X-ray studies on crystalline complexes involving amino acids and peptides. XV. Crystal structures of L-lysine D-glutamate and L-lysine D-aspartate monohydrate and the effect of chirality on molecular aggregation

L-Lysine D-glutamate crystallizes in the monoclinic space group P2(1) with a = 4.902, b = 30.719, c = 9.679 A, beta = 90 degrees and Z = 4. The crystals of L-lysine D-aspartate monohydrate belong to the orthorhombic space group P2(1)2(1)2(1) with a = 5.458, b = 7.152, c = 36.022 A and Z = 4. The structures were solved by the direct methods and refined to R values of 0.125 and 0.040 respectively for 1412 and 1503 observed reflections. The glutamate complex is highly pseudosymmetric. The lysine molecules in it assume a conformation with the side chain staggered between the alpha-amino and the alpha-carboxylate groups. The interactions of the side chain amino groups of lysine in the two complexes are such that they form infinite sequences containing alternating amino and carboxylate groups. The molecular aggregation in the glutamate complex is very similar to that observed in L-arginine D-aspartate and L-arginine D-glutamate trihydrate, with the formation of double layers consisting of both types of molecules. In contrast to the situation in the other three LD complexes, the unlike molecules in L-lysine D-aspartate monohydrate aggregate into alternating layers as in the case of most LL complexes. The arrangement of molecules in the lysine layer is nearly the same as in L-lysine L-aspartate, with head-to-tail sequences as the central feature. The arrangement of aspartate ions in the layers containing them is, however, somewhat unusual. Thus the comparison between the LL and the LD complexes analyzed so far indicates that the reversal of chirality of one of the components in a complex leads to profound changes in molecular aggregation, but these changes could be of more than one type.

New computational approaches for inelastic x-ray scattering

Inelastic x-ray scattering spectroscopy is a versatile experimental technique for probing the electronic structure of materials. It provides a wealth of information on the sample's atomic-scale structure, but extracting this information from the experimental data can be challenging because there is no direct relation between the structure and the measured spectrum. Theoretical calculations can bridge this gap by explaining the structural origins of the spectral features. Reliable methods for modeling inelastic x-ray scattering require accurate electronic structure calculations. This work presents the development and implementation of new schemes for modeling the inelastic scattering of x-rays from non-periodic systems. The methods are based on density functional theory and are applicable for a wide variety of molecular materials. Applications are presented in this work for amorphous silicon monoxide and several gas phase systems. Valuable new information on their structure and properties could be extracted with the combination of experimental and computational methods.

Eigenvalues of kinematical conservation laws (KCL) based 3-D weakly nonlinear ray theory (WNLRT)

System of kinematical conservation laws (KCL) govern evolution of a curve in a plane or a surface in space, even if the curve or the surface has singularities on it. In our recent publication K. R. Arun, P. Prasad, 3-D kinematical conservation laws (KCL): evolution of a surface in R-3-in particular propagation of a nonlinear wavefront, Wave Motion 46 (2009) 293-311] we have developed a mathematical theory to study the successive positions and geometry of a 3-D weakly nonlinear wavefront by adding an energy transport equation to KCL. The 7 x 7 system of equations of this KCL based 3-D weakly nonlinear ray theory (WNLRT) is quite complex and explicit expressions for its two nonzero eigenvalues could not be obtained before. In this short note, we use two different methods: (i) the equivalence of KCL and ray equations and (ii) the transformation of surface coordinates, to derive the same exact expressions for these eigenvalues. The explicit expressions for nonzero eigenvalues are important also for checking stability of any numerical scheme to solve 3-D WNLRT. (C) 2010 Elsevier Inc. All rights reserved.

Disordered matter studied by x-ray Raman scattering

Spectroscopy can provide valuable information on the structure of disordered matter beyond that which is available through e.g. x-ray and neutron diffraction. X-ray Raman scattering is a non-resonant element-sensitive process which allows bulk-sensitive measurements of core-excited spectra from light-element samples. In this thesis, x-ray Raman scattering is used to study the local structure of hydrogen-bonded liquids and solids, including liquid water, a series of linear and branched alcohols, and high-pressure ice phases. Connecting the spectral features to the local atomic-scale structure involves theoretical references, and in the case of hydrogen-bonded systems the interpretation of the spectra is currently actively debated. The systematic studies of the intra- and intermolecular effects in alcohols, non-hydrogen-bonded neighbors in high-pressure ices, and the effect of temperature in liquid water are used to demonstrate different aspects of the local structure that can influence the near-edge spectra. Additionally, the determination of the extended x-ray absorption fine structure is addressed in a momentum-transfer dependent study. This work demonstrates the potential of x-ray Raman scattering for unique studies of the local structure of a variety of disordered light-element systems.

An X-ray and neutron diffraction study of cation substituted TlSr2CuO5

The structures of TlSr(2−x)LaxCuO(5+δ), with x=0.5, 0.75 and 1, and Tl.5Pb0.5Sr2CuO(5+δ) have been examined with X-ray and neutron powder Rietveld refinement. They are isostructural (P4/mmm) with the corresponding thallium-barium cuprate having one Cu-O layer with Cu3+ ions in octahedral coordination with oxygen (structure type 1201). The influence of cation substitution and disorder on the structure and superconducting properties of these phases have been investigated. La3+ substitution for Sr2+ stabilises the structure and reduces Cu3+, permitting superconductivity, while Pb2+ substitution for Tl3+ only stabilises the structure, without reducing Cu3+.

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.

Crystal and molecular structure of sym-homospermidine monohydrate

Sym-homospermidine, [formula; see text] is a naturally occurring rare-polyamine found in relatively large concentration in sandal leaves. As part of our studies on structure and interactions of polyamines, ym-homospermidine was purified from sandal leaves and its structure was determined by single crystal X-ray diffraction technique. The phosphate salt of the molecule crystallized in the triclinic space group P1- with a = 8.246(1)A, b = 8.775(1)A, c = 15.531(2)A, alpha = 74.20(1) degrees, beta = 88.36(1) degrees and gamma = 65.41(1) degrees. The structure was determined by direct methods and refined to a final R factor of 5.4% for 2087 reflections with magnitude of F(obs) greater than 5 sigma [F(obs)]. The amine exists in its most favourable all trans conformation. For each amine molecule three phosphate groups exist in the crystal structure, suggesting that two of the oxygens of each phosphate group are protonated. There is also a single water molecule in the asymmetric unit in contrast to that of spermidine phosphate which has 3 water molecules. These differences probably reflect the hydrogen bonding properties of mono-ionic and di-ionic phosphate groups. The structure is predominantly stabilized by a network of hydrogen bonds.

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.