Increased glycosidic bond stabilities in 4-C-hydroxymethyl linked disaccharides

Three new hydroxymethyl-linked non-natural disaccharide analogues, containing an additional methylene group in between the glycosidic linkage, were synthesized by utilizing 4-C-hydroxymethyl-alpha-D-glucopyranoside as the glycosyl donor. A kinetic study was undertaken to assess the hydrolytic stabilities of these new disaccharide analogues toward acid-catalyzed hydrolysis, at 60 degrees C and 70 degrees C. The studies showed that the disaccharide analogues were stable, by an order of magnitude, than naturally-occurring disaccharides, such as, cellobiose, lactose, and maltose. The first order rate constants were lower than that of methyl glycosides and the trend of hydrolysis rate constants followed that of naturally-occurring disaccharides. alpha-Anomer showed faster hydrolysis than the beta-anomer and the presence of axial hydroxyl group also led to faster hydrolysis among the disaccharide analogues. Energy minimized structures, derived through molecular modeling, showed that dihedral angles around the glycosidic bond in disaccharide analogues were nearly similar to that of naturally-occurring disaccharides. (C) 2011 Elsevier Ltd. All rights reserved.

Structural Annotation of Mycobacterium tuberculosis Proteome

Of the similar to 4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for similar to 2877 ORFs, covering similar to 70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well.

An improved X-ray structural analysis for determining cation distribution in ZnFe2O4 and ZnFe2O4- Fe3O4 solid solutions

The distribution of zinc cation between crystallographically nonequivalent positions in ZnFe204 has been determined by anomalous X-ray scattering near the Zn K absorption edge. Measured intensity ratio with two energies close to the edge can be quantitatively explained only by assigning all zinc cations to the tetrahedral position in the approximately cubic close packed array of oxygen ions. A similar conclusion has also been reached for ZnxFe3-x04 solid solutions with x = 0.73, 0.54 and 0.35 employing the improved X-ray method. This is consistent with the EXAFS results which indicate an almost unchanged environmental structure around zinc cation in these solid solutions.

Structural, optical, and electrical properties of bulk single crystals of InAsxSb(1-x) grown by rotatory Bridgman method

Radially-homogeneous and single-phase InAsxSb(1−x) crystals, up to 5.0 at. % As concentration, have been grown using the rotatory Bridgman method. Single crystallinity has been confirmed by x-ray and electron diffraction studies. Infrared transmission spectra show a continuous decrease in optical energy gap with the increase of arsenic content in InSb. The measured values of mobility and carrier density at room temperature (for x = .05) are 5.6×104 cm2/V s and 2.04×1016 cm−3, respectively.

Usefulness of in Situ Single Crystal to Single Crystal Transformation (SCSC) Studies in Understanding the Temperature-Dependent Dimensionality Cross-over and Structural Reorganization in Copper-Containing Metal-Organic Frameworks (MOFs)

Two copper-containing compounds [Cu(3)(mu(3)-OH)(2)-(H(2)O)(2){(SO(3))-C(6)H(3)-(COO)(2)}(CH(3)COO)] , I, and [Cu(5)(mu(3)-OH)(2)(H(2)O)(6){(NO(2))-C(6)H(3)-(COO)(2)}(4)]center dot 5H(2)O, II, were prepared using sulphoisophthalic and nitroisophthalic acids. The removal of the coordinated water molecules in the compounds was investigated using in situ single crystal to single crystal (SCSC) transformation studies, temperature-dependent powder X-ray diffraction (PXRD), and thermogravimetric analysis (TGA). The efficacy of SCSC transformation studies were established by the observation of dimensionality cross-over from a two-dimensional (I) to a three-dimensional structure, Cu(6)(mu(3)-OH)(4){(SO(3))-C(6)H(3)-(COO)(2)}(2)(CH(3)COO)(2), Ia, during the removal of the coordinated water molecules. Compound H exhibited a structural reorganization forming Cu(5)(mu(2)-OH)(2){(NO(2))C(6)H(3)-(COO)(2))(4)], Ha, possessing trimeric (Cu(3)O(12)) and dimeric (Cu(2)O(8)) copper clusters. The PXRD studies indicate that the three-dimensional structure (Ia) is transient and unstable, reverting back to the more stable two-dimensional structure (I) on cooling to room temperature. Compound Ha appears to be more stable at room temperature. The rehydration/dehydration studies using a modified TGA setup suggest complete rehydration of the water molecules, indicating that the water molecules in both compounds are labile. A possible model for the observed changes in the structures has been proposed. Magnetic studies indicate changes in the exchanges between the copper centers in Ha, whereas no such behavior was observed in Ia.

Structural, thermal, and electrical properties of CrSi2

Stoichiometric CrSi2 was prepared by arc melting and compacted by uniaxial hot pressing for property measurements. The crystal structure of CrSi2 was investigated using the powder x-ray diffraction method. From the Rietveld refinement, the lattice parameters were found to be a = 4.427 57 (7) and c = 6.368 04 (11) Å, respectively. The thermal expansion measurement revealed an anisotropic expansion in the temperature range from room temperature 800 K with αa = 14.58×10−6/K, αc = 7.51×10−6/K, and αV = 12.05×10−6/K. The volumetric thermal expansion coefficient shows an anomalous decrease in the temperature range of 450–600 K. The measured electrical resistivity ρ and thermoelectric power S have similar trends with a maxima around 550 K. Thermal conductivity measurements show a monotonic decrease with increasing temperature from a room temperature value of 10 W m−1 K−1. The ZT values increase with temperature and have a maximum value of 0.18 in the temperature range studied. An analysis of the electronic band structure is provided.

Bi4Ti3O12–5BiFeO3 Aurivillius intergrowth: Structural and ferroelectric properties

Aurivillus intergrowth Bi4Ti3O12–5BiFeO3 was demonstrated to be ferroelectric that evoked the possibility of achieving high temperature magnetoelectric property in this family of compounds. X-ray diffraction studies confirmed its structure to be orthorhombic [Fmm2; a = 5.5061(11) Å, b = 5.4857(7) Å, c = 65.742(12) Å]. However, transmission electron microscopy established the random incidence of intergrowth at nanoscale corresponding to n = 6 and n = 7 members of the Aurivillius family. Diffuse ferroelectric orthorhombic to paraelectric tetragonal phase transition around 857 K was confirmed by dielectric and high temperature x-ray diffraction studies. Polarization versus electric field hysteresis loops associated with 2Pr of 5.2 μC/cm2 and coercive field of 42 kV/cm were obtained at 300 K.

Structural and electrical properties of low pressure metalorganic chemical vapor deposition grown Eu2O3 films on Si(100)

Structural and electrical properties of Eu2O3 films grown on Si(100) in 500–600 °C temperature range by low pressure metalorganic chemical vapor deposition are reported. As-grown films also possess the impurity Eu1−xO phase, which has been removed upon annealing in O2 ambient. Film’s morphology comprises uniform spherical mounds (40–60 nm). Electrical properties of the films, as examined by capacitance-voltage measurements, exhibit fixed oxide charges in the range of −1.5×1011 to −6.0×1010 cm−2 and dielectric constant in the range of 8–23. Annealing has resulted in drastic improvement of their electrical properties. Effect of oxygen nonstoichiometry on the film’s property is briefly discussed.

Structural and dielectric behavior of pulsed laser ablated Sr(0.6)Ca(0.4)TiO(3) thin film and asymmetric multilayer of SrTiO(3) and CaTiO(3)

Homogeneous thin films of Sr(0.6)Ca(0.4)TiO(3) (SCT40) and asymmetric multilayer of SrTiO(3) (STO) and CaTiO(3) (CTO) were fabricated on Pt/Ti/SiO(2)/Si substrates by using pulsed laser deposition technique. The electrical behavior of films was observed within a temperature range of 153 K-373 K. A feeble dielectric peak of SCT40 thin film at 273 K is justified as paraelectric to antiferroelectric phase transition. Moreover, the Curie-Weiss temperature, determined from the epsilon'(T) data above the transition temperature is found to be negative. Using Landau theory, the negative Curie-Weiss temperature is interpreted in terms of an antiferroelectric transition. The asymmetric multilayer exhibits a broad dielectric peak at 273 K. and is attributed to interdiffusion at several interfaces of multilayer. The average dielectric constants for homogeneous Sr(0.6)Ca(0.4)TiO(3) films (similar to 650) and asymmetric multilayered films (similar to 350) at room temperature are recognized as a consequence of grain size effect. Small frequency dispersion in the real part of the dielectric constants and relatively low dielectric losses for both cases ensure high quality of the films applicable for next generation integrated devices. (C) 2011 Elsevier B.V. All rights reserved.

Phenylboronic acids in crystal engineering: Utility of the energetically unfavorable syn,syn-conformation in co-crystal design

Phenylboronic acids can exist, in principle, in three different conformers (syn,syn; syn,anti and anti,anti) with distinct energy profiles. In their native state, these compounds prefer the energetically favored syn, anti-conformation. In molecular complexes, however, the functionality exhibits conformational diversity. In this paper we report a series of co-crystals, with N-donor compounds, prepared by a design strategy involving the synthons based on the syn, syn-conformation of the boronic acid functionality. For this purpose, we employed compounds with the 1,2-diazo fragment (alprazolam, 1H-tetrazole, acetazolamide and benzotriazole), 1,10-phenanthroline and 2,2'-bipyridine for the co-crystallization experiments. However, our study shows that the mere presence of the 1,2-diazo fragment in the coformer does not guarantee the successful formation of co-crystals with a syn, syn-conformation of the boronic acid. [GRAPHICS] The -B(OH)(2) fragment makes unsymmetrical O-H center dot center dot center dot N heterosynthons with alprazolam (ALP) and 1,10-phenanthroline (PHEN). In the co-crystals of phenylboronic acids with 1H-tetrazole (TETR) and 2,2'-bipyridine (BPY), the symmetrical boronic acid dimer is the major synthon. In the BPY complex, boronic acid forms linear chains and the pyridine compound interacts with the lateral OH of boronic acid dimers that acts as a connector, thus forming a ladder structure. In the TETR complex, each heterocycle interacts with three boronic acids. While two boronic acids interact using the phenolic group, the third molecule generates O-H center dot center dot center dot N hydrogen bonds using the extra OH group, of -B(OH)(2) fragment, left after the dimer formation. Thus, although molecules were selected retrosynthetically with the 1,2-diazo fragment or with nearby hetero-atoms to induce co-crystal formation using the syn,syn-orientation of the -B(OH)(2) functionality, co-crystal formation is in fact selective and is probably driven by energy factors. Acetazolamide (ACET) contains self-complementary functional groups and hence creates stable homosynthons. Phenylboronic acids being weak competitors fail to perturb the homosynthons and hence the components crystallize separately. Therefore, besides the availability of possible hydrogen bond acceptors in the required position and orientation, the ability of the phenyl-boronic acid to perturb the existing interactions is also a prerequisite to form co-crystals. This is illustrated in the table below. In the case of ALP, PHEN and BPY, the native structures are stabilized by weak interactions and may be influenced by the boronic acid fragment. Thus phenylboronic acids can attain co-crystals with those compounds, wherein the cyclic O-H center dot center dot center dot N hydrogen bonds are stronger than the individual homo-interactions. This can lower the lattice energy of the molecular complex as compared with the individual crystals. [GRAPHICS] Phenylboronic acids show some selectivity in the formation of co-crystals with N-heterocycles. The differences in solubility of the components fall short to provide a possible reason for the selective formation of co-crystals only with certain compounds. These compounds, being weak acids, do not follow the Delta pK(a) analysis and hence fail to provide any conclusive observation. Theoretical results show that of the three conformers possible, the syn,anti conformer is the most stable. The relative stabilities of the three conformers syn,anti,syn,syn and anti,anti are 0.0, 2.18 and 3.14 kcal/mol, respectively. The theoretical calculations corroborate the fact that only energetically favorable synthons can induce the formation of heterosynthons, as in ALP and PHEN complexes. From a theoretical and structural analysis it is seen that phenylboronic acids will form interactions with those molecules wherein the heterocyclic and acidic fragments can interrupt the homosynthons. However, the energy profile is shallow and can be perturbed easily by the presence of competing functional groups (such as OH and COOH) in the vicinity. [GRAPHICS] .

Structural, electrical, and optical properties of as-grown and heat treated ultra-thin SnS films

The composition, structural, electrical, and optical properties of as-grown and heat treated tin-mono-sulfide (SnS) ultra-thin films have been studied. The ultra-thin SnS films were prepared on glass substrates by thermal resistive evaporation technique. All the SnS films contained nanocrystallites and exhibited p-type conductivity with a low Hall-mobility, <50 cm(2)/Vs. All these films are highly tin rich in nature and exhibited orthorhombic crystal structure. As compared to other films, the SnS films annealed at 300 degrees C showed a low electrical resistivity of similar to 36 Omega cm with an optical band gap of similar to 1.98 eV. The observed electrical and optical properties of all the films are discussed based on their composition and structural parameters. These nanocrystalline ultra-thin SnS films could be expected as a buffer layer for the development of tandem solar cell devices due to their low-resistivity and high absorbability with an optimum band gap. (C) 2011 Elsevier B.V. All rights reserved.