DOT2: Macromolecular docking with improved biophysical models

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. © 2013 Wiley Periodicals, Inc.     

Solvent extraction with organophosphorus extractants in environmental samples: determination of cadmium(II) in natural water

In this work, Cd(II) extraction in natural waters by organophosphorus extractants as organic phase, as well as its back-extraction in an acidic media, has been studied. Cadmium extraction behavior at natural waters’ pH conditions (values in the range 7–8) was studied with two different extractants and co-ions, obtaining the highest extraction efficiency when using 0.1M Cyanex 272 in kerosene as organic phase and 0.1 M NO₃ ^? as co-ion. Once they were selected, the effect on the extraction efficiency of sample pH, buffer concentration, extraction time, Cyanex 272 concentration as well as back-extractant concentration, was studied. The presence of the main inorganic and organic ligands in the sample was also studied, observing that extraction efficiency was affected most significantly when chlorides were present, with a decrease of about 14%, proving negligible for the others. Under the selected conditions, spiked real samples were successfully analyzed.      

Methodology for measuring the thermal conductivity of insulating samples with small dimensions by heat flow meter technique

Journal of Thermal Analysis and Calorimetry - Nowadays, developing advanced, highly insulating materials for minimizing heat losses in buildings is of utmost relevance. Thus, there is a constant...     

Magnetic and structural properties of FeCr alloys

Synergistic synchrotron x-ray absorption experiments using imaging magnetic microspectroscopy, x-ray magnetic circular dichroism, and ab initio calculations on FeCr alloys reveal that the Cr content strongly influences the ferromagnetic microstructure and the Fe magnetic moments. The Cr local structure resolved by extended x-ray absorption fine structure (EXAFS) is also found to be affected by the alloy's composition. Both EXAFS and ab initio calculations show a change in the Cr local atomic structure above 10 at.% Cr content from the distance contraction of the first two coordination shells around the Cr absorbing atom. These results indicate the strong dependence of magnetic and structural properties of these alloys on Cr concentration.     

Phosphatidylcholine‐Coated Iron Oxide Nanomicelles for In Vivo Prolonged Circulation Time with an Antibiofouling Protein Corona

We report the synthesis of micellar phosphatidylcholine‐coated superparamagnetic iron oxide nanoparticles as a new long circulation contrast agents for magnetic resonance imaging. Oleic acid‐coated Fe₃O₄ nanoparticles were first prepared through thermal degradation and then encapsulated into small clusters with a phosphatidylcholine coating to obtain hydrophilic nanomicelles. A thorough characterization confirmed the chemical nature of the coating and the excellent colloidal stability of these nanomicelles in aqueous media. Magnetization and relaxivity properties proved their suitability as magnetic resonance imaging (MRI) contrast agent and in vitro cell viability data showed low toxicity. Vascular lifetime and elimination kinetics in the liver were assessed by blood relaxometry and by in vivo MRI in rats and compared with “control” particles prepared with a polyethylene glycol derivative. These micellar particles had a lifetime in blood of more than 10 h, much longer than the control nanoparticles (≈2 h), which is remarkable considering that the coating molecule is a small biocompatible zwitterionic phospholipid. The protein corona was characterized after incubation with rat serum at different times by high‐throughput proteomics, showing a higher proportion of bound apolipoproteins and other dysopsonins for the phosphatidylcholine particles. The antibiofouling properties of this corona and its resistance to the adsorption of proteins corroborate the observed enhanced stability and prolonged systemic circulation.     

Unprecedented 1,14‐seco‐Crotofolanes from Croton insularis: Oxidative Cleavage of Crotofolin C by a Putative Homo‐Baeyer–Villiger Rearrangement

EBC‐162 isolated from Croton insularis, obtained from the northern rainforest of Australia, was structurally affirmed as crotofolin C ( 4 ). Novel oxidative degradation products, EBC‐233 and EBC‐300, which are the first crotofolane endoperoxides, were also isolated. Both endoperoxides were found to be stable intermediates, which are proposed to undergo an unprecedented homo‐Baeyer–Villiger biosynthetic rearrangement to give a new class of 1,14‐seco‐crotofolane diterpenes. Prolonged storage of all isolates assisted in authenticating their natural product status. Anticancer activities of reported compounds are presented.     

Tailoring a Zinc Oxide Nanorod Surface by Adding an Earth-Abundant Cocatalyst for Induced Sunlight Water Oxidation

Herein, a detailed investigation of the surface modification of a zinc oxide (ZnO) nanorod electrode with FeOOH nanoparticles dispersed in glycine was conducted to improve the water oxidation reaction assisted by sunlight. The results were systematically analysed in terms of the general parameters (light absorption, charge separation, and surface for catalysis) that govern the photocurrent density response of metal oxide as photoanode in a photoelectrochemical (PEC) cell. ZnO electrodes surface were modified with different concentration of FeOOH nanoparticles using the spin-coating deposition method, and it was found that 6-layer deposition of glycine-FeOOH nanoparticles is the optimum condition. The glycine plays an important role decreasing the agglomeration of FeOOH nanoparticles over the ZnO electrode surface and increasing the overall performance. Comparing bare ZnO electrodes with the ones modified with glycine-FeOOH nanoparticles an enhanced photocurrent density can be observed from 0.27 to 0.57 mA/cm² at 1.23 V_RHE under sunlight irradiation. The impedance spectroscopy data aid us to conclude that the higher photocurrent density is an effect associated with more efficient surface for chemical reaction instead of electronic improvement. Nevertheless, the charge separation efficiency remains low for this system. The present discovery shows that the combination of glycine-FeOOH nanoparticle is suitable and environmentally-friend cocatalyst to enhance the ZnO nanorod electrode activity for the oxygen evolution reaction assisted by sunlight irradiation.     

Synthesis and magnetic characterization of cobalt-substituted ferrite (CoxFe3−xO4) nanoparticles

Cobalt-substituted ferrite nanoparticles were synthesized with a narrow size distribution using reverse micelles formed in the system water/AOT/isooctane. Fe:Co ratios of 3:1, 4:1, and 5:1 were used in the synthesis, obtaining cobalt-substituted ferrites (Co_xFe_3−xO₄) and some indication of γ-Fe₃O₄ when 4:1 and 5:1 Fe:Co ratios were used. Inductively coupled plasma mass spectroscopy (ICP-MS) verified the presence of cobalt in all samples. Fourier transform infrared (FTIR) showed bands at ∼560 and ∼400 cm⁻¹, characteristic of the metal–oxygen bond in ferrites. Transmission electron microscopy showed that the number median diameter of the particles was ∼3 nm with a geometric deviation of ∼0.2. X-ray diffraction (XRD) confirmed the inverse spinel structure typical of ferrites with a lattice parameter of a=8.388 Å for Co_0.61Fe_0.39O₄, which is near that of CoFe₂O₄ (a=8.394 Å). Magnetic properties were determined using a superconducting quantum interference device (SQUID). Coercivities higher than 8 kOe were observed at 5 K, whereas at 300 K the particles showed superparamagnetic behavior. The anisotropy constant was determined based on the Debye model for a magnetic dipole in an oscillating field and an expression relating χ′ and the temperature of the in-phase susceptibility peak. Anisotropy constant values in the order of ∼10⁶ erg/cm³ were determined using the Debye model, whereas anisotropy constants in the order of ∼10⁷ erg/cm³ were calculated assuming Ωτ=1 at the temperature peak of the in-phase component of the susceptibility curve as commonly done in the literature. Our analysis demonstrates that the assumption Ωτ=1 at the temperature peak of χ′ is rigorously incorrect.