Protein–small molecule docking with receptor flexibility in iMOLSDOCK

We have earlier reported the iMOLSDOCK technique to perform ‘induced-fit’ peptide–protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLSs) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the optimum pose and conformation. In this paper we report the extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset of 34 protein–ligand complexes as well as with Astex Diverse dataset, with nonpeptide small molecules as ligands. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time. The source code and binary of MOLS 2.0 (under a GNU Lesser General Public License) are freely available for download at https://sourceforge.net/projects/mols2-0/files/.     

Structures of anti,Z-4,4-dimethyl-3-thiosemicarbazide, syn,E,Z-2,4-dimethyl-3-thiosemicarbazide and syn,E-1-cyclopentano-3-thiosemicarbazone

The structures of three alkyl derivatives of thiosemicarbazide are described: anti,Z-4,4-dimethyl-3-thiosemicarbazide (1), syn,E,Z-2,4-dimethyl-3-thiosemicarbazide (2), and syn,E-1-cyclopentano-3-thiosemicarbazone (3). Crystal data: for 1: triclinic, P-1 (#2), a = 5.802(1)Å, b = 6.935(1)Å, c = 8.104(2)Å, = 78.35(1)°, = 82.13(1)°, = 70.71(1)°, and Z = 2; for 2: orthorhombic, Pbca (#61), a = 9.417(3)Å, b = 8.624(2)Å, c = 15.169(3)Å, and Z = 8; for 3: triclinic, P-1 (#2), a = 6.068(3)Å, b = 8.145(4)Å, c = 8.666(5)Å, = 83.75(4)°, = 86.16(5)°, = 74.07(4)°, and Z = 2. In general, molecules are linked by N–H···S hydrogen bonds with sulfurs accepting two or three hydrogen bonds. Structures 2 and 3, which adopt the syn conformation, form N–H···N intramolecular hydrogen bonds. The solid-state structures are consistent with their infrared and proton nuclear magnetic resonance spectra.     

Hydrothermal decomposition of esters under high pressure

Abstract

The hydrothermal decomposition of two esters (methyl formate and ethyl formate) was studied in the absence of oxygen over the temperature range of 373 – 673 K at pressures from 15 to 35MPa for residence times between 72 and 600s. At hydrothermal conditions, the esters were hydrolyzed to formic acid and the corresponding alcohols in equilibrium yields of more than 90%, and the disappearance rate of ester was more promoted with increasing temperature than with increasing pressure. In supercritical water, the conversion of the esters reached 100% at short times. From reaction experiments with various catalysts, it was found that the hydrolysis of alkyl formates was accelerated by acid, while retarded by base in a manner different from that in usual water. In addition, a delayed reaction start observed in ester disappearance. profiles suggested strongly a catalytic action of formic acid produced by hydrolysis.     

The SURF model and the curvature effect for PBX 9502

SURF is a high explosive burn model based on the ignition & growth concept of hot-spot reaction. For the TATB based explosive PBX 9502, the model has been calibrated to shock-to-detonation transition experiments. To apply the SURF model for propagating detonation waves, the rate has to be extended to a higher pressure regime than is sampled by shock initiation experiments. The experimentally measured curvature effect – detonation speed as a function of front curvature or D _n(κ) – provides the appropriate data for calibrating the propagation regime. The calibration to the curvature effect is based on the ODEs for the reaction zone profile of a detonation wave in conjunction with a shooting algorithm to determine the rate model parameters, for a given κ, needed to obtain a specified detonation speed. A complication for calibrating PBX 9502 rate models arises from the kink in the experimentally measured D _n(κ) curve. This results from the fast and slow reactions that TATB exhibits. To account for this, we use an extension of the SURF model that utilises a sequence of two reactions. The first, with a fast rate, is due to molecular decomposition and is described by the original SURF formulation. The second, with a slow rate, is due to carbon clustering and is used to contribute additional energy from the formation of carbon bonds. The wave profile equations are generalised to the SURF-plus model. Model parameters are then determined for the propagation regime to fit the curvature effect data. The extended model is applicable to both the shock initiation regime and the propagating detonation wave regime.     

Structural,optical and electrical properties of tin oxide thin films by electrostatic spray deposition

Tin oxide (SnO₂) thin films were deposited by electrostatic spray deposition (ESD). The structural, optical and electrical properties of the films for different solvents were studied. The morphology of the deposited thin films was investigated by scanning electron microscopy. The optical transmission spectra of the films showed 66–75% transmittance in the visible region of spectrum. The electrical resistivity of thin films deposited using the different solvents ranged 1.08 × 10^?3–1.34 × 10^?3 Ω-cm. Overall, EG and PG were good solvents for depositing SnO₂ thin films by the ESD technique with stable cone jet.     

Synthesis and characterization of a new acceptor (n‐type) fluorinated and terminal‐functionalized polythiophene

Donor‐ or acceptor‐substituted polythiophenes have many potential applications in optoelectronics. Fluorinated polythiophenes are particularly attractive because of the presence of fluorine, which can withdraw electrons and also improve polymer chemical stability. Because of the promising future of these polymers, there has been much interest in identifying favorable synthetic routes to new fluorinated monomers and polymers. In this study, the monomer had an electron‐withdrawing fluorinated ester and was derived from 3‐thiophene carboxylic acid and 2,2,3,3,4,4,4‐heptafluoro‐1‐butanol. The synthesis of an n‐type fluorinated and terminal‐functionalized polythiophene was accomplished with the Ullmann coupling reaction. A polymer soluble in tetrahydrofuran was obtained with a molecular weight of approximately 15,000 g/mol. In solution, it exhibited a band gap of 2.4 eV, and the photoluminescent excitation and emission maxima were 370 nm and 555 nm, respectively. All peaks were bathochromically shifted when they were measured in the solid state. The glass‐transition and decomposition (in air) temperatures were 129 and 493 °C, respectively. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4280–4287, 2005     

Regioregularity and solar cell device performance of poly(3‐dodecylthienylenevinylene)

Influence of side chain regioregularity on photovoltaic performance has been investigated in bulk heterojunction solar cells based on a series of poly(3‐dodecylthienylenevinylene)s (C₁₂‐PTV) and 6,6‐phenyl‐C₆₁‐butyric acid methyl ester (PCBM). Performance of each C₁₂‐PTV is optimized for fair comparison. It is found that regiorandomness has no detrimental effect on device performance, in sharp contrast to poly(3‐hexylthiophene) (P3HT). Fully regioregular C₁₂‐PTV performs slightly poorer than less regioregular ones mainly due to its fast crystallization behavior. The results suggest that introduction of side chain regiorandomness is an effective strategy to enhance processability of certain types of polymers without a reduction in photovoltaic performance. The better polymer:PCBM weight ratio, found to be 3:7 for all C₁₂‐PTVs, and improved device performance, as compared with the literature work on the same polymer synthesized by a different method, demonstrate again the importance of the integrity of polymer main chain structure. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

Pep-Calc.com: a set of web utilities for the calculation of peptide and peptoid properties and automatic mass spectral peak assignment

The ability to calculate molecular properties such as molecular weights, isoelectric points, and extinction coefficients is vital for scientists using and/or synthesizing peptides and peptoids for research. A suite of two web utilities: Peptide Calculator and Peptoid Calculator, available free at http://www.pep-calc.com, are presented. Both tools allow the calculation of peptide/peptoid chemical formulae and molecular weight, ChemDraw structure file export and automatic assignment of mass spectral peaks to deletion sequences and metal/protecting group adducts. Peptide Calculator also provides a calculated isoelectric point, molar extinction coefficient, graphical peptide charge summary and β-strand contiguity profile (for aggregation-prone sequences), indicating potential regions of synthesis difficulty. In addition to the unique automatic spectral assignment features offered across both utilities, Peptoid Calculator represents a first-of-a-kind resource for researchers in the field of peptoid science. With a constantly expanding database of over 120 amino acids, non-natural peptide building blocks and peptoid building blocks, it is anticipated that Pep-Calc.com will act as a valuable asset to those working on the synthesis and/or application of peptides and peptoids in the biophysical and life sciences fields.     

Hydrogen‐Bonding Interactions Trigger a Spin‐Flip in Iron(III) Porphyrin Complexes

A key step in cytochrome P450 catalysis includes the spin‐state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin‐state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen‐bonding interactions on the electronic structure of a five‐coordinate iron(III) octaethyltetraarylporphyrin chloride. The spin state of the metal was found to switch reversibly between high (S=⁵/₂) and intermediate spin (S=³/₂) with hydrogen bonding. Our study highlights the possible effects and importance of hydrogen‐bonding interactions in heme proteins. This is the first example of a synthetic iron(III) complex that can reversibly change its spin state between a high and an intermediate state through weak external perturbations.     

Probing Reversible Chemistry in Coenzyme B12‐Dependent Ethanolamine Ammonia Lyase with Kinetic Isotope Effects

Coenzyme B₁₂‐dependent enzymes such as ethanolamine ammonia lyase have remarkable catalytic power and some unique properties that enable detailed analysis of the reaction chemistry and associated dynamics. By selectively deuterating the substrate (ethanolamine) and/or the β‐carbon of the 5′‐deoxyadenosyl moiety of the intrinsic coenzyme B₁₂, it was possible to experimentally probe both the forward and reverse hydrogen atom transfers between the 5′‐deoxyadenosyl radical and substrate during single‐turnover stopped‐flow measurements. These data are interpreted within the context of a kinetic model where the 5′‐deoxyadenosyl radical intermediate may be quasi‐stable and rearrangement of the substrate radical is essentially irreversible. Global fitting of these data allows estimation of the intrinsic rate constants associated with Co?C homolysis and initial H‐abstraction steps. In contrast to previous stopped‐flow studies, the apparent kinetic isotope effects are found to be relatively small.