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PubMed2004

Crystal and magnetic structure of the double perovskite Sr2CoUO6: a neutron diffraction study.

Sr2CoUO6 double perovskite has been prepared as a polycrystalline powder by solid-state reaction, in air. This material has been studied by X-ray, neutron powder diffraction (NPD) and magnetic measurements. At room temperature, the crystal structure is monoclinic, space group P2(1)/n, Z= 2, with a= 5.7916(2), b= 5.8034(2), c= 8.1790(3) A, beta= 90.1455(6)degrees. The perovskite lattice consists of a completely ordered array of CoO6 and UO6 octahedra, which exhibit an average tilting angle phi= 11.4 degrees. Magnetic and neutron diffraction measurements indicate an antiferromagnetic ordering below TN = 10 K. The low-temperature magnetic structure was determined by NPD, selected among the possible magnetic solutions compatible with the P2(1)/n space group, according with the group theory representation. The propagation vector is k= 0. A canted antiferromagnetic structure is observed below TN = 10 K, which remains stable down to 3 K, with an ordered magnetic moment of 2.44(7)mu(B) for Co2+ cations. The magnetic moment calculated from the Curie-Weiss law at high temperatures (5.22 mu(B)/f.u.) indicates that the orbital contribution is unquenched at high temperatures, which is consistent with high-spin Co2+((4)T(1g) ground state) in a quasi-regular octahedral environment. Magnetic and structural features are consistent with an electronic configuration Co2+[3d(7)]-U6+[Rn].

Journal Article↗
PubMed1983

Neutron diffraction analysis of cytochrome b5 reconstituted in deuterated lipid multilayers.

Cytochrome b5 was reconstituted with a highly deuterated phospholipid to form ordered multilayers consisting of repeated centrosymmetric pairs of asymmetric lipid-protein bilayers. Lamellar neutron diffraction data were collected to approximately 29 A resolution, and have been interpreted using models for the interaction of the membrane-binding domain of cytochrome b5 with the lipid bilayer. A range of different models was examined, and those in which the protein penetrates well into the bilayer, possibly spanning it, are favored.

Animals↗
PubMed1999

Single-crystal neutron diffraction study of beta-Cs3(HSO4)2

The structure of beta-Cs(3)(HSO(4))(2)[H(2-x)(S(x)P(1-x))O(4)] has been examined by single-crystal neutron diffraction at 15 K. The compound crystallizes in space group C2/c and contains four formula units in the unit cell, with lattice parameters a = 19.769 (9), b = 7.685 (2), c = 8.858 (3) Å and beta = 100.60 (4) degrees. Refinement of P, S and H site occupancies indicated that the value of x (in the stoichiometry) is 0.500 (6). This, together with the unit-cell volume of 1322.8 (14) Å(3), implies a density of 3.463 Mg m(-3). The structure contains zigzag rows of XO(4) anions, where X = P or S, that alternate, in a checkerboard fashion, with zigzag rows of Cs cations. Moreover, there is one proton site, H(3), with an occupancy of 0.25 and one X-atom site, X(1), that is occupied by 0.5 P and 0.5 S. These features are in general agreement with a previous X-ray structure determination carried out at 298 K. In contrast to the X-ray study, however, it was found that two different structural models adequately fit the diffraction data. In the first model, the proton vacancies and the P atoms were assumed to be randomly distributed over the H(3) and X(1) sites, respectively, and to have no impact on the local structure. In the second model, several atoms were assigned split occupancies over two neighboring sites, to reflect the presence or absence of a proton vacancy, and the presence of P or S on the X(1) site. Refinement assuming the first model, in which anisotropic displacement parameters for 12 of 14 atom sites in the asymmetric unit were employed, yielded residuals wR(F(2)) = 0.084 and wR(F) = 0.038. For the second model, in which anisotropic displacement parameters were utilized for only the five atoms that were not split relative to the first model, the residuals were wR(F(2)) = 0.081 and wR(F) = 0.036.

Journal Article↗
PubMed1988

On the occurrence of three-center hydrogen bonds in cyclodextrins in crystalline form and in aqueous solution: comparison of neutron diffraction and molecular dynamics results.

Three-center (bifurcated) hydrogen bonds may play a role by serving as an intermediate state between different dynamically changing hydrogen bonding patterns. Hydrogen bonding configurations can be studied experimentally by neutron diffraction and theoretically by computer simulation techniques. Here, both methods are used to analyse the occurrence of three-center hydrogen bonds in crystals of cyclodextrins. Almost all experimentally observed three-center hydrogen bonds in the crystal are reproduced in the molecular dynamics (MD) simulations, even as far as the detailed asymmetric geometry is concerned. On the basis of this result a MD simulation of cyclodextrin in aqueous solution is searched for the occurrence of three-center hydrogen bonds. Significant differences are found. In solution more different three-center hydrogen bonds per alpha-cyclodextrin molecule are observed than in the crystal but the population (existence as percent of the simulation period) of each three-center hydrogen bond is lower in solution than in crystal. These may indeed serve as intermediate states in the process of changing one hydrogen bonding pattern into another.

Chemical Phenomena↗
PubMed1986

Protein dynamics investigated by neutron diffraction.

The most correct model of the molecular structure of a protein molecule is one which describes it as having a number of variable conformational states. These states differ in degree over a large spectrum of structural variation ranging from individual atomic vibrational motion to significant tertiary denaturation. The application of the neutron diffraction techniques discussed above dealt with two classes of conformational fluctuation, "protein breathing" and "regional melting." The utility of the neutron technique stems from the ability to locate hydrogen atoms and to discriminate between hydrogens and deuteriums. This latter attribute allows for performing H/D exchange experiments by identifying individual sites of exchange. With this information it has been possible to discern which regions of the protein molecule undergo regional melting. Protein breathing was explored by analyzing the rotational properties of side chain methyl groups. Such information clearly suggested that most of these groups reside in "staggered" (low energy) conformation in the time averaged structure and are not greatly affected by local structural packing. Together these two classes of conformational fluctuation span nearly the full range of all motions that might play a role in biological activity. Information about such motions can be obtained from other types of physicochemical methods, but in most cases the interpretation of the data is considerably less definitive than that which can be obtained from a neutron analysis.

Crystallography↗
PubMed2005

Distorted hexagonal phase studied by neutron diffraction: lipid components demixed in a bent monolayer.

The recent discovery of a distorted hexagonal phase in 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine/1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPE/DOPC) mixtures raised the intriguing question as to whether lipid mixtures demix in a bent monolayer. We performed neutron diffraction on a mixture of headgroup deuterated DOPC-d(13) and nondeuterated DOPE to study the lipid distribution in the distorted hexagonal phase. The 1:1 lipid mixture in full hydration and 25 degrees C was in a homogeneous lamellar phase. Upon dehydration the mixture transformed to a rhombohedral phase, then to a distorted inverted hexagonal phase, and finally to a regular inverted hexagonal phase. In the distorted hexagonal phase, the diffraction pattern showed a two-dimensional monoclinic lattice with two reciprocal vectors of equal length (1.5 nm(-)(1)) forming an angle 53 degrees between them. Diffraction intensities measured while varying the D(2)O/H(2)O ratio in the humidity was used to solve the phase problem. The neutron scattering length density distribution of the distorted hexagonal phase was constructed. The constant density contours are approximately elliptical. The difference in the eccentricities of the contours between the water and lipid distributions indicates that the DOPE/DOPC ratio is not uniform around the elliptical lipid tube in the unit cell. DOPE is preferentially distributed at the vertex regions where the curvature is the highest. Thus for the first time it is shown that when a monolayer of a homogeneous lipid mixture is bent, the lipid components are partially demixed in reaching the free energy minimum.

Lipids↗
PubMed2001

Neutron diffraction study of phi-Bi(8)Pb(5)O(17): structure refinement and analysis of cationic ordering.

The triclinic crystal structure of the varphi phase in the structure of the Bi(2)O(3)-PbO phase diagram has been recently solved by the synergetic use of electron and X-ray diffraction on a polycrystalline Bi(8)Pb(5)O(17) sample. In the present work the problem is re-examined on the basis of powder neutron diffraction data: the structure has been confirmed and refined by the Rietveld method. The increased accuracy of the O-atom positions allowed the study of the cationic ordering in this structure by means of bond-valence calculations and charge distribution analysis. The results, confirmed by the refinement of the site occupancies, indicate that the structure is ordered to a large extent, with Bi and Pb atoms occupying preferentially different lattice sites. In this frame, the varphi phase being the most ordered one in the considered region of the Bi(2)O(3)-PbO phase diagram, it should represent the thermodynamically stable low-temperature polymorph.

Journal Article↗
PubMed1998

Localization of glycolipids in membranes by in vivo labeling and neutron diffraction.

Evidence is accumulating for the lateral organization of cell membrane lipids and proteins in the context of sorting or intracellular signaling. So far, however, information has been lacking on the details of protein-lipid interactions in such aggregates. Purple membranes are patches made up of lipids and the protein bacteriorhodopsin in the plasma membrane of certain Archaea. Naturally crystalline, they provide a unique opportunity to study the structure of a natural membrane at submolecular resolution by diffraction methods. We present a direct structural determination of the glycolipids with respect to bacteriorhodopsin in these membranes. Deuterium labels incorporated in vivo into the sugar moieties of the major glycolipid were localized by neutron diffraction. The data suggest a role for specific aromatic residue-carbohydrate stacking interactions in the formation of the purple membrane crystalline patches.

Amino Acids↗
PubMed1999

Orientation of the headgroup of phosphatidylinositol in a model biomembrane as determined by neutron diffraction.

Derivatives of the sodium salt of dimyristoylphosphatidylinositol (DMPI) have been synthesized specifically deuterated in the headgroup. A 50:50 (molar) mixture of DMPI with dimyristoylphosphatidylcholine (DMPC) hydrated to the level of 16 waters/lipid gives a biomembrane-like Lalpha phase at 50 degrees C. Comparison of the neutron diffraction scattering profiles for deuterated and undeuterated membranes allowed the depth of each deuterium (hydrogen) within the bilayer to be determined to +/-0.5 A. This gave the orientation of the inositol ring which lies more-or-less along the bilayer normal projecting directly out into the water. This orientation is similar to that of the sugar residue in glycolipids and confirms previous models for PI. On the assumption that the (P)O-DAG bond is more-or-less parallel to the bilayer normal, it is consistent with a roughly trans, trans, trans, gauche- conformation for the glyceryl-phosphate-inositol link. In the case of DMPI, it is the C4-hydroxy group which is most fully extended into the water layer, but when this is phosphorylated, the inositol ring turns over and tilts so that the C5-hydroxy group is now the one furthest extended into the water layer. Hence, at each stage in the pathway PI --> PI-4P --> PI-4,5-P2, it is the hydroxy position most exposed to the water which undergoes phosphorylation. Whereas the orientation of the inositol ring in DMPI can be seen simply as maximizing its hydration, the tilt of the ring in DMPI-4P cannot be explained in this way. It is suggested that it is due to an electrostatic interaction.

Carbohydrate Conformation↗
PubMed1991

Neutron diffraction studies of the structure of filamentous bacteriophage Pf1. Demonstration that the coat protein consists of a pair of alpha-helices with an intervening, non-helical surface loop.

The structure of filamentous bacteriophage Pf1 has been studied using neutron diffraction from magnetically oriented gels of native and specifically deuterated phage. These methods have been used to determine the positions of the two methionine, two tyrosine and six isoleucine residues of the coat protein. Combined with the positions of the five valine residues previously determined, they represent one third (15 of 46) of the residues of the coat protein. These 15 amino acid residue positions have been used as the basis for constructing a model for the protein consisting of two alpha-helices with an intervening surface loop. The first helix extends from near the amino terminus to Ile12. The second helix extends from Lys20 to at least Met42, and may contain a bend between Ile32 and Val35. The two helices are tilted by about 15 degrees relative to one another, and are positioned in such a way that they appear to be bound end-to-end by main-chain hydrogen bonds. The intervening, non-helical loop, made up of Thr13 to Met19, connects the two helices without disrupting the pattern of main-chain hydrogen bonding, but does not result in a bend in the otherwise continuous helical structure. This model is used to predict the approximate positions of all amino acid residues in the Pf1 protein coat, providing a basis for further understanding of a number of viral properties including the symmetry transitions, the non-isomorphism of heavy-atom derivatives, and the protein-protein and protein-DNA interactions in the virion.

Amino Acid Sequence↗
PubMedDate not supplied

A combined X-ray and neutron diffraction study of selectively deuterated melittin in phospholipid bilayers: effect of pH.

In order to study consequences of protonation of the N-terminus upon the interaction of the bee venom melittin with phospholipid bilayers, analogues of melittin, some of which were specifically deuterated at either Ala-12 or 15, were synthesized. These peptides were incorporated into bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine at either low pH (N-terminus protonated) or high pH (N-terminus unprotonated). X-ray and neutron diffraction data were collected from ordered stacks of these bilayers and from peptide-free controls. Phase determination was carried out using the swelling series (X-ray) and isomorphous derivative (neutron) methods. The water distribution between adjacent bilayers in the stacks may be described by a pair of Gaussians whose position and width change with the protonation state of the melittin. Difference Fourier profiles reveal that the melittin largely incorporates into the phospholipid bilayers. Changes in the water, melittin and deuterium label distributions fit a model in which the melittin lies both at the surface and close to the centre of the bilayer, the distribution of peptide between these locations being pH-dependent, with a larger population of surface melittin when the N-terminus is unprotonated.

Amino Acid Sequence↗
PubMed1981

The reaction center profile structure derived from neutron diffraction.

Both reaction center protein from the photosynthetic bacteria Rhodopseudomonas sphaeroides and egg phosphatidylcholine can be deuterium labelled; the reaction center protein can be incorporated into the phosphatidylcholine bilayers forming a homogeneous population of unilamellar vesicles. The lipid profile and the reaction center profile within these reconstituted membrane profiles were directly determined to 32 A resolution using lamellar neutron diffraction from oriented membrane multilayers containing either deuterated or protonated reaction centers, and either deuterated or protonated phosphatidylcholine. The 32 A resolution reaction center profile shows that the protein spans the membranes, and has an asymmetric mass distribution along the perpendicular to the membrane plane. These results were combined with previously described X-ray diffraction results in order to extend the resolution of the derived reaction center profile to 9 A.

Bacterial Proteins↗
PubMed1991

Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution.

This is the first in a series of papers concerned with methods for the determination of the structures of fluid phospholipid bilayers in the liquid-crystalline (L alpha) phase. The basic approach is the joint refinement of quasimolecular models (King and White, 1986. Biophys. J. 49:1047-1054) using x-ray and neutron diffraction data. We present here (a) the rationale for quasimolecular models, (b) the nature of the resolution problem for thermally disordered bilayers, and (c) an analysis of the resolution of experiments in which Gaussian functions are used to describe the distribution of submolecular components. We show that multilamellar liquid-crystalline bilayers are best described by the convolution of a perfect lattice function with a thermally disordered bilayer unit cell. Lamellar diffraction measurements on such a system generally yield only 5-10 orders of diffraction data from which transbilayer profiles of the unit cell can be constructed. The canonical resolution of these transbilayer profiles, defined as the Bragg spacing divided by the index of the highest recorded diffraction order, is typically 5-10 A. Using simple model calculations, we show that the canonical resolution is a measure of the widths of the distributions of constituents of the unit cell rather than a measure of the spatial separation of the distributions. The widths provide a measure of the thermal motion of the bilayer constituents which can be described by Gaussian functions. The equilibrium positions of the centers of the distributions can be determined with a precision of 0.1-0.5 A based upon typical experimental errors.

Lipid Bilayers↗
PubMed2004

Crystalline, mixed-valence manganese analogue of prussian blue: magnetic, spectroscopic, X-ray and neutron diffraction studies.

The compound of stoichiometry Mn(II)3[Mn(III)(CN)6]2.zH2O (z = 12-16) (1) forms air-stable, transparent red crystals. Low-temperature single crystal optical spectroscopy and single crystal X-ray diffraction provide compelling evidence for N-bonded high-spin manganese(II), and C-bonded low-spin manganese(III) ions arranged in a disordered, face-centered cubic lattice analogous to that of Prussian Blue. X-ray and neutron diffraction show structured diffuse scattering indicative of partially correlated (rather than random) substitutions of [Mn(III)(CN)6] ions by (H2O)6 clusters. Magnetic susceptibility measurements and elastic neutron scattering experiments indicate a ferrimagnetic structure below the critical temperature Tc = 35.5 K.

Journal Article↗
PubMed2002

Structure and dynamics of ND3BF3 in the solid and gas phases: a combined NMR, neutron diffraction, and Ab initio study.

The decrease in D-->A bond lengths, previously reported for some Lewis acid/base complexes, in going from the gas to the solid phases is investigated by obtaining an accurate crystal structure of solid ND(3)BF(3) by powder neutron diffraction. The B-N internuclear distance is 1.554(3) A, 0.118 A shorter than the most recent gas-phase microwave value and 0.121 A shorter than the single molecule geometry optimized (1.672 A, CISD/6-311++G(d,p)) bond length. The crystal structure also shows N-D.F-B hydrogen bonds. The effects of this change in structure and of intermolecular hydrogen-bonding on nuclear magnetic shielding (i.e., chemical shifts) and the nuclear quadrupolar coupling constants (QCC) are investigated by ab initio molecular orbital and density functional theory calculations. These calculations show that the nitrogen ((15)N and (14)N) and boron ((11)B and (10)B) chemical shifts should be rather insensitive to changes in r(BN) and that the concomitant changes in molecular structure. Calculations on hydrogen-bonded clusters, based on the crystal structure, indicate that H-bonding should also have very little effect on the chemical shifts. On the other hand, the (11)B and (14)N QCCs show large changes because of both effects. An analysis of the (10)B[(19)F] line shape in solid ND(3)(10)BF(3) yields a (11)B QCC of +/-0.130 MHz. This is reasonably close an earlier value of +/-0.080 MHz and the value of +/-0.050 MHz calculated for a [NH(3)BF(3)](4) cluster. The gas-phase value is 1.20 MHz. Temperature-dependent deuterium T(1) measurements yield an activation energy for rotation of the ND(3) group in solid ND(3)BF(3) of 9.5 +/- 0.1 kJ/mol. Simulations of the temperature-dependent T(1) anisotropy gave an E(a) of 9.5 +/- 0.2 kJ/mol and a preexponential factor, A, of 3.0 +/- 0.1 x 10(12) s(-)(1). Our calculated value for a [NH(3)BF(3)](4) cluster is 16.4 kJ/mol. Both are much higher than the previous value of 3.9 kJ/mol, from solid-state proton T(1) measurements.

Journal Article↗
PubMed1983

The determination of the separate Ca2+ pump protein and phospholipid profile structures within reconstituted sarcoplasmic reticulum membranes via X-ray and neutron diffraction.

We have previously compared the electron density profiles for several highly-functional reconstituted sarcoplasmic reticulum membranes with that for the isolated sarcoplasmic reticulum membrane (Herbette, L., Scarpa, A., Blasie, J.K., Wang, C.T., Saito, A. and Fleischer, S. (1981) Biophys. J. 36, 47-72). In this paper, we compare the separate calcium pump protein profile within these reconstituted sarcoplasmic reticulum membranes, as derived by X-ray and neutron diffraction methods, with that within isolated sarcoplasmic reticulum membranes. In addition, the time-average perturbation of the lipid bilayer by the incorporated calcium pump protein within these reconstituted sarcoplasmic reticulum membranes has been determined in some detail.

Animals↗
PubMed1980

Neutron diffraction identifies His 57 as the catalytic base in trypsin.

The mechanism of action of trypsin and other serine proteases has been widely debated, particularly with regard to the identification of the group at the active site which functions as the chemical base during the catalytic process. Attempts to resolve this question by a number of indirect techniques, including NMR, isotope exchange, difference IR and quantum mechanical calculations, have resulted in different identifications of this group. Neutron diffraction, because of its ability to locate hydrogen atoms experimentally, offers the most direct way of resolving this issue. Results are presented here from a 2.2-A neutron data set for bovine trypsin covalently inhibited by a transition-state analogue, the monoisopropylphosphoryl (MIP) group. His 57 is clearly identified as the base in the catalytic process.

Amino Acid Sequence↗
PubMed2002

Electron distribution and molecular motion in crystalline benzene: an accurate experimental study combining CCD X-ray data on C6H6 with multitemperature neutron-diffraction results on C6D6.

The electronic properties of the benzene molecule, for example its quadrupole moment and the electric field gradients (EFG's) at the H nuclei, are of fundamental importance in theoretical and experimental chemistry. With this in mind, single-crystal X-ray diffraction data on C(6)H(6) were collected with a charge-coupled device detector at T approximately 110 K. As accurate modelling of the thermal motion in the crystal was regarded as vital, especially for the hydrogen atoms, anisotropic-displacement parameters (ADP's) for the C and H atoms in C(6)H(6) were derived in a straightforward fashion from analysis of the temperature dependence of ADP's for the C and D atoms in C(6)D(6) at 15 K and 123 K obtained by neutron diffraction. Agreement between C-atom ADP's derived from thermal-motion analysis of neutron data and those obtained from multipole refinement by using the X-ray data is extraordinarily good; this gives confidence in the modelling of vibrational motion for the H atoms. The molecular quadrupole moment derived from the total charge density of the molecule in the crystal is (-29.7+/-2.4)x10(-40) C m(2), in excellent agreement with measurements made in the gas phase and in solution. The average deuterium nuclear quadrupole coupling constant (DQCC) derived from EFG tensors at H atoms is 182+/-17 kHz, also in excellent agreement with independent measurements. The strategy employed in this work may be of more general applicability for future accurate electron density studies.

Benzene↗