Pristine graphite oxide

Graphite oxide (GO) is a lamellar substance with an ambiguous structure due to material complexity. Recently published GO-related studies employ only one out of several existing models to interpret the experimental data. Because the models are different, this leads to confusion in understanding the nature of the observed phenomena. Lessening the structural ambiguity would lead to further developments in functionalization and use of GO. Here, we show that the structure and properties of GO depend significantly on the quenching and purification procedures, rather than, as is commonly thought, on the type of graphite used or oxidation protocol. We introduce a new purification protocol that produces a product that we refer to as pristine GO (pGO) in contrast to the commonly known material that we will refer to as conventional GO (cGO). We explain the differences between pGO and cGO by transformations caused by reaction with water. We produce ultraviolet-visible spectroscopic, Fourier transform infrared spectroscopic, solid-state nuclear magnetic resonance spectroscopic, thermogravimetric, and scanning electron microscopic analytical evidence for the structure of pGO. This work provides a new explanation for the acidity of GO solutions and allows us to add critical details to existing GO models.     

High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.     

Molecular dynamics simulations of the interfacial and structural properties of dimethyldodecylamine-N-oxide micelles

A series of large-scale atomistic molecular dynamics simulations were conducted to study the structural and interfacial properties of nonionic dimethyldodecylamine-N-oxide (DDAO) micelles with an aggregation number of 104 in pure water, which was determined using small-angle neutron scattering (SANS). From these simulations, the micelles were found to be generally ellipsoidal in shape with axial ratios of ～1.3-1.4, which agrees well with that found from small-angle neutron scattering measurements. The resulting micelles have an area per DDAO molecule of 94.8 ?(2) and an average number of hydration water molecules per DDAO molecule of ～8. The effect of the encapsulation of ethyl butyrate (CH(3)(CH(2))(2)COOCH(2)CH(3), C(4)) and ethyl caprylate (CH(3)(CH(2))(6)COOCH(2)CH(3), C(8)) on the structural and interfacial properties of the nonionic DDAO aggregates was also examined. In the presence of the C(4) oil molecules, the aggregates were found to be less ellipsoidal and more spherical than the pure DDAO micelles, while the aggregates in the presence of the C(8) oil molecules were almost perfect spheres. In addition, the C(4) oil molecules move into the core of the aggregates, while the C(8) oil molecules stay in the headgroup region of the aggregates. Finally, the structural properties of two micelles formed from different starting states (a "preassembled" sphere and individual DDAO molecules distributing in water) were found to be nearly identical.     

Nonpeptide inhibitors of cathepsin G: optimization of a novel beta-ketophosphonic acid lead by structure-based drug design

The serine protease cathepsin G (EC 3.4.21.20; Cat G), which is stored in the azurophilic granules of neutrophils (polymorphonuclear leukocytes) and released on degranulation, has been implicated in various pathological conditions associated with inflammation. By employing high-throughput screening, we identified beta-ketophosphonic acid 1 as a moderate inhibitor of Cat G (IC(50) = 4.1 microM). We were fortunate to obtain a cocrystal of 1 with Cat G and solve its structure by X-ray crystallography (3.5 A). Structural details from the X-ray analysis of 1.Cat G served as a platform for optimization of this lead compound by structure-based drug design. With the aid of molecular modeling, substituents were attached to the 3-position of the 2-naphthyl ring of 1, which occupies the S1 pocket of Cat G, to provide an extension into the hydrophobic S3 region. Thus, we arrived at analogue 7 with an 80-fold potency improvement over 1 (IC(50) = 53 nM). From these results, it is evident that the beta-ketophosphonic acid unit can form the basis for a novel class of serine protease inhibitors.     

Syntheses of 3-Chloro-7-[(Chlorocarbonyl)Methoxy]-4-Methylcoumarin

Two efficient syntheses of 3-chloro-7-[(chlorocarbonyl)methoxy]-4-methylcoumarin are described, one utilizing traditional chemistry starting from 3-chloro-7-hydroxy-4-methylcoumarin, while the other uses a novel reagent, sulfuryl chloride/thionyl chloride, in a one-pot reaction starting from 7-(carboxymethoxy)-4-methylcoumarin.     

High-resolution electron microscopy of montmorillonite and montmorillonite/epoxy nanocomposites

With the use of high-resolution transmission electron microscopy the structure and morphology of montmorillonite (MMT), a material of current interest for use in polymer nanocomposites, was characterized. Using both imaging theory and experiment, the procedures needed to generate lattice images from MMT were established. These procedures involve careful control of the microscope's objective lens defocus to maximize contrast from features of a certain size, as well as limiting the total dose of electrons received by the sample. Direct images of the MMT lattice were obtained from neat Na+ MMT, organically modified MMT, and organically modified MMT/epoxy nanocomposites. The degree of crystallinity and turbostratic disorder were characterized using electron diffraction and high-resolution electron microscopy (HREM). Also, the extent of the MMT sheets to bend when processed into an epoxy matrix was directly visualized. A minimum radius of curvature tolerable for a single MMT sheet during bending deformation was estimated to be 15 nm, and from this value a critical failure strain of 0.033 was calculated. HREM can be used to improve the understanding of the structure of polymer nanocomposites at the nanometer-length scale.     

Electrochemical detection of amino acids at carbon nanotube and nickel-carbon nanotube modified electrodes

The oxidation and enhanced detection of traditionally 'non-electroactive' amino acids at a single-wall carbon nanotube (SWNT) surface and at a nickel hydroxide film electrochemically deposited and generated upon the SWNT layer is reported. Different CNT are compared, with Nafion-dispersed SWNT offering the most favorable layer for constant-potential amperometric detection. Factors affecting the oxidation process, including the pH or applied potential, are assessed. The response of the SWNT-Nafion coated electrode compares favorably with that of copper and nickel disk electrodes under flow injection analysis (FIA) conditions. The electrodeposition of nickel onto the SWNT-Nafion layer (Ni-CNT) led to a dramatic enhancement of the analytical response (vs. that observed at the SWNT or nickel electrodes alone). The oxidative process at the Ni(OH)(2) layer has been studied and the increase in sensitivity rationalized. In the presence of amino acid the Ni-CNT layer undergoes an electrocatalytic process in which the amino acid reduces the newly formed NiO(OH) species. Furthermore, the attractive response of both the CNT and Ni-CNT layers has allowed these electrodes to be used for constant-potential FIA of various amino acids and indicates great promise for monitoring chromatographic effluents. Once again an improved signal was observed at the Ni-CNT electrode compared to nickel deposited upon a bare glassy carbon electrode (Ni-GC).     

Mechanistic studies on the formation and reactivity of dioxygen adducts of diiron complexes supported by sterically hindered carboxylates

Dioxygen activation by enzymes such as methane monooxygenase, ribonucleotide reductase, and fatty acid desaturases occurs at a nonheme diiron active site supported by two histidines and four carboxylates, typically involving a (peroxo)diiron(III,III) intermediate in an early step of the catalytic cycle. Biomimetic tetracarboxylatodiiron(II,II) complexes with the familiar "paddlewheel" topology comprising sterically bulky o-dixylylbenzoate ligands with pyridine, 1-methylimidazole, or THF at apical sites readily react with O(2) to afford thermally labile peroxo intermediates that can be trapped and characterized spectroscopically at low temperatures (193 K). Cryogenic stopped-flow kinetic analysis of O(2) adduct formation carried out for the three complexes reveals that dioxygen binds to the diiron(II,II) center with concentration dependences and activation parameters indicative of a direct associative pathway. The pyridine and 1-methylimidazole intermediates decay by self-decomposition. However, the THF intermediate decays much faster by oxygen transfer to added PPh(3), the kinetics of which has been studied with double mixing experiments in a cryogenic stopped-flow apparatus. The results show that the decay of the THF intermediate is kinetically controlled by the dissociation of a THF ligand, a conclusion supported by the observation of saturation kinetic behavior with respect to PPh(3), inhibition by added THF, and invariant saturation rate constants for the oxidation of various phosphines. It is proposed that the proximity of the reducing substrate to the peroxide ligand on the diiron coordination sphere facilitates the oxygen-atom transfer. This unique investigation of the reaction of an O(2) adduct of a biomimetic tetracarboxylatodiiron(II,II) complex provides a synthetic precedent for understanding the electrophilic reactivity of like adducts in the active sties of nonheme diiron enzymes.