X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.

Nanoscale studies of materials using x-ray synchrotron radiation and mesoscopic modelling

X-ray synchrotron radiation was used to study the nanostructure of cellulose in Norway spruce stem wood and powders of cobalt nanoparticles in cellulose support. Furthermore, the growth of metallic clusters was modelled and simulated in the mesoscopic size scale. Norway spruce was characterized with x-ray microanalysis at beamline ID18F of the European Synchrotron Radiation Facility in Grenoble. The average dimensions and the orientation of cellulose crystallites was determined using x-ray microdiffraction. In addition, the nutrient element content was determined using x-ray fluorescence spectroscopy. Diffraction patterns and fluorescence spectra were simultaneously acquired. Cobalt nanoparticles in cellulose support were characterized with x-ray absorption spectroscopy at beamline X1 of the Deutsches Elektronen-Synchrotron in Hamburg, complemented by home lab experiments including x-ray diffraction, electron microscopy and measurement of magnetic properties with a vibrating sample magnetometer. Extended x-ray absorption fine structure spectroscopy (EXAFS) and x-ray diffraction were used to solve the atomic arrangement of the cobalt nanoparticles. Scanning- and transmission electron microscopy were used to image the surfaces of the cellulose fibrils, where the growth of nanoparticles takes place. The EXAFS experiment was complemented by computational coordination number calculations on ideal spherical nanocrystals. The growth process of metallic nanoclusters on cellulose matrix is assumed to be rather complicated, affected not only by the properties of the clusters themselves, but essentially depending on the cluster-fiber interfaces as well as the morphology of the fiber surfaces. The final favored average size for nanoclusters, if such exists, is most probably a consequence of these two competing tendencies towards size selection, one governed by pore sizes, the other by the cluster properties. In this thesis, a mesoscopic model for the growth of metallic nanoclusters on porous cellulose fiber (or inorganic) surfaces is developed. The first step in modelling was to evaluate the special case of how the growth proceeds on flat or wedged surfaces.

Amino acid-lanthanide interactions, Part 2. The X-ray crystal structures of lanthanide and calcium complexes of 1-amino-cyclohexane-1-carboxylic acid (Acc6)

The structures of [Nd-2(Acc(6))(H2O)(6)](ClO4)(6) .(H2O)(6) (1) [Er-2(Acc(6))(4)(H2O)(8)](ClO4)(6) .(H2O)(11) (2) and [Ca-5(Acc(6))(12)(H2O)(6)](ClO4)(10).(H2O)(4) (3) (Acc(6) = 1-aminocyclohexane-1-carboxylic acid) have been determined by X-ray crystallography. The lanthanide complexes 1 and 2 are dimeric in which two lanthanide cations are bridged by four carboxylato groups of Acc(6) molecules. In addition, the neodymium complex (1) features the unidentate coordination of the carboxyl group of an Acc(6) molecule in place of a water molecule in the erbium complex (2). The coordination number in both 1 and 2 is eight. The calcium Acc(6) complex (3) is polymeric; three different calcium environments are observed in the asymmetric unit. Two calcium ions are hexa-coordinated and one is hepta-coordinated. Considerable differences are observed between the solid state structures of Ln(III) and Ca-II complexes of Acc(6

Transition metal oxide perovskites by photoelectron and x-ray absorption spectroscopy

X-ray and ultraviolet photoelectron spectroscopy as well as x-ray absorption spectroscopy have been employed to investigate transition metal oxide perovskites of the general formula ABOs (A=La or rare-earth ion, B=trivalent transition metalion). Systematics in the core levels and in the valence bands in the series of LaBOa compounds have been discussed. Lanthanum chemical shifts in the x-ray absorption spectra in this series show interesting trends. Photoelectron spectra of the solid solutions, LaNil_x Coxes, LaNix_x FexO8 and LaFel_x Coxes show that the rigid band model is applicable to these systems. It is shown that x-ray photoelectron spectroscopy can be employed to identify multiple oxidation states of transition metal ions in oxide perovskites.

C-H…O hydrogen bond mediated chain reversal in a peptide containing g-amino acid residue, determined directly from powder X-ray diffraction data

The finding that peptides containing -amino acid residues give rise to folding patterns hitherto unobserved in -amino acid peptides[1] has stimulated considerable interest in the conformational properties of peptides built from , and residues,[2] as the introduction of additional methylene (CH2) units into peptide chains provides further degrees of conformational freedom.

Structure of the rhenium X-ray LIII absorption edge in caesium hexachlororhenate(IV)

The X-ray LIII absorption-edge structure of rhenium in Cs2[ReCl6] has been measured with a bent-crystal X-ray spectrograph. An analysis in terms of molecular-orbital (m.o.) theory has been attempted. The energies of the m.o. levels, crystal-field splitting parameter, effective magnetic moment, magnetic susceptibility, and Landég parameter have been determined from this analysis. An estimate of the Re–Cl bond length has also been made.

Nucleophilic attacks of 1,2-diaminoethane on MeCN ligands: synthesis, x-ray structure, and spectral and electrochemical properties of [Ru(.mu.-O)(.mu.-O2CAr)2[NH2CH2CH2NHC(Me)NH]2(PPh3)2](ClO4)2(Ar = C6H4-p-X; X = H, Me, OMe, Cl)

The diruthenium(III) complex [Ru2O(O2CAr)2(MeCN)4(PPh3)2](ClO4)2 (1), on reaction with 1,2-diaminoethane (en) in MeOH at 25-degrees-C, undergoes nucleophilic attacks at the carbon of two facial MeCN ligands to form [(Ru2O)-O-III(O2CAr)2-{NH2CH2CH2NHC(Me)NH}2(PPh3)2](ClO4)2 (2) (Ar = C6H4-p-X, X = H, Me, OMe, Cl) containing two seven-membered amino-amidine chelating ligands. The molecular structure of 2 with Ar = C6H4-p-OMe was determined by X-ray crystallography. Crystal data are as follows: triclinic, P1BAR, a = 13.942 (5) angstrom, b = 14.528 (2) angstrom, c = 21.758 (6) angstrom, alpha = 109.50 (2)-degrees, beta = 92.52 (3)-degrees, gamma = 112.61 (2)-degrees, V = 3759 (2) angstrom 3, and Z = 2. The complex has an {Ru2(mu-O)(mu-O2CAr2)2(2+)} core. The Ru-Ru and average Ru-O(oxo) distances and the Ru-O-Ru angle are 3.280 (2) angstrom, 1.887 [8] angstrom, and 120.7 (4)-degrees, respectively. The amino group of the chelating ligand is trans to the mu-oxo ligand. The nucleophilic attacks take place on the MeCN ligands cis to the mu-oxo ligand. The visible spectra of 2 in CHCl3 display an absorption band at 565 nm. The H-1 NMR spectra of 2 in CDCl3 are indicative of the formation of an amino-amidine ligand. Complex 2 exhibits metal-centered quasireversible one-electron oxidation and reduction processes in the potential ranges +0.9 to +1.0 V and -0.3 to -0.5 V (vs SCE), respectively, involving the Ru(III)2/Ru(III)Ru(IV) and Ru(III)2/Ru(II)Ru(III) redox couples in CH2Cl2 containing 0.1 M TBAP. The mechanistic aspects of the nucleophilic reaction are discussed.

Organometallic derivatives of diphosphazanes. 2. Seven-coordinated Group 6 metal tricarbonyl complexes of diphosphazane ligands. X-ray crystal structure of [WI2(CO)3{P(OPh)2}2NPh]

The reactions of the complexes [MI2(CO)3-(NCMe)2] (M = Mo, W) with the diphosphazane ligands RN{P(OPh)2}2 (R = Me, Ph) in CH2Cl2 at room temperature afford new seven-coordinated complexes of the type [MI2(CO)3{P(OPh)2}2NR]. The molybdenum complexes are sensitive to air oxidation even in the solid state, whereas the tungsten complexes are more stable in the solid state and in solution. The structure of the tungsten complex [WI2(CO)3{P(OPh)2}2NPh] has been determined by single-crystal X-ray diffraction. It crystallizes in the orthorhombic system with the space group Pna 2(1), a = 19.372 (2) angstrom, b = 11.511 (1) angstrom, c = 15.581 (1) angstrom, and Z = 4. Full-matrix least-squares refinement with 3548 reflections (I > 2.5-sigma-(I)) led to final R and R(w) values of 0.036 and 0.034, respectively. The complex adopts a slightly distorted pentagonal-bypyramidal geometry rarely observed for such a type of complexes; two phosphorus atoms of the diphosphazane ligand, two iodine atoms, and a carbonyl group occupy the equatorial plane, and the other two carbonyl groups, the apical positions.

Origin of nonmetallicity in PrBa2Cu3O7 from a study of Gd1−xPrxBa2Cu3O7 using soft x-ray absorption at the oxygen K-edge

We present the x-ray absorption data at the oxygen K-edge using total yield technique for Gd1−xPrxba2Cu3O7 (x= 0.0, 0.2, 0.4, 0.6, 0.8, and 1.0). The data clearly to oxygen that the holes doped in the GdBa2Cu3O7 due to oxygen composition are not removed by Pr doping even for the x = 1.0 sample, suggesting that Pr is predominantly in the formally trivalent state. However, the data also clearly indicate the evidence of hybridization effects between the Pr3+ and the adjacent CuO2 layers. This is suggested to be responsible for the progressive suppression of Tc and the metallicity with Pr doping in these systems.

Cloning, expression, purification and preliminary X-ray crystallographic studies of 2-methylisocitrate lyase from Salmonella typhimurium. Acta Crystallogr

In Salmonella typhimurium, propionate is oxidized to pyruvate via the 2-methylcitric acid cycle. The last step of this cycle, the cleavage of 2-methylisocitrate to succinate and pyruvate, is catalysed by 2-methylisocitrate lyase (EC 4.1.3.30). Methylisocitrate lyase (molecular weight 32 kDa) with a C-terminal polyhistidine affinity tag has been cloned and overexpressed in Escherichia coli and purified and crystallized under different conditions using the hanging-drop vapour-diffusion technique. Crystals belong to the orthogonal space group P2(1)2(1)2(1), with unit-cell parameters a = 63.600, b = 100.670, c = 204.745 Angstrom. A complete data set to 2.5 Angstrom resolution has been collected using an image-plate detector system mounted on a rotating-anode X-ray generator.

Relation between effective atomic charge and chemical shifts in X-ray absorption spectra of transition-metal compounds

Chemical shifts of K absorption discontinuities, Delta E, of several manganese, iron and cobalt oxides with the metal in the formal oxidation states between +2 and +4, have been measured. These data, together with data in the literature on other compounds of these metals, can be fitted into the expression Delta E=aq+bq2, where q is the effective atomic charge on the metal. Theoretical considerations also support this functional relationship between Delta E and q.

Steric and rotational constraints in the X-ray structure of the animalarial drug amodiaquine

In the crystal structure of the antimalarial drug amodiaquine, the bonds linking the quinoline and the phenyl groups show partial double-bond character. The partial double-bond character of the two exocyclic bonds, together with stereochemical constraints, reduce flexibility of the two ring systems of the molecule. The dihedral angle between the two ring planes is lowest compared to those in the antileukaemic drug amsacrine and its derivatives. CPK-modelling studies suggest the way amodiaquine can bind to DNA. Stacking interaction between the quinoline and phenyl groups of independent molecules and the hydrogen-bond network stabilize the crystal structure.

Syntheses, X-ray structure and properties of (5-cyclopentadienyl)ruthenium(II) complexes of pyridyl-2-hydrazone ligands

Complexes of the formulae [(-Cp)Ru(PPh3)(2-PPH)]Cl and [(Cp)Ru(PPh3) (py)(1-PPH)]Cl were prepared by reacting pyridyl-2-phenylhydrazone [PPH, C5H4N-2-CH=NNHPh] with (-Cp)Ru(PPh3)2Cl and (-Cp)Ru(PPh3)(py)Cl, respectively. In these complexes the PPH ligand displays bidentate chelating and unidentate modes of bonding. The molecular structure of [(-Cp)Ru(PPh3)(2-PPH)](ClO4)·CH2Cl2 was determined by X-ray crystallography. In this complex the metal is bonded to the N-pyridyl and N-imine atoms of the chelating ligand. 1H NMR spectral data suggests that PPH is bonded to ruthenium through the pyridine moiety of the PPH ligand in [(η-Cp)Ru(PPh3)(py)(η1-PPH)]Cl.