The carboxylate shift in zinc enzymes: a computational study

Zinc is the second most abundant transition element in biology and the only metal known to be represented in enzymes from each one of the six classes established by the International Union of Biochemistry. The flexible coordination geometry, the fast ligand exchange, the lack of redox activity, and its role as Lewis acid are just some of the features that make zinc an invaluable element in biological catalysis. In this study, we have analyzed the importance in mononuclear Zn enzymes of an interesting mechanistic phenomenon known as carboxylate shift, which is characterized by a change in the coordination mode of a carboxylate group (mono to bidentate or vice versa) with both ligand entrance or exit from the metal coordination sphere. Using B3LYP calculations, we were able to unveil in detail patterns relating the intrinsic characteristics of a given Zn coordination sphere with the existence or not of a carboxylate-shift mechanism and the additional energy stabilization arising from it. In particular, a specific Zn coordination sphere containing a carboxylate ligand (Asp or Glu), a cysteine, and a histidine has been shown to have the most favorable combination of amino acid residues that ensures a fast ligand exchange.     

Supported ionic liquids: ordered mesoporous silicas containing covalently linked ionic species

Ordered mesoporous silicas with hexagonal or lamellar architectures incorporating covalently bound ionic species were synthesized via a template directed hydrolysis-polycondensation of tetraethoxysilane (TEOS) with triethoxysilylated imidazole [(EtO)(3)Si(CH(2))(3)-Im] or alkylimidazolium halides [(EtO)(3)Si(CH(2))(3)-Im(+)-R Hal(-)].     

Non-destructive method for determination of hydroxyl value of soybean polyol by LS-SVM using HATR/FT-IR

This paper presents the use of least-squares support vector machine (LS-SVM) for quantitative determination of hydroxyl value (OHV) of hydroxylated soybean oils by horizontal attenuated total reflection Fourier transform infrared (HATR/FT-IR) spectroscopy. A least-squares support vector machine (LS-SVM) calibration model for the prediction of hydroxyl value (OHV) was developed using the range 1805.1-649.9 cm(-1). Validation of the method was carried out by comparing the OHV of a series of hydroxylated soybean oil predicted by the LS-SVM model to the values obtained by the AOCS standard method. A correlation coefficient equal to 0.989 and RMSEP = 4.96 mg of KOH/g was obtained. This study demonstrates a better prediction ability of the LS-SVM technique to determine OHV in hydroxylated soybean oil samples by HATR/FT-IR spectra.     

Infrared spectroscopy of racemic and enantiomeric forms of atenolol

The molecular structure of conformational isomorphs given by X-ray diffraction for racemic and enantiomeric atenolol were optimized at the HF/6-31G* level of theory and the infrared spectra of the structure were calculated. These spectra are used to characterize the differences between the various atenolol conformers. The spectra of the (R,S)- and S-atenolol solid forms were recorded and the bands corresponding to the functional groups identified with the aid of the calculated spectra, fitting analysis, temperature effect and H/D isotopic exchange. Particular attention was paid to the stretch vibration modes of the functional groups present in the atenolol.     

Feasibility of light-emitting diode uses for annular reactor inner-coated with TiO2 or nitrogen-doped TiO2 for control of dimethyl sulfide

Limited environmental pollutants have only been investigated for the feasibility of light‐emitting diodes (LED) uses in photocatalytic decomposition (PD). The present study investigated the applicability of LEDs for annular photocatalytic reactors by comparing PD efficiencies of dimethyl sulfide (DMS), which has not been investigated with any LED‐PD system, between photocatalytic systems utilizing conventional and various LED lamps with different wavelengths. A conventional 8 W UV/TiO₂ system exhibited a higher DMS PD efficiency as compared with UV‐LED/TiO₂ system. Similarly, a conventional 8 W visible‐lamp/N‐enhanced TiO₂ (NET) system exhibited a higher PD efficiency as compared with six visible‐LED/NET systems. However, the ratios of PD efficiency to the electric power consumption were rather high for the photocatalytic systems using UV‐ or visible‐LED lamps, except for two LED lamps (yellow‐ and red‐LED lamps), compared to the photocatalytic systems using conventional lamps. For the photocatalytic systems using LEDs, lower flow rates and input concentrations and shorter hydraulic diameters exhibited higher DMS PD efficiencies. An Fourier‐transformation infrared analysis suggested no significant absorption of byproducts on the catalyst surface. Consequently, it was suggested that LEDs can still be energy‐efficiently utilized as alternative light sources for the PD of DMS, under the operational conditions used in this study.     

Thickness and refractive index of DPPC and DPPE monolayers by multiple-beam interferometry

The thickness and refractive index of 1,2-dipalmitoyl-sn-glycero-3-phosphatidyl choline (DPPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE) monolayers Langmuir--Blodgett (LB) deposited on mica were measured in dry air and bulk water using multiple-beam interferometry (MBI). Measurements of thickness using atomic force microscopy (AFM) of identical monolayers, and X-ray reflectivity (XRR) of the monolayers on quartz were taken for comparison. The measurement of the properties of solid-supported monolayers in dry air allows lipid optical properties to be determined free from solvent effects. The thickness and refractive index measured by MBI were 25.5?±?0.6 Å and 1.485?±?0.007 for DPPE monolayers, and 23.9?±?0.5 Å and 1.478?±?0.006 for DPPC monolayers in dry air. These thicknesses are consistent with the other techniques used in this work as well as other measurements in the literature. The refractive indices of solid-supported lipid monolayers have not been previously measured. The values are higher than previous measurements on black lipid films done by reflectometry, which is attributed to increased lipid packing density and the absence of hydrocarbon solvents. Applying water to the monolayers had no measurable effect on their properties, indicating that any change in hydration was below detection.

99mTc(CO)3-labeled pamidronate and alendronate for bone imaging

Bone scintigraphy with (99m)Technetium-methylenediphosphonate ((99m)Tc-MDP) or (99m)Technetium-hydroxymethylenediphosphonate ((99m)Tc-HMDP) presents several limitations, namely low specificity, uncertainty in the radiopharmaceutical's molecular structure and long acquisition time after injection. Aiming to find bone-seeking radiotracers based on the core fac-[(99m)Tc(CO)(3)](+) with improved chemical and biological properties, we synthesized new conjugates (pz-PAM and pz-ALN), comprising a pyrazolyl-diamine chelating unit (pz: N,N,N donor atom set) for metal stabilization and a pendant pamidronate (PAM) or alendronate (ALN) moiety for bone targeting. The reaction of the conjugates with fac-[(99m)Tc(CO)(3)](+) yielded (> 95%) the stable complexes fac-[(99m)Tc(CO)(3)(pz-PAM)](-) (2a) and fac-[(99m)Tc(CO)(3)(pz-ALN)](-) (3a), which have been characterized by comparing their HPLC gamma-traces with the UV-vis traces of the Re surrogates 2 and 3, respectively. 2a and 3a bind strongly onto hydroxyapatite. The biodistribution studies in Balb-c mice have shown that 2a and 3a presented an high bone uptake (2a 18.3 ± 0.6% I.D./g, 3a 17.3 ± 6.1% I.D./g, at 1 h post injection), similar to (99m)Tc-MDP (17.1 ± 2.4% I.D./g, at 1 h post injection), with comparable clearance from most tissues and increased total excretion (2a 66% I.D., 3a 67% I.D. and (99m)Tc-MDP 49% I.D., at 1 h post injection). The bone-to-blood (2a 86.2, 3a 74.7) and the bone-to-muscle ratios (2a 77.7, 3a 79.0) are higher than the ones found for (99m)Tc-MDP (70.9, 47.9), at 4 h post injection. Planar whole-body gamma camera images of the rats injected with the (99m)Tc(CO)(3)-labeled pamidronate (2a) and alendronate (3a) confirmed the overall adequate biological profile of the new radiotracers for bone imaging.     

Polymer microfluidic chips for electrochemical and biochemical analyses

Our recent developments concerning the fabrication of polymer microchips and their applications for biochemical analyses are reviewed. We first describe two methods of fabrication of polymer microfluidic chips, namely UV-laser photoablation and plasma etching that are well suited for the prototyping and mass fabrication of microchannel networks with integrated microelectrodes. These microanalytical systems can be coupled with various detection means including mass spectrometry, and their applications in capillary electrophoresis are presented here. We also present how UV laser photoablation can be used for the patterning of biomolecules on polymer surfaces for generating two-dimensional arrays of microspots to carry out affinity assays. Finally, the use of the microchips for the development of fast affinity and immunological assays with electrochemical detection is presented, demonstrating the potential of these polymer microchips for medical diagnostics and drug discovery.     

Gas chromatography-mass spectrometry as a tool for estimating odour concentrations of biofilter effluents at aerobic composting and rendering plants

The relationship between chemical concentrations (gas chromatography–mass spectrometry analysis) and odour concentrations (olfactometry) was studied for biofilter emissions from four aerobic vegetable, fruit and garden waste (VFG) composting plants and one animal rendering plant. For the VFG composting plants, the study revealed a good linear relationship of the odour concentration with the total volatile organic compounds (VOC) concentration (R²=0.97, n=16) as well as with the concentration of esters and ketones (R²=0.9, n=19). For biofilter emissions of the animal rendering plant, the total VOC concentration was a poor estimator for odour concentration. However, for this type of odour, concentrations of organic sulphur containing compounds correlated well with odour concentrations (R²=0.94, n=8). The results of the study also showed that the relationship between chemical and odour concentrations is specific for each type of odour and cannot be generalized.     

The search for a new model structure of β-Factor XIIa

We present the search for a new model of -factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and -factor XIIa, in particular.