Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2

Knowledge-based energy profiles combined with secondary structure prediction have been applied to molecular modelling refinement. To check the procedure, three different models of human procarboxypeptidase A2 (hPCPA2) have been built using the 3D structures of procarboxypeptidase A1 (pPCPA1) and bovine procarboxypeptidase A (bPCPA) as templates. The results of the refinement can be tested against the X-ray structure of hPCPA2 which has been recently determined. Regions miss-modelled in the activation segment of hPCPA2 were detected by means of pseudo-energies using Prosa II and modified afterwards according to the secondary structure prediction. Moreover, models obtained by automated methods as COMPOSER, MODELLER and distance restraints have also been compared, where it was found possible to find out the best model by means of pseudo-energies. Two general conclusions can be elicited from this work: (1) on a given set of putative models it is possible to distinguish among them the one closest to the crystallographic structure, and (2) within a given structure it is possible to find by means of pseudo-energies those regions that have been defectively modelled.     

Synthesis,crystal structure and magnetic properties of the helical oxalate-bridged copper(II) chain {[(CH3)4N]2[Cu(C2O4)2] · H2O}n

The preparation, crystal structure and magnetic properties of a new oxalate-containing copper(II) chain of formula {[(CH₃)₄N]₂[Cu(C₂O₄)₂] · H₂O}_n (1) [(CH₃)₄N⁺ = tetramethylammonium cation] are reported. The structure of 1 consists of anionic oxalate-bridged copper(II) chains, tetramethylammoniun cations and crystallization water molecules. Each copper(II) ion in 1 is surrounded by three oxalate ligands, one being bidentate and the other two exhibiting bis-bidenate coordination modes. Although all the tris-chelated copper(II) units from a given chain exhibit the same helicity, adjacent chains have opposite helicities and then an achiral structure results. Variable-temperature magnetic susceptibility measurements of 1 show the occurrence of a weak ferromagnetic interaction through the oxalate bridge [J = +1.14(1) cm⁻¹, the Hamiltonian being defined as H = –J ∑_nmS_i · S_j]. This value is analyzed and discussed in the light of available magneto-structural data for oxalate-bridged copper(II) complexes with the same out-of-plane exchange pathway.     

One-dimensional metal-organic framework with unprecedented heptanuclear copper units

The reaction of copper(II) sulfate, copper(II) chloride, 3,5-diacetylamino-1,2,4-triazole, and 3-acetylamino-5-amino-1,2,4-triazole in water yields green, plate-shaped crystals of [[{Cu3(mu3-OH(1/2))L(H2O)2Cl}2{mu-Cu(H2O)2Cl2}].12H2O]n (1), where L is a new triazole-derived macrocyclic ligand. The structure of 1 consists of heptanuclear (H)OCuII(3)-CuII-CuII(3)O(H) entities linked in pairs through symmetric mu3-O...H...O-mu3 hydrogen bonds to form a double-stranded one-dimensional network. A significant overall antiferromagnetic behavior has been observed for 1.     

Radical-Mediated Photocatalysis for Lignocellulosic Biomass Conversion into Value-Added Chemicals and Hydrogen: Facts,Opportunities and Challenges

Photocatalytic biomass conversion into high-value chemicals and fuels is considered one of the hottest ongoing research and industrial topics toward sustainable development. In short, this process can cleave C_β−O/C_α−C_β bonds in lignin to aromatic platform chemicals, and further conversion of the polysaccharides to other platform chemicals and H₂. From the chemistry point of view, the optimization of the unique cooperative interplay of radical oxidation species (which are activated via molecular oxygen species, ROSs) and substrate-derived radical intermediates by appropriate control of their type and/or yield is key to the selective production of desired products. Technically, several challenges have been raised that face successful real-world applications. This review aims to discuss the recently reported mechanistic pathways toward selective biomass conversion through the optimization of ROSs behavior and materials/system design. On top of that, through a SWOT analysis, we critically discussed this technology from both chemistry and technological viewpoints to help the scientists and engineers bridge the gap between lab-scale and large-scale production.     

The fate of optical excitations in small hydrated ZnS clusters: a theoretical study into the effect of hydration on the excitation and localisation of electrons in Zn4S4 and Zn6S6

In this paper we explore the effect of water on the excited state properties of ZnS nanostructures by means of time-dependent density functional theory (TD-DFT) calculations. Using these TD-DFT calculations we show that the effect of water on the optical absorption spectra is primarily a small blue-shift and that a secondary effect is that spectroscopic features that correspond to dark excitations for the anhydrous nanostructures gain intensity and new absorption peaks are predicted to appear. The effect of adsorbed water on the localisation of excited states is to produce small shifts in the values of the excited stabilisation energies but, more importantly, it results in the formation of extra minima when compared with the case for anhydrous ZnS. Finally, the effect of water on photoluminescence (PL) energies is predicted to be small but the appearance of extra minima induced by the presence of adsorbed water is expected to lead to a splitting/broadening of the PL signal.     

Very long-distance magnetic coupling in a dicopper(II) metallacyclophane with extended π-conjugated diphenylethyne bridges

Self-assembly of the rigid rodlike ligand N,N'-4,4'-diphenylethynebis(oxamate) (dpeba) and Cu(2+) ions affords a novel dinuclear copper(II) metallacyclophane (nBu(4)N)(4)[Cu(2)(dpeba)(2)]·4MeOH·2Et(2)O (1) featuring a very long intermetallic distance (r = 15.0 ?). Magnetic susceptibility measurements for 1 reveal a moderately weak but nonnegligible intramolecular antiferromagnetic coupling between the two metal centers across the double para-substituted diphenylethynediamidate bridge (J = -3.9 cm(-1); H = -JS(1)S(2), where S(1) = S(2) = S(Cu) = (1)/(2)). Density functional electronic structure calculations on 1 support the occurrence of a spin polarization mechanism.     

Determination of musk fragrances in sewage sludge by pressurized liquid extraction coupled to automated ionic liquid‐based headspace single‐drop microextraction followed by GC‐MS/MS

A method for the quantitative determination of ten musk fragrances extensively used in personal care products from sewage sludge was developed by using a pressurized liquid extraction (PLE) followed by an automated ionic liquid‐based headspace single‐drop microextraction and gas chromatography‐tandem mass spectrometry. The influence of main factors on the efficiency of PLE was studied. For all musks, the highest recovery values were achieved using 1 g of pretreated sewage sludge, H₂O/methanol (1:1) as an extraction solvent, a temperature of 80°C, a pressure of 1500 psi, an extraction time of 5 min, 2 cycles, a 100% flush volume, a purge time of 120 s, and 1 g Florisil as in‐cell clean‐up extraction sorbent. The use and optimization of an in‐cell clean‐up sorbent was necessary to remove fatty interferents of the PLE extract that make the subsequent ionic liquid‐based headspace single‐drop microextraction difficult. Validation parameters, namely LODs and LOQs, ranged from 0.5–1.5 to 2.5–5 ng/g, respectively. Good levels of intra‐ and interday repeatabilities were obtained analyzing sewage sludge samples spiked at 10 ng/g (n = 3, RSDs < 10%). The method applicability was tested with sewage sludge from different wastewater treatment plants. The analysis revealed the presence of all the polycyclic musks studied at concentrations higher than the LOQs, ranging from 6 to 530 ng/g. However, the nitro musk concentrations were below the LOQs or, in the case of musk xylene, was not detected.     

An automated headspace solid-phase microextraction followed by gas chromatography–mass spectrometry method to determine macrocyclic musk fragrances in wastewater samples

A fully automated method has been developed for determining eight macrocyclic musk fragrances in wastewater samples. The method is based on headspace solid-phase microextraction (HS-SPME) followed by gas chromatography–mass spectrometry (GC-MS). Five different fibres (PDMS 7 μm, PDMS 30 μm, PDMS 100 μm, PDMS/DVB 65 μm and PA 85 μm) were tested. The best conditions were achieved when a PDMS/DVB 65 μm fibre was exposed for 45 min in the headspace of 10 mL water samples at 100 °C. Method detection limits were found in the low ng L^?1 range between 0.75 and 5 ng L^?1 depending on the target analytes. Moreover, under optimized conditions, the method gave good levels of intra-day and inter-day repeatabilities in wastewater samples with relative standard deviations (n?=?5, 1,000 ng L^?1) less than 9 and 14 %, respectively. The applicability of the method was tested with influent and effluent urban wastewater samples from different wastewater treatment plants (WWTPs). The analysis of influent urban wastewater revealed the presence of most of the target macrocyclic musks with, most notably, the maximum concentration of ambrettolide being obtained in WWTP A (4.36 μg L^?1) and WWTP B (12.29 μg L^?1), respectively. The analysis of effluent urban wastewater showed a decrease in target analyte concentrations, with exaltone and ambrettolide being the most abundant compounds with concentrations varying between below method quantification limit (<MQL) and 2.46 μg L^?1.