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PubMed1965

ALPHA-D-GLUCOSE: PRECISE DETERMINATION OF CRYSTAL AND MOLECULAR STRUCTURE BY NEUTRON-DIFFRACTION ANALYSIS.

This analysis provides the first precise crystal and molecular structural parameters for alpha-D-glucose. The C-C, C-H, and O-H bond lengths deviate only slightly from their means of 1.523 A, 1.098 A, and 0.968 A. The C(1)-O(1) bond length, 1.389 A, is significantly shorter than the mean value, 1.420 A, of the other C-O bonds. The valence angle of the ring oxygen is 113.8 degrees.

Biophysical Phenomena↗
PubMed2001

Cubic aluminum silicides RE8Ru12Al49Si9(Al(x)Si12-x) (RE = Pr, Sm) from liquid aluminum. Empty (Si,Al)12 cuboctahedral clusters and assignment of the Al/Si distribution with neutron diffraction.

Two new quaternary aluminum silicides, RE8Ru12Al49Si9(Al(x)Si12-x) (x approximately 4; RE = Pr, Sm), have been synthesized from Sm (or Sm2O3), Pr, Ru, and Si in molten aluminum between 800 and 1000 degrees C in sealed fused silica tubes. Both compounds form black shiny crystals that are stable in air and NaOH. The Nd analog is also stable. The compounds crystallize in a new structural type. The structure, determined by single-crystal X-ray diffraction, is cubic, space group Pm3m with Z = 1, and has lattice parameters of a = 11.510(1) A for Sm8Ru12Al49Si9(Al(x)Si12-x) and a = 11.553(2) A for Pr8Ru12Al49Si9(Al(x)Si12-x) (x approximately 4). The structure consists of octahedral units of AlSi6, at the cell center, Si2Ru4Al8 clusters, at each face center, SiAl8 cubes, at the middle of the cell edges, and unique (Al,Si)12 cuboctohedral clusters, at the cell corners. These different structural units are connected to each other either by shared atoms, Al-Al bonds, or Al-Ru bonds. The rare earth metal atoms fill the space between various structural units. The Al/Si distribution was verified by single-crystal neutron diffraction studies conducted on Pr8Ru12Al49Si9(Al(x)Si12-x). Sm8Ru12Al49Si9(Al(x)Si12-x) and Pr8Ru12Al49Si9(Al(x)Si12-x) show ferromagnetic ordering at Tc approximately 10 and approximately 20 K, respectively. A charge of 3+ can be assigned to the rare earth atoms while the Ru atoms are diamagnetic.

Journal Article↗
PubMed1988

High-sensitivity neutron diffraction of membranes: Location of the Schiff base end of the chromophore of bacteriorhodopsin.

THREE IMPORTANT EVENTS IN THE FUNCTIONAL CYCLE OF BACTERIORHODOPSIN OCCUR AT THE CHROMOPHORE: the primary absorption of light, the isomerization from the alltrans to the 13-cis form, and the deprotonation and reprotonation of its Schiff base. The protonated Schiff base linkage of the chromophore with lysine-216 plays an essential role in the color regulation of the pigment and is most likely directly involved in the charge translocation of this light-driven proton pump. Although much is known about the structure of the protein, the position of this key functional group has not yet been determined. We have synthesized a retinal in which the five protons closest to the Schiff base are replaced by deuterons. The labeled retinal was spontaneously incorporated into bacteriorhodopsin by using a mutant of Halobacterium halobium that is deficient in the synthesis of retinal. The position of the labeled Schiff base end of the chromophore was determined in the two-dimensional projected density of dark-adapted bacteriorhodopsin by neutron diffraction. The result fits very well with our previous work using retinals that were selectively deuterated in the middle of the polyene chain or in the cyclohexene ring. A coherent structure emerges with the three labeled positions on one line, separated by distances that are in good agreement with the tilt angle of the polyene chain (about 20 degrees ). The chromophore is located in the interior of the protein with the nitrogen of the Schiff base between helices 2 and 6 and with its ring in the vicinity of helix 4. Our results show that it is possible to locate a small group containing as few as five deuterons in a membrane protein of molecular weight 27,000.

Journal Article↗
PubMed2004

Hydrogen-bonded polyrotaxane-like structure containing cyclic (H2O)4 in [Zn(OAc)2(mu-bpe)]2.H2O: X-ray and neutron diffraction studies.

The reaction of 4,4'-bipyridylethane (bpe) and 4,4'-dipyridyl disulfide (dpds) with Zn(OAc)2.2H2O has led to the formation of two coordination polymers, [Zn(OAc)2(mu-bpe)].2H2O (1) and [Zn(OAc)2(mu-dpds)] (2). Both the compounds have zigzag coordination polymeric structures as revealed by X-ray crystallography. However, the presence of two lattice water molecules in 1 results in an interesting difference between the crystal structures. In 1, the carboxylate carbonyl oxygen atoms of the Zn(OAc)2 groups from two different adjacent zigzag polymers and four lattice water molecules form 24-membered hydrogen-bonded rings (graph set notation, R6 (6)(24)). One of the two bpe ligands associated with each Zn(II) center passes through the center of this ring to form a two-dimensional hydrogen-bonded coordination polymeric structure. In the solid state, the adjacent 24-membered hydrogen-bonded rings further fuse together through O-H...O hydrogen bonds among four waters to form cyclic (H2O)4. This results in a one-dimensional hydrogen-bonded ribbon-like polymer comprising fused alternating 24- and eight-membered O-H...O hydrogen-bonded rings. One of the bpe ligands passes through the center of the larger ring to produce an unexpected single self-penetrating three-dimensional hydrogen-bonded network with polyrotaxane-like association. A neutron diffraction study provides a detailed description of the hydrogen bonds involved.

Journal Article↗
PubMed2006

Crystal structures of thermoelectric n- and p-type Ba8Ga16Ge30 studied by single crystal, multitemperature, neutron diffraction, conventional X-ray diffraction and resonant synchrotron X-ray diffraction.

Comprehensive single-crystal structural investigations of n- and p-type Ba8Ga16Ge30 have been carried out using multitemperature neutron and conventional X-ray diffraction as well as resonant synchrotron X-ray diffraction. The data show that the guest atom positions and dynamics are very similar in the two structures, although the barium atoms are slightly more displaced from the cage centers in the p-type structure than in the n-type structure (Deltad = 0.025 A). For both structures Fourier difference maps calculated from very high-resolution neutron diffraction data (sin theta/lambda > 2 A-1) show that the Ba nuclear density at lowest temperatures (15 K) is distributed in a torus around the crystallographic 6d site with maxima in the 24j positions. At room temperature the maxima have shifted to the 24k position. Analysis of atomic displacement parameters give Einstein temperatures of approximately 60(1) K for both structures. Thus, the fundamental difference in the low temperature thermal conductivity observed for p- and n-type Ba8Ga16Ge30 appear not to be directly related to the guest atom behavior as is commonly assumed in thermoelectric research. The neutron data and the resonant synchrotron X-ray data facilitate refinement of Ga/Ge framework occupancies. The Ga atoms have a clear preference for the 6c site with the preference being somewhat stronger for the n-type structure.

Journal Article↗
PubMed2004

Incommensurate magnetic ordering in Cu2Te2O5X2 (X = Cl,Br) studied by neutron diffraction.

We present the results of the first neutron powder and single crystal diffraction studies of the coupled spin tetrahedra systems Cu2Te2O5X2 (X = Cl,Br). Incommensurate antiferromagnetic order with the propagation vectors kCl approximately [0.150,0.422,1/2], kBr approximately [0.158,0.354,1/2] sets in below TN = 18 K for X = Cl and 11 K for X = Br. No simple collinear antiferromagnetic or ferromagnetic spin arrangements within Cu2+ tetrahedra fit these observations. Fitting the diffraction data to more complex but physically reasonable models with multiple helices leads to a moment of 0.67(1)microB/Cu2+ at 1.5 K for the Cl compound. The reason for such a complex ground state may be geometrical frustration of the spins due to the intratetrahedral and intertetrahedral couplings having similar strengths. In neither compound has any evidence for a structural transition accompanying the magnetic ordering been found.

Journal Article↗
PubMed2006

High-pressure neutron diffraction study of L-serine-I and L-serine-II, and the structure of L-serine-III at 8.1 GPa.

The hydrostatic compression of L-serine-d(7) has been studied to 8.1 GPa by neutron powder diffraction. Over the course of this pressure range the compound undergoes two phase transitions, the first between 4.6 and 5.2 GPa, yielding L-serine-II, and the second between 7.3 and 8.1 GPa, yielding L-serine-III. All three polymorphs are orthorhombic, P2(1)2(1)2(1), and feature chains of serine molecules connected via head-to-tail ND...O hydrogen bonds formed between ammonium and carboxylate groups. The chains are linked into a ribbon by a second set of ND...O hydrogen bonds. The hydroxyl moieties are distributed along the outer edges of the ribbon and in phase I they connect the ribbons into a layer by chains of OD...OD hydrogen bonds. The layers are connected together by a third set of ND...O hydrogen bonds, forming R;3_4(14) rings with substantial voids at their centres. In the transition from phase I to II these voids begin to close up, but at the cost of breaking the OD...OD chains. The OD...OD hydrogen bonds are replaced by shorter OD...O hydrogen bonds to carboxylate groups. At 7.3 GPa the O...O distance in the OD...O hydrogen bonds measures only 2.516 (17) A, which is short, and we propose that the phase transition to phase III that occurs between 7.3 and 8.1 GPa relieves the strain that has built up in this region of the structure. The hydroxyl D atom now bifurcates between the OD...O contact that had been present in phase II and a new OD...O contact formed to a carboxylate in another layer. Hirshfeld surface fingerprint plots show that D...D interactions become more numerous, while hydrogen bonds actually begin to lengthen in the transition from phase II to III.

Hydrogen Bonding↗
PubMed1992

Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure.

We present in this paper the complete structure of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) in the L alpha phase (66% RH, 23 degrees C) obtained by the joint refinement of neutron and x-ray lamellar diffraction data. The structural details obtained have previously required a large number of neutron diffraction experiments, using numerous specifically-deuterated phospholipid isomorphs (Büldt et al., 1978. Nature (Lond.). 271:182-184). The joint-refinement approach minimizes specific deuteration by utilizing independent neutron and x-ray data sets. The method yields a quasimolecular structure consisting of a series of multiatomic fragments that are each represented by one or several Gaussian distributions whose positions and widths can be determined to within 0.06 to 0.52 A exclusive of the methylene region. The image of DOPC at 66% RH (5.36 +/- 0.08 waters per lipid) is consistent with many aspects of bilayer structure previously determined by structural and spectroscopic studies. The most striking feature of the structure is the large amount of transbilayer thermal motion suggested by the widths and overlaps of the Gaussian envelopes of the quasimolecular fragments. We discuss the "dynamic bilayer thickness" which describes the minimum effective thickness of the hydrocarbon permeability barrier in terms of the thermal motion of the water. A gradient of thermal motion exists that increases in either direction away from the glycerol backbone which is the most constrained portion of the bilayer. The steric interactions between headgroups of apposed bilayers, expected at the hydration level of our experiments, are clearly revealed. A useful consequence of the quasimolecular structure is that average boundaries within bilayers calculated using composition and volumetric data and ad hoc assumptions can be related to the positions of the principal structural groups. Several measures of "bilayer thickness" in common use can be identified as the positions of the cholines for Luzzati's d1 (Luzzati and Husson. 1962. J. Cell Biol. 12:207-219) and the glycerols for Small's dL (Small. 1967. J. Lipid Res. 8:551-556). We do not know if these relations will be true at other hydrations or for other lipids. Of particular interest is the fact that the position of the carbonyl groups marks the average hydrocarbon/headgroup boundary. It must be emphasized, however, that this region of the bilayer must be generally characterized as one of tumultuous chemical heterogeneity because of the thermal motion of the bilayer.

Biophysical Phenomena↗
PubMed2003

Neutron diffraction study of the size-induced tetragonal to monoclinic phase transition in zirconia nanocrystals.

Accurate neutron powder diffraction experiments at several temperatures allow one to monitor the reconstructive tetragonal to monoclinic phase transition as a function of the size of zirconia nanoparticles. The structure of the tetragonal phase observed in the nanocrystals is identical to that observed in micrometric zirconia above 1400 K. A uniaxial strain depending on grain size is observed. The phase transition occurs above a threshold crystal size. These results are analyzed within the Landau theory and can be understood as a mechanism of size-dependent phase transition where the primary order parameter is altered by the nanoparticle size.

Journal Article↗
PubMed2003

In situ neutron diffraction studies of single crystals and powders during microwave irradiation.

Microwave dielectric heating has become an important method in chemical synthesis and materials processing over the past 15 years, and in the case of the reactions in solutions, there is a well-developed understanding of heating mechanisms and their influence on reaction rate. In the solid-state however, there is much less clarity, despite the advantages to be gained from better insight into the way in which such electromagnetic radiation may couple directly to charge carriers, accelerating reactions in good conductors. The related issue of the influence of microwave irradiation on biological systems, in particular, proteins, and the way in which this may pose hazards to health is similarly poorly understood despite the obvious relevance this may have to the current debate on the influence of electromagnetic radiation, in particular, microwave transmission, on human health. One reason for the paucity of fundamental insight in both fields is because most work has been performed with microwave equipment whose design is derived from that of a domestic oven, and which is not ideal for in situ studies of microwave driven processes. We have been developing new methods of irradiating a variety of solid samples while measuring structural parameters through a range of diffraction techniques, and describe apparatus that will enable X-ray or neutron scattering measurements to be performed on powders or single crystals under microwave irradiation with controlled power level. We also describe preliminary studies of a single crystal of the molecular solid aspirin, and a powder of the microwave-susceptible ionic material BaTiO3, during microwave irradiation.

Aspirin↗
PubMed2003

X-ray and neutron diffraction studies on "Li4.4Sn".

A chemical analysis and detailed structural characterization, using X-ray single crystal and neutron powder diffraction, of the binary lithium-tin compound "Li(4.4)Sn" is presented. Phase analyses and subsequent structural refinements result in the reformulation of "Li(4.4)Sn" as Li(17)Sn(4). The lithium-rich binary phase crystallizes with a complex cubic structure in the space group Ffourmacr;3m, with a = 19.6907(11) A, Z = 20. The improved crystal structure determination indicates well-defined lithium atom positions, some of which differ from those previously reported. The nearly Zintl phase Li(17)Sn(4) exhibits poor metallic behavior similar to that of heavily doped semiconductors. Comparisons of the refined crystal structure with previously reported X-ray crystal structures associated with "Li(4.4)Sn" are discussed.

Journal Article↗
PubMedDate not supplied

Preparation of large crystals of photoactive yellow protein for neutron diffraction and high resolution crystal structure analysis.

The exact positions of all the hydrogen atoms in photoactive yellow protein (PYP) is important for understanding the molecular mechanism of the photoreaction because the protonation/deprotonation of certain amino acid residues and rearrangements in the hydrogen bond network are involved in the conformational changes of PYP. Neutron crystallography is one of the most effective methods to determine the hydrogen positions. However, a large crystal is required for neutron crystallography because a neutron-incident flux is quite limited. In addition, the crystal should be grown from heavy water to reduce the incoherent background from hydrogen. We prepared a large crystal of PYP (dimensions: 1.5 x 0.7 x 0.7 mm3) for neutron crystallography using ammonium sulfate with sodium chloride. The obtained large crystal gave X-ray diffraction spots up to 0.84 angstroms. Although some of the hydrogen atoms could be observed in the high resolution X-ray crystal structure, functionally important hydrogen atoms were impossible to see, indicating the importance of neutron crystallography. Thus, we optimized the crystallization conditions with heavy water and successfully obtained neutron diffraction spots up to 2.1 angstroms with the crystal in D2O.

Bacterial Proteins↗
PubMed2001

Liquid alumina: detailed atomic coordination determined from neutron diffraction data using empirical potential structure refinement.

The neutron scattering structure factor S(N)(Q) for a 40 mg drop of molten alumina (Al2O3) held at 2500 K, using a laser-heated aerodynamic levitation furnace, is measured for the first time. A 1700 atom model of liquid alumina is generated from these data using the technique of empirical potential structural refinement. About 62% of the aluminum sites are 4-fold coordinated, matching the mostly triply coordinated oxygen sites, but some 24% of the aluminum sites are 5-fold coordinated. The octahedral aluminum sites found in crystalline alpha-Al2O3 occur only at the 2% level in liquid alumina.

Journal Article↗
PubMed2006

Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate.

Hydrogen atoms play a central role in many biochemical processes yet are difficult to visualize by x-ray crystallography. Spallation neutron sources provide a new arena for protein crystallography with TOF measurements enhancing data collection efficiency and allowing hydrogen atoms to be located in smaller crystals of larger biological macromolecules. Here we report a 2.2-A resolution neutron structure of Escherichia coli dihydrofolate reductase (DHFR) in complex with methotrexate (MTX). Neutron data were collected on a 0.3-mm(3) D(2)O-soaked crystal at the Los Alamos Neutron Scattering Center. This study provides an example of using spallation neutrons to study protein dynamics, to identify protonation states directly from nuclear density maps, and to analyze solvent structure. Our structure reveals that the occluded loop conformation [monomer (mon.) A] of the DHFR.MTX complex undergoes greater H/D exchange compared with the closed-loop conformer (mon. B), partly because the Met-20 and beta(F-G) loops readily exchange in mon. A. The eight-stranded beta sheet of both DHFR molecules resists H/D exchange more than the helices and loops. However, the C-terminal strand, betaH, in mon. A is almost fully exchanged. Several D(2)Os form hydrogen bonds with exchanged amides. At the active site, the N1 atom of MTX is protonated and thus charged when bound to DHFR. Several D(2)Os are observed at hydrophobic surfaces, including two pockets near the MTX-binding site. A previously unidentified D(2)O hydrogen bonds with the catalytic D27 in mon. B, stabilizing its negative charge.

Binding Sites↗
PubMed2000

Neutron diffraction evidence of microscopic charge inhomogeneities in the CuO2 plane of superconducting La2-xSrxCuO4 (0<or=x<or=0. 30).

High-resolution atomic pair distribution functions have been obtained using neutron powder diffraction data from La2-xSrxCuO4 over the range of doping 0<or=x<or=0.30 at 10 K. Despite the average structure getting less orthorhombic, we see a broadening of the in-plane Cu-O bond distribution as a function of doping up to optimal doping. Thereafter the peak abruptly sharpens. The peak broadening can be well explained by a local microscopic coexistence of doped and undoped material. This suggests a crossover from a charge inhomogeneous state at and below optimal doping to a homogeneous charge state above optimal doping.

Journal Article↗
PubMed2001

Ordering of nitrogen in nickel nitride Ni(3)N determined by neutron diffraction.

The metallic interstitial nitride Ni(3)N was prepared from Ni(NH(3))(6)Cl(2) and NaNH(2) in supercritical ammonia (p(NH(3)) approximately 2 kbar) at 523 K. Its previously reported crystal structure, as determined from X-ray powder data, was confirmed by neutron powder diffraction: Ni(3)N crystallizes in the hexagonal epsilon-Fe(3)N-type structure (P6(3)22, Z = 2, a = 4.6224 A and c = 4.3059 A at room temperature). The N atoms on the octahedral sites of an hcp arrangement of Ni show virtually complete occupational order at ambient temperatures, which is preserved up to its thermal decomposition at T approximately 600 K. This behavior is in marked contrast to that of the isotypic iron nitride, epsilon-Fe(3)N, which shows reversible partial disordering within the same range of temperatures. Possible reasons for the different behaviors of the two nitrides epsilon-Fe(3)N and Ni(3)N are discussed.

Journal Article↗
PubMed2000

Oblique membrane insertion of viral fusion peptide probed by neutron diffraction.

Fusion peptides mimic the membrane fusion activities of the larger viral proteins from which they derive their sequences. A possible mode of activity involves their oblique insertion into lipid bilayers, causing membrane disruption by promoting highly curved hemifusion intermediates, leading to fusion. We have determined the location and orientation of the simian immunodeficiency virus (SIV) fusion peptide in planar lipid bilayers using neutron lamellar diffraction. The helical axis of the peptide adopts an angle of 55 degrees relative to the membrane normal, while it positions itself nearest the lipid bilayer surface. This is the first direct observation of the structural interaction between a fusion peptide and a phospholipid bilayer.

Deuterium↗
PubMed2001

Time-resolved in situ neutron diffraction studies of gas hydrate: transformation of structure II (sII) to structure I (sI).

We report the in situ observation from diffraction data of the conversion of a gas hydrate with the structure II (sII) lattice to one with the structure I (sI) lattice. Initially, the in situ formation, dissociation, and reactivity of argon gas clathrate hydrate was investigated by time-of-flight neutron powder diffraction at temperatures ranging from 230 to 263 K and pressures up to 5000 psi (34.5 MPa). These samples were prepared from deuterated ice crystals and transformed to hydrate by pressurizing the system with argon gas. Complete transformation from D(2)O ice to sII Ar hydrate was observed as the sample temperature was slowly increased through the D(2)O ice melting point. The transformation of sII argon hydrate to sI hydrate was achieved by removing excess Ar gas and exposing the hydrate to liquid CO(2) by pressurizing the Ar hydrate with CO(2). Results suggest the sI hydrate formed from CO(2) exchange in argon sII hydrate is a mixed Ar/CO(2) hydrate. The proposed exchange mechanism is consistent with clathrate hydrate being an equilibrium system in which guest molecules are exchanging between encapsulated molecules in the solid hydrate and free molecules in the surrounding gas or liquid phase.

Journal Article↗