1H NMR study of internal motions and quantum rotational tunneling in (CH3)4NGeCl3

(CH3)4NGeCl3 is prepared, characterized and studied using 1H NMR spin lattice relaxation time and second moment to understand the internal motions and quantum rotational tunneling. Proton second moment is measured at 7 MHz as function of temperature in the range 300-77 K and spin lattice relaxation time (T1) is measured at two Larmor frequencies, as a function of temperature in the range 270-17 K employing a homemade wide-line/pulsed NMR spectrometers. T1 data are analyzed in two temperature regions using relevant theoretical models. The relaxation in the higher temperatures (270-115 K) is attributed to the hindered reorientations of symmetric groups (CH3 and (CH3)4N). Broad asymmetric T1 minima observed below 115 K down to 17 K are attributed to quantum rotational tunneling of the inequivalent methyl groups.

Modeling of magnetostrictive materials and structures

The constitutive model for a magnetostrictive material and its effect on the structural response is presented in this article. The example of magnetostrictive material considered is the TERFENOL-D. As like the piezoelectric material, this material has two constitutive laws, one of which is the sensing law and the other is the actuation law, both of which are highly coupled and non-linear. For the purpose of analysis, the constitutive laws can be characterized as coupled or uncoupled and linear or non linear. Coupled model is studied without assuming any explicit direct relationship with magnetic field. In the linear coupled model, which is assumed to preserve the magnetic flux line continuity, the elastic modulus, the permeability and magneto-elastic constant are assumed as constant. In the nonlinear-coupled model, the nonlinearity is decoupled and solved separately for the magnetic domain and the mechanical domain using two nonlinear curves, namely the stress vs. strain curve and the magnetic flux density vs. magnetic field curve. This is performed by two different methods. In the first, the magnetic flux density is computed iteratively, while in the second, the artificial neural network is used, where in the trained network will give the necessary strain and magnetic flux density for a given magnetic field and stress level. The effect of nonlinearity is demonstrated on a simple magnetostrictive rod.

Structures and molecular-dynamics studies of three active-site mutants of bovine pancreatic phospholipase A(2)

Phospholipase A(2) hydrolyzes phospholipids at the sn-2 position to cleave the fatty-acid ester bond of L-glycerophospholipids. The catalytic dyad (Asp99 and His48) along with a nucleophilic water molecule is responsible for enzyme hydrolysis. Furthermore, the residue Asp49 in the calcium-binding loop is essential for controlling the binding of the calcium ion and the catalytic action of phospholipase A2. To elucidate the structural role of His48 and Asp49, the crystal structures of three active-site single mutants H48N, D49N and D49K have been determined at 1.9 angstrom resolution. Although the catalytically important calcium ion is present in the H48N mutant, the crystal structure shows that proton transfer is not possible from the catalytic water to the mutated residue. In the case of the Asp49 mutants, no calcium ion was found in the active site. However, the tertiary structures of the three active-site mutants are similar to that of the trigonal recombinant enzyme. Molecular-dynamics simulation studies provide a good explanation for the crystallographic results.

Scanning Tunneling Spectroscopy on Pr0.68Pb0.32MnO3 single crystals

Scanning tunneling microscopy/spectroscopy studies were carried out on single crystals of colossal magnetoresistive manganite Pr0.68Pb0.32MnO3 at different temperatures in order to probe their spatial homogeneity across the metal-insulator transition temperature TM-I(similar to 255 K). A metallic behavior of the local conductance was observed for temperatures T < TM-I. Zero bias conductance (dI/dV)v=(0), which is directly proportional to the local surface density of states at the Fermi level, shows a single distribution at temperatures T < 200 K suggesting a homogeneous electronic phase at low temperatures. In a narrow temperature window of 200 K < T < TM-I, however, an inhomogeneous distribution of (dI/dV)v=(0) has been observed. This result gives evidence for phase separation in the transition region in this compound.

Scanning Tunneling Spectroscopy on Pr0.68Pb0.32MnO3 single crystals

Scanning tunneling microscopy/spectroscopy studies were carried out on single crystals of colossal magnetoresistive manganite Pr0.68Pb0.32MnO3 at different temperatures in order to probe their spatial homogeneity across the metal-insulator transition temperature TM-I(similar to 255 K). A metallic behavior of the local conductance was observed for temperatures T < TM-I. Zero bias conductance (dI/dV)v=(0), which is directly proportional to the local surface density of states at the Fermi level, shows a single distribution at temperatures T < 200 K suggesting a homogeneous electronic phase at low temperatures. In a narrow temperature window of 200 K < T < TM-I, however, an inhomogeneous distribution of (dI/dV)v=(0) has been observed. This result gives evidence for phase separation in the transition region in this compound.

Observation of three-photon absorption and saturation of two-photon absorption in amorphous nanolayered Se/As2S3 thin film structures

We have studied the nonlinear optical properties of nanolayered Se/As2S3 film with a modulation period of 10 nm and a total thickness of 1.15 mu m at two [1064 nm (8 ns) and 800 nm (20 ps)] wavelengths using the standard Z-scan technique. Three-photon absorption was observed at off-resonant excitation and saturation of two-photon absorption at quasiresonant excitation. The observation of the saturation of two-photon absorption is because the pulse duration is shorter than the thermalization time of the photocreated carriers in their bands and three-photon absorption is due to high excitation irradiance. (c) 2007 American Institute of Physics.

Vector evaluated particle swarm optimization (VEPSO) for multi-objective design optimization of composite structures

We present a generic method/model for multi-objective design optimization of laminated composite components, based on vector evaluated particle swarm optimization (VEPSO) algorithm. VEPSO is a novel, co-evolutionary multi-objective variant of the popular particle swarm optimization algorithm (PSO). In the current work a modified version of VEPSO algorithm for discrete variables has been developed and implemented successfully for the, multi-objective design optimization of composites. The problem is formulated with multiple objectives of minimizing weight and the total cost of the composite component to achieve a specified strength. The primary optimization variables are - the number of layers, its stacking sequence (the orientation of the layers) and thickness of each layer. The classical lamination theory is utilized to determine the stresses in the component and the design is evaluated based on three failure criteria; failure mechanism based failure criteria, Maximum stress failure criteria and the Tsai-Wu failure criteria. The optimization method is validated for a number of different loading configurations - uniaxial, biaxial and bending loads. The design optimization has been carried for both variable stacking sequences, as well fixed standard stacking schemes and a comparative study of the different design configurations evolved has been presented. (C) 2007 Elsevier Ltd. All rights reserved.

The generalized anomeric effect in the 1,3-thiazolidines: Evidence forboth sulphur and nitrogen as electron donors. Crystal structures of various N-acylthiazolidines including mercury(II) complexes. Possible relevance to penicillin action

Evidence for the generalized anomeric effect (GAE) in the N-acyl-1,3-thiazolidines, an important structural motif in the penicillins, was sought in the crystal structures of N-(4-nitrobenzoyl)-1,3-thiazolidine and its (2:1) complex with mercuric chloride, N-acetyl-2-phenyl-1,3-thiazolidine, and the (2:1) complex of N-benzoyl-1,3-thiazolidine with mercuric bromide. An inverse relationship was generally observed between the. C-2-N and C-2-S bond lengths of the thiazolidine ring, supporting the existence of the GAE. (Maximal bond length changes were similar to 0.04 angstrom for C-2-N-3, S-1-C-2, and similar to 0.08 angstrom for N-3-C-6.) Comparison with N-acylpyrrolidines and tetrahydrothiophenes indicates that both the nitrogen-to-sulphur and sulphur-to-nitrogen GAE's operate simultaneously in the 1,3-thiazolidines, the former being dominant. (This is analogous to the normal and exo-anomeric effects in pyranoses, and also leads to an interesting application of Baldwin's rules.) The nitrogen-to-sulphur GAE is generally enhanced in the mercury(II) complexes (presumably via coordination at the sulphur); a 'competition' between the GAE and the amide resonance of the N-acyl moiety is apparent. There is evidence for a 'push-pull' charge transfer between the thiazolidine moieties in the mercury(II) complexes, and for a 'back-donation' of charge from the bromine atoms to the thiazolidine moieties in the HgBr2 complex. (The sulphur atom appears to be sp(2) hybridised in the mercury(II) complexes, possibly for stereoelectronic reasons.) These results are apparently relevant to the mode of action of the penicillins. (c) 2006 Elsevier B.V. All rights reserved.

Reliability assessment of internal stability of reinforced soil structures: A pseudo-dynamic approach

A methodology for reliability based optimum design of reinforced soil structures subjected to horizontal and vertical sinusoidal excitation based on pseudo-dynamic approach is presented. The tensile strength of reinforcement required to maintain the stability is computed using logarithmic spiral failure mechanism. The backfill soil properties, geometric and strength properties of reinforcement are treated as random variables. Effects of parameters like soil friction angle, horizontal and vertical seismic accelerations, shear and primary wave velocities, amplification factors for seismic acceleration on the component and system probability of failures in relation to tension and pullout capacities of reinforcement have been discussed. In order to evaluate the validity of the present formulation, static and seismic reinforcement force coefficients computed by the present method are compared with those given by other authors. The importance of the shear wave velocity in the estimation of the reliability of the structure is highlighted. The Ditlevsen's bounds of system probability of failure are also computed by taking into account the correlations between three failure modes, which is evaluated using the direction cosines of the tangent planes at the most probable points of failure. (c) 2009 Elsevier Ltd. All rights reserved.

Study of (Ba3MMWO9)-M-II-W-IV (M-II = Ca, Zn; M-IV = Ti, Zr) perovskite oxides: Competition between 3C and 6H perovskite structures

We describe an investigation of (Ba3MMWO9)-M-II-W-IV oxides for M-II = Ca, Zn, and other divalent metals and M-IV = Ti, Zr. In general, a 1:2-ordered 6H (hexagonal, P6(3)/mmc) perovskite structure is stabilized at high temperatures (1300 degrees C) for all of the (Ba3MTiWO9)-Ti-II oxides investigated. An intermediate phase possessing a partially ordered 1:1 double perovskite (3C) structure with the cation distribution, Ba-2(Zn2/3Ti1/3)(W2/3Ti1/3)O-6, is obtained at 1200 degrees C for Ba3ZnTiWO9. Sr substitution for Ba in the latter stabilizes the cubic 3C structure instead of the 6H structure. A metastable Ba3CaZrWO9 that adopts the 3C (cubic, Fm (3) over barm) structure has also been synthesized by a low-temperature metathesis route. Besides yielding several new perovskite oxides that may be useful as dielectric ceramics, the present investigation provides new insights into the complex interplay of crystal chemistry (tolerance factor) and chemical bonding (anion polarization and d(0)-induced distortion of metal-oxygen octahedra) in the stabilization of 6H versus 3C perovskite structures for the (Ba3MMWO9)-M-II-W-IV series.

Structural plasticity and enzyme action: Crystal structures of Mycobacterium tuberculosis peptidyl-tRNA hydrolase

Peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis. The structure of the enzyme from Mycobacteritan tuberculosis has been determined in three crystal forms. This structure and the structure of the enzyme frorn Escherichia coli in its crystal differ substantially on account of the binding of the C terminus of the E. coli enzyme to the peptide-binding site of a neighboring molecule in the crystal. A detailed examination of this difference led to an elucidation of the plasticity of the binding site of the enzyme. The peptide-binding site of the enzyme is a cleft between the body, of the molecule and a polypepticle Y stretch involving a loop and a helix. This stretch is in the open conformation when the enzyme is in the free state as in the crystals of M. tuberculosis peptidyl-tRNA hydrolase. Furthermore, there is no physical continuity between the tRNA and the peptide-binding sites. The molecule in the E. coli crystal mimics the peptide-bound enzyme molecule. The peptide stretch referred to earlier now closes on the bound peptide. Concurrently, a channel connecting the tRNA and the peptide-binding site opens primarily through the concerted movement of two residues. Thus, the crystal structure of M. tuberculosis peptidyl-tRNA hydrolase when compared with the crystal structure of the E. coli enzyme, leads to a model of structural changes associated with enzyme action on the basis of the plasticity of the molecule. (c) 2007 Elsevier Ltd. All rights reserved.

Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 Dye

Experimental charge density distributions in two known conformational polymorphs (orange and yellow) of coumarin 314 dye are analyzed based on multipole modeling of X-ray diffraction data collected at 100 K. The experimental results are compared with the charge densities derived from multipole modeling of theoretical structure factors obtained from periodic quantum calculation with density functional theory (DFT) method and B3LYP/6-31G(d,p) level of theory. The presence of disorder at the carbonyl oxygen atom of ethoxycarbonyl group in the yellow form, which was not identified earlier, is addressed here. The investigationof intermolecular interactions, based on Hirshfeld surface analysis and topological properties via quantum theory of atoms in molecule and total electrostatic interaction energies, revealed significant differences between the polymorphs. The differences of electrostatic nature in these two polymorphic forms were unveiled via construction of three-dimensional deformation electrostatic potential maps plotted over the molecular surfaces. The lattice energies evaluated from ab initio calculations on the two polymorphic forms indicate that the yellow form is likely to be the most favorable thermodynamically. The dipole moments derived from experimental and theoretical charge densities and also from Lorentz tensor approach are compared with the single-molecule dipole moments. In each case, the differences of dipole moments between the polymorphs are identified.

A network representation of protein structures: Implications for protein stability

This study views each protein structure as a network of noncovalent connections between amino acid side chains. Each amino acid in a protein structure is a node, and the strength of the noncovalent interactions between two amino acids is evaluated for edge determination. The protein structure graphs (PSGs) for 232 proteins have been constructed as a function of the cutoff of the amino acid interaction strength at a few carefully chosen values. Analysis of such PSGs constructed on the basis of edge weights has shown the following: 1), The PSGs exhibit a complex topological network behavior, which is dependent on the interaction cutoff chosen for PSG construction. 2), A transition is observed at a critical interaction cutoff, in all the proteins, as monitored by the size of the largest cluster (giant component) in the graph. Amazingly, this transition occurs within a narrow range of interaction cutoff for all the proteins, irrespective of the size or the fold topology. And 3), the amino acid preferences to be highly connected (hub frequency) have been evaluated as a function of the interaction cutoff. We observe that the aromatic residues along with arginine, histidine, and methionine act as strong hubs at high interaction cutoffs, whereas the hydrophobic leucine and isoleucine residues get added to these hubs at low interaction cutoffs, forming weak hubs. The hubs identified are found to play a role in bringing together different secondary structural elements in the tertiary structure of the proteins. They are also found to contribute to the additional stability of the thermophilic proteins when compared to their mesophilic counterparts and hence could be crucial for the folding and stability of the unique three-dimensional structure of proteins. Based on these results, we also predict a few residues in the thermophilic and mesophilic proteins that can be mutated to alter their thermal stability.

Scanning Tunneling Spectroscopy on Pr0.68Pb0.32MnO3 single crystals

Scanning tunneling microscopy/spectroscopy studies were carried out on single crystals of colossal magnetoresistive manganite Pr0. 68Pb0.32MnO3 at different temperatures in order to probe their spatial homogeneity across the metal-insulator transition temperature TM-I(similar to 255 K). A metallic behavior of the local conductance was observed for temperatures T < TM-I. Zero bias conductance (dI/dV)v=(0), which is directly proportional to the local surface density of states at the Fermi level, shows a single distribution at temperatures T < 200 K suggesting a homogeneous electronic phase at low temperatures. In a narrow temperature window of 200 K < T < TM-I, however, an inhomogeneous distribution of (dI/dV)v=(0) has been observed. This result gives evidence for phase separation in the transition region in this compound.

Parallel and antiparallel aggregation of alpha-helices. Crystal structures of two apolar decapeptides X-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe (X = Boc, Ac)

An apolar helical decapeptide with different end groups, Boc- or Ac-, crystallizes in a completely parallel fashion for the Boc-analog and in an antiparallel fashion for the Ac-analog. In both crystals, the packing motif consists of rows of parallel molecules. In the Boc-crystals, adjacent rows assemble with the helix axes pointed in the same direction. In the Ac-crystals, adjacent rows assemble with the helix axes pointed in opposite directions. The conformations of the molecules in both crystals are quite similar, predominantly alpha-helical, except for the tryptophanyl side chain where chi 1 congruent to 60 degrees in the Boc- analog and congruent to 180 degrees in the Ac-analog. As a result, there is one lateral hydrogen bond between helices, N(1 epsilon)...O(7), in the Ac-analog. The structures do not provide a ready rationalization of packing preference in terms of side-chain interactions and do not support a major role for helix dipole interactions in determining helix orientation in crystals. The crystal parameters are as follow. Boc-analog: C60H97N11O13.C3H7OH, space group Pl with a = 10.250(3) A, b = 12.451(4) A, c = 15.077(6) A, alpha = 96.55(3) degrees, beta = 92.31(3) degrees, gamma = 106.37(3) degrees, Z = 1, R = 5.5% for 5581 data ([F] greater than 3.0 sigma(F)), resolution 0.89 A. Ac-analog: C57H91N11O12, space group P2(1) with a = 9.965(1) A, b = 19.707(3) A, c = 16.648(3) A, beta = 94.08(1), Z = 2, R = 7.2% for 2530 data ([F] greater than 3.0 sigma(F)), resolution 1.00 A.