REMGa3Ge and RE3Ni3Ga8Ge3 (M = Ni, Co; RE = rare-earth element): new intermetallics synthesized in liquid gallium. X-ray, electron, and neutron structure determination and magnetism

New quaternary intermetallic phases REMGa(3)Ge (1) (RE = Y, Sm, Tb, Gd, Er, Tm; M = Ni, Co) and RE(3)Ni(3)Ga(8)Ge(3) (2) (RE = Sm, Gd) were obtained from exploratory reactions involving rare-earth elements (RE), transition metal (M), Ge, and excess liquid Ga the reactive solvent. The crystal structures were solved with single-crystal X-ray and electron diffraction. The crystals of 1 and 2 are tetragonal. Single-crystal X-ray data: YNiGa(3)Ge, a = 4.1748(10) A, c = 23.710(8) A, V = 413.24(2) A(3), I4/mmm, Z = 4; Gd(3)Ni(3)Ga(8)Ge(3), a = 4.1809(18) A, c = 17.035(11) A, V = 297.8(3) A(3), P4/mmm, Z = 1. Both compounds feature square nets of Ga atoms. The distribution of Ga and Ge atoms in the REMGa(3)Ge was determined with neutron diffraction. The neutron experiments revealed that in 1 the Ge atoms are specifically located at the 4e crystallographic site, while Ga atoms are at 4d and 8g. The crystal structures of these compounds are related and could be derived from the consecutive stacking of disordered [MGa](2) puckered layers, monatomic RE-Ge planes and [MGa(4)Ge(2)] slabs. Complex superstructures with modulations occurring in the ab-plane and believed to be associated with the square nets of Ga atoms were found by electron diffraction. The magnetic measurements show antiferromagnetic ordering of the moments located on the RE atoms at low temperature, and Curie-Weiss behavior at higher temperatures with the values of mu(eff) close to those expected for RE(3+) free ions.     

Crystal structure and hydrogen-bonding system in cellulose Ibeta from synchrotron X-ray and neutron fiber diffraction

The crystal and molecular structure together with the hydrogen-bonding system in cellulose Ibeta has been determined using synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from tunicin. These samples diffracted both synchrotron X-rays and neutrons to better than 1A resolution (>300 unique reflections; P2(1)). The X-ray data were used to determine the C and O atom positions. The resulting structure consisted of two parallel chains having slightly different conformations and organized in sheets packed in a "parallel-up" fashion, with all hydroxymethyl groups adopting the tg conformation. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The hydrogen atoms involved in the intramolecular O3...O5 hydrogen bonds have well-defined positions, whereas those corresponding to O2 and O6 covered a wider volume, indicative of multiple geometry with partial occupation. The observation of this disorder substantiates a recent infrared analysis and indicates that, despite their high crystallinity, crystals of cellulose Ibeta have an inherent disorganization of the intermolecular H-bond network that maintains the cellulose chains in sheets.     

Synchrotron X-ray and Neutron Diffraction Studies in Solid-State Chemistry

Neutron diffraction studies, especially with powders, play an important role in structural solid-state chemistry, making possible the precise determination of the location of light atoms, particularly hydrogen, and enabling a distinction to be made between certain neighboring elements in the periodic table that are difficult to distinguish in experiments with X-rays. Neutron diffraction investigations also make a unique contribution in the area of magnetic structure determination. The availability of intense synchrotron X-rays sources, however, is opening up new opportunities to the structural chemist, many of them complementary to the “traditional” strengths of neutron methods. The key features of synchrotron radiation in relation to structural studies are the wavelength tunability, which facilitates the use of resonant diffraction methods, and the high brightness and excellent vertical collimation of the source, which make possible the construction of diffractometers with unparalleled angular and spatial resolution. The following types of experiments are now possible with synchrotron X-ray diffraction: (1) The ab initio determination of structures from powder diffraction data. (2) The differentiation between different oxidation states of an element (valence contrast experiments) based upon the sensitivity of an absorption edge to the valence of the element in question. (3) The differentiation of elements adjacent to each other in the periodic table, which is now feasible with synchrotron X-rays for all elements beyond chromium. (4) Site-selective X-ray absorption spectroscopy. (5) The study of cation occupancies in materials where more than one element occupies a site that is, or may be, partially occupied. (Such problems are important in zeolite chemistry and high-temperature superconductors.) (6) The determination of crystal structures from microcrystals. (7) In situ and rapid, time-resolved diffraction studies. This review examines the roles played by X-ray and neutron diffraction studies in modern solid-state chemistry, and describes some recent examples in which the use of neutron radiation or synchrotron X-rays has been advantageous.     

Disorder in BaThF6--refinement of anharmonic displacement parameters from high-pressure single-crystal X-ray diffraction data

The structure of BaThF(6) has been investigated as a function of temperature and pressure with single-crystal X-ray diffraction using synchrotron radiation. The compound crystallizes in the tysonite structure, space group P6(3)/mmc (a = 4.296(1) ? and c = 7.571(1) ? at ambient conditions). It is stable at least down to 150 K and up to 4 GPa. In the entire range of pressures and temperatures studied here, the compound is characterized by a high degree of disorder, both on the cationic and anionic positions. Despite the different valence states and sizes, both cations occupy the same crystallographic site in the ideal tysonite structure. The cationic disorder is described by two alternative approaches. The first model corresponds to a split-atom position model in which Ba(2+) is maintained on a special position with site symmetry 6m2, while Th(4+) is slightly displaced from the respective position. In the second model, both cations are maintained on the ideal position and anharmonic displacement parameters using a tensor of third order are introduced. Anharmonic displacement parameters have been refined from high-pressure single-crystal X-ray data measured in situ in a diamond anvil cell for the first time. The feasibility and general problems of anharmonic refinements of high-pressure X-ray data are further commented.     

Crystal structure and hydrogen bonding system in cellulose I(alpha) from synchrotron X-ray and neutron fiber diffraction

The crystal and molecular structure, together with the hydrogen-bonding system in cellulose I(alpha), has been determined using atomic-resolution synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from the cell wall of the freshwater alga Glaucocystis nostochinearum. The X-ray data were used to determine the C and O atom positions. The resulting structure is a one-chain triclinic unit cell with all glucosyl linkages and hydroxymethyl groups (tg) identical. However, adjacent sugar rings alternate in conformation giving the chain a cellobiosyl repeat. The chains organize in sheets packed in a "parallel-up" fashion. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The differences between the structure and hydrogen-bonding reported here for cellulose I(alpha) and previously for cellulose I(beta) provide potential explanations for the solid-state conversion of I(alpha) --> I(beta) and for the occurrence of two crystal phases in naturally occurring cellulose.     

Valence instabilities, phase transitions, and abrupt lattice expansion at 5 K in the YbGaGe system

The powder synchrotron X-ray diffraction technique was used to study the thermal expansion behavior of the mixed valence layered compound, YbGa1.05Ge0.95 in the temperature range 3-1123 K. A surprising abrupt isosymmetric phase transition, accompanied by a dramatic volume increase (negative thermal expansion), was found at 5 K induced by a sudden Yb valence transition from +(2 + epsilon) toward +2. At high temperatures, the material undergoes a transformation to a highly disordered structure until it eventually collapses at 1123 K to a structure with isovalent Yb ions and flat Ga/Ge planes (AlB2 type).     

Synthesis, structure, and properties of BaAl2Si2

Single crystals of BaAl2Si2 were grown from an Al molten flux and characterized using single-crystal X-ray diffraction at 10 and 90 K and neutron diffraction at room temperature. BaAl2Si2 crystallizes with the alpha-BaCu2S2 structure type (Pnma), is isostructural with alpha-BaAl2Ge2, and is an open 3D framework compound, where Al and Si form a covalent cagelike network with Ba2+ cations residing in the cages. BaAl2Si2 has a unit cell of a=10.070(3) A, b=4.234(1) A, and c=10.866(3) A, as determined by room-temperature single-crystal neutron diffraction (R1=0.0533, wR2=0.1034). The structure as determined by single-crystal neutron and X-ray diffraction (10 and 90 K) indicates that BaAl2Si2 (Pnma) is strictly isostructural to other (alpha)-BaCu2S2-type structures, requiring site specificity for Al and Si. Unlike BaAl2Ge2, no evidence for an alpha to beta (BaZn2P2-type, I4/mmm) phase transition was observed. This compound shows metallic electronic resistivity and Pauli paramagnetic behavior.     

Origins of superstructure ordering and incommensurability in stuffed CoSn-type phases

The CoSn structure type contains large interstitial void spaces that frequently host electropositive guest atoms, such as rare earth elements. In this stuffing process, an intriguing ordering occurs between the neighboring void spaces leading to a family of long-period superstructures comprising intergrowths of the ScFe6Ge6 and ScFe6Ga6 structure types. This superstucture ordering culminates in incommensurability in the REFe6Ge6-deltaGa delta systems with RE = Sc, Tb, and Lu. In this work, we derive a 3 + 1D superspace model encompassing this series of structures and investigate the origins of the structural trends in this family with electronic structure calculations, at both the LDA-DFT and extended Hückel levels. Using our 3 + 1D model, we refine the structures of four new ErFe6Ge6-deltaGa delta (0 < or = delta < or = 6) phases, two commensurate and two incommensurate, from powder X-ray diffraction data. The refinement results confirm trends observed in the Sc-, Tb-, and Lu-based series: a gradual lengthening and, eventually, turning of the q-vector as Ge is progressively exchanged for Ga. These trends, and the incommensurate ordering as a whole, are traced to a tension between two modes by which the host lattice responds to stuffing atom insertion: (1) an atomic charge modulation enhancing the anionic character of the cavity walls around the guest atoms, and (2) a positional modulation expanding the cavities occupied by guest atoms. These two modes direct the stuffing atom ordering pattern toward opposite ends of the ScFe6Ge6-ScFe6Ga6 intergrowth series. The full series of structures, complex and incommensurate, reflects various degrees of balance between these two factors.     

The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction

Hydrogen atoms play key roles in enzyme mechanism, but as this study shows, even high-quality X-ray data to a resolution of 1 A cannot directly visualize them. Neutron diffraction, however, can locate deuterium atoms even at resolutions around 2 A. Both neutron and X-ray diffraction data have been used to investigate the transition state of the aspartic proteinase endothiapepsin. The different techniques reveal a different part of the story, revealing the clearest picture yet of the catalytic mechanism by which the enzyme operates. Room temperature neutron and X-ray diffraction data were used in a newly developed joint refinement software package to visualize deuterium atoms within the active site of the enzyme when a gem-diol transition state analogue inhibitor is bound at the active site. These data were also used to estimate their individual occupancy, while analysis of the differences between the bond lengths of the catalytic aspartates was performed using atomic resolution X-ray data. The two methods are in agreement on the protonation state of the active site with a transition state analogue inhibitor bound confirming the catalytic mechanism at which the enzyme operates.     

Novel characterization of the adsorption sites in large pore metal-organic frameworks: combination of X-ray powder diffraction and thermal desorption spectroscopy

The preferred adsorption sites of xenon in the recently synthesized metal-organic framework MFU-4l(arge) possessing a bimodal pore structure (with pore sizes of 12 ? and 18.6 ?) were studied via the combination of low temperature thermal desorption spectroscopy and in situ X-ray powder diffraction. The diffraction patterns were collected at 110 K and 150 K according to the temperature of the desorption maxima. The maximum entropy method was used to reconstruct the electron density distribution of the structure and to localize the adsorbed xenon using refined data of the Xe-filled and empty sample. First principles calculations revealed that Xe atoms exclusively occupy the Wyckoff 32f position at approximately 2/3 2/3 2/3 along the body diagonal of the cubic crystal structure. At 110 K, Xe atoms occupy all 32 f positions (8 atoms per pore) while at 150 K the occupancy descends to 25% (2 atoms per pore). No Xe occupation of the small pores is observed by neither experimental measurements nor theoretical studies.     

Atomic interactions in the p-type clathrate I Ba8Au5.3Ge40.7

Single crystals of Ba(8)Au(5.3)Ge(40.7) [space group Pm(3)n (No. 223), a = 10.79891(8) ?] were prepared by a Bridgman technique. The crystal structure refinement based on single-crystal X-ray diffraction data does not reveal any vacancies in the Au/Ge framework or in the cages. In addition to the ionic bonding between Ba and the anionic framework, a direct interaction between Ba and Au atoms was identified in Ba(8)Au(5.3)Ge(40.7) by applying the electron localizability indicator. As expected by the chemical-bonding picture, Ba(8)Au(5.3)Ge(40.7) is a diamagnet and shows p-type electrical conductivity with a hole carrier concentration of 7.14 × 10(19) cm(-3) at 300 K and very low lattice thermal conductivity of ≈0.6 W m(-1) K(-1) at 500 K. The thermoelectric figure of merit ZT of single crystals of Ba(8)Au(5.3)Ge(40.7) attains 0.3 at 511 K and reaches 0.9 at 680 K in a polycrystalline sample of closely similar composition. This opens up an opportunity for tuning of the thermoelectric properties of materials in the Ba-Au-Ge clathrate system by changing the chemical composition.     

Low-temperature Na4Ti5O12 from X-ray and neutron powder diffraction data

The crystal structure of the low-temperature Na₄Ti₅O₁₂ (tetra­sodium penta­titanium dodeca­oxide) phase has been solved and refined from X-ray and neutron powder diffraction data at 295 K. The structure is trigonal, space group P3, with Z = 1, although it is pseudo-centrosymmetric. The O and Na atoms form a distorted close-packed structure, where Ti atoms occupy octahedral sites.     

Single-crystal X-ray diffraction analysis of pyrene II at 93 K

The crystal and molecular structure of the low temperature phase of the polycyclic aromatic hydrocarbon pyrene has been determined for the first time by single-crystal X-ray diffraction methods. The crystal structure at 93 K is shown to be in excellent agreement with that obtained by the refinement of powder neutron diffraction data for pyrene II obtained at 4.2 K.     

Structure determination from powder diffraction

The review surveys modern methods for the determination of unknown crystal structures of organic and inorganic compounds from powder diffraction data. The main stages of this process, from the preparation of the specimen to a search for the structural motif followed by the Rietveld refinement, are considered. The results obtained on different diffractometers using X-ray, synchrotron, and neutron radiations are demonstrated to be well reproducible. Examples of successful structure solution are cited, which provide evidence that powder diffraction is a reliable tool in establishing structures of a wide range of compounds for which single crystals are unavailable.     

Propene adsorption sites in zeolite ITQ-12: a combined synchrotron X-ray and neutron diffraction study

The adsorption site of propene in the small-pore, pure silica zeolite [Si24O48]-ITW-ITQ-12 has been characterized via Rietveld refinement of the crystal structure of propene-loaded ITQ-12 on the basis of synchrotron X-ray and neutron diffraction data taken at 298 K. The structure can be described with a monoclinic unit cell having Cm symmetry and unit cell parameters a = 10.436 angstroms, b = 15.018 angstroms, c = 8.855 angstroms, beta = 105.74 degrees, and volume = 1335.9 angstroms3. Four-fold disordered adsorption sites that are nearly equivalent relative to the cage's 2/m pseudosymmetry are located near the center of each ellipsoidally shaped [4(4)5(4)6(4)8(4)] cage. At this site, the adsorbed propene molecule lies on a plane close and approximately parallel to the equatorial plane of the cage and is aligned with its methylene group pointing toward the pore's eight-ring window. The refined propene concentration, 1.8 per unit cell content, is close to one propene molecule per [4(4)5(4)6(4)8(4)] cage and the amount observed in adsorption experiments at 298 K and 1 atm propene partial pressure.     

Crystalline, mixed-valence manganese analogue of prussian blue: magnetic, spectroscopic, X-ray and neutron diffraction studies

The compound of stoichiometry Mn(II)3[Mn(III)(CN)6]2.zH2O (z = 12-16) (1) forms air-stable, transparent red crystals. Low-temperature single crystal optical spectroscopy and single crystal X-ray diffraction provide compelling evidence for N-bonded high-spin manganese(II), and C-bonded low-spin manganese(III) ions arranged in a disordered, face-centered cubic lattice analogous to that of Prussian Blue. X-ray and neutron diffraction show structured diffuse scattering indicative of partially correlated (rather than random) substitutions of [Mn(III)(CN)6] ions by (H2O)6 clusters. Magnetic susceptibility measurements and elastic neutron scattering experiments indicate a ferrimagnetic structure below the critical temperature Tc = 35.5 K.     

K and Ba distribution in the structures of the clathrate compounds KxBa16−x(Ga,Sn)136 (x = 0.8, 4.4, and 12.9) and KxBa8−x(Ga,Sn)46 (x = 0.3)

Studies of the K–Ba–Ga–Sn system produced the clathrate compounds K_0.8(2)Ba_15.2(2)Ga_31.0(5)Sn_105.0(5) [a = 17.0178 (4) Å], K_4.3(3)Ba_11.7(3)Ga_27.4(4)Sn_108.6(4) [a = 17.0709 (6) Å] and K_12.9(2)Ba_3.1(2)Ga_19.5(4)Sn_116.5(4) [a = 17.1946 (8) Å], with the type‐II structure (cubic, space group Fdm), and K_7.7(1)Ba_0.3(1)Ga_8.3(4)Sn_37.7(4) [a = 11.9447 (4) Å], with the type‐I structure (cubic, space group Pmn). For the type‐II structures, only the smaller (Ga,Sn)₂₄ pentagonal dodecahedral cages are filled, while the (Ga,Sn)₂₈ hexakaidecahedral cages remain empty. The unit‐cell volume is directly correlated with the K:Ba ratio, since an increasing amount of monovalent K occupying the cages causes a decreasing substitution of the smaller Ga in the framework. All three formulae have an electron count that is in good agreement with the Zintl–Klemm rules. For the type‐I compound, all framework sites are occupied by a mixture of Ga and Sn atoms, with Ga showing a preference for Wyckoff site 6c. The (Ga,Sn)₂₀ pentagonal dodecahedral cages are occupied by statistically disordered K and Ba atoms, while the (Ga,Sn)₂₄ tetrakaidecahedral cages encapsulate only K atoms. Large anisotropic displacement parameters for K in the latter cages suggest an off‐centering of the guest atoms.     

Guest-framework interaction in type I inorganic clathrates with promising thermoelectric properties: on the ionic versus neutral nature of the alkaline-earth metal guest A in A8Ga16Ge30 (A=Sr, Ba)

Periodic density functional calculations using pseudopotentials and a local basis set were performed on the type I clathrates A(8)Ga(16)Ge(30) (A=Sr, Ba). Both are known to show promising thermoelectric properties. Ab initio wave functions were analyzed within the framework of the quantum theory of atoms in molecules. This enabled us to analyze both the charge transfer and bonding properties of the clathrate from a rigorous quantum mechanical viewpoint. The Ba and Sr centers were found to be largely ionic (charge: ca. +1.7 e) both in the smaller 20-atom and in the larger 24-atom cages, consistent with a Zintl-phase view of these type I clathrates. The assertion that the Sr atoms in the different cages have similar oxidation states is shown to be consistent with multiwavelength diffraction experiments on Sr(8)Ga(16)Ge(30); while the assertion of ionicity of the Sr center is supported by the observation that the adsorption edge lies close to that previously found in the Sr K-edge XANES spectra of Sr(OH)(2).8 H(2)O. As such, this work contradicts previous experimental and theoretical studies that claim that the guest atoms are neutral. We show that the discrepancy is related to the definitions used for electron transfer. Definitions based on electron displacement (rearrangement) in space, as in previous works, do not account for the variation in shape and volume of the atomic catchment regions upon change in the number and average locations of the particles in the system. Eventually, such definitions lead to underestimation of charge transfer. The large binding energy found in earlier work for Ba and Sr in these materials is found to be consistent with a simple picture of charge transfer from the guest to the frame. Preliminary investigations on a clathrate of perfect stoichiometry appear to rule out any important relationship between the observed increase in the thermoelectric figure of merit with increasing external pressure and host-guest charge transfer.     

"Nanoscale zippers" in Gd5(SixGe(1-x))4: symmetry and chemical influences on the nanoscale zipping action

One critical parameter influencing the structural nature of the phase transitions in magnetocaloric materials Gd5(SixGe(1-x))4 is the Si/Ge ratio (x/1-x), because transition temperatures and structures depend crucially on this value. In this study, single-crystal X-ray diffraction indicates that Si and Ge atoms are neither completely ordered nor randomly mixed among the three crystallographic sites for these elements in these structures. Ge atoms enrich the T sites linking the characteristic slabs in these structures, while Si atoms enrich the T sites within them. Decomposition of the total energy into site and bond energy terms provides a rationale for the observed distribution, which can be explained by symmetry and electronegativity arguments. For any composition in Gd5(SixGe(1-x))4, a structure map is presented that will allow for a rapid assessment of the specific structure type.     

Synchrotron X-ray charge-density study of coordination polymer [Mn(HCOO)2(H2O)2]infinity

Three high-quality single-crystal X-ray diffraction data sets have been measured under very different conditions on a structurally simple, but magnetically complex, coordination polymer, [Mn(HCOO)(2)(H(2)O)(2)](infinity) (1). The first data set is a conventional 100(2) K Mo(Kalpha) data set, the second is a very high resolution 100(2) K data set measured on a second-generation synchrotron source, while the third data set was measured with a tiny crystal on a high brilliance third-generation synchrotron source at 16(2) K. Furthermore, the magnetic susceptibility (chi) and the heat capacity (C(p)) have been measured from 2 to 300 K on pressed powder. The charge density of 1 was determined from multipole modeling of the experimental structure factors, and overall there is good agreement between the densities obtained separately from the three data sets. When considering the fine density features, the two 100 K data sets agree well with each other, but show small differences to the 16 K data set. Comparison with ab initio theory suggests that the 16 K APS data set provides the most accurate density. Topological analysis of the metal-ligand bonding, experimental 3d orbital populations on the Mn atoms, and Bader atomic charges indicate quite ionic, high-spin metal atoms. This picture is supported by the effective moment estimated from the magnetization measurements (5.840(2) mu(B)), but it is at variance with earlier spin density measurements from polarized neutron diffraction. The magnetic ordering originates from superexchange involving covalent interactions with the ligands, and non-ionic effects are observed in the static deformation density maps as well as in plots of the valence shell charge concentrations. Overall, the present study provides a benchmark charge density that can be used in comparison with future metal formate dihydrate charge densities.