Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism

Mycobacterium tuberculosis is the causative agent of human tuberculosis. The nitric oxide reaction with oxy-truncated hemoglobin N (trHbN) has been proposed to be responsible for the resistance mechanism by which this microorganism can evade the toxic effects of NO. In this work, we explore the molecular basis of the NO detoxification mechanism using a combination of classical and hybrid quantum-classical (QM-MM) simulation techniques. We have investigated the structural flexibility of the protein, the ligand affinity properties, and the nitric oxide reaction with coordinated O2. The analysis of the classical MD trajectory allowed us to identify Phe62 as the gate of the main channel for ligand diffusion to the active site. Moreover, the opening of the channel stems from the interplay between collective backbone motions and local rearrangements in the side chains of the residues that form the bottleneck of the tunnel. Even though the protein environment is not found to make a significant contribution to the heme moiety catalyzed reaction, the binding site influences the physiological function of the enzyme at three different levels. First, by isolating the intermediates formed in the reaction, it prevents nondesired reactions from proceeding. Second, it modulates the ligand (O2, NO) affinity of the protein, which can be ascribed to both distal and proximal effects. Finally, the stabilization of the Tyr33-Gln58 pair upon O2 binding might alter the essential dynamics of the protein, leading in turn to a mechanism for ligand-induced regulation.     

Photodetachment spectrum of OHF-: three-dimensional study of the heavy-light-heavy resonances

In this work a simulation of the OHF(-) photodetachment spectrum is performed in a three-dimensional potential energy surface recently developed for OHF((3)A(")). The ground (2)A(') state potential of the anion is calculated in three dimensions based on accurate ab initio calculations and the reaction dynamics is studied using a wave packet method. The calculated spectrum shows a sequence of bands associated to vibrational HF(v) up to v=3. Each band is formed by a continuous spectrum and resonant structures. These resonances are associated to the OH-F channel well of the (3)A(") PES, in which fragmentation occurs through vibrational predissociation. Above the OH(v=0) threshold a new resonant pattern appears corresponding to heavy-light-heavy resonances. Special attention is paid to the assignment of these resonances because they mediate the reaction dynamics in the OH+F collision at low kinetic energies. The sequence of bands is in rather good agreement with that appearing in the experimental spectrum, especially at higher electron kinetic energies. At low kinetic energies, however, some other electronic states may contribute. The resonance structures might be washed out by the rotational average and the relatively low energy resolution of the experiment.     

Intramolecular interactions in the triplet excited states of benzophenone-thymine dyads

Time-resolved and product studies on the synthesized dyads 1 and 2 have provided evidence that the benzophenone-to-thymine orientation strongly influences intramolecular photophysical and photochemical processes. The prevailing reaction mechanism has been established as a Paterno-Büchi cycloaddition to give oxetanes 3-6; however, the ability of benzophenone to achieve a formal hydrogen abstraction from the methyl group of thymidine has also been evidenced by the formation of photoproducts 7 and 8. These processes have been observed only in the case of the cisoid dyad 1. Adiabatic photochemical cycloreversion of the oxetane ring is achieved upon direct photolysis to give the starting dyad 1 in its excited triplet state. The photobiological implications of the above results are discussed with respect to benzophenone-photosensitized damage of thymidine.     

2-Oxopiperazine-based gamma-turn conformationally constrained peptides: synthesis of CCK-4 analogues

2-Oxopiperazine derivatives 1 have been designed as mimetics of gamma-turn conformationally constrained tripeptides. The synthetic pathway devised for the preparation of both epimers of 1 at C(5) involves a reductive amination of cyanomethyleneamino pseudopeptides with amino acid derivatives, followed by regiospecific lactamization of the resulting C-backbone branched pseudopeptides. The versatility of this methodology is illustrated in the synthesis of analogues of the tetrapeptides Boc-[Nle(31)]-CCK-4 and Boc-[Lys(o-tolylaminocarbonyl)(31)]-CCK-4. The introduction of the new conformational restriction into these Boc-CCK-4 analogues led to a loss of 2 or 3 orders of magnitude in the affinity at CCK receptors. These results suggest the absence of a gamma-turn in the bioactive conformation of the C-terminal tripeptide of CCK-4.     

An integrated electrochemical fructose biosensor based on tetrathiafulvalene-modified self-assembled monolayers on gold electrodes

An integrated amperometric fructose biosensor based on a gold electrode (AuE) modified with a self-assembled monolayer (SAM) of 3-mercaptopropionic acid (MPA) on which fructose dehydrogenase (FDH) and the mediator tetrathiafulvalene (TTF) are co-immobilized by cross-linking with glutaraldehyde is reported. Variables concerning the behavior of the biosensor were optimized by taking the slope value obtained for the fructose calibration plot in the 0.1–1.0 mM concentration range as a criterion of selection. At an applied potential of +0.20 V, a good repeatability of such slope values (RSD=6.7%, n=10) was obtained with no need to apply a cleaning or pretreatment procedure to the modified electrode. Moreover, results from five different TTF-FDH-MPA-AuEs yielded a RSD of 5.8%. The useful lifetime of one single biosensor was approximately 30 days, exhibiting a 93% of the original response on the 33rd day. A linear calibration graph was obtained for fructose over the 1.0×10^–5–1.0×10^–3 M range, with a limit of detection of 2.4×10^–6 M. The effect of potential interferents was evaluated. The TTF-FDH-MPA-AuE also performed well in the flow-injection mode. The biosensor was used for the determination of fructose in real samples, and the results compared with those provided by using a commercial enzyme test kit.     

Volatile compounds of red and white wines by headspace--solid-phase microextraction using different fibers

The behavior of four fibers [polydimethylsiloxane (PDMS), PDMS-divinylbenzene (DVB), carboxen (CAR)-PDMS, PDMS-DVB-CAR), is tested for the analysis of volatile compounds of white and red wine. The PDMS-DVB-CAR fiber is the most appropriate to obtain the most wide volatile profile of wines. The better extraction conditions are 40 min at 35 degrees C. Satisfactory data about the reproducibility and uptake are obtained for more than 40 volatile compounds of red and white wine.     

“On line” mass spectrometric detection of ammonia oxidation products generated by polypyrrole based amperometric sensors

Polypyrrole (PPy) is the conducting polymer most widely employed in electrochemical sensors for ammonia detection in the last decade. Although sensors have been described in depth in the literature, the mechanism of ammonia detection by polypyrrole is still a matter of controversy. The differential electrochemical mass spectrometry (DEMS) technique, together with UV-Vis spectroscopy, gives direct and conclusive evidence with respect to the ammonia oxidation products formed in NaOH solution (pH=10) at polyrrole or N-methyl polypyrrole film sensors polarized at 0.35 V (Ag/AgCl). Monitoring of the different possible ammonia oxidation products by on-line DEMS measurements indicates that only NO is formed and that other species such as N₂ or N₂O are absent. UV-Vis absorption spectroscopy also showed that ionic products such as nitrate or nitrite are not formed.     

Soil characterization by energy dispersive X-ray fluorescence: sampling strategy for in situ analysis.

This work describes a sampling strategy that will allow the use of portable EDXRF (energy dispersive X-ray fluorescence) instruments for "in situ" soil analysis. The methodology covers a general approach to planning field investigations for any type of environmental studies and it was applied for a soil characterization study in the zone of Campana, Argentina, by evaluating data coming from an EDXRF spectrometer with a radioisotope excitation source. Simulating non-treated sampled as "in situ" samples and a soil characterization for Campana area was intended. "In situ" EDXRF methodology is a powerful analytical modality with the advantage of providing data immediately, allowing a fast general screening of the soil composition.     

Ethyl 3,5‐dimethyl‐4‐phenyl‐1H‐pyrrole‐2‐carboxylate

In the title compound, C₁₅H₁₇NO₂, the ethoxy­carbonyl group is anti with respect to the pyrrole N atom. The angle between the planes of the phenyl and pyrrole rings is 48.26 (9)°. The mol­ecules are joined into dimeric units by a strong hydrogen bonds between pyrrole N—H groups and carbonyl O atoms. The geometry of the isolated mol­ecule was studied by ab initio quantum mechanical calculations, employing both molecular orbital Hartree–Fock (MO–HF) and density functional theory (DFT) methods. The minimum energy was achieved for a conformation where the angle between the planes of the phenyl and pyrrole rings is larger, and that between the ethoxy­carbonyl and pyrrole planes is smaller than in the solid‐state mol­ecule.     

Qualitative and quantitative analysis of THC, 11‐hydroxy‐THC and 11‐nor‐9‐carboxy‐THC in whole blood by ultra‐performance liquid chromatography/tandem mass spectrometry

A qualitative and quantitative analytical method was developed for the simultaneous determination of Δ⁹‐tetrahydrocannabinol (THC), 11‐hydroxy‐Δ⁹‐tetrahydrocannabinol (11‐OH‐THC) and l1‐nor‐9‐carboxy‐Δ⁹‐tetrahydrocannabinol (THC‐COOH) in whole blood. The samples were prepared by solid‐phase extraction followed by ultra‐performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) analysis using positive ion electrospray ionization and multiple reaction monitoring. The chromatographic separation was performed with an Acquity UPLC® HSS T3 (50 × 2.1 mm i.d., 1.8 µm) reversed‐phase column using a methanol/2 mM ammonium formate (formic acid 0.1%) gradient in a total run time of 9.5 min. MS/MS detection was achieved with two precursor‐product ion transitions per substance. The method was fully validated, including selectivity and capacity of identification, according to the identification criteria (two transitions per substance, signal‐to‐noise ratio, relative retention time and ion ratio) without the presence of interferences, limit of detection (0.2 µg/L for THC and 0.5 µg/L for 11‐OH‐THC and THC‐COOH), limit of quantitation (0.5 µg/L for all cannabinoids), recovery (53–115%), carryover, matrix effect (34‐43%), linearity (0.5‐100 µg/L), intra‐assay precision (CV < 10% for the relative peak area ratios and <0.1% for the relative retention time), inter‐assay accuracy (mean relative error <10%) and precision (CV <11%). The method has already been successfully used in proficiency tests and subsequently applied to authentic samples in routine forensic analysis. Copyright © 2011 John Wiley & Sons, Ltd.