Neutron Structure Refinement Research Articles

A neutron diffraction study of the hydrous borate inderborite, CaMg[B3O3(OH)5]2(H2O)4·2H2O

Abstract The crystal chemistry of inderborite, a B-rich mineral (B2O3 ~41 wt%) with ideal formula CaMg[B3O3(OH)5]2·6H2O or CaMg[B3O3(OH)5]2(H2O)4·2H2O from the Inder Deposit, Kazakhstan, was re-investigated by a multi-methodological approach (single-crystal X-ray and neutron diffraction, electron probe micro-analysis in wavelength-dispersive mode, laser ablation multi-collector inductively mass spectrometry). The experimental findings show that the real chemical formula of inderborite from the Inder Deposit is virtually identical to the ideal one: the fraction of potential isomorphic substituents is insignificant. Boron is, therefore, the only industrially relevant element occurring in this mineral. The in situ B isotope composition of the Inder inderborite shows enrichment in the heavy 11B isotope, giving a weighted mean δ11BNIST951 of +35.15 ± 0.49 ‰ (2σ, N = 6). Such a positive δ11B value falls within the range of values in which the source of boron is ascribable to marine reservoirs rather than to terrestrial ones. X-ray (at 293 K) and neutron (at 20 K) structure refinements confirm that the principal building block unit of the structure is a [B3O3(OH)5]2– ring, consisting of two BO2(OH)2 tetrahedra (B-ion in sp3 electronic configuration) and one planar-triangular BO2OH group (B-ion in sp2 electronic configuration). In the [B3O3(OH)5]2– ring, all the oxygen atoms that are not shared between two boron atoms are protonated. The building units share corners with the CaO2(OH)4(OH2)2 polyhedra and Mg(OH)4(OH2)2 octahedra, forming hetero-polyhedral sheets parallel to (100). Subsequent hetero-polyhedral sheets are mutually connected only by H-bonding interactions, even mediated by the zeolitic (“interstitial”) H2O molecules. Ten out of 11 independent oxygen sites in the structure of inderborite are involved in H-bonds as donors or acceptors, and this reflects the pervasive effect of the H-bonding network. The role played by the complex H-bond network is expected to be substantial on the stability of the crystalline edifice, having effects within the single hetero-polyhedral sheet, between subsequent sheets, and in the bonding with the interstitial zeolitic H2O molecules. Finally, the potential utilizations of inderborite, as a B-bearing mineral, are discussed.

On the crystal-chemistry of inderite, Mg[B3O3(OH)5](H2O)4·H2O

The crystal chemistry of inderite, a hydrous borate with known ideal formula MgB3O3(OH)5·5H2O from the Kramer deposit, was re-investigated by electron probe micro-analysis in wavelength dispersive mode, laser ablation-(multi collector-)inductively coupled plasma-mass spectrometry and single-crystal neutron diffraction. The chemical data prove that the real composition of the investigated inderite is substantially identical to the ideal one, with insignificant content of potential isomorphic substituents, so that, excluding B, inderite does not contain any other industrially-relevant element (e.g., Li concentration is lower than 2.5 wt ppm, Be or REE lower than 0.1 wt ppm). The average δ11BNIST951 value of ca. − 7 ‰ lies within the range of values in which the source of boron is ascribable to terrestrial reservoirs (e.g., hydrothermal brines), rather than to marine ones. Neutron structure refinements, at both 280 and 10 K, confirm that the building units of the structure of inderite consist of: two BO2(OH)2 tetrahedra (B-ion in sp3 electronic configuration) and one BO2(OH) triangle (B-ion in sp2 electronic configuration), linked by corner-sharing to form a (soroborate) B3O3(OH)5 ring, and a Mg-octahedron Mg(OH)2(OH2)4. The B3O3(OH)5 ring and the Mg-octahedron are connected, by corner-sharing, to form an isolated Mg(H2O)4B3O3(OH)5 (molecular) cluster. The tri-dimensional edifice of inderite is therefore built by heteropolyhedral Mg(H2O)4B3O3(OH)5 clusters mutually connected by H-bonds, mediated by the zeolitic (“interstitial”) H2O molecules lying between the clusters, so that the correct form of the chemical formula of inderite is Mg[B3O3(OH)5](H2O)4·H2O, rather than MgB3O3(OH)5·5H2O. All the thirteen independent oxygen sites of the structure are involved in H-bonding, as donors or as acceptors. This confirms the pervasive nature and the important role played by the H-bonding network on the structural stability of inderite. The differences between the crystal structure of the two dimorphs inderite and kurnakovite are discussed.

Optimizing Li+ transport in Li7La3Zr2O12 solid electrolytes

The Li + conductivity of Li7La3Zr2O12 (LLZO) solid electrolytes was optimized by controlling the addition of the dopant (Al) into the crystal structure. A solution-based synthesis method was used to minimize Al segregation and ensure a homogeneous substitution into the garnet framework. Neutron and x-ray diffraction were used to monitor the structural transition from tetragonal to cubic LLZO. It was found that the critical dopant concentration (xc) required to stabilize the cubic phase was 0.18 mol pfu. The maximum ionic conductivity of 5.54 × 10−4 S/cm was obtained at the critical composition. The enhanced conductivity was achieved by accurately controlling the vacancy density at the active Li octahedral sites. Neutron structure refinements were used to validate the changes in Li vacancy distribution at different dopant concentrations. Impedance measurements reveal a strong dependence of Li+ transport properties on Al concentration, specifically around the critical dopant concentration xc = 0.18 mol pfu. These findings demonstrate the importance of fine-tuning composition and provide guidance for engineering improvements in ionic conductivity.

On the crystal-chemistry of meyerhofferite, CaB3O3(OH)5·H2O

The crystal structure and crystal chemistry of meyerhofferite, ideally CaB3O3(OH)5·H2O, was investigated by a multi-methodological approach based on titrimetric determination of boron, gravimetric determination of calcium, determination of fluorine by ion selective electrode, determination of water content by heating, other minor elements by inductively coupled plasma atomic emission spectroscopy, along with single-crystal synchrotron X-ray and neutron diffraction. The concentration of more than 50 chemical elements was measured. The combination of these techniques proves that the composition of meyerhofferite approaches the ideal one (i.e., (Ca1.012Mg0.003) (B2.984Si0.001)O3(OH)5·1.018H2O), with only a modest fraction of Mg (with MgO ≈ 0.03 wt%) replacing Ca, and with Si the only potential substituent of tetrahedral B (with SiO2 ≈ 0.02 wt%). The content of REE and other minor elements is, overall, not significant, including that of fluorine as a potential OH− substituent (i.e., < 0.01 wt%). These findings have some relevant geochemical and technical implications, here discussed. The X-ray and neutron structure model obtained in this study prove that the building units of the structure of meyerhofferite consist of: two BO2(OH)2 tetrahedra and one BO2(OH) triangle, linked by corner-sharing to form [B3O3(OH)5]2− rings, and distorted Ca-polyhedra (with CN = 8, CaO3(OH)4(OH2)), linked by edge-sharing to form infinite chains along [001]. The B3O3(OH)5 rings are connected to the Ca-polyhedra chains by corner- and edge-sharing, on two sides of the chains. These heteropolyhedral chains, made by Ca-polyhedra and B3O3(OH)5 rings, are mutually connected through hydrogen bonding only, giving rise to the tri-dimensional edifice of meyerhofferite. The neutron structure refinement showed no evidence of static or dynamic disorder pertaining to the H sites; their libration regime was found to be significantly anisotropic. At least seven of the nine oxygen sites of the structure are involved in H-bonding, as donors or as acceptors. The role played by the H-bonding scheme on the physical properties of meyerhofferite is discussed.

Allanite at high temperature: effect of REE on the thermal behaviour of epidote-group minerals

The thermal behaviour of a natural allanite-(Ce) has been investigated up to 1073 K (at room pressure) by means of in situ synchrotron powder X-ray diffraction and single-crystal neutron diffraction. Allanite preserves its crystallinity up to 1073 K. However, up to 700 K, the thermal behaviour along the three principal crystallographic axes, of the monoclinic β angle and of the unit-cell volume follow monotonically increasing trends, which are almost linear. At T > 700–800 K, a drastic change takes place: an inversion of the trend is observed along the a and b axes (more pronounced along b) and for the monoclinic β angle; in contrast, an anomalous increase of the expansion is observed along the c axis, which controls the positive trend experienced by the unit-cell volume at T > 700–800 K. Data collected back to room T, after the HT experiments, show unit-cell parameters significantly different with respect to those previously measured at 293 K: allanite responds with an ideal elastic behaviour up to 700 K, and at T > 700–800 K its behaviour deviates from the elasticity field. The thermo-elastic behaviour up to 700 K was modelled with a modified Holland–Powell EoS; for the unit-cell volume, we obtained the following parameters: VT0 = 467.33(6) Å3 and αT0(V) = 2.8(3) × 10–5 K−1. The thermal anisotropy, derived on the basis of the axial expansion along the three main crystallographic directions, is the following: αT0(a):αT0(b):αT0(c) = 1.08:1:1.36. The T-induced mechanisms, at the atomic scale, are described on the basis of the neutron structure refinements at different temperatures. Evidence of dehydroxylation effect at T ≥ 848 K are reported. A comparison between the thermal behaviour of allanite, epidote and clinozoisite is carried out.

Influence of Alkaline-Earth-Metal Substitutions on the Bismuth Ruthenate Structure: Bi2-xA'xRu2O6O'1-y (A' = Mg, Ca, Sr).

Solid solutions with the formula of Bi2-xA'xRu2O7-y (A' = Mg, Ca, Sr; 0 ≤ x ≤ 0.2 for Mg, 0 ≤ x ≤ 1 for Ca, and 0 ≤ x ≤ 0.5 for Sr) have been synthesized and characterized. The crystal structures for these phases are found to be in the pyrochlore family, crystallizing in the cubic space group Fd3̅m with complex A/A' cation coordination environments. The Bi cation is found to be off-center from the ideal position because of a lone-pair distortion, while the positions of the substituted A' cations vary based on the size and ionicity. The neutron structure refinements reveal a similar propensity to off-center regarding Ca and Sr, while Mg features the largest static displacement of up to 0.48 Å. Interestingly, this is one of only two known pyrochlores with Mg2+ located in an 8-coordinated site. The average Ru oxidation state for each substitution is found to increase, and charge compensates for the lower divalent A' substitution. The solid solutions show temperature-independent resistance across the series with small changes in magnitude that scale with the amount of substitution, while displaying Pauli paramagnetic behavior throughout.

A multi-methodological study of kernite, a mineral commodity of boron

Abstract Kernite, ideally Na2B4O6(OH)2∙3H2O, is a major constituent of borate deposits and one of the most important mineral commodities of B. The chemical composition and crystal structure of kernite from the Kramer Deposit (Kern County, California) were investigated by a suite of analytical techniques (i.e., titrimetric determination of B content, gravimetric method for Na, ion selective electrode for F, high-T mass loss for H2O content, inductively coupled plasma atomic emission spectroscopy for REE and other minor elements, elemental analysis for C, N, and H contents) and single-crystal X-ray (at 293 K) and neutron (at 20 K) diffraction. The concentrations of more than 50 elements were measured. The general experimental formula of the kernite sample used in this study is Na1.99B3.99O6(OH)2∙3.01H2O. The fraction of other elements is, overall, insignificant: excluding B, kernite from the Kramer Deposit does not act as geochemical trap of other technologically relevant elements (e.g., Li, Be, or REE). The X-ray and neutron structure model obtained in this study confirms that the structure of kernite is built up by: two (crystallographically independent) triangular BO2OH groups and two tetrahedral BO4 groups, which share corner-bridging O atoms to form threefold rings, giving chains running along [010], and NaO4(OH)(OH2) and NaO2(OH)(OH2)3 polyhedra. Positional disorder of two H sites of H2O molecules was observed by the neutron structure refinement and corroborated by the maximum-entropy method calculation, which consistently provided a model based on a static disorder, rather than a dynamic one. The H-bonding network in the structure of kernite is complex, pervasive, and plays a primary role on its structural stability: the majority of the oxygen sites are involved in H-bonding, as donors or as acceptors. The potential utilizations of kernite, as a source of B (B2O3 ~50 wt%), are discussed, on the basis of the experimental findings of this study.

Na-feldspar: temperature, pressure and the state of order

Abstract. In feldspars, mean tetrahedral T–O bond lengths (T = Al,Si) are the standard measure of the tetrahedral Al content. However, for a sophisticated assessment of the Al,Si distribution, factors have to be accounted for (1) that cause individual T–O bond lengths to deviate from their tetrahedral means and (2) that cause mean tetrahedral lengths to deviate from values specified by the Al content. We investigated low albite, Na[AlSi3O8], from six X-ray crystal structure refinements available in the literature. The Al,Si distribution of low albite is fully ordered so that Al,Si–O bond length variations result only from bond perturbing factors. For the intra-tetrahedral variation ΔT–O≡T–O-〈T–O〉, only two factors turned out to be effective: (1) the sum of bond critical point electron densities in the Na–O and T–O bonds neighbouring the T–O bond under consideration and (2) the fractional s-bond character of the bridging oxygen atom. This model resulted in a root mean square (rms) value for ΔT–O of only 0.002 Å, comparable to the estimated standard deviations (esd's) routinely quoted in X-ray and neutron structure refinements. In the second step, the inter-tetrahedral differences Δ〈T–O〉≡〈T–O〉-〈〈T–O〉〉 were considered. Here, apart from the tetrahedral Al content, the only size-perturbing factor is the difference between the tetrahedral and the grand mean fractional s-characters. The resulting rms value was as small as 0.0003 Å. From this analysis, Al site occupancies, t, can be derived from observed mean tetrahedral distances, 〈T–O〉obs, as t=0.25(1+nAn)+〈T–O〉adj-〈〈T–O〉〉/0.12466(17), with the observed distance 〈T–O〉obs adjusted for the influence of the fractional s-character, 〈T–O〉adj=〈T–O〉obs+0.1907(51)[〈fs(O)〉-〈〈fs(O)〉〉]. This equation served to determine the site occupancies of 16 intermediate to high albites and one analbite from their mean tetrahedral distances. It was found that the individual site occupancies t10, t1m and t20= t2m all vary linearly with the difference Δt1= t10− t1m. Δt1, in turn, varies linearly with the length difference, Δtr[110], between the unit cell repeat distances [1∕2a, 1∕2b, 0] and [1∕2a, -1/2b, 0]. Then, from the Δtr[110] indicator, values of t were obtained as t10=(1-b0)+b0(b1+b2Δtr[110])t1m=(1-b0)-(1-b0)(b1+b2Δtr[110])t20=t2m=(b0-0.5)-(b0-0.5)(b1+b2Δtr[110]), with b0=0.7288(16), b1=0.1103(59) and b2=3.234(32) Å−1. Finally, from an expression that converts the Δ2θ(131) measure of order into Δtr[110] and thus into site occupancies, it was possible to obtain from the unique suite of bracketed high-pressure experiments performed on albites by Goldsmith and Jenkins (1985) the evolution with equilibrium temperature of the thermodynamic order parameter Qod and of the individual Al site occupancies t at a pressure of 1 bar. For that purpose, since the Goldsmith and Jenkins experiments were performed at ≈18 kbar, a procedure was devised that accounts for the effect of pressure on the state of order. At 1 bar, low albite is stable up to 590 ∘C, where it begins to disorder, turning into high albite above 720 ∘C. The highly though not fully disordered monoclinic state (monalbite) is reached at 980 ∘C, 1 bar, and 1055 ∘C, 18 kbar, respectively. Eventually, when applying the determinative equations given above to low microcline, full order is predicted as in low albite.

Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27

The IBARAKI biological crystal diffractometer (iBIX) was used in single-crystal time-of-flight neutron diffraction experiments on manganese catalase from Thermus thermophilus. The unit-cell dimensions were 133 × 133 × 133 Å, which is close to the designed maximum limitation of iBIX (135 × 135 × 135 Å). The optimum integration box sizes were set and the degree of integration box overlap was calculated for each Laue spot. Using the overlap ratio as the criterion, the selection of the diffraction intensity data was performed to give a minimum R p.i.m.. Subsequently, diffraction intensity data from Laue spots with overlap ratios ≤0.1 were selected and a complete reflection data set with d min = 2.35 Å was obtained. Joint X-ray and neutron structure refinements were also successfully performed. It was difficult to determine the structures and protonation states of all the oxygen atoms in the manganese cluster owing to the disordered structure. No hydrogen atom was observed on the ordered μ-bridging oxygen atom O1003. Instead, this oxygen atom probably forms a hydrogen bond with Thr39. In addition, the refinements clearly showed the protonation states of the amino acid residues and hydrogen bonds, as observed in Tyr192, Glu167 and Glu280. This first neutron crystal structure of manganese catalase shows that iBIX can provide acceptable diffraction data for neutron single-crystal analyses of at least 2.4 Å resolution within the original targeted unit-cell dimensions of 135 × 135 × 135 Å.

Tuning color through sulfur and fluorine substitutions in the defect tin(II, IV) niobate pyrochlores

Sulfur and fluorine substituted Sn2Nb2O7 pyrochlore compounds were synthesized to produce brilliant orange/red colors as an environmentally friendly alternative to other toxic inorganic pigments. Neutron structure refinements indicate that the studied compositions crystallize in the pyrochlore structure with a large number of cation and/or anion vacancies and significant local structural disorder. The cubic unit cell decreases with increasing sulfur and fluorine content. The Sn2+ cation is off-center by 0.39–0.48 Å from the ideal site, and the oxygen O′ is strongly displaced to the 32e position by an extraordinarily large distance that has never been reported for a pyrochlore type phase. The unprecedented displacive disorder and unusual lattice evolution upon sulfur substitution are presumably driven by the strong lone pair stereoactivity associated with Sn2+. Chemical analysis confirmed the existence of sulfur and fluorine, and 119Sn Mössbauer spectroscopy quantified the presence of both Sn2+ and Sn4+ in all compositions. The general formula representative of sulfur-containing pigments is nonstoichiometric Sn2−z2+(Nb2-ySny4+)O7-z-y/2-xSx with the color varying according to x. The fluorine compound is refined to be Sn22+(Nb0·958Ti0.984Sn0.0584+)O6·376F0.206 with exclusively anion vacancies. Optical characterization was performed through diffuse reflectance and color meter measurements. The band gap is determined to be in the range of 2.35 to 2.05 eV as sample color changes from yellow to orange/red. All powder samples show 60–95% reflectance in the near-infrared (NIR) region, adding new functionality to the application of these compounds as “cool” pigments.

On the labyrinthine world of arsenites: a single-crystal neutron and X-ray diffraction study of cafarsite

The crystal chemistry of a cafarsite sample from the fengitic orthogneisses of the Mt. Leone-Arbola nappe (Lower Penninic), forming the central body of Mount Cervandone and cropping out both in Switzerland and Italy (Alpe Devero area, Verbano–Cusio–Ossola province), was investigated by electron microprobe analysis in wavelength-dispersive mode (EPMA-WDS), single-crystal Raman spectroscopy, and single-crystal X-ray and neutron diffraction at 293 K. The sample of cafarsite of this study was found experimentally to be anhydrous and the chemical formula obtained on the basis of the EPMA-WDS data and structural refinements is the following: Ca1,Ca2(Ca15.56Na0.44)Σ16Fe1(Na0.53Fe2+0.17REE0.30)Σ1.00Mn1,Ti,Fe2(Ti7.46Fe3+4.47Fe2+3.20Mn2+0.85Al0.11) Σ16.11As1,As2,As3(AsO3)28 FF, with the general chemical formula Ca16(Na,Fe2+,REE)(Ti, Fe3+,Fe2+,Mn2+,Al)16(AsO3)28F [or Ca16(Na,Fe2+,REE)(Ti,Fe3+,Al)12(Fe2+,Mn)4(AsO3)28F]. Our experimental findings show that fluorine, which was unconsidered in the previous studies, is a key element. The anhydrous nature of this sample is also confirmed by its Raman spectrum, which does not show any evidence of active bands ascribable to the O–H stretching region. The X-ray and neutron structure refinements provide a structure model that is partially in agreement with the previous experimental findings. The space group (i.e. Pn3) and the unit-cell constant [i.e. 15.9507(4) A] are conform to the literature data, but the structure of cafarsite, here refined, contains the following building units: three independent AsO3 groups (trigonal pyramids), one CaO6F polyhedron, one CaO8 polyhedron, two independent (Ti,Fe)O6 octahedra, one (Na,Fe,REE)O8 polyhedron, and one (Mn,Fe)O6 octahedron. Connections among polyhedra are mainly due to edge- or vertex-sharing; the AsO3 groups are not connected to each other.

Order of [6]Ti4+ in a Ti-rich calcium amphibole from Kaersut, Greenland: a combined X-ray and neutron diffraction study

In order to characterize the role of Ti in the crystal structure of calcium amphiboles with high or even dominant oxo-component, the crystal structure of a Ti-rich calcium amphibole from a gabbro at Kaersut, Greenland, has been refined with single-crystal MoKα X-ray intensity data to an R 1(F) index of ~0.025, and with single-crystal Laue neutron intensity data to an R 1(F) index of ~0.053. The crystal used for X-ray structure refinement was characterized by electron- and ion-microprobe analysis. The site populations of the C-group cations Mg, Fe and Ti were calculated from the refined site-scattering values for the M(1), M(2) and M(3) sites derived by both X-ray and neutron diffraction. Ti is distributed among all the three sixfold coordinated M sites, with a strong preference for the M(1) and M(3) sites, where its main role is maintaining electroneutrality at the deprotonated O(3) site. The pattern of distortion of the M(1), M(2) and M(3) octahedra differs from that in F-free deprotonated or partly deprotonated amphiboles, where Ti4+ does not occur at the M(3) site. The neutron structure refinement provides also a clear picture of the environment of the proton, anisotropic displacement behaviour and potential hydrogen-bonding arrangements. A trifurcated hydrogen-bonding configuration has been identified, with two O(6) and one O(7) oxygen atoms as acceptors of weak hydrogen-bonds.

H-bonding scheme in allactite: a combined single-crystal X-ray and neutron diffraction, optical absorption spectroscopy, FTIR and EPMA-WDS study

AbsatractThe crystal chemistry of allactite from Långban, Värmland (Sweden) was investigated by single-crystal X-ray and neutron diffraction, optical absorption spectroscopy, Fourier-transform infra-red spectroscopy (FTIR) and electron microprobe analysis by wavelength-dispersive spectroscopy (EPMA-WDS). The optical spectra indicate the presence of Mn in valence state 2+ only. Assuming 16 O atoms per formula unit, arsenic as As5+ and the (OH) content calculated by charge balance, the resulting formula based on the EPMA-WDS data is (Mn2+6.73Ca0.13Mg0.12Zn0.02)∑7.00(As5+)2.00O16H8, very close to the ideal composition Mn7(AsO4)2(OH)8. In the unpolarized FTIR spectrum of allactite, fundamental (OH)-stretching bands are observed at 3236, 3288, 3387, 3446, 3484, 3562 and 3570 cm–1, suggesting that a number of OH environments, with different hydrogen bond strengths, occur in the structure. The neutron structure refinement shows that four independent H sites occur in allactite with full site occupancy, all as members of hydroxyl groups. The complex hydrogen-bonding scheme in the allactite structure is now well defined, with at least nine hydrogen bonds energetically favourable with mono-, bi- and trifurcated configurations.

Single-crystal neutron diffraction and Mössbauer spectroscopic study of hureaulite, (Mn,Fe)5(PO4)2 (HPO4)2 (H2O)4

The crystal chemistry of hureaulite from the Jocao (Cigana) pegmatite, Conselheiro Pena, Doce Valley, Minas Gerais (Brazil), was investigated by electron microprobe analysis in wavelength-dispersive mode, single-crystal Laue (at 293 K) and monochromatic neutron diffraction (at 2.3 K), and 57 Fe-Mossbauer spectroscopy [ M(1),M(2),M(3) (Mn 2+ 3.61 Fe 2+ 1.21 Ca 0.11 Mg 0.03 ) ∑=4.96 ( P(2) (PO 4 ) 2 (H 1.04 P(1) PO 4 ) 2 (H 2 O) 3.92 , Z = 4, a = 17.603(6), b = 9.087(2), c = 9.404(4) A, β = 96.66(4)°, and V = 1494.1(9) A 3 at 293 K, space group C 2 /c ]. The neutron refinements confirm the general structure model previously reported, showing that five independent H sites (with full site occupancy) occur in the hureaulite structure, one of them as member of the unique hydroxyl group ( i.e. , O(1)-H(1) ) and the other four belonging to two independent H 2 O molecules ( i.e. , H(2)-O(9)-H(3) and H(4)-O(10)-H(5) ). The hydroxyl group is the vertex of one of the two independent P-tetrahedra ( i.e. , HOPO 3 ), whereas the two H 2 O molecules are the vertices of the (Mn,Fe)-octahedra. No zeolitic H 2 O occurs in hureaulite structure. The complex hydrogen bonding scheme in hureaulite is now well defined, with five hydrogen bonds energetically favorable. The element distribution among the octahedral sites, deduced on the basis of the neutron structure refinements, shows that the highest fraction of Fe populates the M(2) site (~36%), whereas lower fractions are observed at M(1) and M(3) ( i.e. , ~13–15 and 11–12%, respectively). The 57 Fe Mossbauer spectrum of hureaulite confirms the absence of ferric iron in the sample. The spectrum shows four well-separated absorption lines which are best fitted with three doublets. The well-resolved doublet (with the largest quadrupole splitting) is here assigned to the M(3) site, in line with the pronounced preference of Mn 2+ for the M(3) site as shown by the neutron structure refinements. The two innermost doublets have almost identical isomer shifts, though with slightly different quadrupole splitting values; the smaller quadrupole splitting value is assigned to the M(2) site, which is expected to have a slightly lower polyhedral distortion than the M(1) site, according to the experimental findings based on the neutron refinements.

H-bonding scheme and cation partitioning in axinite: a single-crystal neutron diffraction and Mössbauer spectroscopic study

The crystal chemistry of a ferroaxinite from Colebrook Hill, Rosebery district, Tasmania, Australia, was investigated by electron microprobe analysis in wavelength-dispersive mode, inductively coupled plasma–atomic emission spectroscopy (ICP–AES), 57Fe Mossbauer spectroscopy and single-crystal neutron diffraction at 293 K. The chemical formula obtained on the basis of the ICP–AES data is the following: $$ ^{X1,X2} {\text{Ca}}_{4.03} \,^{Y} \left( {{\text{Mn}}_{0.42} {\text{Mg}}_{0.23} {\text{Fe}}^{2 + }_{1.39} } \right)_{\varSigma 2.04} \,^{Z1,Z2} \left( {{\text{Fe}}^{3 + }_{0.15} {\text{Al}}_{3.55} {\text{Ti}}_{0.12} } \right)_{\varSigma 3.82} \,^{T1,T2,T3,T4} \left( {{\text{Ti}}_{0.03} {\text{Si}}_{7.97} } \right)_{\varSigma 8} \,^{T5} {\text{B}}_{1.96} {\text{O}}_{30} \left( {\text{OH}} \right)_{2.18} $$ . The 57Fe Mossbauer spectrum shows unambiguously the occurrence of Fe2+ and Fe3+ in octahedral coordination only, with Fe2+/Fe3+ = 9:1. The neutron structure refinement provides a structure model in general agreement with the previous experimental findings: the tetrahedral T1, T2, T3 and T4 sites are fully occupied by Si, whereas the T5 site is fully occupied by B, with no evidence of Si at the T5, or Al or Fe3+ at the T1–T5 sites. The structural and chemical data of this study suggest that the amount of B in ferroaxinite is that expected from the ideal stoichiometry: 2 a.p.f.u. (for 32 O). The atomic distribution among the X1, X2, Y, Z1 and Z2 sites obtained by neutron structure refinement is in good agreement with that based on the ICP–AES data. For the first time, an unambiguous localization of the H site is obtained, which forms a hydroxyl group with the oxygen atom at the O16 site as donor. The H-bonding scheme in axinite structure is now fully described: the O16–H distance (corrected for riding motion effect) is 0.991(1) A and an asymmetric bifurcated bonding configuration occurs, with O5 and O13 as acceptors [i.e. with O16···O5 = 3.096(1) A, H···O5 = 2.450(1) A and O16–H···O5 = 123.9(1)°; O16···O13 = 2.777(1) A, H···O13 = 1.914(1) A and O16–H···O13 = 146.9(1)°].

Neutron diffraction study to elucidate reaction mechanism of RNase A

Ribonuclease A (RNase A) is a pyrimidine-specific endoribonuclease that claves and hydrolyzes single-stranded RNA in two distinct steps. The mechanism of the cleavage reaction catalyzed by RNase A involves two key histidine residues, His12 and His119. It is important to know the protonation states of them in order to understand the hydrolysis mechanism of RNase A. Neutron protein crystallography is a powerful technique for solving the problems. In previous reports, the protonation states of them for RNase A complexed with phosphate ion, uridine vanadate and phosphate free one have been investigated by neutron diffraction analysis [1-3]. In this study, neutron diffraction analysis of phosphate free RNase A has been carried out with high resolution and completeness data set in order to clarify the protonation states of two active site histidine residues, and to elucidate the detailed mechanism of the cleavage reaction. Neutron diffraction data of bovine pancreatic RNase A were collected by IBARAKI biological crystal diffractometer iBIX in J-PARC. The structure was determined by joint neutron and X-ray structure refinement. The final values of Rcryst and Rfree were 19.5% and 22.0%, respectively, for completeness of 86.7% to a resolution of 1.4Å. The structure with high reliability and good data statistics could be obtained by comparing with the already-reported one [3]. We calculated |Fo|-|Fc| neutron scattering length density map after omitting Dδ1 and Dε2 of His12 and His119 in order to confirm the protonation states of them. These omit maps indicated that His12 is completely singly protonated and Hi119 is doubly protonated. The protonation states of them are consistent with those in the first step of the putative mechanism of catalysis by RNase A. We could also observed a D atom of water molecule which is hydrogen bonded to Nε2 of His12.

Single-crystal neutron diffraction and Raman spectroscopic study of hydroxylherderite, CaBePO4(OH,F)

AbstractThe crystal structure, H bonding and chemical composition of hydroxylherderite from the Bennett pegmatite, Buckfield, Oxford County, Maine, USA were investigated by single-crystal X-ray diffraction and neutron Laue diffraction, electron microprobe analysis in wavelength-dispersive mode, inductively coupled plasma-atomic emission spectrometry and polarized Raman spectroscopy [Ca(Na0.01Ca1.01)∑1.02Be(Be0.98Li0.01)∑0.99P(Si0.03P0.98)∑1.01O4(OH0.67F0.33)∑1,Z= 4,a= 9.7856(5),b= 7.6607(5),c= 4.8025(3) Å, β = 90.02(3)°,V= 360.02(4) Å3, space groupP21/a]. The neutron-structure refinement converged with fully anisotropic displacement parameters to give a final agreement indexR1= 0.0363 for 85 refined parameters and 1614 unique reflections withFo&gt;4σ(Fo). The structure refinement was used to determine the H position and geometry of H bonding in the structure. OneHsite was found on theO5 anion with an O–H interatomic distance, corrected for “riding motion”, of 0.996(2) Å. The H bond of hydroxylherderite is bifurcated withO2 andO4 acceptors forming H bonds withO5⋯O2 = 3.163(1) Å,H⋯O2 = 2.544(2) ÅandO5–H⋯O2 = 121.8(1)°;O5⋯O4 = 3.081(1) Å,H⋯O4 = 2.428(2) Å andO5–H⋯O4 = 124.4(1)°. The highly non-linear O–H⋯O hydrogen bonds in hydroxylherderite and in the isotypic datolite [ideally CaBSiO4(OH)] are constrained by the tetrahedral network topology. Two main O–H stretching modes were observed in the Raman spectra at 3565 and 3620 cm–1, which are attributed to the bifurcated H bond. Two additional weak bands at 3575 and 3610 cm–1are attributed to Si–P disorder in the tetrahedral sites. Results of this study will contribute to the correlation of H-bonding geometry and O–H stretching frequencies of highly non-linear H bonds.

A single-crystal neutron and X-ray diffraction study of a Li, Be-bearing brittle mica

AbstractThe crystal chemistry of a meso-octahedral Li,Be-bearing mica from the Harding pegmatite (Dixon, Taos County, New Mexico, USA) has been investigated by constant-wavelength single-crystal neutron diffraction at 20 K, single-crystal X-ray diffraction at 100 K and inductively coupled plasma-atomic emission spectrometry (ICP-AES). The chemical composition based on ICP-AES analysis leads to the following chemical formula (calculated on the basis of 12 oxygen atoms):Ca(Na0.26K0.04Ca0.69)∑0.99M(Li0.29Mg0.03Fe0.023+Al1.78)∑2.12T(Al1.73Be0.16Si2.11)S4.00O12H2.53. The apparent excess of H is probably due to the fact that the fraction of H2O was assumed by difference to 100 wt.%, and slightly overestimated. On the basis of the previous experimental findings on Li,Be-bearing mica, X-ray (at 100 K) and neutron (at 20 K) structure refinements were performed in the space groupsCcandC2/c. The neutron structure refinement in the space groupCcoffers a view about the (Al,Be,Si)-tetrahedral ordering: the best fit of the refinement was reached with theT1 andT4 sites occupied by (Be + Al) andT2 andT3 fully occupied by Si. This leads to a final population ofT(Al1.88Be0.12Si2.00)∑4.00p.f.u., in reasonable agreement with the chemical analysis. The neutron refinement provides unambigous evidence of the occurrence of Li at theM1 site. The refined fraction of Li at theM1 site ranges between 0.27 and 0.29 a.p.f.u., in excellent agreement with the chemical analysis. The presence of Li, at least at a significant level, at theM2 (andM3) site can be ruled out, as a full site occupancy with the scattering length of Al was obtained. The location of the H sites and the complex hydrogen-bonding scheme are described. A comparison between the structure features of this Li,Be-mica and other brittle micas is carried out.

On the crystal structure and low-temperature behaviour of davyne: A single-crystal X-ray and neutron diffraction study

The crystal structure of a natural davyne [(Na3.98K1.79Ca1.89Mg0.02Fe0.01)∑7.69(Al5.99Si6.01O24)(SO4)0.65Cl1.96, a=12.7908(5)Å, c=5.3469(2)Å and V=757.59(6)Å3, space group P63], its thermoelastic behaviour and low-temperature induced structural evolution have been investigated by single-crystal neutron diffraction and in situ single-crystal X-ray diffraction within the range 110⩽T (K)⩽293. X-ray and neutron structure refinements provided a better picture of the disordered configuration of the SO4-groups and of the cation sites into the [0001]-channel. No evidence of phase transition or change of the thermoelastic behavior have been observed within the T-range investigated. The volume thermal expansion coefficient is αV=4.2(4)∗10−5K−1, and the axial thermal coefficients are αa=1.4(1)∗10−5K−1 and αc=1.6(1)∗10−5K−1. A series of structure refinements based on X-ray intensity data collected between 293 and 110K showed that the structural evolution of davyne is driven by the rotation of the rigid TO4 framework tetrahedra. The main deformation mechanisms of framework and extraframework population, in response to the applied temperature, are described. A comparison between the low-temperature structure evolution of the isotypic davyne, balliranoite and cancrinite is carried out.

On the crystal structure and compressional behavior of talc: a mineral of interest in petrology and material science

The crystal structure of a natural triclinic talc (1Tc polytype) [with composition: (Mg2.93Fe0.06)Σ2.99(Al0.02Si3.97)Σ3.99O10(OH)2.10] has been investigated by single-crystal X-ray diffraction at 223 and 170 K and by single-crystal neutron diffraction at 20 K. Both the anisotropic X-ray refinements (i.e. at 223 and 170 K) show that the two independent tetrahedra are only slightly distorted. For the two independent Mg-octahedra, the bond distances between cation-hydroxyl groups are significantly shorter than the others. The ditrigonal rotation angle of the six-membered ring of tetrahedra is modest (α ~ 4°). The neutron structure refinement shows that the hydrogen-bonding scheme in talc consists of one donor site and three acceptors (i.e. trifurcated configuration), all the bonds having O···O ≤ 3.38 Å, H···O ~ 2.8 Å, and O–H···O ~ 111–116°. The three acceptors belong to the six-membered ring of tetrahedra juxtaposed to the octahedral sheet. The vibrational regime of the proton site appears being only slightly anisotropic. The elastic behavior of talc was investigated by means of in situ synchrotron single-crystal diffraction up to 16 GPa (at room temperature) using a diamond anvil cell. No evidence of phase transition has been observed within the pressure range investigated. P–V data fit, with an isothermal third-order Birch-Murnaghan equation of state, results as follows: V 0 = 454.7(10) Å3, K T0 = 56(3) GPa, and K′ = 5.4(7). The “Eulerian finite strain” versus “normalized stress” plot yields: Fe(0) = 56(2) GPa and K′ = 5.3(5). The compressional behavior of talc is strongly anisotropic, as reflected by the axial compressibilities (i.e. β(a):β(b):β(c) = 1.03:1:3.15) as well as by the magnitude and orientation of the unit-strain ellipsoid (with ε 1:ε 2:ε 3 = 1:1.37:3.21). A comparison between the elastic parameters of talc obtained in this study with those previously reported is carried out.