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PubMed2003

Experimental and theoretical charge distribution in (Z)-N-methyl-C-phenylnitrone.

The total experimental charge density in (Z)-N-methyl-C-phenylnitrone (1) has been determined using high-resolution X-ray diffraction data in combination with neutron diffraction data measured at 100 K in terms of the rigid pseudoatom model. Multipole refinement converged at R = 0.03 for 7163 reflections with I > 2 sigma(I). Topological analysis of the total experimental charge density rho(r) and its Laplacian, -[symbol: see text]2 rho(r) and a comparison with high level theoretical gas-phase calculations reveals an unexpected electron distribution in the N-O group, both atoms having negative atomic charges, contrary to that commonly assumed in nitrone species. This observation is confirmed on examination of both the theoretical charges and the molecular electrostatic potential. Compound 1 contains a large number of hydrogen bonds and these are analysed using the atoms in molecules approach leading to quantitative values for bond strength, ranging from medium to very weak.

Journal Article↗
PubMed2003

X-N charge density analysis of the hydrogen bonding motif in 1-(2-hydroxy-5-nitrophenyl)ethanone.

The total experimental charge density in 1-(2-hydroxy-5-nitrophenyl)ethanone (1) has been determined using high-resolution X-ray diffraction data in combination with neutron diffraction data measured at 100 K. Multipole refinement was carried out in terms of the rigid pseudoatom model. Multipole refinement converged at R = 0.026 for 5415 reflections with I > 2 sigma(I). Topological analysis of the total experimental charge density rho(r) and its Laplacian, -[symbol: see text]2 rho(r) together with a comparison against high level theoretical gas-phase calculations reveals fine details of intra- and intermolecular bonding features, in particular the extent of the pi-delocalisation throughout the molecule.

Journal Article↗
PubMed2000

Ce4

The yellow-orange oxonitridosilicate oxide Ce4[Si4O4N6]O was obtained by the reaction of cerium metal with Si(NH)2 and SiO2 in a radiofrequency furnace at 1560 degrees C. The crystal structure was determined by single-crystal X-ray diffraction (a = 1033.67(6) pm, P2,3, Z = 4, R1 = 0.0412, wR2 = 0.0678) and powder neutron diffraction. In the solid there are complex cations [Ce4O]10+ that are enveloped by a hyperbolical layer structure [Si4O4N6]10-. The layer is built up by corner-sharing SiON3 tetrahedra of Q3 type. The oxygen atoms of the SiON3 tetrahedra are terminally bound to Si, while all nitrogen atoms bridge two neighboring Si centres. The crystallographic differentiation of O and N was unequivocally possible by a careful evaluation of the single-crystal X-ray diffraction data combined with lattice-energy calculations by using the MAPLE concept (Madelung part of lattice energy). Furthermore the results were confirmed by the chemical analyses. Subsequently, the determined N/O distribution and their crystallographic ordering was proved by neutron powder diffraction. In accordance with the molar ratio Si:(O,N) = 2:5 the [Si4O4N6]10- network may be classified as a layer silicate. In this specific case a hyperbolically corrugated topology of the layers is observed; this is correlated to periodic nodal surface (PNS) representatives.

Journal Article↗
PubMed2003

W3Y single mutant of rubredoxin from Pyrococcus furiosus: a preliminary time-of-flight neutron study.

Rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus maintains its native structure at high temperatures (373 K). In order to investigate the role of hydrogen bonding, hydration and chain dynamics in this thermostability, wavelength-resolved Laue neutron diffraction data have been collected from the W3Y single mutant (Trp3-->Tyr3) on the spallation neutron protein crystallography station (PCS) at Los Alamos Neutron Science Center. Data were measured at room temperature from nine crystal settings, each of approximately 12 h duration. The total data-measurement period was less than 5 d from a single crystal that had undergone H(2)O/D(2)O exchange. The nominal resolution of the data is 2.1 A.

Crystallization↗
PubMed2004

Hydrogen and hydration in proteins.

Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins. High-resolution neutron diffractometers dedicated to biological macromolecules (BIX-type diffractometer) have been constructed at the Japan Atomic Energy Research Institute and they have been used in the 1.5A-resolution crystal structure analyses of several proteins. Interesting topics relevant to hydrogen and hydration in proteins, such as (1) the detailed geometry of hydrogen bonds; (2) information regarding hydrogen/deuterium exchange behavior; (3) the acidities of certain H atoms; (4) the role of hydrogen atoms in enzyme mechanisms and thermostability; (5) the location methyl hydrogen atoms; and (6) dynamical behavior of hydration structures that include H positions have been extracted from these structural results. In addition, a method for the systematic growth of large single crystals based on phase diagrams has been introduced and will be briefly described in this article.

Crystallization↗
PubMed1996

Understanding water: molecular dynamics simulations of myoglobin.

Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulation. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

Computer Simulation↗
PubMed2006

Ba2[Ni3N2]: a low-valent nitridonickelate-synthesis, crystal structure, and physical properties.

The ternary alkaline-earth nitridonickelate Ba2[Ni3N2] (Ba2[NiI2Ni0N2]) was prepared by the reaction of mixtures of Ba2N and Ni in nitrogen gas of ambient back-pressure at 1173 K. The crystal structure determined by X-ray single-crystal and powder diffraction methods as well as from neutron diffraction data at various temperatures between 2 and 298 K is orthorhombic (Cmca (no. 64), 298 K: a=715.27(18) pm, b=1032.99(21) pm, c=740.12(20) pm) and provides the first example of a nitridonickelate with a two-dimensional complex anion. The Ni2 atom is described with a split position and the corresponding superstructure variants are investigated by theoretical full-potential nonorthogonal local-orbital calculations (FPLO). The average oxidation state of Ni in Ba2[Ni3N2] is +0.67, the lowest average value observed in nitridonickelates so far. Investigations of the physical properties demonstrate that Ba2[Ni3N2] acts as a "poor" metal with a large resistivity of approximately 2.7 mOmega cm at 300 K and exhibits low-dimensional magnetism with antiferromagnetic ordering at T approximately 90 K. XAS spectra correspond with low-valent Ni states.

Journal Article↗
PubMed2005

X-ray spectroscopy and X-ray diffraction at wavelengths near the K-absorption edge of phosphorus.

Phosphorus is an abundant element in living organisms. It is traceable by its X-ray absorption spectrum which shows a strong white line at its K-edge, comparable with that observed for the L(III) edges of rare earth ions. With purple membrane, the variation of the imaginary part of the anomalous dispersion of phosphorus is found to be close to 20 anomalous electron units. Anomalous diffraction experiments at wavelengths near the K-absorption edge of phosphorus confirm this result. The spatial distribution of lipids derived from anomalous diffraction agrees with earlier results from neutron diffraction. Test experiments on single crystals of the carrier protein using 5.76 A photons gave a first low-resolution diffraction pattern. Various techniques of crystal mounting were attempted. In addition, fluorescence measurements on a solution of threonine synthase appear to hint at a change of the phosphate environment of the cofactor upon activator binding.

Carbon-Oxygen Lyases↗
PubMed2006

Simultaneous fitting of X-ray and neutron diffuse scattering data.

Conventional crystallographic refinement uses the Bragg-peak intensities and gives the single-site average crystal structure. Information about short-range order and local order is contained in the diffuse scattering that is distributed throughout reciprocal space. Models of the short-range order in materials can now be automatically refined. The complementarity of X-ray and neutron diffraction data, and the value of simultaneously refining a structural model against both types of data, has long been known. This paper presents the first refinement of a short-range-order model against comprehensive X-ray and neutron diffuse scattering data simultaneously. The sample is the organic molecular crystal benzil, C(14)H(10)O(2) (for neutron work H is replaced by D). The technique gives new insights into local order in crystalline materials, including the dynamic correlation structure indicative of the dynamics of molecules in the crystalline state, and successfully overcomes limitations of using only the X-ray data set.

Crystallography, X-Ray↗
PubMed2004

Prospects for atomic resolution and neutron crystallography in drug design.

The number of protein crystal structures being refined to atomic resolution is increasing each year as well as the size of proteins being studied. There are currently 346 structures in the protein data bank which have been refined to or beyond atomic resolution. The benefits of atomic resolution X-ray data are discussed along with a number of structural examples of biomedically relevant proteins. The complementary role of neutron diffraction will also be discussed.

Animals↗
PubMed2006

The use of advanced diffraction methods in the study of the structure of a bioactive calcia: silica sol-gel glass.

Sol-gel derived calcium silicate glasses may be useful for the regeneration of damaged bone. The mechanism of bioactivity is as yet only partially understood but has been strongly linked to calcium dissolution from the glass matrix. In addition to the usual laboratory-based characterisation methods, we have used neutron diffraction with isotopic substitution to gain new insights into the nature of the atomic-scale calcium environment in bioactive sol-gel glasses, and have also used high energy X-ray total diffraction to probe the nature of the processes initiated when bioactive glass is immersed in vitro in simulated body fluid. The data obtained point to a complex calcium environment in which calcium is loosely bound within the glass network and may therefore be regarded as facile. Complex multi-stage dissolution and mineral growth phases were observed as a function of reaction time between 1 min and 30 days, leading eventually, via octacalcium phosphate, to the formation of a disordered hydroxyapatite (HA) layer on the glass surface. This methodology provides insight into the structure of key sites in these materials and key stages involved in their reactions, and thereby more generally into the behaviour of bone-regenerative materials that may facilitate improvements in tissue engineering applications.

Calcium Compounds↗
PubMed2002

A 3-D structural model of solid self-assembled chlorophyll a/H(2)O from multispin labeling and MAS NMR 2-D dipolar correlation spectroscopy in high magnetic field.

Magic angle spinning (MAS) NMR with Lee-Goldburg cross-polarization (LG-CP) is used to promote long-range heteronuclear transfer of magnetization and to constrain a structural model for uniformly labeled chlorophyll a/H(2)O. An effective maximum transfer range d(max) can be determined experimentally from the detection of a gradually decreasing series of intramolecular correlations with the (13)C along the molecular skeleton. To probe intermolecular contacts, d(max) can be set to approximately 4.2 A by choosing an LG-CP contact time of 2 ms. Long-range (1)H-(13)C correlations are used in conjunction with carbon and proton aggregation shifts to establish the stacking of the chlorophyll a (Chl a) molecules. First, high-field (14.1 T) 2-D MAS NMR homonuclear ((13)C-(13)C) dipolar correlation spectra provide a complete assignment of the carbon chemical shifts. Second, proton chemical shifts are obtained from (1)H-(13)C heteronuclear dipolar correlation spectroscopy in high magnetic field. The shift constraints and long-range (1)H-(13)C intermolecular correlations reveal a 2-D stacking homologous to the molecular arrangement in crystalline solid ethyl-chlorophyllide a. A doubling of a small subset of the carbon resonances, in the 7-methyl region of the molecule, provides evidence for two marginally different well-defined molecular environments. Evidence is found for the presence of neutral structural water molecules forming a hydrogen-bonded network to stabilize Chl a sheets. In line with the microcrystalline order observed for the rings, the long T(1)'s, and absence of conformational shifts for the (13)C in the phytyl tails, it is proposed that the Chl a form a rigid 3-D space-filling structure. Probably the only way this can be realized with the sheets is by forming bilayers with interpenetration of elongated tails. Such a 3-D space-filling organization of the aggregated Chl a from MAS NMR would match existing models inferred from electron microscopy and low-resolution X-ray powder diffraction, while a micellar model based on neutron diffraction and antiparallel stacking observed in solution can be discarded.

Carbon Isotopes↗
PubMed2005

La4Cu(3-x)Zn(x)MoO12: zinc-doped cuprates with Kagomé lattices.

Two solid solutions, La4Cu(3-x)Zn(x)MoO12 (0.05 < or = x < or = 0.20, SS1) and La4Cu(3-x)Zn(x)MoO12 (0.30 < or = x < or = 2.40, SS2), were synthesized at ambient pressure and at temperatures from 1025 to 1200 degrees C by traditional solid-state reactions. Their structures were determined from X-ray powder diffraction with the help of electron and neutron diffraction. The atomic arrangements of SS1 and SS2 are similar, but their space groups are different, Pmnm for SS1 and P-1 for SS2, respectively. The copper, zinc, and molybdenum are coordinated by oxygen in corner-sharing trigonal bipyramids that are sandwiched between layers of lanthanum cations. In the transition metal cations layer of SS2, the copper and zinc cations order into a Kagomé-like lattice of triangular clusters. The magnetism has been measured from 2 to 300 K and is highly influenced by the geometric arrangement of the Cu(II) and Zn(II) cations. The number of free electrons per three Cu atoms is close to one for all samples in SS1 and SS2 indicating that the system can be well expressed by independent Cu(II)3 clusters. Spontaneous magnetization was observed in the system.

Copper↗
PubMed2006

A comparison of united atom, explicit atom, and coarse-grained simulation models for poly(ethylene oxide).

We compare static and dynamic properties obtained from three levels of modeling for molecular dynamics simulation of poly(ethylene oxide) (PEO). Neutron scattering data are used as a test of each model's accuracy. The three simulation models are an explicit atom (EA) model (all the hydrogens are taken into account explicitly), a united atom (UA) model (CH(2) and CH(3) groups are considered as a single unit), and a coarse-grained (CG) model (six united atoms are taken as one bead). All three models accurately describe the PEO static structure factor as measured by neutron diffraction. Dynamics are assessed by comparison to neutron time of flight data, which follow self-motion of protons. Hydrogen atom motion from the EA model and carbon/oxygen atom motion from the UA model closely follow the experimental hydrogen motion, while hydrogen atoms reinserted in the UA model are too fast. The EA and UA models provide a good description of the orientation properties of C-H vectors measured by nuclear magnetic resonance experiments. Although dynamic observables in the CG model are in excellent agreement with their united atom counterparts, they cannot be compared to neutron data because the time after which the CG model is valid is greater than the neutron decay times.

Journal Article↗
PubMed2003

Secondary extinction and diffraction behaviors in cylindrical crystals.

The X-ray and neutron diffraction properties in absorbing cylindrical crystals are systematically explored within the framework of transfer equations and the kinematic diffraction approximation. The calculated power ratio distribution, the integrated reflection power ratio and the secondary-extinction factor y( micro ) are expressed as functions of the Bragg angle theta(B), the reduced radius sigma(0)rho = tau(0) and the ratio of absorption coefficient to diffraction cross section micro /sigma(0) = xi(0). Numerical solutions were obtained for all theta(B) (0-90 degrees ) and samples with tau(0) from 0 to 30, and xi(0) from 0 to 25. The relationship between the power ratio distribution curves, the integrated reflection power ratio and the diffraction geometry of cylindrical crystals is obtained for the first time and analyzed in detail. A dip was found in the curve of the extinction factor y( micro ) against tau(0) for given theta(B) and xi(0), and the position of this minimum shifts toward smaller tau(0) with increasing xi(0) or theta(B). A large decrease of y( micro ) with decreasing theta(B) at low angle appears when micro rho > 3.5 and 25 > xi(0) > 0.2. The rate of change of y( micro ) in this region increases with tau(0). All of this will be important for the refinement of diffraction data. The influence of different kinds of mosaic distributions on the integrated reflection power ratio and the extinction factor was also studied. The transmission coefficients A(*) were calculated using two different methods, and an inaccuracy of these numbers in Vol. II of International Tables for X-ray Crystallography (1972) in the range theta(B) < or = 15 degrees and micro rho > or = 15 was found by comparison.

Journal Article↗
PubMed1987

Considerations regarding the structure of the mammalian mineralized osteoid from viewpoint of the generalized packing model.

The relative magnitudes of mineral, organic and water contents of dense mammalian bone are calculated by a new theory based on recent findings: (1) The neutron diffraction studies of mineralized tissues with different densities demonstrated an inverse relationship between wet density and the equatorial diffraction spacing of the collagen. (2) The neutron studies showed there was very little mineral within the collagen fibrils. (3) A generalized packing model for collagen has been advanced to show how the equatorial spacing can be varied depending on tissue type, water content, and mineral content. (4) The water content of collagen fibrils when calculated from the generalized packing model matches the experimentally determined values for rat tail tendon fibers, bone matrix, and fully mineralized bone. A computational model was developed based on the generalized packing model. It provides a unifying approach to explain many features of mineralized fibrous collagenous tissues. The results are presented as estimates of the mineralized collagen fibril density, the volume fraction of collagen in bone, the density of the extrafibrillar space, the fraction of the e.f. space occupied by mineral and the ratio of mineral within collagen to total mineral content, each expressed as a function of wet bone density. A useful data base, available from previous studies, related mineral, organic and water weight fractions to wet bone density, for a density range from 1.7 g/cc for deer antler to 2.7 g/cc for porpoise petrosal. A second order polynomial was found for each weight fraction component, with bone density as the input variable, with a standard deviation less than 2% of total bone weight. This permits the bone properties to be related to a single variable, the wet bone density. It is seen that compacting the collagen fibrils as well as reducing the organic component weight fraction are two important factors determining the structure of the mineralized osteoid. It was concluded that voids and pore spaces may occupy at least 5% of the bone volume.

Animals↗
PubMed2005

Refinements in the collection of energy filtered diffraction patterns from disordered materials.

In this paper a method for collecting electron diffraction patterns using a Gatan imaging filter is presented. The method enables high-quality diffraction data to be measured at scattering angles comparable to those that can be obtained using X-ray and neutron diffraction. In addition, the method offers the capability for examining small regions of sample in, for example, thin films and nano-structures. Using X-ray, neutron and electron diffraction data collected from the same sample, we demonstrate quantitative agreement between all three. We also present a novel method for obtaining the single scattering contribution to the total diffracted intensity by collecting data at various electron wavelengths. This approach allows pair distribution functions to be determined from electron diffraction in cases where there exists significant multiple scattering.

Journal Article↗
PubMed2004

The structure of aqueous guanidinium chloride solutions.

The combination of neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations to characterize the structuring in an aqueous solution of the denaturant guanidinium chloride is described. The simulations and experiments were carried out at a concentration of 3 m at room temperature, allowing for an examination of any propensity for ion association in a realistic solution environment. The simulations satisfactorily reproduced the principal features of the neutron scattering and indicate a bimodal hydration of the guanidinium ions, with the N-H groups making well-ordered hydrogen bonds in the molecular plane, but with the planar faces relatively deficient in interactions with water. The most striking feature of these solutions is the rich ion-ion ordering observed around the guanidinium ion in the simulations. The marked tendency of the guanidinium ions to stack parallel to their water-deficient surfaces indicates that the efficiency of this ion as a denaturant is due to its ability to simultaneously interact favorably with both water and hydrophobic side chains of proteins.

Cations↗