Single-crystal Neutron Diffraction Data Research Articles

No Evidence for Proton Transfer along the N−H···O Hydrogen Bond in N-Methylacetamide: Neutron Single Crystal Structure at 250 and 276 K

The crystal structure of N-methylacetamide (C3H7NO), Mr = 73.095, has been determined from single-crystal neutron diffraction data at two temperatures, 250 and 276 K, above and below the previously reported phase transition located at 274 K in this work. Crystal data: 250 K [276 K]: space group Pn21a [Pn21m], a = 9.671(2) [4.878(1)] A, b = 6.613(6) [6.567(1)] A, c = 7.218(1) [7.332(2)] A; V = 465.7(6) [234.9(5)] A3; Dn = 1.043 [1.034] g·cm-3, R(F2) = 0.168 [0.134], wR(F2) = 0.062 [0.051], S = 1.18 [1.11]. This new investigation of the structure of N-methylacetamide was undertaken in order to assess a recent suggestion based on inelastic neutron scattering spectroscopy that transfer of the amide proton along the peptide hydrogen bond may be responsible for the vibrational anomalies. While we found no evidence for proton transfer along the N−H···O hydrogen bond (d(NH) = 1.025(17) A, and d(H···O) = 1.856(14) A for at T = 250 K) at either temperature evidence for some molecular disorder is present in accord...

Crystal Growth and Structural Investigations of the Oxygen Ion Conductor BaBi3O5.5

Large single crystals of the oxygen ion conductor BaBi3O5.5 have been obtained, and its structure was investigated by single-crystal X-ray diffraction (XRD) and neutron diffraction (ND), electron diffraction, and high-resolution electron microscopy (HREM). The basic three-dimensional structure was refined, using single crystal ND data, in space group Im3m to a weighted R value of 5.3% for 17 unique reflections, with Ba and Bi atoms statistically distributed on the 2(a) sites (0, 0, 0) and the O atoms on the 6(b) sites (12, 0, 0) with a refined occupancy of 36(1)%. The refined thermal-displacement parameters for the O atoms are highly anisotropic, with U11=U22=0.27(1) and U33=0.082(7) Å2. In addition, the structure is incommensurately modulated with the systematic absence conditions F〈hklmnp〉=0 unless h+k+l=2j and m+n+p=2j, implying the six-dimensional superspace group P:Im3m:Im3m, with a=4.3798(2) Å and modulation vectors q1=[α, 0, 0]*, q2=[0, α, 0]*, and q3=[0, 0, α]* with α=0.3835(1). The diffraction data and the HREM images indicate that the modulation is predominantly occuptional. The satellite reflections have comparable intensities in powder XRD and ND patterns, indicating furthermore that the modulation originates from ordering of both O atoms/vacancies and metal atoms.

A SINGLE-CRYSTAL NEUTRON-DIFFRACTION INVESTIGATION OF DIOPSIDE AT 10 K

Single-crystal neutron-diffraction data, collected at 10 K on a natural sample of diopside, provided a structure that refined t o R = 4.5% for 415 independent reflections. The structure refinement showed significant reduction of the M(2)‐O(3C2),(3D2) bond lengths, resulting in a more regular M(2) polyhedron than at higher temperatures. A significant zero-point contribution to the atomic displacement parameters (ADP) was found. On average, it accounts for the 35% of the room-temperature determination. Such results confirm previous predictions based on lattice-dynamics calculations.

The Structures of C–Ce2O3+δ, Ce7O12, and Ce11O20

The crystal structures of CeO1.68 (C–Ce2O3+δ), Ce7O12, and Ce11O20 with ordered oxygen vacancy distributions have been determined by refinement of single crystal neutron diffraction data collected at ambient temperature. CeO1.68 is cubic, of space group Ia3 with a=11.111(2) Å; one of the two oxygen positions is partially occupied with a probability of 37(3)%. For Ce7O12 the rhombohedral space group R3 with a=6.785(1) Å, α=99.42(1)° was confirmed. Ce11O20 is isomorphous to Tb11O20 with the triclinic space group P1. The lattice parameters are a=6.757(3) Å, b=10.260(5) Å, c=6.732(3) Å, α=90.04(4)°, β=99.80(4)°, and γ=96.22(4)°. For Ce11O20 there are no 12[1, 1, 1]F oxygen vacancy pairs, i.e., pairs corresponding to half of the space diagonal of the fluorite lattice along [1, 1, 1]F. The shortest vacancy pair type in that structure is 12[1, 1, 1]F, which is also present in the two other phases. High temperature neutron diffraction measurements showed that Ce7O12 is stable up to 1072 K. Then it transforms into a fluorite type structure with disordered oxygen vacancies.

Structure and dynamics of the symmetric hydrogen bond in potassium hydrogen maleate: a neutron scattering study

The crystal structure of potassium hydrogen maleate KH(OOC–CHCH–COO) has been studied at 300, 14 and 5 K using three-dimensional single-crystal neutron diffraction data. There is no evidence for any phase transition. The crystal structure is orthorhombic, P bcm (D 2h ll), with four entities in the unit cell ( Z=4), in accord with previous X-ray diffraction work. The ion is nearly planar and deviation from C 2v symmetry is negligible. The short internal hydrogen bond parallel to the c axis, R O⋯O=2.427(1) Å at 5 K, is symmetrical with the proton located at the center. Inelastic neutron scattering (INS) spectra, from 16 to 4000 cm −1, of the fully hydrogenated sample and partially deuterated analogues, KH(OOC–CDCD–COO) and KD(OOC–CHCH–COO), have been recorded for powdered samples and aligned single crystals at 20 K. Complex spectral profiles are observed for the stretching mode of the hydrogen bond, ν a OHO, and for the totally symmetric out-of-plane deformation of the maleate ion. An isotopic mixture of KH(OOC–CDCD–COO), 20%, and KD(OOC–CDCD–COO), 80%, reveals that intermolecular coupling is negligible. Frequencies and intensities are amenable to symmetrical potential functions with a central minimum between secondary minima at higher energy. The INS and infrared band profiles suggest that the planar conformation with C 2v symmetry of the maleate ring is unstable in excited vibrational states. The quantum nature of the hydrogen bond is emphasised with the concept of `hydrogen bonding/anti-bonding' states.

Isotope Effect in TlH2PO4 and TlD2PO4

The crystal structure of the antiferroelectric phase of TlD2PO4, deuterated thallium dihydrogenphosphate, has been determined from single-crystal neutron diffraction data collected at room temperature. The para-antiferroelectric transition (T_c^d = 353 K) of TlD2PO4 is analysed from a structural point of view and compared with the phase transition of TlH2PO4 at TI = 357 K, already characterized. The distinct phase sequences observed in the two compounds when decreasing temperature from that of the high-temperature prototype phase (prototype phase/room-temperature phase/low-temperature phase) are discussed and associated with the different ordering of the two crystallographically inequivalent H (D) atoms existing in the prototype phase.

Structural Studies of the Fast Oxygen Ion Conductor BICOVOX.15 by Single-Crystal Neutron Diffraction at Room Temperature

The room temperature crystal structure of the fast oxygen ion conductor Bi4(V0.85Co0.15)2O11−δ(BICOVOX.15) was refined within the average tetragonal unit cell from single-crystal neutron diffraction data. The unit cell dimensions areaT=3.929(2) Å andcT=15.476(9) Å in space groupI4/mmmwithZ=1. The conventionalRwfactor is 0.067. The structure consists of intergrowth, along the c-axis, of alternating (Bi2O2)2+sheets and (VO3.5□0.5)2−oxygen-deficient perovskite-like layers. The compound, which exhibits a high ionic conductivity at moderate temperatures, undergoes a phase transition around 780 K between the disordered high-temperatureγ-phase and the lower temperatureγ′-phase, showing a modulated superstructure. Oxygen vacancies are localized in the perovskite-like layers, oxygen stoichiometry is derived, and oxygen diffusion paths are proposed for theγ′-phase at room temperature.

Refinement of Ibuprofen at 100K by Single-Crystal Pulsed Neutron Diffraction

The structure of racemic ibuprofen [α-methyl-4-(2-methylpropyl)benzeneacetic acid], C13H18O2, has been refined using single-crystal pulsed neutron diffraction data collected at 100 K. Accurate positional and anisotropic displacement (vibration) parameters have been determined for all 33 atoms and the hydrogen-bond geometry of the dimeric crystal-packing motif is well defined.

Structure of Ce2Pt6Ga15: interplanar disorder from the Ce2Ga3 layers

The structure of the heavy fermion compound Ce2Pt6Ga15 has been determined from neutron powder and X-ray/neutron single-crystal diffraction. Examination of symmetry equivalence among the single-crystal data, as well as the good fit of the powder data to the final structural arrangement, with all the atoms on symmetry sites, suggests that the correct space group is P63/mmc. The structure is unusual in that Ce layers have 1/3 of the Ce atoms replaced by groups of three Ga atoms; distances between atoms in these planes suggest this substitution must occur in a concerted fashion. The refined occupancies lead to a stoichiometry near Ce2Pt6Ga15, consistent with such an arrangement. In addition, single-crystal neutron diffraction data show columns of weak diffuse scattering along the <001> axes, suggesting disorder arising from a lack of registration of successive Ce2Ga3 layers (lying half a cell length or 8.27 Å apart along z) and a 3 × 3 × 1 supercell. This disorder is very likely responsible for the low resistance ratio of approximately unity measured for single-crystal samples.

H in rutile-type compounds: I. Single-crystal neutron and X-ray diffraction study of H in rutile

The crystal structure of natural hydrous rutile from a mantle eclogite nodule has been refined from single-crystal neutron diffraction data collected at 24 K. The chemical composition was 95.52 wt% Ti02, 0.74 wt% Fe203, 0.68 wt% A1203, 1.16 wt% Cr203, 1.86 wt% Nb205, and 0.04 wt% MnO, with approximately 13000 ppm OH-, as estimated by IR spectroscopy. The position of the H atom was located by examining the negative residuals in the difference Fourier maps. The refined position is near the shared edge of the cation octahedron at xl a = 0.42(1), ylb = 0.50(1), and zlc = 0 with a site occupancy of 2.7%, which is consistent with the H concentration estimated by IR spectroscopy. The O-H bond distance is 1.05 A and the OH vector is in the (001) plane, which is consistent with the strong w-polarization of the OH absorption observed in the IR spectra. Single-crystal X-ray data were collected from a synthetic anhydrous rutile crystal and a hydrous rutile crystal from the same mantle nodule as the sample used in the neutron study. The detailed X-ray structures of both rutiles were compared and no significant differences were found; the ale ratios and the 0 position were identical within error. Therefore, we conclude that the addition of H into rutile for the purpose of charge-balancing excess 3 + cations does not significantly change the structure.

Refinement strategy in structural studies of crystalline solid proton conductors

The strategy applied in the structure refinement of accurate single-crystal neutron diffraction data for pseudo-centrosymmetric proton conducting systems can often be decisive. The application of a combination of judicious symmetry constraints and symmetry-lowering procedures can expose the likely route for proton transfer, otherwise not revealed by a disordered centrosymmetric model involving partially occupied H-sites, e.g. OH/2…H/2O. This procedure will be illustrated for the simple case of an apparently disordered structure which has recently appeared in the literature. The structure was stated to involve an H 3O 2 − ion lying across a centre of symmetry. Use of the strategy suggested here resulted in an ordered H 2O…OH − arrangement, involving a quite reasonable OH…O hydrogen-bond geometry, and low correlations between all parameters varied in the refinement. Interestingly, it is shown that the proton can be placed equally successfully on either side of the central H-bond, implying that the entire crystal comprises extended regions (domains) which are dominated by one or other of the H-bond orientations, i.e. one or other of the non-centrosymmetric structural enantiomorphs. The size of these domains must be well in excess of the coherence length of the diffraction experiment. Indeed, a single domain can, in principle, extend across the whole crystal.

Localization of Protons in Li 1- xH xIO 3 by Single-Crystal Neutron Diffraction

Structural parameters of lithium iodate-iodic acid solid solution Li 1- x H x IO 3 ( x = 0.28) have been refined at 60 K and at room temperature from single-crystal neutron diffraction data with a good reliability factor (about 2%). The lattice parameters are a = 5.494(7) Å, c = 4.924(2) Å at 60 K and a = 5.514(3) Å, c = 4.960(3) Å at RT. The proton does not replace the lithium atom but is located in a general position of the space group P6 3, x = 0.240(4), y = 0.299(4), and z = -0.042(6) at RT, and its thermal ellipsoid is well defined. Hydrogen sites are located on three of the six lateral edges of the distorted oxygen octahedron around the lithium site.

Thallous nitrate (III): a single-crystal neutron study

The structure of TlNO 3 (III) is refined from single-crystal neutron diffraction data with significantly improved accuracy compared to the reported X-ray structure. Rigid-body thermal-motion analysis indicates that the largest amplitude of libration is about the plane normal to one of the nitrate ions and about an in-plane axis for the other. The maximum librational frequencies for both nitrate groups, however, are about the in-plane axes, and are in close agreement with the values reported from a Raman scattering study

Proton density and orientational potential in nickelhexammine salts: a thermodynamic analysis of rotation-translation coupling

The scattering densities of the orientationally disordered protons and deuterons in Ni(NX3)6Y2 (X=H or D; Y=Br, I, NO3 or PF6) are obtained from neutron single-crystal diffraction data at room temperature. While we observe a nearly circular density distribution for Y=PF6, a nuclear density distribution with four maxima on a square shows up for Y=Br, I and NO3. This is a pronounced deviation from the circular distribution that is expected from uniaxial rotational diffusion or reorientational jump models for the dynamics of the orientational disordered ammonia groups. All observed density distributions are consistently explained as the consequence of rotation-translation coupling in an anharmonic crystal potential. The calculated potential parameters, i.e. anharmonicity and strength of the coupling, depend on the type of anion present in the crystal frame. The weak anisotropy in the Y=NO3 and PF6 compounds is the consequence of a nearly eightfold non-crystallographic symmetry of the atoms establishing the hindrance potential.

Anomalous X-ray diffraction study of the AlPdMn icosahedral phase

The atomic structure of the perfect AlPdMn icosahedral phase has been studied on a single grain by anomalous X-ray diffraction close to the Pd edge. A method is proposed for relative normalization of the data, in order to extract the partial structure factor FPd of the Pd atoms. The Pd is found to be very ordered in the six-dimensional description of the quasicrystal, as was previously inferred from X-ray and neutron single-crystal diffraction data. However, a phason Debye-Waller-like term has to be introduced to account for the data. Comparison of the present data set with low-resolution data indicates the existence of diffuse scattering located close to the Bragg reflections whose intensity scales as (1-exp(-BperpQ2perp)) as expected from random fluctuations of the atomic surfaces. The average fluctuation is found to be of the order of 1 AA. Moreover the comparison of the data with a spherical model shows that the atomic surface describing Pd atoms is likely to be made of several disjointed pieces.

Single-crystal neutron diffraction study of ferroelectric Ba0·92Ca0·08TiO3

Crystal structure of BaTiO3 doped with 8% Ca2+ is refined using single-crystal neutron diffraction data and it is shown that the doped Ca2+ ion substitutes only at the Ba sites. The refined cell (P4 mm) parameters area=b=3·982(3) Å,c=4·003(3) Å with a finalR value of 0·02 (onF). Existence of multiple domains in the crystal is ruled out based on refinement with multidomain model.

A direct investigation of thermal vibrations of beryllium in real space through the maximum-entropy method applied to single-crystal neutron diffraction data

The thermal vibrations of beryllium metal were determined directly from the nuclear densities obtained by the maximum-entropy method (MEM) using neutron single-crystal data. A high-resolution nuclear density distribution of beryllium was obtained by applying the MEM to the 48 structure factors with sin θ/λ < 1.41 A−1 from a previous study [Larsen, Lehmann & Merisalo (1980). Acta Cryst. A36, 159–163], which showed small but significant cubic anharmonicity in beryllium by least-squares refinement of the structure factors. In the present study, quartic as well as cubic anharmonicities are clearly visible in the MEM nuclear density. In order to determine anharmonic thermal-vibration parameters, a three-dimensional function was fitted to the MEM nuclear density around the atom site. The one-particle potential was used to model the thermal vibrations up to quartic terms. The least-squares-fit values were γ = −0.306 eV A−3 for the third- and α40 = − 1.02, β20 = 2.95 and γ00 = − 3.28 eV A−4 for the fourth-order anharmonic parameters. Thus, the atomic potential in the basal plane is hardened against the bipyramidal space around the tetrahedral holes of the hexagonal-close-packed structure. It is softened towards the center of the octahedral voids. Least-squares refinement of the MEM nuclear density gives a standard deviation of about 5 for the last digit of the anharmonic parameters. However, there is added uncertainty in the parameters because of the relationship of the reliability of the MEM density distribution to the standard deviations of the measured intensities. Judging from previous studies of the thermal parameters for beryllium based on least-squares refinement of observed structure factors, it is estimated that values determined here for the anharmonic parameters are reliable to the first digit after the decimal point.

Charge Density Study on Bullvalene (C10H10 )

Abstract Low-temperature single-crystal neutron and X-ray diffraction data were collected for bullvalene (Figure 1). X -N Fourier and multipole static deformation electron density maps were calculated and compared. Atomic mean-square-displacement parameters were analysed in the framework of the rigid-body motion model and the residual amplitudes (UOBS - UTLS) were graphically interpreted. The preliminary results presented here reveal either a bias in the X-ray anisotropic displacement parameters (ADPs) due to improper modelling of the electron density or unresolved errors in the neutron data.

Hydrogen bonding in Be[C 2(COO) 2]·4H 2O—A neutron diffraction study at 15 K

Lattice constants for orthorhombic Be[C 2 (COO) 2 ]·4H 2 O at 15 K are a =1006.4(6), b =663.0(4), and c =1263.1(7) pm, Z =4, space group Cmcm . Anisotropic refinement on single crystal neutron diffraction data led to R w =0.0229. The crystal structure is made up by slightly distorted Be(H 2 O) 2+ / 4 tetrahedra (Be−H 2 O 161. 3 and 162.0 pm) and planar [C 2 (COO) 2 ] 2− anions linked together by strong (O… H 2 O 262.0 and 263.5 pm) asymmetric hydrogen bonds. A layer-like arrangement extending parallel to (010) consisting of [C 2 (COO) 2 ] 2− anions and hydrogen bound water molecules of the Be(H 2 O 2+ / 4 tetrahedra is the primary structural feature of Be[C 2 (COO) 2 ]·4H 2 O. These layers are stacked in … ABAB … sequence and interlinked by coordinative bonds between Be 2− and H 2 O to yield a rigid three-dimensional framework. O−H bond length corrected for thermal motion are 100.4 and 100.5 pm, respectively. The H−O−H angle are rather wide (111.12 and 114.36°). The anion has mmm symmetry.

On hydrogen atom positions in 3-deazauracil

The positions of the contentious and important hydrogen atoms in the modified nucleic acid base 3-deazauracil are determined from single crystal neutron diffraction data, with the fully characterised hydrogen bonding scheme emphasising the strength of this interaction in the structure.