywords: 1,3,4-thiadiazole, antibacterial activity, antifungal activity.

Sodium niobate (NaNbO3) fine powders were synthesized by hydrothermal method using ammonium niobate (V) oxalate hydrate (C4H4NNbO9 x H2O), sodium hydroxide (NaOH) and sodium citrate hydrate (C6H9Na3O9) as precursors. The samples were characterized by X-Ray diffraction (XRD), scanning electron microscopy (SEM), AFM (Atomic Force Microscopy), UV-VIS spectroscopy and Fourier Transform Infrared Spectroscopy (FTIR). X-ray diffraction for powder obtained by hydrothermal method revealed three phases mixture (NaNbO3, Nb2O5, Na2C2O4). In order to obtain a material with perovskite structure, the powder was treated for 6 h at 600°C. After calcination, the X-ray powder diffraction (XRD) patterns shown reflections of a pure cubic structure (space group Pm-3m) with lattice parameters (a=b=c=3.909Å) comparable to those reported in the literature. The average particle sizes estimated by SEM image were 2-3 micrometers.

Keywords: sodium niobate, hydrothermal method, X-ray diffraction, scanning electron microscopy

Dendrimers are macromolecules with well-defined shape and size, being typically symmetric around the core. A new class of aromatic core 0 generation dendrimers and their Cu(0) complexes were synthetized. The obtained adducts were tested as catalysts for reduction of 4-nitrophenol. Higher catalytic activity was observed in each case compared to Cu(0) prepared in situ.

Keywords: dendrimer complexes, aromatic core, catalyst, Cu(0), p-nitrophenol

The paper presents a study regarding the correlation of the transition temperature for nine derivatives of the tetraphenylethene, a class of columnar liquid crystals, with 35 molecular descriptors (22 topological indices and 13 Van der Waals parameters), calculated for these compounds. Their transition temperature was modelled in mono- and multivariate linear regression equations. In linear, simple correlations, 19 out of the 22 topological indices and 3 out of the 13 Van der Waals parameters show a correlation coefficient higher than 0,8; in multivariate linear correlations the results are even better, with correlation coefficients larger than 0,9.

Keywords: correlation, columnar crystals, topological indices

Discrete Adriatic indices have been defined by Vukičević and Gašperov (2010), as a way of generalizing well-known molecular descriptors defined as the sum of individual bond contributions. One of these indices is the inverse sum indeg index which is a significant predictor of total surface area of octane isomers. In this paper, exact formulas for computing the inverse sum indeg index of some nanotubes are presented.

Keywords: ISI index, Nanotube.

A QSPR (Quantitative Structure-Property Relationship) model was derived for a set of forty 7 beta-hydroxysteroid compounds selected from PubChem database in order to assess the link between structural features and lipophilicity expressed as logP. After optimization and topological indices data collecting, the cluster of molecules was superposed onto a representative hypermolecule. Based on each molecule atoms positions, a binary vector and its weighted by mass fragments was computed for each molecule in the set. A model relating the structure with logP was identified based on the contributions of statistically significant positions of each molecule superposed on the hypermolecule and based on structural descriptors. The obtained model was validated in leave-one-out analysis as well as on training versus test analysis.

Keywords: 7 beta-Hydroxysteroid, QSPR (Quantitative Structure-Property Relationships), logP, hypermolecule

Zinc oxide has been investigated due to its large band gap and several applications in science and industry. However, doping extrinsic impurities would change the resistivity of ZnO films which enhance their properties. In the present study, nano-structured ZnO and Cu-doped ZnO photocatalysts were successfully prepared on glass substrates by sol-gel dip-coatig method. Various techniques such as X-ray diffraction (XRD), scanning electron microscopy (SEM), field emission scanning electron microscopy (FESEM) and UV-VIS absorption spectroscopy were used to investigate the effect of the Cu-doped on ZnO thin film. The results showed that the doping greatly changed the microstructure, morphology and optical properties of ZnO, which may contribute to the enhancement of photocatalytic activity. The photocatalytic activity of the prepared pure ZnO and Cu-doped ZnO photocatalyst was investigated by the degradation of Methylene Blue solution. The results indicated that Cu-doped ZnO had a higher photocatalytic activity and Cu dopant greatly increased the photocatalytic activity of ZnO. Using C # programming language, we developed a software for more analyzing results.

Keyword: Cu-doped ZnO, Thin film, Sol-Gel, Photocatalyst.

The eigenvalues of a graph are the eigenvalues of its adjacency matrix and the energy of a molecular graph is defined as the sum of absolute values of its eigenvalues. In this paper, some classical methods are used to evaluate the energy of nanotubes.

Keywords: Eigenvalue, energy, nanotube.

Abstract: Pure and Nb doped titanium dioxide films were grown by magnetron sputtering, for integration in hybrid polymer-semiconductor solar cells. The effect of the thickness of the films on their physical properties was investigated, emphasis given on the optical transparency, the surface morphology, the wettability and the conductivity. Particular surface parameters were determined and their variation with film thickness was investigated. Finally, a hydrophobic to hydrophilic transition under UV irradiation was studied.

Keywords: metal oxides, titanium dioxide, thin films, thickness, solar cells applications.

Abstract: Diamond-like carbon (DLC) films are metastable amorphous hydrogenated or non-hydrogenated forms of carbon, with excellent properties that make them reliable to use in various fields of science and technology. However, poor adhesion of DLC films to the substrate limits their performance. Using an interlayer is one of the methods to reduce the stress in films and improve the adhesion. In this study, different thickness of the nickel nano layers was deposited on the silicon substrates as an interlayer for the growth of DLC films. The Ni nano layers with the thickness of 10, 20, 40 and 80 nanometers were deposited on the substrates by DC magnetron sputtering while DLC films were synthesized by plasma enhancement chemical vapor deposition (PECVD) system with a mixture of argon and methane gases as the precursors. Morphology and the surface roughness of Ni interlayers were investigated by atomic force microscopy (AFM) which showed low surface roughness changing with thickness of interlayer. For the characterization of DLC films, Raman spectroscopy was used; it proved high degree of diamond-like character for the films grown on 10 nanometers nickel interlayer, as given by the ratio of ID to IG. FE-SEM (Field emission scanning electron microscopy) cross-section images of DLC films showed increasing of the thickness of DLC films by increasing of nickel nano layer thickness. The adhesion strength also was investigated by the nanoscratch test.

Keywords: Nickel Nano Layer, Diamond-Like Carbon film, Adhesion Strength, Raman Spectroscopy

The crystal network named flu, belonging to the symmetry group Fm-3m, can be designed by map operations Medial and Dual, applied subsequently on the Cube. The topology of the network was characterized by Omega, Cluj and related polynomials.

Keywords: Crystal like network, Omega polynomial, Cluj polynomial, Map operation

In this paper, we give some theoretical results about nanostar dendrimers by topological indices. Formulas for computing topological indices based on distance and degree in a graph such as eccentric connectivity, total eccentricity, fourth version of atom-bond connectivity and fifth version of geometric-arithmetic indices of two types of nanostar dendrimers are presented.

Keywords: Dendrimers, Eccentric, Vertex-degree, Connectivity indices.

Let G=(V,E) be a graph, where G is a non-empty set of vertices V(G) and E(G) is a set of edges. In such chemical graphs the vertices of the graph corresponds to the atoms of the molecule, and the edges represent the chemical bonds. The aim of this paper is to compute the modified eccentric connectivity polynomial for the naphthylenic molecular graph.

Keywords: modified eccentric connectivity polynomial, molecular graph, naphthylenic lattice

A computational study on water-ions clusters for six ions (NH4+ , F-, Cl-, Li+ , Na+ , and K+ ) is described. Restricted Hartree-Fock method with 6-31G* basis set was used to optimize the investigated water ion-clusters. Stable ion-water clusters proved to form with four (NH4+ •4H2O and Li+•4H2O), five (Cl-•5H2O and Na+ •5H2O) and respectively six water molecules (F-•6H2O and K •6H2O). The arrangement of water molecules around the investigated ions proved not be symmetrical. Furthermore, the investigation of the stability of dodecahedral cages constructed with the investigated ions showed a stable symmetry for O12N8H50, O12Li8H18, and O15K5H29.

Keywords: ion-water cluster; monovalent ion; stabilization

Cu(In,Ga)Se2 films were prepared via a sputtering route followed by a selenization process, on glass substrates. Having a layer sequence Mo/In/Cu-Ga with preferred thicknesses, the metallic layers were selenized at vacuum of 6×10-3 mbar and 1 atm pressure with a total gas inlet of 7 sccm. Under vacuum, only single-phase CIGS was observed while at 1 atm, other phases in addition to CIGS were formed. The metallic layers were selenized at several temperatures. Pure-phased CIGS films were obtained by selenization at 600˚C. The crystallinity of the obtained films was further enhanced by increasing the selenization temperature. The produced CIGS films were studied by X-ray diffraction (XRD), scanning electron microscope (SEM) and energy dispersion spectroscopy (EDS) techniques.

Keywords: Cu(In,Ga)Se2 thin film, sputtering, selenization.

Adsorption of tetracyanoethylene molecule on graphene and graphyne was investigated in view of finding an effective way to control their electronic properties. The electronic properties of graphene, α-, β- and γ- graphyne were studied by using the density functional theory. The binding energy, equilibrium adsorption distance, amount of charge transfer, electronic band structure, and density of states were calculated. The small adsorption energy and large adsorption distance identified physisorption of tetracyanoethylene molecule on graphene and graphyne sheets. It was found that charge is transferred from sheets to tetracyanoethylene molecule. In the presence of this acceptor molecule, the graphene and α-, β- and γ-graphynes, with semimetallic properties, show semiconducting behaviour. The tetracyanoethylene molecule has no considerable effect on the semiconducting property of γ-graphyne. Our results reveal that adsorption of organic molecules, such as tetracyanoethylene, is a proper method to open a band gap in graphene and graphyne.

Keywords: Organic molecule, Graphene, Graphyne, Band gap, Density functional theory.

Studies on the effects of electromagnetic field (EMF) exposure on cardiovascular function have provided some evidence of a possible action. Low density lipoprotein (LDL) modifications appear as an early step in the promotion and progression of atherosclerosis, the most causes of death in cardiovascular disease (CVD) patients. This study aimed to evaluate the effects of extremely low frequency (ELF) of electromagnetic fields on LDL physico-chemical modifications. LDL was separated by sequential ultracentrifugation and its susceptibility to oxidation was evaluated by continuous monitoring of conjugated dienes formation, using a spectrophotometer. LDL size and zeta potential is determined by zetasizer instrument. The results indicated that moderate ELF-EMFs of 2-4 mT can induce the susceptibility of LDL to oxidation and aggregation. Weak ELF-EMFs of 0.125-0.5 mT caused a decrease in LDL zeta potential in a time and dose dependent manner while in moderate ELF-EMFs of 1-4 mT LDL zeta potential was started to increase after an initial decrease at the first hour of exposure. LDL oxidation and aggregation are two important modifications of LDL, involved in the promotion and progression of atherosclerosis. On the other hand, alteration of the LDL surface charge can interfere with the metabolism of LDL and its interaction with other molecules. Therefore with regard to the atherogenic effects of ELF-EMFs on LDL, it can be considered as a risk factor in atherosclerosis.

Keywords: Electromagnetic field, LDL oxidation, LDL aggregation, LDL zeta potential, LDL mean size

A polyvinyl chloride membrane chromium(III)-selective electrode based on a synthesized A3B free base porphyrin, namely 5-(4-pyridyl)-10,15, 20-tris(phenoxy-phenyl)porphyrin, as membrane carrier was formulated and evaluated. The electrode exhibits a near-Nernstian response over the chromium(III) concentration range of 3x10−5 ÷ 1x10−1 M and shows good selectivity with respect to a wide range of cations. The aggregation behavior of the porphyrin macrocycle was investigated using TEM and STEM analytic techniques and revealed the formation of different shapes of nanostructures. Electron tomography was also employed in the study of the porphyrin aggregates.

Keywords: membrane carrier, A3B porphyrin, aggregation behavior, electron tomography

Sensitive, precise and accurate analytical methods for free amino acids determination in biological samples were developed. Purification by ion exchange technique was followed by two steps derivatization method to obtain trifluoroacetyl ester derivatives. GC/MS analysis was performed by using scan or SIM mode. Known amounts of internal standard, the isotopic labelled analogue of glycine, methionine or isoleucine were added to the sample, before extraction, for the quantitative analysis, followed by matrix and regression curves calculation. The methods were validated using amino acid standard samples. Analyses of dairy, corn grain, fish plasma and meat are presented. Also a trace level (picogram) analysis method of blood spots, for diagnosis of inborn errors of metabolism, is described.

Keywords: amino acids, GC-MS, isotopic dilution, blood

In this paper, a preliminary result from a property-property analysis on a series of chemical compounds in regards of quantitative relationship between two properties is communicated. The study was conducted on a series of 190 inorganic chemical compounds for which both properties taken into study are known. The correlation analysis revealed that is a strong relationship between the boiling point and the heat of vaporization at the boiling temperature, having the variance in the paired series of data explained over 90%.

Keywords: Property-property relationship, Distribution analysis, Regression analysis

Diamond coating is one of the hot research topic due to its various industrial applications; for the diamond growth, several techniques, such as PECVD and HFCVD, have been reported. In this paper, we investigate the effects of different CVD techniques on synthesis of diamond crystals, grown on silicon and aluminum substrates, at temperature of 550˚ C and the reaction pressure of 30 Torr, in which CH4 and H2 act as a source and diluting gases, respectively. The hydrogen was used as the etching gas to enhance the diamond nucleation. As a result, we obtained a high distribution of nanodiamond with (111) crystallite structure on gold-coated silicon in HFCVD system. The samples were analyzed using AFM, SEM and XRD.

Keywords: Hot filament chemical vapor deposition; Plasma enhanced chemical vapor deposition; Etching gas; NCD.

An (r, s)fullerene graph is a planar 3regular graph with only Cr and Cs faces, where Cn denotes a cycle of length n. In this paper the (3,6)fullerene Cayley graphs constructed from finite groups are classified. A characterization of (4,6)fullerene Cayley graphs is also presented.

Keywords: Fullerene, Cayley graph, finite group.

The nature of interactions between Polyethylenimine and glucose oxidase 3QVR enzyme was studied by docking and Molecular dynamics procedures. The docking procedure evidenced two active sites, one located inside the enzyme body and the second at the enzyme surface. In view of deeply understand the interactions ligand – enzyme, a Molecular dynamics study followed to the docking. This provided a detailed information on the type, intensity and frequency of these interactions.

Keywords: PEI, 3QVR, Glucose oxidase (GOx), Docking, Molecular Dynamics

A modified Wiener number was proposed by Graovać and Pisanski. It is based on the full automorphism group of a graph. In this paper, we compute the difference between these topological indices for some polyhedral graphs.

Keywords: automorphism, polyhedral graphs, topological indices.

In this paper, the edge version geometric-arithmetic index of certain nanocones is presented.

Keywords: Geometric-arithmetic (GA) index, GAe index, Nanocones

The measure of bipartivity is one of the important topological and structural property which describes the chemical stability of underlying chemical structures. Bipartite edge frustration is one of the topological descriptors which calculate measure of bipartivity of a chemical structure. Carbon hexagonal nanotubes, boron triangular nanotubes and boron -nanotubes are important nanostructures, which have been studied extensively by both of the theoretical and computational chemists. In this article, we consider carbon hexagonal nanotubes, boron triangular nanotubes and boron -nanotubes for the study of bipartite edge frustration.

Keywords: Bipartite edge frustration, Carbon hexagonal nanotube, Boron triangular nanotube, Boron -nanotube

A topological index is a single number descriptor that characterizes the molecular graph topology up to isomorphism. Hyper-tubes, open or closed, consisting of hyper-cubes of n-dimensions have been designed and formulas for some topological indices, counting vary substructures or characteristics, were established.

Keywords: graph, topological index, n-cube, hyper-tube, hyper-torus, n-dimensional space

A QSAR study on a set of 30 phenothiazines performed within a hypermolecule frame, to model their logP and LD50 values, is reported. The initial set of molecules was split into a training set and the test set; Cluj topological indices and some quantum mechanical descriptors have been used to derive the models, which were next tested for predictability by LOO, external validation and similarity clustering.

Key words: phenothiazine, hypermolecule, LD50, logP, topological indices.

STUDIA UBB CHEMIA, Volume 60 (LX), 4, 2015 (p. 179)