Neutron Structure Refinement Research Articles

A single-crystal neutron and X-ray diffraction study of pezzottaite, Cs(Be2Li)Al2Si6O18

The chemical composition and the crystal structure of pezzottaite [ideal composition Cs(Be2Li)Al2Si6O18; space group: $${\it{R}} \overline{\text{3}} $$ c, a = 15.9615(6) A, c = 27.8568(9) A] from the type locality in Ambatovita (central Madagascar) were investigated by electron microprobe analysis in wavelength dispersive mode, thermo-gravimetric analysis, Fourier-transform infrared spectroscopy, single-crystal X-ray (at 298 K) and neutron (at 2.3 K) diffraction. The average chemical formula of the sample of pezzottaite resulted Cs1,Cs2(Cs0.565Rb0.027K0.017)Σ0.600 Na1,Na2(Na0.101Ca0.024)Σ0.125Be2.078Li0.922 Al1,Al2(Mg0.002Mn0.002Fe0.003Al1.978)Σ1.985 Si1,Si2,Si3(Al0.056Si5.944)Σ6O18·0.27H2O. The (unpolarized) IR spectrum over the region 3,800–600 cm−1 was collected and a comparison with the absorption bands found in beryl carried out. In particular, two-weak absorption bands ascribable to the fundamental H2O stretching vibrations (i.e. 3,591 and 3,545 cm−1) were observed, despite the mineral being nominally anhydrous. The X-ray and neutron structure refinements showed: (a) a non-significant presence of aluminium, beryllium or lithium at the Si1, Si2 and Si3 sites, (b) the absence (at a significant level) of lithium at the octahedral Al1, Al2 and Al3 sites and (c) a partial lithium/beryllium disordering between tetrahedral Be and Li sites.

A single-crystal neutron and X-ray diffraction study of elbaite

The crystal chemistry and crystal structure of gem-quality elbaite from the Pederneira mine, Sao Jose da Safira, Minas Gerais, Brazil, were investigated by electron microprobe analysis in wavelength dispersive mode, un-polarized Fourier transform infrared spectroscopy, single-crystal neutron and X-ray diffraction. The average chemical formula of the sample resulted X(Na0.73Ca0.06□0.21)Y(Al1.24Li1.02Fe0.41Mn0.18Mg0.07)ZAl6TSi6O18B(BO3)3V(OH)3W(OH0.46F0.54) and the chemical analysis showed an almost homogeneous distribution of the principal elements over the crystal, with significant amounts of Fe (wt% FeO ~ 3.1) and Mn (wt% MnO ~ 1.3) which substitute YAl. The infrared spectrum over the diagnostic range of fundamental hydroxyl stretching vibrations is characterized by three strong absorption bands at 3,591 (ν1), 3,562 (ν2), and 3,491 (ν3) cm−1, respectively. The neutron structure refinement showed: (a) the presence of boron at the B site only and (b) the absence (at a significant level) of aluminum at the T site, which appears to be fully occupied by silicon. Only one proton site was successfully located. The H bond configuration is described with O3 as “donor” and O5 as “acceptor.” The O3–H bond distance corrected for “riding motion” is 0.9834 A, and H···O5 = 2.238(7) A, O3···O5 = 3.152(4) A and O3–H···O5 = 157.7(5)°. The reasons of the positional disorder at the O1 and O2 sites, observed in both neutron and X-ray refinements, are discussed.

Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP)

Photoactive yellow protein (PYP) from Halorhodospira halophila is a soluble 14 kDa blue-light photoreceptor. It absorbs light via its para-coumaric acid chromophore (pCA), which is covalently attached to Cys69 and is believed to be involved in the negative phototactic response of the organism to blue light. The complete structure (including H atoms) of PYP has been determined in D(2)O-soaked crystals through the application of joint X-ray (1.1 A) and neutron (2.5 A) structure refinement in combination with cross-validated maximum-likelihood simulated annealing. The resulting XN structure reveals that the phenolate O atom of pCA accepts deuterons from Glu46 O(epsilon2) and Tyr42 O(eta) in two unusually short hydrogen bonds. This arrangement is stabilized by the donation of a deuteron from Thr50 O(gamma1) to Tyr42 O(eta). However, the deuteron position between pCA and Tyr42 is only partially occupied. Thus, this atom may also interact with Thr50, possibly being disordered or fluctuating between the two bonds.

Time-of-flight Rietveld neutron structure refinement and quantum chemistry study of Y-α-sialon

A Y-α-sialon was prepared using a specially designed temperature regime supporting formation of α-sialon and the amount of non-crystalline phase was remarkably reduced by a chemical treatment. Chemical composition of the sample was determined by EDX analysis. Crystal structure of Y-α-sialon was refined using high quality time-of-flight neutron powder diffraction data taken with the General Purpose Powder Diffractometer (GPPD) at the IPNS, Argonne National Laboratory. Unrestrained structure refinement was done in the P31 c space group. The list of simultaneously refined parameters included profile parameters, atomic coordinates, individual isotropic temperature parameters and the occupancy parameter of Y. The contents of Y in the cell refined to 0.38(1) and calculated Si–N distances in tetrahedra varied from 1.716(3) to 1.773(3) Å, but their distributions in the respective tetrahedra differ as in the parent structure of α-Si 3N 4. Anisotropic temperature parameters refinement, as well as constrained refinements of the occupancy parameters of Si–Al and N–O pairs, were also attempted, but they all ended with unphysical values. Variation of the background was analyzed using RDF formalism. Three peaks centered around 1.7 Å (with a shoulder at 2.2 Å), 2.8 Å and 3.5 Å proved that the composition of amorphous phase was close to that of crystalline. Ab initio cluster calculations performed at the B3LYP/6-31G** level of theory excluded configuration with O atoms bonded to three Si atoms and proved that the most probable is the configuration where an O atom is shared by three Al atoms.

Neutron and X-Ray Structure Refinements between 15 and 1073 K of Piezoelectric Gallium Arsenate, GaAsO4: Temperature and Pressure Behavior Compared with Other α-Quartz Materials

Previous X-ray crystal structure refinement of GaAsO4 gave spurious As–O (1.72 Å) and Ga–O (1.77 Å) bond distances by comparison with theoretical values and with experimental values from AlAsO4 and GaPO4 ([As–O]≅1.67 Å and [Ga–O]≅1.82 Å). Therefore, a complete structural reinvestigation of gallium arsenate was carried out between 15 and 1073 K by both neutron and X-ray diffraction. All new analyses led to experimental bond values in agreement with those predicted, i.e., close to 1.67 and 1.82 Å. This new structural investigation of GaAsO4 over a wide range of temperatures emphasizes the high thermal stability of the α-quartz packing in this compound, the best amongst quartz-like materials. The experimental relation between structural deformation and piezoelectric properties of these quartz-like materials also allows us to predict that GaAsO4 would have the best piezoelectric characteristics for its AT-cut. Conversely, its higher covalent character should imply a greater pressure sensitivity, with a crystal structure transition around 9 GPa. Thus, GaAsO4 would be the best piezoelectric candidate for high temperature applications but not for high pressure devices.

IR spectroscopy of hemimorphite between 82 and 373 K and optical evidence for a low-temperature phase transition

Polarized IR absorption spectra of oriented hemimorphite single-crystals were recorded in the region of the O-H fundamentals and combination bands between 82 and 373 K. The almost exclusive orientation of the absorption bands in the (010) plane is in agreement with previous neutron structure refinements. The weak H bonds of the OH groups and water molecules are confirmed by the energies of the OH stretching fundamentals around 3350-3600 cm^(-1). However, even though two O-H stretching bands in both ɑ and c are predicted by factor group analysis, three strong bands in ɑ, and two in c are observed. This fact, as well as the occurrence of weak satellite bands in the a and c spectra, and a minor component parallel to the b axis direction, indicate complicated dynamics of the water molecules and OH groups within the structural channels. These motions can be partly explained by a twisting motion of the water molecule around its two-fold molecular axis. A much better interpretation for these motions, however, is found in dynamic proton disorder, which describes a hopping motion between disordered proton sites. A possible dynamic disorder-order phase transition at low temperatures was tested by determination of birefringence values (Δn) of hemimorphite between 82 and 373 K. A strong discontinuity in the slope of Δn_(x,γ) and Δn_(γ,z) was observed at 98(2) K. This, together with considerable energy shifts of IR bands upon cooling, provides evidence for a low-temperature second-order phase transition in hemimorphite.

Fe, Ti ordering and octahedral distortions in acentric neptunite: Temperature dependent X-ray and neutron structure refinements and M�ssbauer spectroscopy

Single-crystal X-ray and neutron structure refinements carried out on neptunite (KNa2Li(Fe, Mg, Mn)2Ti2Si8O24) from San Benito, California at various temperatures (neutrons: 15 K and 293 K; X-rays: 110 K, 293 K and 493 K) indicate that this mineral crystallizes in the acentric space group Cc (T=293K: a=16.427 A, b=12.478 A, c=9.975 A, β= 115.56°, Z=4, V=1844.53 A3) due to ordering of octahedrally coordinated metals (Ti, Fe, Mn, Mg). In the neptunite structure, Ti and (Fe, Mn, Mg) octahedra share edges to form chains that run along [110] and [110]. These chains are, in turn, linked through shared corners along [001]. The resulting octahedral framework is interwoven by a similar [Si8O22] tetrahedral framework. Li, Na and K occupy 6-, 8- and 10- coordinated sites within the framework. The metal-containing polyhedra show strong distortions at all temperatures. In particular, Ti exhibits a strong off-center displacement (≈0.25 A) within its octahedron, leading to four Ti-O distances of 2.0 A, one of 2.2 A and one of 1.7 A. The displaced Ti position is in good agreement with a position that minimizes differences between ionic bond strengths and is interpreted as an energy minimum in an ionic potential model. Mossbauer spectra collected at 77 K, 293 K and 400 K indicate all Fe to be present as octahedral Fe2+. Although two distinct Fe positions were found in the structure, 77 K and 293 K spectra display only one quadrupole doublet. Two Fe sites can only be resolved in the 400 K spectrum. It is suggested that the temperature dependence of octahedral edge distortions is responsible for the separation of the Mossbauer doublets.

Neutron structure refinement of barium oxalate–oxalic acid dihydrate, BaC2O4.H2C2O4.2H2O and of related nonstoichiometric hydrates

Neutron structure refinement of barium oxalate–oxalic acid dihydrate, BaC2O4.H2C2O4.2H2O and of related nonstoichiometric hydrates

Neutron structure refinement of γ- and β-lithium lodate: Comparison between α, γ, and β phases

Neutron powder diffraction patterns of (γ + α) and β lithium iodate samples are used to refine the structure of γ (at 488 K) and β (at 513 K) LiIO 3. All three modifications are built up from Li + and (IO 3) − pyramids but lithium is six-, five-, and fourfold-coordinated to oxygen in the α-, γ-, and β-phases, respectively. The study of IO 3 group displacements through the α → γ phase transition suggests that the γ phase structure is closely related to a mixed orthohexagonal description of the α structure where both enantiomorphic forms of the hexagonal unit cell are present. The existence of a new α′ modification is postulated in view of neutron diffraction and NMR results. A simulation of the structure of hexagonal α-LiIO 3 is also presented.

Extinction in deformed copper single crystals. A combined study by γ-ray diffractometry and neutron structure refinement

Neutron diffraction and γ-ray rocking-curve measurements were performed on plastically deformed single crystals of Cu in order to compare the mosaic distribution parameters obtained from least-squares structural refinement with those seen by the γ-diffractometer. Neutron data were collected at two wavelengths (λ = 0.538 and 0.741 A) for one crystal with very homogeneous mosaic distribution, and for another crystal with less good but more typical mosaic structure data were collected for λ = 0.538 A. Maximum sin θ/λ was 1.52 A-1 and maximum extinction correction was less than 30%. For the latter crystal no comparison could be made between the two sets of observed distribution parameters because of the uneven mosaic distribution. The former crystal was found from the γ-ray measurements to be bent, but when this was taken into consideration in the Coppens-Hamilton [Acta Cryst. (1970), A26, 71-83] formalism for anisotropic extinction correction good agreement was found between mosaic parameters obtained by γ-ray and neutron measurements for directions not affected by the crystal curvature, whereas the structure refinement did not, as expected, reflect the complete crystal curvature when this effect was dominant.