Visualisation of a 2′-5′ parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2′,5′-adenosine

X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

Synthesis and characterization of flexible epoxy nanocomposites reinforced with amine functionalized alumina nanoparticles: a potential encapsulant for organic devices

Research on conducting polymers, organic light emitting diodes and organic solar cells has been an exciting field for the past decade. The challenge with these organic devices is the long term stability of the active material. Organic materials are susceptible to chemical degradation in the presence of oxygen and moisture. The sensitivity of these materials towards oxygen and moisture makes it imperative to protect them by encapsulation. Polymer nanocomposites can be used as encapsulation materials in order to prevent material degradation. In the present work, amine functionalized alumina was used as a cross-linking and reinforcing material for the polymer matrix in order to fabricate the composites to be used for encapsulation of devices. Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy and Raman spectroscopy were used to elucidate the surface chemistry. Thermogravimetric analysis techniques and CHN analysis were used to quantify grafting density of amine groups over the surface of the nanoparticles. Mechanical characterizations of the composites with various loadings were carried out with dynamic mechanical analyzer. It was observed that the composites have good thermal stability and mechanical flexibility, which are important for an encapsulant. The morphology of the composites was evaluated using scanning electron microscopy and atomic force microscopy.

Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures

Analysis of continuum using boundary compatibility conditions of integrated force method

Static and vibration problems of an indeterminate continuum are traditionally analyzed by the stiffness method. The force method is more or less non-existent for such problems. This situation is primarily due to the incomplete state of development of the compatibility conditions which are essential for the analysis of indeterminate structures by the flexibility method. The understanding of the Compatibility Conditions (CC) has been substantially augmented. Based on the understanding of CC, a novel formulation termed the Integrated Force Method (IFM) has been established. In this paper IFM has been extended for the static and vibration analyses of a continuum. The IFM analysis is illustrated taking three examples: 1. (1) rectangular plate in flexure 2. (2) analysis of a cantilevered dam 3. (3) free vibration analysis of a beam. From the examples solved it is observed that the force response of an indeterminate continuum with mixed boundary conditions can be generated by IFM without any reference to displacements in the field or on the boundary. Displacements if required can be calculated by back substitution.

Structural effects on the vaporization of high molecular weight esters

To understand the effect of molecular weight and branching on the heats of vaporization (AH,) and their flow behavior, AH, and viscosity (7) were measured at different temperatures in the high molecular weight ester series: linear flexible di-n-alkyl sebacates and compact branched triglycerides with molecular weight ranging from 300 to 900. AHv" values (AHv corrected to 298 K) have been obtained with experimental AH, and also computed according to the group additivity method; a smaller-CH,- group value of 3.8 kJ mol-' compared to the normal value of 5.0 kJ mol-' is found to give good agreement with the experimental data (within 2-5% error). Both ester series have the same AH," irrespective of their molecular features, namely,shape, flexibility, and polarity, suggesting the coiling of the molecules during vaporization. The segmental motion of these ester series during their flow and its dependence on their molecular features unlike AH,' are demonstrated by the correlation of the enthalpy of activation for viscous flow (AH*) and the ratio AE,/AH* = n (AE, is the energy of vaporization) with molecular weight.

Evaluation of interfacial frictional resistance

Three distinct mechanisms — sliding, bonding and bearing — for the mobilisation of interfacial friction have been identified. In the light of these mechanisms, the effect of variation in reinforcement parameters, such as extensibility, flexibility and hardness on mobilisation of interfacial friction, and the mechanisms themselves has been examined. The influence of boundary effects of apparatus on the interfacial friction has been discussed and a method of estimating the same in a pull-out box has been proposed.

Dynamics of zeolite cage and its effect on the diffusion properties of sorbate: persistence of diffusion anomaly in NaA zeolite

Recent computer simulations on zeolites Y and A have found that the diffusion coefficient and the rate of intercage diffusion exhibit, apart from a linear dependence on the reciprocal of the square of the sorbate diameter, an anomalous peak as sorbate diameter approaches the window diameter. Here we report molecular dynamics simulations of zeolite NaA incorporating framework flexibility as a function of sorbate diameter in order to verify the existence of anomalous diffusion. Results suggest persistence of anomalous diffusion or ring effect. This suggests that the anomalous behavior is a general effect characteristic of zeolites Y and A. The barrier for diffusion across the eight-ring window is seen to be negative and is found to decrease with sorbate size. The effect of sorbate on the cage motion has also been investigated. Results suggest that the window expands during intercage migration only if the sorbate size is comparable to the window diameter. Flexible cage simulations yield a higher value for the diffusion coefficient and also the rate of intercage diffusion. This increase has been shown to be due to an increase in the intercage diffusions via the centralized diffusion mode rather than the surface-mediated mode. It is shown that this increase arises from an increase in the single particle density distribution in the region near the cage center.

Effect of the valine-threonine constraint on the dynamics of the proline helix — A molecular dynamics study

Proline residues in helices play an important role in the structure of proteins. The proline residue introduces a kink in the helix which varies from about 5-degrees to 50-degrees. The presence of other residues such as threonine or valine near the proline region can influence the flexibility exhibited by the kinked helix, which can have an important biological role. In the present paper, the constraint introduced by threonine and valine on a proline helix is investigated by molecular dynamics studies. The systems considered am (1) a poly-alanine helix with threonine-proline residues (TP) and (2) a poly-alanine helix with valine-threonine-proline residues (VTP), in the middle. Molecular dynamics simulations are carried out on these two systems for 500 ps. The results are analyzed in terms of structural transitions, bend-related parameters and sidechain orientations.

Sputter deposited LiPON thin films from powder target as electrolyte for thin film battery applications

Lithium phosphorus oxynitride (LiPON) thin films as solid electrolytes were prepared by reactive radio frequency (rf) magnetron sputtering from Li3PO4 powder compact target. High deposition rates and ease of manufacturing powder target compared with conventional ceramic Li3PO4 targets offer flexibility in handling and reduce the cost associated. Rf power density varied from 1.7 Wcm(-2) to 3 Wcm(-2) and N-2 flow from 10 to 30 sccm for a fixed substrate to target distance of 4 cm for best ionic conductivity. The surface chemical analysis done by X-ray photoelectron spectroscopy showed incorporation of nitrogen into the film as both triply, NE and doubly. Nd coordinated form. With increased presence of NE, ionic conductivity of LiPON was found to be increasing. The electrochemical impedance spectroscopy of LiPON films confirmed an ionic conductivity of 1.1 x 10(-6) Scm(-1) for optimum rf power and N-2 flow conditions. (C) 2011 Elsevier B.V. All rights reserved.

Molecular dynamics studies on nucleoside 2',3'-cyclic phosphates

2',3'-cyclic nucleotides are intermediates and substrates of Ribonuclease (RNase)-catalysed reactions. The characterization of the equilibrium conformation as well as the flexibility inherent in these molecules helps in understanding the enzymatic action of RNases. The present study explores parameters like phase angle, glycosydic torsion angle and hydrogen bond to find possible interrelationship between them through Molecular Dynamics (MD) simulations on 3'-GMP, 3'-UMP, A>p, G>p, U>p, C>p, GpA>p and UpA>p. Interesting results of the effect of cyclisation and other constraints such as hydrogen bond between certain groups on the equilibrium ribose conformation have emerged from this study.

Plates on Elastic Foundation

Analysis of rectangular plates resting on a Winkler-type, one-parameter foundation is studied. The finite element method is applied and a 12-degree-of-freedom, nonconforming rectangular plate element is adopted. Based on shape functions of the plate element, an energy approach is used to derive a closed-form, 12-by-12, consistent foundation stiffness matrix for a rectangular plate on an elastic subgrade. A commonly used method of modeling structural elements on an elastic foundation is the application of discrete springs at the element nodes. The model developed in this paper is compared with the discrete spring model and the convergence of both models is discussed. The convergence of the models is compared with the well-known classical solution of plates on elastic foundation developed in the 1950s. Both models show good convergence to the classical solution. The continuous subgrade response model converges in a manner more consistent with the flexibility of the plate element.

The effect of traffic shaping in efficiently providing end-to-end performance guarantees

This paper reports new results concerning the capabilities of a family of service disciplines aimed at providing per-connection end-to-end delay (and throughput) guarantees in high-speed networks. This family consists of the class of rate-controlled service disciplines, in which traffic from a connection is reshaped to conform to specific traffic characteristics, at every hop on its path. When used together with a scheduling policy at each node, this reshaping enables the network to provide end-to-end delay guarantees to individual connections. The main advantages of this family of service disciplines are their implementation simplicity and flexibility. On the other hand, because the delay guarantees provided are based on summing worst case delays at each node, it has also been argued that the resulting bounds are very conservative which may more than offset the benefits. In particular, other service disciplines such as those based on Fair Queueing or Generalized Processor Sharing (GPS), have been shown to provide much tighter delay bounds. As a result, these disciplines, although more complex from an implementation point-of-view, have been considered for the purpose of providing end-to-end guarantees in high-speed networks. In this paper, we show that through ''proper'' selection of the reshaping to which we subject the traffic of a connection, the penalty incurred by computing end-to-end delay bounds based on worst cases at each node can be alleviated. Specifically, we show how rate-controlled service disciplines can be designed to outperform the Rate Proportional Processor Sharing (RPPS) service discipline. Based on these findings, we believe that rate-controlled service disciplines provide a very powerful and practical solution to the problem of providing end-to-end guarantees in high-speed networks.

Covalent Grafting of Polydimethylsiloxane over Surface-Modified Alumina Nanoparticles

The synthesis of ``smart structured'' conducting polymers and the fabrication of devices using them are important areas of research. However, conducting polymeric materials that are used in devices are susceptible to degradation due to oxygen and moisture. Thus, protection of such devices to ensure long-term stability is always desirable. Polymer nanocomposites are promising materials for the encapsulation of such devices. Therefore, it is important to develop suitable polymer nanocomposites as encapsulation materials to protect such devices. This work presents a technique based on grafting between surface-decorated gamma-alumina nanoparticles and polymer to make nanocomposites that can be used for the encapsulation of devices. Alumina was functionalized with allyltrimethoxysilane and used to conjugate polymer molecules (hydride-terminated polydimethylsiloxane) through a platinum-catalyzed hydrosilylation reaction. Fourier transform infrared spectroscopy, X-ray-photoelectron spectroscopy, and Raman spectroscopy were used to characterize the surface chemistry of the nanoparticles after surface modification. The grafting density of alkene groups on the surface of the modified nanoparticles was calculated using CHN and thermogravimetric analyses. The thermal stability of the composites was also evaluated using thermogravimetric analysis. The nanoindentation technique was used to analyze the mechanical characteristics of the composites. The densities of the composites were evaluated using a density gradient column, and the morphology of the composites was evaluated by scanning electron microscopy. All of our studies reveal that the composites have good thermal stability and mechanical flexibility and, thus, can potentially be used for the encapsulation of organic photovoltaic devices.

New open-framework phosphate and phosphite compounds of gallium

Five new open-framework compounds of gallium have been synthesized by hydrothermal methods and their structures determined by single crystal X-ray diffraction studies. The compounds, C8N4H26]Ga6F4(PO4)(6)], I, C5N3H11]Ga3F2(PO4)(3)]center dot H2O, II, C6N3H19]Ga-4(C2O4)(PO4)(4)(H2PO4)]center dot 2H(2)O, III, Ga2F3(HPO4)(PO4)]center dot 2H(3)O, IV, and C3N2H5](2)Ga-4(H2O)(3)(HPO3)(7)], V, possess three-dimensional structures. All the compounds are formed by the connectivity between the Ga polyhedra and phosphite/phosphate units. The observation of SBU-6 (I and II) and spiro-5 (IV) secondary building units (SBUs) are noteworthy. The flexibility of the formation of gallium phosphate frameworks has been established by the isolation of two related structures (I and II) from the same SBU units but different organic amines. Some of the present structures have close resemblance to the gallium phosphate phases known earlier. The compounds have been characterized by CHN analysis, powder XRD, IR, and TGA. (C) 2011 Elsevier B. V. All rights reserved.

Water-mediated ionic interactions in protein structures

It is well known that water molecules play an indispensable role in the structure and function of biological macromolecules. The water-mediated ionic interactions between the charged residues provide stability and plasticity and in turn address the function of the protein structures. Thus, this study specifically addresses the number of possible water-mediated ionic interactions, their occurrence, distribution and nature found in 90% non-redundant protein chains. Further, it provides a statistical report of different charged residue pairs that are mediated by surface or buried water molecules to form the interactions. Also, it discusses its contributions in stabilizing various secondary structural elements of the protein. Thus, the present study shows the ubiquitous nature of the interactions that imparts plasticity and flexibility to a protein molecule.