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PubMed2001

Ti location in the MFI framework of Ti-Silicalite-1: a neutron powder diffraction study.

The first direct evidence that Ti atoms are not equally distributed in the 12 crystallographically independent T sites of the MFI framework is presented on the basis of neutron diffraction data collected at the HRPD instrument of the ISIS pulsed neutron source. We found strong evidence indicating that T6, T7, and T11 are the most populated sites and weak evidence that Ti may be hosted in T10. Ti occupancy can be excluded for sites T1, T2, T4, T5, T9, and T12. The occupancy of the remaining sites is doubtful. Since defective silicalite has been shown to exhibit the same preferential sites (T6, T7, T11, and T10) for Si vacancies, it may be suggested that the incorporation mechanism of the Ti atoms in the MFI framework occurs via the insertion of titanium in the defective sites. This hypothesis implies that titanium has a mineralizing effect on the MFI framework, and it is supported by independent spectroscopic data on both TS-1 and defective silicalite. The results are discussed in comparison with the known substitution mechanisms in the T-sites of MFI-type structures.

Journal Article↗
PubMed2006

Adsorption structures of water in NaX studied by DRIFT spectroscopy and neutron powder diffraction.

Diffuse reflectance infrared Fourier transform spectroscopic (DRIFTS) measurements (4000-1500 cm(-1)) and the results of neutron powder diffraction have been combined to study the structure of adsorption complexes of water in a NaX zeolite at different water loadings (25, 48, 72, and 120 water molecules per unit cell, respectively). Sharp bands corresponding to non-hydrogen-bonded OH groups of water molecules and broad associate bands due to hydrogen-bonded molecules are observed in the DRIFT spectra. We observe a remarkable downshift of the high-frequency associate band in a narrow temperature interval when the water amount decreases from 120 to 72 molecules per unit cell, which could signify some kind of "phase transition" for the water inside the zeolite cavities. Neutron powder diffraction results show that water molecules are predominantly localized in or near the 12-ring windows. Water molecules with hydrogen-bonded and non-hydrogen-bonded OH groups were found, in agreement with the observation of sharp and broad bands in the DRIFT spectra. We find strong evidence for the formation of cyclic hexamers of water molecules localized in the 12-ring windows, which are further stabilized by hydrogen bonds to framework oxygen atoms.

Adsorption↗
PubMed1997

A high-angle neutron fibre diffraction study of the hydration of deuterated A-DNA.

A high-angle neutron fibre diffraction study of the hydration of A-DNA has been performed using the single-crystal diffractometer D19 at the Institut Laue-Langevin (Grenoble, France). The sample was prepared using deuterated DNA extracted from E. Coli cells cultured on deuterated nutrients. In common with our previous neutron fibre diffraction studies of DNA, this work exploits the ability to isotopically replace H2O around the DNA by D2O. However this study benefitted additionally from the fact that the hydrogen atoms which are covalently bonded to carbon atoms in the DNA sugars and bases were replaced by deuterium so that incoherent scattering and absorption effects were minimised. Successive cycles of Fourier synthesis and Fourier difference synthesis allowed water peaks to be identified and their positional and occupancy parameters to be refined against the observed diffraction data. The results confirm the main hydration features noted in our earlier studies with a clear network of water running along the inside edge of the major groove linking successive OI phosphate oxygen atoms. The central core of water running along the axis of the double helix is very much clearer in this work. Additionally this study shows chains of ordered water lying in the centre of the major groove.

Crystallography↗
PubMed2001

A neutron Laue diffraction study of endothiapepsin: implications for the aspartic proteinase mechanism.

Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing nonhydrolyzable analogues of the scissile peptide bond. However, the positions of protons on the catalytic aspartates and the ligand in these complexes have not been determined with certainty. Thus, our objective was to locate crucial protons at the active site of an inhibitor complex since this will have major implications for a detailed understanding of the mechanism of action. We have demonstrated that high-resolution neutron diffraction data can be collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex has been refined at a resolution of 2.1 A to an R-factor of 23.5% and an R(free) of 27.4%. This work represents the largest protein structure studied to date by neutron crystallography at high resolution. The neutron data demonstrate that 49% of the main chain nitrogens have exchanged their hydrogen atoms with D2O in the mother liquor. The majority of residues resisting exchange are buried within core beta-sheet regions of the molecule. The neutron maps confirm that the protein has a number of buried ionized carboxylate groups which are likely to give the molecule a net negative charge even at very low pH, thereby accounting for its low pI. The functional groups at the catalytic center have clearly undergone H-D exchange despite being buried by the inhibitor occupying the active site cleft. Most importantly, the data provide convincing evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. This has an important bearing on mechanistic proposals for this class of proteinase.

Aspartic Acid↗
PubMed1988

Unified structure theory of icosahedral quasicrystals: Evidence from neutron powder diffraction patterns that AlCrFeMnSi, AlCuLiMg, and TiNiFeSi icosahedral quasicrystals are twins of cubic crystals containing about 820 or 1012 atoms in a primitive unit cube.

A unified structure theory of icosahedral quasicrystals, combining the twinned-cubic-crystal theory and the Penrose-tiling-six-dimensional-projection theory, is described. Values of the primitive-cubic lattice constant for several quasicrystals are evaluated from x-ray and neutron diffraction data. The fact that the low-angle diffraction maxima can be indexed with cubic unit cells provides additional support for the twinned-cubic-crystal theory of icosahedral quasicrystals.

Journal Article↗
PubMed2000

NaDNA-bipyridyl-(ethylenediamine)platinum (II) complex: structure in oriented wet-spun films and fibers.

Complexes of NaDNA with bipyridyl-(ethylenediamine)platinum(II) (abbreviated [(bipy)Pt(en)](2+)) in solid, oriented films, prepared with a wet-spinning method, have been studied using x-ray diffraction, elastic neutron scattering, two-dimensional magic-angle-spinning nuclear magnetic resonance (NMR), infrared (IR) linear dichroism, and IR absorption. All of these experiments indicate that the DNA in this complex is in the B conformation. The neutron diffraction experiments reveal that the rise per residue is 3.31 A, indicating that the [(bipy)Pt(en)](2+) molecular ion causes a small distortion of the B conformation. The neutron data in the direction perpendicular to the helical axis are consistent with a centered orthorhombic unit cell with a=22.65 A and b=32.2 A. The NMR and IR experiments show that the orientation of phosphate groups in the DNA small middle dot[(bipy)Pt(en)](2+) complex is the same as that observed for pure DNA in the B conformation. The IR experiments also show that the [(bipy)Pt(en)](2+) molecular ion stabilizes the B conformation of DNA down to 59% relative humidity, a low water activity. Mechanochemical experiments on wet-spun NaDNA fibers in 68% ethanol with and without [(bipy)Pt(en)](2+) reveal a 9% elongation of the DNA fibers as the complex is formed.

2,2'-Dipyridyl↗
PubMed2002

Stress influence on interface in plasma-sprayed hydroxyapatite coatings on titanium alloy.

During clinical use of hydroxyapatite-coated implants, mechanical stresses are added to pre-existing residual stresses. The magnitude of these stresses affects the coating's performance. In this work we studied, by neutron diffraction and conventional X-ray diffraction methods, the macrostresses induced by a plasma-spraying process in the coating and at the interface. Neutron diffraction is one of the most suitable techniques for studying the strain distribution in a bulk material. X-ray diffraction was used to determine residual stress in the hydroxyapatite coating. Using a neutron diffraction method at the nearest point to the interface, we saw no real difference between the stress observed on coated and that on non-coated samples. With the X-ray diffraction method, it appeared that the stress level was compressive on every sample. The major advantage of the neutron diffraction method is that measurements can be made on a thick coating in a nondestructive way. The disadvantage is the large-gauge volume that we had to use because of the relatively low intensity of the neutron beam. Polishing is necessary for measurements inside the material when using the X-ray method. This destructive method may alter the stress field of the deposit.

Durapatite↗
PubMed2006

Single-crystal X-ray and neutron powder diffraction investigation of the phase transition in tetrachlorobenzene.

The polymorphic phase transition of 1,2,4,5-tetrachlorobenzene (TCB) has been investigated using neutron powder diffraction and single-crystal X-ray diffraction. The diffraction experiments show a reversible phase change that occurs as a function of temperature with no apparent loss of sample quality on transition between the two phases. Neutron powder diffraction gives detailed information on the molecular structural changes and lattice parameters from 2 K to room temperature. The structure of the low-temperature form has been elucidated for the first time using single-crystal X-ray diffraction. Comparison of the alpha and beta structures show that they are both based on the same sheet motif, with the differences between the two being very subtle, except in terms of crystal symmetry. Detailed analysis of the structures revealed the changes required for inter-conversion. A computational polymorph search showed that these two sheet structures are more thermodynamically stable than alternative herringbone-type structures.

Journal Article↗
PubMed2000

Structure of the defect perovskite Ce1/3NbO3: a redetermination by electron and neutron powder diffraction

The crystal structure of the defect perovskite Ce1/3NbO3, cerium niobium oxide, has been re-examined by neutron powder and electron diffraction. The results of a powder neutron Rietveld refinement indicate that the structure is monoclinic: space group P2/m with Z = 4, a = 5.5267 (3), b = 7.8824 (2), c = 5.5245 (3) A, beta = 90.294 (1)degrees, V= 240.67 (2) A3 at 298 K with chi2 = 2.570. Previous reports have described the Ce1/3NbO3 structure in a smaller (V/2) orthorhombic cell based solely upon X-ray powder diffraction data. The presence of weak reflections in the electron diffraction pattern provides conclusive evidence for a monoclinic superstructure of the orthorhombic cell. While these superlattice reflections are barely detectable with X-ray radiation, they are clearly visible in the neutron diffraction experiments. The superlattice reflections are shown to arise from a tilting of the NbO6 octahedra which results in the reduction of symmetry from orthorhombic to monoclinic. It is also found that the Ce3+ and Nb5+ cations are displaced from the centres of their respective polyhedra to accommodate the bond-valence requirements of the crystal structure. It is likely that distortions of this type are present in other Ln1/3NbO3 and Ln1/3TaO3 defect perovskites.

Journal Article↗
PubMed1994

Langevin dynamics of the choline head group in a membrane environment.

Computer simulations of dipalmitoylphosphatidylcholine (DPPC) have been performed using Langevin dynamics and a Marcelja-type mean field. This work has focused on the dynamics of the choline head group to parameterize the empirical constraints against phosphorus-carbon dipolar couplings (Dp-c) as measured by nuclear magnetic resonance (13C-NMR). The results show good agreement with experimental values at constraints equivalent to the choline tilt observed in joint refinement of x-ray diffraction and neutron diffraction scatterings. Quadrupolar splittings for the alpha and beta positions are also calculated and compared with 2H-NMR experiments. The model predicts torsional transition rates around the alpha-beta bonds and for the two C-O-P-O torsions. It also predicts T1 relaxation times for the alpha and beta carbons.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2002

Magnetism and structural chemistry of the n = 1 Ruddlesden-Popper phases La4LiMnO8 and La3SrLiMnO8.

Polycrystalline samples of La4LiMnO8 and La3SrLiMnO8 have been studied by a combination of X-ray diffraction (XRD), neutron diffraction (ND), 6Li MAS NMR, electron microscopy (EM), and magnetometry. Room-temperature XRD and ND measurements suggest that both compounds have the K2NiF4 structure, with a disordered arrangement of Li and Mn over the six-coordinate sites. However, MAS NMR and EM demonstrate the presence of local 1:1 Li:Mn order on these sites, and EM shows that although cation order is well-developed in each xy sheet of corner-sharing octahedra, the sheets are stacked randomly along z. The structures are best described as paracrystalline, and many of the concepts of conventional crystallography are inapplicable. Magnetometry and low-temperature ND experiments show that, despite their paracrystallinity, the two compounds are ordered antiferromagnetically with susceptibility maxima at 26 and 18 K, respectively, and with ordered magnetic moments of 3.61(6) and 2.3(1) muB per Mn cation at 2 K. Anisotropic peak broadening reveals a 2D character in the magnetic behavior of both compounds, and La3SrLiMnO8 is well-modeled as a quadratic layer S = 3/2 Heisenberg antiferromagnet.

Journal Article↗
PubMed2006

Polyanionic hydrides from polar intermetallics AeE2 (Ae = Ca, Sr, Ba; E = Al, Ga, In).

The hydrogenation behavior of the polar intermetallic systems AeE2 (Ae = Ca, Sr, Ba; E = Al, Ga, In) has been investigated systematically and afforded the new hydrides SrGa2H2 and BaGa2H2. The structure of these hydrides was characterized by X-ray powder diffraction and neutron diffraction of the corresponding deuterides. Both compounds are isostructural to previously discovered SrAl2H2 (space group P3m1, Z = 1, SrGa2H2/D2: a = 4.4010(4)/4.3932(8) A, c = 4.7109(4)/4.699(1) A; BaGa2H2/D2: a = 4.5334(6)/4.5286(5) A, c = 4.9069(9)/4.8991(9) A). The three hydrides SrAl2H2, SrGa2H2, and BaGa2H2 decompose at around 300 degrees C at atmospheric pressure. First-principles electronic structure calculations reveal that H is unambiguously part of a two-dimensional polyanion [E2H2]2- in which each E atom is tetrahedrally coordinated by three additional E atoms and H. The compounds AeE2H2 are classified as polyanionic hydrides. The peculiar feature of polyanionic hydrides is the incorporation of H in a polymeric anion where it acts as a terminating ligand. Polyanionic hydrides provide unprecedented arrangements with both E-E and E-H bonds. The hydrogenation of AeE2 to AeE2H2 takes place at low reaction temperatures (around 200 degrees C), which suggests that the polyanion of the polar intermetallics ([E2]2-) is employed as precursor.

Journal Article↗
PubMed1993

High resolution electron microscopic study on the human dentine crystal.

The direct atomic images in single dentine crystals were investigated using high resolution electron microscope. High resolution electron microscopy clarified the unit cell (each side: 0.94 nm) and 6 columnar calcium (Ca) atoms. This (001) plane image of a dentine crystal was similar to enamel hydroxyapatite. The sublattice image of the (011) plane in a dentine crystal has revealed that lattice fringes consist of a linkage of atoms. Furthermore, the present observation made clear that a different focus and a specimen thickness affect sublattice images. These findings suggest that the character of a single crystal plane can be determined contrasting analytical data by X-ray diffraction and neutron diffraction with atomic images in high resolution transmission electron microscopy.

Calcium↗
PubMed2004

Modeling of the nuclear parameters for H atoms in X-ray charge-density studies.

Extensive and precise X-ray diffraction data for xylitol have been used to test different approaches to estimate nuclear parameters for H atoms in charge-density studies. The parameters from a neutron diffraction study of the same compound were taken as a reference. The resulting static charge densities obtained for the different approaches based on a multipole model were subjected to a topological analysis. The comparative analysis led to the following results. The procedure of extending the X-H bond to match bond lengths from neutron diffraction studies provides the best agreement with the neutron positional parameters. An isotropic model for the atomic displacements of H atoms is highly unsatisfactory and leads to significant deviations for the properties of the bond critical points including those that only involve non-H atoms. Anisotropic displacement parameters for H atoms can be derived from the X-ray data that are in agreement with the values from the neutron study, and the resulting charge-density models are in good agreement with the reference model. The anisotropic displacement parameters for H atoms are derived from the X-ray data as a sum of the external (rigid-body) and internal vibrations. The external vibrations are obtained from a TLS analysis of the ADPs of the non-H atoms and the internal vibrations from analysis of neutron diffraction studies of related compounds. The results from the analysis of positional and thermal parameters were combined to devise a 'best anisotropic' model, which was employed for three other systems where X-ray and neutron data were available. The results from the topological analysis of these systems confirm the success of the 'best anisotropic' model in providing parameters for the H atoms that give charge densities in agreement with the reference models based on H-atom parameters derived from neutron diffraction.

Journal Article↗
PubMed1999

Temperature-dependent neutron powder diffraction evidence for splitting of the cationic sites in ferroelectric PbHf0.4Ti0.6O3.

Temperature-dependent neutron powder diffraction experiments (diffractometer 3T2-LLB, Saclay, France, lambda = 1.227 Å) have been performed on the perovskite-like lead hafnate titanate PbHf(0.4)Ti(0.6)O(3). This compound belongs to the solid solution denoted PHT, which derives from the well known ferroelectric PZT series. It exhibits a ferroelectric-to-paraelectric phase transition around 620 K, between the low-temperature tetragonal phase and the high-temperature cubic phase. The tetragonal structure of the ferroelectric phase has been refined at 10 and 300 K using a Rietveld-type method: space group P4mm with Z = 1; a(t) = 3.999 (1), c(t) = 4.120 (1) Å, c/a = 1.030, V = 65.89 Å(3) at 10 K; a(t) = 4.012 (1) and c(t) = 4.100 (1) Å, c/a = 1.022, V = 65.99 Å(3) at 300 K. The cubic structure of the paraelectric phase has also been refined at 720 K: space group Pm3;m, Z = 1, a(c) = 4.046 (1) Å, V = 66.23 Å(3). Cation displacements and oxygen-octahedra elongations have been observed as a function of temperature. Evidence for peculiar behaviour associated with the relative shifts of the Hf and Ti atoms (thought until now to be on the same crystallographic site) was found through an anomaly of the mean-square atomic displacements of the Hf/Ti pseudo-nucleus. The PDF Nos for PbHf(0.4)Ti(0.6)O(3) are 48-49-9 and 48-49-10.

Journal Article↗
PubMed2000

Hydroxo hydrido complexes of iron and cobalt (Sn-Fe-Sn, Sn-Co-Sn): probing agostic Sn...H-M interactions in solution and in the solid state

Bis(toluene)iron 9 reacts with Lappert's stannylene [Sn[CH(SiMe3)2]2] (4) to form the paramagnetic bis-stannylene complex [[(eta6-toluene)Fe-Sn-[CH(SiMe3)2]2]2] (10). Compound 10 reacts with H2O to form the hydroxo hydrido complex [(eta6-C7H8)(mu-OH)(H)-Fe-[Sn[CH(SiMe3)2]2]2] (12) in high yield; its solid-state structure has been elucidated by X-ray and neutron diffraction analysis. In agreement with the 1H NMR results, 12 contains a hydridic ligand whose exact coordination geometry could be determined by neutron diffraction. The 1H and 119Sn NMR analysis of 12 suggested a multicenter Sn/Sn/H/Fe bonding interaction in solution, based on significantly large values of J(Sn,H,Fe) = 640+/-30 Hz and J(119Sn,119Sn) = 4340+/-100 Hz. In solution, complex 12 exists as two diastereomers in a ratio of about 2:1. Neutron diffraction analysis has characterized 12 as a classical metal hydride complex with very little Sn...H interaction and a typical Fe-H single bond (1.575(8) A). This conclusion is based on the fact that the values of the Sn...H contact distances (2.482(9) and 2.499(9) A) are not consistent with strong Fe-H...Sn interactions. This finding is discussed in relation to other compounds containing M-H...Sn units with and without strong three-center interactions. The neutron diffraction analysis of 12 represents the first determination of a Sn-H atomic distance employing this analytical technique. The cobalt analogues [(eta5-Cp)(mu-OH)(H)Co-[Sn[CH(SiMe3)2]2]2] (15) and [(eta5-Cp)(OD)(D)Co-[Sn[CH-(SiMe3)2]2]2] [D2]15, which are isolobal with 12, were prepared by the reaction of [(eta5-Cp)Co-Sn[CH(SiMe3)2]2] (14) with H2O and D2O, respectively. The magnitude of J(Sn,H) (539 Hz) in 15 is in the same range as that found for 12. The molecular structure of 15 has been determined by X-ray diffraction which reveals it to be isostructural with 12. The coordination geometries of the Co(Fe)-Sn1-O-Sn2 arrangements in 12 and 15 are fully planar within experimental error. Compounds 10 and 15 are rare examples of fully characterized complexes obtained as primary products from water activation reactions.

Journal Article↗
PubMed1999

Neutron Laue diffraction studies of coenzyme cob(II)alamin.

Using a recently designed neutron single-crystal diffractometer utilizing a narrow-band Laue concept (LADI), diffraction data were collected from a crystal of the coenzyme cob(II)alamin (B12r), crystallized from a mixture of D2O and perdeuterated acetone. The instrument was placed at the end of a cold neutron guide at the Institute Laue Langevin (ILL, Grenoble, France), and data collection with neutrons of 1.8-8.0 A wavelength to a crystallographic resolution of 1.43 A was complete after about 36 h. This compares favourably with a previous experiment utilizing the same crystal specimen, where more than four weeks were required to collect monochromatic diffraction data to about 1 A resolution. Using the Laue data, the structure was solved by molecular replacement with the known X-ray crystal structure. Difference density maps revealed the atomic positions (including deuterium atoms) of seven ordered solvent water molecules and two (partially disordered) acetone molecules. These density maps were compared with corresponding maps computed with monochromatic neutron-diffraction data collected to 1. 0 A resolution using the same crystal specimen, as well as to maps derived from high-resolution (0.90 A) synchrotron X-ray data. In spite of the better definition of atomic positions in the two high-resolution maps, the 1.43 A LADI maps show considerable power for the determination of the location of hydrogen and deuterium positions.

Coenzymes↗
PubMed2004

Water-DNA interactions as studied by X-ray and neutron fibre diffraction.

X-ray fibre-diffraction studies indicate a high degree of stereochemical specificity in interactions between water and the DNA double helix. Evidence for this comes from data that show that the molecular conformations assumed by DNA in fibres are highly reproducible and that the hydration-driven transitions between these conformations are fully reversible. These conformational transitions are induced by varying the relative humidity of the fibre environment and hence its water content. Further evidence for stereochemical specificity comes from the observed dependence of the conformation assumed on the ionic content of the fibre and the nucleotide sequence of the DNA. For some transitions, information on stereochemical pathways has come from real-time X-ray fibre diffraction using synchrotron radiation; information on the location of water with respect to the double helix for a number of DNA conformations has come from neutron fibre diffraction. This structural information from fibre-diffraction studies of DNA is complemented by information from X-ray single-crystal studies of oligonucleotides. If the biochemical processes involving DNA have evolved to exploit the structural features observed in DNA fibres and oligonucleotide single crystals, the challenges in developing alternatives to a water environment can be expected to be very severe.

DNA↗