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PubMed2005

Structure of strontium hydroxide octahydrate, Sr(OH)2.8H2O, at 20, 100 and 200 K from neutron diffraction.

The crystal structure of Sr(OH)2*8H2O has been determined at 20, 100 and 200 K from neutron diffraction data. The structure consists of double layers of H2O and OH- ions separated by Sr2+ along the c axis. The Sr2+ ions are eight-coordinated by water O atoms in a square antiprism configuration. Each H2O molecule is engaged in three hydrogen bonds. The OH- ions form chains of acceptor and donor bonds along the fourfold axis with O atoms engaged in four bonds with H2O molecules, such that both non-equivalent O atoms have square-pyramidal environments of five H atoms and the overall bonding configurations of distorted octahedra.

Journal Article↗
PubMed1989

Binding of dimethyl sulfoxide to lysozyme in crystals, studied with neutron diffraction.

Crystals of hen egg white lysozyme soaked in 15% (v/v) dimethyl sulfoxide have been studied with single-crystal neutron diffraction to determine the effect of the solvent molecules on the protein configuration. A total of 9423 statistically significant Bragg reflections to a resolution of approximately 1.8 A were used to locate 6 dimethyl sulfoxide molecules, and structure refinements including a model for the flat solvent lead to a final crystallographic agreement factor of 0.130. The mode of location of the dimethyl sulfoxide molecules was compared with that in previous studies employing ethanol. This showed that hydrophobic interactions can be an essential factor in fixing the probe molecules on the protein surface. There was, however, no sign of any significant change in the protein configuration; so although possibly at higher concentrations of dimethyl sulfoxide the protein will unfold, there was no indication of any precursor effect.

Dimethyl Sulfoxide↗
PubMed2002

Direct observation of deuterium migration in crystalline-state reaction by single crystal neutron diffraction IV. "Hula-twist" rotation of a long alkyl radical produced by photoirradiation.

When the crystal of [(R)-1,2-bis(ethoxycarbonyl)ethyl](pyridine)bis(dimethylglyoximato)cobalt(III) was exposed to a xenon lamp, the chiral 1,2-bis(ethoxycarbonyl)ethyl group was partly inverted to the opposite configuration and finally the racemic group was produced with retention of the single crystal form. To make clear the mechanism, the hydrogen atom bonded to the chiral carbon of the chiral group was exchanged with the deuterium atom and the crystal was exposed to the xenon lamp for 3 days. The crystal after irradiation was analyzed by neutron diffraction. About 33% of the (R)-isomers were inverted to the (S) isomers in a crystal. The deuterium atom in the (S)-isomer was bonded to the same chiral carbon atom. This result clearly indicates that the inversion proceeds in the three steps; (i) the Co-C bond was homolytically cleaved by photoirradiation and the 1,2-bis(ethoxycarbonyl)ethyl radical and Co(II) were produced, (ii) the radical rotated by 180 degrees directing the C-D bond to the cobalt atom and the opposite plane of the radical faced to the cobalt atom, and (iii) the radical made a bond with Co(II). Because the peripheral atoms of the long radical occupy approximately the same positions in the process of the radical rotation, the crystal was not decomposed. The above rotation is a good example of hula-twist rotation in the process of photoisomerization of polyenes such as rhodopsin.

Cobalt↗
PubMed2004

Powder neutron diffraction of SrNbO2N at room temperature and 1.5 K.

The structure of strontium niobium dioxygen nitride, SrNbO2N, has been solved by powder neutron diffraction at room temperature and 1.5 K. SrNbO2N crystallizes in the tetragonal space group I4/mcm, with a = 5.7056 (4) and c = 8.1002 (9) A at room temperature, and a = 5.6938 (4) and c = 8.0974 (8) A at 1.5 K. The crystal structure is derived from the cubic perovskite archetype by a slight rotation of the Nb(O,N)6 octahedra with respect to the tetragonal axis. A partially ordered distribution of oxygen and nitrogen on the anionic sites was found.

Journal Article↗
PubMed2001

Hydrogen-bond network in cyclodecaamylose hydrate at 20 K; neutron diffraction study of novel structural motifs band-flip and kink in alpha-(1-->4)-D-glucoside oligosaccharides.

A single-crystal neutron diffraction study of cyclodecaamylose (CA10) was carried out at 20 K. CA10 crystallizes with 27.18 water molecules [(C(6)H(10)O(5))(10).27.18H(2)O] in space group C2 with unit-cell constants a = 29.31 (5), b = 9.976 (10), c = 19.34 (2) A, beta = 121.07 (2) degrees. The asymmetric unit contains a half molecule of CA10 and 13.59 water molecules, the other half being related by a crystallographic twofold rotation axis. All H atoms except two water H atoms could be located from difference neutron-density maps; structure refinement converged at R = 0.635. Two of the five CH(2)-O6 groups and one of the 15 O2, O3 hydroxyl groups of CA10 are twofold orientationally disordered. A total of 13.59 water molecules in the asymmetric unit are distributed over 23 positions; 20 of which are in the CA10 cavity, and the other three occupy intermolecular interstices. Of the 123 symmetry-independent hydrogen bonds, 25 (= 20%) are three-centered and 7 (= 6%) are four-centered. Water molecules and O-H groups of CA10 form an extended network with cooperative O-H...O-H...O-H hydrogen bonds. They are arranged in 11 polygons with three, four, five, six and eight O-H bonds and in homodromic, antidromic and heterodromic arrangements. Nine polygons are located within the cavity and the others are outside.

Journal Article↗
PubMed2004

No evidence for large-scale proton ordering in Antarctic ice from powder neutron diffraction.

We have examined a sample of 3000 year old Antarctic ice, collected at the Kohnen Station, by time-of-flight powder neutron diffraction to test the hypothesis of Fukazawa et al. [e.g., Ann. Glaciol. 31, 247 (2000)] that such ice may be partially proton ordered. Great care was taken to keep our sample below the proposed ordering temperature (237 K) at all times, but we did not observe any evidence of proton ordering.

Journal Article↗
PubMed1991

Structure of the adipate complex [Na2(C6H9O4)2(C6H10O4)].2H2O from neutron diffraction at 220 and 295 K.

The crystal structure of sodium hydrogen adipate-adipic acid (2/1) dihydrate, [Na2(C6H9O4)2(C6H10O4)].2H2O, Mr = 518.4, has been determined from neutron diffraction data collected at 220 and 295 K. Crystals are monoclinic, space group C2/m, with Z = 2. At 295 K, a = 9.378 (2), b = 13.379 (5), c = 10.247 (3) A, beta = 95.93 (3) degrees, V = 1278.8 (7) A3, Dn = 1.346, Dm = 1.348 (1) g cm-3 (in dibromomethane/bromobutane), lambda = 1.1588 (2) A, mu = 2.186 cm-1, F(000) = 176.4 fm, R(F2) = 0.108 for all 1995 nonequivalent reflections with sin theta/lambda less than 0.71 A-1. The crystal structure is similar at 220 K except for reduced nuclear mean-square displacements. Hydrogen adipate subunits (called A) are linked end-to-end in infinite chains by very short O...O (2.44 A) hydrogen bonds where the H nuclei are on centers of symmetry within the experimental error. The Na cation is octahedrally coordinated by O atoms from molecules A and also by non-ionized adipic acid molecules (called B). The B molecules have large mean-square nuclear displacements which are described in terms of anharmonicity and disorder.

Adipates↗
PubMed2004

A new crystal phase of barium nitroprusside trihydrate studied by neutron diffraction at 20 K.

The crystal of barium pentacyanonitrosylferrate trihydrate [barium nitroprusside trihydrate, Ba[Fe(CN)5(NO)] x 3H2O] has been studied by neutron diffraction at 20 K. The study was performed to characterize the structural phase generated by the phase transition undergone by the crystals at 80 K, at which temperature the unit-cell volume doubles. This crystal phase still exists at 20 K. The crystal structure, in space group P1, is completely ordered. The positional changes of the water molecules in the present structure with respect to those of the compound at 105 K are presented.

Journal Article↗
PubMed1984

A neutron diffraction study of the bones of the foot.

The preferential orientation of the apatite crystals in the lower tibia, talus and calcaneus, as determined by neutron diffraction, serves as an indicator of the lines of stress in the foot. The main stress flows down from the tibia to the heel and the ball of the foot and there is noteworthy orientation along the line of the plantar aponeurosis which acts as a tie. Orientation is particularly marked above the point of attachment of the Achilles tendon, where the edge of the calcaneus functions as a beam. The centre of the talus serves as a junctional region for forces and is relatively unoriented.

Calcaneus↗
PubMed1997

The headgroup orientation of dimyristoylphosphatidylinositol-4-phosphate in mixed lipid bilayers: a neutron diffraction study.

The trisodium salt of dimyristoylphosphatidylinositol-4-phosphate (DMPI-4P) has been synthesised specifically deuterated at particular sites in the headgroup. These materials have been used in neutron diffraction experiments, which successfully located the position (depth) of each of these deuterated sites to within +/- 0.5 A in a mixed model membrane (a 1:1 molar mixture of DMPI-4P with dimyristoyl-phosphatidylcholine, DMPC, in the L alpha phase, hydrated to the level of 28 water molecules per lipid molecule). The diffracted intensities were measured at four different D2O/H2O ratios and six orders of diffraction were obtained. These data sets, in conjunction with computer modelling, have been used to determine the orientation of the inositol ring of DMPI-4P, localising each vertical H-H distance to within approximately +/- 0.03 A. The orientation of the inositol ring is found to be one in which the C5 hydroxyl is extended out into the aqueous medium. This is, therefore, the most accessible site for water-borne reagents. This may be significant for the important pathway leading from PI-4P to PI-4,5P2. On the assumption that the P/ODAG bond is orientated parallel to the bilayer normal, these results are consistent with two possible conformations for the portion of the headgroup connecting the diacylglycerol to the inositol ring. Distinction between these two is difficult, but one may be favoured since the other involves close atom-atom contacts.

Computer Simulation↗
PubMed1999

Total neutron diffraction: a route to the correct local structure of disordered LaMo2O5 and its application to the model compound Zn2Mo3O8.

Analysis of Bragg diffraction is the normal route to the structure of crystalline materials. Here we demonstrate the use of total neutron diffraction in determining the local structure in the disordered lanthanum molybdate LaMo(2)O(5). An average structure with space-group symmetry P6(3)/mmc accounts for the Bragg scattering and shows that the compound contains the rare Mo(6)O(18) cluster and a unique type of Mo-Mo bonded sheet. However, this gives an incomplete picture of the structure, since it does not reveal how the sites with fractional occupancy are occupied at a local level. Two models describing possible local structures are constructed by removing symmetry elements present in the average structure. Total correlation functions, T(r), calculated from these structures, with space-group symmetry P6(3)mc and P3;m1, are compared with the experimental T(r) to show the validity of these local structures. The close relationship between the T(r)'s of the component structures gives an insight into why disorder occurs in LaMo(2)O(5). The calculated and experimental T(r)'s for a model compound, Zn(2)Mo(3)O(8), are compared to show the agreement expected from an ordered crystalline material. Remaining discrepancies between our model and the experimental T(r) give an insight into the origin of additional disorder in LaMo(2)O(5).

Journal Article↗
PubMed2005

Powder neutron diffraction of Tl2BeF4 at six temperatures from room temperature to 1.5 K.

The structure of thallium fluoroberyllate, Tl2BeF4, has been analysed by the Rietveld method on neutron diffraction patterns collected at 1.5, 50, 100, 150, 200 and 300 K, with the aim of detecting low-temperature instabilities. Atomic parameters based on the isomorphic beta-K2SO4 crystal in the paraelectric phase were used as the starting model at room temperature; no evidence for any phase transition has been detected at lower temperature. The structure was determined in the orthorhombic space group Pnma. All the atoms (except one F atom) occupy sites with m symmetry. We have compared the structure with those of other compounds of the beta-K2SO4 family, at room temperature, in order to gain insight into their observed instabilities. The irregular coordination of the cations may indicate stereochemical activity of the TlI lone pair but does not indicate a possible structural instability.

Journal Article↗
PubMed2001

Crystal engineering in the gem-alkynol family: the key role of water in the structure of 2,3,5,6-tetrabromo-trans-1,4-diethynyl-cyclohexa-2,5-diene-1,4-diol dihydrate determined by X-ray and neutron diffraction at 150 K.

The structure of the title compound has been determined using low-temperature (150 K) single-crystal X-ray and neutron diffraction data. Crystals adopt the uncommon space group P4(2)/ncm and display a complex set of intermolecular interactions in which the water molecules play the crucial role: the water O-atom [O2(w)] accepts two hydrogen bonds and both water H atoms act as bifurcated donors. A set of O--H...O hydrogen bonds is formed around the 4(2) axis comprising (a) a cyclic tetrameric synthon involving four donor-H from two water molecules and two O(hydroxy) acceptors from two parent molecules, and (b) short discrete O(hydroxy)--H...O2(w) hydrogen bonds which link these tetramers along the c axis. Four Br...Br interactions [3.708 (1) A] form cyclic Br(4) tetramers around the 4 axis and are linked to the O--H...O system via O2(w)--H...Br bonds with H...Br = 2.995 (2) A. Finally, the O--H...O system is further linked to the parent molecules via C identical with C...H...O2(w) bonds of 2.354 (3) A. The supramolecular structure of the title hydrate is compared with that of the non-hydrated parent molecule, which also forms cyclic O--H...O bonded tetrameric synthons, and with its (non-hydrated) tetrachloro analogue, which forms cyclic tetrameric Cl(4) synthons [Madhavi, Desiraju et al. (2000b). Acta Cryst. B56, 1063--1070].

Journal Article↗
PubMed1995

A comparison of neutron diffraction and molecular dynamics structures: hydroxyl group and water molecule orientations in trypsin.

A comparison is presented of experimentally observed hydroxyl and water hydrogen atoms in trypsin determined from neutron density maps with the results of a 140 ps molecular dynamics simulation. Experimental determination of hydrogen and deuterium atom positions in molecules as large as proteins is a unique capability of neutron diffraction. The comparison addresses the degree to which a standard force-field approach can adequately describe the local electrostatic and van der Waals forces that determine the orientations of these hydrogen atoms. The molecular dynamics simulation, based on the all-atom AMBER force-field, allowed free rotation of all hydroxyl groups and movement of water molecules making up a bath surrounding the protein. The neutron densities, derived from 2.1 A 2H2O-H2O difference Fourier maps, provide a database of 27 well-ordered hydroxyl hydrogen atoms. Virtually all of the simulated hydroxyl orientations are within a standard deviation of the experimentally observed positions, including several examples in which both the simulation and the neutron density indicate that a hydroxyl group is shifted from a "standard" rotamer. For the most highly ordered water molecules, the hydrogen distributions calculated from the trajectory were in good agreement with neutron density; simulated water molecules that displayed multiple hydrogen-bonding networks had correspondingly broadened neutron density profiles. This comparison was facilitated by development of a method to construct a pseudo 2 A density map based on the hydrogen atom distributions from the simulation. This method is particularly useful for statically disordered water molecules, in which the average location assigned from a trajectory may represent a site of relatively low occupancy. The degree of disorder of internal water molecules is shown to result primarily from the electrostatic environment surrounding that water molecule as opposed to the cavity size available to the molecule.

Crystallography, X-Ray↗
PubMed2003

Low-temperature single-crystal Raman and neutron-diffraction study of the hydrogenous ammonium copper(II) Tutton salt and the deuterated analogue in the metastable state.

Low-temperature (15 K) single-crystal neutron-diffraction structures and Raman spectra of the salts (NX4)2[Cu(OX2)6](SO4)2, where X=H or D, are reported. This study is concerned with the origin of the structural phase change that is known to occur upon deuteration. Data for the deuterated salt were measured in the metastable state, achieved by application of 500 bar of hydrostatic pressure at approximately 303 K followed by cooling to 281 K and the subsequent release of pressure. This allows for the direct comparison between the hydrogenous and deuterated salts, in the same modification, at ambient pressure and low temperature. The Raman spectra provide no intimation of any significant change in the intermolecular bonding. Furthermore, structural differences are few, the largest being for the long Cu-O bond, which is 2.2834(5) and 2.2802(4) A for the hydrogenous and the deuterated salts, respectively. Calorimetric data for the deuterated salt are also presented, providing an estimate of 0.17(2) kJ/mol for the enthalpy difference between the two structural forms at 295.8(5) K. The structural data suggest that substitution of hydrogen for deuterium gives rise to changes in the hydrogen-bonding interactions that result in a slightly reduced force field about the copper(II) center. The small structural differences suggest different relative stabilities for the hydrogenous and deuterated salts, which may be sufficient to stabilize the hydrogenous salt in the anomalous structural form.

Journal Article↗
PubMed2004

Investigation of structure of liquid 2,2,2 trifluoroethanol: neutron diffraction, molecular dynamics, and ab initio quantum chemical study.

The molecular conformation and intermolecular H bonding in liquid 2,2,2 trifluoroethanol (TFE) have been studied by neutron diffraction with hydrogen/deuterium isotopic substitution at room temperature. For comparison, conformations of molecules and their dimers in the gas phase have also been calculated, based on the density functional theory. Energies, geometry, and vibrational frequencies of dimers were analyzed. Diffraction data analyzed by the "Monte Carlo determination of g(r)" (MCGR) method resulted in a molecular structure in agreement with the findings from gas phase electron diffraction experiments and density functional calculations. The intermolecular structure functions were compared to the same functions obtained from a molecular dynamics simulation. All of the composite radial distribution functions are in good agreement with the simulation results. According to our calculation the hydrogen-bonded aggregation size is smaller in pure liquid TFE than in pure liquid ethanol.

Journal Article↗