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At least 973 records · Page 54Linked to original sources
PubMed1999

Electron density in ammonium dihydrogen phosphate: non-uniqueness of the multipolar model in simple inorganic structures.

X-ray and neutron diffraction data of a single crystal of ammonium dihydrogen phosphate have been used for the determination of the electron density using multipolar expansion of the density around each nucleus. As the ammonium group was found to be nearly neutral from unconstrained multipole refinement, constrained refinements have been performed with the charge of the ammonium group ranging from zero to one. On the other hand, the expansion of the radial functions of the phosphorus atom was varied. All refinements led to almost the same agreement factors and residual densities. The consequences of such uncertainties on the topology of the electron density are discussed, namely the topology of the P-O bond critical point.

Journal Article↗
PubMed2001

Structure of the X-phase of 38% brominated betaine calcium chloride dihydrate.

The structures of the high- and low-temperature phases of 38% brominated BCCD [betaine (trimethylammonioacetate) calcium chloride dihydrate], the latter being known as the X-phase, have been determined by single-crystal neutron diffraction at 295 and 20 K, respectively. The symmetry of the X-phase is described by the P2(1)2(1)2(1) space group. The distortion with respect to the high-temperature Pnma phase is characterized by anti-symmetric displacements of the betaine molecules as well as of the Ca octahedra. On the basis of a symmetry-mode analysis, we propose an interpretation of the direct phase transition that occurs around 80 K between these two phases.

Journal Article↗
PubMed2001

Asymmetric hydrogen bonds in centrosymmetric environment: neutron study of very short hydrogen bonds in potassium hydrogen dichloromaleate.

The structure of the title compound has been studied by neutron diffraction at 30 and 295 K, with the emphasis on the location of the protons. There are two crystallographically independent H atoms in two very short hydrogen bonds, 2.437 (2) and 2.442 (2) A at 30 K. The structure could be refined successfully in the centrosymmetric space group P1;, with the H atoms located at the centres of symmetry. However, the form of the thermal ellipsoids of hydrogen indicated either asymmetric hydrogen bonds or overlap of two closely spaced, partially occupied positions around the centres of symmetry. Several different types of refinements have then been applied, including unconventional models; with all atoms except hydrogen constrained in P1;, but with hydrogen allowed to refine without any constraints in P1, anisotropic refinement of all atoms resulted in clearly off-centred hydrogen positions. Significance tests clearly showed that the results from this constrained refinement give the most satisfactory description of the structure. This structure may be described as 'pseudo-centrosymmetric with non-centred protons'. The results demonstrate that it is very important to also include refinement models with non-centrosymmetric hydrogen in a centrosymmetric environment when studying very short hydrogen bonds. The shifts of the two H atoms from the centres of symmetry are 0.15 (1) and 0.12 (1) A, respectively, at 30 K, and 0.15 (1) A for both H atoms at room temperature. At 30 K: R(F) = 0.036 for 1485 reflections; at 295 K: R(F) = 0.035 for 1349 reflections.

Journal Article↗
PubMed2001

Experimental electron density of urea-phosphoric acid (1/1) at 100 K.

The deformation electron density of the urea-phosphoric acid adduct has been studied from 100 K X-ray and neutron diffraction experiments. Data were interpreted according to the Hirshfeld model. The long hydrogen bonds show characteristics of electrostatic interaction. Deformation density maps on the short hydrogen bond shows hydrogen more strongly bonded to urea than to phosphoric acid, and peak maxima at almost midway between the two O-H bonds.

Journal Article↗
PubMed2001

Charge distribution as a tool to investigate structural details. II. Extension to hydrogen bonds, distorted and hetero-ligand polyhedra.

It is shown that one of the main reasons for most failures of the methods for calculating distance-dependent bond strengths is related to the distortion of the coordination polyhedra. The charge distribution (CD) method which depends on only one universal empirical parameter (contraction parameter) is modified to include: (i) an iterative calculation of the effective coordination number (ECoN), to deal with structures containing very distorted coordination polyhedra; (ii) a specific contraction parameter to treat structures containing any type of hydrogen bond; (iii) scale factors for coordination subshells, to treat structures with hetero-ligand polyhedra. The contraction parameter for the hydrogen bonds was obtained from 119 well refined structures based on neutron diffraction data. Examples of the application of the iterative charge distribution (CD-IT) are presented to show the efficiency of the new method in dealing with distorted (including hydrogen bonding) and hetero-ligand polyhedra. In particular, analysis of a series of 74 structures with pentacoordinated cations shows that deviations from overall trends are related to structure instability. The possible failure of the method with polyionic structures and 'dynamic' structures is discussed.

Journal Article↗
PubMed2002

Synthesis and characterization of the barium oxalates BaC2O4.0.5H2O, alpha-BaC2O4 and beta-BaC2O4.

The synthesis of BaC(2)O(4).0.5H(2)O and its thermal decomposition to alpha-BaC(2)O(4) and beta-BaC(2)O(4) was investigated. BaC(2)O(4).0.5H(2)O is precipitated at room temperature from aqueous solutions of barium chloride and ammonium oxalate. The deuterated compound BaC(2)O(4).0.5D(2)O was made in analogy with D(2)O as the solvent. The compounds were characterized by X-ray and neutron diffraction analysis. Single-crystal X-ray diffraction of BaC(2)O(4).0.5H(2)O measured at 120 K gave the triclinic cell a = 8.692 (1), b = 9.216 (1), c = 6.146 (1) A, alpha = 95.094 (3), beta = 95.492 (3), gamma = 64.500 (3) degrees, space group P1, Z = 4. Two independent Ba atoms are each coordinated to nine O atoms at distances from 2.73 (1) to 2.99 (1) A. One of the two oxalate ions deviates significantly from planarity. The water molecule does form weak hydrogen bonds. In situ X-ray powder diffraction was used to study the thermal decomposition of BaC(2)O(4).0.5H(2)O and the formation of alpha-BaC(2)O(4). The X-ray powder pattern of alpha-BaC(2)O(4) measured at 473 K was indexed on a triclinic cell with a = 5.137 (3), b = 8.764 (6), c = 9.006 (4) A, alpha = 83.57 (4), beta = 98.68 (5), gamma = 99.53 (5) degrees, and the space group P1 with Z = 4.

Journal Article↗
PubMed2002

Structural characterization of crystals of alpha-glycine during anomalous electrical behaviour.

The crystal structure of alpha-glycine has been investigated in the temperature range 288-427 K using neutron diffraction. The molecular structure does not change significantly and the putative crystallographic phase transition associated with anomalous electrical behaviour in this temperature range is not observed. The unit cell expands anisotropically with increasing temperature, with the unique monoclinic b axis, corresponding to the stacking direction of molecular layers, changing the most. The increasing separation of antiferroelectric molecular layers with increasing temperature is driven by an increase in molecular libration about an axis that lies perpendicular to the b axis. There is also a weakening of the interlayer hydrogen bonds with temperature. These structural and dynamic changes will affect the response of molecular dipoles to an applied electric field and provide a possible mechanism for the anomalous electrical behaviour.

Crystallography, X-Ray↗
PubMed2002

Asymmetric hydrogen bonds in centrosymmetric environment. II. Neutron study of very short hydrogen bonds in potassium hydrogen dichloromaleate at 90 K and 170 K.

In our earlier neutron diffraction study of the title compound at 30 K and 295 K an unconventional strategy in the refinement of hydrogen was applied and the same procedure has now been followed in the present investigation at 170 K and 90 K. There are two short O...H...O hydrogen bonds [2.437 (2) A and 2.442 (2) A at 30 K] and the 'heavy-atom' structure is centrosymmetric (P1) with centres of symmetry in the middle of the O...O bonds. However, statistical significance tests clearly show that an asymmetric location of both H atoms gives the most satisfactory description of the structure at all temperatures. The shift of hydrogen from the centre of symmetry is 0.15, 0.14, 0.15 and 0.15 A for H2 at 30, 90, 170 and 295 K, respectively, and 0.15, 0.15, 0.15 and 0.12 A for H4 (sigma = 0.01 A). Furthermore, the behaviour of H2 is very interesting: at 295 K and 170 K it is located on one side of the symmetry centre but at 90 K and 30 K it is located on the other side. A detailed determination of the unit-cell parameters by X-ray diffraction in the whole temperature range from 30 K to 295 K has revealed that the data points of the cell parameters as a function of temperature fall on two different straight lines with a sudden change in the slope around 135 K. It appears likely that the change in the location of H2 as the temperature is lowered is related to this behaviour. At 170 K, R(F) = 0.029 for 1236 reflections; at 90 K, R(F) = 0.030 for 1457 reflections.

Journal Article↗
PubMed2003

Structure-property correlation over five phases and four transitions in Pb5Al3F19.

The calorimetric and dielectric properties of Pb(5)Al(3)F(19) in the five phases stable under ambient pressure are correlated with structure for fuller characterization of each phase. The first-order transition between ferroelectric phase V and antiferroelectric phase IV at T(V,IV) = 260 (5) K exhibits a thermal hysteresis of 135 (5) K on heating, with a maximum atomic displacement Delta(xyz)(max) = 1.21 (6) A; the transition from phase IV to ferroelastic phase III at 315 (5) K is also first order but with a thermal hysteresis of 10 (5) K and Delta(xyz)(max) = 0.92 (7) A; that from phase III to paraelastic phase II at 360 (5) K is second order without hysteresis and has Delta(xyz)(max) = 0.69 (4) A; and the transition from phase II to paraelectric phase I at 670 (5) K is second or higher order, with Delta(xyz)(max) = 0.7 (4) A. The measured entropy change DeltaS at T(V,IV) agrees well with DeltaS as derived from the increased configurational energy by Stirling's approximation. For all other phase transitions, 0.5 > or = DeltaS > 0 J mol(-1) K(-1) is consistent with an entropy change caused primarily by the changes in the vibrational energy. The structure of phase III is determined both by group theoretical/normal mode analysis and by consideration of the structures of phases II, IV and V reported previously; refinement is by simultaneous Rietveld analysis of the X-ray and neutron diffraction powder profiles. The structure of prototypic phase I is predicted on the basis of the atomic arrangement in phases II, III, IV and V. The introduction of 3d electrons into the Pb(5)Al(3)F(19) lattice disturbs the structural equilibrium, the addition of 0.04% Cr(3+) causing significant changes in atomic positions and increasing T(IV,III) by approximately 15 K. Substitution of Al(3+) by 20% or more Cr(3+) eliminates the potential minima that otherwise stabilize phases IV, III and II.

Journal Article↗
PubMed1995

Computational studies of crystalline H3PO4.

A polarized split-valence wavefunction was computed for the H3PO4 molecule at its neutron crystallographic valence geometry, and the wavefunction was used to map the molecular electron-density distribution and to simulate X-ray crystal structure factors for both static, at-rest and dynamic thermally averaged structures. The thermal vibrational averaging was approximated using anisotropic mean-square atomic displacements from approximately 300 K neutron diffraction data. The simulated X-ray data were used to test pseudoatom multipole modeling of the valence electron-density distribution, in particular, radial modeling of the M valence shell of the P atom, and deconvolution of the nonspherical density features from anisotropic vibrational smearing.

Crystallography, X-Ray↗
PubMed1996

Effects of H/D substitution on thermal vibrations in piperazinium hexanoate-h11, d11.

The crystal structures of piperazinium hexanoate-h11, 1/2C4H12N2(2+).C6H11O2-, and piperazinium hexanoate-d11, 1/2C4H12N2(2+).C6D11O2-, have been determined from neutron diffraction data collected at 15 K. Nuclear anisotropic displacement parameters have been analyzed to obtain the internal molecular displacements of the H and D nuclei, given by (u(obs)2)-(u(ext)2) where (u(ext)2) is the contribution assuming all H/D to be carried rigidly on the vibrating molecular framework consisting of the heavier nuclei. In both crystal structures the cation ring is well fitted by the rigid-body model and the anion chain by a model with two rigid segments. In the piperazinium cations the corresponding protons in the two structures have about the same internal vibrational directions and magnitudes except for the two N--H protons, perhaps owing to differences in N--H...O hydrogen bonding. The internal vibrations of corresponding H/D in the h11 and d11 anions have approximately the same vibrational directions. The internal mean-square displacements of the H nuclei are systematically greater than the values of the corresponding D nuclei by an average factor 1.7(3). For both anions, normal-mode analyses have been carried out using the force fields derived from ab initio quantum-mechanical calculations with HF/3-21G and HF/6-31G** basis sets. The values of the resultant H/D internal displacements for C--H(D) bond stretching and methylene out-of-plane vibrations are in good agreement with experiment. However, with either basis set, theory predicts methylene in-plane mean-square displacements significantly greater than the experimental values.

Caproates↗
PubMed1999

Experimental charge density and electrostatic potential in nicotinamide.

The accurate crystal structure of nicotinamide, 3-pyridinecarboxamide, was determined from X-ray and neutron diffraction experiments: C(6)H(6)N(2)O, M(r) = 122.13, monoclinic, P2(1)/c, Z = 4. The electron distribution at 150 K was determined by the maximum entropy method and the electrostatic potential in the crystal was calculated by Fourier convolution of the electron distribution. The electrostatic properties of the nicotinamide molecule depend on the molecular conformation. The asymmetric electrostatic potential field observed above and below the pyridine-ring plane is related to the rotation of the carboxamide group with respect to the pyridine plane. The positive potential peak at the C4 atom of the pyridine ring extends to the C=O-group side of the plane. The asymmetry of the potential on the C4 atom is consistent with the stereospecificity of hydride transfer in NAD(+)/NADH oxidoreduction.

Journal Article↗
PubMed1999

Disparate atomic displacements in skutterudite-type LaFe3CoSb12, a model for thermoelectric behavior.

Mean-square atomic displacements in lanthanum triiron cobalt dodecaantimonide, determined as a function of temperature using single-crystal neutron diffraction, show that the La atom exhibits an anomalously large displacement at room temperature, U(eq) = 0.0196 (9) Å(2), because it is too small to fill the atomic cage formed by the corner-linked octahedral framework of M(4)Sb(12), M = Fe, Co. Site-occupancy refinements show 25% vacancies on the La site and an actual Fe:Co ratio of 2.17:1. Analysis of the temperature dependence of the atomic displacements identifies a significant temperature-independent component for the La atom ascribed to static disorder, which amounts to 19% of the room-temperature value. The large-amplitude rattling of the La atom can be effectively linked to the dramatic decrease of the lattice contribution to the thermal conductivity, which is a key factor for improving the thermoelectric behavior of these materials. This structure-property relationship offers a new paradigm for the exploration of thermoelectric materials.

Journal Article↗
PubMed2000

Structure of the inclusion complex of beta-cyclodextrin with 1,12-dodecanedioic acid using synchrotron radiation data; a detailed dimeric beta-cyclodextrin structure

A detailed crystal structure study of the dimeric inclusion complex of beta-cyclodextrin (betaCD) with 1,12-dodecanedioic acid is presented [IUPAC name: beta-cyclodextrin-1,12-dodecanedioic acid (2/1)]. The structure was solved with synchrotron high-resolution data (0.65 A) at 100 K [crystal data: P1, Z= 1, a = 18.153 (7), b = 15.456 (8), c = 15.251 (4) A, alpha = 102.81 (2), beta = 113.13 (2), gamma = 99.90 (3)degrees, V = 3,673 (3) A3, R = 0.0474 for 25,134 unique reflections with I > 2sigma(I)]. Moreover, the room-temperature structure is used for comparison [crystal data: P1, Z = 1, a = 18.220 (3), b = 15.488 (3), c = 15.409 (3) A, alpha = 102.903 (6), beta = 113.122 (5), gamma = 99.708 (5)degrees, V = 3735.2 (12) A3, R = 0.0828 for 8,235 unique reflections with I > 2sigma(I)]. Combining the high-resolution data and the low-temperature made possible the location of the disordered guest molecule, 1,12-dodecanedioic acid, inside the wide cavity of the macrocycle formed by two betaCD monomers. Moreover, almost all the H atoms of the betaCD macrocycle and many of the water molecules have been located in the low-temperature structure. Thus, for the first time, it has been possible to show in detail, up to now only given by neutron diffraction data, that two betaCD monomers self-assemble through O3...O3 intermolecular hydrogen bonds to form the betaCD dimer, as well as describe the hydrogen-bonding scheme between the dimer's hydroxyl groups among themselves and with water molecules in the lattice. The long guest threads through two host molecules forming a [3]pseudorotaxane. Its polar carboxyl groups, fully hydrated at the primary faces of the betaCD dimers, influence their packing so that those faces are exposed to the solvent. This is in contrast to the packing of the beta-cyclodextrin complexes of the corresponding aliphatic monoacids, where the dimeric complexes form channels in order to isolate the terminal methyl group from the water environment of the lattice.

Journal Article↗
PubMed2000

The geometry of metal-ligand interactions relevant to proteins. II. Angles at the metal atom, additional weak metal-donor interactions.

Geometrical data which could be of relevance in the structure determination, structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from 'small-molecule' structures determined by X-ray or neutron diffraction to an accuracy and precision much better than that of most current protein structure determinations. Structures of Mg, Mn, Fe, Cu and Zn complexes with ligands whose donor atoms may be only N, O, S or Cl have been selected and analysed in terms of the geometry of the metal coordination group - octahedral, tetrahedral, tetragonal pyramidal etc. The r.m.s. deviation of all the interbond angles around the metal atom provides a measure, delta, of the deviation from ideal geometry. Average values of delta are tabulated for the different metals in each type of complex. For simple non-chelated complexes of Mn, Fe and Zn, distortions of up to 5 degrees in octahedral complexes and 10 degrees in tetrahedral complexes are found to be normal and seem likely to be a consequence of packing effects, ligand bulk or intramolecular effects. Substantially larger distortions are found for some other metals and geometries and are common for chelated complexes. Brief comments on six-, seven- and eight-coordinate Ca complexes are included. Tables are also presented showing that for four- and five-coordinate complexes of Zn and Cu it is quite common to find additional weakly coordinated ligands, usually with N or O donor atoms and with M.N,O distances longer than a normal bond length but shorter than a van der Waals contact, e.g. in the range 2.4-3.0 A for Zn and 2.6-3.0 A for Cu. Although the contributions to bond valency or bonding energy of such interactions may not be great, their effect on geometry can be considerable; they can, for example, cause much larger distortions of tetrahedral Zn complexes than indicated above.

Chelating Agents↗
PubMed2006

Structure of human ferritin L chain.

Ferritin is the major iron-storage protein present in all cells. It generally contains 24 subunits, with different ratios of heavy chain (H) to light chain (L), in the shape of a hollow sphere hosting up to 4500 ferric Fe atoms inside. H-rich ferritins catalyse the oxidation of iron(II), while L-rich ferritins promote the nucleation and storage of iron(III). Several X-ray structures have been determined, including those of L-chain ferritins from horse spleen (HoSF), recombinant L-chain ferritins from horse (HoLF), mouse (MoLF) and bullfrog (BfLF) as well as recombinant human H-chain ferritin (HuHF). Here, structures have been determined of two crystal forms of recombinant human L-chain ferritin (HuLF) obtained from native and perdeuterated proteins. The structures show a cluster of acidic residues at the ferrihydrite nucleation site and at the iron channel along the threefold axis. An ordered Cd2+ structure is observed within the iron channel, offering further insight into the route and mechanism of iron transport into the capsid. The loop between helices D and E, which is disordered in many other L-chain structures, is clearly visible in these two structures. The crystals generated from perdeuterated HuLF will be used for neutron diffraction studies.

Amino Acids↗
PubMed1994

Water structure associated with proteins and its role in crystallization.

X-ray or neutron diffraction studies have shown, at the atomic level, that water molecules occupy well determined sites inside or at the surface of biological macromolecules. These water molecules are constitutive of biomolecules and play a crucial role in their structural and functional properties. Upon crystallization some water molecules are either desolvated or involved in crystal packing. The role of water in determining crystal packing has been experimentally confirmed by several X-ray analyses.

Journal Article↗
PubMed1995

On the ab initio solution of the phase problem for macromolecules at very low resolution: the few atoms model method.

A method is proposed for the solution of the phase problem at very low resolution for macromolecules. It generates randomly a very large number of models, each consisting of a few (two to ten) pseudo-atoms. The corresponding amplitudes are used for selecting a subset of 'best' models by choosing those with the highest correlation with experimental values. The phases calculated from these 'best' models are analysed by a clusterization procedure leading to a few possible solutions, from which the correct one can be recognized by simple additional criteria. This method has been successfully applied to the neutron diffraction data of the AspRS-tRNA(Asp) complex at 50 A resolution and to data calculated from a model ribosome crystal at 60 A resolution.

Journal Article↗