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PubMed1998

Phospholipid component volumes: determination and application to bilayer structure calculations.

We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2006

Are recent water models obtained by fitting diffraction data consistent with infrared/Raman and x-ray absorption spectra?

X-ray absorption (XA) spectra have been computed based on water structures obtained from a recent fit to x-ray and neutron diffraction data using models ranging from symmetrical to asymmetrical local coordination of the water molecules [A. K. Soper, J. Phys.: Condens. Matter 17, S3273 (2005)]. It is found that both the obtained symmetric and asymmetric structural models of water give similar looking XA spectra, which do not match the experiment. The fitted models both contain unphysical structures that are allowed by the diffraction data, where, e.g., hydrogen-hydrogen interactions may occur. A modification to the asymmetric model, in which the non-hydrogen-bonded OH intramolecular distance is allowed to become shorter while the bonded OH distance becomes longer, improves the situation somewhat, but the overall agreement is still unsatisfactory. The electric field (E-field) distributions and infrared (IR) spectra are also calculated using two established theoretical approaches, which, however, show significant discrepancies in their predictions for the asymmetric structural models. Both approaches predict the Raman spectrum of the symmetric model fitted to the diffraction data to be significantly blueshifted compared to experiment. At the moment no water model exists that can equally well describe IR/Raman, x-ray absorption spectroscopy, and diffraction data.

Journal Article↗
PubMed2006

On the structure of simple molecular liquids SbCl5 and WCl6.

Neutron diffraction measurements on liquid antimony pentachloride and tungsten hexachloride have been carried out using the Studsvik liquids and amorphous diffractometer (SLAD) at the Studsvik Neutron Research Laboratory. The corrected structure factors have been interpreted by means of reverse Monte Carlo modeling which provides large structural models, containing thousands of atoms, that are consistent with the experimental data within their uncertainties. From these models, partial structure factors and pair correlation functions can be calculated. It is demonstrated that the intramolecular structure can be determined on the basis of data extending up to 10 Angstrom (-1). SbCl(5) is found to have a trigonal bipyramidal shape in the liquid, while liquid WCl(6) consists of octahedral molecules. The intermolecular structure of liquid SbCl(5) and WCl(6) seems to be determined largely by steric effects (excluded volume and molecular shape).

Journal Article↗
PubMed1996

X-ray structure determination of fully hydrated L alpha phase dipalmitoylphosphatidylcholine bilayers.

Bilayer form factors obtained from x-ray scattering data taken with high instrumental resolution are reported for multilamellar vesicles of L alpha phase lipid bilayers of dipalmitoylphosphatidylcholine at 50 degrees C under varying osmotic pressure. Artifacts in the magnitudes of the form factors due to liquid crystalline fluctuations have been eliminated by using modified Caillé theory. The Caillé fluctuation parameter eta 1 increases systematically with increasing lamellar D spacing and this explains why some higher order peaks are unobservable for the larger D spacings. The corrected form factors fall on one smooth continuous transform F(q); this shows that the bilayer does not change shape as D decreases from 67.2 A (fully hydrated) to 60.9 A. The distance between headgroup peaks is obtained from Fourier reconstruction of samples with four orders of diffraction and from electron density models that use 38 independent form factors. By combining these results with previous gel phase results, area AF per lipid molecule and other structural quantities are obtained for the fluid L alpha phase. Comparison with results that we derived from previous neutron diffraction data is excellent, and we conclude from diffraction studies that AF = 62.9 +/- 1.3 A2, which is in excellent agreement with a previous estimate from NMR data.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1993

Structure and dynamics of bacteriorhodopsin. Comparison of simulation and experiment.

Global features of the structure and dynamics of bacteriorhodopsin are investigated using molecular modelling, dynamical simulations and neutron scattering experiments. The simulations are performed on a model system consisting of one protein molecule plus intrinsic water molecules. The simulation-derived structure is compared with neutron diffraction data on the location of water and with the available electron microscopy structure of highest resolution. The simulated water geometry is in good accord with the neutron data. The protein structure deviates slightly but significantly from the experiment. The low-frequency vibrational frequency distribution of a low-hydration purple membrane is derived from inelastic neutron scattering data and compared with the corresponding simulation-derived quantity.

Bacteriorhodopsins↗
PubMed1980

X-ray and neutron scattering density profiles of the intact human red blood cell membrane.

Hemoglobin-free human red blood cell membranes have been prepared with glutaraldehyde to maintain an intact structure on partial dehydration. Treatment of resealed ghosts with poly(L-lysine) produced an essentially constant structural unit and permitted correlation of electron microscopy results with x-ray and neutron diffraction profiles. These profiles provide detailed information, for the intact membrane, on the location and relative distribution of lipids and proteins.

Erythrocyte Membrane↗
PubMed2004

Neutron imaging of Zr-1%Nb fuel cladding material containing hydrogen.

Hydrogen distribution and hydride phases were analyzed in reactor fuel cladding pressure tube Zr-1%Nb material up to 13,300 ppm. From neutron diffraction measurements, formation of cubic delta-ZrH2 and a small amount of tetragonal gamma-ZrH was established. Texture effects were analyzed by imaging plate technique. From neutron radiography images a linear model was set up that adequately described the relationship between gray levels and nominal H-concentrations. The H-distribution was unveiled by 3D intensity histograms and fractal analysis of multilevel-segmented neutron radiography images.

Journal Article↗
PubMed2003

Multiple Li positions inside oxygen octahedra in lithiated TiO2 anatase.

Intercalation of Li in TiO2 anatase results in a phase separation in a Li-poor and a Li-rich phase. The local lithium configuration in the coexisting crystallographic phases is resolved by detailed analysis of neutron diffraction data. In each of the phases, two distinct positions within the octahedral interstices are found, with a temperature-dependent occupancy. A combination of quasi-elastic neutron scattering and force field molecular dynamics simulations shows that Li is hopping on a picosecond time scale between the two sites in the octahedral interstices. The results also suggest a specific Li arrangement along the crystallographic a direction, albeit without long range order. It is likely that multiple discrete Li sites within a distorted oxygen octahedron occur not only in intercalated TiO2 anatase but also in other (transition metal) oxides.

Journal Article↗
PubMed1994

Image plate detectors for macromolecular neutron diffractometry.

Neutron diffraction studies of macromolecules require large position sensitive detectors. It is proposed that such a device can be based on image plate technology, which relies on re-usable photostimuable phosphors, combined with a neutron to gamma-ray converter. Design parameters such as the best wavelength for the neutron radiation and the optimum sample to detector distance are discussed, and a design for a cylindrical detector is outlined. Presently a prototype of such a detector is being built, and the very first test-recording of an X-ray diffraction pattern from a protein crystal is presented.

Journal Article↗
PubMed2006

Structural phase transition and hydrogen ordering of TlH2PO4 at low temperature.

The crystal structure of TlH(2)PO(4) (TDP) has been studied at low temperature. The lattice parameters were derived from high-resolution X-ray powder diffraction in the temperature range between 8 and 300 K. A detailed crystal structure analysis of the antiferroelectric low-temperature phase TDP-III has been performed based on neutron diffraction data measured at 210 K on a twinned crystal consisting of two domain states. The structure model in the triclinic space group P\bar 1 is characterized by a complete ordering of all the H atoms in the asymmetric O-H...O hydrogen bonds. The phase transition from the ferroelastic TDP-II to the antiferroelectric TDP-III phase at 229.5 +/- 0.5 K is only slightly of first order and shows no detectable hysteresis effects. Its mechanism is driven by the hydrogen ordering between the partially ordered TDP-II state and the completely ordered TDP-III state. The polymorphism of TDP and the fully deuterated TlD(2)PO(4) (DTDP) is presented in the form of group-subgroup relations between the different space groups.

Journal Article↗
PubMed1987

The partial molar volume of water in biological membranes.

A new algorithm is presented for interpreting the hydration dependence of x-ray diffraction measurements. The method assumes that the volume of the hydrocarbon phase of the lipid bilayer is not affected by hydration and that the volume expansion between bilayers at maximum hydration is caused by incorporation of water molecules whose partial molar volume is that of pure bulk water. These simple assumptions lead to a determination of the area expansion (and hence change in hydrocarbon-phase thickness) as a function of hydration. An analysis is made of x-ray data of the L alpha and L beta' phases of dimyristoyl phosphatidylcholine and the L alpha phase of egg phosphatidylcholine. The partial molar volume of water depends critically on the degree of lipid hydration and the presence of voids between the head groups of adjacent lipids. The calculated head-group spacings at minimum hydration are consistent with those obtained from neutron diffraction and indicate that the methyl groups of the choline are almost in contact with corresponding groups in the opposing bilayer. This calls into question the origin of the repulsive forces observed in dehydration experiments.

Algorithms↗
PubMedDate not supplied

Frozen spin targets in ribosomal structure research.

Polarized neutron scattering strongly depends on nuclear spin polarisation, particularly on proton spin polarisation. A single proton in a deuterated environment then is as efficient as 10 electrons in X-ray anomalous diffraction. Neutron scattering from the nuclear spin label is controlled by the polarisation of neutron spins and nuclear spins. Pure deuteron spin labels and proton spin labels are created by NMR saturation. We report on results obtained from the large subunit of E. coli ribosomes which have been obtained at the research reactor of GKSS using the polarized target facility developed by CERN. The nuclear spins were oriented with respect to an external field by dynamic nuclear polarisation. Proton spin polarisations of more than 80% were obtained in ribosomes at temperatures below 0.5 K. At T = 130 mK the relaxation time of the polarized target is one month (frozen spin target). Polarized small-angle neutron scattering of the in situ structure of rRNA and the total ribosomal protein (TP) has been determined from the frozen spin targets of the large ribosomal subunit, which has been deuterated in the TP and rRNA respectively. The results agree with those from neutron scattering in H2O/D2O mixtures obtained at room temperature. This is a necessary prerequisite for the planned determination of the in situ structure of individual ribosomal proteins and especially of that of ribosome bound mRNA and tRNAs.

Deuterium↗
PubMed2006

Ion association in aqueous LiCl solutions at high concentration: predicted results via molecular simulation.

We perform molecular dynamics simulations to study the ionic solvation and association behavior in concentrated aqueous LiCl solutions at ambient conditions, including consideration of expected signatures of ion pairing that might be found in neutron diffraction experiments with isotopic substitution. The ten possible pair radial distribution functions that define the microstructure of the systems are determined and used to assess the first-order difference of the neutron-weighted correlation functions for these solutions in heavy and null water. Then, both sets of correlation functions are applied to the interpretation of the ion's local environment in terms of the location of the relevant peaks and the penetration of ions into the counterion solvation shells as a signature of ion-pair formation. Finally, we illustrate how first-order difference experiments involving null and heavy water might be used to assess the magnitude of the M(v+) - X(v-) ion-pair formation for a salt M(v+)X(n) v- in an aqueous solution, provided the significant experimental challenges in these studies could be overcome.

Journal Article↗
PubMed1995

Experimental electron density in crystalline H3PO4.

X-ray diffraction data for H3PO4 crystals have been measured to dmin = 0.46 A resolution, and used to model the electron-density distribution with the hydrogen structure of the crystals adopted from an earlier neutron diffraction analysis. The molecule is asymmetric in the crystal with site symmetry 1 (C1), but the local symmetries of the pseudoatomic densities are, within experimental error, equivalent as they would be under idealized 3m (C3v) molecular symmetry. Although the experimental analysis entailed substantial problems with absorption and extinction corrections, the static deformation density from the experiment agrees very well with that from a polarized split-valence molecular orbital wavefunction for an isolated molecule with the crystallographic molecular geometry. Hydrogen bonding in the crystal polarizes the molecule's P==O acceptor group towards P(+)--O-, and appears to relocalize the lone-pair density of the P--OH donor groups. Crystal data: anhydrous orthophosphoric acid, H3PO4, M(r) = 98.00, room temperature, P2(1)/c, a = 5.7572 (13), b = 4.8310 (17), c = 11.5743 (21) A, beta = 95.274 (12) degrees, V = 320.55 (25) A3, Z = 4, dx = 2.030 mg mm-3, mu = 0.660 mm-1 for lambda(Mo K alpha) = 0.7107 A, F(000) = 200 e-, R(parallel F) = 0.026 for 3512 unique reflections.

Crystallography, X-Ray↗
PubMed1999

Electron density study of urea using TDS-corrected X-ray diffraction data: quantitative comparison of experimental and theoretical results.

The electron-density distribution in urea, CO(NH(2))(2), was studied by high-precision single-crystal X-ray diffraction analysis at 148 (1) K. An experimental correction for TDS was applied to the X-ray intensities. R(merge)(F(2)) = 0.015. The displacement parameters agree quite well with results from neutron diffraction. The deformation density was obtained by refinement of 145 unique low-order reflections with the Hansen & Coppens [Acta Cryst. (1978), A34, 909-921] multipole model, resulting in R = 0.008, wR = 0.011 and S = 1.09. Orbital calculations were carried out applying different potentials to account for correlation and exchange: Hartree-Fock (HF), density-functional theory/local density approximation (DFT/LDA) and density-functional theory/generalized gradient approximation (DFT/GGA). Extensive comparisons of the deformation densities and structure factors were made between the results of the various calculations and the outcome of the refinement. The agreement between the experimental and theoretical results is excellent, judged by the deformation density and the structure factors [wR(HF) = 0.023, wR(DFT) = 0.019] and fair with respect to the results of a topological analysis. Density-functional calculations seem to yield slightly better results than Hartree-Fock calculations.

Journal Article↗
PubMed2004

Structural investigations of polymer electrolyte poly(propylene oxide)-LiClO4 using diffraction experiments and reverse Monte Carlo simulation.

The structure of an amorphous polymer electrolyte, poly(propylene oxide) (PPO) complexed with LiClO4, has been studied using reverse Monte Carlo (RMC) simulations. The simulations require no force field but are based on experimental data only, in this case from x-ray and neutron diffraction experiments. Excellent agreement between the experimental data and the structures resulting from the RMC simulation is obtained. Samples with ether-oxygen to lithium concentrations (molar ratios) O:Li=16:1 and 5:1 were studied and compared to results of pure PPO from a previous study. We focus on the effects of the solvated salt on the structure of the polymer matrix, the spatial distribution of ions, and the correlations between the anions and the polymer chains. Analyzing the structures produced in the simulations, we find that for a concentration 16:1, the interchain distance is approximately the same as in pure PPO but more well defined. For a concentration 5:1, we find a larger and less well-defined interchain distance compared to the 16:1 concentration. This signifies that at the 16:1 salt concentration, there is enough free volume in the polymer host to accommodate the ions, and that the solvation of salt induces ordering of the polymer matrix. At the higher salt concentration 5:1, the polymer network must expand and become less ordered to host the ions. We also note, in accordance with previous studies, that the solvation of salt changes the conformation of the polymer chain towards more gauche states. The simulations furthermore reveal marked correlations between the polymer chains and the anions, which we suggest arise predominantly from an interaction mediated via cations, which can simultaneously coordinate both ether oxygens in the polymer chains and anions. Interanionic distances at 5 A, which are consistent with two or more anions being coordinated around the same cation, are also observed. On a larger scale, the RMC structure of PPO-LiClO4 16:1 clearly indicates the presence of salt-rich and salt-depleted domains having a length scale of <20 A. In view of such a heterogeneous structure of PPO-LiClO4 16:1, it is plausible that the increased ordering of the polymer matrix is due to rather well-defined structural arrangements within the salt-rich domains, and that the characteristic interchain distance in the salt-rich domains is similar to that of the pure polymer.

Journal Article↗
PubMed1978

Where do general anaesthetics act?

General anaesthetics were found to have no effect on lipid bilayer structures when studied using X-ray and neutron diffraction. Combined gaseous and aqueous phase solubility data suggested that the primary site of action of general anaesthetics has both polar and nonpolar characteristics, and probably involves protein.

Anesthetics↗