Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

Mechanistic studies on the effect of ferrocene bonding agents in composite solid propellents

Five compounds, viz. 1,1'-ferrocenediyldiethylidene bis(thiocarbonohydrazide) (DAFT), 1,1-diacetylferrocene disemicarbazone (DAFS), 1,1-diacetylferrocenebenzoyl hydrazone (FDBAH), 1,1-diacetylferrocene-p-nitrobenzoyl hydrazone (FDNBAH), and p-toluenesulfonic acid 1,1'-ferrocenediyldiethylidene dihydrazide (TFDD) were found to be bonding agents as well as burning-rate modifiers for the ammonium perchlorate + hydroxy-terminated polybutadiene system. The tensile strength and percentage elongation significantly increased in the presence of these bonding agents (except FDBAH). The bonding agents generally did not adversely affect the slurry viscosity during processing. The bonding sites were located by infrared spectroscopy, supported by determination of the dissolution kinetics of the bonding agents and scanning electron microscopy. The bonding agents did not undergo any side-reactions with the curing agents.

Multi-Agent Rendezvous Algorithm with Rectilinear Decision Domain

The aim of this paper is to develop a computationally efficient decentralized rendezvous algorithm for a group of autonomous agents. The algorithm generalizes the notion of sensor domain and decision domain of agents to enable implementation of simple computational algorithms. Specifically, the algorithm proposed in this paper uses a rectilinear decision domain (RDD) as against the circular decision domain assumed in earlier work. Because of this, the computational complexity of the algorithm reduces considerably and, when compared to the standard Ando's algorithm available in the literature, the RDD algorithm shows very significant improvement in convergence time performance. Analytical results to prove convergence and supporting simulation results are presented in the paper.

Positional Consensus of Multi-Agent Systems Using Linear Programming Based Decentralized Control with Rectilinear Decision Domain

In this paper we develop a Linear Programming (LP) based decentralized algorithm for a group of multiple autonomous agents to achieve positional consensus. Each agent is capable of exchanging information about its position and orientation with other agents within their sensing region. The method is computationally feasible and easy to implement. Analytical results are presented. The effectiveness of the approach is illustrated with simulation results.

Mechanistic studies on the effect of ferrocene bonding agents in composite solid propellents

Five compounds, viz. 1,1'-ferrocenediyldiethylidene bis(thiocarbonohydrazide) (DAFT), 1,1-diacetylferrocene disemicarbazone (DAFS), 1,1-diacetylferrocenebenzoyl hydrazone (FDBAH), 1,1-diacetylferrocene-p-nitrobenzoyl hydrazone (FDNBAH), and p-tolenesulfonic acid, 1,1'-ferrocenediyldiethylidene dihydrazide (TFDD) were found to be bonding agents as well as burning-rate modifiers for the ammonium perchlorate + hydroxy-terminated polybutadiene system. The tensile strength and percentage elongation significantly increased in the presence of these bonding agents (except FDBAH). The bonding agents generally did not adversely affect the slurry viscosity during processing. The bonding sites were located by infrared spectroscopy, supported by determination of the dissolution kinetics of the bonding agents and scanning electron microscopy. The bonding agents did not undergo any side-reactions with the curing agents.

Microwave assisted synthesis and UV-Vis spectroscopic studies of silver nanoparticles synthesized using vanillin as a reducing agent

The present investigation explores the adaptability of a microwave assisted route to obtain silver nanoparticles by the reduction of AgNO3 with vanillin, an environmentally benign material. Anionic surfactants such as AOT and SDS were used separately for encapsulating AgNPs and their role was compared. The UV-Visible absorption spectra present a broad SPR band consisting of two peaks suggesting the formation of silver nanoparticle with bimodal size distribution. The TEM image shows particles with spherical and hexagonal morphologies which confirms the results of UV-Vis studies. The anisotropy in the particle morphology can be attributed to the surface oxidation which in turn produces Ag@Ag2O core-shell nanostructures. Thus an intriguing feature of this system is that the obtained colloid is a mixture of AgNPs with and without Ag2O layers. Studies on the influence of pH on the stability of the synthesized nanoparticles revealed that the presence of excess Ag2O layers has a profound influence on it. Ag2O layers can be removed from AgNPs' surface by changing the solution pH to the acidic regime. The present study attests the enhanced ability of AOT in stabilizing the AgNPs in aqueous media. (C) 2011 Elsevier B.V. All rights reserved.

Automated Multi-Agent Search Using Centroidal Voronoi Configuration

This paper addresses the problem of automated multiagent search in an unknown environment. Autonomous agents equipped with sensors carry out a search operation in a search space, where the uncertainty, or lack of information about the environment, is known a priori as an uncertainty density distribution function. The agents are deployed in the search space to maximize single step search effectiveness. The centroidal Voronoi configuration, which achieves a locally optimal deployment, forms the basis for the proposed sequential deploy and search strategy. It is shown that with the proposed control law the agent trajectories converge in a globally asymptotic manner to the centroidal Voronoi configuration. Simulation experiments are provided to validate the strategy. Note to Practitioners-In this paper, searching an unknown region to gather information about it is modeled as a problem of using search as a means of reducing information uncertainty about the region. Moreover, multiple automated searchers or agents are used to carry out this operation optimally. This problem has many applications in search and surveillance operations using several autonomous UAVs or mobile robots. The concept of agents converging to the centroid of their Voronoi cells, weighted with the uncertainty density, is used to design a search strategy named as sequential deploy and search. Finally, the performance of the strategy is validated using simulations.

Stabilisation of unusual simultaneous binding of four cytosine nucleobases to copper(II) by a novel network of bifurcated hydrogen bonding

The crystal structure of tetrakis(cytosine)copper(II) perchlorate dihydrate has been determined. All the hydrogen atoms were obtained from Fourier-difference synthesis. The geometry around. copper is a bicapped octahedron (4 + 2 + 2*). The adjacent cytosine rings are oriented head-to-tail with respect to each other and are roughly at right angles to the co-ordination plane. The exocyclic oxo groups form an interligand, intracomplex hydrogen-bonding network above and below the co-ordination plane with the exocyclic amino groups of alternate cytosine bases. The EPR and electronic spectra are consistent with the retention of the solid-state structure in solution. The steric effect of the C(2)=O group of cytosine is offset by the presence of the intracomplex hydrogen-bonding network. The trend in Ei values of Cu-II-Cu-I couples for 1.4 complexes of cytosine, cytodine, pyridine, 2-methylpyridine and N-methylimidazole suggests that both steric effects and pi-delocalization in imidazole and pyridine ligands and the steric effect of C(2)=O in pyrimidine ligands are important in stabilising Cu-I relative to Cu-II.

Simple Structural And Bonding Representations Of Fullerenes

Bonding in buckminsterfullerene, C60, can be described in terms of a unique canonical representation in which all six membered rings have a benzenoid Kekule structure while the pentagons are all made of exclusively single bonds. The corresponding valence bond structure reflects the full symmetry of the molecule and is consistent with the observed bond length variations. Computational support for the bonding description is provided using localized MO's obtained at the MNDO level. The requirement of benzenoid structures for all the hexagons can be used as a criterion of stability of fullerenes which complements the pentagon isolation rule. A convenient two-dimensional representation of the fullerene structures incorporating the above bonding description is suggested, especially for use in mechanistic discussions.

Synthesis of epoxy-terminated polymers by radical polymerization using alpha-(t-butylperoxymethyl)styrene as chain transfer agent

Epoxy-terminated polystyrene has been synthesized by radical polymerization using alpha-(t-butylperoxymethyl) styrene (TPMS) as the chain transfer agent. The chain transfer constants were found to be 0.66 and 0.80 at 60 and 70 degrees C, respectively. The presence of epoxy end groups was confirmed by functional group modification of epoxide to aldehyde by treatment with BF3.Et(2)O. Thermal stability of TPMS was followed by differential scanning calorimetry and iodimetry. Thermal decomposition of TPMS in toluene follows first order kinetics with an activation energy of 23 kcal/mol. (C) 1996 John Wiley & Sons, Inc.

Studies on adsorption of guar gum onto biotite mica

The interaction of guar gum with biotite mica has been investigated through adsorption, flotation and electrokinetic measurements. The adsorption densities of guar gum increase with increase of pH and the isotherms exhibit Langmuirian behaviour. Pretreatment of mica with a complexing agent such as EDTA results in a decrease in the adsorption density, highlighting the contribution of metal ions to the adsorption process. An increase in the surface face-to-edge ratio lends to an increase in the adsorption density. The flotation recoveries decrease as a function of pH, complementing the adsorption results. However, polymer depressant ability is reduced in the case of EDTA treated mica, consequent to reduction of metallic sites. Electrokinetic measurements portray conformational rearrangements of macromolecules with the loading, resulting in the shift of the shear plane, further away from the interface. Dissolution experiments indicate release of metal ions from mica, while co-precipitation tests confirm polymer-metal ion interaction in the bulk solution. The adsorption process is governed by hydrogen bonding as well as chemical interaction between guar gum and the surface metal hydroxide groups of mica. (C) 1997 Published by Elsevier Science Ltd.

Halogen Bonding in 2,5-Dichloro-1,4-benzoquinone: Insights from Experimental and Theoretical Charge Density Analysis

Experimental charge density distribution in 2, 5-dichloro-1, 4-benzoquinone has been carried out using high resolution X-ray diffraction data at 90 K to quantitatively evaluate the nature of C-Cl center dot center dot center dot O=C halogen bond in molecular crystals. Additionally, the halogen bond is studied from geometrical point of view and the same has been visualized using Hirshfeld surface analysis. The obtained results from experimental charge density analysis are compared with periodic quantum calculations using B3LYP 6-31G(d,p) level of theory. The topological values at bond critical point, three-dimensional static deformation density features and electrostatic potential isosurfaces unequivocally establish the attractive nature of C-Cl center dot center dot center dot O=C halogen bond in crystalline lattice.

Molecular self-assembly of cadmium-triazolate complexes via hydrogen bonding: Synthesis, structures and photoluminescent properties

Two new cadmium coordination polymers namely Cd(HAmTrz-COO)(4)(NH4+)(2)] 1; and Cd(HAmTrz)(2)I-2](n) 2; (HAmTrz-COOH = 3-amino-1,2,4-triazole-5-carboxylic acid), have been prepared based on HAmTrz-COOH as ligand. The crystal structures of 1 and 2 have been determined by single-crystal X-ray diffraction technique. In coordination-complex 1 four triazole ligands coordinate via N1 nitrogen leading to a tetrahedral geometry around cadmium ion, while in 2 the ligand prefers to coordinate to the metal in a bidentate bridging mode. The structures of both the coordination polymers can be envisaged as 3D hydrogen bonded networks. Thermogravimetric analysis shows that 2 is more stable than 1 owing to different coordination numbers of cadmium atoms. Photoluminescence properties of both the compounds have been investigated in the solid state. (C) 2011 Elsevier B.V. All rights reserved.

Propargyloxycarbonyl (Poc) amino acid chlorides as efficient coupling reagents for the synthesis of 100% diastereopure peptides and resin bound tetrathiomolybdate as an effective deblocking agent for the Poc group

Synthesis of short peptides using propargyloxycarbonyl amino acid chlorides as effective coupling reagents and polymer supported tetrathiomolybdate as an efficient deblocking agent are reported.

Theoretical Studies on the Structure and Bonding of Metallacyclocumulenes, -cyclopentynes, and -cycloallenes

In this paper, we compare the electronic structure of the hafnacycloallene complex Cp(2)HfC(4)Rr'(2)R `' (5Hf), which was previously described by Erker et al., with those of the titanium, zirconium, and hafnium complexes Cp(2)M(eta(4)-RHC(4)HR) (3M; i.e. metallacyclopent-2,3,4-trienes, metallacyclocumulenes) and Cp(2)M(eta(2)-R(2)C(4)R(2)) (4M; i.e. 1-metallacyclopent-3-ynes) using density functional theory (BP86/LANL2DZ) calculations. Moreover, the eta(3)-phenylallenyl zirconocene complex 7Zr, which was synthesized by Wojcicki et al., is included for the comparison. These calculations and extended Huckel calculations show that the bonding in complex 5Hf is remarkably similar to that of complexes 4M and 7Zr. An analysis of the structural parameters and bonding reveals that the unique interaction of the internal carbon atoms along with the terminal carbon atoms with the bent-metallocene moiety is the reason for the unusual stability of these metallacycles. The molecular orbital analysis further suggests that complex 5Hf can react with another metal fragment to give the bimetallic complexes 9 and 10. The electronic structures of complexes 3M, 4M, 5Hf, and 7Zr have been comparatively studied to get a general understanding of the bonding in these metallacycles.