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PubMed1986

Quantitation of water in membranes by neutron diffraction and X-ray techniques.

The general principle of placing neutron and X-ray scattering density profiles on an absolute scale is being applied to an increasing number of problems in structural biology. This maximizes the information from the experiments by facilitating the identification of various molecular species. The greater detail available on the membrane water distribution has been highlighted in this chapter. The quantitative analysis of water in the headgroup region and the intermembrane water layer provides valuable information on membrane structure and function. The single most important limitation of the method is the lack of resolution. Improvements in experimental techniques will improve the resolution in a number of situations.

Lipid Bilayers↗
PubMed1998

Plant sterols: a neutron diffraction study of sitosterol and stigmasterol in soybean phosphatidylcholine membranes.

Neutron scattering experiments have been performed on oriented Soybean phosphatidylcholine (SPC) bilayers, containing sitosterol or stigmasterol, two major sterols of plant plasma membranes. Sitosterol and stigmasterol were either protonated or deuterated on position C25 of the lateral chain. Incorporation of sitosterol leads to an increase of the hydrophobic thickness of SPC bilayers of 1.2 and 2 A when present, at 16 and 30 mol%, respectively. On the other hand, no change was observed when stigmasterol is present in the bilayer at its maximal solubility of 16 mol%. These results are in agreement with the fact that sitosterol is more efficient than stigmasterol to order acyl chains of SPC, as already shown with other biophysical techniques. In order to get more insight into the behavior of the lateral chains of the two sterols, the proton-deuterium contrast method was used in order to locate the (2)H25 atoms of the two sterols. For sitosterol, this atom was found close to the center of the bilayer at +/-(1.6+/-0.2 A), with a width, nu=2.5+/-0.5 A. For stigmasterol, the difference profile could be fitted in two different ways: either two possible locations are found at +/-(2.3+/-0.2 A) and +/-(10+/-0.2 A) with the same width, nu=2.5+/-0.5 A or only one broad distribution at +/-(6.1+/-0.3 A), nu=8.5+/-0.7 A. The results are discussed in terms of difference of dynamics for the lateral chain of the two sterols.

Journal Article↗
PubMed2000

Evolution of the Jahn-Teller distortion of MnO6 octahedra in RMnO3 perovskites (R = Pr, Nd, Dy, Tb, Ho, Er, Y): a neutron diffraction study.

Stoichiometric RMnO3 perovskites have been prepared in the widest range of R3+ ionic sizes, from PrMnO3 to ErMnO3. Soft-chemistry procedures have been employed; inert-atmosphere annealings were required to synthesize the materials with more basic R cations (R = Pr, Nd), in order to minimize the unwanted presence of Mn4+. On the contrary, annealings in O2 flow were necessary to stabilize the perovskite phases for the last terms of the series, HoMnO3, ErMnO3, and YMnO3, thus avoiding or minimizing the formation of competitive hexagonal phases with the same stoichiometry. The samples have been investigated at room temperature by high-resolution neutron powder diffraction to follow the evolution of the crystal structures along the series. The results are compared with reported data for LaMnO3. The distortion of the orthorhombic perovskite (space group Pbnm), characterized by the tilting angle of the MnO6 octahedra, progressively increases from Pr to Er due to simple steric factors. Additionally, all of the perovskites show a distortion of the MnO6 octahedra due to the orbital ordering characteristic of the Jahn-Teller effect of Mn3+ cations. The degree of orbital ordering slightly increases from La to Tb and then remains almost unchanged for the last terms of the series. The stability of the crystal structure is also discussed in light of bond-valence arguments.

Journal Article↗
PubMed2000

Halogen trimer synthons in crystal engineering: low-temperature X-ray and neutron diffraction study of the 1:1 complex of 2,4, 6-tris(4-chlorophenoxy)-1,3,5-triazine with tribromobenzene

The title complex has been studied using low-temperature X-ray (150 K) and neutron (100 K) diffraction. Molecules of the triazine host form a two-dimensional hexagonal network mediated by trigonally symmetric Cl(3) synthons having Cl.Cl interactions of 3.441 (3) A, a C-Cl.Cl angle of 165 degrees and a Cl.Cl-C angle of 105 degrees, close to the ideal values of 180 and 90 degrees, respectively. The guest molecules are of an appropriate size to fit the hexagonal networks and interact with the host via C-H.pi (phenyl) and C-Br.pi (phenyl) interactions which stabilize the overall structure. Both C-donor bond vectors are directed more closely towards the mid-point (X) of an individual aromatic bond, rather than the ring centroid, with H.X 2.817 (9) A and C-H.X 174.0 (9) degrees, and Br.X 3.353 (4) A and C-Br.X 158.1 (2) degrees.

Journal Article↗
PubMed1992

Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. II. Distribution and packing of terminal methyl groups.

We continue in this paper the presentation of theoretical and experimental methods for the joint refinement of neutron and x-ray lamellar diffraction data for the analysis of fluid (L alpha phase) bilayer structure (Wiener, M. C., and S. H. White. 1991 a, b, c. Biophys. J. 59:162-173 and 174-185; Biochemistry. 30:6997-7008; Wiener, M. C., G. I. King, and S. H. White. Biophys. J. 60: 568-576). We show how to obtain the distribution and packing of the terminal methyls in the interior of a fluid dioleoylphosphatidylcholine bilayer (66% RH) by combining x-ray and neutron scattering-length transbilayer profiles with no a priori assumptions about the functional form of the distribution. We find that the methyls can be represented by a Gaussian function with 1/e-halfwidth of 2.95 +/- 0.28 A situated at the bilayer center. There is substantial mixing of the methyls and methylenes in the bilayer center. The Gaussian representation of the methyl distribution is narrower and has a different shape than predicted by several simulations of fluid bilayers (Gruen, D. W. R., and E. H. B. de Lacey. 1984. Surfactants in Solution, Vol. 1. Plenum Publishing Corp., New York. 279-306; de Loof, H., et al. 1991. Biochemistry. 30:2099-2133) but this may be due to the smaller area/lipid of our experiments and the presence of the double-bonds. Determination of the absolute specific volume of DOPC and an analysis of bulk alkane volumetric data over a range of hydrostatic pressures lead to estimates of methylene and methyl volumes at the bilayer center of 27 +/- 1 A3 and 57.2 +/- 3.6 A3, respectively. This result provides direct confirmation of the common assumption that the molecular packing of methyl and methylene groups in bilayers is the same as in bulk liquid alkanes.

Biophysical Phenomena↗
PubMed2005

X-ray and neutron diffraction studies and MD simulation of atomic configurations in polyamorphic Y2O3-Al2O3 systems.

Supercooled liquids in the Y(2)O(3)-Al(2)O(3) system undergo a liquid-liquid phase transition between a high-temperature, high-density amorphous (HDA) polymorph form and one with lower density (LDA form) that is stable at lower temperature. The two amorphous polymorphs have the same chemical composition, but they differ in their density (ca. 4% difference) and in their heat content (enthalpy) and entropy determined by calorimetry. Here we present new results of structural studies using neutron and high-energy X-ray diffraction to study the structural differences between HDA and LDA polyamorphs. The combined datasets show no large differences in the average nearest-neighbour Al-O or Y-O bond lengths or coordination numbers between the low- and high-density liquids. However, the data indicate that substantial changes occur among the packing geometries and clustering of the Al-O and Y-O coordination polyhedra, i.e. within the second-nearest-neighbour shell defined by the metal-metal (i.e. Y-Y, Y-Al, Al-Al) interactions. Polarizable ion model molecular dynamics simulations of Y(2)O(3)-Al(2)O(3) liquids are used to help interpret the pair-correlation functions obtained from X-ray and neutron scattering data. Unexpectedly large density fluctuations are observed to occur during the simulation of nominally equilibrated systems. These are interpreted as being due to dynamic sampling of high- and low-density configurations within the single-phase liquid at temperatures above the critical point or phase transition line. Calculated partial radial distribution functions indicate that the primary differences between HDA and LDA configurations occur among the Y-Y correlations.

Aluminum Oxide↗
PubMed1983

Active site of RNase: neutron diffraction study of a complex with uridine vanadate, a transition-state analog.

A complex of RNase A with a transition-state analog, uridine vanadate, has been studied by a combination of neutron and x-ray diffraction. The vanadium atom occupies the center of a distorted trigonal bipyramid, with the ribose oxygen O2' at the apical position. Contrary to expectations based on the straightforward interpretation of the known in-line mechanism of action of RNase, nitrogen NE2 of histidine-12 was found to form a hydrogen bond to the equatorial oxygen O8, while nitrogen NZ of lysine-41 makes a clear hydrogen bond to the apical oxygen O2'. Nitrogen ND1 of histidine-119 appears to be within a hydrogen-bond distance of the other apical oxygen, O7. Two other hydrogen bonds between the vanadate and the protein are made by nitrogen NE2 of glutamine-11 and by the amide nitrogen of phenylalanine-120. The observed geometry of the complex may necessitate reinterpretation of the mechanism of action of RNase.

Animals↗
PubMed1988

New analysis of the neutron diffraction data for anhydrous orthophosphoric acid and the structure of H3PO4 molecules in crystals.

Two neutron data sets, which had been analyzed separately to determine the H-atom positions in H3PO4 crystals [Cole (1966). PhD Thesis, Univ. of Washington, Pullman, USA], have been re-analyzed in a joint refinement, fitting separate scale and extinction parameters for each data set, in order to obtain more precise positional and vibrational parameters. The new refinement gave R(F) = 0.036 for the combined 743 data. For the new results, and for six other H3PO4 molecules from four other, different crystal structures, thermal vibration analyses have been performed, and the molecular structures, thermal vibrations and hydrogen-bonding effects are compared. The rigid-body model is found to be better than the riding model for the PO4 groups. The P-OH bond lengths are markedly affected by hydrogen bonding, but seem to be independent of O = P-O-H conformation. These effects are interpreted in terms of the P-O partial double-bond character. Crystal data (Cole, 1966): anhydrous orthophosphoric acid, H3PO4, Mr = 98.00, room temperature, P2(1)/c, a = 5.779(9), b = 4.826 (4), c = 11.606 (40) A, beta = 95.26 (18) degrees, V = 322.3 (20) A3, Z = 4, Dx = 2.019 mg mm-3, mu = 0.1687 mm-1 for neutrons with lambda = 1.450 A.

Hydrogen Bonding↗
PubMed2006

Synchrotron and neutron diffraction study of 4-methylpyridine-N-oxide at low temperature.

The structure of 4-methylpyridine-N-oxide has been determined at 250, 100 and 10 K by combined synchrotron (C(6)H(7)NO) and neutron (C(6)D(7)NO) powder diffraction experiments. At 250 K the space group is I4(1)/amd and the tetragonal unit cell [a = b = 7.941 (2), c = 19.600 (5) A] contains eight equivalent molecules. At 100 K the structure is orthorhombic, with space group Fddd, a = 12.138 (2), b = 10.237 (2) and c = 19.568 (3) A. The 16 equivalent molecules are rotated by about 8 degrees around the c axis with respect to positions at high temperature. At 10 K the best structural model corresponds to a tetragonal unit cell with the space group P4(1), a = b = 15.410 (2) A and c = 19.680 (3) A. The 32 molecules (eight molecules in the asymmetric unit) show complex reorientations around the three cell axes. Whereas at 250 and 100 K the deuterated methyl groups are largely disordered, at 10 K they are ordered in-phase along infinite chains parallel to a and b. Face-to-face methyl groups along c are in an eclipsed configuration. The structure at 10 K suggests that the manifold of rotational tunnelling transitions could be due to inequivalent lattice sites for crystallographically independent methyl groups.

Journal Article↗
PubMed1992

Distribution of decane within the unit cell of the inverted hexagonal (HII) phase of lipid-water-decane systems determined by neutron diffraction.

The addition of a free alkane such as decane to lipid-water systems is known to promote the formation of a low-temperature inverted hexagonal (HII) phase [Kirk, G. L., & Gruner, S. M. (1985) J. Phys. (Paris) 46, 761]. Kirk et al. [Kirk, G. L., Gruner, S. M., & Stein, D. E. (1984) Biochemistry 23, 1093] have discussed the hydrocarbon packing anisotropy in the HII unit cell and have suggested that free alkane will distribute in a way that reduces this packing anisotropy by allowing the lipid chain environment to become more uniform. By combining neutron and X-ray diffraction data to do a Fourier reconstruction of the HII phase of dioleoylphosphatidylethanolamine (DOPE) + water + deuterated decane, it was found that the decane preferentially partitions into the interstitial regions of the HII unit cell where it should be the most effective in alleviating the hydrocarbon chain packing stress, supporting the suggestion of Kirk et al. Using the distribution of decane within the unit cell, we have calculated the lipid length distribution for the situations with and without added alkane. With a suitable molecular model, this lipid length distribution may eventually be used to calculate the free energy change upon the addition of alkane. Such a measurement is important for a more realistic understanding of the interactions which lead to the formation of the HII phase.

Alkanes↗