Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Magnetism and local distortions near carbon impurity in gamma-iron

Local perturbations of the crystal and magnetic structure of gamma-iron near carbon interstitial impurity is investigated by ab initio electronic structure calculations. It is shown that the carbon impurity creates locally a region of ferromagnetic ordering with substantial tetragonal distortions. Exchange integrals and solution enthalpy are calculated, the latter being in very good agreement with experimental data. The effect of the local distortions on the carbon-carbon interactions in gamma-iron is discussed.     

Tuneable molecular doping of corrugated graphene

Density functional theory (DFT) modeling of the physisorption of four different types of molecules (toluene, bromine dimmer, water and nitrogen dioxide) over and under graphene ripples has been performed. For all types of molecules changes of charge transfer and binding energies in respect to flat graphene are found. The changes in the electronic structure of corrugated graphene and turn of π-orbitals of carbon atoms in combination with the chemical structure of adsorbed molecules are proposed as the causes of difference with the perfect graphene case and variety of adsorption properties of different types of molecules. The results of calculation suggest that the tops of the ripples are more attractive for large molecules and valley between ripples for small molecules. Stability of molecules on the ripples and energy barriers for migration over flat and corrugated graphene is also discussed.     

Modeling of hydrogen and hydroxyl group migration on graphene

Density functional calculations of optimized geometries for the migration of single hydrogen and hydroxyl groups on graphene are performed. It is shown that the migration energy barrier for the hydroxyl group is three times larger than for hydrogen. The crucial role of supercell size for the values of the migration barriers is discussed. The paired migration of hydrogen and hydroxyl groups has also been examined. It could be concluded that hydroxyl group based magnetism is rather stable in contrast with unstable hydrogen based magnetism of functionalized graphene. The role of water in the migration of hydroxyl groups is also discussed, with the results of the calculations predicting that the presence of water weakens the covalent bonds and makes these groups more fluid. Increasing the number of water molecules associated with hydroxyl groups provides an increase of the migration energy.     

Computable error bounds for pointwise derivatives of a Neumann problem

In this paper we discuss the recovery of derivatives and thecomputation of rigorous and useful upper bounds for the pointwiseerror in the recovered derivatives, for finite element approximationsof the Laplace equation with Neumann boundary conditions, especiallyat points close to or on a smooth, curved boundary. We analyzethe dipole image technique for the case of curved boundaries,and show how to compute reliable recovered derivatives and errorbounds even in the limiting case of points lying on the curvedboundary. Numerical experiments show reasonably tight errorbounds for points both close to and away from a curved boundary.     

Mn clusterisation in Ga1−xMnxN

The local structure of Mn atoms in Ga_1?xMn_xN has been investigated by the Mn L₃ edge x-ray absorption spectrum (XAS) at total electron yield mode, which preferentially looks at atoms near the surface. A modeling defects configuration, Mn₅ micro-clusters complexed with substitutional Mn_Ga and interstitial Mn_I is found for a higher Mn doping concentration. This new configuration is also confirmed by the total energy calculations.     

Effect of ligand substitution on the exchange interactions in {Mn(12)}-type single-molecule magnets

We investigate how ligand substitution affects the intramolecular spin exchange interactions, studying a prototypical family of single-molecule magnets comprising dodecanuclear cluster molecules [Mn(III)(8)Mn(IV)(4)O(12)(COOR)(16)]. We identify a simple scheme based on accumulated Pauling electronegativity numbers (AEN) of the carboxylate ligand groups (R). The redistribution of the electron density, controlled by the AEN of a ligand, changes the degree of hybridization between 3d electrons of manganese and 2p electrons of oxygen atoms, thus changing the exchange interactions. This scheme, despite its conceptual simplicity, provides a strong correlation with the exchange energies associated with carboxylate bridges and is confirmed by the electronic structure calculations taking into account the Coulomb correlations in magnetic molecules.     

Interplay of ballistic and chemical effects in the formation of structural defects for Sn and Pb implanted silica

The electronic structures of Sn and Pb implanted SiO₂ are studied using soft X-ray absorption (XAS) and emission (XES) spectroscopy. We show, using reference compounds and ab initio calculations, that the presence of PbO and SnO interactions can be detected in the pre-edge region of the oxygen K-edge XAS. Via analysis of this interaction-sensitive pre-edge region, we find that Pb implantation results primarily in the clustering of Pb atoms. Conversely, with Sn implantation using identical conditions, strong SnO interactions are present, showing that Sn is coordinated with oxygen. The varying results between the two ion types are explained using both ballistic considerations and density functional theory calculations. We find that the substitution of Pb into Si sites in SiO₂ requires much more energy than substituting Sn in these same sites, primarily due to the larger size of the Pb ions. From these calculated formation energies it is evident that Pb requires far higher temperatures than Sn to be soluble in SiO₂. These results help explain the complex processes which take place upon implantation and determine the final products.