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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↗

PubMed2006

On the crystal structure of Cr2N precipitates in high-nitrogen austenitic stainless steel. III. Neutron diffraction study on the ordered Cr2N superstructure.

The ordered structure of Cr(2)N precipitates in high-nitrogen austenitic steel was investigated utilizing high-resolution neutron powder diffractometry (HRPD). On the basis of the Rietveld refinement of neutron diffraction patterns, the ordered Cr2N superstructure was confirmed to be trigonal (space group P31m), with lattice parameters a=4.800 (4) and c=4.472 (5) A, as suggested in previous transmission electron microscopy studies [Lee, Oh, Han, Lee, Kim & Takaki (2005). Acta Cryst. B61, 137-144; Lee, Kim & Takaki (2006). Acta Cryst. B62, 190-196]. The occupancies of the N atoms in four crystallographic sites [1(a), 1(b), 2(d) and 2(c) Wyckoff sites] were determined to be 1.00 (5), 0.0, 0.74 (9) and 0.12 (3), respectively, reflecting a partial disordering of N atoms along the c axis. The position of the metal atom was specified to be x=0.346 (8) and z=0.244 (6), corresponding to a deviation from the ideal position (x=0.333 and z=0.250). This deviation caused the ((1/3 1/3)(0))-type superlattice reflection to appear. A comparison between the ideal and measured crystal structures of Cr2N was performed using a computer simulation of selected-area diffraction patterns.

Journal Article↗

PubMed1975

Neutron diffraction analysis of myoglobin: structure of the carbon monoxide derivative.

The locations of hydrogen and deuterium atoms and water molecules have been investigated in carbon monoxide myoglobin using neutron diffraction, and the results are compared with earlier work on metmyoglobin. Parallel real space refinements on the two molecules show relatively few changes, but do show the carbon monoxide molecule with the iron atom moving into the heme plane.

Carbon Monoxide↗

PubMed1989

Crystal structure of 1-methyluracil from neutron diffraction at 15, 60 and 123 K.

The crystal structure of 1-methylpyrimidine-2,4-dione (1-methyluracil, C5H6N2O2) has been determined at 15, 60 and 123 K from neutron diffraction data. Molecules lie in the eightfold special positions (symmetry m) of space group Ibam, with a = 13.213 (2), b = 13.172 (2), c = 6.163 (1) A at 15 K. Full-matrix least-squares refinements based on 807 (15 K), 805 (60 K) and 815 (123 K) reflections with sin theta/lambda less than 0.69 A-1 converged with R(F2) = 0.023, 0.024 and 0.024 respectively. Bond lengths and angles have e.s.d.'s less than 0.002 A and 0.2 degrees. Detailed analysis of the anisotropic thermal parameters gives estimates of the zero-point internal vibrations for all nuclei and also for molecular rigid-body thermal vibrations at 15, 60 and 123 K. With thermal-vibration corrections there is good agreement in bond lengths and angles at the three temperatures.

Crystallography↗

PubMedDate not supplied

The interplay between X-ray crystallography, neutron diffraction, image reconstruction, organo-metallic chemistry and biochemistry in structural studies of ribosomes.

Crystals of ribosomes, their complexes with components of protein biosynthesis, their natural, mutated and modified subunits, have been subjected to X-ray and neutron crystallographic analyses. Electron microscopy and 3-dimensional image reconstruction, supported by biochemistry, genetic, functional and organo-metallic studies were employed for facilitating phasing of the crystallographic data. For example, a monofunctional multi heavy-atom cluster (undecagold) was designed for covalent and quantitative binding to ribosomes. The modified particles were crystallized isomorphously with the native ones. Their difference-Patterson maps contain indications for the usefulness of these derivatives for subsequent phasing. Models of the ribosome and its large subunit were reconstructed from tilt series of 2-dimensional sheets. The comparison of the various reconstructed images enabled an initial assessment of the reliability of these models and led to tentative assignments of several functional features. These include the presumed sites for binding mRNA and for codon-anticodon interactions, the path taken by the nascent protein chain and the mode for tRNA binding to ribosomes. These assignments assisted in the design of biologically meaningful crystal systems. The reconstructed models are being used to identify structural features in initial density maps derived from X-ray and neutron diffraction data.

Crystallography↗

PubMed2005

Short- and long-range order in the positive electrode material, Li(NiMn)0.5O2: a joint X-ray and neutron diffraction, pair distribution function analysis and NMR study.

The local environments and short-range ordering of LiNi(0.5)Mn(0.5)O(2), a potential Li-ion battery positive electrode material, were investigated by using a combination of X-ray and neutron diffraction and isotopic substitution (NDIS) techniques, (6)Li Magic Angle Spinning (MAS) NMR spectroscopy, and for the first time, X-ray and neutron Pair Distribution Function (PDF) analysis, associated with Reverse Monte Carlo (RMC) calculations. Three samples were studied: (6)Li(NiMn)(0.5)O(2), (7)Li(NiMn)(0.5)O(2), and (7)Li(NiMn)(0.5)O(2) enriched with (62)Ni (denoted as (7)Li(ZERO)Ni(0.5)Mn(0.5)O(2)), so that the resulting scattering length of Ni atoms is null. LiNi(0.5)Mn(0.5)O(2) adopts the LiCoO(2) structure (space group Rm) and comprises separate lithium layers, transition metal layers (Ni, Mn), and oxygen layers. NMR experiments and Rietveld refinements show that there is approximately 10% of Ni/Li site exchange between the Li and transition metal layers. PDF analysis of the neutron data revealed considerable local distortions in the layers that were not captured in the Rietveld refinements performed using the Bragg diffraction data and the LiCoO(2) structure, resulting in different M-O bond lengths of 1.93 and 2.07 Angstroms for Mn-O and Ni/Li-O, respectively. Large clusters of 2400-3456 atoms were built to investigate cation ordering. The RMC method was then used to improve the fit between the calculated model and experimental PDF data. Both NMR and RMC results were consistent with a nonrandom distribution of Ni, Mn, and Li cations in the transition metal layers; both the Ni and Li atoms are, on average, close to more Mn ions than predicted based on a random distribution of these ions in the transition metal layers. Constraints from both experimental methods showed the presence of short-range order in the transition metal layers comprising LiMn(6) and LiMn(5)Ni clusters combined with Ni and Mn contacts resembling those found in the so-called "flower structure" or structures derived from ordered honeycomb arrays.

Journal Article↗

PubMed2004

Neutron diffraction study of [H(4)Co(4)(C(5)Me(4)Et)(4)], a tetrahedral metal cluster complex with four face-bridging hydride ligands.

A single-crystal neutron diffraction analysis of the cluster complex [H(4)Co(4)(C(5)Me(4)Et)(4)] was carried out on the new quasi-Laue diffractometer VIVALDI at the Institut Laue-Langevin. The structure consists of four face-bridging hydrides attached to a tetrahedral cobalt metal core. Average distances and angles in the core of the molecule are as follows: Co-Co = 2.571(8), Co-C = 2.158(6), Co-H = 1.749(7), H.H = 2.366(9) A; Co-H-Co = 94.6(3), H-Co-H = 85.1(3) degrees. The hydride ligands are located off the Co-Co-Co planes by an average distance of 0.923(8) A. It is suggested that the dimensions of the HCo(3) fragments found in this molecule provide reasonable estimates for analogous distances and angles associated with chemisorbed H atoms situated on the 3-fold hollows of a cobalt surface. Crystallographic details: space group P2(1)/a (monoclinic); a = 21.979(2), b = 10.924(1), c = 34.406(2) A; beta = 90.81(1) degrees; Z = 8. Final agreement factor: R(F) = 0.099 for 3779 reflections [I > 2sigma(I)] collected at 20 K.

Journal Article↗

PubMed2001

A study of heat-treatment induced framework contraction in strontium-ETS-4 by powder neutron diffraction and vibrational spectroscopy.

The effects of heat-treatment on the structure of the strontium ion-exchanged titanosilicate ETS-4 have been studied by Rietveld analysis of powder neutron diffraction data and by FT-Raman spectroscopy. Hydrous Sr-ETS-4 (space group Cmmm), upon heat-treatment under inert atmosphere at temperatures between 423 and 573 K, exhibits framework contraction as evinced by the decrease in the unit cell dimensions. The effects of heat-treatment on the dimensions of the transport-controlling eight-membered ring (8MR) are elucidated by Rietveld analysis. It is also found that during heat-treatment: (a) the double three membered rings (D3MRs) in ETS-4 are sites of structural instability, (b) the titania chains running along [010] exhibit a large degree of disorder in the bridging oxygen atoms, and (c) significant relocations of the strontium cations take place, which may affect the separation properties of the heat-treated materials. Raman spectra of heat-treated ETS-4 crystals exhibit strong cation-framework interaction effects. Vibrational modes involving the atoms in the titania chains show progressive frequency shifts and loss of intensity with increasing heat-treatment temperature, in a manner consistent with the crystallographic results. The study indicates the potential for continuously varying the effective pore dimension of ETS-4 by combining heat-treatment with appropriate ion-exchange procedures.

Journal Article↗

PubMed2005

Variable-temperature neutron diffraction studies of the short, strong hydrogen bonds in the crystal structure of pyridine-3,5-dicarboxylic acid.

Pyridine-3,5-dicarboxylic acid has been studied by single-crystal neutron diffraction at 15 and 296 K. Pyridine-3,5-dicarboxylic acid, in which the carboxylic acid protons have been replaced by deuterons, has also been studied at 15, 150 and 296 K. The protonated structure contains a short N...H...O hydrogen bond [N...O 2.523 (2) Angstrom at 15 K]. Temperature-dependent proton migration occurs where the N--H distance in the hydrogen bond changes from 1.213 (4) Angstrom at 15 K to 1.308 (6) Angstrom at 300 K. In the deuterated structure the overall hydrogen-bond length increased [N...O 2.538 (3) Angstrom at 15 K] and the magnitude of the migration increased so that the N--D distance changes from 1.151 (3) Angstrom at 15 K to 1.457 (4) Angstrom at 300 K.

Journal Article↗

PubMed1973

Neutron diffraction structure of melampodin: its role in the reclassification of the germacranolides.

The precise crystal and molecular structure of melampodin, C(21)H(24)O(9), was determined from three-dimensional neutron diffraction data collected by counter techniques and phases by direct statistical methods. Crystals are orthorhombic, P2(1)2(1)2(1), a = 8,990(9), b = 14.352(14), c = 16.294(16) A, V = 2102 A(3), d(calc.) = 1.328 g.cm(-3), Z = 4 molecules per unit cell. The structural model was refined by full matrix least-squares of 2303 observed independent reflections, with all 54 atoms treated anisotropically, to R(F) = 5.0%. Hydrogen bonds link melampodin molecules together in the solid state. The conformation of the cyclodeca-1,5-diene ring is such that one intraannular hydrogen atom interacts strongly with one double bond, but there is little or no transannular interaction between double bonds. Strain in the ten-membered ring and in the trans-fused lactone ring is discussed, as are chemical implications of the unsymmetric epoxide in the epoxyangelic acid side chain. The previously suggested reclassification of germacranolide sesquiterpene lactones into four subgroups is supported, and a new convention for configurational representations of the four subgroups is proposed.

Journal Article↗

PubMed2001

Rapid neutron-diffraction data collection for hydrogen-bonding studies: application of the Laue diffractometer (LADI) to the case study zinc (tris)thiourea sulfate.

The successful application of the newly developed image-plate neutron Laue diffractometer (LADI) at the Institut Laue-Langevin (ILL), Grenoble, France, for rapid hydrogen-bonding characterization is reported. The case study concerns the promising non-linear optical material zinc (tris)thiourea sulfate (ZTS), which contains 30 atoms in the asymmetric unit and crystallizes in the orthorhombic space group, Pca2(1), a = 11.0616 (9), b = 7.7264 (6), c = 15.558 (1) A [T = 100.0 (1) K]. The results from a 12 h data collection from ZTS on LADI are compared with those obtained over 135 h using the monochromatic four-circle diffractometer D9 at the same reactor source with a crystal 13 times larger in volume. Both studies reveal the extensive hydrogen bonding and other close non-bonded contacts within the material. As expected, the results from D9 are more precise than those obtained from LADI; however, the bond geometry determined from the two experiments is the same within the larger estimated standard deviations. Furthermore, the conclusions drawn from the two studies separately regarding the nature of all supramolecular features are identical. This illustrates that LADI is eminently suitable for rapid characterization of hydrogen-bonded structures by neutron diffraction, with the gain in speed compared with traditional instrumentation being several orders of magnitude.

Journal Article↗

PubMed1990

Cross-linkage sites in type I collagen fibrils studied by neutron diffraction.

Cross-links in tendon collagen are essential for the biomechanical strength of healthy tissue. The nature and position of these cross-links has long been a subject for conjecture. We have approached this problem in a non-destructive manner, by studying neutron diffraction from collagen fibrils that have been specifically deuterated by reduction at keto-amine and Schiff base groups with sodium borodeuteride (NaB2H4). The intensities of the first 23 meridional reflections were recorded for both native and reduced tendons. These data were used to calculate the neutron-scattering density profile of the 67 nm (D) repeat of type I collagen fibrils in rat tail tendon. This approach not only succeeds in determining the location of the cross-linkage sites with respect to the fibril structure, as projected onto the fibre axis, but also presents a novel form of the isomorphous derivative solution to the phase problem.

Animals↗

PubMed1995

Neutron diffraction analysis of the solvent accessible volume in cubic insulin crystals.

The average contact distance between protein and solvent surface atoms in cubic insulin crystals has been determined from two sets of 15 A resolution neutron diffraction data. A contact distance between the water hydrogen sites and the protein surface that is significantly shorter than the average protein-water oxygen contact distance implies that many water molecules are oriented with hydrogen atoms pointed towards the protein surface. The shape of the protein/solvent interface is consistent with the protein envelope obtained from atomic co-ordinates.

Animals↗

PubMed1985

A neutron diffraction study on the location of the polyene chain of retinal in bacteriorhodopsin.

We report on the location of the chain part of the retinylidene chromophore in the projected density of bacteriorhodopsin as determined by neutron diffraction from the two-dimensional purple membrane lattice. For this purpose, partially deuterated retinal was synthesized containing 10 deuterons at positions C-8, C-10, C-12, C-14, C-19(3), and C-20(3) of the polyene chain. Two sets of dark-adapted samples were prepared in entirely different ways: (i) Deuterated retinal was incorporated biosynthetically during growth of the bacteria by using the mutant JW5, which is deficient in the synthesis of retinal. (ii) The chromophore was converted to retinal oxime, the resulting colorless apomembrane was regenerated with deuterated retinal, and the residual retinal oxime was removed by washing with bovine serum albumin. Characterization of these samples by x-ray diffraction, absorption, and flash spectroscopy showed that they were identical to native purple membrane samples as judged by these criteria. Fourier difference maps were calculated from the differences in inplane diffraction from the deuterated membranes and from protonated samples that were prepared in exactly the same way. At 8.7 A resolution, both maps show a single major peak at the same position with the center of mass of the labeled part of the chain (C-11) between helices 6 and 3 but closer to helix 6. It appears likely that the COOH-terminal helix G, to which retinal is attached at lysine-216, is either helix 2 or 6.

Apoproteins↗

PubMed2002

Spin densities in a ferromagnetic bimetallic chain compound: polarized neutron diffraction and DFT calculations.

The spin population distribution in the ferromagnetically coupled hetero-bimetallic chain compound [MnNi(NO(2))(4)(en)(2)] (en = 1,2-ethanediamine) has been investigated by means of polarized neutron diffraction experiments, and the results compared with those from theoretical estimates obtained via calculations based on density functional theory on dinuclear molecular models of the chain. The spin distributions obtained from experiment and from theory are consistent and reflect a larger spin delocalization from the Ni atom due to the more covalent character of the Ni-N bonds compared to the Mn-O ones. Also a nearly isotropic spin distribution is observed for the more ionic d(5) Mn(2+) ion and a clearly anisotropic distribution for the d(8) Ni(2+) ion. The use of dinuclear molecular models for the calculation of the exchange coupling constant between Ni and Mn provide upper and lower limits (+17.6 and -4.2 cm(-)(1)) for the experimentally determined value (+1.3 cm(-)(1)), depending on how the missing part of the chain is simulated, but yield essentially the same spin distribution. The Mn(II)-Ni(II) weak ferromagnetic coupling in the chain is interpreted in a spin delocalization mechanism as resulting from the weakness of the overlap between the magnetic orbitals centered on nickel and those centered on manganese which are only weakly delocalized on the ligands.

Journal Article↗