Fully automated molecular mechanics based induced fit protein-ligand docking method

We describe a method for docking a ligand into a protein receptor while allowing flexibility of the protein binding site. The method employs a multistep procedure that begins with the generation of protein and ligand conformations. An initial placement of the ligand is then performed by computing binding site hotspots. This initial placement is followed by a protein side-chain refinement stage that models protein flexibility. The final step of the process is an energy minimization of the ligand pose in the presence of the rigid receptor. Thus the algorithm models flexibility of the protein at two stages, before and after ligand placement. We validated this method by performing docking and cross docking studies of eight protein systems for which crystal structures were available for at least two bound ligands. The resulting rmsd values of the 21 docked protein-ligand complexes showed values of 2 A or less for all but one of the systems examined. The method has two critical benefits for high throughput virtual screening studies. First, no user intervention is required in the docking once the initial binding site selection has been made in the protein. Second, the initial protein conformation generation needs to be performed only once for a given binding region. Also, the method may be customized in various ways depending on the particular scenario in which dockings are being performed. Each of the individual steps of the method is fully independent making it straightforward to explore different variants of the high level workflow to further improve accuracy and performance.     

Monomeric fullerenes in lipid membranes: effects of molecular shape and polarity

We report a combined theoretical and experimental study on the single-molecule interaction of fullerenes with phospholipid membranes. We studied pristine C(60) (1) and two N-substituted fulleropyrrolidines (2 and 3), one of which (3) bore a paramagnetic nitroxide group. Theoretical predictions of fullerene distribution and permeability across lipid bilayers were combined with electron paramagnetic resonance (EPR) experiments in aligned DMPC/DHPC bicelles containing the paramagnetic fulleropyrrolidine 3 or either one of the diamagnetic fullerenes together with spin-labeled lipids. We found that, at low concentrations, fullerenes are present in the bilayer as single molecules. Their preferred location in the membrane is only slightly influenced by the derivatization: all derivatives were confined just below the hydrophilic/hydrophobic interface, because of the key role played by dispersion interactions between the highly polarizable fullerene cage and the hydrocarbon chains, which are especially tight within this region. However, the deviation from spherical shape is sufficient to induce a preferential orientation of 2 and 3 in the membrane. We predict that monomeric fullerenes spontaneously penetrate the bilayer, in agreement with the results of molecular dynamics simulations, but we point out the limits of the currently used permeability model when applied to hydrophobic solutes.     

Erratum to: Organic–inorganic hybrid melting gels

Melting gels are a class of organically modified silica gels that are rigid at room temperature, flow at temperature T1 and consolidate at temperature T2 (T2 > T1), when crosslinking is complete. The process of (a) softening, (b) becoming rigid and (c) re-softening can be repeated many times. Mixtures of mono-substituted alkoxysilanes and di-substituted alkoxysilanes have been studied in a systematic way to identify suitable melting gel compositions. The mixtures and the resulting melting gels have been characterized for their softening temperatures and consolidation temperatures. With an interest in using these materials for sealing microelectronics, their physical properties have been measured.     

Ring Expansions of Boroles with Diazo Compounds: Steric Control of C or N Insertion and Aromatic/Nonaromatic Products

Access to novel imine‐substituted 1,2‐azaborinines, as well as highly arylated boracyclohexa‐3,5‐dienes has been developed by ring expansion of boroles with diazoalkanes with varying degrees of steric bulk. The formation of a diazoalkane intermediate is also discussed for the reaction of ortho‐brominated p‐tolyl‐azide with 1,2,3,4,5‐pentaphenylborole. Structural details as well as UV/Vis spectroscopic and cyclic voltammetric data are provided. These boron‐containing heterocycles have the potential to serve as building blocks for boron‐containing materials.     

N-Heterocyclic carbene catalysed redox isomerisation of esters to functionalised benzaldehydes

N-Heterocyclic carbene catalysed redox isomerisation with reduction about the carbonyl has been developed in the transformation of trienyl esters to tetrasubstituted benzaldehydes. The reaction proceeds in good to excellent yield, and in cases that provide 2,2′-biaryls, enantioselectivity is observed. Mechanistic studies demonstrate the intermediacy of a cyclohexenyl β-lactone, while implicating formation of the homoenolate as turnover limiting.     

Laser-printed lithium-sulphur micro-electrodes for Li/S batteries

A novel path for the preparation of electrodes for lithium-sulphur cells was developed using a very fast laser-printing setup for the direct and dry i.e., solvent-free transfer of electrode materials onto the current collectors. Model electrodes could be prepared at very small dimensions enabling these batteries to be used even in portable small devices. The initial specific charge was remarkably high at about 1300 A h kg^?1 (relating to the active material content of the electrode) with a loss of specific charge of about 75% after about 400 cycles at 1C. In addition, the dry transfer technique has highly beneficial effects on the environmental sustainability and, therefore, supports the concept of the use of “green” power storage.     

Determination of bis-carboxyethyl germanium sesquioxide by gas chromatography with microwave-induced plasma-atomic emission detection after derivatization with alkyl chloroformates

Organic germanium compounds, especially Ge-132, more corrctly denoted as bis-beta-carboxyethyl germanium sesquioxide ([Ge(=O)CH₂CH₂CO₂H]₂O), are of continued interest as they are said to promote health and display anticancer activity. Although these beneficial effects have never been substantiated by comprehensive clinical studies, this drug can still be obtained through various sources and is usually marketed as a nutritional supplementation rather than an anticancer medication. As the quality standards under which this drug is produced are unknown, the need for an effective quality control of these products arises. To date, Ge-132 is considered generally as a safe compound for application in contrast to inorganic germanium which demonstrates severe renal toxicity. In this paper, a new approach to the determination of Ge-132, based on derivatization by ethyl chloroformate reagent (ECF), in the presence of ethanol and pyridine in the mixture, and subsequent analysis by gas chromatography coupled with microwave-induced plasma-atomic emission detection (GC-MIP-AED), is reported. Reaction conditions of the derivatization procedure were optimized with particular respect to the reagent (ECF) and catalyst (pyridine) concentrations. The proposed method is capable of distinguishing Ge-132 from inorganic germanium. The derivatization procedure was also tested with the use of methyl chloroformate (MCF) as alternative reagent, providing interesting additional information about the nature of the final product and the proposed reaction scheme. Among the two types of chloroformates, i.e., MCF and ECF, the latter proved to be more suitable for the proposed method, providing a calibration curve of superior sensitivity and linearity compared with the one obtained with MCF. The method was applied successfully in three real samples, two food supplements, and one commercially available fertilizer. The analysis of the Ge-132 derivative showed good linearity in the concentration of 1–250 mg L^?1 (r ²?=?0.9986) and a satisfactory precision (RSD?=?6.8 %), which qualifies the proposed method for the speciation analysis of Ge in various matrices.     

Antiaromaticity to Aromaticity: From Boroles to 1,2‐Azaborinines by Ring Expansion with Azides

We have exploited the reactivity of antiaromatic boroles, gaining access to aryl‐substituted monocyclic 1,2‐azaborinines. The observed ring‐expansion reaction of inherently electron‐deficient boroles with organometallic and organic azides is demonstrated for representative examples. This substance class is expected to provide a new avenue into 1,2‐azaborinine chemistry, especially in the area of functional organoboron materials. Our results are based on NMR and UV/Vis spectroscopy as well as single‐crystal X‐ray crystallography and provide a virtually quantitative approach that also offers numerous points of variation.