Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP)

Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.     

Evaluation and application of bismuth as an internal standard for the determination of lead in wines by simultaneous electrothermal atomic absorption spectrometry

A method for the direct determination of Pb in wines by simultaneous multi-element atomic absorption spectrometry (SIMAAS) using a transversely heated graphite atomizer, Zeeman-effect background corrector and internal standardization is proposed. Bismuth was used as an internal standard and Pd(NO3)2 plus Mg(NO3)2 as chemical modifier to stabilize both the analyte and the internal standard. The implementation of two pyrolysis steps avoided any build-up of carbonaceous residues on the graphite platform. All diluted samples (1 + 1 v/v) in 0.2% v/v HNO3 and reference solutions (5.0-50 microg l(-1) Pb in 0.2% v/v HNO3) were spiked with 25 microg l(-1) Bi. For a 20 microl aliquot dispensed into the graphite tube, a good correlation (r = 0.9997) was obtained between the ratio of the analyte signal to the internal standard signal and the analyte concentration of the reference solutions. The electrothermal behaviour of Pb and Bi in red, white and rosé wines were compared. In addition, absorbance variations due to changes in experimental conditions, such as atomizer temperature, integration time, injected sample volume, radiation beam intensity, graphite tube surface, dilution and sample composition, were minimized by using Bi as internal standard. Relative standard deviations of measurements based on integrated absorbance varied from 0.1 to 3.4% and from 0.5 to 7.3% (n = 12) with and without internal standard correction, respectively. Good recoveries (91-104%) for Pb spikes were obtained. The characteristic mass was 45 pg Pb and the limit of detection based on integrated absorbance was 0.9 microg l(-1) Pb. Internal standardization increased the lifetime of the tube by 25%. Direct determinations of Pb in wines with and without internal standardization approaches were in agreement at the 95% confidence level. The repeatability and the tube lifetime were improved when using Bi as internal standard. The improvement in accuracy using an internal standard was only observed when the analytical results were affected by errors.     

The Fermi doublet V2−V3 + V4 of CH3CN as a probe of molecular interactions

The Fermi doublet V₂?V₃ + V₄ of CH₃CN in basic, inert and acidic solvents has been studied by IR and Raman spectroscopy. The values of W, the Fermi coupling coefficient, obtained from IR spectra varies with the nature of the solvent while W evaluated from Raman data remains constant at 12.5 ± 0.5 cm^?1. The similar effects of Bronsted and Lewis acids on the band frequencies and intensities is evidence that the CN group complexes with acids via the N atom “n” electron pair and not the π bond.     

Modeling of temperature-programmed desorption thermograms for the determination of adsorption heat considering pore and surface diffusion

In this work, two partial differential equation-based models have been proposed for the quantitative analysis of temperature-programmed desorption (TPD) thermograms when the adsorption cell can be modeled as a well-mixed reactor, using the Langmuir equation as the adsorption isotherm and including the effect of diffusional resistance. One model considers pore diffusion, and the other considers surface diffusion. For both models, the rate of adsorption is proportional to the gas pressure. By nondimensionalizing these models, the range of design parameters for which the accumulation in the gas cell, diffusional resistance, and readsorption have an important effect on the TPD signal is proposed. An important conclusion is that the dimensionless numbers accounting for the diffusional resistance and the corresponding range of parameters are quite different for both mechanisms. The models have been validated with two systems where surface and pore diffusion are the relevant mechanisms: (i) CO2-Na-mordenite and (ii) CO2-Na-mordenite pellets.     

Complexes of TiCl4, VCl4 and SnX4 (X = Cl or Br) with Schiff bases derived from 2-aminobenzimidazole

Summary The reactions of anhydrous titanium(IV), tin(IV) and vanadium(IV) halides with Schiff bases derived from 2-aminobenzimidazole and 4-methylbenzaldehyde (abimbz) and salicylaldehyde (abisal), yield hexacoordinated complexes M(abimbz)Cl₄ and M(abisal)₂X₄ (M = Ti, Sn or V; X = Cl or Br).The compounds have been characterized by elemental analyses, magnetic measurements, e.p.r., electronic and i.r. spectral studies. I.r. spectra suggest that the Schiff base (abimbz) is coordinated as a bidentate ligand with the metal ion and the (abisal) base acts as a monodentate ligand.     

Catalyzed oxidation of alcohols and aldehydes with iodosylbenzene

RuCl₂(PPh₃)₃ catalyzes oxidation of alcohols to carbonyi compounds by iodosylbenzene and that of aldehydes to carboxylic acids. Catalyzed oxidation of primary alcohols with phenyliodosodiacetate affords aldehydes.     

Ab Initio (GIAO) Calculations of Absolute Nuclear Shieldings for Representative Compounds Containing 1(2)H, 6(7)Li, 11B, 13C, 14(15)N, 17O, 19F, 29Si, 31P, 33S,and 35Cl Nuclei

Two kinds of ab initio calculations (B3LYP and HF) using the GIAO approach have been carried out for fifteen H, three Li, three B, eleven C, seven N, nine O, four F, three Si, four P, six S and five Cl containing derivatives. The calculated absolute nuclear shieldings have been compared with experimental absolute values (either measured or estimated from relative chemical shifts) when available or with relative chemical shifts (¹¹B, ³⁵Cl). The correlations range from good to excellent and only three compounds (PN, P₂H₂, SO₂) deviate significantly.     

Complexes of divalent nickel and copper with the Schiff base derived from 2-(2-aminophenyl)benzimidazole and benzaldehyde

Summary The reactions of divalent nickel and copper salts with the Schiff base derived from 2-(2-aminophenyl)benzimidazole and benzaldehyde, L, yield complexes of general formulae [CuL₂X₂] (X=Cl, Br, or ClO₄), [CuL(SO₄)], [CuL(SO₄)] · 4H₂O, and NiLX₂ (X=Cl, Br, or NCS).All the complexes have been characterized by elemental analyses, magnetic measurements, e.s.r. electronic and i.r. spectral studies. The results show that the Schiff base acts as bidentate ligand through the pyridine-like imine nitrogen of imidazole ring and the azomethine nitrogen. Tentative structures of the complexes are suggested.     

Pyrylium-containing polymers as sensory materials for the colorimetric sensing of cyanide in water

A sensory polymeric material for the colorimetric sensing of cyanide in water has been developed based on the reactivity of this anion with the pyrylium cation.