Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Short range side chain-backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution = 1.5 angstrom). Hydrogen bonds involving residues i - 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (Cn, where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C10 (COdi .NHi + 2), C13 (COdi .NHi + 3) and C17 (NdHi .COi - 4) structures. In contrast, Gln predominantly forms C16 (COei .NHi - 3), C12 (NeHi .COi - 2), C15 (NeHi .COi - 3) and C18 (NeHi .COi - 4) motifs, with only the C18motif being analogous to the Asn C17structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone beta-turns and a-turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain-backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.

3-D acoustic analysis of elliptical chamber mufflers having an end-inlet and a side-outlet: An impedance matrix approach

The acoustical behavior of an elliptical chamber muffler having an end-inlet and side-outlet port is analyzed semi-analytically. A uniform piston source is assumed to model the 3-D acoustic field in the elliptical chamber cavity. Towards this end, we consider the modal expansion of acoustic pressure field in the elliptical cavity in terms of angular and radial Mathieu functions, subjected to rigid wall condition, whereupon under the assumption of a point source, Green's function is obtained. On integrating this function over piston area of the side or end port and dividing it by piston area, one obtains the acoustic field, whence one can find the impedance matrix parameters characterizing the 2-port system. The acoustic performance of these configurations is evaluated in terms of transmission loss (TL). The analytical results thus obtained are compared with 3-D HA carried on a commercial software for certain muffler configurations. These show excellent agreement, thereby validating the 3-D semi-analytical piston driven model. The influence of the chamber length as well as the angular and axial location of the end and side ports on TL performance is also discussed, thus providing useful guidelines to the muffler designer. (c) 2011 Elsevier B.V. All rights reserved.

Intra-molecular hydrogen bonding with organic fluorine in the solution state: Deriving evidence by a two dimensional NMR experiment

The direct evidence for the existence of intra-molecular C-F center dot center dot center dot H-N hydrogen bond in organofluorine molecules, in the liquid state, is derived using NMR spectroscopy by the detection of long range interactions among fluorine, nitrogen and hydrogen atoms. The present study reports the determination of the relative signs and magnitudes of through space and through bond couplings to draw unambiguous evidence on the existence of weak molecular interactions involving organic fluorine. It is a simple, easy to implement, N-15 natural abundant two dimensional heteronuclear N-15-H-1 double quantum-single quantum correlation experiment. The existence of intra-molecular hydrogen bond is conclusively established in the investigated molecules. (C) 2011 Elsevier B.V. All rights reserved.

The inhomogeneous extended Bose-Hubbard model: A mean-field theory

We develop an inhomogeneous mean-field theory for the extended Bose-Hubbard model with a quadratic, confining potential. In the absence of this potential, our mean-field theory yields the phase diagram of the homogeneous extended Bose-Hubbard model. This phase diagram shows a superfluid (SF) phase and lobes of Mott-insulator (MI), density-wave (DW), and supersolid (SS) phases in the plane of the chemical potential mu and on-site repulsion U; we present phase diagrams for representative values of V, the repulsive energy for bosons on nearest-neighbor sites. We demonstrate that, when the confining potential is present, superfluid and density-wave order parameters are nonuniform; in particular, we obtain, for a few representative values of parameters, spherical shells of SF, MI, DW, and SS phases. We explore the implications of our study for experiments on cold-atom dipolar condensates in optical lattices in a confining potential.

Monodispersity and stability: case of ultrafine aluminium nanoparticles (< 5 nm) synthesized by the solvated metal atom dispersion approach

The synthesis of THF coordinated aluminium nanoparticles by the solvated metal atom dispersion (SMAD) method is described. These colloids are not stable with respect to precipitation of aluminium nanoparticles. The precipitated aluminium nanopowder is highly pyrophoric. Highly monodisperse colloidal aluminium nanoparticles (3.1 +/- 0.6 nm) stabilized by a capping agent, hexadecyl amine (HDA), have also been prepared by the SMAD method. They are stable towards precipitation of particles for more than a week. The Al-HDA nanoparticles are not as pyrophoric as the Al-THF samples. Particles synthesized in this manner were characterized by high-resolution electron microscopy and powder X-ray diffraction. Annealing of the Al-HDA nanoparticles resulted in carbonization of the capping agent on the surface of the particles which imparts air stability to them. Carbonization of the capping agent was established using Raman spectroscopy and TEM. The annealed aluminium nanoparticles were found to be stable even upon their exposure to air for over a month which was evident from the powder XRD, TGA/DSC, and TEM studies. The successful passivation was further confirmed with the determination of high active aluminium content (95 wt%) upon exposure and storage under air.

Estimation of the shear transformation zone size fin a bulk metallic glass through statistical a analysis of the first pop-in stresses during spherical nanoindentation

The size of the shear transformation zone (STZ) that initiates the elastic to plastic transition in a Zr-based bulk metallic glass was estimated by conducting a statistical analysis of the first pop-in event during spherical nanoindentation. A series of experiments led us to a successful description of the distribution of shear strength for the transition and its dependence on the loading rate. From the activation volume determined by statistical analysis the STZ size was estimated based on a cooperative shearing model. (C) 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Homo- or Heterosynthon? A Crystallographic Study on a Series of New Cocrystals Derived from Pyrazinecarboxamide and Various Carboxylic Acids Equipped with Additional Hydrogen Bonding Sites

Four new cocrystals of a well studied active pharmaceutical ingredient (API), namely, pyrazinecarboxamide (PZA), with various monocarboxylic acids equipped with additional hydrogen bonding sites such as vanillic acid (VA), gallic acid (GA), 1-hydroxy-2-naphthoic acid (1HNA), and indole-2-carboxylic acid (I2CA) have been successfully prepared and characterized by FTIR, H-1 NMR, differential scanning calorimetry (DSC), and single crystal and powder X-ray diffraction (SXRD and PXRD, respectively) techniques. In the majority of the cases, preferential occurrence amide amide and acid acid homosynthons has been observed. Since the heterosynthon is energetically preferred to homosynthon, such unusual occurrence of homosynthon in these cocrystals is intriguing.

Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

Benzene carboxylic acids and Benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by H-1, C-13 and N-15 NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations. (C) 2012 Elsevier B.V. All rights reserved.

On the structure of analytic vectors for the Schrodinger representation

This article deals with the structure of analytic and entire vectors for the Schrodinger representations of the Heisenberg group. Using refined versions of Hardy's theorem and their connection with Hermite expansions we obtain very precise representation theorems for analytic and entire vectors.

Spherical and rod-like Gd2O3:Eu3+ nanophosphors-Structural and luminescent properties

A comparative study of spherical and rod-like nanocrystalline GdO:Eu (GdEuO) red phosphors prepared by solution combustion and hydrothermal methods have been reported. Powder X-ray diffraction (PXRD) results confirm the as-formed product in combustion method showing mixed phase of monoclinic and cubic of GdO:Eu. Upon calcinations at 800C for 3 h, dominant cubic phase was achieved. The as-formed precursor hydrothermal product shows hexagonal Gd(OH):Eu phase and it converts to pure cubic phase of GdO:Eu on calcination at 600C for 3 h. TEM micrographs of hydrothermally prepared cubic GdO:Eu phase shows nanorods with a diameter of 15 nm and length varying from 50 to 150 nm, whereas combustion product shows the particles to be of irregular shape, with different sizes in the range 50-250 nm. Dominant red emission (612 nm) was observed in cubic GdO:Eu which has been assigned to transition. However, in hexagonal Gd(OH):Eu, emission peaks at 614 and 621 nm were observed. The strong red emission of cubic GdO:Eu nanophosphors by hydrothermal method are promising for high performance display materials. The variation in optical energy bandgap () was noticed in as-formed and heat treated systems in both the techniques. This is due to more ordered structure in heat treated samples and reduction in structural defects.

Novel tetranuclear distorted open-cubane copper complex containing oximate bridges: Synthesis, crystal structure, DNA binding and cleavage activity

The synthesis, molecular structure, DNA binding and nuclease activity of Cu4O4 open-cubane tetranuclear copper(II) complex with 3-2-(ethyl amino)ethyl]imino]-2-butanoneoxime (HL) are reported for the first time. The neutral tetranuclear Cu4L4(ClO4)(4)] complex crystallizes in tetragonal space group P (4) over bar2(1)c with the unit cell parameters; a = 13.798(4) angstrom, b = 13.798(4) angstrom, c = 14.119(6) angstrom, V = 2688(16) angstrom(3), Z = 8, R = 0.0636. Symmetrically equivalent copper atoms exhibit a CuN3O3 elongated distorted octahedral coordination environment, with three nitrogen atoms of the L ligand and one oxime-oxygen atom of second L ligand at equatorial positions, one oxime-oxygen atom of the third L ligand and perchlorate oxygen at axial positions. The complex shows quasireversible cyclic voltammetric response at 0.805 V (Delta E-p = 277 mV) at 100 mV s (1) in DMF for the Cu(II)/Cu(I) redox couple. The binding study of the complex with calf-thymus DNA has been investigated using absorption spectrophotometry. The complex shows strong nuclease activity on stranded pBR 322 plasmid DNA in the presence of hydrogen peroxide and marginal nuclease activity in the presence of reducing agent (dithiothreitol). (C) 2012 Elsevier B. V. All rights reserved.

On the Role of Higher-Order Evanescent Modes in End-Offset Inlet and End-Centered Outlet Elliptical Flow-Reversal Chamber Mufflers

This paper deals with the role of the higher-order evanescent modes generated at the area discontinuities in the acoustic attenuation characteristics of an elliptical end-chamber muffler with an end-offset inlet and end-centered outlet. It has been observed that with an increase in length, the muffler undergoes a transition from being acoustically short to acoustically long. Short end chambers and long end chambers are characterized by transverse plane waves and axial plane waves, respectively, in the low-frequency range. The nondimensional frequency limit k(0)(D-1/2) or k(0)R(0) as well as the chamber length to inlet/outlet pipe diameter ratio, i.e., L/d(0), up to which the muffler behaves like a short chamber and the corresponding limit beyond which the muffler is acoustically long are determined. The limits between which neither the transverse plane-wave model nor the conventional axial plane-wave model gives a satisfactory prediction have also been determined, the region being called the intermediate range. The end-correction expression for this muffler configuration in the acoustically long limit has been obtained using 3-D FEA carried on commercial software, covering most of the dimension range used in the design exercise. Development of a method of combining the transverse plane wave model with the axial plane wave model using the impedance Z] matrix is another noteworthy contribution of this work.

MODELING HETEROSTRUCTURES WITH SCHRODINGER-POISSON-NAVIER ITERATIVE SCHEMES, EFFECT OF CARRIER CHARGE, AND INFLUENCE OF ELECTROMECHANICAL COUPLING

This paper presents a detailed investigation of the erects of piezoelectricity, spontaneous polarization and charge density on the electronic states and the quasi-Fermi level energy in wurtzite-type semiconductor heterojunctions. This has required a full solution to the coupled Schrodinger-Poisson-Navier model, as a generalization of earlier work on the Schrodinger-Poisson problem. Finite-element-based simulations have been performed on a A1N/GaN quantum well by using both one-step calculation as well as the self-consistent iterative scheme. Results have been provided for field distributions corresponding to cases with zero-displacement boundary conditions and also stress-free boundary conditions. It has been further demonstrated by using four case study examples that a complete self-consistent coupling of electromechanical fields is essential to accurately capture the electromechanical fields and electronic wavefunctions. We have demonstrated that electronic energies can change up to approximately 0.5 eV when comparing partial and complete coupling of electromechanical fields. Similarly, wavefunctions are significantly altered when following a self-consistent procedure as opposed to the partial-coupling case usually considered in literature. Hence, a complete self-consistent procedure is necessary when addressing problems requiring more accurate results on optoelectronic properties of low-dimensional nanostructures compared to those obtainable with conventional methodologies.

Analyticity of the Schrodinger propagator on the Heisenberg group

We discuss the analytic extension property of the Schrodinger propagator for the Heisenberg sublaplacian and some related operators. The result for the sublaplacian is proved by interpreting the sublaplacian as a direct integral of an one parameter family of dilated special Hermite operators.

1-D Hydrogen bonded water in Cu(II)-picolinate coordination polymer: synthesis, crystal structure, and thermogravimetric analysis

A new Cu(II)-picolinate complex was synthesized and characterized by single crystal X-ray crystallography. The complex crystallizes in the centrosymmetric triclinic space group P (1) over bar (no. 2). Picolinate in the complex extends the neutral unit into a 1-D chain through mu(2)-bridging carboxylate. The complex has a hydrogen bonding acceptor in the second coordination sphere allowing lattice water to assemble neighboring chains. Water self-assembles to form a zig-zag 1-D chain. The adjacent chains are assembled by C-H center dot center dot center dot O interactions result in the formation 2-D hydrogen bonded network. The overall hydrogen bonding between water chain and Cu-picolinate network yields a 3-D hydrogen bonded coordination network. X-ray structural analysis, FTIR and thermal analysis have been used to characterize the reported compound in the solid state.