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PubMed2005

Gas-phase electron diffraction studies of the icosahedral carbaboranes, ortho-, meta- and para-C2B10H12.

The molecular structures of the three closo-carbaboranes, ortho-, meta- and para-C2B10H12, were experimentally determined using gas-phase electron diffraction (GED). All unique bond distances for ortho and meta carbaboranes were determined experimentally for the first time. For ortho-carbaborane (RG= 0.046), a model with C2v symmetry refined to give bond distances of 1.624(8) A for C-C, 1.093(8)A for C-H and 1.192(3)-1.196(3) A for B-H. For meta-carbaborane (RG= 0.040) a model with C2v symmetry refined to give a CC distance of 2.575(9) A. For para-carbaborane (RG= 0.062) a model with D5d symmetry refined to give a C-B bond distance of 1.698(3) A, B2-B3 of 1.785(1), B2-B7 of 1.774(4) and CC of 3.029(5)A. These GED structures are compared with geometries from other experimental diffraction methods (neutron, X-ray) and ab initio calculations.

Journal Article↗
PubMed2005

Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models.

The present article gives an overview of analytical and simulation approaches to describe the relaxation dynamics of proteins. Particularly emphasised are recent developments of theoretical models, such as fractional Brownian dynamics. The latter connects dynamical events seen on the pico- to nanosecond time scale, accessible to quasielastic neutron scattering, and functional dynamics of proteins on much longer time scales.

Computer Simulation↗
PubMed2005

Rotational tunneling of methyl groups in low temperature phases of mesitylene: potentials and structural implications.

Mesitylene can be stabilized at He temperature in three solid phases of so far unknown crystal structures. Rotational tunneling of methyl groups is based on rotational potentials and used to characterize structural aspects. In phase III found after the first fast cooling of the sample three nonequivalent methyl rotors with splittings of 2.7, 4.1 and 16.3 microeV are observed. Three other unresolved bands are identified by their librational modes. In the second phase II the metastability is emphasized by tunneling energies still changing at temperatures T< or = 12 K. Above this temperature tunneling bands at 6.6, 12.5, 15.0 and 18.3 microeV evolve in the manner characteristic of coupling to phonons. In the equilibrium phase I a single tunnel splitting of 10.2 microeV represents all methyl groups. A unit cell containing a single molecule at a site of threefold symmetry explains quantitatively this spectrum. Phases II and III most likely contain two nonequivalent molecules in the unit cell with no local symmetry in phase II and a mirror plane in phase III. The good moderator properties for neutrons are most likely not connected to the low energy tunneling bands but to a dense vibrational phonon density of states.

Benzene Derivatives↗
PubMed2005

The high resolution inelastic neutron scattering spectrum of ammonium fluoride.

The measured high resolution (deltaE/E approximately 2-3%) incoherent inelastic neutron scattering spectrum of ammonium fluoride is presented and discussed with reference to the available optical spectra. In addition, a full set of dispersion curves have been obtained from a new ab initio lattice dynamics calculation and these have been used to produce a rigorous interpretation of the spectrum. The librational modes of the ammonium ion occur at 560 cm(-1) and the anharmonicity in these modes is estimated to be 4%, about half that observed in the other ammonium halides. The reduction in anharmonicity is attributed to stronger hydrogen bonding and a deeper potential well. The calculations agree well with the observed spectrum apart from the librational modes which are shifted upwards by around 40 cm(-1) from the measured values. Dispersion and LO-TO splitting are important in this system with modes changing frequency by up to 135 cm(-1). The nature of the calculated LO-TO splitting in the optic mode region is indicative of a pseudo-cubic system confirming that the site symmetry of the ammonium ion is very close to T(d). Because of LO-TO splitting the ammonium ion asymmetric stretch, nu3, has components calculated to be at higher frequencies than those of the symmetric stretch, nu1, which contradicts the assignment scheme produced from optical data.

Algorithms↗
PubMed2005

An infrared and inelastic neutron scattering spectroscopic investigation on the interaction of eta-alumina and methanol.

The industrially important interaction of methanol with an eta-alumina catalyst has been investigated by a combination of infrared spectroscopy (diffuse reflectance and transmission) and inelastic neutron scattering (INS) spectroscopy. The infrared and INS spectra together show that chemisorbed methoxy is the only surface species present. Confirmation of the assignments was provided by a periodic DFT calculation of methoxy on eta-alumina (110). The thermal conversion of adsorbed methoxy groups to form dimethylether was also followed by INS, with DFT calculations assisting assignments. An intense feature about 2600 cm(-1) was observed in the diffuse reflectance spectrum. This band is poorly described in the extensive literature on the alumina/methanol adsorption system and its observation raised the possibility of a new surface species existing on this particular catalyst surface. INS measurements established that the 2600 cm(-1) feature could be assigned to a combination band of the methyl rock with the methyl deformation modes. This assignment was reinforced by an analysis of the neutron scattering intensity at a particular energy as a function of momentum transfer, which confirmed this particular adsorbed methoxy feature to arise from a second order transition. Similar behaviour was observed in the model compound Al(OCH3)3. The anomalous infrared intensity of the 2600 cm(-1) peak in the diffuse reflectance spectrum is a consequence of the different absorption coefficients of the C-H stretch and the combination mode. The implications for catalyst studies are discussed.

Aluminum Oxide↗
PubMed2005

Nuclear and magnetic structures and magnetic properties of synthetic brochantite, Cu4(OH)6SO4.

Cu4(OH)6SO4 (1) and Cu4(OD)6SO4 (2) were obtained by hydrothermal syntheses from copper sulfate and sodium hydroxide in H2O and D2O, respectively. They crystallize in the monoclinic system, space group P2(1)/a (14), a = 13.1206(5), b = 9.8551(3), c = 6.0295(2) Angstroms, beta = 103.432(3) degrees, V = 758.3(1) Angstroms(3), Z = 4 and a = 13.1187(5), b = 9.8552(3), c = 6.0293(2) Angstroms, beta = 103.410(3) degrees, V = 758.3(1) Angstroms(3), Z = 4, respectively. They are iso-structural to the mineral brochantite and consist of double chains of edge-sharing copper octahedra that are connected to one another by corners to form corrugated planes along bc; these planes are in-turn bridged by the unprecedented mu7-sulfate tetrahedra to give a 3D-structure. All the hydrogen atoms were precisely located from refinement of the neutron powder diffraction data of the deuterated sample. Magnetic susceptibility data reveal a low-dimensional behavior at high temperature and the presence of both ferromagnetic and antiferromagnetic super-exchanges resulting in a 3D long-range antiferromagnetic ordering at 7.5 K accompanied by a small canting of the moments. The transition is confirmed by a lambda-peak in the specific heat. The magnetic structure at 1.4 K shows the moments are oriented perpendicular to the corrugated planes with alternation along +/-a for neighboring chains within the double chains. The enhanced incoherent scattering at low-angle suggests the existence of short-range ferromagnetic clusters.

Journal Article↗
PubMed2006

The solubilisation behaviour of some dichloroalkanes in aqueous solutions of PEO-PPO-PEO triblock copolymers: a dynamic light scattering, fluorescence spectroscopy, and SANS study.

The aggregation behaviour of PEO-PPO-PEO triblock copolymers in water and in water + chlorinated additive mixtures was studied by means of fluorescence spectroscopy, dynamic light scattering (DLS), and small-angle neutron scattering (SANS). The copolymers were chosen such as to investigate the effects of molecular architecture (L35 and 10R5) and molecular weight by keeping constant the hydrophilic/hydrophobic balance (F88 and F108). 1,2-Dichloroethane was used as a prototype of water basins contaminants. The hydrodynamic radius of the block copolymer aggregates (R(h,M)) and the intensity ratio of pyrene of the first and the third vibrational band (I(1)/I(3)) were determined as a function of temperature (10-45 degrees C) and concentration. The copolymer architecture essentially does not affect R(h,M) in the entire range of temperature and concentration investigated. At a given temperature, increasing macromolecular size leads to a decrease of R(h,M). With rising temperature R(h,M) also decreases. According to the DLS results, the I(1)/I(3) change with temperature clearly detects the aggregation only for F88 and F108. The presence of 1,2-dichloroethane, at concentrations close to its solubility in water, does not lead to changes in the distribution of hydrodynamic radii for L35 and 10R5. Larger quantities of additive induce the formation of quite polydisperse mixed aggregates for L35 and of networks for 10R5. In the case of F88 and F108, low concentrations of additive lead to formation of mixed aggregates with smaller R(h,M). The SANS results corroborate the DLS and fluorescence findings proving enhancement of the copolymer aggregation through the presence of 1,2-dichloroethane. The DLS findings combined with those from the fluorescence spectroscopy provide some insight into the site of solubilisation of the additive in the aggregates.

Alkanes↗
PubMed2006

Effect of Sr content on the crystal structure and electrical properties of the system La2-xSrxNiO4+delta (0 <or=x<or= 1).

Materials formulated as La(2-x)Sr(x)NiO(4+delta) (0 <or=x<or= 1) have been prepared and investigated by high-resolution neutron powder diffraction in order to correlate the structural variation induced by the incorporation of Sr into the crystal lattice with the electronic and thermal properties of each material. The evolution of the electrical conductivity and thermal expansion coefficients with temperature have been determined in order to study the potential use of these compounds as cathodes for intermediate-temperature solid oxide fuel cells (IT-SOFC). These oxides show a good thermal expansion coefficient (TEC = 11-13 x 10(-6) K(-1)), and high electronic conductivity up to 273 S cm(-1). It is noticeable that a great enhancement of the electrical conductivity with the Sr content is concomitant with the shortening of the Ni-O1 bond length.

Journal Article↗
PubMed2006

Conformational heterogeneity and low-frequency vibrational modes of proteins.

Molecular dynamics simulation and normal mode analysis are used to calculate the vibrational density of states of dihydrofolate reductase complexed with nicotinamide adenine dinucleotide phosphate at 120 K and the results are compared with the experimental spectrum derived from inelastic neutron scattering. The simulation results indicate that the experimental spectrum arises from an average over proteins trapped in different conformations with structural differences mainly in the loop regions, and that these conformations have significantly different low-frequency (<20 cm(-1)) spectra. Thus, the experimentally measured spectrum is an average over the vibrational modes of different protein conformations and is thus inhomogeneously broadened. The implications of this broadening for future neutron scattering experiments and ligand binding calculations are discussed.

Computer Simulation↗
PubMed2004

Small-angle neutron scattering study of structural changes in temperature sensitive microgel colloids.

The structure of temperature-sensitive poly(N-isopropylacrylamide) microgels in dilute suspension was investigated by means of small-angle neutron scattering. A direct modeling expression for the scattering intensity distribution was derived which describes very well the experimental data at all temperatures over an extensive q range. The overall particle form as well as the internal structure of the microgel network is described by the model. The influence of temperature, cross-linking density, and particle size on the structure was revealed by radial density profiles and clearly showed that the segment density in the swollen state is not homogeneous, but gradually decays at the surface. The density profile reveals a box profile only when the particles are collapsed at elevated temperatures. An increase of the cross-linking density resulted in both an increase of the polymer volume fraction in the inner region of the particle and a reduction of the smearing of the surface. The polymer volume fraction inside the colloid decreased with increasing particle size. The structural changes are in good agreement with the kinetics of the emulsion copolymerization used to prepare the microgel colloids.

Acrylic Resins↗
PubMed2004

Freezing on heating of liquid solutions.

We report a reversible liquid-solid transition upon heating of a simple solution composed of a-cyclodextrine (alpha CD), water, and 4-methylpyridine. These solutions are homogeneous and transparent at ambient temperature and solidify when heated to temperatures between 45 degrees and 75 degrees. Quasielastic and elastic neutron scattering show that molecular motions are slowed down in the solid and that crystalline order is established. The solution "freezes on heating." This process is fully reversible, on cooling the solid melts. A rearrangement of hydrogen bonds is postulated to be responsible for the observed phenomenon.

Crystallization↗
PubMed2005

Calculation of crystal and molecular structures of carbon disulfide CS2.

Crystal and molecular structures of carbon disulfide CS(2) were investigated by molecular packing analysis with a computed dynamical model. This model includes thermal motions, molecular deformations, and anisotropic atomic repulsive interactions. Several crystalline structures with orthorhombic symmetry Cmca have been found by the calculation. The lowest energy structure agrees with the experimental one. The temperature dependence of the crystal structure parameters reproduces the general features and the particular increase with decreasing temperature of the lattice parameter c (and orientational angle psi) as determined by x-ray diffraction or neutron scattering experiments. The pressure behavior of the crystal structure parameters up to 12 GPa at room temperature is also correctly reproduced.

Journal Article↗
PubMed2004

Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules.

The structure of a partially deuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, was determined by using the neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-3) at the JRR-3M reactor of the Japan Atomic Energy Research Institute. Data were collected at room temperature up to a resolution of 1.5 A, and the completeness factor of the data set was 81.9%. The model contains 306 H and 50 D atoms. A total of 37 hydration water molecules were identified, with 15 having all three atoms fully located and the remaining D2O molecules partially defined. The model has been refined to final agreement factors of R = 18.6% and Rfree = 21.7%. Several orientations of the O-D bonds of side chains, whose assignments from x-ray data were previously ambiguous, were clearly visible in the neutron structure. Although most backbone N-H bonds had undergone some degree of H/D exchange throughout the rubredoxin molecule, 5 H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND3+ terminus that may contribute to the unusual thermostability of this molecule.

Deuterium Exchange Measurement↗
PubMed2004

The 15-K neutron structure of saccharide-free concanavalin A.

The positions of the ordered hydrogen isotopes of a protein and its bound solvent can be determined by using neutron crystallography. Furthermore, by collecting neutron data at cryo temperatures, the dynamic disorder within a protein crystal is reduced, which may lead to improved definition of the nuclear density. It has proved possible to cryo-cool very large Con A protein crystals (>1.5 mm3) suitable for high-resolution neutron and x-ray structure analysis. We can thereby report the neutron crystal structure of the saccharide-free form of Con A and its bound water, including 167 intact D2O molecules and 60 oxygen atoms at 15 K to 2.5-A resolution, along with the 1.65-A x-ray structure of an identical crystal at 100 K. Comparison with the 293-K neutron structure shows that the bound water molecules are better ordered and have lower average B factors than those at room temperature. Overall, twice as many bound waters (as D2O) are identified at 15 K than at 293 K. We note that alteration of bound water orientations occurs between 293 and 15 K; such changes, as illustrated here with this example, could be important more generally in protein crystal structure analysis and ligand design. Methodologically, this successful neutron cryo protein structure refinement opens up categories of neutron protein crystallography, including freeze-trapped structures and cryo to room temperature comparisons.

Binding Sites↗
PubMed2004

Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functions.

The concept that proteins exist in numerous different conformations or conformational substates, described by an energy landscape, is now accepted, but the dynamics is incompletely explored. We have previously shown that large-scale protein motions, such as the exit of a ligand from the protein interior, follow the dielectric fluctuations in the bulk solvent. Here, we demonstrate, by using mean-square displacements (msd) from Mossbauer and neutron-scattering experiments, that fluctuations in the hydration shell control fast fluctuations in the protein. We call the first type solvent-slaved or alpha-fluctuations and the second type hydration-shell-coupled or beta-fluctuations. Solvent-slaved motions are similar to the alpha-fluctuations in glasses. Their temperature dependence can be approximated by a Vogel-Tammann-Fulcher relation and they are absent in a solid environment. Hydration-shell-coupled fluctuations are similar to the beta-relaxation in glasses. They can be approximated by a Ferry or an Arrhenius relation, are much reduced or absent in dehydrated proteins, and occur in hydrated proteins even if embedded in a solid. They can be responsible for internal processes such as the migration of ligands within myoglobin. The existence of two functionally important fluctuations in proteins, one slaved to bulk motions and the other coupled to hydration-shell fluctuations, implies that the environment can control protein functions through different avenues and that no real protein transition occurs at approximately 200 K. The large number of conformational substates is essential; proteins cannot function without this reservoir of entropy, which resides mainly in the hydration shell.

Animals↗
PubMed2004

C subunits binding to the protein kinase A RI alpha dimer induce a large conformational change.

We present structural data on the RI alpha isoform of the cAMP-dependent protein kinase A that reveal, for the first time, a large scale conformational change within the RI alpha homodimer upon catalytic subunit binding. This result infers that the inhibition of catalytic subunit activity is not the result of a simple docking process but rather is a multi-step process involving local conformational changes both in the cAMP-binding domains as well as in the linker region of the regulatory subunit that impact the global structure of the regulatory homodimer. The results were obtained using small-angle neutron scattering with contrast variation and deuterium labeling. From these experiments we derived information on the shapes and dispositions of the catalytic subunits and regulatory homodimer within a holoenzyme reconstituted with a deuterated regulatory subunit. The scattering data also show that, despite extensive sequence homology between the isoforms, the overall structure of the type I alpha holoenzyme is significantly more compact than the type II alpha isoform. We present a model of the type I alpha holoenzyme, built using available high-resolution structures of the component subunits and domains, which best fits the neutron-scattering data. In this model, the type I alpha holoenzyme forms a flattened V shape with the RI alpha dimerization domain at the point of the V and the cAMP-binding domains of the RI alpha subunits with their bound catalytic subunits at the ends.

Animals↗
PubMed1983

Yeast tRNAAsp-aspartyl-tRNA synthetase: the crystalline complex.

Aspartyl-tRNA synthetase from yeast, a dimer of molecular weight 125,000 and its cognate tRNA (Mr = 24,160) were co-crystallized using ammonium sulfate as precipitant agent. The presence in the crystals of both components in the two-to-one stoichiometric ratio was demonstrated by electrophoresis, biological activity assays and crystallographic data. Crystals belong to the cubic space group I432 with cell parameter of 354 A and one complex particle per asymmetric unit. The solvent content of about 78% is favorable for a low resolution structural investigation. By exchanging H2O for D2O in mother liquors, advantage can be taken from contrast variation techniques with neutron radiations. Diffraction data to 20 A resolution were measured at five different contrasts, two of them being close to the theoretical matching point of RNA and protein in the presence of ammonium sulfate. The experimental extinction of the diffracted signal was observed to be close to 36% D2O, significantly different from the predicted value of 41%. The phenomenon can be explained by the existence of a large interface region between the two tRNAs and the enzyme. These parts of the molecules are hidden from the solvent and their protons are less easily exchangeable. Accessibility studies toward chemicals of tRNAAsp in solution and in the presence of synthetase are in agreement with such a model.

Amino Acyl-tRNA Synthetases↗