Chemistry

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Macroscopic properties of biomolecular systems are a straightforward consequence of time dependent microscopic interactions. Molecular Dynamics (MD) Simulations provide a time dependent microscopic properties of biomolecules, which could not be explained by experimental methods like X-ray crystallography. These specifications enable MD simulations as most widely used computational techniques for the study of dynamical properties of proteins, DNAs and other bio-macromolecules. In the present chapter, we focus the scopes, applicability and major case studies of MD simulations. The chapter also provides some lucid discussions about the pros and cons of free energy pathways like MM-PB (GB)/SA, LIE and other alchemical methods which are frequently used to study the binding mode of several biomolecular complexes. © 2013 by Apple Academic Press, Inc.

(SoNS) School of Natural Sciences

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Nanoscience and Computational Chemistry: Research Progress

Molecular dynamics simulations: Applicability and scopes in computational biochemistry

The activity of gelatin and collagen proteins towards C-C bond formation via Henry (nitroaldol) reaction between aldehydes and nitroalkanes is demonstrated for the first time. Among other variables, protein source, physical state and chemical modification influence product yield and kinetics, affording the nitroaldol products in both aqueous and organic media under mild conditions. Significantly, the scale-up of the process between 4-nitrobenzaldehyde and nitromethane is successfully achieved at 1 g scale and in good yield. A comparative kinetic study with other biocatalysts shows an increase of the first-order rate constant in the order chitosan < gelatin < bovine serum albumin (BSA) < collagen. The results of this study indicate that simple edible gelatin can promote C-C bond forming reactions under physiological conditions, which may have important implications from a metabolic perspective. © 2013 Kühbeck et al; licensee Beilstein-Institut.

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Beilstein Journal of Organic Chemistry

C-C bond formation catalyzed by natural gelatin and collagen proteins

An enhanced dielectric permittivity of polyethylene and related polymers, while not overly sacrificing their excellent insulating properties, is highly desirable for various electrical energy storage applications. In this computational study, we use density functional theory (DFT) in combination with modified group additivity based high throughput techniques to identify promising chemical motifs that can increase the dielectric permittivity of polyethylene. We consider isolated polyethylene chains and allow the CH2 units in the backbone to be replaced by a number of Group IV halides (viz., SiF 2, SiCl2, GeF2, GeCl2, SnF 2, or SnCl2 units) in a systematic, progressive, and exhaustive manner. The dielectric permittivity of the chemically modified polyethylene chains is determined by employing DFT computations in combination with the effective medium theory for a limited set of compositions and configurations. The underlying chemical trends in the DFT data are first rationalized in terms of various tabulated atomic properties of the constituent atoms. Next, by parametrizing a modified group contribution expansion using the DFT data set, we are able to predict the dielectric permittivity and bandgap of nearly 30 000 systems spanning a much larger part of the configurational and compositional space. Promising motifs which lead to simultaneously large dielectric constant and band gap in the modified polyethylene chains have been identified. Our theoretical work is expected to serve as a possible motivation for future experimental efforts. © 2013 American Chemical Society.

Journal of Chemical Information and Modeling

New group IV chemical motifs for improved dielectric permittivity of polyethylene

The first high-resolution neutron protein structure of perdeuterated rubredoxin from Pyrococcus furiosus (PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory is reported. Neutron diffraction data extending to 1.6514;Å resolution were collected from a relatively small 0.714;mm3 PfRd crystal using 2.514;d (6014;h) of beam time. The refined structure contains 371 out of 391, or 95%, of the D atoms of the protein and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolution (1.514;Å) from crystals with volume &lt;1.014;mm3 and with unit-cell edges &lt;10014;Å. Beamline features include novel elliptical focusing mirrors that deliver neutrons into a 2.0 × 3.214;mm focal spot at the sample position with full-width vertical and horizontal divergences of 0.5 and 0.6°, respectively. Variable short- and long-wavelength cutoff optics provide automated exchange between multiple-wavelength configurations (λmin = 2.0, 2.8, 3.314;Å to λmax = 3.0, 4.0, 4.5, ∼2014;Å). These optics produce a more than 20-fold increase in the flux density at the sample and should help to enable more routine collection of high-resolution data from submillimetre-cubed crystals. Notably, the crystal used to collect these PfRd data was 5-10 times smaller than those previously reported. © 2013 International Union of Crystallography Printed in Singapore - all rights reserved. © 2013.

Acta Crystallographica Section D: Biological Crystallography

The IMAGINE instrument: First neutron protein structure and new capabilities for neutron macromolecular crystallography

An electron rich porous metal–organic framework (MOF) has been synthesized, which acts as an effective heterogeneous catalyst for Diels–Alder reactions through encapsulation of the reactants in confined nano-channels of the framework. {\textcopyright} 2013 The Royal Society of Chemistry.

Chemical Communications

An electron rich porous extended framework as a heterogeneous catalyst for diels–alder reactions

Two new anthracene-functionalized fluorescent tris-imidazolium salts have been synthesized, characterized and proven to be selective sensors for picric acid, which is a common constituent of many powerful explosives. Theoretical studies revealed an unusual ground-state electron transfer from picrate anion to the sensor molecules. {\textcopyright} 2013 American Chemical Society.

Journal of Organic Chemistry

Fluorescent tris-imidazolium sensors for picric acid explosive

Riboflavin tetraacetate-catalyzed aerobic photooxidation of 1-(4-methoxyphenyl)ethanol was investigated as a model reaction under blue visible light in different soft gel materials, aiming to establish their potential as reaction vessels for photochemical transformations. Three strategies involving different degrees of organization of the catalyst within the gel network were explored, and the results compared to those obtained in homogeneous and micellar solutions. In general, physical entrapment of both the catalyst and the substrate under optimized concentrations into several hydrogel matrices (including low-molecular-weight and biopolymer-based gels) allowed the photooxidation with conversions between 55 and 100% within 120 min (TOF ∼ 0.045-0.08 min-1; kobs ∼ 0.011-0.028 min -1), albeit with first-order rates ca. 1-3-fold lower than in solution under comparable non-stirred conditions. Remarkably, the organogel made of a cyclohexane-based bisamide gelator in CH3CN not only prevented the photodegradation of the catalyst but also afforded full conversion in less than 60 min (TOF ∼ 0.167 min-1; kobs ∼ 0.073 min-1) without the need of additional proton transfer mediators (e.g., thiourea) as it occurs in CH3CN solutions. In general, the gelators could be recycled without detriment to their gelation ability and reaction rates. Moreover, kinetics could be fine-tuned according to the characteristics of the gel media. For instance, entangled fibrillar networks with relatively high mechanical strength were usually associated with lower reaction rates, whereas wrinkled laminated morphologies seemed to favor the reaction. In addition, the kinetics results showed in most cases a good correlation with the aeration efficiency of the gel media. © The Royal Society of Chemistry.

Journal of Materials Chemistry A

Organophotocatalysis in nanostructured soft gel materials as tunable reaction vessels: Comparison with homogeneous and micellar solutions

In the present study, we have demonstrated the diversity oriented synthesis of nitrogen heterocycles viz. chiral piperidinones, quinolizidinones and diaryl pyrrolidinones from Michael adducts generated via a TiCl4-catalyzed highly stereoselective Michael reaction with nitrostyrenes and an Evans chiral auxiliary. We also reported a Cu-4,4'-(isopropyl)-substituted isopropylidene-bridged 2,2'-bis-1,3'-oxazoline catalyst mediated catalytic asymmetric version of this reaction. In silico analysis is utilized to evaluate the diversity of the set of compounds against shape space (PMI), polar surface area (PSA) calculations and relevant drug like properties (viz. HBA, HBD, PSA, mol. wt., log P and log D). Finally, the molecules were screened against microorganisms to assess their antimicrobial properties. © 2013 The Royal Society of Chemistry.

RSC Advances

A reagent based DOS strategy via Evans chiral auxiliary: Highly stereoselective Michael reaction towards optically active quinolizidinones, piperidinones and pyrrolidinones

An elegant reagent-controlled strategy has been developed for the generation of a diverse range of biologically active scaffolds from a chiral bicyclic lactam. Reduction of the chiral lactam with LAH or alkylation with LHMDS to trigger different cyclization reactions have been shown to generate privileged scaffolds, such as pyrrolidines, indolines, and cyclotryptamines. Their amenability to substitution allows us to create various compound libraries by using these scaffolds. In silico studies were used to estimate the drug-like properties of these compounds. Selected compounds were subjected to anticancer screening by using three different cell lines. In addition, all these compounds were subjected to antibacterial screening to gauge the spectrum of biological activity that was conferred by our DOS methodology. Gratifyingly, with no additional iterative cycles, our method directly generated anticancer compounds with potency at low nanomolar concentrations, as represented by spiroindoline 14. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemistry - An Asian Journal

Synthesis of privileged scaffolds by using diversity-oriented synthesis

In this paper I discuss some consequences and manifestations of a mereology of structured wholes in chemistry, with particular reference to the concept of atoms in molecules. © 2012 Springer Science+Business Media Dordrecht.