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Investigation of structure of liquid 2,2,2 trifluoroethanol: neutron diffraction, molecular dynamics, and ab initio quantum chemical study.

The molecular conformation and intermolecular H bonding in liquid 2,2,2 trifluoroethanol (TFE) have been studied by neutron diffraction with hydrogen/deuterium isotopic substitution at room temperature. For comparison, conformations of molecules and their dimers in the gas phase have also been calculated, based on the density functional theory. Energies, geometry, and vibrational frequencies of dimers were analyzed. Diffraction data analyzed by the "Monte Carlo determination of g(r)" (MCGR) method resulted in a molecular structure in agreement with the findings from gas phase electron diffraction experiments and density functional calculations. The intermolecular structure functions were compared to the same functions obtained from a molecular dynamics simulation. All of the composite radial distribution functions are in good agreement with the simulation results. According to our calculation the hydrogen-bonded aggregation size is smaller in pure liquid TFE than in pure liquid ethanol.

Journal Article↗

Neutron diffraction analysis of myoglobin: structure of the carbon monoxide derivative.

The locations of hydrogen and deuterium atoms and water molecules have been investigated in carbon monoxide myoglobin using neutron diffraction, and the results are compared with earlier work on metmyoglobin. Parallel real space refinements on the two molecules show relatively few changes, but do show the carbon monoxide molecule with the iron atom moving into the heme plane.

Carbon Monoxide↗

Crystal structure of 1-methyluracil from neutron diffraction at 15, 60 and 123 K.

The crystal structure of 1-methylpyrimidine-2,4-dione (1-methyluracil, C5H6N2O2) has been determined at 15, 60 and 123 K from neutron diffraction data. Molecules lie in the eightfold special positions (symmetry m) of space group Ibam, with a = 13.213 (2), b = 13.172 (2), c = 6.163 (1) A at 15 K. Full-matrix least-squares refinements based on 807 (15 K), 805 (60 K) and 815 (123 K) reflections with sin theta/lambda less than 0.69 A-1 converged with R(F2) = 0.023, 0.024 and 0.024 respectively. Bond lengths and angles have e.s.d.'s less than 0.002 A and 0.2 degrees. Detailed analysis of the anisotropic thermal parameters gives estimates of the zero-point internal vibrations for all nuclei and also for molecular rigid-body thermal vibrations at 15, 60 and 123 K. With thermal-vibration corrections there is good agreement in bond lengths and angles at the three temperatures.

Crystallography↗

The interplay between X-ray crystallography, neutron diffraction, image reconstruction, organo-metallic chemistry and biochemistry in structural studies of ribosomes.

Crystals of ribosomes, their complexes with components of protein biosynthesis, their natural, mutated and modified subunits, have been subjected to X-ray and neutron crystallographic analyses. Electron microscopy and 3-dimensional image reconstruction, supported by biochemistry, genetic, functional and organo-metallic studies were employed for facilitating phasing of the crystallographic data. For example, a monofunctional multi heavy-atom cluster (undecagold) was designed for covalent and quantitative binding to ribosomes. The modified particles were crystallized isomorphously with the native ones. Their difference-Patterson maps contain indications for the usefulness of these derivatives for subsequent phasing. Models of the ribosome and its large subunit were reconstructed from tilt series of 2-dimensional sheets. The comparison of the various reconstructed images enabled an initial assessment of the reliability of these models and led to tentative assignments of several functional features. These include the presumed sites for binding mRNA and for codon-anticodon interactions, the path taken by the nascent protein chain and the mode for tRNA binding to ribosomes. These assignments assisted in the design of biologically meaningful crystal systems. The reconstructed models are being used to identify structural features in initial density maps derived from X-ray and neutron diffraction data.

Crystallography↗

Short- and long-range order in the positive electrode material, Li(NiMn)0.5O2: a joint X-ray and neutron diffraction, pair distribution function analysis and NMR study.

The local environments and short-range ordering of LiNi(0.5)Mn(0.5)O(2), a potential Li-ion battery positive electrode material, were investigated by using a combination of X-ray and neutron diffraction and isotopic substitution (NDIS) techniques, (6)Li Magic Angle Spinning (MAS) NMR spectroscopy, and for the first time, X-ray and neutron Pair Distribution Function (PDF) analysis, associated with Reverse Monte Carlo (RMC) calculations. Three samples were studied: (6)Li(NiMn)(0.5)O(2), (7)Li(NiMn)(0.5)O(2), and (7)Li(NiMn)(0.5)O(2) enriched with (62)Ni (denoted as (7)Li(ZERO)Ni(0.5)Mn(0.5)O(2)), so that the resulting scattering length of Ni atoms is null. LiNi(0.5)Mn(0.5)O(2) adopts the LiCoO(2) structure (space group Rm) and comprises separate lithium layers, transition metal layers (Ni, Mn), and oxygen layers. NMR experiments and Rietveld refinements show that there is approximately 10% of Ni/Li site exchange between the Li and transition metal layers. PDF analysis of the neutron data revealed considerable local distortions in the layers that were not captured in the Rietveld refinements performed using the Bragg diffraction data and the LiCoO(2) structure, resulting in different M-O bond lengths of 1.93 and 2.07 Angstroms for Mn-O and Ni/Li-O, respectively. Large clusters of 2400-3456 atoms were built to investigate cation ordering. The RMC method was then used to improve the fit between the calculated model and experimental PDF data. Both NMR and RMC results were consistent with a nonrandom distribution of Ni, Mn, and Li cations in the transition metal layers; both the Ni and Li atoms are, on average, close to more Mn ions than predicted based on a random distribution of these ions in the transition metal layers. Constraints from both experimental methods showed the presence of short-range order in the transition metal layers comprising LiMn(6) and LiMn(5)Ni clusters combined with Ni and Mn contacts resembling those found in the so-called "flower structure" or structures derived from ordered honeycomb arrays.

Journal Article↗

Neutron diffraction study of [H(4)Co(4)(C(5)Me(4)Et)(4)], a tetrahedral metal cluster complex with four face-bridging hydride ligands.

A single-crystal neutron diffraction analysis of the cluster complex [H(4)Co(4)(C(5)Me(4)Et)(4)] was carried out on the new quasi-Laue diffractometer VIVALDI at the Institut Laue-Langevin. The structure consists of four face-bridging hydrides attached to a tetrahedral cobalt metal core. Average distances and angles in the core of the molecule are as follows: Co-Co = 2.571(8), Co-C = 2.158(6), Co-H = 1.749(7), H.H = 2.366(9) A; Co-H-Co = 94.6(3), H-Co-H = 85.1(3) degrees. The hydride ligands are located off the Co-Co-Co planes by an average distance of 0.923(8) A. It is suggested that the dimensions of the HCo(3) fragments found in this molecule provide reasonable estimates for analogous distances and angles associated with chemisorbed H atoms situated on the 3-fold hollows of a cobalt surface. Crystallographic details: space group P2(1)/a (monoclinic); a = 21.979(2), b = 10.924(1), c = 34.406(2) A; beta = 90.81(1) degrees; Z = 8. Final agreement factor: R(F) = 0.099 for 3779 reflections [I > 2sigma(I)] collected at 20 K.

Journal Article↗

A study of heat-treatment induced framework contraction in strontium-ETS-4 by powder neutron diffraction and vibrational spectroscopy.

The effects of heat-treatment on the structure of the strontium ion-exchanged titanosilicate ETS-4 have been studied by Rietveld analysis of powder neutron diffraction data and by FT-Raman spectroscopy. Hydrous Sr-ETS-4 (space group Cmmm), upon heat-treatment under inert atmosphere at temperatures between 423 and 573 K, exhibits framework contraction as evinced by the decrease in the unit cell dimensions. The effects of heat-treatment on the dimensions of the transport-controlling eight-membered ring (8MR) are elucidated by Rietveld analysis. It is also found that during heat-treatment: (a) the double three membered rings (D3MRs) in ETS-4 are sites of structural instability, (b) the titania chains running along [010] exhibit a large degree of disorder in the bridging oxygen atoms, and (c) significant relocations of the strontium cations take place, which may affect the separation properties of the heat-treated materials. Raman spectra of heat-treated ETS-4 crystals exhibit strong cation-framework interaction effects. Vibrational modes involving the atoms in the titania chains show progressive frequency shifts and loss of intensity with increasing heat-treatment temperature, in a manner consistent with the crystallographic results. The study indicates the potential for continuously varying the effective pore dimension of ETS-4 by combining heat-treatment with appropriate ion-exchange procedures.

Journal Article↗

Rapid neutron-diffraction data collection for hydrogen-bonding studies: application of the Laue diffractometer (LADI) to the case study zinc (tris)thiourea sulfate.

The successful application of the newly developed image-plate neutron Laue diffractometer (LADI) at the Institut Laue-Langevin (ILL), Grenoble, France, for rapid hydrogen-bonding characterization is reported. The case study concerns the promising non-linear optical material zinc (tris)thiourea sulfate (ZTS), which contains 30 atoms in the asymmetric unit and crystallizes in the orthorhombic space group, Pca2(1), a = 11.0616 (9), b = 7.7264 (6), c = 15.558 (1) A [T = 100.0 (1) K]. The results from a 12 h data collection from ZTS on LADI are compared with those obtained over 135 h using the monochromatic four-circle diffractometer D9 at the same reactor source with a crystal 13 times larger in volume. Both studies reveal the extensive hydrogen bonding and other close non-bonded contacts within the material. As expected, the results from D9 are more precise than those obtained from LADI; however, the bond geometry determined from the two experiments is the same within the larger estimated standard deviations. Furthermore, the conclusions drawn from the two studies separately regarding the nature of all supramolecular features are identical. This illustrates that LADI is eminently suitable for rapid characterization of hydrogen-bonded structures by neutron diffraction, with the gain in speed compared with traditional instrumentation being several orders of magnitude.

Journal Article↗

Cross-linkage sites in type I collagen fibrils studied by neutron diffraction.

Cross-links in tendon collagen are essential for the biomechanical strength of healthy tissue. The nature and position of these cross-links has long been a subject for conjecture. We have approached this problem in a non-destructive manner, by studying neutron diffraction from collagen fibrils that have been specifically deuterated by reduction at keto-amine and Schiff base groups with sodium borodeuteride (NaB2H4). The intensities of the first 23 meridional reflections were recorded for both native and reduced tendons. These data were used to calculate the neutron-scattering density profile of the 67 nm (D) repeat of type I collagen fibrils in rat tail tendon. This approach not only succeeds in determining the location of the cross-linkage sites with respect to the fibril structure, as projected onto the fibre axis, but also presents a novel form of the isomorphous derivative solution to the phase problem.

Animals↗

Neutron diffraction analysis of the solvent accessible volume in cubic insulin crystals.

The average contact distance between protein and solvent surface atoms in cubic insulin crystals has been determined from two sets of 15 A resolution neutron diffraction data. A contact distance between the water hydrogen sites and the protein surface that is significantly shorter than the average protein-water oxygen contact distance implies that many water molecules are oriented with hydrogen atoms pointed towards the protein surface. The shape of the protein/solvent interface is consistent with the protein envelope obtained from atomic co-ordinates.

Animals↗

A neutron diffraction study on the location of the polyene chain of retinal in bacteriorhodopsin.

We report on the location of the chain part of the retinylidene chromophore in the projected density of bacteriorhodopsin as determined by neutron diffraction from the two-dimensional purple membrane lattice. For this purpose, partially deuterated retinal was synthesized containing 10 deuterons at positions C-8, C-10, C-12, C-14, C-19(3), and C-20(3) of the polyene chain. Two sets of dark-adapted samples were prepared in entirely different ways: (i) Deuterated retinal was incorporated biosynthetically during growth of the bacteria by using the mutant JW5, which is deficient in the synthesis of retinal. (ii) The chromophore was converted to retinal oxime, the resulting colorless apomembrane was regenerated with deuterated retinal, and the residual retinal oxime was removed by washing with bovine serum albumin. Characterization of these samples by x-ray diffraction, absorption, and flash spectroscopy showed that they were identical to native purple membrane samples as judged by these criteria. Fourier difference maps were calculated from the differences in inplane diffraction from the deuterated membranes and from protonated samples that were prepared in exactly the same way. At 8.7 A resolution, both maps show a single major peak at the same position with the center of mass of the labeled part of the chain (C-11) between helices 6 and 3 but closer to helix 6. It appears likely that the COOH-terminal helix G, to which retinal is attached at lysine-216, is either helix 2 or 6.

Apoproteins↗

Spin densities in a ferromagnetic bimetallic chain compound: polarized neutron diffraction and DFT calculations.

The spin population distribution in the ferromagnetically coupled hetero-bimetallic chain compound [MnNi(NO(2))(4)(en)(2)] (en = 1,2-ethanediamine) has been investigated by means of polarized neutron diffraction experiments, and the results compared with those from theoretical estimates obtained via calculations based on density functional theory on dinuclear molecular models of the chain. The spin distributions obtained from experiment and from theory are consistent and reflect a larger spin delocalization from the Ni atom due to the more covalent character of the Ni-N bonds compared to the Mn-O ones. Also a nearly isotropic spin distribution is observed for the more ionic d(5) Mn(2+) ion and a clearly anisotropic distribution for the d(8) Ni(2+) ion. The use of dinuclear molecular models for the calculation of the exchange coupling constant between Ni and Mn provide upper and lower limits (+17.6 and -4.2 cm(-)(1)) for the experimentally determined value (+1.3 cm(-)(1)), depending on how the missing part of the chain is simulated, but yield essentially the same spin distribution. The Mn(II)-Ni(II) weak ferromagnetic coupling in the chain is interpreted in a spin delocalization mechanism as resulting from the weakness of the overlap between the magnetic orbitals centered on nickel and those centered on manganese which are only weakly delocalized on the ligands.

Journal Article↗

Neutron diffraction reveals the site of amantadine blockade in the influenza A M2 ion channel.

The influenza A M2 protein forms proton channels which are blocked by the anti-influenza drug amantadine. Using the technique of neutron diffraction with both deuterium-labeled amantadine and influenza A M2 peptides, this study has directly located the position of interaction between the drug and the transmembrane domain of M2. Amantadine is found 0.5 nm from the center of the bilayer in an area between Val 27 and Ser 31, a location consistent with the formation of a steric block within the ion channel. Similar experiments with amantadine and an amantadine-resistant mutant peptide showed no such interaction.

Amantadine↗

Crystal and magnetic structure of the double perovskite Sr2CoUO6: a neutron diffraction study.

Sr2CoUO6 double perovskite has been prepared as a polycrystalline powder by solid-state reaction, in air. This material has been studied by X-ray, neutron powder diffraction (NPD) and magnetic measurements. At room temperature, the crystal structure is monoclinic, space group P2(1)/n, Z= 2, with a= 5.7916(2), b= 5.8034(2), c= 8.1790(3) A, beta= 90.1455(6)degrees. The perovskite lattice consists of a completely ordered array of CoO6 and UO6 octahedra, which exhibit an average tilting angle phi= 11.4 degrees. Magnetic and neutron diffraction measurements indicate an antiferromagnetic ordering below TN = 10 K. The low-temperature magnetic structure was determined by NPD, selected among the possible magnetic solutions compatible with the P2(1)/n space group, according with the group theory representation. The propagation vector is k= 0. A canted antiferromagnetic structure is observed below TN = 10 K, which remains stable down to 3 K, with an ordered magnetic moment of 2.44(7)mu(B) for Co2+ cations. The magnetic moment calculated from the Curie-Weiss law at high temperatures (5.22 mu(B)/f.u.) indicates that the orbital contribution is unquenched at high temperatures, which is consistent with high-spin Co2+((4)T(1g) ground state) in a quasi-regular octahedral environment. Magnetic and structural features are consistent with an electronic configuration Co2+[3d(7)]-U6+[Rn].

Journal Article↗

Neutron diffraction analysis of cytochrome b5 reconstituted in deuterated lipid multilayers.

Cytochrome b5 was reconstituted with a highly deuterated phospholipid to form ordered multilayers consisting of repeated centrosymmetric pairs of asymmetric lipid-protein bilayers. Lamellar neutron diffraction data were collected to approximately 29 A resolution, and have been interpreted using models for the interaction of the membrane-binding domain of cytochrome b5 with the lipid bilayer. A range of different models was examined, and those in which the protein penetrates well into the bilayer, possibly spanning it, are favored.

Animals↗

Single-crystal neutron diffraction study of beta-Cs3(HSO4)2

The structure of beta-Cs(3)(HSO(4))(2)[H(2-x)(S(x)P(1-x))O(4)] has been examined by single-crystal neutron diffraction at 15 K. The compound crystallizes in space group C2/c and contains four formula units in the unit cell, with lattice parameters a = 19.769 (9), b = 7.685 (2), c = 8.858 (3) Å and beta = 100.60 (4) degrees. Refinement of P, S and H site occupancies indicated that the value of x (in the stoichiometry) is 0.500 (6). This, together with the unit-cell volume of 1322.8 (14) Å(3), implies a density of 3.463 Mg m(-3). The structure contains zigzag rows of XO(4) anions, where X = P or S, that alternate, in a checkerboard fashion, with zigzag rows of Cs cations. Moreover, there is one proton site, H(3), with an occupancy of 0.25 and one X-atom site, X(1), that is occupied by 0.5 P and 0.5 S. These features are in general agreement with a previous X-ray structure determination carried out at 298 K. In contrast to the X-ray study, however, it was found that two different structural models adequately fit the diffraction data. In the first model, the proton vacancies and the P atoms were assumed to be randomly distributed over the H(3) and X(1) sites, respectively, and to have no impact on the local structure. In the second model, several atoms were assigned split occupancies over two neighboring sites, to reflect the presence or absence of a proton vacancy, and the presence of P or S on the X(1) site. Refinement assuming the first model, in which anisotropic displacement parameters for 12 of 14 atom sites in the asymmetric unit were employed, yielded residuals wR(F(2)) = 0.084 and wR(F) = 0.038. For the second model, in which anisotropic displacement parameters were utilized for only the five atoms that were not split relative to the first model, the residuals were wR(F(2)) = 0.081 and wR(F) = 0.036.

Journal Article↗

On the occurrence of three-center hydrogen bonds in cyclodextrins in crystalline form and in aqueous solution: comparison of neutron diffraction and molecular dynamics results.

Three-center (bifurcated) hydrogen bonds may play a role by serving as an intermediate state between different dynamically changing hydrogen bonding patterns. Hydrogen bonding configurations can be studied experimentally by neutron diffraction and theoretically by computer simulation techniques. Here, both methods are used to analyse the occurrence of three-center hydrogen bonds in crystals of cyclodextrins. Almost all experimentally observed three-center hydrogen bonds in the crystal are reproduced in the molecular dynamics (MD) simulations, even as far as the detailed asymmetric geometry is concerned. On the basis of this result a MD simulation of cyclodextrin in aqueous solution is searched for the occurrence of three-center hydrogen bonds. Significant differences are found. In solution more different three-center hydrogen bonds per alpha-cyclodextrin molecule are observed than in the crystal but the population (existence as percent of the simulation period) of each three-center hydrogen bond is lower in solution than in crystal. These may indeed serve as intermediate states in the process of changing one hydrogen bonding pattern into another.

Chemical Phenomena↗

Protein dynamics investigated by neutron diffraction.

The most correct model of the molecular structure of a protein molecule is one which describes it as having a number of variable conformational states. These states differ in degree over a large spectrum of structural variation ranging from individual atomic vibrational motion to significant tertiary denaturation. The application of the neutron diffraction techniques discussed above dealt with two classes of conformational fluctuation, "protein breathing" and "regional melting." The utility of the neutron technique stems from the ability to locate hydrogen atoms and to discriminate between hydrogens and deuteriums. This latter attribute allows for performing H/D exchange experiments by identifying individual sites of exchange. With this information it has been possible to discern which regions of the protein molecule undergo regional melting. Protein breathing was explored by analyzing the rotational properties of side chain methyl groups. Such information clearly suggested that most of these groups reside in "staggered" (low energy) conformation in the time averaged structure and are not greatly affected by local structural packing. Together these two classes of conformational fluctuation span nearly the full range of all motions that might play a role in biological activity. Information about such motions can be obtained from other types of physicochemical methods, but in most cases the interpretation of the data is considerably less definitive than that which can be obtained from a neutron analysis.

Crystallography↗