Solution nuclear magnetic resonance structure of the GATase subunit and structural Basis of the interaction between GATase and ATPPase subunits in a two-subunit-type GMPS from methanocaldococcus jannaschii

The solution structure of the monomeric glutamine amidotransferase (GATase) subunit of the Methanocaldococcus janaschii (Mj) guanosine monophosphate synthetase (GMPS) has been determined using high-resolution nuclear magnetic resonance methods. Gel filtration chromatography and N-15 backbone relaxation studies have shown that the Mj GATase subunit is present in solution as a 21 kDa (188-residue) monomer. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35 +/- 0.06 angstrom for backbone atoms and 0.8 +/- 0.06 angstrom for all heavy atoms. Furthermore, 99.4% of the backbone dihedral angles are present in the allowed region of the Ramachandran map, indicating the stereochemical quality of the structure. The core of the tertiary structure of the GATase is composed of a seven-stranded mixed beta-sheet that is fenced by five alpha-helices. The Mj GATase is similar in structure to the Pyrococcus horikoshi (Ph) GATase subunit. Nuclear magnetic resonance (NMR) chemical shift perturbations and changes in line width were monitored to identify residues on GATase that were responsible for interaction with magnesium and the ATPPase subunit, respectively. These interaction studies showed that a common surface exists for the metal ion binding as well as for the protein-protein interaction. The dissociation constant for the GATase-Mg2+ interaction has been found to be similar to 1 mM, which implies that interaction is very weak and falls in the fast chemical exchange regime. The GATase-ATPPase interaction, on the other hand, falls in the intermediate chemical exchange regime on the NMR time scale. The implication of this interaction in terms of the regulation of the GATase activity of holo GMPS is discussed.

The X-C center dot center dot center dot Y (X = O/F, Y = O/S/F/Cl/Br/N/P) `carbon bond' and hydrophobic interactions

While the tetrahedral face of methane has an electron rich centre and can act as a hydrogen bond acceptor, substitution of one of its hydrogens with some electron withdrawing group (such as -F/OH) can make the opposite face electron deficient. Electrostatic potential calculations confirm this and high level quantum calculations show interactions between the positive face of methanol/methyl fluoride and electron rich centers of other molecules such as H2O. Analysis of the wave functions of atoms in molecules shows the presence of an unusual C center dot center dot center dot Y interaction, which could be called `carbon bonding'. NBO analysis and vibrational frequency shifts confirm the presence of this interaction. Given the properties of alkyl groups bonded to electronegative elements in biological molecules, such interactions could play a significant role, which is yet to be recognized. This and similar interactions could give an enthalpic contribution to what is called the `hydrophobic interactions'.

Li diffusion through doped and defected graphene

We investigate the effect of nitrogen and boron doping on Li diffusion through defected graphene using first principles based density functional theory. While a high energy barrier rules out the possibility of Li-diffusion through the pristine graphene, the barrier reduces with the incorporation of defects. Among the most common defects in pristine graphene, Li diffusion through the divacancy encounters the lowest energy barrier of 1.34 eV. The effect of nitrogen and boron doping on the Li diffusion through doped defected-graphene sheets has been studied. N-doping in graphene with a monovacancy reduces the energy barrier significantly. The barrier reduces with the increasing number of N atoms. On the other hand, for N doped graphene with a divacancy, Li binds in the plane of the sheet, with an enhanced binding energy. The B doping in graphene with a monovacancy leads to the enhancement of the barrier. However, in the case of B-doped graphene with a divacancy, the barrier reduces to 1.54 eV, which could lead to good kinetics. The barriers do not change significantly with B concentration. Therefore, divacancy, B and N doped defected graphene has emerged as a better alternative to pristine graphene as an anode material for Li ion battery.

Microwave, infrared-microwave double resonance, and theoretical studies of C2H4 center dot center dot center dot H2S complex

In this manuscript, rotational spectra of four new isotopologues of the S-H center dot center dot center dot pi bonded C2H4 center dot center dot center dot H2S complex, i.e., C2D4 center dot center dot center dot H2S, C2D4 center dot center dot center dot D2S, C2D4 center dot center dot center dot HDS, and (CCH4)-C-13 center dot center dot center dot H2S have been reported and analyzed. All isotopologues except C2D4 center dot center dot center dot HDS show a four line pattern whereas a doubling of the transition frequencies was observed for C2D4 center dot center dot center dot HDS. These results together with our previous report on the title complex M. Goswami, P. K. Mandal, D. J. Ramdass, and E. Arunan, Chem. Phys. Lett. 393(1-3), 22-27 (2004)] confirm that both subunits (C2H4 and H2S) are involved in large amplitude motions leading to a splitting of each rotational transition to a quartet. Further, the results also confirm that the motions which are responsible for the observed splittings involve both monomers. Molecular symmetry group analysis, considering the interchange of equivalent H atoms in H2S and C2H4 could explain the observed four line pattern and their intensities in the microwave spectrum. In addition, hydride stretching fundamentals of the complex were measured using coherence-converted population transfer Fourier Transform Microwave-infrared (IR-MW double resonance) experiments in the S-H and C-H stretch regions. Changes in the tunneling splittings upon vibrational excitation are consistent with the isotopic dependence of pure rotational transitions. A complexation shift of 2.7-6.5 cm(-1) has been observed in the two fundamental S-H stretching modes of the H2S monomer in the complex. Vibrational pre-dissociation in the bound S-H stretch has been detected whereas the instrument-limited line-shapes in other S-H and C-H stretches indicate slower pre-dissociation rate. Some local perturbations in the vibrational spectra have been observed. Two combination bands have been observed corresponding to both the S-H stretching fundamentals and what appears to be the intermolecular stretching mode at 55 cm(-1). The tunneling splitting involved in the rotation of C2H4 unit has been deduced to be 1.5 GHz from the IR-MW results. In addition, ab initio barrier heights derived for different motions of the monomers support the experimental results and provide further insight into the motions causing the splitting. (C) 2013 AIP Publishing LLC.

Fe as Hydrogen/Halogen Bond Acceptor in Square Pyramidal Fe(CO)(5)

Hydrogen bonded complexes formed between the square pyramidal Fe(CO)(5) with HX (X = F, Cl, Br), showing X-H center dot center dot center dot Fe interactions, have been investigated theoretically using density functional theory (DFT) including dispersion correction. Geometry, interaction energy, and large red shift of about 400 cm(-1) in the FIX stretching frequency confirm X-H center dot center dot center dot Fe hydrogen bond formation. In the (CO)(5)Fe center dot center dot center dot HBr complex, following the significant red shift, the HBr stretching mode is coupled with the carbonyl stretching modes. This clearly affects the correlation between frequency shift and binding energy, which is a hallmark of hydrogen bonds. Atoms in Molecule (AIM) theoretical analyses show the presence of a bond critical point between the iron and the hydrogen of FIX and significant mutual penetration. These X-H center dot center dot center dot Fe hydrogen bonds follow most but not all of the eight criteria proposed by Koch and Popelier (J. Phys. Chem. 1995, 99, 9747) based on their investigations on C-H center dot center dot center dot O hydrogen bonds. Natural bond orbital (NBO) analysis indicates charge transfer from the organometallic system to the hydrogen bond donor. However, there is no correlation between the extent of charge transfer and interaction,energy, contrary to what is proposed in the recent IUPAC recommendation (Pure Appl.. Chem. 2011, 83, 1637). The ``hydrogen bond radius'' for iron has been determined to be 1.60 +/- 0.02 angstrom, and not surprisingly it is between the covalent (127 angstrom) and van der Waals (2.0) radii of Fe. DFT and AIM theoretical studies reveal that Fe in square pyramidal Fe(CO)(5) can also form halogen bond with CIF and ClH as ``halogen bond donor''. Both these complexes show mutual penetration as well, though the Fe center dot center dot center dot Cl distance is closer to the sum of van der Waals radii of Fe and Cl in (CO)5Fe center dot center dot center dot ClH, and it is about 1 angstrom less in (CO)(5)Fe center dot center dot center dot ClF.

New rock salt-related oxides Li3M2RuO6 (M=Co, Ni): Synthesis, structure, magnetism and electrochemistry

We describe the synthesis, crystal structure, magnetic and electrochemical characterization of new rock salt-related oxides of formula, Li3M2RuO6 (M=Co, Ni). The M=Co oxide adopts the LiCoO2 (R-3m) structure, where sheets of LiO6 and (Co-2/Ru)O-6 octahedra are alternately stacked along the c-direction. The M=Ni oxide also adopts a similar layered structure related to Li2TiO3, where partial mixing of Li and Ni/Ru atoms lowers the symmetry to monoclinic (C2/c). Magnetic susceptibility measurements reveal that in Li3Co2RuO6, the oxidation states of transition metal ions are Co3+ (S=0), Co2+ (S=1/2) and Ru4+ (S=1), all of them in low-spin configuration and at 10 K, the material orders antiferromagnetically. Analogous Li3Ni2RuO6 presents a ferrimagnetic behavior with a Curie temperature of 100 K. The differences in the magnetic behavior have been explained in terms of differences in the crystal structure. Electrochemical studies correlate well with both magnetic properties and crystal structure. Li-transition metal intermixing may be at the origin of the more impeded oxidation of Li3Ni2RuO6 when compared to Li3CO2RuO6. Interestingly high first charge capacities (between ca. 160 and 180 mAh g(-1)) corresponding to ca. 2/3 of theoretical capacity are reached albeit, in both cases, capacity retention and cyclability are not satisfactory enough to consider these materials as alternatives to LiCoO2. (C) 2013 Elsevier Inc. All rights reserved.

Formation energies and the stability of the oxides of K

The most common valencies associated with K and O atoms are 1+ and 2-. As a result, one expects K2O to be the oxide of potassium which is the most stable with respect to its constituents. Calculating the formation energy within electronic structure calculations using hybrid functionals, one finds that K2O2 has the largest formation energy, implying the largest stability of this oxide of potassium with respect to its constituents. This is traced to the presence of oxygen dimers in the K2O2 structure which interact strongly resulting in a larger formation energy compared to the more ionic K2O.

New insights into designing metallacarborane based room temperature hydrogen storage media

Metallacarboranes are promising towards realizing room temperature hydrogen storage media because of the presence of both transition metal and carbon atoms. In metallacarborane clusters, the transition metal adsorbs hydrogen molecules and carbon can link these clusters to form metal organic framework, which can serve as a complete storage medium. Using first principles density functional calculations, we chalk out the underlying principles of designing an efficient metallacarborane based hydrogen storage media. The storage capacity of hydrogen depends upon the number of available transition metal d-orbitals, number of carbons, and dopant atoms in the cluster. These factors control the amount of charge transfer from metal to the cluster, thereby affecting the number of adsorbed hydrogen molecules. This correlation between the charge transfer and storage capacity is general in nature, and can be applied to designing efficient hydrogen storage systems. Following this strategy, a search for the best metallacarborane was carried out in which Sc based monocarborane was found to be the most promising H-2 sorbent material with a 9 wt.% of reversible storage at ambient pressure and temperature. (C) 2013 AIP Publishing LLC.

Projection-based atom selection in orthogonal matching pursuit for compressive sensing

For compressive sensing, we endeavor to improve the atom selection strategy of the existing orthogonal matching pursuit (OMP) algorithm. To achieve a better estimate of the underlying support set progressively through iterations, we use a least squares solution based atom selection method. From a set of promising atoms, the choice of an atom is performed through a new method that uses orthogonal projection along-with a standard matched filter. Through experimental evaluations, the effect of projection based atom selection strategy is shown to provide a significant improvement for the support set recovery performance, in turn, the compressive sensing recovery.

Strong-coupling expansion for ultracold bosons in an optical lattice at finite temperatures in the presence of superfluidity

We develop a strong-coupling (t << U) expansion technique for calculating the density profile for bosonic atoms trapped in an optical lattice with an overall harmonic trap at finite temperature and finite on-site interaction in the presence of superfluid regions. Our results match well with quantum Monte Carlo simulations at finite temperature. We also show that the superfluid order parameter never vanishes in the trap due to the proximity effect. Our calculations for the scaled density in the vacuum-to-superfluid transition agree well with the experimental data for appropriate temperatures. We present calculations for the entropy per particle as a function of temperature which can be used to calibrate the temperature in experiments. We also discuss issues connected with the demonstration of universal quantum critical scaling in the experiments.

Electronic transport in patterned graphene nanoroads

Graphane, hydrogenated graphene, can be patterned into electronic devices by selectively removing hydrogen atoms. The most simple of such devices is the so-called nanoroad, analogous to the graphene nanoribbon, where confinement-and the opening of a gap-is obtained without the need for breaking the carbon bonds. In this work we address the electronic transport properties of such systems considering different hydrogen impurities within the conduction channel. We show, using a combination of density functional theory and non-equilibrium Green's functions, that hydrogen leads to significant changes in the transport properties and in some cases to current polarization.

X-ray diffraction and Mossbauer spectroscopy studies of cementite dissolution in cold-drawn pearlitic steel

Cementite dissolution in cold-drawn pearlitic steel (0.8 wt.% carbon) wires has been studied by quantitative X-ray diffraction (XRD) and Mossbauer spectroscopy up to drawing strain 1.4. Quantification of cementite-phase fraction by Rietveld analysis has confirmed more than 50% dissolution of cementite phase at drawing strain 1.4. It is found that the lattice parameter of the ferrite phase determined by Rietveld refinement procedure remains nearly unchanged even after cementite dissolution. This confirms that the carbon atoms released after cementite dissolution do not dissolve in the ferrite lattice as Fe-C interstitial solid solution. Detailed analysis of broadening of XRD line profiles for the ferrite phase shows high density of dislocations (approximate to 10(15)/m(2)) in the ferrite matrix at drawing strain 1.4. The results suggest a dominant role of 111 screw dislocations in the cementite dissolution process. Post-deformation heat treatment leads to partial annihilation of dislocations and restoration of cementite phase. Based on these experimental observations, further supplemented by TEM studies, we have suggested an alternative thermodynamic mechanism of the dissolution process.

Highly Stable Hexacoordinated Nonoxidovanadium(IV) Complexes of Sterically Constrained Ligands: Syntheses, Structure, and Study of Antiproliferative and Insulin Mimetic Activity

Three highly stable, hexacoordinated nonoxidovanadium(IV), V-IV(L)(2), complexes (1-3) have been isolated and structurally characterized with tridentate aroylhydrazonates containing ONO donor atoms. All the complexes are stable in the open air in the solid state as well as in solution, a phenomenon rarely observed in nonoxidovanadium(IV) complexes. The complexes have good solubility in organic solvents, permitting electrochemical and various spectroscopic investigations. The existence of nonoxidovanadium(IV) complexes was confirmed by elemental analysis, ESI mass spectroscopy, cyclic voltammetry, EPR, and magnetic susceptibility measurements. X-ray crystallography showed the N3O3 donor set to define a trigonal prismatic geometry in each case. All the complexes show in vitro insulin mimetic activity against insulin responsive L6 myoblast cells, with complex 3 being the most potent, which is comparable to insulin at the complex concentration of 4 mu M, while the others have moderate insulin mimetic activity. In addition, the in vitro antiproliferative activity of complexes 1-3 against the He La cell line was assayed. The cytotoxicity of the complexes is affected by the various functional groups attached to the bezoylhydrazone derivative and 2 showed considerable antiproliferative activity compared to the most commonly used chemotherapeutic drugs.

Crystal structures of SCP2-thiolases of Trypanosomatidae, human pathogens causing widespread tropical diseases: the importance for catalysis of the cysteine of the unique HDCF loop

Thiolases are essential CoA-dependent enzymes in lipid metabolism. In the present study we report the crystal structures of trypanosomal and leishmanial SCP2 (sterol carrier protein, type-2)-thiolases. Trypanosomatidae cause various widespread devastating (sub)-tropical diseases, for which adequate treatment is lacking. The structures reveal the unique geometry of the active site of this poorly characterized subfamily of thiolases. The key catalytic residues of the classical thiolases are two cysteine residues, functioning as a nucleophile and an acid/base respectively. The latter cysteine residue is part of a CxG motif. Interestingly, this cysteine residue is not conserved in SCP2-thiolases. The structural comparisons now show that in SCP2-thiolases the catalytic acid/base is provided by the cysteine residue of the HDCF motif, which is unique for this thiolase subfamily. This HDCF cysteine residue is spatially equivalent to the CxG cysteine residue of classical thiolases. The HDCF cysteine residue is activated for acid/base catalysis by two main chain NH-atoms, instead of two water molecules, as present in the CxG active site. The structural results have been complemented with enzyme activity data, confirming the importance of the HDCF cysteine residue for catalysis. The data obtained suggest that these trypanosomatid SCP2-thiolases are biosynthetic thiolases. These findings provide promise for drug discovery as biosynthetic thiolases catalyse the first step of the sterol biosynthesis pathway that is essential in several of these parasites.

Performance analysis of boron nitride embedded armchair graphene nanoribbon metal-oxide-semiconductor field effect transistor with Stone Wales defects

We study the performance of a hybrid Graphene-Boron Nitride armchair nanoribbon (a-GNR-BN) n-MOSFET at its ballistic transport limit. We consider three geometric configurations 3p, 3p + 1, and 3p + 2 of a-GNR-BN with BN atoms embedded on either side (2, 4, and 6 BN) on the GNR. Material properties like band gap, effective mass, and density of states of these H-passivated structures are evaluated using the Density Functional Theory. Using these material parameters, self-consistent Poisson-Schrodinger simulations are carried out under the Non Equilibrium Green's Function formalism to calculate the ballistic n-MOSFET device characteristics. For a hybrid nanoribbon of width similar to 5 nm, the simulated ON current is found to be in the range of 265 mu A-280 mu A with an ON/OFF ratio 7.1 x 10(6)-7.4 x 10(6) for a V-DD = 0.68 V corresponding to 10 nm technology node. We further study the impact of randomly distributed Stone Wales (SW) defects in these hybrid structures and only 2.5% degradation of ON current is observed for SW defect density of 3.18%. (C) 2014 AIP Publishing LLC.