Structural,electronic properties and intramolecular hydrogen bonding of substituted 2-[(E)-imino methyl] benzenethiol in ground and first excited state by quantum chemical methods

Quantum chemical calculations of geometric structure, the intramolecular hydrogen bond, harmonic vibrational frequencies, NMR spin–spin coupling constants, and physical properties such as chemical potential and chemical hardness of the 2-(E)-imino methyl benzenethiol and its nineteen derivatives were carried out using density functional theory (DFT/B3LYP/6-311++G**) method in the gas phase and the water solution. Furthermore, the topological properties of the electron density distributions for S–H···N intramolecular hydrogen bond have been analyzed in terms of the Bader’s theory of atoms in molecules (AIM). Natural bond orbital (NBO) analysis also performed for better understanding the nature of intramolecular interactions, the results of analysis by quantum theory of AIM and NBO method fairly supported the DFT results. Besides, MEP was performed by the DFT method. On the other hand, the aromaticity of the formed ring has been measured using several well-established indices of aromaticity such as nucleus-independent chemical shift, harmonic oscillator models of the aromaticity, para-delocalization index, average two-center indices, and aromatic fluctuation index. Also, the excited-state properties of intramolecular hydrogen bonding in these systems have been investigated theoretically using the time-dependent DFT method.     

Rank annihilation factor analysis for spectrophotometric study of complex formation equilibria

The use rank annihilation factor analysis (RAFA) for spectrophotometric studies of complex formation equilibria are proposed. One-step complex formation and two successive and mononuclear complex formation systems studied successfully by proposed methods. When the complex stability constant acts as an optimizing object, and simply combined with the pure spectrum of ligand, the rank of original data matrix can be reduced by one by annihilating the information of the ligand from the original data matrix. The residual standard deviation (R.S.D.) of the residual matrix after bilinearization of the background matrix is regarded as the evaluation function. The performance of the method has been evaluated by using synthetic data. For two-step successive complex formation systems, the effects of noise level and equilibrium constants K₁ and K₂ on output of algorithm are investigated. The applicability of method for resolving the two-step successive complex formation systems with full spectral overlapping of two complex species also is shown. Spectrophotometric studies of murexide-calcium, dithiazone-nickel and methyl thymol blue (MTB)-copper are used as experimental model systems with different complexation stoichiometries and spectral overlapping of involved components.     

Investigation of the Role of Ionic Liquids in Imparting Electrocatalytic Behavior to Carbon Paste Electrode

In this paper, a survey has been undertaken to clarify the possible reasons for the electrocatalytic activity obtained by the presence of ionic liquid in carbon paste electrode (CPE). For this purpose, the effect of the addition of traces of ionic liquid to conventional CPE was investigated. Fe(CN)₆^3?/4? was used as a probe and two ionic liquids, namely n‐octylpyridinum hexafluorophosphate and 1‐octyl‐3‐methylimidazolium hexaflourophosphate were tested for their electrocatalytic activity. The reasons for this electrocatalytic behavior were evaluated and it was found that different factors such as increase in the ionic conduction of the binder, decrease in the resistance of the modified electrode, increase in ion exchange properties of the electrode and the inherent catalytic activity of ionic liquids are responsible for the considerable improved electrochemical response obtained in the presence of traces of ionic liquid.     

Multi-criteria decision making in micellar liquid chromatographic separation of chlorophenols

Simultaneous optimization of separation quality and analysis time of the micellar liquid chromatography of nine chlorophenol isomers was investigated. The effect on retention of three experimental parameters was studied using multivariate analysis. The factors studied were the concentration of sodium dodecyl sulfate, propanol content, and pH of the mobile phase. The experiments were performed according to the face-centered cube central composite design and the inverse form of the experimental retention times of analytes was fitted to polynomial models. The results of the analysis of variance showed that the models obtained explain over 99% of the variance observed in the chromatograms. The good predictive ability of the models was verified by high correlation coefficient (R2 > 0.99) and F ratio values for the plots of predicted cross-validated versus experimental retention times. The study showed that the use of the Pareto-Optimality method, an approach from multi-criteria decision making, allows selection of the best possible combinations of separation quality and analysis time in micellar liquid chromatography of chlorophenols.     

Human genomic DNA analysis using a semi-automated sample preparation, amplification, and electrophoresis separation platform

The growing importance of analyzing the human genome to detect hereditary and infectious diseases associated with specific DNA sequences has motivated us to develop automated devices to integrate sample preparation, real-time PCR, and microchannel electrophoresis (MCE). In this report, we present results from an optimized compact system capable of processing a raw sample of blood, extracting the DNA, and performing a multiplexed PCR reaction. Finally, an innovative electrophoretic separation was performed on the post-PCR products using a unique MCE system. The sample preparation system extracted and lysed white blood cells (WBC) from whole blood, producing DNA of sufficient quantity and quality for a polymerase chain reaction (PCR). Separation of multiple amplicons was achieved in a microfabricated channel 30 microm x 100 microm in cross section and 85 mm in length filled with a replaceable methyl cellulose matrix operated under denaturing conditions at 50 degrees C. By incorporating fluorescent-labeled primers in the PCR, the amplicons were identified by a two-color (multiplexed) fluorescence detection system. Two base-pair resolution of single-stranded DNA (PCR products) was achieved. We believe that this integrated system provides a unique solution for DNA analysis.     

A molecular dynamics investigation on the interaction properties of AzrC and its cofactor

In this report, the main contributions of FMN were employed in the reductive cleavage reaction of AzrC protein (as a member of azoreductase family). Molecular dynamics simulations of three models in the presence and absence of FMN and ligand were performed to gather information about the dynamic nature of active site residues of AzrC. Combination of pairwise decomposition and alanine scanning calculations provides critical information about the FMN binding sites. The MD results analyzed by alanine scanning method revealed the high negative scores for N 10 (A) A, N 12 (A) A, S 17 (A) A and Y 151 (A) A mutations, which were in agreement with pairwise decomposition analyses. Hydrogen bond analyses indicated that these residues play critical roles in establishing appropriate hydrogen bonds between AzrC and FMN. Negative energy results for nonpolar residues such as W 103 (A), M 102 (A) and F 105 (A) and binding free energy analyses of three complexes indicate that the VDW interactions could be regarded as some favorable contribution in FMN and AzrC protein and confirmed the critical role of FMN in ligand binding (35.84 %), in addition to its catalytic function. This information could be used for future experimental investigations.     

An ab initio investigation of chalcogen–hydride interactions involving HXeH as a chalcogen bond acceptor

This work presents an ab initio study on chalcogen–hydride interactions in several binary complexes of chalcogen-containing molecules with HXeH. The geometries, H–Xe stretching frequencies and interaction energies of XCY···HXeH binary complexes are investigated at MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ levels of theory, where X = O, S, Se, Te and Y = S, Se, Te. For each XCY···HXeH complex, a chalcogen–hydride bond is formed between the negatively charged hydrogen atom of the HXeH molecule and the most positive electrostatic potential region (σ-hole) on the surface of the interacting atom Y. Upon complex formation, a notable blue shift is found for the H–Xe stretch vibration. This result reveals that there is a stronger H^?(XeH)⁺ ion-pair character in XCY···HXeH complexes than in free HXeH molecule. In order to shed light on the origin of the chalcogen–hydride interactions, molecular electrostatic potential, quantum theory of atoms in molecules and interaction energy decomposition analyses are performed. Cooperative effects between a conventional chalcogen bond and the chalcogen–hydride interaction in OCY···OCY···HXeH complexes are also investigated.