Computational clues for a new mechanism in the glycosylase activity of the human DNA repair protein hOGG1. A generalized paradigm for purine-repairing systems?

A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle responsible for the glycosylase activity of the human DNA repair protein hOGG1: enzyme activation, cleavage of the glycosidic bond, and expulsion of the damaged base. An unprecedented large quantum mechanics (QM) model system has been used, which includes a complete oxoG molecule, the deoxyribose ring bonded to the phosphate groups, and most of the surrounding residues that simulate the protein binding pocket. It has been found that Asp268 does not play any role in Lys249 activation and that the oxoG basis acts as a coenzyme, triggering nucleophile activation by Lys249 deprotonation. An SN2 nucleophilic attack by Lys249 on the anomeric carbon then follows. This is the rate-determining step of the process with an activation barrier of 16.7 kcal mol(-1) in good agreement with the experimental value of 17.1 kcal mol(-1). The expelled oxoG plays again as an enzyme cofactor at the end of the process by activating (via proton transfer) ribose ring opening and Schiff base formation. This study suggests a recurring catalytic strategy in the enzymatic cleavage of purine nucleoside where the activation of the leaving group by protonation of the nucleoside base (via an enzymatic general acid) triggers the cleavage of the glycosidic bond.     

Synthesis, solution thermodynamics, and X-ray study of CuII [12]metallacrown-4 with GABA hydroxamic acid: an unprecedented crystal structure of a [12]MC-4 with a gamma-aminohydroxamate

The solution equilibria of gamma-aminobutanehydroxamic acid (GABAha) with H+ and Cu2+ were investigated by potentiometry, titration calorimetry, spectrophotometry, NMR spectroscopy, and ESI-MS. The thermodynamic parameters of the CuII [12]metallacrown-4 obtained for GABAha were compared with those of the corresponding complexes of (S)-alpha-Alaha and beta-Alaha. The stability (-DeltaG0) sequence was beta-Alaha>alpha-Alaha>GABAha, whereas the order of formation enthalpies (-DeltaH0) was beta-Alaha>GABAha>alpha-Alaha. These data were interpreted on the basis of the dimensions of the chelate rings and the planarity of the metallamacrocycles. The CuII [12]metallacrown-4 ([12]MC-4) complex of GABAha was isolated and its crystal structure, which is the first reported for a [12]MC-4 of a gamma-aminohydroxamic acid, fully supports the structural features interpreted from the thermodynamic data.     

Voltammetric Detection of Free Sulfhydryl Compounds in Food Flours

Cyclic voltammetry has been applied to the rapid measurement of free SH‐compounds in food flours samples. The protocol is based on the electrochemical adaptation of the Ellman's test, where the DTNB reacts with SH‐compounds present in food flour extracts, resulting in the equimolar production of the electroactive compound TNBA which, in turns, reacts with phenylendiamine. The reaction is found to provide an analytical signal from which to quantify indirectly free sulfhydryl compounds in flours extracts.     

Nonperiodic boundary conditions for solvated systems

The simulation of charged and/or strongly polar solutes represents a challenge for standard molecular-dynamics techniques. The use of periodic boundary conditions (PBCs) leads to artifacts due to the interaction between two replicas in the presence of the long-range Coulomb forces. A way to avoid these problems is the use of nonperiodic boundary conditions. A possible realization is to consider a finite system, a sphere, embedded in a reaction field described by the method of the images. In the present work the modified image approximation has been implemented in a molecular-dynamics code and optimized for the use of two standard solvents, water and acetonitrile. The methodology has then been applied to investigate the conformational changes in water-solvated alanine dipeptide. The free-energy surface calculated with this method is comparable to that obtained with PBC.     

The role of dispersive forces determining the energetics of adsorption in Ti zeolites

Ti‐zeolites are interesting materials because of their key role in partial oxidation reactions, as well as under a fundamental point of view being regarded as single site catalysts. Both experimental and computational approaches have been widely applied to the characterization of their active sites, reaching a level of knowledge unmatchable by most other important catalysts. However, several questions are still open, being a proper energetic simulation of the adsorption process of simple molecules, fitting with the experimental outcomes, still missing. The present work wants to underline the role of dispersive forces in correctly determining the adsorption energies of H₂O and NH₃ in Ti chabazite: first dispersive contributions have been included through an ONIOM scheme, comparing the results from semiempirical Grimme scheme and fully ab initio MP2. Being the key contribution of dispersion proved, a fully periodic, Grimme dispersions inclusive approach has been applied, coming to results close to the experimental values. © 2016 Wiley Periodicals, Inc.     

Direct flow injection profiling of acyl glycerols from food products using isopropanol as solvent

This work proposes a novel method for the direct flow injection profiling of acylglycerols in edible oils and fats without preliminary extraction and consequent reconstitution in the injection solvent. The work exploits the outstanding performance of high‐resolution mass spectrometry to target unique elemental compositions even in the most complex matrices. The performance of isopropanol as the unique solvent for both the solubilization and analysis of acylglycerols was investigated in comparison with other classical methods involving preliminary extractions, sample recovery, and analysis. The calibrations of two triglyceride standards (triolein and trilinolenin) were successfully performed in presence and absence of oil matrix. As final application, the effects on the acylglycerol fraction of a heat treatment on three different fat samples (extra virgin olive oil, lard oil, and fat from dry cured ham—speck) were monitored. The proposed method is therefore suitable for a rapid evaluation of acylglycerol fractions in food lipid samples.     

Synthesis of α-trifluoromethyl-α-amino-β-sulfone hydroxamates: novel nanomolar inhibitors of matrix metalloproteinases

The racemic α-trifluoromethyl-α-amino-β-sulfone hydroxamates 1 were synthesized by means of a nucleophilic addition of sulfur-stabilized carbanions to a N-Cbz imine of trifluoropyruvate (4). The free amino derivative 1a was the most potent inhibitor of both MMP-3 (stromelysin-1) and MMP-9 (gelatinase-B), showing an IC₅₀ = 14 nM and 1 nM, respectively, and excellent selectivity versus MMP-1 (>5000-fold difference in inhibitory capacity). The N-Me derivative 1b was the most selective for MMP-3 with respect to MMP-9 (62-fold difference).     

Determination of metal concentration in fat supplements for swine nutrition by atomic absorption spectroscopy

The presence of some essential and toxic metals in fat supplements for swine diet was investigated. Collected samples represented a relevant production of the Italian industry. In particular, some samples were enriched with antioxidants or waste cooking oils. The method for the determination of Ca, Cu, Cd, Fe, Mg, Mn, Ni, Pb, and Zn in fat samples was developed by means of a certified reference material (CRM 186) and a representative fatty sample (RFS). All samples were digested in closed vessels in a microwave oven and then analyzed by flame atomic absorption or graphite furnace atomic absorption spectrometry. The entire analytical method provided a satisfactory repeatability and reproducibility confirmed by agreement between the experimental recovery data obtained for the CRM 186 sample and, with the method of standard additions, for the RFS material. The samples generally showed a small amount of metals compared with the recommended daily intake for the essential elements. On the other hand, some samples contained a significant concentration, from an analytical point of view, of Cd, Ni, and Pb. Principal component analysis (PCA) was applied to inspect the experimental data obtained from samples analysis. Basically no differences were detected in terms of metal concentration among the fat supplements analyzed.     

q value and parent energy optimization using a low-voltage ionization approach increases resolution in linear ion trap mass spectrometry

In this work, the isolation step in the linear ion trap was performed using different “q values” conditions at a low collision-induced dissociation (CID) energy leading to the parent ion resolution improvements, reasonably due to better ion energy distribution. According to the results, we obtained a greater resolution and mass accuracy operating in both traditional electrospray and low voltage ionization near the q value = 0.778 and with a CID energy of 10%. This effect was evaluated with low-molecular-mass compounds (skatole and arginine). The proposed optimization yielded a superior instrument performance without adding technological complexity to mass spectrometry analyses.