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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↗
PubMed1997

The headgroup orientation of dimyristoylphosphatidylinositol-4-phosphate in mixed lipid bilayers: a neutron diffraction study.

The trisodium salt of dimyristoylphosphatidylinositol-4-phosphate (DMPI-4P) has been synthesised specifically deuterated at particular sites in the headgroup. These materials have been used in neutron diffraction experiments, which successfully located the position (depth) of each of these deuterated sites to within +/- 0.5 A in a mixed model membrane (a 1:1 molar mixture of DMPI-4P with dimyristoyl-phosphatidylcholine, DMPC, in the L alpha phase, hydrated to the level of 28 water molecules per lipid molecule). The diffracted intensities were measured at four different D2O/H2O ratios and six orders of diffraction were obtained. These data sets, in conjunction with computer modelling, have been used to determine the orientation of the inositol ring of DMPI-4P, localising each vertical H-H distance to within approximately +/- 0.03 A. The orientation of the inositol ring is found to be one in which the C5 hydroxyl is extended out into the aqueous medium. This is, therefore, the most accessible site for water-borne reagents. This may be significant for the important pathway leading from PI-4P to PI-4,5P2. On the assumption that the P/ODAG bond is orientated parallel to the bilayer normal, these results are consistent with two possible conformations for the portion of the headgroup connecting the diacylglycerol to the inositol ring. Distinction between these two is difficult, but one may be favoured since the other involves close atom-atom contacts.

Computer Simulation↗
PubMed1999

Total neutron diffraction: a route to the correct local structure of disordered LaMo2O5 and its application to the model compound Zn2Mo3O8.

Analysis of Bragg diffraction is the normal route to the structure of crystalline materials. Here we demonstrate the use of total neutron diffraction in determining the local structure in the disordered lanthanum molybdate LaMo(2)O(5). An average structure with space-group symmetry P6(3)/mmc accounts for the Bragg scattering and shows that the compound contains the rare Mo(6)O(18) cluster and a unique type of Mo-Mo bonded sheet. However, this gives an incomplete picture of the structure, since it does not reveal how the sites with fractional occupancy are occupied at a local level. Two models describing possible local structures are constructed by removing symmetry elements present in the average structure. Total correlation functions, T(r), calculated from these structures, with space-group symmetry P6(3)mc and P3;m1, are compared with the experimental T(r) to show the validity of these local structures. The close relationship between the T(r)'s of the component structures gives an insight into why disorder occurs in LaMo(2)O(5). The calculated and experimental T(r)'s for a model compound, Zn(2)Mo(3)O(8), are compared to show the agreement expected from an ordered crystalline material. Remaining discrepancies between our model and the experimental T(r) give an insight into the origin of additional disorder in LaMo(2)O(5).

Journal Article↗
PubMed2001

Crystal engineering in the gem-alkynol family: the key role of water in the structure of 2,3,5,6-tetrabromo-trans-1,4-diethynyl-cyclohexa-2,5-diene-1,4-diol dihydrate determined by X-ray and neutron diffraction at 150 K.

The structure of the title compound has been determined using low-temperature (150 K) single-crystal X-ray and neutron diffraction data. Crystals adopt the uncommon space group P4(2)/ncm and display a complex set of intermolecular interactions in which the water molecules play the crucial role: the water O-atom [O2(w)] accepts two hydrogen bonds and both water H atoms act as bifurcated donors. A set of O--H...O hydrogen bonds is formed around the 4(2) axis comprising (a) a cyclic tetrameric synthon involving four donor-H from two water molecules and two O(hydroxy) acceptors from two parent molecules, and (b) short discrete O(hydroxy)--H...O2(w) hydrogen bonds which link these tetramers along the c axis. Four Br...Br interactions [3.708 (1) A] form cyclic Br(4) tetramers around the 4 axis and are linked to the O--H...O system via O2(w)--H...Br bonds with H...Br = 2.995 (2) A. Finally, the O--H...O system is further linked to the parent molecules via C identical with C...H...O2(w) bonds of 2.354 (3) A. The supramolecular structure of the title hydrate is compared with that of the non-hydrated parent molecule, which also forms cyclic O--H...O bonded tetrameric synthons, and with its (non-hydrated) tetrachloro analogue, which forms cyclic tetrameric Cl(4) synthons [Madhavi, Desiraju et al. (2000b). Acta Cryst. B56, 1063--1070].

Journal Article↗
PubMed1995

A comparison of neutron diffraction and molecular dynamics structures: hydroxyl group and water molecule orientations in trypsin.

A comparison is presented of experimentally observed hydroxyl and water hydrogen atoms in trypsin determined from neutron density maps with the results of a 140 ps molecular dynamics simulation. Experimental determination of hydrogen and deuterium atom positions in molecules as large as proteins is a unique capability of neutron diffraction. The comparison addresses the degree to which a standard force-field approach can adequately describe the local electrostatic and van der Waals forces that determine the orientations of these hydrogen atoms. The molecular dynamics simulation, based on the all-atom AMBER force-field, allowed free rotation of all hydroxyl groups and movement of water molecules making up a bath surrounding the protein. The neutron densities, derived from 2.1 A 2H2O-H2O difference Fourier maps, provide a database of 27 well-ordered hydroxyl hydrogen atoms. Virtually all of the simulated hydroxyl orientations are within a standard deviation of the experimentally observed positions, including several examples in which both the simulation and the neutron density indicate that a hydroxyl group is shifted from a "standard" rotamer. For the most highly ordered water molecules, the hydrogen distributions calculated from the trajectory were in good agreement with neutron density; simulated water molecules that displayed multiple hydrogen-bonding networks had correspondingly broadened neutron density profiles. This comparison was facilitated by development of a method to construct a pseudo 2 A density map based on the hydrogen atom distributions from the simulation. This method is particularly useful for statically disordered water molecules, in which the average location assigned from a trajectory may represent a site of relatively low occupancy. The degree of disorder of internal water molecules is shown to result primarily from the electrostatic environment surrounding that water molecule as opposed to the cavity size available to the molecule.

Crystallography, X-Ray↗
PubMed2003

Low-temperature single-crystal Raman and neutron-diffraction study of the hydrogenous ammonium copper(II) Tutton salt and the deuterated analogue in the metastable state.

Low-temperature (15 K) single-crystal neutron-diffraction structures and Raman spectra of the salts (NX4)2[Cu(OX2)6](SO4)2, where X=H or D, are reported. This study is concerned with the origin of the structural phase change that is known to occur upon deuteration. Data for the deuterated salt were measured in the metastable state, achieved by application of 500 bar of hydrostatic pressure at approximately 303 K followed by cooling to 281 K and the subsequent release of pressure. This allows for the direct comparison between the hydrogenous and deuterated salts, in the same modification, at ambient pressure and low temperature. The Raman spectra provide no intimation of any significant change in the intermolecular bonding. Furthermore, structural differences are few, the largest being for the long Cu-O bond, which is 2.2834(5) and 2.2802(4) A for the hydrogenous and the deuterated salts, respectively. Calorimetric data for the deuterated salt are also presented, providing an estimate of 0.17(2) kJ/mol for the enthalpy difference between the two structural forms at 295.8(5) K. The structural data suggest that substitution of hydrogen for deuterium gives rise to changes in the hydrogen-bonding interactions that result in a slightly reduced force field about the copper(II) center. The small structural differences suggest different relative stabilities for the hydrogenous and deuterated salts, which may be sufficient to stabilize the hydrogenous salt in the anomalous structural form.

Journal Article↗
PubMed1975

Neutron diffraction analysis of myoglobin: structure of the carbon monoxide derivative.

The locations of hydrogen and deuterium atoms and water molecules have been investigated in carbon monoxide myoglobin using neutron diffraction, and the results are compared with earlier work on metmyoglobin. Parallel real space refinements on the two molecules show relatively few changes, but do show the carbon monoxide molecule with the iron atom moving into the heme plane.

Carbon Monoxide↗
PubMed1989

Crystal structure of 1-methyluracil from neutron diffraction at 15, 60 and 123 K.

The crystal structure of 1-methylpyrimidine-2,4-dione (1-methyluracil, C5H6N2O2) has been determined at 15, 60 and 123 K from neutron diffraction data. Molecules lie in the eightfold special positions (symmetry m) of space group Ibam, with a = 13.213 (2), b = 13.172 (2), c = 6.163 (1) A at 15 K. Full-matrix least-squares refinements based on 807 (15 K), 805 (60 K) and 815 (123 K) reflections with sin theta/lambda less than 0.69 A-1 converged with R(F2) = 0.023, 0.024 and 0.024 respectively. Bond lengths and angles have e.s.d.'s less than 0.002 A and 0.2 degrees. Detailed analysis of the anisotropic thermal parameters gives estimates of the zero-point internal vibrations for all nuclei and also for molecular rigid-body thermal vibrations at 15, 60 and 123 K. With thermal-vibration corrections there is good agreement in bond lengths and angles at the three temperatures.

Crystallography↗
PubMedDate not supplied

The interplay between X-ray crystallography, neutron diffraction, image reconstruction, organo-metallic chemistry and biochemistry in structural studies of ribosomes.

Crystals of ribosomes, their complexes with components of protein biosynthesis, their natural, mutated and modified subunits, have been subjected to X-ray and neutron crystallographic analyses. Electron microscopy and 3-dimensional image reconstruction, supported by biochemistry, genetic, functional and organo-metallic studies were employed for facilitating phasing of the crystallographic data. For example, a monofunctional multi heavy-atom cluster (undecagold) was designed for covalent and quantitative binding to ribosomes. The modified particles were crystallized isomorphously with the native ones. Their difference-Patterson maps contain indications for the usefulness of these derivatives for subsequent phasing. Models of the ribosome and its large subunit were reconstructed from tilt series of 2-dimensional sheets. The comparison of the various reconstructed images enabled an initial assessment of the reliability of these models and led to tentative assignments of several functional features. These include the presumed sites for binding mRNA and for codon-anticodon interactions, the path taken by the nascent protein chain and the mode for tRNA binding to ribosomes. These assignments assisted in the design of biologically meaningful crystal systems. The reconstructed models are being used to identify structural features in initial density maps derived from X-ray and neutron diffraction data.

Crystallography↗
PubMed2004

Neutron diffraction study of [H(4)Co(4)(C(5)Me(4)Et)(4)], a tetrahedral metal cluster complex with four face-bridging hydride ligands.

A single-crystal neutron diffraction analysis of the cluster complex [H(4)Co(4)(C(5)Me(4)Et)(4)] was carried out on the new quasi-Laue diffractometer VIVALDI at the Institut Laue-Langevin. The structure consists of four face-bridging hydrides attached to a tetrahedral cobalt metal core. Average distances and angles in the core of the molecule are as follows: Co-Co = 2.571(8), Co-C = 2.158(6), Co-H = 1.749(7), H.H = 2.366(9) A; Co-H-Co = 94.6(3), H-Co-H = 85.1(3) degrees. The hydride ligands are located off the Co-Co-Co planes by an average distance of 0.923(8) A. It is suggested that the dimensions of the HCo(3) fragments found in this molecule provide reasonable estimates for analogous distances and angles associated with chemisorbed H atoms situated on the 3-fold hollows of a cobalt surface. Crystallographic details: space group P2(1)/a (monoclinic); a = 21.979(2), b = 10.924(1), c = 34.406(2) A; beta = 90.81(1) degrees; Z = 8. Final agreement factor: R(F) = 0.099 for 3779 reflections [I > 2sigma(I)] collected at 20 K.

Journal Article↗