SEARCH · PubMed Health
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Neutron diffraction measurements on isolated retinal rod outer segments show that most of the visual pigment protein, rhodopsin, is embedded in the hydrophobic core of the disk membrane. A very slight outward shift of protein at the cytoplasmic side of the membrane is associated with pigment bleaching.
Neutron-diffraction studies of the compounds 5-nitro-2-[[1-phenylethyl]amino]pyridine (methylbenzylaminonitropyridine, hereafter MBANP) and 3,5-dinitro-2-[[1-phenylethyl]amino]pyridine (methylbenzylaminodinitropyridine, hereafter MBADNP) are presented, and a charge-density study of the latter is reported. The studies were conducted in order to relate the structural attributes of these materials to their physical properties. MBANP exhibits a second-harmonic generation (SHG) output, chi(2), over eight times higher than that of MBADNP, despite their very similar molecular characteristics and the seemingly more SHG-favourable molecular features present in MBADNP. The neutron-diffraction studies show that intramolecular hydrogen bonding is responsible for this apparent discrepancy. The charge-density study on MBADNP confirms this and reveals that the pyridine group is the principal moiety responsible for the SHG effect on the molecular scale. Moreover, the strong intramolecular hydrogen bond present in MBADNP is proven to result from an electrostatic interaction. The dipole moment of MBADNP is also deduced from the charge-density study.
The crystal structure of adenosine, C10H13N5O4, Mr = 267.24, has been refined by full-matrix least-squares methods using single-crystal neutron diffraction data (sin theta/lambda less than 0.79 A-1) measured at 123 K. Crystal data at 123 K: monoclinic, P2l, Z = 2, a = 4.7885 (8), b = 10.240 (2), c = 11.772 (2) A, beta = 99.59 (2) degrees, V = 569.2 A3, lambda = 1.0402 (1) A, Dn = 1.559 Mg m-3, mu = 191.1 m-1, F(000) = 175.72 fm, R(F2) = 0.044, wR(F2) = 0.055, S = 1.13 for 2450 reflections with F2 greater than 0.0. Bond lengths and angles have e.s.d.'s less than 0.002 A and 0.1 degrees for non-H atoms and less than 0.004 A and 0.3 degrees for H atoms. Values are in general agreement with those previously obtained from room-temperature X-ray data and with those obtained for 9-methyladenine by neutron diffraction at 126 K. Small displacements of amino H atoms from the least-squares plane through the non-H atoms of the adenine part appear to be the result of hydrogen bonding. There is an intermolecular interaction C2--H2...O2' with an H...O distance of 2.20 A. In its thermal vibrations, the adenosine molecule behaves as two rigid segments with a torsional libration about the glycosidic bond of 14.4 deg2 at 123 K. The force constant for this libration, as determined from the diffraction data, is 73 (10) J mol-1 deg-2.
Variation of the equatorial diffraction spacing of soft type I collagen tissues with water content using X-rays has been known for many years. Recently, a generalized model for collagen molecule packing within fibrils was deduced from this information for different collagenous tissues. It is now known that the eq. diff. sp. of mineralized tissues can be less than for soft tissues and is inversely dependent on the wet density. A determination of the eq. dif. sp. dependence on water content using neutron diffraction of fully mineralized cow bone was undertaken for comparison. Specimens with various partial water content between 0 and 100% were tested. Data show collagen molecules pack more closely together as water content decreases, just as for soft tissues.
A method has been developed to determine the structure of bound solvent and the positions of exchanged hydrogens in proteins, on the basis of neutron diffraction from hydrogenous and deuterated crystals. In this method phases for the hydrogenous and for the deuterated model are refined simultaneously, and an average model is imposed in the volume occupied by non-hydrogen atoms. The densities in the areas of bulk solvent are replaced by their average values, while no modifications are performed in the vicinity of ordered solvents and potentially exchangeable hydrogens. The method was tested on 1.8 A neutron diffraction data collected from two crystals of bovine pancreatic trypsin inhibitor, one of them deuterated and the other hydrogenous. Significant improvement was observed for the densities corresponding to many partially occupied solvent sites, as well as to partially exchanged hydrogens. The algorithm presented here has been compared with a different approach published recently by Shpungin & Kossiakoff [Methods Enzymol.(1986), 127, 329-342].
A neutron diffraction study of the complex RuCl(2)[PPh(2)(2,6-Me(2)C(6)H(3))](2) (1) defines the precise nature of the delta agostic interactions between the unsaturated metal center and two o-methyl groups of the xylyl substituents. The CH(3) carbon atoms lie in the RuP(2) equatorial plane with Ru...C distances of 2.637(7) and 2.668(6) A, whereas four short Ru.H distances (from 2.113(11) to 2.507(11) A) indicate that each methyl group interacts with two C-H bonds. A survey of the X-ray structures with beta, gamma, delta, and epsilon M...H(3)C-C moieties (no neutron data have been previously reported) shows a linear correlation between the angle M.C-C and the torsion of the methyl group about the C-C bond. Thus, the agostic interactions span the range between the classical (M...eta(2)-HC) and the nonclassical (M...eta(3)-H(2)C) types. A solution study of 1 shows intramolecular rearrangement of each xylyl substituent that equilibrates the environments of its two ortho CH(3) groups. Activation parameters, evaluated from the analysis of (1)H NMR line shape as a function of temperature, are Delta H(++) = 9.6 +/- 0.2 kcal mol(-1) with Delta S(++) = -15.4 +/- 0.7 eu (CDCl(3)). The related 14-electron complexes RuX(2)[PPh(2)(2,6-Me(2)C(6)H(3))](2) (X = I, 2; NCO, 3), prepared from 1 and NaX, show a similar dynamic process in solution, with the iodo derivative displaying the most hindered rotation of the xylyl group. A DFT optimization of the complex RuCl(2)[PH(2)(2,6-Me(2)C(6)H(3))](2) (1a) reproduces well the nonclassical Ru...eta(3)-H(2)C agostic mode, whereas the classical Ru...eta(2)-HC one corresponds to a transition state 1b, destabilized by 3.4 kcal mol(-1). A similar barrier (ca. 3.8 kcal mol(-1)) is calculated for the xylyl rotation in the further simplified model RuCl(2)[PH(2)(2,6-Me(2)C(6)H(3))][PH(2)CH[double bond]CHCH(3)] (1c), the absence of bulky phenyl substituents being largely responsible for the difference with respect to the experimental value. Finally, the MO analysis addresses the intrinsic stability of the 14-electron complex RuCl(2)(PH(3))(2) and, in agostic complexes, accounts for the different interactions between the methyl group and the metal atom in relation to the length of their interconnecting chain.
A neutron diffraction study of the non-linear optical (NLO) material 4-nitro-4'-methylbenzylidene aniline (NMBA) is presented. NMBA exhibits a large macroscopic second-order NLO susceptibility, chi((2)), and this study shows that hydrogen bonding is, in part, responsible for this. No hydrogen bonding was reported in the X-ray study [Ponomarev et al. (1977). Sov. Phys. Crystallogr. 22, 223-225], whereas the present work shows that C-H.X hydrogen bonds (where X = N, O or pi) direct the nature of the three-dimensional lattice. C-H.X (X = N or O) hydrogen bonds are common; however, C-H.pi hydrogen-bond motifs are relatively rare. Such intermolecular interactions help extend the molecular charge transfer into the supramolecular realm, the charge transfer originating as a consequence of the high level of molecular planarity and strong donor-to-acceptor interactions. Molecular planarity, coupled with the favourable nature of the hydrogen bonds, results in parallel stacking of molecules in both the a and c crystallographic directions with extremely close interplanar spacings. Such a combination of influential hydrogen-bonding characteristics accounts, in part, for the large second-order NLO output of the material since the phenomenon is so critically dependent upon the nature of the charge transfer.
Yeast inorganic pyrophosphatase (Y-PPase) is a model system for studying phosphoryl-transfer reactions catalysed by multiple metal ions. To understand the process requires knowledge of the positions of the protons in the active site, which can be best achieved by neutron diffraction analysis. In order to reduce the hydrogen incoherent-scattering background and to improve the signal-to-noise ratio of the neutron reflections, deuterated protein was produced. Deuterated protein 96% enriched with deuterium was produced in high yield and crystals as large as 2 mm on one side were obtained. These crystals have unit-cell parameters a = 58.9, b = 103.9, c = 117.0 A, alpha = beta = gamma = 90 degrees at 273 K and diffract neutrons to resolutions of 2.5-3 A. The X-ray structure of the perdeuterated protein has also been refined at 273 K to 1.9 A resolution.
The location of acetaldehyde binding sites in the axial unit cell of tendon collagen was investigated by neutron diffraction. Acetaldehyde forms spontaneous cross-links with specific residues in collagen. The use of deuterated acetaldehyde increased the neutron scattering length of these groups. The introduction of deuterated acetaldehyde at specific locations allowed the acetaldehyde-reacted collagen to be treated as multiple isomorphous derivatives for neutron fibre diffraction. The low resolution axially projected structure was determined using amplitudes of the first eight meridional reflections (d = 67 nm). Results indicate that the process of acetaldehyde labelling takes place at different rates at different sites within the collagen fibril. The position of acetaldehyde attachment correlates well with the position of lysine and hydroxylysine residues especially in the regions of the molecular termini. This information is relevant to the process of cirrhosis and fibrosis of the liver since adduction of collagen by acetaldehyde may interfere with normal Schiff base cross-link formation at the C- and N-termini. This may result in subsequent alterations in the intra- and inter-molecular cross-linking pattern of collagen molecules.
Mixtures of egg phosphatidylcholine and phosphonic acid diethyl or dibutyl esters of the general type RP(O)(OR')2 with R = hexane or dodecane were studied at room temperature in the fluid lamellar state by X-ray and by neutron diffraction. Generally a molar ratio of lipid and ester of 1:0.5 was used. Additionally an equimolar lipid/ester mixture of hexane phosphonic acid diethyl ester was studied. Depending on the ester used and its concentration a single L alpha-phase was observed above a certain water content which changes to an L alpha + water two phase system at high water concentration. Despite the large amounts of the amphiphilic ester molecules incorporated in the membrane and their high molecular asymmetry, the mixtures qualitatively show the typical hydration and swelling behaviour of non-charged lipid membranes. However, the incorporation of the esters induces a higher hydration capacity, a lateral extension and a decrease in membrane thickness. The position of the ester molecules and their orientation in the membrane were determined by neutron diffraction using partially deuterated esters. The esters were found to be located with their phosphonic moiety near or in the lipid/water interface. The lamellar structure contradicts this location of the cone-shaped ester molecules which should increase the tendency to form hexagonal structures. However, the experimental findings can be understood if one considers a partial interdigitation of the last hydrocarbon groups of the lipid chains accompanied by a larger disorder in the hydrophobic centre of the membrane. In the case of hexane phosphonic acid dibutyl ester, a vertical translocation of the ester takes place below a certain water content where it is distributed between two locations at the lipid water interface and the centre of the membrane.
The complex of ribonuclease A (RNase A) with uridine vanadate (U-V), a transition-state analogue, has been studied with 51V and proton NMR spectroscopy in solution and by neutron diffraction in the crystalline state. Upon the addition of aliquots of U-V at pH 6.6, the C epsilon-H resonances of the two active-site histidine residues 119 and 12 decrease in intensity while four new resonances appear. Above pH 8 and below pH 5, these four resonances decrease in intensity as the complex dissociates. These four resonances are assigned to His-119 and His-12 in protonated and unprotonated forms in the RNase-U-V complex. These resonances do not titrate or change in relative area in the pH range 5-8, indicating a slow protonation process, and the extent of protonation remains constant with ca. 58% of His-12 and ca. 26% of His-119 being protonated. The results of diffraction studies show that both His-12 and His-119 occupy well-defined positions in the RNase-U-V complex and that both are protonated. However, while the classic interpretation of the mechanism of action of RNase based on the proposal of Findlay et al. [Findlay, D., Herries, D. G., Mathias, A. P., Rabin, B. R., & Ross, C. A. (1962) Biochem. J. 85, 152-153] requires both His-12 and His-119 to be in axial positions relative to the pentacoordinate transition state, in the diffraction structure His-12 is found to be in an equatorial position, while Lys-41 is close to an axial position. Hydrogen exchange data show that the mobility and accessibility of amides in the RNase-U-V complex do not significantly differ from what was observed in the native enzyme. The results of both proton NMR in solution and neutron diffraction in the crystal are compared and interpreted in terms of the mechanism of action of RNase.
The structure of gold cyanide, AuCN, has been determined at 10 and 300 K using total neutron diffraction. The structure consists of infinite [bond]Au[bond](CN)[bond]Au[bond](CN)[bond] linear chains, hexagonally packed, with the gold atoms in sheets. The Au-C and Au-N bond lengths are found to be identical, with d(Au(-C/N) = 1.9703(5) A at 300 K. This work supersedes a previous study, by others, which used Rietveld analysis of neutron Bragg diffraction in isolation, and found these bonds to have significantly different lengths (Delta d = 0.24 A) at 300 K. The total correlation function, T(r), at 10 and 300 K, has been modeled using information derived from total diffraction. The broadening of inter- and intrachain correlations differs markedly due to random displacements of the chains in the direction of the chain axes. This is a consequence of the relatively weak bonding between the chains. An explanation for the negative thermal expansion in the c-direction, which occurs between 10 and 300 K, is presented.
The new oxothiomolybdate anion [Mo8S8O8(OH)8[HWO5(H2O)]]3- (denoted HMo8W3-) has been synthesized in aqueous solution by an acido-basic condensation reaction. Four (Mo(V)2S2O2) building blocks are connected through hydroxo bridges around a central [W(VI)O6] octahedron. X-ray and neutron diffraction studies have been performed on single crystals of the lithium salt Li3[Mo8S8O8(OH)8[HWO5(H2O)]] x 18H2O (Li3HMo8W x 18H2O) in an aqueous grown from HMo8W3- solution of LiCl (1 M). The neutron diffraction experiment enabled us to locate both the protons and the lithium ions. In the structure of Li3HMo8W x 18H20, ring-shaped anions interleaved by a cluster of disordered hydrogen-bonded water molecules stack on top of each other along lithium pillars. The lithium columns are formed by alternating edge-sharing octahedra and tetrahedra, with one lithium site in four being totally vacant. Ionic conductivity measurements on pressed pellets have shown that Li3HMo8W x 18H2O is a good ionic conductor at room temperature (sigma = 10(-5) S cm(-1)), but the ionic conductivity on single crystals is smaller by two orders of magnitude and is isotropic; this suggests the main path of conduction involves surface protons rather than lithium ions of the bulk.
The 1:2 adduct of benzene-1,2,4,5-tetracarboxylic acid and 4,4'-bipyridyl at 100 K has been studied by single-crystal neutron diffraction at 20, 200 and 296 K. The structure contains two short, strong N...O hydrogen bonds: one O-H...N hydrogen bond [O...N 2.6104 (17) A at 20 K] and one short N-H...O hydrogen bond [N...O 2.5220 (17) A at 20 K]. The N-H distance in the N-H...O hydrogen bond changes from 1.207 (3) A at 20 K to 1.302 (4) A at 296 K and the N...O distance increases to 2.5315 (16) A at 296 K. At 200 K the H atom lies in an intermediate position 1.251 (6) A from the N atom with an N...O separation of 2.520 (4) A. The O-H...N hydrogen bond, on the other hand, does not change with temperature.
Three-dimensional coordination network solids of MII[C(CN)3]2 (M = V, Cr) composition possess interpenetrating rutile-like network structures. Each [C(CN)3]- bonds to three different metal ions in a triangular array, affording a geometrical topology akin to a Kagomé lattice leading to competing spin exchange interactions and spin frustration. The crystal and magnetic structure of CrII[C(CN)3] was determined by Rietveld refinement of the powder neutron diffraction data at 2 and 15 K and belongs to the orthorhombic space group Pmna [a = 7.313(1) A, b = 5.453(1) A, c = 10.640(1) A, Z = 2, T = 15 K]. Each CrII has a tetragonally elongated octahedral structure with four Cr-N(1) distances of 2.077(2) A and two significantly longer axial Cr-N(2) distances of 2.452(2) A. Magnetic susceptibility measurements between 1.7 and 300 K reveal strong antiferromagnetic interactions for both V- and Cr[C(CN)3]2 with theta = -67 and -46 K, respectively, from a fit to the Curie-Weiss law. Long-range magnetic ordering does not occur for M = V above 1.7 K, in contrast to M = Cr, which antiferromagnetically orders at low temperature. This is attributed to Jahn-Teller distorted CrII site relieving frustration in one dimension, leading to 2-D Ising antiferromagnetism, as observed by both magnetic susceptibility and specific heat studies. Neutron diffraction experiments at 2 K for Cr[C(CN)3]2 yielded additional Bragg reflections as a result of antiferromagnetic ordering with the moments on the CrII atoms aligned parallel to c and 4.7(1) microB. Fitting of the magnetic order parameter to a power law yielded TN = 6.12(4) K and beta = 0.18(1) consistent with 2-D Ising behavior. A TN of 6.13 K is also observed from the specific heat data.
Neutron diffraction is used to examine the effects of Ca2+ and ClO4- ions on interactions and some structural features of dipalmitoylphosphatidylcholine membranes in both solid and fluid lamellar phases. The results are described within the framework of Derjaguin-Landau-Verwey-Overbeek (DLVO) theory with reference to electrostatic, van der Waals, and hydration components of disjoining pressure. The Hamaker constants are evaluated under equilibrium conditions. Addition of 100 mM CaCl2 to the aqueous phase substantially increases the lamellar repeat spacing (d), which is interpreted in terms of adsorption of Ca2+ ions to bilayers followed by electrostatic repulsion between membranes. The rise of NaClO4 concentration in the presence of 100 mM CaCl2 leads to gradual decrease in d, evidently resulted from the diminution of Ca(2+)-induced positive surface potential by both electrostatic screening and binding of ClO4- ions. In the absence of CaCl2, elevation of NaClO4 concentration to 100-300 mM drastically enhances the repeat spacing and then dramatically decreases d at about 1 M NaClO4. Estimation of the hydration coefficients showed that the pronounced decrease of the repeat spacing at high NaClO4 concentrations was resulted mainly from the (partial) disruption of the structure of intermembrane bound water by chaotropic ClO4- ions and subsequent decrease in hydration repulsive pressure. Moreover, in the case of solid membranes (20 degrees C) high concentrations of ClO4- induced formation of interdigitated phase paralleled with marked reduction in bilayer thickness and corresponding increase in the effective cross-sectional area per lipid molecule.
We have studied the spin liquid Tb2Ti2O7 by single crystal neutron diffraction under high pressure up to 2.8 GPa, together with uniaxial stress, down to 0.1 K, in zero and high magnetic fields up to 7 T. In zero magnetic field, a long-range ordered antiferromagnetic structure is induced by pressure. The Néel temperature and ordered magnetic moment can be tuned by the anisotropic pressure component. Under magnetic field, the antiferromagnetic structure transforms into a canted ferromagnetic one at 0.6 T. Spin canting persists even at 7 T. The magnetic phase diagram under pressure shows a strong increase of the Néel temperature with the field.
Crystals of barium pentacyanonitrosylferrate trihydrate (barium nitroprusside trihydrate), Ba[Fe(CN)(5)(NO)].3H(2)O, have been studied by neutron diffraction in order to examine the structural behaviour of the compound in the 20-120 K temperature range and to determine the structure at 105 K. The results show the existence of a new crystal phase of the compound at 80 K (with a duplicated a parameter), which still exists at 20 K. The crystal structure at 105 K shows a rearrangement of the water molecules, which results in an ordered structure with P1 symmetry. Two of the four independent nitroprusside cations are rotated by 4.5 degrees around the [100] direction.