Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme

Pyridoxal 5-phosphate (PLP), the phosphorylated and the oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with the ?-amino group of a lysine residue of PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase is a PLP-dependent enzyme that degrades GABA to succinic semialdehyde, while reduction of GABA concentration in the brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for the inactivation of the GABA-AT are synthesized extensively in cases where the inactivation mechanisms involve HF elimination. Although two proposed mechanisms are present for the HF elimination, the details of the base-induced HF elimination are not well identified. In this density functional theory (DFT) study, fluorine-containing substrate analogue, 5-amino-2-fluorocyclohex-3-enecarboxylic acid, is particularly chosen in order to explain the details of the HF elimination reactions. On the other hand, the experimental studies revealed that aromatization competes with Michael addition mechanism in the presence of 5-amino-2-fluorocyclohex-3-enecarboxylic acid. The results allowed us to draw a conclusion for the nature of HF elimination, besides the elucidation of the mechanism preference for the inactivation mechanism. Furthermore, the solvent phase calculations carried out in this study ensure that the proton transfer steps should be assisted either by a water molecule or a base for lower activation energy barriers.     

Synthesis, photophysical and thermal studies of symmetrical and unsymmetrical zinc phthalocyanines

The novel zinc phthalocyanine (3) with malonylester and chloro groups on each benzo unit was synthesized from 4-diethoxymalonyl-5-chloro-phthalonitrile (1). The unsymmetrically substituted zinc phthalocyanine (5), carrying hexylthio, malonylester and chloro groups at the periphery, was obtained from 4-diethoxymalonyl-5-chloro-phthalonitrile (1) and 4,5-bis-hexylsulfanyl-phthalonitrile (2) by a statistical condensation method as an A₃B type unsymmetrical phthalocyanine compound. Transesterification of the malonyl esters of the new symmetrical and unsymmetrical phthalocyanines occurred during the cyclotetramerization of dinitriles with Zn(CH₃COO)₂ in 1-pentanol in the presence of DBU. Octa-hexylthio-substituted zinc phthalocyanine (4) was prepared according to the literature. The photophysical and thermal properties of all the phthalocyanine complexes are described for the first time. These novel symmetrical and unsymmetrical phthalocyanine macrocycles have been characterized by a series of spectroscopic methods including ¹H NMR, electronic absorption, IR and mass spectroscopy, in addition to elemental analysis. Their narrow long wavelength absorption band shows that the bulky substituents on the periphery prevent aggregation. The unsymmetrically substituted phthalocyanine (5) gave a greater fluorescence quantum yield in chloroform than the symmetrical analogues (3 and 4).     

Heterogeneous Suzuki reactions catalyzed by Pd(0)-Y zeolite

The Pd(0)-Y zeolite showed high activity in the Suzuki cross-coupling reactions of aryl bromides without added ligands. The type of base and organic solvent were found to be critical for the efficiency of the reaction. The presence of water was essential within the reaction medium. The coupling reactions occurred on the external surface of the zeolite. The catalyst is reusable.     

A preliminary approach to the separation of Leishmania cell-surface antigens

The purpose of the current study was to characterize Leishmania cell-surface antigens by two different methods established for the purification of glycoproteins and proteins, and to point out a useful approach to define their size and mass heterogeneity. L. tropica parasites were initially isolated from patients with active cutaneous leishmaniasis and were then cultured in vitro. The parasite-cell layer was solubilised with 6 M guanidinium chloride (GuHCl) and subsequently prepared for the purification procedure. The methods used in this work were gel filtration chromatography and isopycnic density-gradient centrifugation. Because of the presence of a substantial amount of non-specific proteins in the culture medium, these methods were not effective alone in distinguishing these antigens. However, a good idea of their N-glycosylated structures could be obtained by using Periodic acid-Schiffs (PAS) and Con A lectin, and also size and mass heterogeneity. A combination of these methods effected a clear separation of the antigens. Amino acid analysis of the purified antigens was performed to positively identify them as well-known Leishmania cell-surface antigen gene products. The results confirmed the presence of more than one cell-surface antigen on the Leishmania parasite and the combination of gel chromatography and density-gradient centrifugation could be useful for their isolation.     

Synthesis of trifluoromethylated pyrazoles from trifluoromethylenaminones and monosubstituted hydrazines

Cyclocondensation of monosubstituted hydrazines 2a-c with trifluoromethylenaminones 1a-c afforded 3-CF₃ and (or) 5-CF₃ pyrazoles 3-6. Addition of N-methylhydrazine to enaminone led to 3-CF₃ pyrazole as the major product, whereas phenylhydrazine gave regiospecific formation of 5-CF₃ pyrazole.Structural assignment of regioisomers is based on NMR chemical shifts, long-range carbon-fluorine and hydrogen-fluorine coupling constants and - NOE.The pyrazole 4ac was characterized by X-ray diffraction analysis.     

Nonlinear two-phase equilibrium model for the binding of arsenic anions to cationic micelles

The binding of arsenic ions to cationic cetylpyridinium chloride (CPC) micelles has been investigated using the semiequilibrium dialysis (SED) technique. In SED experiments, it has been shown that CPC micelles are very effective in binding arsenic ions in the retentate. At the studied pH (pH 8), the unbound and bound arsenic exists primarily as divalent anions (HAsO₄²⁻) while CPC molecules exist as monovalent cations. Therefore, arsenic ions are bound electrostatically to the cationic micelle. The resultant colloid is large enough not to pass through the dialysis membrane, producing a rejection greater than 99.59%. The concentration of the unbound arsenic anions passing through the dialysis membrane is practically the same as the permeate concentration of these species in the analogous micellar-enhanced ultrafiltration (MEUF) experiments. Therefore, a nonlinear equilibrium model which combines thermodynamic relations, charge balance equations, and material balance equations with the Oosawa two-phase polyelectrolyte theory has been developed to correlate the binding of arsenic to CPC micelles in SED and MEUF. It was shown that the equilibrium model successfully accounts for the experimental data in both SED and MEUF in the absence and presence of monovalent (HCO₃¹⁻) and divalent co-ions (HPO₄²⁻). Because of their small sizes (less than 10 nm), micelles should retain their equilibrium shapes in the presence of hydrodynamic shear typically attained in most dynamic processes. Therefore, the equilibrium model can be used to predict separation efficiencies in other ultrafiltration units such as in crossflow ultrafiltration processes.     

Determination of Melatonin Hormone and Neurotransmitters in Cerebrospinal Fluid: Method Validation and Uncertainty Calculations

The uncertainty of measurement for well-known neurotransmitters like serotonin, noradrenalin and gamma-aminobutyric acid (GABA), glutamate and melatonin hormone with high performance liquid chromatography?fluorescence detection was calculated after the method validation. Two methods were developed for the determination of the neurotransmitters. A derivatization step was performed for the determination of GABA and glutamate. Sensitivity, method detection limit, limit of quantification, linearity, recovery, interday and intraday precision values were calculated. Low detection limit values were obtained especially for the determination of GABA and glutamate. Then, bottom-up approach was used to calculate measurement uncertainty. The critical stages of the method were evaluated. The major sources of the uncertainty budget were calibration curves, stock solution and recovery. The calculated percentage relative uncertainty values for the compounds changed between 10.1 and 16.7.     

Reactions of pentachloro-2-nitrobutadiene with some aliphatic and heterocyclic thiols and a crystallographic study

In this study, S-, S,S- and S,O-substituted novel nitrodiene compounds were synthesized. Cyclization products were formed when difunctional nucleophiles were used. The stereoisomerism of a heterocyclic nitrodiene is discussed with the help of XRD studies. The structures of all compounds were characterized by spectroscopic methods (FT-IR, ¹H NMR, ¹³C NMR, ¹⁹F NMR, MS) and microanalysis.     

A mixed experimental and theoretical study on chelidamate copper(II) complex with 4-methylpyrimidine

A new chelidamate complex, [Cu(chel)(H₂O)₂(mpd)] (chel = chelidamate; mpd = 4-methylpyrimidine), has been synthesized and characterized through a combination of single crystal X-ray analysis, electron paramagnetic resonance (EPR), ultraviolet-visible (UV-vis), and fourier transform infrared spectroscopy (FT-IR). The complex has six-coordinate distorted octahedral geometry around Cu(II). The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and angles) have been calculated using Density Functional Theory (DFT)/B3LYP and Hartree Fock quantum chemical methods with 6-31G(d, p) basis set by Gaussian 09W software. The EPR spectrum of the compound showed that the paramagnetic center has rhombic symmetry. The EPR studies were carried out using the following unrestricted hybrid density functionals: B3LYP, CAM-B3LYP, HSEH1PBE, WB97XD, MPW1PW91, and BPV86. The UV–vis absorption spectra have been examined in different media and compared with the calculated one using TD-DFT method by applying the polarizable continuum model. Natural bond orbital property of complex has been performed by DFT/B3LYP with 6-31G (d, p) basis set.