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The local and intermediate range structures of the five amorphous ices at 80 K and ambient pressure: a Faber-Ziman and Bhatia-Thornton analysis.

Using isotope substitution neutron scattering data, we present a detailed structural analysis of the short and intermediate range structures of the five known forms of amorphous ice. Two of the lower density forms--amorphous solid water and hyperquenched glassy water--have a structure very similar to each other and to low density amorphous ice, a structure which closely resembles a disordered, tetrahedrally coordinated, fully hydrogen bonded network. High density and very high density amorphous ices retain this tetrahedral organization at short range, but show significant differences beyond about 3.1 A from a typical water oxygen. The first diffraction peak in all structures is seen to be solely a function of the intermolecular organization. The short range connectivity in the two higher density forms is more homogeneous, while the hydrogen site disorder in these forms is greater. The low Q behavior of the structure factors indicates no significant density or concentration fluctuations over the length scale probed. We conclude that these three latter forms of ice are structurally distinct. Finally, the x-ray structure factors for all five amorphous systems are calculated for comparison with other studies.

Journal Article↗

Variable-temperature studies of the 4-isopropylphenol crystal structure from X-ray diffraction. Comparison of thermal expansion and molecular dynamics with spectroscopic results.

Crystalline 4-isopropylphenol, C(9)H(12)O, an optically non-linear material, was studied by X-ray diffraction in order to determine its structure at several temperatures in the 95-300 K range. The thermal expansion coefficients have been calculated from the lattice parameters' dependence on temperature. The rigid-body analysis of the anisotropic displacement parameters including the correlation with the internal motion of large amplitude provided the values of the molecular translation and libration tensors at the temperatures studied and was used to characterize the torsional motion of the isopropyl group. The calculated normal modes and internal torsion frequency were compared with the wave numbers at the maximum of bands in the low-frequency Raman scattering, FTIR and inelastic neutron scattering spectra.

Journal Article↗

Electron densities in relation to magnetism: gamma-ray diffraction from transition-metal monoxides and difluorides.

In this article, results are described from an area of solid-state physics that heretofore has remained unexplored by Bragg charge-scattering experiments. It is shown that gamma-ray electron densities can provide detailed information on magnetic ground-state properties at a subatomic resolution. The use of 316 keV gamma radiation has allowed low-order structure factors at better than 0.1% accuracy to be determined and, at the same time, extended data sets to be collected up to high momentum transfer. Prototypic antiferromagnets such as the late 3d transition-metal monoxides and difluorides have been systematically investigated, in most cases both in the paramagnetic and in the fully ordered phase. At transitions with a lowering of symmetry, multidomain formation was suppressed by application of external mechanical stress or magnetic fields. The results are considered in the context of information provided by recent magnetic neutron and X-ray studies.

Journal Article↗

Focusing Optics for High-Energy X-ray Diffraction.

Novel focusing optical devices have been developed for synchrotron radiation in the energy range 40-100 keV. Firstly, a narrow-band-pass focusing energy-tuneable fixed-exit monochromator was constructed by combining meridionally bent Laue and Bragg crystals. Dispersion compensation was applied to retain the high momentum resolution despite the beam divergence caused by the focusing. Next, microfocusing was achieved by a bent multilayer arranged behind the crystal monochromator and alternatively by a bent Laue crystal. A 1.2 micro m-high line focus was obtained at 90 keV. The properties of the different set-ups are described and potential applications are discussed. First experiments were performed, investigating with high spatial resolution the residual strain gradients in layered polycrystalline materials. The results underline that focused high-energy synchrotron radiation can provide unique information on the mesoscopic scale to the materials scientist, complementary to existing techniques based on conventional X-ray sources, neutron scattering or electron microscopy.

Journal Article↗

Structure of 1,8-bis(hydroxymethyl)naphthalene.

1,8-Naphthalenedimethanol, C12H12O2, M(r) = 188.24, monoclinic, P2(1)/n, a = 8.549(4), b = 4.856(3), c = 22.604(4) A, beta = 94.24(3) degrees, V = 935.8(7) A 3, Z = 4, Dx = 1.34 g cm-3, lambda(Mo K alpha) = 0.71073 A, mu = 0.84 cm-1, F(000) = 400, T = 295 K, R = 0.042 for 1455 unique reflections having I > 3 sigma I. In the title structure the exterior angles at ring atoms C(1), C(8) and C(9) deviate significantly from 120 degrees as a result of the steric interactions of the hydroxymethyl substituents. The ten C atoms comprising the naphthalene core have an average deviation of 0.012 (7) A from the best least-squares plane describing the core. The conformation of the title compound is compared to those of other 1,8-disubstituted naphthalenes. Each hydroxy group is involved in hydrogen bonding as both acceptor and donor, creating infinite chains that propagate in the [010] directions. The neutron-adjusted parameters for the two H...O(acceptor) distances are 1.78 (3) and 1.80 (3) A and for the two O--H...O(acceptor) angles are 165 (2) and 170 (2) degrees. The packing arrangement can be described as a modified herringbone structure with the shortest crystallographic axis coinciding with the b axis of the standard monoclinic setting.

Molecular Structure↗

Rotation-libration and rotor-rotor coupling in 4-methylpyridine.

The low temperature rotational dynamics of methyl groups in 4-methylpyridine is analyzed in terms of a model potential including rotation-libration and rotor-rotor coupling. The parameters of the model potential are adjusted by comparison of calculated with published and newly recorded inelastic neutron scattering spectra. Initial evaluations of the potential parameters of the model are obtained from molecular mechanics calculations. Experimental spectra are calculated from these potentials by numerical solution of Schrödinger's equation for clusters of coupled rotors embedded in a bigger ensemble of rotors treated in the mean field approximation. Adjustment of the potential parameters leads to excellent agreement with the experimental spectra of protonated 4-methylpyridine, measured at well-defined spin temperatures. At higher levels of deuteration, agreement with experiment is qualitative, only. The observed deviations are attributed to the increasing frustration of the system of coupled methyl groups and mutual localization, effects leading to a phase transition around 5.5 K in isotopic mixtures, as shown in diffraction experiments.

Journal Article↗

Refinement of the crystal structural parameters of the intermediate phase of h-BaTiO3 using convergent-beam electron diffraction.

Crystal structural parameters (21 positional parameters and nine isotropic Debye-Waller factors) of the intermediate phase of hexagonal barium titanate (h-BaTiO3) have been refined by a structure analysis method using convergent-beam electron diffraction (CBED); this method was developed by Tsuda & Tanaka [Acta Cryst. (1999), A55, 939-954]. In order to perform the analysis, a parallel computation using a computer cluster composed of 16 connected Pentium 4 PCs was introduced. A function of parallel computation has been implemented in our analysis software, MBFIT, with the aid of the Message Passing Interface (MPI). Parallel computation enabled the present refinement to be conducted using a [001] CBED pattern and a [010] CBED pattern simultaneously. Reliable errors for the refined structural parameters have been obtained from the analyses of four independent experimental data sets instead of using the errors obtained by the error-propagation rule of least-squares fitting. The parameters obtained have been found to agree well with those determined by a neutron Rietveld analysis.

Journal Article↗

The structure of the chromatin core particle in solution.

The shape and size of the nucleosomal core particle from chromatin has been examined by analysis of neutron and X-ray scattering data from dilute solutions. Calculations of scattering for many different models have been made and only one model was able to account for both the X-ray and neutron profiles. This model is an oblate structure with height about 50A and diameter 110A. The DNA is mainly confined to two annuli located at the top and bottom respectively of the core particle positioned on the outside of a compact protein core which has a height of about 40A and diameter about 73A.

Animals↗

Physical characteristics of ribosomal protein S4 from Escherichia coli.

A hydrodynamic study of protein S4 from Escherichia coli 30 S ribosomal subunits indicates that this protein is moderately asymmetric. A sedimentation coefficient of 1.69 S and a diffusion coefficient of 7.58 X 10(-7) cm2/s suggest that S4 has an axial ratio of about 5:1 using a prolate ellipsoidal model. This structure should give a radius of gyration of about 29-30 A from small-angle neutron or small-angle x-ray scattering studies. This study has utilized quasi-elastic light scattering as an analytical tool to obtain a diffusion coefficient as well as a method to monitor sample quality. Using quasi-elastic light scattering in this manner allows an assessment of problems associated with protein purity which may be responsible for the many disparate results reported for ribosomal proteins and especially protein S4.

Chemical Phenomena↗

Carboxyl group hydrogen bonding in X-ray protein structures analysed using neutron studies on amino acids.

A method is proposed to make a distinction between ionized and neutral carboxyl groups in X-ray protein structures. This is based on an analysis of the relative hydrogen bonding populations and bond-length bond-valence correlations in high-precision neutron studies of amino acids and small peptides. With the help of this method, four amino acid residues containing carboxyl groups in the refined structure of triclinic hen egg-white lysozyme have been analysed. Two of these, Glu-35 and Asp-52, are involved in lysozyme function, while the other two, Glu-7 and Asp-101, form a protein-protein inter-molecular contact in the triclinic structure.

Amino Acid Sequence↗

Conformational distinguishability of medium cycloalkanes in crystals via inelastic neutron scattering.

This paper begins an exploration of the use of the combination of DFT computations with experimental inelastic neutron scattering (INS) spectra as a method for establishing what conformation is present in a molecular crystal at low temperature. Presented here are INS spectra of a series of medium-sized cycloalkanes: C6H12, C7H14, C8H16, C10H20, C12H24, and C14H28. Optimized geometries and normal mode calculations were performed at B3LYP/6-311G(d,p) on the lowest energy conformations (i.e., those thermally accessible at the experimental temperature of 30 K). The calculated and observed spectra were analyzed for the best fit from each set of conformers, allowing a prediction of the dominant conformation in a conformationally rich system. For each cycloalkane, the calculated spectrum for the lowest energy conformer shows good agreement with experiment while the higher energy conformations have a much poorer fit. With little ambiguity, the lowest energy conformer is therefore predicted to be the dominant conformation, consistent with the diffraction data available for C6H12, C10H20, C12H24, and C14H28. These results indicate that INS spectroscopy may be a useful tool in determining the dominant conformation in a crystal lattice in cases such as this in which the intermolecular interactions are weak and the different conformers are calculated to have distinguishable spectra. Such an analysis is applied to the cases of C7H14 and C8H16 for which no low-temperature X-ray analysis is available. Clear structure predictions result, and the conformer observed is that computed to be of lowest energy for the molecule in isolation.

Journal Article↗

ASAXS, SAXS and SANS investigations of vulcanized elastomers filled with carbon black.

Small-angle X-ray scattering (SAXS) performed down to small q values (q <or= 10(-3) A(-1)) is a powerful method for investigating the arrangement of filler aggregates in filled elastomers under uniaxial strain. Meanwhile, for vulcanized samples, zinc oxide is used as an additive. Owing to their high contrast, the ZnO particles remaining in the manufactured composite are strong X-ray scatterers. In the low-q domain, their scattering hides that of filler aggregates (carbon black, pyrogenic silica) and must be quantified in order to be suppressed. To this end, anomalous SAXS (ASAXS) and small-angle neutron scattering (SANS) have been performed. It is shown that ASAXS measurements can be performed down to small q values (q <or= 10(-3) A(-1)). Therefore ASAXS is well adapted to separate the contributions of ZnO and filler scattering. For neutron scattering the contrast of the ZnO particles is similar to that of carbon. Because the amount of ZnO is much smaller than that of filler, ZnO scattering can be neglected. Owing to multiple scattering effects, however, SANS can only be used for very thin samples (less than about 0.25 mm). It is shown that, providing multiple scattering is avoided, ASAXS and SANS yield similar scattering curves for the filler aggregates.

Elastomers↗

Solution structure of the Tn3 resolvase-crossover site synaptic complex.

Tn3 resolvase is a site-specific DNA recombinase, which catalyzes strand exchange in a synaptic complex containing twelve resolvase subunits and two res sites. Hyperactive mutants of resolvase can form a simpler complex (X synapse) containing a resolvase tetramer and two shorter DNA segments at which strand exchange takes place (site I). We have solved the low-resolution solution structure of the purified, catalytically competent X synapse from small-angle neutron and X-ray scattering data, using methods in which the data are fitted with models constructed by rigid body transformations of a published crystallographic structure of a resolvase dimer bound to site I. Our analysis reveals that the two site I fragments are on the outside of a resolvase tetramer core and provides some information on the quaternary structure of the tetramer. We discuss implications of our structure for the architecture of the natural synaptic complex and the mechanism of strand exchange.

Bacterial Proteins↗

Solution structure of human and mouse immunoglobulin M by synchrotron X-ray scattering and molecular graphics modelling. A possible mechanism for complement activation.

The pentameric 71-domain structure of human and mouse immunoglobulin M (IgM) was investigated by synchrotron X-ray solution scattering and molecular graphics modelling. The radii of gyration RG of human IgM Quaife and its Fc5, IgM-S, Fab'2 and Fab fragments were determined as 12.2 nm, 6.1 nm, 6.1 nm, 4.9 nm and 2.9 nm in that order. The RG values were similar for mouse IgM P8 and its Fab'2 and Fab fragments, despite the presence of an additional carbohydrate site. The IgM scattering curves, to a nominal resolution of 5 nm, were compared with molecular graphics models based on published crystallographic alpha-carbon co-ordinates for the Fab and Fc structures of IgG. Good curve fits for Fab were obtained based on the crystal structure of Fab from IgG. A good curve fit was obtained for Fab'2, if the two Fab arms were positioned close together at their contact with the C mu 2 domains. The addition of the Fc fragment close to the C mu 2 domains of this Fab'2 model, to give a planar structure, accounted for the scattering curve of IgM-S. The Fc5 fragment was best modelled by a ring of five Fc monomers, constrained by packing considerations and disulphide bridge formation. A position for the J chain between two C mu 4 domains rather than at the centre of Fc5 was preferred. The intact IgM structure was best modelled using a planar arrangement of these Fab'2 and Fc5 models, with the side-to-side displacement of the Fab'2 arms in the plane of the IgM structure. All these models were consistent with hydrodynamic simulations of sedimentation data. The solution structure of IgM can therefore be reproduced quantitatively in terms of crystallographic structures for the fragments of IgG. Putative Clq binding sites have been identified on the C mu 3 domain. These would become accessible for interaction with Clq when the Fab'2 arms move out of the plane of the Fc5 disc in IgM, that is, a steric mechanism exposing pre-existing Clq sites. Comparison with a solution structure for Clq by neutron scattering shows that two or more of the six globular Clq heads in the hexameric head-and-stalk structure are readily able to make contacts with the putative Clq sites in the C mu 3 domains of free IgM if if the Clq arm-axis angle in solution is reduced from 40 degrees-45 degrees to 28 degrees. This could be the trigger for Cl activation.

Amino Acid Sequence↗

Configurational distribution of denatured phosphoglycerate kinase.

Physiochemical characterization of the denatured states of proteins is important for a complete understanding of the factors stabilizing their folded conformations. Using a combination of small angle neutron scattering (SANS), statistical mechanical modelling and molecular mechanics calculations, we examine the configurational distribution of phosphoglycerate kinase denatured in 4 M guanidine hydrochloride solution. The denaturing of the protein produces a clear change in the form of the SANS profile and a large increase of the radius of gyration. In the statistical mechanical model, the region of contrast neutron scattering density associated with the protein is pictured as a chain of freely jointed spheres. The model is fitted to the SANS data for the denatured protein. It is found that a model with a small number of spheres cannot account for the higher resolution scattering, indicating an absence of detectable structuration; a good fit is found with 100 spheres of 8.5 A radius. Single configurations of the fitted chain of spheres are used as low-resolution bounds for model-building and molecular mechanics calculations to obtain plausible atomic-detail models of the denatured chain.

Computer Simulation↗

Physical properties of the Escherichia coli transcription termination factor rho. 1. Association states and geometry of the rho hexamer.

To function as a DNA-RNA helicase in rho-dependent transcript termination, six genetically identical subunits of the Escherichia coli transcription termination protein rho must first assemble into a hexameric complex. To help determine the quaternary structure of this complex, we have studied the association equilibria of the rho protomers. Sedimentation equilibrium, sedimentation velocity, diffusion, X-ray scattering, and neutron-scattering data have been combined to create a "phase diagram" of the association states of this protein as a function of protein concentration and ionic environment. The results show that rho exists predominantly as a hexamer under approximately physiological conditions and that this hexamer is in equilibrium with both lower and higher states of association that may also have physiological relevance. Small-angle X-ray scattering measurements and theoretical calculations indicate that the rho hexamer has a radius of gyration of 50 +/- 3 A. The radius of gyration measured by small-angle neutron scattering in 2H2O is 47 +/- 3 A. These scattering studies also support earlier models of rho as a planar hexagon which have been developed on the basis of electron microscopy. In the following paper in this issue [Geiselmann, J., Seifried, S. E., Yager, T. D., Liang, C., & von Hippel, P. H. (1992)], these results are combined with information on symmetry, subunit interactions, and packing geometry to obtain a model of the quaternary structure of the functional rho hexamer.

DNA↗

Neutron and x-ray scatter studies of the histone octamer and amino and carboxyl domain trimmed octamers.

The structure of the nucleosome has been under intense investigation using neutron crystallography, x-ray crystallography, and neutron solution scattering. However the dimension of the histone octamer inside the nucleosome is still a subject of controversy. The radius of gyration (Rg) of the octamer obtained from solution neutron scattering of core particles at 63% 2H2O, 37% 1H2O is 33 A, and x-ray crystallography study of isolated histone octamer gives a Rg of 32.5 A, while the reported values using x-ray crystallography of core particles from two individual studies are 29.7 and 30.4 A, respectively. We report here studies of isolated histone octamer and trypsin-limited digested octamer using both neutron solution scattering and small angle x-ray scattering. The Rg of the octamer obtained is 33 A, whereas that of the trimmed octamer is 29.8 A, similar to the structure obtained from the crystals of the core particles. The N-terminal domains of the core histones in the octamer have been shown by high resolution nuclear magnetic resonance (Schroth, G.P., Yau, P., Imai, B.S., Gatewood, J.M., and Bradbury, E.M. (1990) FEBS Lett. 268, 117-120) to be mobile and flexible; it is likely that these regions are disordered and "not seen" by x-ray crystallography.

Animals↗

S-alkylation and S-amination of methyl thioethers--derivatives of closo-[B(12)H(12)](2-). synthesis of a boronated phosphonate, gem-bisphosphonates, and dodecaborane-ortho-carborane oligomers.

A variety of S-alkylated products was prepared by alkylation of methyl thioethers [MeSB(12)H(11)](2-) (5), [1-(MeS)-2(7,12)-(Me(2)S)B(12)H(10)](-) (6-8), and [1,2(7,12)-(MeS)(2)B(12)H(10)](2-) (9-11) with alkyl halides and tosylates in acetonitrile. Since these methyl thioethers can be prepared easily in B-10-enriched form on a large scale and due to their chemical versatility, they are potentially very attractive boron entities for the design and synthesis of therapeutics for boron neutron capture therapy of cancer. It was found that alkylation of 6-8 can be complicated by an equilibrium which establishes between, on the one hand, one of the former species and, on the other hand, 1,2(7,12)-(Me(2)S)(2)B(12)H(10) (2-4) and [1,2(7,12)-(MeS)(2)B(12)H(10)](2-) (9-11). A boronated phosphonate 1-(MeS(CH(2))(4)P(O)(OEt)(2))-7-(Me(2)S)B(12)H(10) (14g) and a gem-bisphosphonate 1-(MeS(CH(2))(3)CH[P(O)(OEt)(2)](2))-7-(Me(2)S)B(12)H(10) (14h) were prepared from thioether 7 and the corresponding iodide and tosylate, respectively, and subsequently converted to their sodium salts. The propargyl sulfonium salts obtained by alkylation of thioethers 7, 8, 10, and 11 with propargyl bromide have been further converted to two- and three-cage oligomers containing both ortho-carborane and dodecaborane moieties. Methyl thioethers derived from closo-[B(12)H(12)](2-) are excellent participants in Michael addition reactions in the presence of a strong acid. The sulfonium salts with tertiary alkyl and vinyl substituents have been prepared by this method. Methyl thioethers 5-11 react with hydroxylamine-O-sulfonate yielding the corresponding aminosulfonium salts, albeit in lower yields as compared to those in the alkylation reactions. Several derivatives of methyl thioethers 5-11 have been characterized by single-crystal X-ray diffraction.

Journal Article↗