Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Neutron Diffraction”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,279 records · Page 71Linked to original sources
PubMed1997

Differences in hydration structure near hydrophobic and hydrophilic amino acids.

We use molecular dynamics to simulate recent neutron scattering experiments on aqueous solutions of N-acetyl-leucine-amide and N-acetyl-glutamine-amide, and break down the total scattering function into contributions from solute-solute, solute-water, water-water, and intramolecular correlations. We show that the shift of the main diffraction peak to smaller angle that is observed for leucine, but not for glutamine, is attributable primarily to alterations in water-water correlations relative to bulk. The perturbation of the water hydrogen-bonded network extends roughly two solvation layers from the hydrophobic side chain surface, and is characterized by a distribution of hydrogen bonded ring sizes that are more planar and are dominated by pentagons in particular than those near the hydrophilic side chain. The different structural organization of water near the hydrophobic solute that gives rise to the inward shift in the main neutron diffraction peak under ambient conditions may also provide insight into the same directional shift for pure liquid water as it is cooled and supercooled.

Amino Acids↗
PubMed2000

The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments.

We present results from an extensive molecular dynamics simulation study of water hydrating the protein Ribonuclease A, at a series of temperatures in cluster, crystal, and powder environments. The dynamics of protein hydration water appear to be very similar in crystal and powder environments at moderate to high hydration levels. Thus, we contend that experiments performed on powder samples are appropriate for discussing hydration water dynamics in native protein environments. Our analysis reveals that simulations performed on cluster models consisting of proteins surrounded by a finite water shell with free boundaries are not appropriate for the study of the solvent dynamics. Detailed comparison to available x-ray diffraction and inelastic neutron-scattering data shows that current generation force fields are capable of accurately reproducing the structural and dynamical observables. On the time scale of tens of picoseconds, at room temperature and high hydration, significant water translational diffusion and rotational motion occur. At low hydration, the water molecules are translationally confined but display appreciable rotational motion. Below the protein dynamical transition temperature, both translational and rotational motions of the water molecules are essentially arrested. Taken together, these results suggest that water translational motion is necessary for the structural relaxation that permits anharmonic and diffusive motions in proteins. Furthermore, it appears that the exchange of protein-water hydrogen bonds by water rotational/librational motion is not sufficient to permit protein structural relaxation. Rather, the complete exchange of protein-bound water molecules by translational displacement seems to be required.

Computer Simulation↗
PubMed2000

Thermotropic and lyotropic properties of long chain alkyl glycopyranosides. Part II. Disaccharide headgroups.

We have investigated the thermotropic and lyotropic properties of some long chain alkyl glycosides with disaccharide headgroups. The thermotropism was measured with polarising microscopy and additionally the lyotropism with the contact preparation method, Fourier-transform Infrared (FTIR) spectroscopy, X-ray diffraction and small angle neutron scattering. A broad thermotropic as well as lyotropic polymorphism was found. The compounds displayed thermotropic S(A) (lamellar) and cubic phases, and the investigation of the lyotropic phase behaviour led to the observation of inverted bicontinuous cubic V(II) phases, lamellar L(alpha) phases, normal bicontinuous cubic V(I) phases, normal columnar H(I) phases, normal discontinuous cubic I(I) phases and lyotropic cholesteric phases. The phases are discussed with respect to the chemical structures that have been varied systematically to derive structure-property relationships.

Carbohydrate Conformation↗
PubMed2000

Review: model peptides and the physicochemical approach to beta-amyloids.

beta-Amyloid peptides are the main protein components of neuritic plaques and may be important in the pathogenesis of Alzheimer's Disease. The determination of the structure of beta-amyloid fibrils poses a challenge because of the limited solubility of beta-amyloid peptides and the noncrystalline nature of fibrils formed from these peptides. In this paper, we describe several physicochemical approaches which have been used to examine fibrils and the fibrillogenesis of peptide models of beta-amyloid. Recent advances in solid state NMR, such as the DRAWS pulse sequence, have made this approach a particularly attractive one for peptides such as beta-amyloid, which are not yet amenable to high-resolution solution phase NMR and crystallography. The application of solid state NMR techniques has yielded information on a model peptide comprising residues 10-35 of human beta-amyloid and indicates that in fibrils, this peptide assumes a parallel beta-strand conformation, with all residues in exact register. In addition, we discuss the use of block copolymers of Abeta peptides and polyethylene glycol as probes for the pathways of fibrillogenesis. These methods can be combined with other new methods, such as high-resolution synchrotron X-ray diffraction and small angle neutron and X-ray scattering, to yield structural data of relevance not only to disease, but to the broader question of protein folding and self-assembly.

Amyloid beta-Peptides↗
PubMed2005

Molecular dynamics simulations of side chain liquid crystal polymer molecules in isotropic and liquid-crystalline melts.

A detailed molecular dynamics simulation study is described for a polysiloxane side chain liquid crystal polymer (SCLCP). The simulations use a coarse-grained model composed of a combination of isotropic and anisotropic interaction sites. On cooling from a fully isotropic polymer melt, we see spontaneous microphase separation into polymer-rich and mesogen-rich regions. Upon application of a small aligning potential during cooling, the structures that form on microphase separation anneal to produce a smectic-A phase in which the polymer backbone is largely confined between the smectic layers. Several independent quenches from the melt are described that vary in the strength of the aligning potential and the degree of cooling. In each quench, defects were found where the backbone chains hop from one backbone-rich region to the next by tunneling through the mesogenic layers. As expected, the number of such defects is found to depend strongly on the rate of cooling. In the vicinity of such a defect, the smectic-A structure of the mesogen-rich layers is disrupted to give nematiclike ordering. Additionally, several extensive annealing runs of approximately 40 ns duration have been carried out at the point of microphase separation. During annealing the polymer backbone is seen to be slowly excluded from the mesogenic layers and lie perpendicular to the smectic-A director. These observations agree with previous assumptions about the structure of a SCLCP and with interpretations of x-ray diffraction and small angle neutron scattering data. The flexible alkyl spacers, which link the backbone to the mesogens, are found to form sublayers around the backbone layer.

Journal Article↗
PubMed2003

Intermediate-range order in permanently densified GeO2 glass.

Information about the partial structure factors of densified GeO2 glass has been obtained from neutron and x-ray diffraction measurements. Densification causes a reduction in the length scale of the intermediate range order (IRO). The difference structure factors obtained by combining the x-ray and neutron data so as to eliminate one partial structure factor at a time shows the greatest effects when the Ge-Ge correlations are eliminated and least when O-O correlations are eliminated. This implies that the reduced length scale results from a decrease in the next-nearest neighbor Ge-O and O-O distance caused by a rotation about the Ge-O-Ge bonds and a distortion of the GeO4 tetrahedra.

Journal Article↗
PubMed1998

On the electronic nature of low-barrier hydrogen bonds in enzymatic reactions.

The electronic nature of low-barrier hydrogen bonds (LBHBs) in enzymatic reactions is discussed based on combined low temperature neutron and x-ray diffraction experiments and on high level ab initio calculations by using the model substrate benzoylacetone. This molecule has a LBHB, as the intramolecular hydrogen bond is described by a double-well potential with a small barrier for hydrogen transfer. From an "atoms in molecules" analysis of the electron density, it is found that the hydrogen atom is stabilized by covalent bonds to both oxygens. Large atomic partial charges on the hydrogen-bonded atoms are found experimentally and theoretically. Therefore, the hydrogen bond gains stabilization from both covalency and from the normal electrostatic interactions found for long, weak hydrogen bonds. Based on comparisons with other systems having short-strong hydrogen bonds or LBHBs, it is proposed that all short-strong and LBHB systems possess similar electronic features of the hydrogen-bonded region, namely polar covalent bonds between the hydrogen atom and both heteroatoms in question.

Butanones↗
PubMed2002

Structural studies of several distinct metastable forms of amorphous ice.

Structural changes during annealing of high-density amorphous ice were studied with both neutron and x-ray diffraction. The first diffraction peak was followed from the high- to the low-density amorphous form. Changes were observed to occur through a series of intermediate forms that appear to be metastable at each anneal temperature. Five distinct amorphous forms were studied with neutron scattering, and many more forms may be possible. Radial distribution functions indicate that the structure evolves systematically between 4 and 8 angstroms. The phase transformations in low-temperature liquid water may be much more complex than currently understood.

Journal Article↗
PubMed1997

Highly aligned lipid membrane systems in the physiologically relevant "excess water" condition.

The "excess water" condition in biologically relevant systems is met when a membrane mesophase coexists with excess bulk water. Further addition of water to such a system results in no change to any of the system's physical properties (e.g., transition temperature, repeat spacing, and structural mesophases). Moreover, because biological membranes are anisotropic systems, many of their properties are best studied using aligned samples. Although model membrane systems are routinely aligned, they have traditionally been hydrated with water vapor. It is well known that membranes exposed to water vapor at 100% humidity do not imbibe the same quantity of water as a sample in contact with liquid water. As such, membranes that have been hydrated with water vapor have physical properties different from those of membranes dispersed in water. Because of this shortcoming, aligned membranes have not been utilized to their full potential. Here we present a novel and simple method of aligning model membrane systems under conditions of excess water, which will make possible, for the first time, a variety of techniques (e.g., neutron and x-ray diffraction, nuclear magnetic resonance, electron spin resonance, attenuated total reflection infrared spectroscopy, etc.) for studying such systems under physiologically relevant conditions. In addition, when dealing with samples of limited availability, the system allows for the conditions (buffer pH and ionic strength) to be altered without any effect on the sample's alignment.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1999

Supramolecular structures of peptide assemblies in membranes by neutron off-plane scattering: method of analysis.

In a previous paper (Yang et al., Biophys. J. 75:641-645, 1998), we showed a simple, efficient method of recording the diffraction patterns of supramolecular peptide assemblies in membranes where the samples were prepared in the form of oriented multilayers. Here we develop a method of analysis based on the diffraction theory of two-dimensional liquids. Gramicidin was used as a prototype model because its pore structure in membrane in known. At full hydration, the diffraction patterns of alamethicin and magainin are similar to gramicidin except in the scale of q (the momentum transfer of scattering), clearly indicating that both alamethicin and magainin form pores in membranes but of different sizes. When the hydration of the multilayer samples was decreased while the bilayers were still fluid, the in-plane positions of the membrane pores became correlated from one bilayer to the next. We believe that this is a new manifestation of the hydration force. The effect is most prominent in magainin patterns, which are used to demonstrate the method of analysis. When magainin samples were further dehydrated or cooled, the liquid-like diffraction turned into crystal-like patterns. This discovery points to the possibility of investigating the supramolecular structures with high-order diffraction.

Cell Membrane↗
PubMed1989

Study of temperature factors in cubic crystals by high-voltage electron diffraction.

The critical voltages for systematic reflections and splits of Kikuchi lines were measured using a high-voltage electron microscope to investigate the atomic temperature factors in cubic crystals. The split of the Kikuchi line at the intersection with the forbidden 222 Kikuchi line as well as the critical voltage of the 333 reflection for Si and Ge decreased steeply with temperature. The temperature dependence showed that the anharmonic contribution to the atomic-temperature factor for Si and Ge is extremely weak in the temperature range 300 approximately 1078 K. On the contrary, the B factors obtained from the measured critical voltages for Al, Cu, and Fe varied nonlinearly with temperature, suggesting the importance of the anharmonic effect in the vibration of atoms. The observed temperature dependence of the critical voltages for the metals were compared with calculations based on harmonic, quasi-harmonic, and anharmonic approximations. The quasi-harmonic approximation that takes into account the thermal expansion modification reproduces well the observed values for Fe but not those for Al and Cu. The effect of intrinsic anharmonic vibration should be considered for reproducing the results for Al and Cu. Fitting the measured critical voltages with the calculated ones, we estimated the values for coefficients of the isolated atom potentials. The results are in good agreement with those obtained by neutron and X-ray diffraction.

Aluminum↗
PubMed2003

Small-angle neutron scattering study of the lipid bilayer thickness in unilamellar dioleoylphosphatidylcholine vesicles prepared by the cholate dilution method: n-decane effect.

Previous X-ray diffraction studies on fully hydrated fluid lamellar egg phosphatidylcholine phases indicated a approximately 10 A increase of bilayer thickness in the presence of excess n-decane [Biochim. Biophys. Acta 597 (1980) 455], while the small-angle neutron scattering (SANS) on unilamellar extruded dioleoylphosphatidylcholine (DOPC) vesicles detected substantially smaller 2.4+/-1.3 A bilayer thickness increase at n-decane/DOPC molar ratio of 1.2 [Biophys. Chem. 88 (2000) 165]. The purpose of the present study is to investigate the n-decane effect on the bilayer thickness in unilamellar DOPC vesicles prepared by the sodium cholate (NaChol) dilution method. Mixed DOPC+NaChol micelles at DOPC and NaChol concentrations of 0.1 mol/l were prepared in 2H(2)O containing 0.135 mol/l NaCl. This micellar solution was diluted in 0.135 mol/l NaCl in 2H(2)O to reach the final DOPC and NaChol concentrations of 0.008 mol/l. Thirty microliters of n-decane solution in methanol was added to 1 ml of this dispersion. After methanol evaporation, SANS was conducted on the dispersions. From the Kratky-Porod plot ln[I(Q)Q(2)] vs. Q(2) of SANS intensity I(Q) in the range of scattering vector values Q corresponding to interval 0.001 A(-2)<or=Q(2)<or=0.006 A(-2), the bilayer radius of gyration R(g) and the bilayer thickness parameter d(g)=12(0.5)R(g) were obtained. The values of d(g) indicate that the bilayer thickness increases by 2.4+/-0.9 A up to n-decane/DOPC molar ratio of 1.6. This result confirms the previous SANS findings obtained with extruded vesicles.

Alkanes↗
PubMed1993

Hexamethylenetetramine at 298 K: new refinements.

New refinements of the crystal structure of hexamethylenetetramine (HMT, C6H12N4) have been carried out using previously reported neutron and X-ray diffraction data collected at 298 K. A new feature in the structure model is the inclusion of third-order Gram-Charlier coefficients for the description of the anharmonic C-H bond stretching, which is found to be significant. The charge-density distribution is analyzed in terms of the pseudoatom model of Stewart [Acta Cryst. (1976). A32, 565-574]. Our experimental determination of the molecular octapole moment gives = +1.0 (3)/e/ A3. The refinement involving HMT provides a worst-case example of a general deficiency in the application of the multipole model to noncentrosymmetric structures. Strong least-squares correlations occur involving the electron population parameters of all atoms for certain of the multipole terms, namely those odd-order terms that are invariant under the symmetry operations of the space group.

Crystallography, X-Ray↗
PubMed2001

A note on the problem of scattering from a single atomic plane and a stack of planes. Differences between the Ewald and other diffraction theories.

The scattering of a scalar plane wave (neutrons) from a single atomic plane consisting of any two-dimensional lattice with a basis is studied using the Ewald dynamical theory of diffraction. Formulae for the reflection and transmission coefficients obtained by evaluating the optical plane lattice sums are valid for general geometries, including nonsymmetrical and noncoplanar diffractions. The approach adopted is different from and more general than that by Yashiro & Takahashi [Acta Cryst. (2000), A56, 1663-167]. The structure factor yielded by this procedure differs from that used in the kinematical or Laue dynamical diffraction theories.

Journal Article↗
PubMed1985

Effect of proteolipid protein on central nervous system myelin membrane fluidity.

The effect which intrinsic (proteolipid) protein has on fluidity of central nervous system myelin membrane was measured through differences in temperature-dependent anisotropy of the lipid-soluble fluorescence probe, 1,6-diphenyl-1,3,5-hexatriene (DPH), in multilamellar vesicles (MLV) prepared from total myelin lipids in the presence and absence of proteolipid protein. Very little difference was observed in the anisotropies of DPH incorporated into intact myelin membrane vesicles compared with MLV reconstituted from total myelin lipid plus proteolipid protein but excluding myelin basic protein. In contrast, a significant decrease (P less than 0.01) in anisotropy was observed when MLV prepared from total myelin lipids depleted of proteolipid protein were compared with vesicles containing proteolipid protein. Given the different distributions of myelin basic protein and proteolipid protein suggested by freeze-fracture, neutron and X-ray diffraction studies, and the fact that the hydrophobic DPH probe is known to distribute in the non-polar regions of lipid bilayers, we interpret the marked decrease in anisotropy when proteolipid protein is excluded from MLV to suggest that at least part of the proteolipid is distributed in the hydrocarbon region of the MLV. These findings are consistent with the earlier physical studies and recent postulations that extensive hydrophobic segments exist in proteolipid protein and that these hydrophobic segments are buried in the myelin lipid bilayer and alternate with hydrophilic extra-membrane segments.

Brain↗
PubMed1992

The effect of fluoride treatment on bone mineral crystals in the rat.

In order to investigate the effect of fluoride on bone mineral crystals, we gave groups of female rats 8 mM NaF/L water and distilled water to control groups. The rats were sacrificed at six weeks, three months, and six months. The fluor content of the bone was determined by neutron activation. X-ray diffraction showed no difference in bone crystal size/strain with fluoride treatment. Fourier transform Infrared Spectroscopy (FTIR) showed an increased crystallinity in fluoride-fed animals, which seems to be associated with a decrease of labile phosphate environment. Three carbonate bands have been found in fluoridated and normal bone samples. The distribution of carbonate ions on type A and B sites is strongly affected by fluoride. Type A carbonate is always present in bone, but decreases with increasing bone fluoride content. A carbonate band found at 866 cm-1 may correspond to a fluoride interaction with type B carbonate ions. Lastly, phosphate bands have been found to be shifted towards high wave number, which is probably related to the change in unit cell size induced by the fluoride ion. All these changes induced by fluoride reduce the solubility of bone crystals by direct incorporation of fluoride ions in the apatite lattice and by decreasing the labile phosphate environments.

Animals↗
PubMed2004

Ions from the Hofmeister series and osmolytes: effects on proteins in solution and in the crystallization process.

Sephadex G-10 gel sieving chromatography, Jones-Dole viscosity B coefficients, and solution neutron and X-ray diffraction are used to show that small ions of high charge density (e.g., sulfate, phosphate, the carboxylate, sodium, and fluoride) are strongly hydrated (kosmotropes) whereas large monovalent ions of low charge density (e.g., ammonium, chloride, potassium, and the positively charged amino acid side chains) are weakly hydrated (chaotropes). The heats of solution of the crystalline alkali halides are then used to show that only oppositely charged ions of equal water affinity spontaneously form inner sphere ion pairs, and that this controls ion binding to proteins. The net charge on a protein is a major determinant of its solubility. Finally, the surface potential difference and surface tension at an air-salt solution interface are used to generate a simple model for how ions affect protein stability and solubility through indirect interactions at the protein-solution interface. A few comments about small neutral osmolytes are also included.

Chemistry Techniques, Analytical↗