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PubMed1998

Direct detection of domains in phospholipid bilayers by grazing incidence diffraction of neutrons and atomic force microscopy.

The geometry of domains in phospholipid bilayers of binary (1:1) mixtures of synthetic lecithins with a difference in chain length of four methylene groups has been studied by two independent, direct and complementary methods. Grazing incidence diffraction of neutrons provided gel domain sizes of less than 10 nm in both the gel and the coexistence phase of the mixture, while no domains were detected for the fluid phase. For the coexistence region, the neutron data suggest that domains grow in number rather than in size with decreasing temperature. Atomic force microscopy was used to study gel phase size and shape of the domains. The domains imaged by atomic force microscopy exhibit a rather irregular shape with an average size of 10 nm, thus confirming the neutron results for this phase. The good agreement between atomic force microscopy and neutron results, despite the completely different nature of their observables, has potential for the future development of refined models for the interpretation of neutron data from heterogeneous membranes in terms of regularly spaced and spatially extended scatterers.

Calorimetry, Differential Scanning↗
PubMed2006

Anisotropic displacement parameters for H atoms using an ONIOM approach.

X-ray diffraction data cannot provide anisotropic displacement parameters (ADPs) for H atoms, a major outstanding problem in charge-density analysis of molecular crystals. Although neutron diffraction experiments are the preferred source of this information, for a variety of reasons they are possible only for a minority of materials of interest. To date, approximate procedures combine rigid-body analysis of the molecular heavy-atom skeleton, based on ADPs derived from the X-ray data, with estimates of internal motion provided by spectroscopic data, analyses of neutron diffraction data on related compounds, or ab initio calculations on isolated molecules. Building on these efforts, an improved methodology is presented, incorporating information on internal vibrational motion from ab initio cluster calculations using the ONIOM approach implemented in GAUSSIAN03. The method is tested by comparing model H-atom ADPs with reference values, largely from neutron diffraction experiments, for a variety of molecular crystals: benzene, 1-methyluracil, alpha-glycine, xylitol and 2-methyl-4-nitroaniline. The results are impressive and, as the method is based on widely available software, and is in principle widely applicable, it offers considerable promise in future charge-density studies of molecular crystals.

Journal Article↗
PubMed2001

Temperature-dependent neutron powder diffraction study of the Ba(OD)(2) polymorphs: a new low-temperature phase.

The structural behaviour of both low-temperature beta- and high-temperature alpha-Ba(OD)(2), barium dihydroxide-d, was investigated at temperatures between 10 and 552 K by neutron powder diffraction. While the beta phase (P2(1)/n) remains stable to the lowest temperature investigated, the quenchable alpha phase (Pnma) shows a reversible orthorhombic-to-monoclinic phase transition between 100 and 150 K. The structure of the new alpha(m) phase (P2(1)/n) is quite similar to that of the alpha phase. This behaviour is unusual as a metastable phase transforms to another metastable phase. The Pnma <--> P2(1)/n low-temperature phase transition is driven by an order-disorder mechanism, mainly caused by one of the D atoms, which is disordered on positions off the mirror plane, mimicking a special position on the mirror plane in the orthorhombic phase. Refinements of the alpha phase above the phase transition indicate this disorder across the mirror plane through a conspicuously high isotropic displacement parameter if compared to the other D atoms. At low temperature the energy of the vibration is lowered and the D atom is frozen at a general position in a correlated way, thus violating the mirror plane and reducing the space-group symmetry.

Journal Article↗
PubMed2006

Structure of Ce2RhIn8: an example of complementary use of high-resolution neutron powder diffraction and reciprocal-space mapping to study complex materials.

The room-temperature crystal structure of the heavy fermion antiferromagnet Ce2RhIn8, dicerium rhodium octaindide, has been studied by a combination of high-resolution synchrotron X-ray reciprocal-space mapping of single crystals and high-resolution time-of-flight neutron powder diffraction. The structure is disordered, exhibiting a complex interplay of non-periodic, partially correlated planar defects, coexistence and segregation of polytypic phases (induced by periodic planar ;defects'), mosaicity (i.e. domain misalignment) and non-uniform strain. These effects evolve as a function of temperature in a complicated way, but they remain down to low temperatures. The room-temperature diffraction data are best represented by a complex mixture of two polytypic phases, which are affected by non-periodic, partially correlated planar defects, differ slightly in their tetragonal structures, and exhibit different mosaicities and strain values. Therefore, Ce2RhIn8 approaches the paracrystalline state, rather than the classic crystalline state and thus several of the concepts of conventional single-crystal crystallography are inapplicable. The structural results are discussed in the context of the role of disorder in the heavy-fermion state and in the interplay between superconductivity and magnetism.

Journal Article↗
PubMed2004

Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy.

The atomic resolution structure of Pf1 coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles in solution is compared to the structures previously determined by X-ray fiber and neutron diffraction, the structure of its membrane-bound form, and the structure of fd coat protein. These structural comparisons provide insights into several biological properties, differences between class I and class II filamentous bacteriophages, and the assembly process. The six N-terminal amino acid residues adopt an unusual "double hook" conformation on the outside of the bacteriophage particle. The solid-state NMR results indicate that at 30 degrees C, some of the coat protein subunits assume a single, fully structured conformation, and some have a few mobile residues that provide a break between two helical segments, in agreement with structural models from X-ray fiber and neutron diffraction, respectively. The atomic resolution structure determined by solid-state NMR for residues 7-14 and 18-46, which excludes the N-terminal double hook and the break between the helical segments, but encompasses more than 80% of the backbone including the distinct kink at residue 29, agrees with that determined by X-ray fiber diffraction with an RMSD value of 2.0 A. The symmetry and distance constraints determined by X-ray fiber and neutron diffraction enable the construction of an accurate model of the bacteriophage particle from the coordinates of the coat protein monomers.

Bacteriophage Pf1↗
PubMed2003

Structural and physical properties of the ferromagnetic tris-dithiooxalato compounds, A[M(II)Cr(III)(C(2)S(2)O(2))(3)], with A(+) = N(n-C(n)()H(2)(n)(+1))(4)(+) (n = 3-5) and P(C(6)H(5))(4)(+) and M(II) = Mn, Fe, Co, and Ni.

The structural and magnetic properties of the tris-dithiooxalato salts, A[M(II)Cr(C(2)S(2)O(2))(3)], have been investigated with A(+) = PPh(4)(+), N(n-C(n)()H(2)(n)()(+1))(4)(+), with n = 3-5, where M(II) is Mn, Fe, Co, and Ni. With the exception of A[MnCr(C(2)S(2)O(2))(3)], all the salts are ferromagnets with Curie temperatures, T(c), between 5 and 16 K. In contrast to the corresponding oxalates which are ferromagnetic, the A[MnCr(C(2)S(2)O(2))(3)] compounds are paramagnetic above 2 K. Powder neutron diffraction studies of d(20)-PPh(4)[FeCr(C(2)S(2)O(2))(3)] indicate that no structural phase transitions occur between 2.4 and 285 K and that the coefficient of linear expansion is four times larger for the c-axis than for the a-axis. The crystal structure refined from powder neutron diffraction data confirms the honeycomb layer arrangement observed in the related bimetallic tris-oxalate salts. The Mössbauer spectra reveal that the iron(II) in PPh(4)[FeCr(C(2)S(2)O(2))(3)] is coordinated mainly to six oxygen atoms of the dithiooxalato ligand but with a minor component of sulfur coordination that increases with aging of the sample; the iron(II) is high-spin in both cases. Powder neutron diffraction profiles of d(20)-PPh(4)[FeCr(C(2)S(2)O(2))(3)] below T(c) show magnetic intensity with a q = 0 propagation vector, confirming the presence of ferromagnetic order.

Journal Article↗
PubMed1984

Phospholipid asymmetry in the isolated sarcoplasmic reticulum membrane.

The total phospholipid content and distribution of phospholipid species between the outer and inner monolayers of the isolated sarcoplasmic reticulum membrane was measured by phospholipase A2 activities and neutron diffraction. Phospholipase measurements showed that specific phospholipid species were asymmetric in their distribution between the outer and inner monolayers of the sarcoplasmic reticulum lipid bilayer; phosphatidylcholine (PC) was distributed 48/52 +/- 2% between the outer and inner monolayer of the sarcoplasmic reticulum bilayer, 69% of the phosphatidyl-ethanolamine (PE) resided mainly in the outer monolayer of the bilayer, 85% of the phosphatidylserine (PS) and 88% of the phosphatidylinositol (PI) were localized predominantly in the inner monolayer. The total phospholipid distribution determined by these measurements was 48/52 +/- 2% for the outer/inner monolayer of the sarcoplasmic reticulum lipid bilayer. Sarcoplasmic reticulum phospholipids were biosynthetically deuterated and exchanged into isolated vesicles with both a specific lecithin and a general exchange protein. Neutron diffraction measurements directly provided lipid distribution profiles for both PC and the total lipid content in the intact sarcoplasmic reticulum membrane. The outer/inner monolayer distribution for PC was 47/53 +/- 1%, in agreement with phospholipase measurements, while that for the total lipid was 46/54 +/- 1%, similar to the phospholipase measurements. These neutron diffraction results regarding the sarcoplasmic reticulum membrane bilayer were used in model calculations for decomposing the electron-density profile structure (10 A resolution) of isolated sarcoplasmic reticulum previously determined by X-ray diffraction into structures for the separate membrane components. These structure studies showed that the protein profile structure within the membrane lipid bilayer was asymmetric, complementary to the asymmetric lipid structure. Thus, the total phospholipid asymmetry obtained by two independent methods was small but consistent with a complementary asymmetric protein structure, and may be related to the highly vectorial functional properties of the calcium pump ATPase protein in the sarcoplasmic reticulum membrane.

Animals↗
PubMed2003

Impact of urea on water structure: a clue to its properties as a denaturant?

A new investigation of the structure of urea-water solutions at a mole ratio of 1 urea to 4 water molecules is described. Neutron diffraction is used in conjunction with isotope labelling on the water and urea hydrogen atoms and on the nitrogen atom of urea. The diffraction data are analysed using the empirical potential structure refinement procedure to yield a set of site-site radial distribution functions and spatial density functions that are consistent with the diffraction data. The results are discussed in relation to recent and past X-ray and neutron diffraction experiments and theoretical studies of this system. It is found that urea incorporates readily into water, forming pronounced hydrogen bonds with water at both the amine and carbonyl headgroups. In addition the urea also hydrogen bonds to itself, forming chains or clusters consisting of up to approximately 60 urea molecules in a cluster. There, is however, little or no evidence of urea segregating itself from water, in marked contrast to a recent study of the methanol-water system. This behaviour is discussed in the context of the great propensity of urea to effect protein denaturation.

Hydrogen Bonding↗
PubMed1998

15R SrMn(1-)(x)()Fe(x)()O(3)(-)(delta) (x approximately 0.1); A New Perovskite Stacking Sequence.

A polycrystalline sample of a new phase in the Sr-Fe-Mn-O system has been prepared by standard solid-state techniques. Characterization at room temperature by X-ray diffraction, high-resolution electron microscopy, Mössbauer spectroscopy and neutron diffraction has led to it being described as a 15-layered, rhombohedral (15R) perovskite [space group R&thremacr;m: a = 5.4489(1) Å, c = 33.8036(7) Å] with a previously unobserved structure. The pseudo close-packed SrO(3) layers have a (cchch)(3) stacking sequence such that the occupation of the interstitial 6-coordinate sites by Mn (or Fe) leads to the formation of Mn(2)O(9) units which are linked to each other either directly by a common vertex, or indirectly via a single, vertex-sharing MnO(6) octahedron. The stoichiometry of the compound was determined to be SrMn(0.915(5))Fe(0.085(5))O(2.979(3)). The face-sharing sites are occupied by 0.957(3)Mn/0.043(3)Fe while the exclusively corner-linked sites show a higher Fe occupation; 0.745(4)Mn/ 0.255(4)Fe. A neutron diffraction experiment carried out at 3 K indicated the presence of long-range magnetic order with the Mn(4+) cations aligned antiferromagnetically with an ordered moment of 2.26(3)&mgr;(B)/Mn(4+). Both the neutron and the susceptibility data are consistent with the Fe cations remaining magnetically disordered to 3 K. The latter data show T(N) = 220 K, and suggest that some spin frustration is present at low temperatures.

Journal Article↗
PubMed2005

Electron and nuclear positions in the short hydrogen bond in urotropine-N-oxide.formic acid.

The crystal structure of urotropine-N-oxide.formic acid, as determined from multiple temperature single-crystal X-ray diffraction experiments in the range 123-295 K and from neutron diffraction at 123 K, is reported. There is a strong hydrogen bonding interaction between the OH of formic acid and the N-oxide of urotropine, with the oxygen-oxygen distance ranging from 2.4300(10) to 2.4469(10) A. The electron density of the hydrogen atom associated with this interaction was located in the Fourier difference maps of the spherical atom refinement after all heavy atom positions were determined. The maximum of the electron density associated with the hydrogen bond is located approximately 1.16 A from the formate segment, though the distribution of electron density is very broad. The electron density associated with the H atom is thus shown by these accurate X-ray diffraction experiments to be approximately centered at all temperatures studied. This was conclusively confirmed by single-crystal neutron diffraction data obtained at 123 K, from which statistically equivalent O-H distances of 1.221(7) and 1.211(7) A were obtained.

Journal Article↗
PubMed2005

High-resolution neutron protein crystallography with radically small crystal volumes: application of perdeuteration to human aldose reductase.

Neutron diffraction data have been collected to 2.2 Angstrom resolution from a small (0.15 mm(3)) crystal of perdeuterated human aldose reductase (h-AR; MW = 36 kDa) in order to help to determine the protonation state of the enzyme. h-AR belongs to the aldo-keto reductase family and is implicated in diabetic complications. Its ternary complexes (h-AR-coenzyme NADPH-selected inhibitor) provide a good model to study both the enzymatic mechanism and inhibition. Here, the successful production of fully deuterated human aldose reductase [h-AR(D)], subsequent crystallization of the ternary complex h-AR(D)-NADPH-IDD594 and neutron Laue data collection at the LADI instrument at ILL using a crystal volume of just 0.15 mm(3) are reported. Neutron data were recorded to 2 Angstrom resolution, with subsequent data analysis using data to 2.2 Angstrom. This is the first fully deuterated enzyme of this size (36 kDa) to be solved by neutron diffraction and represents a milestone in the field, as the crystal volume is at least one order of magnitude smaller than those usually required for other high-resolution neutron structures determined to date. This illustrates the significant increase in the signal-to-noise ratio of data collected from perdeuterated crystals and demonstrates that good-quality neutron data can now be collected from more typical protein crystal volumes. Indeed, the signal-to-noise ratio is then dominated by other sources of instrument background, the nature of which is under investigation. This is important for the design of future instruments, which should take maximum advantage of the reduction in the intrinsic diffraction pattern background from fully deuterated samples.

Aldehyde Reductase↗
PubMed2005

Combined charge and spin density experimental study of the yttrium(III) semiquinonato complex Y(HBPz3)2(DTBSQ) and DFT calculations.

High-resolution X-ray diffraction and polarized neutron diffraction experiments have been performed on the Y-semiquinonate complex, Y(HBPz3)2(DTBSQ), in order to determine the charge and spin densities in the paramagnetic ground state, S = (1/2). The aim of these combined studies is to bring new insights to the antiferromagnetic coupling mechanism between the semiquinonate radical and the rare earth ion in the isomorphous Gd(HBPz3)2(DTBSQ) complex. The experimental charge density at 106 K yields detailed information about the bonding between the Y3+ ion and the semiquinonate ligand; the topological charge of the yttrium atom indicates a transfer of about 1.5 electrons from the radical toward the Y3+ ion in the complex, in agreement with DFT calculations. The electron density deformation map reveals well-resolved oxygen lone pairs with one lobe polarized toward the yttrium atom. The determination of the induced spin density at 1.9 K under an applied magnetic field of 9.5 T permits the visualization of the delocalized magnetic orbital of the radical throughout the entire molecule. The spin is mainly distributed on the oxygen atoms [O1 (0.12(1) mu B), O2(0.11(1) mu B)] and the carbon atoms [C21 (0.24(1) mu B), C22(0.20(1) mu B), C24(0.16(1) mu B), C25(0.12(1) mu B)] of the carbonyl ring. A significant spin delocalization on the yttrium site of 0.08(2) mu B is observed, proving that a direct overlap with the radical magnetic orbital can occur at the rare earth site and lead to antiferromagnetic coupling. The DFT calculations are in good quantitative agreement with the experimental charge density results, but they underestimate the spin delocalization of the oxygen toward the yttrium and the carbon atoms of the carbonyl ring.

Journal Article↗
PubMed2004

Cooperative ordering of gapped and gapless spin networks in Cu2Fe2Ge4O13.

The unusual magnetic properties of a novel low-dimensional quantum ferrimagnet Cu2Fe2Ge4O13 are studied using bulk methods, neutron diffraction, and inelastic neutron scattering. It is shown that this material can be described in terms of two low-dimensional quantum spin subsystems, one gapped and the other gapless, characterized by two distinct energy scales. Long-range magnetic ordering observed at low temperatures is a cooperative phenomenon caused by weak coupling of these two spin networks.

Journal Article↗
PubMed2006

The crystal structure of Zr2NiD4.5.

The crystal structure of Zr2NiD4.5 has been determined by a combination of synchrotron radiation powder X-ray diffraction, electron diffraction and powder neutron diffraction data. Deuterium ordering results in a triclinic supercell given by asuper=6.81560 (7), bsuper=8.85137 (9), csuper=8.88007 (10) A, alphasuper=79.8337 (8), betasuper=90.0987 (9), gammasuper=90.3634 (9) degrees, which relates to the non-super unit cell as asuper=-a, bsuper=-b-c, csuper=-b+c. The centrosymmetric and fully ordered deuterium sublattice was determined by simulated annealing and Rietveld refinement. Deuterium was found to occupy three types of tetrahedral sites: two that are coordinated by four Zr atoms and one that is coordinated by three Zr atoms and one Ni atom. All D-D distances are longer than 2 A. The feasibility of the crystal structure was supported by density functional theory calculations.

Journal Article↗
PubMed2003

Crystallization of a large single crystal of cubic insulin for neutron protein crystallography.

The growth of a large single crystal of cubic porcine insulin for characterization of hydrogen and hydration in cubic insulin crystals by neutron diffraction analysis is reported. Growth in D2O was investigated based on the phase diagram for cubic insulin to determine appropriate growth conditions, and a large single crystal was then successfully grown by a dialysis method to a size of 4.0 x 4.0 x 1.3 mm3. Neutron diffraction analysis of the cubic insulin crystals was carried out using a single-crystal diffractometer at the JRR-3M reactor of the Japan Atomic Energy Research Institute. In preliminary analysis, Npi appears to be protonated and Ntau deprotonated in His5 in the B-chain, whereas both Npi and Ntau are protonated in His10.

Crystallization↗
PubMed2006

Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography.

Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins, a technique complimentary to ultra-high-resolution [1, 2] X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the United States, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5-2.5 A. Results relating to hydrogen positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, H/D exchange in proteins and oligonucleotides, the role of hydrogen atoms in enzymatic activity and thermostability, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals, the preparation of fully deuterated proteins, the use of cryogenic techniques, and a data base of hydrogen and hydration in proteins, will be described.

Biology↗
PubMed2005

Nanometer-scale ion aggregates in aqueous electrolyte solutions: guanidinium sulfate and guanidinium thiocyanate.

Neutron diffraction experiments and molecular dynamics simulations are used to study the structure of aqueous solutions of two electrolytes: guanidinium sulfate (a mild protein conformation stabilizer) and guanidinium thiocyanate (a powerful denaturant). The MD simulations find the unexpected result that in the Gdm2SO4 solution the ions aggregated into mesoscopic (nanometer-scale) clusters, while no such aggregation is found in the GdmSCN solution. The neutron diffraction studies, the most direct experimental probe of solution structure, provide corroborating evidence that the predicted very strong ion pairing does occur in solutions of 1.5 m Gdm2SO4 but not in 3 m solutions of GdmSCN. A mechanism is proposed as to how this mesoscopic solution structure affects solution denaturant properties and suggests an explanation for the Hofmeister ordering of these solutions in terms of this ion pairing and the ability of sulfate to reverse the denaturant power of guanidinium.

Electrolytes↗