First-Principles Study of the Effect of Organic Ligands on the Crystal Structure of CdS Nanoparticles

We show with the aid of first-principles electronic structure calculations that suitable choice of the capping ligands may be an important control parameter for crystal structure engineering of nanoparticles. Our calculations on CdS nanocrystals reveal that the binding energy of model trioctylphosphine molecules on the (001) facets of zincblende nanocrystals is larger compared to that on wurtzite facets. Similarly, the binding energy of model cis-oleic acid is found to be dominant for the (10 (1) over bar0) facets of wurtzite structure. As a consequence, trioctylphosphine as a capping agent stabilizes the zincblende structure while cis-oleic acid stabilizes the wurtzite phase by influencing the surface energy, which has a sizable contribution to the energetics of a nanocrystal. Our detailed analysis suggests that the binding of molecules on the nanocrystalline facets depends on the surface topology of the facets, the coordination of the surface atoms where the capping molecule is likely to attach, and the conformation of the capping molecule.

Effect of charge asymmetry and charge screening on structure of superlattices formed by oppositely charged colloidal particles

Colloidal suspensions made up of oppositely charged particles have been shown to self-assemble into substitutionally ordered superlattices. For a given colloidal suspension, the structure of the superlattice formed from self-assembly depends on its composition, charges on the particles, and charge screening. In this study we have computed the pressure-composition phase diagrams of colloidal suspensions made up of binary mixtures of equal sized and oppositely charged particles interacting via hard core Yukawa potential for varying values of charge screening and charge asymmetry. The systems are studied under conditions where the thermal energy is equal or greater in magnitude to the contact energy of the particles and the Debye screening length is smaller than the size of the particles. Our studies show that charge asymmetry has a significant effect on the ability of colloidal suspensions to form substitutionally ordered superlattices. Slight deviations of the charges from the stoichiometric ratio are found to drastically reduce the thermodynamic stability of substitutionally ordered superlattices. These studies also show that for equal-sized particles, there is an optimum amount of charge screening that favors the formation of substitutionally ordered superlattices. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.3700226]

Synthesis and characterization of cobalt(II), nickel(II), copper(II) and zinc(II) complexes of 2-nitrobenzoic acid with methyl carbazate as ancillary ligand. Crystal structure of the copper(II) complex

Divalent metal complexes of general formula M(2-nb)(2)(mc)(2)].2(2-nbH), where M = Co(II), Ni(II), Cu(II) or Zn(II), 2-nbH = 2-nitrobenzoic acid and mc = methyl carbazate (NH2NHCOOCH3), have been prepared and characterized by physicochemical and spectroscopic methods. Single-crystal X-ray study of the Cu(II) complex revealed that the molecule is centrosymmetric, with two N,O-chelating mc ligands in equatorial positions and a pair of monodentate 2-nb anions in the axial positions. The lattice 2-nbH molecules help to establish the packing of monomers through hydrogen-bonding interactions. Thermal stability and reactivity of the complexes were studied by TG-DTA. Emission studies show that these complexes are fluorescent.

Hardness and Nitrogen Bonding Structure of A(x)Ti(1-x)N/CrN Multilayer Hard Coating

AlxTi1-xN/CrN multilayer coatings were fabricated by magnetron sputtering and those hardness variations were studied by observing the crack propagation and measuring the chemical bonding state of nitrides by Ti addition. While AlN/CrN multilayer shown stair-like crack propagation, AlxTi1-xN/CrN multilayer illustrated straight crack propagation. Most interestingly, Ti addition induced more broken nitrogen bonds in the nitride multilayers, leading to the reduction of hardness. However, the hardness of Al0.25Ti0.75N/CrN multilayer, having high Ti contents, increased by the formation of many Ti-N bond again instead of Al-N bond. From these results, we found that linear crack propagation behavior was dominated by broken nitrogen bonds in the AlxT1-xN/CrN multilayer coatings.

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.

Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis

Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize the unique chemistry of a pyridine ring to carry out diverse reactions involving amino acids. Diaminopropionate (DAP) ammonia-lyase (DAPAL) is a prokaryotic PLP-dependent enzyme that catalyzes the degradation of D-and L-forms of DAP to pyruvate and ammonia. Here, we report the first crystal structure of DAPAL from Escherichia coli (EcDAPAL) in tetragonal and monoclinic forms at 2.0 and 2.2 angstrom resolutions, respectively. Structures of EcDAPAL soaked with substrates were also determined. EcDAPAL has a typical fold type II PLP-dependent enzyme topology consisting of a large and a small domain with the active site at the interface of the two domains. The enzyme is a homodimer with a unique biological interface not observed earlier. Structure of the enzyme in the tetragonal form had PLP bound at the active site, whereas the monoclinic structure was in the apo-form. Analysis of the apo and holo structures revealed that the region around the active site undergoes transition from a disordered to ordered state and assumes a conformation suitable for catalysis only upon PLP binding. A novel disulfide was found to occur near a channel that is likely to regulate entry of ligands to the active site. EcDAPAL soaked with DL-DAP revealed density at the active site appropriate for the reaction intermediate aminoacrylate, which is consistent with the observation that EcDAPAL has low activity under crystallization conditions. Based on the analysis of the structure and results of site-directed mutagenesis, a two-base mechanism of catalysis involving Asp(120) and Lys(77) is suggested.

Synthesis and structure of Bi2Ce2O7: a new compound exhibiting high solar photocatalytic activity

A facile method of solution combustion was used to synthesize a new solid solution Bi2Ce2O7. The structure was determined from powder X-ray diffraction (PXRD) and found to crystallize in the space group Fm (3) over barm with cell parameter a = 5.46936(9) angstrom. The particle sizes varied from 5 to 6 nm. The degradation of cationic dye malachite green (MG) was investigated under solar radiation as the band gap of the material is 2.34 eV.

Analysis of Strain Rates and Microstructural Evaluation during Metal Forming: Role of Surface Texture and Friction

The surface texture of a die plays an important role in friction during metal forming. In the present study, unidirectional and random surface finishes were produced on hardened steel plate surfaces. To understand the influence of surface texture on friction, experiments were conducted using Al-Mg alloy pins that slid against steel plates of different surface textures. In the sliding experiments, a high coefficient of friction was observed when the pins slid perpendicular to the unidirectional grinding marks and low friction occurred when the pins slid on the random surfaces. Finite element simulations were performed using the measured friction values to understand the stress and strain evolutions in the deforming material using dies with various friction. The numerical results showed that the states of stress and strain rates are strongly influenced by the friction at the interface and hence would influence the final material microstructure. To substantiate the numerical results, laboratory compression tests were conducted. Different surface textures were obtained in order to experience different friction values at different locations. A large variation in the microstructure at these locations was observed during experiments, verifying that surface texture and die friction significantly influence fundamental material formation behavior.

Retrobiosynthetic Approach Delineates the Biosynthetic Pathway and the Structure of the Acyl Chain of Mycobacterial Glycopeptidolipids

Glycopeptidolipids (GPLs) are dominant cell surface molecules present in several non-tuberculous and opportunistic mycobacterial species. GPLs from Mycobacterium smegmatis are composed of a lipopeptide core unit consisting of a modified C-26-C-34 fatty acyl chain that is linked to a tetrapeptide (Phe-Thr-Ala-alaninol). The hydroxyl groups of threonine and terminal alaninol are further modified by glycosylations. Although chemical structures have been reported for 16 GPLs from diverse mycobacteria, there is still ambiguity in identifying the exact position of the hydroxyl group on the fatty acyl chain. Moreover, the enzymes involved in the biosynthesis of the fatty acyl component are unknown. In this study we show that a bimodular polyketide synthase in conjunction with a fatty acyl-AMP ligase dictates the synthesis of fatty acyl chain of GPL. Based on genetic, biochemical, and structural investigations, we determine that the hydroxyl group is present at the C-5 position of the fatty acyl component. Our retrobiosynthetic approach has provided a means to understand the biosynthesis of GPLs and also resolve the long-standing debate on the accurate structure of mycobacterial GPLs.

Crystal Structure of a Monomeric Thiolase-Like Protein Type 1 (TLP1) from Mycobacterium smegmatis

An analysis of the Mycobacterium smegmatis genome suggests that it codes for several thiolases and thiolase-like proteins. Thiolases are an important family of enzymes that are involved in fatty acid metabolism. They occur as either dimers or tetramers. Thiolases catalyze the Claisen condensation of two acetyl-Coenzyme A molecules in the synthetic direction and the thiolytic cleavage of 3-ketoacyl-Coenzyme A molecules in the degradative direction. Some of the M. smegmatis genes have been annotated as thiolases of the poorly characterized SCP2-thiolase subfamily. The mammalian SCP2-thiolase consists of an N-terminal thiolase domain followed by an additional C-terminal domain called sterol carrier protein-2 or SCP2. The M. smegmatis protein selected in the present study, referred to here as the thiolase-like protein type 1 (MsTLP1), has been biochemically and structurally characterized. Unlike classical thiolases, MsTLP1 is a monomer in solution. Its structure has been determined at 2.7 angstrom resolution by the single wavelength anomalous dispersion method. The structure of the protomer confirms that the N-terminal domain has the thiolase fold. An extra C-terminal domain is indeed observed. Interestingly, it consists of six beta-strands forming an anti-parallel beta-barrel which is completely different from the expected SCP2-fold. Detailed sequence and structural comparisons with thiolases show that the residues known to be essential for catalysis are not conserved in MsTLP1. Consistent with this observation, activity measurements show that MsTLP1 does not catalyze the thiolase reaction. This is the first structural report of a monomeric thiolase-like protein from any organism. These studies show that MsTLP1 belongs to a new group of thiolase related proteins of unknown function.

Severe diffraction anisotropy, rotational pseudosymmetry and twinning complicate the refinement of a pentameric coiled-coil structure of NSP4 of rotavirus

The crystal structure of the region spanning residues 95-146 of the rotavirus nonstructural protein NSP4 from the asymptomatic human strain ST3 was determined at a resolution of 2.5 angstrom. Severe diffraction anisotropy, rotational pseudo-symmetry and twinning complicated the refinement of this structure. A systematic explanation confirming the crystal pathologies and describing how the structure was successfully refined is given in this report.

Activation of Lattice Oxygen of TiO2 by Pd2+ Ion: Correlation of Low-Temperature CO and Hydrocarbon Oxidation with Structure of Ti1-xPdxO2-x (x=0.01-0.03)

Lattice oxygen of TiO2 is activated by the substitution of Pd ion in its lattice. Ti1-xPdxO2-x (x = 0.01-0.03) have been synthesized by solution combustion method crystallizing in anatase TiO2 structure. Pd is in +2 oxidation state and Ti is in +4 oxidation state in the catalyst. Pd is more ionic in TiO2 lattice compared to Pd in PdO. Oxygen storage capacity defined by ``amount of oxygen that is used reversibly to oxidize CO'' is as high as 5100 mu mol/g of Ti0.97Pd0.03O1.97. Oxygen is extracted by CO to CO2 in absence of feed oxygen even at room temperature which is more than 20 times compared to pure TiO2. Rate of CO oxidation is 2.75 mu mol g(-1) s(-1) at 60 degrees C over Ti0.97Pd0.03O1.97 and C2H2 gets oxidized to CO2 and H2O at room temperature. Catalyst is not poisoned on long time operation of the reactor. Such high catalytic activity is due to activated lattice oxygen created by the substitution of Pd ion as seen from first-principles density functional theory (DFT) calculations with 96 atom supercells of Ti32O64, Ti31Pd1O63, Ti30Pd2O62, and Ti29Pd3O61. The compounds crystallize in anatase TiO2 structure with Pd2+ ion in nearly square planar geometry and TiO6 octahedra are distorted by the creation of weakly bound oxygens. Structural analysis of Ti31Pd1O63 which is close to 3% Pd ion substituted TiO2 shows that oxygens associated with both Ti and Pd ions in the lattice show bond valence sum of 1.87, a low value characteristic of weak oxygen in the lattice compared to oxygens with valence 2 and above in the same lattice. Exact positions of activated oxygens have been identified in the lattice from DFT calculations.

Precision and long-term stability of clumped-isotope analysis of CO2 using a small-sector isotope ratio mass spectrometer

RATIONALE The ratio of the measured abundance of 13C18O bonding CO2 to its stochastic abundance, prescribed by the delta 13C and delta 18O values from a carbonate mineral, is sensitive to its growth temperature. Recently, clumped-isotope thermometry, which uses this ratio, has been adopted as a new tool to elucidate paleotemperatures quantitatively. METHODS Clumped isotopes in CO2 were measured with a small-sector isotope ratio mass spectrometer. CO2 samples digested from several kinds of calcium carbonates by phosphoric acid at 25 degrees C were purified using both cryogenic and gas-chromatographic separations, and their isotopic composition (delta 13C, delta 18O, Delta 47, Delta 48 and Delta 49 values) were then determined using a dual-inlet Delta XP mass spectrometer. RESULTS The internal precisions of the single gas Delta 47 measurements were 0.005 and 0.02 parts per thousand (1 SE) for the optimum and the routine analytical conditions, respectively, which are comparable with those obtained using a MAT 253 mass spectrometer. The long-term variations in the Delta 47 values for the in-house working standard and the heated CO2 gases since 2007 were close to the routine, single gas uncertainty while showing seasonal-like periodicities with a decreasing trend. Unlike the MAT 253, the Delta XP did not show any significant relationship between the Delta 47 and delta 47 values. CONCLUSIONS The Delta XP gave results that were approximately as precise as those of the MAT 253 for clumped-isotope analysis. The temporal stability of the Delta XP seemed to be lower, although an advantage of the Delta XP was that no dependency of delta 47 on Delta 47 was found. Copyright (c) 2012 John Wiley & Sons, Ltd.

Structure of a carbon nanotube-dendrimer composite

Using all atomistic molecular dynamics (MD) simulations we report a microscopic picture of the carbon nanotube (6,5)-dendrimer complex for PAMAM dendrimers of generations 2 to 4. We study the compact wrapping conformations of the dendrimer onto the nanotube surface for all the three generations of PAMAM dendrimer. A high degree of wrapping for the non-protonated dendrimer is observed as compared to the protonated dendrimer. For comparison, we also study the interaction of another dendrimer, poly(propyl ether imine) (PETIM), with the nanotube. The results of the distance of closest approach as well as the number of close contacts between the nanotube and the dendrimer reveal that the PAMAM dendrimer interacts strongly as compared to the PETIM dendrimer. We also calculate the binding energy between the nanotube and the dendrimer using MM/PBSA methods and attribute the strong binding to the charge transfer between them. Dendrimer wrapping on the CNT will make it soluble and the dendrimer can act as an efficient dispersing agent for the nanotubes.

Exploiting the Structure of the Constraint Graph for Efficient Points-to Analysis

Points-to analysis is a key compiler analysis. Several memory related optimizations use points-to information to improve their effectiveness. Points-to analysis is performed by building a constraint graph of pointer variables and dynamically updating it to propagate more and more points-to information across its subset edges. So far, the structure of the constraint graph has been only trivially exploited for efficient propagation of information, e.g., in identifying cyclic components or to propagate information in topological order. We perform a careful study of its structure and propose a new inclusion-based flow-insensitive context-sensitive points-to analysis algorithm based on the notion of dominant pointers. We also propose a new kind of pointer-equivalence based on dominant pointers which provides significantly more opportunities for reducing the number of pointers tracked during the analysis. Based on this hitherto unexplored form of pointer-equivalence, we develop a new context-sensitive flow-insensitive points-to analysis algorithm which uses incremental dominator update to efficiently compute points-to information. Using a large suite of programs consisting of SPEC 2000 benchmarks and five large open source programs we show that our points-to analysis is 88% faster than BDD-based Lazy Cycle Detection and 2x faster than Deep Propagation. We argue that our approach of detecting dominator-based pointer-equivalence is a key to improve points-to analysis efficiency.