Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Neutron Diffraction”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27Linked to original sources
PubMed2006

Neutron powder diffraction study of D2 sorption in Cu3(1,3,5-benzenetricarboxylate)2.

Rietveld analyses of neutron powder diffraction data of D2 in Cu3(BTC)2, where BTC = 1,3,5-benzenetricarboxylate, reveals the location and progressive filling of six distinct D2 sites within the nanopore structure. Location of the primary site at the coordinatively unsaturated Cu atoms provides direct structural evidence of the potential importance of such metal sites to hydrogen storage. Competitive loading of the other D2 sites proceeds with the pores filling from smallest to largest.

Journal Article↗
PubMed1992

A high angle neutron fibre diffraction study of the hydration of the A conformation of the DNA double helix.

A high angle neutron fibre diffraction study of the distribution of water around the A-form of DNA has been performed using the diffractometer D19 at the Institut Laue-Langevin, Grenoble. These experiments have exploited the ability to replace H2O surrounding the DNA by D2O so that isotopic difference Fourier maps can be computed in which peaks are identified with the distribution of water in the unit cell. All peaks of significant height have been accounted for by four families of water molecules whose positions and occupancies have been determined using least squares refinement. The coordinates of the water peaks making up each family do not deviate significantly from a regular helical arrangement with the same parameters as the DNA. Two of these families are of particular interest. The first consists of water molecules in the major groove linking successive charged phosphate oxygens along the polynucleotide chains. The second is associated with bases in the major groove and forms a central core of density along the helix axis. These two families provide a layer of hydration lining the interior wall of the major groove leaving a central channel to accommodate cations. The relationship between these observations and conformational stability is discussed.

DNA↗
PubMed2006

Observation of hydrogen in deuterated methane hydrate by maximum entropy method with neutron powder diffraction.

The crystal structure of deuterated methane hydrate (structure I, space group: Pm(-)3n) was investigated by neutron powder diffraction at temperatures of 7.7-185 K. The scattering amplitude density distribution was examined by a combination of Rietveld method and maximum entropy method (MEM). The distribution of the D atoms in both D(2)O and CD(4) molecules was clarified from three-dimensional graphic images of the scattering amplitude density. The MEM results showed that there were low-density sites for the D atom of D(2)O in a particular location within the D(2)O cage at low temperatures. The MEM provided more reasonable results because of the decrease in the R factor that is attainable by this method. Accordingly, the low-density sites for the D atom of D(2)O probably exist within the D(2)O cage. This suggests that a spatial disorder of the D atom of D(2)O occurs at these sites and that hydrogen bonds between D(2)O molecules become partially weakened. With regard to the CD(4) molecules, there were high-density sites for the D atom of CD(4), and the density distribution of the C and D atoms was observed separately in the scattering amplitude density image. Consequently, the C-D bonds of CD(4) were not observed clearly because the CD(4) molecules had an orientational disorder. The D atoms of CD(4) were displaced from the line between the C and O atoms, and were located near the face center of the polygon in the cage. Accordingly, the D atoms of CD(4) were not bonded to specific O atoms. This result is consistent with the hydrophobicity of the CD(4) molecule. We also report the difference between the small and the large cages in the density distribution map and the temperature dependence of the scattering amplitude density.

Journal Article↗
PubMed2005

Synthesis, neutron structure, and reactivity of the bis(dihydrogen) complex RuH2(eta(2)-H2)2(PCyp3)2 stabilized by two tricyclopentylphosphines.

Treatment of Ru(eta4-C8H12)(eta6-C8H10) with 3 bar H2 in the presence of 2 equiv of tricyclopentylphosphine (PCyp3) in pentane resulted in the isolation of the new bis(dihydrogen) complex RuH2(eta2-H2)2(PCyp3)2 (2), characterized by NMR and single-crystal X-ray and neutron diffraction. The single-crystal neutron diffraction study is the first carried out for a bis(dihydrogen) complex. The coordination geometry around the metal center is a distorted octahedron defined by the two phosphines in a trans configuration (making an angle of 168.9(1) degrees ), two cis dihydrogen ligands, and two hydrides trans to them, defining the equatorial plane. The H-H bond distances (0.825(8) and 0.835(8) A) are characteristic of two "unstretched" dihydrogen ligands. H/D exchange between the Ru-H and the C-D bonds of deuterated benzene is observed within 1 h, leading to the formation of various isotopomers RuHxD6-x(PCyp3)2 (with x = 0-6). 2 is a catalyst precursor for ethylene coupling (20 bar, 293 K) to a functionalized arene (Murai reaction). We found a 90% conversion of acetophenone to 2-ethylacetophenone within 35 min, whereas 10 h was needed in the same conditions using the analogous tricyclohexylphosphine complex, RuH2(eta2-H2)2(PCy3)2, the best catalyst precursor, at room temperature, prior to this work.

Journal Article↗
PubMed1988

Thermal vibrations and electrostatic properties of parabanic acid at 123 and 298 K.

The crystal structure of parabanic acid (1H,3H-imidazoletrione, C3H2N2O3, Mr = 114.1) at 123 K [monoclinic, P2(1)/n, Z = 4, a = 10.704 (2), b = 8.187 (2), c = 4.969 (1) A, beta = 92.32 (1)o] has been determined by neutron and X-ray diffraction. Neutron reflections [1658, (sin theta)/lambda less than or equal to 0.78 A-1, lambda = 1.0470 (1) A, mu = 0.75 cm-1] in full-matrix least-squares refinement (wR = 0.055) gave nuclear parameters with bond lengths having estimated standard deviations (e.s.d.'s) of 0.001 A. X-ray reflections [3150 with magnitude of F magnitude of greater than or equal to 3 sigma and (sin theta)/lambda less than or equal to 1.3 A-1, Mo Ka, lambda = 0.7093 (1) A, mu = 1.708 cm-1] were used in full-matrix least-squares refinement (R = 0.022) assuming Stewart's rigid pseudoatom model, so as to determine the charge-density distribution. Sharp features near the O nuclei in the residual electron density map noted by Craven & McMullan (CM) [Acta Cryst. (1979), B35, 934-945] in their 298 K study were absent at 123 K. New refinements using CM's 298 K data give significant third-order thermal parameters for O atoms due to anharmonic molecular stretching, with good agreement between probability density functions, (p.d.f.'s) from X-ray and neutron diffraction. When deconvoluted from the thermal vibrations in the crystal, deformation charge densities derived at 298 and 123 K are in satisfactory agreement and conform closely to the 2 mm symmetry of the isolated molecule. The molecular dipole moment is 2.3 (3) D [7.7 (10) x 10(-30) C m]. A map of molecular electrostatic potential indicates that the carbonyl O atoms in parabanic acid are weakly electronegative. This is confirmed by calculation of the electrostatic energy of interaction for the two distinct H-bonded pairs of molecules isolated from the crystal. Energy values are weakly attractive [-7 (3) and 5 (2) kJ mol-1]. Similar calculations are less reliable for pairs of molecules forming intermolecular C....O distances as short as 2.75 A. However, depending on the model, energy values are repulsive or negligibly small. Thus the high stability of parabanic acid crystals (m.p. 516 K with decomposition) cannot be explained.

Chemical Phenomena↗
PubMed1987

Evidence from x-ray and neutron powder diffraction patterns that the so-called icosahedral and decagonal quasicrystals of MnAl(6) and other alloys are twinned cubic crystals.

It is shown that the x-ray powder diffraction patterns of rapidly quenched MnAl(6) and Mg(32)(Al,Zn)(49) and the neutron powder diffraction pattern of MnAl(6) are compatible with the proposed 820-atom primitive cubic structure [Pauling, L. (1987) Phys. Rev. Lett. 58, 365-368]. The values found for the edge of the unit cube are 23.365 A (x-ray) and 23.416 A (neutron) for MnAl(6) and 24.313 A (x-ray) for Mg(32)(Al,Zn)(49).

Journal Article↗
PubMed2000

Neutron powder diffraction study of orthorhombic and monoclinic defective silicalite

The crystal structure of silicalite (SiO2) with a substantial amount of structural hydroxyl groups [Si(1-x)O(2-4x)(OH)4x, with 0.08<x<0.10] has been refined from neutron powder diffraction data measured using the HRPD instrument at the ISIS pulsed neutron source. Powder data were collected on the as-synthesized orthorhombic sample at 298 K, and on the deuterated monoclinic sample at 100 K. Preferential location of Si-atom vacancies was found on four out of 12 independent T sites in the orthorhombic silicalite [Si(6), Si(7), Si(10) and Si(11)], although the H atoms of the substituting hydroxyl groups could not be located because of the low statistical site occupancy on multiple sites. No significant population of D atoms or of Si vacancies was found in the tetrahedral sites of the monoclinic sample. The detected long-range order of adjacent Si atoms in defective orthorhombic [MFI] structures is compatible with a mechanism of Si vacancy clustering and with the model of hydroxyl nests assumed in the literature on the basis of IR spectroscopic evidence. Crystal data: orthorhombic, Pnma, Z = 8, a = 20.0511 (1), b = 19.8757 (1), c = 13.36823 (9) A, V = 5327.62 (5) A3, Dx = 1.798 g cm(-3), Mr = 721.01; monoclinic, P2(1)/n, Z = 4, a = 19.8352 (2), b = 20.0903 (2), c = 13.3588 (1) A, beta = 90.892 (1), V = 5322.78 (6) A3, Dx = 1.799 g cm(-3), Mr = 1442.02.

Journal Article↗
PubMedDate not supplied

Mcg in 2030: new techniques for atomic position determination of immune complexes.

The lambda-type light chain dimer from a patient (Mcg) with multiple myeloma and amyloidosis was a pioneer protein for determining the three-dimensional structures of immunoglobulins, understanding the effects of ligand binding, and exploring the use of combinatorial methods to identify novel peptides complementary to protein active sites. Despite 30 years of intense study, there are still unanswered questions about the structure of the Mcg dimer, especially with respect to positions of hydrogen atoms and solvent molecules. In the present report, we describe two techniques that will help define the roles of solvent in ligand interactions and complex formation with this immunoglobulin fragment: (1) introduction of helium as a cryogenic agent during X-ray data collection; and (2) addition of neutron diffraction analyses. These techniques should provide improved resolution, and a more accurate structure of the Mcg dimer. Resolution enhancements of 0.5 A have been achieved in preliminary experiments with cryogenic helium, as compared with the best X-ray diffraction data obtained previously. In the near future, neutron diffraction studies should produce the first hydrogen structure for the Mcg dimer and help elucidate the ligand preferences and amyloidogenic properties of this eminently useful protein.

Amyloidosis↗
PubMed2002

Squalane is in the midplane of the lipid bilayer: implications for its function as a proton permeability barrier.

A recently proposed model for proton leakage across biological membranes [Prog. Lipid Res. 40 (2001) 299] suggested that hydrocarbons specifically in the center of the lipid bilayer inhibit proton leaks. Since cellular membranes maintain a proton electrochemical gradient as a principal energy transducer, proton leakage unproductively consumes cellular energy. Hydrocarbons in the bilayer are widespread in membranes that sustain such gradients. The alkaliphiles are unique in that they contain up to 40 mol% isoprenes in their membranes including 10-11 mol% squalene [J. Bacteriol. 168 (1986) 334]. Squalene is a polyisoprene hydrocarbon without polar groups. Localizing hydrocarbons in lipid bilayers has not been trivial. A myriad of physical methods including fluorescence spectroscopy, electron-spin resonance, nuclear magnetic resonance as well as X-ray and neutron diffraction have been used to explore this question with various degrees of success and often contradictory results. Seeking unambiguous evidence for the localization of squalene in membranes or lipid bilayers, we employed neutron diffraction. We incorporated 10 mol% perdeuterated or protonated squalane, an isosteric analogue of squalene, into stacked bilayers of dioleoyl phosphatidyl choline (DOPC) doped with dioleoyl phosphatidyl glycerol (DOPG) to simulate the negative charges found on natural membranes. The neutron diffraction data clearly show that the squalane lies predominantly in the bilayer center, parallel to the plane of the membrane.

Animals↗
PubMed2003

Neutron powder diffraction studies of silicon-substituted hydroxyapatite.

The incorporation of a small amount of silicon in the hydroxyapatite (HAp) lattice is known to improve the bioactivity of the material. The effect of silicon substitution was studied by comparing samples of pure and 0.4wt% silicon-substituted HAp prepared by an aqueous precipitation method. High-resolution neutron powder diffraction and Rietveld refinement methods were used to investigate the effect of silicon substitution on the crystal structure parameters of the HAp lattice from room temperature down to 20K. Small structural changes in the lattice constants, interatomic distances, site occupancies and distortion of the phosphate tetrahedron were found. Modifications of the Fourier transform infrared spectra as well as appearance of new modes were observed in the silicon-substituted sample. Heat treatment and silicon substitution also affected the morphology and crystallinity of this bioapatite.

Biocompatible Materials↗
PubMed2006

Structure and thermoelectric characterization of Ba8Al14Si31.

A molten Al flux method was used to grow single crystals of the type I clathrate compound Ba8Al14Si31. Single-crystal neutron diffraction data for Ba8Al14Si31 were collected at room temperature using the SCD instrument at the Intense Pulsed Neutron Source, Argonne National Laboratory. Single-crystal neutron diffraction of Ba8Al14Si31 confirms that the Al partially occupies all of the framework sites (R1 = 0.0435, wR2 = 0.0687). Stoichiometry was determined by electron microprobe analysis, density measurements, and neutron diffraction analysis. Solid-state (27)Al NMR provides additional evidence for site preferences within the framework. This phase is best described as a framework-deficient solid solution Ba8Al14Si31, with the general formula, Ba(8)Al(x)Si(42-3/4x)[](4-1/4x) ([] indicates lattice defects). DSC measurements and powder X-ray diffraction data indicate that this is a congruently melting phase at 1416 K. Temperature-dependent resistivity reveals metallic behavior. The negative Seebeck coefficient indicates transport processes dominated by electrons as carriers.

Journal Article↗
PubMed1999

Structures of Bi14WO24 and Bi14MoO24 from neutron powder diffraction data.

The (isomorphous) structures of Bi(14)WO(24), tetradecabismuth tungsten tetracosaoxide, and Bi(14)MoO(24), tetradecabismuth molybdenum tetracosaoxide, have been solved and refined using neutron powder diffraction data in the space group I4/m. The metal-atom array is fully ordered in terms of composition, and in terms of atomic positions deviates only slightly from a fluorite-type delta-Bi(2)O(3)-related parent structure. Three independent O-atom sites (accounting for 70 out of 78 O atoms in the unit cell) are also very close to fluorite-type parent positions. The remaining two O-atom sites, which coordinate W, exhibit partial occupancies and displacive disorder, neither of which could be better modelled by lowering of symmetry. The W site is coordinated by four O atoms in highly distorted tetrahedral coordination, the tetrahedron necessarily being orientationally disordered on that site. Nonetheless, the structure appears to be chemically reasonable.

Journal Article↗
PubMed2005

Search for memory effects in methane hydrate: structure of water before hydrate formation and after hydrate decomposition.

Neutron diffraction with HD isotope substitution has been used to study the formation and decomposition of the methane clathrate hydrate. Using this atomistic technique coupled with simultaneous gas consumption measurements, we have successfully tracked the formation of the sI methane hydrate from a water/gas mixture and then the subsequent decomposition of the hydrate from initiation to completion. These studies demonstrate that the application of neutron diffraction with simultaneous gas consumption measurements provides a powerful method for studying the clathrate hydrate crystal growth and decomposition. We have also used neutron diffraction to examine the water structure before the hydrate growth and after the hydrate decomposition. From the neutron-scattering curves and the empirical potential structure refinement analysis of the data, we find that there is no significant difference between the structure of water before the hydrate formation and the structure of water after the hydrate decomposition. Nor is there any significant change to the methane hydration shell. These results are discussed in the context of widely held views on the existence of memory effects after the hydrate decomposition.

Chemistry, Physical↗
PubMed1989

Neutron fibre diffraction study of DNA hydration.

Interactions with water are crucial to the conformation assumed by the DNA double helix. The location of water around the D conformation has been investigated in a neutron fibre diffraction study which shows that water is ordered in the minor groove of the DNA. The D conformation is important since its occurrence is limited to specific DNA base pair sequences which have been identified as functionally significant. This study is of particular interest because the D conformation has not been reported in single crystal studies of oligonucleotides.

DNA↗
PubMed2005

Neutron powder diffraction studies of dimethyl sulfoxide.

The crystal structure of perdeuterodimethyl sulfoxide, (CD3)2SO, has been refined at 2 and 100 K, and characterized as a function of temperature up to 275 K against high-resolution neutron powder diffraction data. The structure determined previously by Thomas, Shoemaker & Eriks [Acta Cryst. (1966), 21, 12-20] (T=278 K) is shown to remain down to 2 K. At 2 K, the S-O bond distance is 1.495 (2) A. The fact that the molecule is distorted from ideal Cs point symmetry may be explained by the short D...O contacts of the respective methyl groups.

Journal Article↗
PubMed2007

Neutron powder diffraction with (nat)Sm: crystal structures and magnetism of a binary samarium deuteride and a ternary samarium magnesium deuteride.

Binary SmH(3) (trigonal, a=656.7(3), c=680.1(3) pm, P$\bar 3$c1, Z=6), ternary SmMg2H7 (tetragonal, a=626.47(6), c=937.2(2) pm, P4(1)2(1)2, Z=4) and the corresponding deuterides SmD3 (a=653.9(1)m, c=676.7(2) pm) and SmMg2D7 (a=624.10(1), c=934.81(2) pm) have been prepared by hydrogenation (deuteration) of elemental samarium and the Laves phase SmMg2, respectively, and investigated by X-ray and neutron powder diffraction and SQUID and vibration magnetometry. The problem of the enormous neutron absorption of the natural isotopic mixture (natSm) is circumvented by carefully choosing the neutron wavelength (approximately 50 pm) and the use of double-walled cylindrical sample holders and a high-intensity neutron diffractometer (D4c at ILL). SmD3 crystallises with a tysonite-type structure and has three independently ordered deuterium atom sites with trigonal-planar, trigonal-pyramidal and tetrahedral metal environments and Sm--D bond lengths in the range 220(1)-258(1) pm (average: 235 pm). SmMg2D7 is a new deuteride that crystallises with an LaMg2D7-type structure. It displays four fully occupied deuterium sites having triangular and tetrahedral metal environments and Sm--D bond lengths in the range 227.6(5)-246.8(8) pm (average: 239 pm). These are the first samarium-deuterium bond lengths to be reported. Both deuterides are paramagnetic down to 2 K (SmD3: mueff=0.63(1) muB, thetap approximately -4 K; SmMg2D7: mueff=0.57(2) muB, thetap approximately -4 K). Their crystal structures and chemical and physical properties suggest mainly ionic bonding according to the limiting ionic formulae Sm3+(H-)3 and Sm3+(Mg2+)2(H-)7.

Journal Article↗
PubMed2006

Structures of the cation-deficient perovskite Nd(0.7)Ti(0.9)Al(0.1)O3 from high-resolution neutron powder diffraction in combination with group-theoretical analysis.

The crystal structures of Nd(0.7)Ti(0.9)Al(0.1)O3, taken to represent the ideal Nd(2/3)TiO3, have been elucidated from 4 to 1273 K using high-resolution neutron powder diffraction in combination with group-theoretical analysis. The room-temperature structure is monoclinic in C2/m, on a cell with a = 7.6764 (1), b = 7.6430 (1), c = 7.7114 (1) A, beta = 90.042 (2) degrees . Pertinent features are the layered ordering of the A-site Nd cations/vacancies along the z axis and out-of-phase tilting of the (Ti/Al)O6 octahedra around both the x and z axes. From about 750 to 1273 K, the octahedra are tilted around just one axis (x axis) perpendicular to the direction of the cation ordering, giving rise to an orthorhombic structure with space-group symmetry Cmmm.

Journal Article↗
PubMed2005

Neutron powder diffraction study of Pb(HfxTi1-x)O3 ceramics (0.10<or=x<or=0.50).

The crystal symmetries of lead hafnate titanate (Pb(HfxTi1-x)O3, PHT) powders with 0.10<or=x<or=0.50 were investigated by high-resolution neutron powder diffraction. Samples with x<or=0.40 were tetragonal (space group P4 mm), while the sample with x=0.50 contained both monoclinic Cm and rhombohedral (modeled using the R3c space group) phases. The role of the B cations (Hf and Ti) and the oxygen octahedra network, in addition to the displacement of Pb ions from their ideal sites, in promoting the phase transformation between the P4 mm and Cm phases was considered. Two types of structural disorder were identified. Diffuse scattering between Bragg reflection peaks was assigned to Pb ion displacement. A second type of structural disorder, revealed by the weak intensities of observed pseudo-cubic 00l reflections with l even and as 00l reflection peak widths significantly broader than the l00 reflection peaks, was observed. This behavior was attributed to disorder in the arrangement of the O-B-O rows parallel to the c axis. For small values of x, this shift was predominantly along the c axis, whereas shifts perpendicular to the c axis increased with increasing x. These features were modeled using an hkl-dependent line-broadening model. The origin of the hkl-dependent line broadening was assigned to the microstrain accompanying a spatial-composition variation. Structural models were tested by computing valence sums and spontaneous polarization values.

Journal Article↗