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Neutron scattering combined with selective isotopic labeling and contrast matching is useful for obtaining in situ structural information about a selected particle, or particles, in a macromolecular complex. The observed intensities, however, may be distorted by inter-complex interference and by scattering-length-density fluctuations of the (otherwise) contrast-matched portions. Methods have been proposed to cancel out such distortions (Hoppe's method, the Statistical Labeling Method, and the Triple Isotopic Substitution Method). With these methods as well as related unmixed-sample methods, structural information about the selected particle(s) can be obtained without these distortions. We have generalized these methods so that, in addition to globular particles in solution, they can be applied to in situ structures of systems having underlying symmetry and/or net orientation as well. The information obtainable from such experiments is discussed.
X-ray diffraction, neutron diffraction and differential scanning calorimetry were used to investigate phase transitions in the ternary system phospholipid/dimethyl sulfoxide (DMSO)/water under cooling for three homologous phospholipids: dimyristoylphosphatidylcholine (DMPC), dipalmitoylphosphatidylcholine (DPPC), and distearoylphosphatidylcholine (DSPC). Below the temperature of ice formation from -40 to -113 degrees C, a new lamellar phase of DPPC and DSPC was found at and above a DMSO molar fraction of X(DMSO) = 0.05. Below X(DMSO) = 0.05 only a single dehydrated Lc-phase exists after ice formation. The new phase has an increased membrane repeat distance and coexists with a dehydrated Lc-phase. DPPC with a DMSO molar fraction of X(DMSO) = 0.07 shows a membrane repeat distance of the new phase of d = 6.61 +/- 0.03 nm. The value of d increases at the increase of X(DMSO). The new phase was not observed in the ternary system with DMPC. No correlation between the new phase and the glass transition of bound water in the intermembrane space was detected. The new phase was detected only in the systems with excess of water. The creation of the new phase demonstrates the specific DMSO interaction with hydrocarbon chains.
Crystallization and preliminary neutron-diffraction measurements of wild-type variant Val58-->Ile of the Escherichia coli trp repressor are reported. A vapor-diffusion chamber suitable for initial protein-solution Volumes in the range 0.2-0.5 ml was used to grow cube-shaped crystals with edge dimensions in the range 0.8-1.4 mm. Neutron Laue measurements to a nominal resolution of 2.1 A were recorded from a D(2)O-exchanged crystal using the LADI instrument at ILL. These results demonstrate that it will be possible for the first time to obtain a full-atom neutron structural model of a DNA-binding protein plus its associated solvent. Direct observation of hydrogen bonding between protein and solvent should enhance understanding of the role of solvent in protein-DNA recognition.
High-resolution neutron powder diffraction has been used in order to characterize the order-disorder transition in monoclinic cyclo-octasulphur. Rapid data collection and the novel use of geometrically constrained refinements has enabled a direct and precise determination of the order parameter, based on molecular site occupancies, to be made. The transition is critical and continuous; with a transition temperature, Tc=198.4 (3) K, and a critical exponent, beta=0.28 (3), which is indicative of three-dimensional ordering. Difficulties encountered as a consequence of the low thermal conductivity of the sample are discussed.
The structure of the insulating manganites Nd(1-x)Ca(x)MnO(3) (0.3 </= x </= 0.5) has been studied against temperature using electron diffraction and neutron diffraction. At room temperature, the three compounds with x = 0.3, 0.4 and 0.5 exhibit the orthorhombic GdFeO(3)-type structure (a approximately 2(1/2)a(p), b approximately 2a(p), c approximately 2(1/2)a(p)). Below the charge-ordering temperature of approximately 250 K, a doubling of the lattice is observed along the a axis which could be interpreted as an ordering of the d(z(2)) Mn(3+) orbitals. The low-temperature polymorph has ortho-rhombic symmetry for x = 0.5 and monoclinic symmetry for x = 0.4 and 0.3. The low-temperature structure of the x = 0.4 sample was refined using neutron diffraction data. The HREM study at room temperature confirms the average GdFeO(3)-type structure and indicates the existence of defective areas with a lower symmetry.
Single-crystal neutron diffraction, inelastic neutron scattering, and density functional calculations provide experimental and theoretical analyses of the nature of the osmium-bound, "elongated" dihydrogen ligands in [Cp*OsH(4)(L)][BF(4)] complexes (L = PPh(3), AsPh(3), or PCy(3)). The PPh(3) and AsPh(3) complexes clearly contain one dihydrogen ligand and two terminal hydrides; the H(2) ligand is transoid to the Lewis base, and the H-H vector connecting the central two hydrogen atoms lies parallel to the Ct-Os-L plane (Ct = centroid of Cp* ring). In contrast, in the PCy(3) complex the H-H vector is perpendicular to the Ct-Os-L plane. Not only the orientation of the central two hydrogen atoms but also the H-H bond length between them depends significantly on the nature of L: the H...H distance determined from neutron diffraction is 1.01(1) and 1.08(1) A for L = PPh(3) and AsPh(3), respectively, but 1.31(3) A for L = PCy(3). Density functional calculations show that there is a delicate balance of electronic and steric influences created by the L ligand that change the molecular geometry (steric interactions between the Cp* and L groups most importantly change the Ct-Os-L angle), changing the relative energy of the Os 5d orbitals, which in turn govern the H-H distance, preferred H-H orientation, and rotational dynamics of the elongated dihydrogen ligand. The geometry of the dihydrogen ligand is further tuned by interactions with the BF(4)(-) counterion. The rotational barrier of the bound H(2) ligand in [Cp*OsH(4)(PPh(3))](+), determined experimentally (3.1 kcal mol(-)(1)) from inelastic neutron scattering experiments, is in reasonable agreement with the B3LYP calculated H(2) rotational barrier (2.5 kcal mol(-)(1)).
The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institut Laue-Langevin. Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformational transitions in the DNA double-helix.
The crystal and molecular structure together with the hydrogen-bonding system in cellulose Ibeta has been determined using synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from tunicin. These samples diffracted both synchrotron X-rays and neutrons to better than 1A resolution (>300 unique reflections; P2(1)). The X-ray data were used to determine the C and O atom positions. The resulting structure consisted of two parallel chains having slightly different conformations and organized in sheets packed in a "parallel-up" fashion, with all hydroxymethyl groups adopting the tg conformation. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The hydrogen atoms involved in the intramolecular O3...O5 hydrogen bonds have well-defined positions, whereas those corresponding to O2 and O6 covered a wider volume, indicative of multiple geometry with partial occupation. The observation of this disorder substantiates a recent infrared analysis and indicates that, despite their high crystallinity, crystals of cellulose Ibeta have an inherent disorganization of the intermolecular H-bond network that maintains the cellulose chains in sheets.
Until now, no aspartic proteinase has been subjected to a successful neutron diffraction analysis, owing to the limited size of the crystals. However, the recent development of the neutron Laue technique at ILL and EMBL (Grenoble) has allowed the collection of data to 2.2 A on a complex of endothiapepsin with a transition-state analogue. The objective is to define the positions of the protons at the active site by refinement using the neutron data. In line with work on serine proteinases, where neutron diffraction has provided some of the most definitive data on the catalytic mechanism, it is expected that this work will have a major significance for studies of the aspartic proteinase enzymes.
The crystal and molecular structure, together with the hydrogen-bonding system in cellulose I(alpha), has been determined using atomic-resolution synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from the cell wall of the freshwater alga Glaucocystis nostochinearum. The X-ray data were used to determine the C and O atom positions. The resulting structure is a one-chain triclinic unit cell with all glucosyl linkages and hydroxymethyl groups (tg) identical. However, adjacent sugar rings alternate in conformation giving the chain a cellobiosyl repeat. The chains organize in sheets packed in a "parallel-up" fashion. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The differences between the structure and hydrogen-bonding reported here for cellulose I(alpha) and previously for cellulose I(beta) provide potential explanations for the solid-state conversion of I(alpha) --> I(beta) and for the occurrence of two crystal phases in naturally occurring cellulose.
The hydrothermal crystallization of barium titanate, BaTiO3, has been studied in situ by time-resolved powder neutron diffraction methods using the recently developed Oxford/ISIS hydrothermal cell. This technique has allowed the formation of the ferroelectric ceramic to be followed in a noninvasive manner in real time and under genuine reaction conditions. In a first set of experiments, Ba(OD)2-8D2O was reacted with two different titanium sources, either crystalline TiO2 (anatase) or amorphous TiO2-H2O in D2O, at 100-140 degrees C and the reaction studied using the POLARIS time-of-flight neutron powder diffractometer, at the ISIS Facility. In a second series of experiments, the reaction between barium chloride and crystalline TiO2 (anatase) in NaOD/D2O was studied at temperatures between 100 and 200 degrees C and at different deuterioxide concentrations using the constant-wavelength D20 neutron powder diffractometer at the Institut Laue Langevin. Quantitative growth and decay curves were determined from analysis of the integrated intensities of Bragg reflections of starting materials and product phases. In both sets of experiments the rapid dissolution of the barium source was observed, followed by dissolution of the titanium source before the onset of crystallization of barium titanate. Using a nucleation-growth model we are able to simulate the growth curve of barium titanate at three temperatures. Our results indicate the predominance of a homogeneous dissolution-precipitation mechanism for the hydrothermal formation of barium titanate, rather than other possible mechanisms that have been discussed in the literature. Analysis of the line widths of the Bragg reflections in the neutron diffraction data indicates that the particle size of the BaTiO3 product phase prepared from the amorphous TiO2-H2O is smaller than that prepared from crystalline TiO2 (anatase).
A new approach, using neutron diffraction and the hydrogen exchange (H/D) technique, has been used to study the extent and nature of the inherent conformational fluctuations in the protein, trypsin. The observed pattern of exchange was used to investigate systematic relationships between exchangeable sites and structural and chemical properties of the molecule. Results of this analysis indicate that hydrogen-bonding structure is the dominant factor governing rates of exchange. The model of conformational mobility which best explains the experimental findings involves a localized disruption of the secondary structure within different regions of the protein molecule, each limited in extent to the breaking of a small number of hydrogen bonds.
Neutron powder diffraction data, collected over the temperature range 10-770 K, have been analysed in order to make a detailed characterization of the sequence of phase transitions occurring in the Hf-rich ferroelectric PbHf(0.8)Ti(0.2)O3, titanium hafnium lead oxide. Over the whole temperature range this compound undergoes two phase transitions, which involve cationic displacements and octahedral deformations (tilt and/or distortion) leading to strongly distorted perovskite-type structures. The first transition appears around 415 K between two ferroelectric rhombohedral phases: a low-temperature nonzero-tilt phase F(RL) (space group R3c) and an intermediate zero-tilt phase FRH (space group R3m). The second one, detected around 520 K, is associated with a ferroelectric to-paraelectric transition between the FRH phase and the Pc cubic phase (space group Pm3m). From high-resolution neutron powder diffraction data (diffractometer 3T2-LLB, Saclay, France, lambda = 1.2251 A), the crystallographic structure of the three successive phases has been accurately determined at the following temperatures: T = 10 K (FRL): space group R3c, Z = 6, a(hex) = 5.7827 (1), c(hex) = 14.2702 (4) A, V(hex) = 413.26 (2) A3; T = 150 K (F(RL)): space group R3c, Z = 6, a(hex) = 5.7871 (1), C(hex) = 14.2735 (4) A, V(hex) = 413.98 (3) A3; T = 290 K (FRL): space group R3c, Z = 6, a(hex) = 5.7943 (1), C(hex) = 14.2742 (5) A, V(hex) = 415.04 (3) A3; T = 440 K (F(RH)): space group R3c, Z = 6, a(hex) = 5.8025 (1), c(hex) = 14.2648 (4) A, V(hex) = 415.94 (3) A3; T = 520 K (Pc): space group Pm3m, Z = 1, a(cub) = 4.1072 (2) A, V(cub) = 69.29 (1) A3. In addition, a neutron powder thermodiffractometry experiment, performed between 290 and 770 K (diffractometer D1B-ILL, Grenoble, France, lambda = 2.533 A), has been used to study in situ the temperature-induced phase transitions. From sequential Rietveld refinements, the temperature dependence of the cation displacements and the rotation and/or distortion of oxygen octahedra was derived.
High-resolution fibre neutron diffraction data were recorded from cellulose samples on a D19 diffractometer at the Institut Laue-Langevin (Grenoble). Highly crystalline cellulose I samples from Cladophora (cellulose I alpha + I beta) or Halocynthia (cellulose I beta) origin were prepared in the form of oriented films. Samples were studied in a hydrogenated form and in a hydrogen-deuterium exchanged deuterated form corresponding to all OH moieties being replaced by ODs. These samples, which diffracted to a resolution of around 0.9 A, gave diffraction diagrams consisting of several hundred independent diffraction spots. Crystalline cellulose II fibres resulting from the mercerization of flax were also studied in a hydrogenated form using NaOH/H2O as mercerizing medium and in a deuterated form using NaOD/D2O. Both of these samples diffracted to around 1.2 A, giving fibre diffraction diagrams slightly less resolved than those of cellulose I, but still consisting of more than one hundred independent diffraction spots. For cellulose I as well as for cellulose II, significant differences between the hydrogenated and deuterated patterns were observed and recorded. These new data should lead to improved structures for cellulose and direct identification of the position of hydrogen atoms involved in hydrogen bonding.
We report the first neutron diffraction data from D2SO4.6(1/2)D2O. The crystal is monoclinic, space group Cm, with four formula units per unit cell. At 4.2 K the unit cell dimensions are a = 6.253 26(4) A, b = 26.813 62(10) A, c = 5.908 45(2) A, and beta = 112.1939(3) degrees [V = 917.286(6) A3 and rho(deuterated) = 1664.14(2) kg m(-3)]. The deuteron positions refined from the neutron data are in agreement with those established by single crystal x-ray analysis [D. Mootz and A. Merschenz-Quack, Z. Naturforsch. B 42, 1231 (1987)], but not with those found from the ab initio simulation of Hirsch and Ojamae [Acta Crystallogr, Sect. B: Struct. Sci. 60, 179 (2004)]. The crystal consists of SO4(2-), D3O+ ions, and D2O molecules hydrogen bonded to form a layered structure in which sheets of "icelike" D3O+ and D2O are separated by layers of opposing SO4(2-) tetrahedra.