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PubMed1988

A model for vitamin B6--amino-acid-related metal complexes. Neutron diffraction study of aqua(N-salicylideneglycinato)copper(II) hemihydrate at 130 K.

A neutron diffraction study of aqua(N-salicylideneglycinato)copper(II) hemihydrate, [Cu(C9H7NO3)-(H2O)].0.5H2O, Mr = 267.7, a model for vitamin B6-amino-acid-related metal complexes, has been carried out at 130 K. Least-squares refinement based on 3800 reflections [(sin theta/lambda)max = 0.786 A-1] converged at R(F2) = 4.5%. The crystal is monoclinic, space group C2/c, Z = 8 with cell parameters at 130 K: a = 17.030 (3), b = 6.665 (1), c = 17.469 (5) A, beta = 111.13 (1) degree, V = 1849.50 A3. The bond distances between non-H atoms have been determined with estimated standard deviations in the range 0.0008-0.0012 A; the corresponding values for distances involving H atoms are 0.0017-0.0020 A. The presence of a Cu11 ion does not significantly change the bond distances around the alpha-C atom from those observed in glycine or glycylglycine. There are, however, indications of differences in distance and direction relative to the pi system for the two alpha-C-H bonds. These bond vectors are inclined at angles of 30 and 71 degrees to the plane of the conjugated pi system. A planar conjugated pi-system is stabilized by chelation to the Cu ion.

Amino Acids↗
PubMed1980

Conformation of phosphatidylethanolamine in the gel phase as seen by neutron diffraction.

For confirmation of some general aspects of phospholipid conformation in membranes and extension of previous neutron diffraction studies on dipalmitoyllecithin, measurements have now been made on 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE) in the gel phase by the same method. Three selectively deuterated samples were investigated; in one of the specimens the first methylene segment close to the glycerol backbone in both chains was deuterated, and in the other two samples one of the methylene segments in the phosphoethanolamine group was replaced by CD2. Together with the undeuterated DPPE, these probes were investigated at very low water content (about 1.5--2 molecules of water per lipid) as oriented samples at 25 degrees C. The intensities of the first 12 reflections were collected and phased, and the mean positions of the segments were determined. The results confirm the idea that the conformation of a DPPE molecule in the gel state is very similar to the crystal structure of rac-1,2-dilauroyl-sn-glycero-3-phosphoethanolamine. The two main features are (1) the chains remain in all all-trans conformation having an axial displacement of about 3--4 A, (2) the zwitterionic dipoles in the head groups of both compounds are found to be aligned almost parallel to the bilayer surface. The main advantage of the method results in the fact that the combination of neutron scattering with selectively deuterated probes allows the determination of the mean label position to an accuracy of up to +/- 1 A.

Crystallography↗
PubMed1984

Direct determination of the calcium profile structure for dipalmitoyllecithin multilayers using neutron diffraction.

The distribution of calcium in lamellar phases of dipalmitoyllecthin (DPPC) multilayers was directly determined by neutron diffraction and stable isotope substitution of 44Ca for 40Ca. A significant resonance effect on the intensities of the lamellar diffraction pattern was observed for millimolar concentrations of these calcium isotopes. The calcium difference profile indicated that calcium was localized in the phospholipid headgroup region, being excluded from the hydrocarbon core as was water separately determined from the water profile structure obtained by H2O/D2O exchange. A reciprocal space analysis of the difference structure factors indicated that calcium binds preferentially to within 1-2 A of the phosphate moiety of the phospholipid head groups of the DPPC bilayer.

Calcium↗
PubMed1997

Five-Coordinate Hydrogen: Neutron Diffraction Analysis of the Hydrido Cluster Complex

Pentacoordinate hydrogen atoms were identified by single-crystal neutron diffraction analysis of [N(CH3)4]3[H2Rh13(CO)24]. The hydrogen atoms are located in square pyramidal cavities of the Rh13 cluster, in positions almost coplanar with the Rh4 faces on the surface of the cluster. They are slightly displaced inward, toward the central rhodium atom of the cluster, with average H-Rh(central) and H-Rh(surface) distances of 1.84(2) and 1.97(2) angstroms, respectively. This result shows that hydrogen, which normally forms only one bond, can be attached to five other atoms simultaneously in a large metal cluster.

Journal Article↗
PubMed2000

"NaB15": a new structural description based on X-ray and neutron diffraction, electron microscopy, and solid-state NMR spectroscopy

A boron-rich sodium boride, formerly known as NaB15, has been subjected to a comprehensive structural reinvestigation using X-ray single-crystal and powder diffraction, low-temperature neutron and electron diffraction, high-resolution transmission electron microscopy, and 23Na solid-state NMR spectroscopy. The results indicate that the previously published orthorhombic space group is incorrect. Consistent with all of the experimental results a modified structural description is developed in the monoclinic space group Ilml (a = 585.92(3), b= 1039.92(6), c = 833.17(5) pin, beta = 90.373(5) from powder data). Because one of the interstitial boron atom positions remains unoccupied, the accurate compositional formula is NaB145 or Na2B29.

Journal Article↗
PubMed1986

Localization of two chymotryptic fragments in the structure of renatured bacteriorhodopsin by neutron diffraction.

The structure of crystalline purple membrane reconstituted from purified bacteriorhodopsin (BR) chymotryptic fragments has been studied by neutron diffraction. In one of the samples studied, the fragment C-2, encompassing the first two predicted transmembrane segments, was prepared from deuterated purple membrane. The diffraction changes when the natural C-2 fragment is substituted by a deuterated one are analysed in terms of a seven-helix model for BR. The assignment of the labelled fragment to one end of the molecule placed new constraints on folding models for the protein.

Bacteriorhodopsins↗
PubMed1991

Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. II. "Composition-space" refinement method.

This is the second of two papers describing a method for the joint refinement of the structure of fluid bilayers using x-ray and neutron diffraction data. We showed in the first paper (Wiener, M. C., and S. H. White. 1990. Biophys. J. 59:162-173) that fluid bilayers generally consist of a nearly perfect lattice of thermally disordered unit cells and that the canonical resolution d/hmax is a measure of the widths of quasimolecular components represented by simple Gaussian functions. The thermal disorder makes possible a "composition space" representation in which the quasimolecular Gaussian distributions describe the number or probability of occupancy per unit length across the width of the bilayer of each component. This representation permits the joint refinement of neutron and x-ray lamellar diffraction data by means of a single quasimolecular structure that is fit simultaneously to both diffraction data sets. Scaling of each component by the appropriate neutron or x-ray scattering length maps the composition space profile to the appropriate scattering length space for comparison to experimental data. Other extensive properties, such as mass, can also be obtained by an appropriate scaling of the refined composition space structure. Based upon simple bilayer models involving crystal and liquid crystal structural information, we estimate that a fluid bilayer with hmax observed diffraction orders will be accurately represented by a structure with approximately hmax quasimolecular components. Strategies for assignment of quasimolecular components are demonstrated through detailed parsing of a phospholipid molecule based upon the one-dimensional projection of the crystal structure of dimyristoylphosphatidylcholine. Finally, we discuss in detail the number of experimental variables required for the composition space joint refinement. We find fluid bilayer structures to be marginally determined by the experimental data. The analysis of errors, which takes on particular importance under these circumstances, is also discussed.

Lipid Bilayers↗
PubMed1990

Hydroxyl hydrogen conformations in trypsin determined by the neutron diffraction solvent difference map method: relative importance of steric and electrostatic factors in defining hydrogen-bonding geometries.

Neutron diffraction maps have been used to assign the rotor conformations of the hydroxyl hydrogens in trypsin. Knowledge of these conformations is used to assess the relative importance of steric and electrostatic effects in conferring the H-bonding geometries of these groups. A general finding was that most hydroxyl groups are rotationally ordered with their highest populated conformation near the low-energy staggered orientation. For the low-energy conformers (-60 degrees, 60 degrees, 180 degrees) of serine and threonine, the trans (-180 degrees) position is most highly populated followed by +60 degrees. In trypsin, only 1 of 24 serines was found in the -60 degrees conformer. Serine hydroxyls preferentially act as H-bond acceptors and rarely are observed as H-bond donors alone. Threonines were found to be more likely than serines to participate in two H bonds; tryosines were found to prefer to act as donors. In H-bonding situations in which there was incompatibility between the energies defining the barrier to rotation and the local electrostatics, the electrostatic criteria dominated. Overall, the findings support a model of H bonding where there exists strong inherent complementarity between the low-energy hydroxyl orientations and the local electrostatic environment.

Hydrogen Bonding↗
PubMed1991

Crystal structure and thermal vibrations of cholesteryl acetate from neutron diffraction at 123 and 20 K.

Cholesteryl acetate (C29H48O2) at 20 K is monoclinic, space group P2(1) with a = 16,521 (4), b = 9,220 (2), c = 17,620 (5) A, beta = 107.18 (2) degrees and Z = 4 (two molecules in the asymmetric unit). The crystal structure, earlier determined by X-ray diffraction at 123 K, has been redetermined at 123 and 20 K by neutron diffraction (7447 reflections at 123 K, 7281 at 20 K; sin theta/lambda less than 0.69 A-1) and refined by full-matrix least squares with 1423 variables to give R(F2) = 0.10 at 123 K, 0.06 at 20 K. Results at 20 K are more accurate not only because nuclear thermal vibrations have reduced amplitudes but also because a larger crystal was used for data collection. At 20 K, the average of 44 methylene C-H bond lengths is 1,102 (8) A (sigma from the observed distribution) and 1.103 (6) A for 16 methine groups. The 22 methylene H-C-H angles [106.2 (9) degrees] all fall within a narrow range. Analysis of nuclear anisotropic thermal parameters shows that intramolecular vibrations of the H nuclei are highly significant with similar mean-square amplitudes at 123 and 20 K. Torsional vibrations around the C-CH3 bonds of the C18 and C19 methyl groups have r.m.s. amplitudes of about 7 degrees. For methylene groups, mean-square amplitudes are a minimum for C-H bond stretching (0.006 A2) and a maximum for CH2 in-plane vibrations (0.024 A2). Values of Beq for the H-atom intramolecular vibrations are 0.8, 1.2 and 1.6 A2 for methine, methylene and methyl H atoms respectively. These results can be used to estimate Beq for H atoms in crystal structure determinations carried out by X-ray diffraction. The anisotropic intramolecular vibrations of the H nuclei contribute to the effective shape of the H atoms which, from the observed anisotropy in the distribution of intermolecular H...H distances, appears to be flattened along the direction of the C-H bond.

Cholesterol Esters↗
PubMed1984

5-A Fourier map of gramicidin A phased by deuterium-hydrogen solvent difference neutron diffraction.

Crystals of ion-free gramicidin A (P212121: a = 24.61, b = 32.28, c = 32.52) have been investigated using neutron diffraction. A difference analysis of crystals soaked in ethanol/H2O as opposed to ethanol-d6/D2O has led to single isomorphous replacement Fourier projections of the structure at 5-A resolution. The gramicidin dimer appears to be a 32-A-long cylinder oriented parallel to the c-axis in these crystals.

Crystallography↗
PubMed1976

Direct methods for the analysis of lamellar neutron diffraction from oriented multilayers: a difference Patterson deconvolution approach.

We have described here a direct method for the solution of the phase problem for lamellar neutron diffraction from hydrated oriented multilayers of model membranes. As a result, the neutron-scattering profiles of such model membranes can be uniquely determined. We note that such methods can easily be extended to cases in which the thickness of the water layer w is somewhat greater than d/2 as long as it is substantially less than d [e.g., w less than 3d/4 would suffice, since deltaP(-d/4 less than or equal to x less than or equal to d/4) would contain only contributions from see article without overlapping contributions from see articles and to cases in which isotopic labeling is used instead of partial H2O-D2O exchange.

Cholesterol↗
PubMed1987

Structure of RNA in satellite tobacco necrosis virus. A low resolution neutron diffraction study using 1H2O/2H2O solvent contrast variation.

The crystal structure of satellite tobacco necrosis virus has been studied by neutron diffraction at 16 A resolution using the technique of 1H2O/2H2O solvent contrast variation to distinguish between the regions of protein and nucleic acid. The RNA density is essentially localized in a region just inside the protein coat, leading to a significant interaction between the two components. From the appearance of the RNA density we conclude that the protein coat imposes partial icosahedral symmetry on a significant proportion of the nucleic acid. The shape and dimensions of the major part of this density suggests that about 72% of the total RNA could be double-helical in structure. The most important interaction between the two components of the virus occurs between the N-terminal triple-helical arms of the protein subunits and those regions of the RNA density that could have a double-helical secondary structure.

Amino Acid Sequence↗
PubMed1989

Binding of dimethyl sulfoxide to lysozyme in crystals, studied with neutron diffraction.

Crystals of hen egg white lysozyme soaked in 15% (v/v) dimethyl sulfoxide have been studied with single-crystal neutron diffraction to determine the effect of the solvent molecules on the protein configuration. A total of 9423 statistically significant Bragg reflections to a resolution of approximately 1.8 A were used to locate 6 dimethyl sulfoxide molecules, and structure refinements including a model for the flat solvent lead to a final crystallographic agreement factor of 0.130. The mode of location of the dimethyl sulfoxide molecules was compared with that in previous studies employing ethanol. This showed that hydrophobic interactions can be an essential factor in fixing the probe molecules on the protein surface. There was, however, no sign of any significant change in the protein configuration; so although possibly at higher concentrations of dimethyl sulfoxide the protein will unfold, there was no indication of any precursor effect.

Dimethyl Sulfoxide↗
PubMed2002

Direct observation of deuterium migration in crystalline-state reaction by single crystal neutron diffraction IV. "Hula-twist" rotation of a long alkyl radical produced by photoirradiation.

When the crystal of [(R)-1,2-bis(ethoxycarbonyl)ethyl](pyridine)bis(dimethylglyoximato)cobalt(III) was exposed to a xenon lamp, the chiral 1,2-bis(ethoxycarbonyl)ethyl group was partly inverted to the opposite configuration and finally the racemic group was produced with retention of the single crystal form. To make clear the mechanism, the hydrogen atom bonded to the chiral carbon of the chiral group was exchanged with the deuterium atom and the crystal was exposed to the xenon lamp for 3 days. The crystal after irradiation was analyzed by neutron diffraction. About 33% of the (R)-isomers were inverted to the (S) isomers in a crystal. The deuterium atom in the (S)-isomer was bonded to the same chiral carbon atom. This result clearly indicates that the inversion proceeds in the three steps; (i) the Co-C bond was homolytically cleaved by photoirradiation and the 1,2-bis(ethoxycarbonyl)ethyl radical and Co(II) were produced, (ii) the radical rotated by 180 degrees directing the C-D bond to the cobalt atom and the opposite plane of the radical faced to the cobalt atom, and (iii) the radical made a bond with Co(II). Because the peripheral atoms of the long radical occupy approximately the same positions in the process of the radical rotation, the crystal was not decomposed. The above rotation is a good example of hula-twist rotation in the process of photoisomerization of polyenes such as rhodopsin.

Cobalt↗
PubMed2001

Hydrogen-bond network in cyclodecaamylose hydrate at 20 K; neutron diffraction study of novel structural motifs band-flip and kink in alpha-(1-->4)-D-glucoside oligosaccharides.

A single-crystal neutron diffraction study of cyclodecaamylose (CA10) was carried out at 20 K. CA10 crystallizes with 27.18 water molecules [(C(6)H(10)O(5))(10).27.18H(2)O] in space group C2 with unit-cell constants a = 29.31 (5), b = 9.976 (10), c = 19.34 (2) A, beta = 121.07 (2) degrees. The asymmetric unit contains a half molecule of CA10 and 13.59 water molecules, the other half being related by a crystallographic twofold rotation axis. All H atoms except two water H atoms could be located from difference neutron-density maps; structure refinement converged at R = 0.635. Two of the five CH(2)-O6 groups and one of the 15 O2, O3 hydroxyl groups of CA10 are twofold orientationally disordered. A total of 13.59 water molecules in the asymmetric unit are distributed over 23 positions; 20 of which are in the CA10 cavity, and the other three occupy intermolecular interstices. Of the 123 symmetry-independent hydrogen bonds, 25 (= 20%) are three-centered and 7 (= 6%) are four-centered. Water molecules and O-H groups of CA10 form an extended network with cooperative O-H...O-H...O-H hydrogen bonds. They are arranged in 11 polygons with three, four, five, six and eight O-H bonds and in homodromic, antidromic and heterodromic arrangements. Nine polygons are located within the cavity and the others are outside.

Journal Article↗
PubMed1991

Structure of the adipate complex [Na2(C6H9O4)2(C6H10O4)].2H2O from neutron diffraction at 220 and 295 K.

The crystal structure of sodium hydrogen adipate-adipic acid (2/1) dihydrate, [Na2(C6H9O4)2(C6H10O4)].2H2O, Mr = 518.4, has been determined from neutron diffraction data collected at 220 and 295 K. Crystals are monoclinic, space group C2/m, with Z = 2. At 295 K, a = 9.378 (2), b = 13.379 (5), c = 10.247 (3) A, beta = 95.93 (3) degrees, V = 1278.8 (7) A3, Dn = 1.346, Dm = 1.348 (1) g cm-3 (in dibromomethane/bromobutane), lambda = 1.1588 (2) A, mu = 2.186 cm-1, F(000) = 176.4 fm, R(F2) = 0.108 for all 1995 nonequivalent reflections with sin theta/lambda less than 0.71 A-1. The crystal structure is similar at 220 K except for reduced nuclear mean-square displacements. Hydrogen adipate subunits (called A) are linked end-to-end in infinite chains by very short O...O (2.44 A) hydrogen bonds where the H nuclei are on centers of symmetry within the experimental error. The Na cation is octahedrally coordinated by O atoms from molecules A and also by non-ionized adipic acid molecules (called B). The B molecules have large mean-square nuclear displacements which are described in terms of anharmonicity and disorder.

Adipates↗
PubMed1984

A neutron diffraction study of the bones of the foot.

The preferential orientation of the apatite crystals in the lower tibia, talus and calcaneus, as determined by neutron diffraction, serves as an indicator of the lines of stress in the foot. The main stress flows down from the tibia to the heel and the ball of the foot and there is noteworthy orientation along the line of the plantar aponeurosis which acts as a tie. Orientation is particularly marked above the point of attachment of the Achilles tendon, where the edge of the calcaneus functions as a beam. The centre of the talus serves as a junctional region for forces and is relatively unoriented.

Calcaneus↗