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We present the crystallographic program Jana2020, the successor of Jana2006. Jana2020 has new, technically different graphics and structure plot-driven intuitive control. Tools known from Jana2006 were revised and inserted into a new logical scheme, and their control connected with the structure plot. Some of the tools were considerably improved. We focus on the details of the most dynamically developing parts, namely twinned structures, magnetic structures, and structure analysis based on electron diffraction data.

Two examples of twinning, by metric and reticular merohedry, in uranyl-oxide minerals demonstrate the care that must be taken during structural studies, and not only of such complex materials. This contribution also demonstrates the possibilities of the Jana2020 program in revealing twinning and in subsequent refinement., In this work, the structures of chemically related uranyl-oxide minerals agrinierite and rameauite have been revisited and some corrections to the available structure data are provided. Both structures were found to be twinned. The two minerals are chemically similar, and though their structures differ considerably, their unit-cell metrics are similar. Agrinierite was found to be twinned by metric merohedry (diffraction type I), whereas the structure of rameauite is twinned by reticular merohedry (diffraction type II). The twinning of the monoclinic unit cells (true cells) leads to pseudo-orthorhombic or pseudo-tetragonal supercells in the single-crystal diffraction patterns of both minerals. According to the new data and refinement, agrinierite is monoclinic (space group Cm), with a = 14.069 (3), b = 14.220 (3), c = 13.967 (3) Å, β = 120.24 (12)° and V = 2414.2 (12) Å3 (Z = 2). The twinning can be expressed as a mirror in (101) (apart from the inversion twin), which leads to a supercell with a = 14.121, b = 14.276, c = 24.221 Å and V = 2 × 2441 Å3, which is F centered. The new structure refinement converged to R = 3.54% for 6545 unique observed reflections with I > 3σ(I) and GOF = 1.07. Rameauite is also monoclinic (space group Cc), with a = 13.947 (3), b = 14.300 (3), c = 13.888 (3) Å, β = 118.50 (3)° and V = 2434.3 (11) Å3 (Z = 2). The twinning can be expressed as a mirror in (101) (apart from the inversion twin), which leads to a supercell with a = 14.223, b = 14.300, c = 23.921 Å and V = 2 × 2434 Å3, which is C centered. The new structure refinement of rameauite converged to R = 4.23% for 2344 unique observed reflections with I > 3σ(I) and GOF = 1.48. The current investigation documented how peculiar twinning can be, not only for this group of minerals, and how care must be taken in handling the data biased by twinning.

Iron phosphate materials have attracted a lot of attention due to their potential as cathode materials for lithium-ion rechargeable batteries. It has been shown that lithium insertion or extraction depends on the Fe mixed valence and reduction or oxidation of the Fe ions' valences. In this paper, we report a new synthesis method for the Fe

The crystal structure of the uranyl arsenate mineral hügelite is affected by twinning due to reticular merohedry (diffraction type II). This study documents, apart from the correct description of the unit cell and the nature of the twinning, the possibilities of the JANA2006 program in revealing the real nature of twinning even if using published structural data without the original reflection files., Revisiting the structure of uranyl arsenate mineral hügelite provided some corrections to the available structural data. The previous twinning model (by reticular merohedry) in hügelite has been corrected. Twinning of the monoclinic unit cell [a = 7.0189 (7) Å, b = 17.1374 (10) Å, c = 8.1310 (10) Å and β = 108.904 (10)°], which can be expressed as a mirror in [100], leads to a pseudo-orthorhombic unit cell (a = 7.019 Å, b = 17.137 Å, c = 61.539 Å and β = 90.02°), which is eight times larger, with respect to the unit-cell volume, than a real cell. Moreover, the unit cell of chosen here and the unit cell given by the previous structure description both lead to the same supercell. A new structure refinement undertaken on an untwinned crystal of hügelite resulted in R = 4.82% for 12 864 reflections with I obs > 3σ(I) and GOF = 1.12. The hydrogen-bonding scheme has been proposed for hügelite for the first time.

The new ambient-temperature hexagonal (space group P63 /mmc) polymorph of tripotassium ytterbium(III) disilicate (β-K3YbSi2O7) has been synthesized by the high-temperature flux method and subsequently structurally characterized. In the course of the temperature-dependent single-crystal diffraction experiments, a phase transformation of β-K3YbSi2O7 to a novel low-temperature orthorhombic phase (β′-K3YbSi2O7, space group Cmcm) has been observed at about 210 K. β-K3YbSi2O7 is isostructural with K3ErSi2O7, whereas β′-K3YbSi2O7 adopts a new type of structure. Both compounds can be built up from a regular alternation of layers of two types, which are parallel to the (001) plane. In the octahedral layer, YbO6 octahedra are isolated and linked by K1O6+3 polyhedra. The second, slightly thicker sorosilicate layer is formed by a combination of Si2O7 dimers and K2O6+3 polyhedra. The boundary between the layers is a pseudo-kagome oxide sheet based on 3.6.3.6 meshes. The phase transition is due to a tilt of the two SiO4 tetrahedra forming a single dimer which induces a decrease of the Si—O—Si angle between bridging Si—O bonds from 180° (dictated by symmetry in space group P63/mmc) to ≃164°. Magnetic characterization indicates that K3YbSi2O7 remains paramagnetic down to 2 K, showing no apparent influence of the phase transformation on its magnetic properties. Analysis of the magnetization data revealed the positions of the three lowest crystal field levels of the Yb3+ cations, as well as the corresponding projections of their angular momentum on the direction of the magnetic field.

Here we report the synthesis and characterization of three quaternary complex chalcogenides, Ag0.72Bi5.48Cu0.88S9 (I), Ag0.70Bi5.30Cu1.3S9 (II), Ag0.34Bi4.54Cu1.98PbS9 (III). All the compounds in this homologous series crystallize in the C2/m space group and can be described as Pavonite structures. This structure type consists of alternating NaCl-like layers with varied thickness (nP), separated by a pair of square pyramids. All the compounds reported here are synthetic analogues of the n = 4 pavonite family and are known as makovickyite minerals. Compounds I–III possess complex crystal structures, consisting of mixed occupancies of Bi/Ag/Pb sites, as well as partially occupied Cu sites. These intrinsic assets lead to ultra-low lattice thermal conductivities, in the range of 0.75–0.42 Wm−1 K−1 from 300–500 K, and make these materials promising candidates for thermoelectric applications. All three structures exhibit very narrow indirect band gaps of less than 0.5 eV as confirmed by DRS measurements. Charge transport properties are consistent with n-type semiconducting behavior with moderate electrical conductivities and large Seebeck coefficients. Low temperature electrical resistivity and Seebeck coefficient measurements are also performed on II. A promising figure of merit, zT, of 0.09 for I and II, 0.11 for III can be achieved at 475 K.

Materials 15(22), 8059 (2022). doi:10.3390/ma15228059, Iron phosphate materials have attracted a lot of attention due to their potential as cathode materials for lithium-ion rechargeable batteries. It has been shown that lithium insertion or extraction depends on the Fe mixed valence and reduction or oxidation of the Fe ions’ valences. In this paper, we report a new synthesis method for the Fe$_3$(PO$_3$OH)$_4$(H$_2$O)$_4$ mixed valence iron phosphate. In addition, we perform temperature-dependent measurements of structural and physical properties in order to obtain an understanding of electronic–structural interplay in this compound. Scanning electron microscope images show needle-like single crystals of 50 μm to 200 μm length which are stable up to approximately 200 °C, as revealed by thermogravimetric analysis. The crystal structure of Fe$_3$(PO$_3$OH)$_4$(H$_2$O)$_4$ single crystals has been determined in the temperature range of 90 K to 470 K. A monoclinic isostructural phase transition was found at ~213 K, with unit cell volume doubling in the low temperature phase. While the local environment of the Fe$^{2+}$ ions does not change significantly across the structural phase transition, small antiphase rotations occur for the Fe$^{3+}$ octahedra, implying some kind of electronic order. These results are corroborated by first principle calculations within density functional theory, which also point to ordering of the electronic degrees of freedom across the transition. The structural phase transition is confirmed by specific heat measurements. Moreover, hints of 3D antiferromagnetic ordering appear below ~11 K in the magnetic susceptibility measurements. Room temperature visible light absorption is consistent with the Fe$^{2+}$/Fe$^ {3+}$ mixed valence., Published by MDPI, Basel

Baumoite, Ba0.5[(UO2)3O8Mo2(OH)3](H2O)~3, is a new mineral found near Radium Hill, South Australia, where it occurs in a granite matrix associated with baryte, metatorbernite, phurcalite and kaolinite. Baumoite forms thin crusts of yellow to orange–yellow tabular to prismatic crystals. The mineral is translucent with a vitreous lustre and pale yellow streak. Crystals are brittle, the fracture is uneven and show one excellent cleavage. The Mohs hardness is ~2½. The calculated density is 4.61 g/cm3. Optically, baumoite crystals are biaxial (–), with α = 1.716(4), β = 1.761(4), γ = 1.767(4) (white light); and 2Vcalc= 42.2°. Electron microprobe analyses gave the empirical formula Ba0.87Ca0.03Al0.04U2.97Mo2.02P0.03O22H11.99, based on 22 O atoms per formula unit. The eight strongest lines in the powder X-ray diffraction pattern are [dobsÅ (I) (hkl)]: 9.175(39)(12${\bar 1}$), 7.450(100)(020), 3.554(20)(221), 3.365(31)(004, 202), 3.255(31)(123, 30${\bar 2}$), 3.209(28)(12${\bar 4}$), 3.067(33)(30${\bar 3}$, 222, 32${\bar 2}$) and 2.977(20)(142). Single-crystal X-ray studies (R1= 5.85% for 1892 main reflections) indicate that baumoite is monoclinic, superspace groupX2/m(a0g)0swithX= (0,½,0,½), with unit-cell parameters:a= 9.8337(3),b= 15.0436(5),c= 14.2055(6) Å, β = 108.978(3)°,V= 1987.25(13) Å3andZ= 4. The crystal structure is twinned and incommensurately modulated and is based upon sheets of U6+and Mo6+polyhedra of unique topology. Four independent cationic sites partially occupied by Ba atoms are located between the sheets, together with H2O molecules.

19 pags., 8 figs., 5 tabs. -- Open Access funded by Creative Commons Atribution Licence 3.0, The full crystal structure of the copper-uranyl tetrahydroxide mineral (vandenbrandeite), including the positions of the hydrogen atoms, is established by the first time from X-ray diffraction data taken from a natural crystal sample from the Musonoi Mine, Katanga Province, Democratic Republic of Congo. The structure is verified using first-principles solid-state methods. From the optimized structure, the mechanical and dynamical stability of vandenbrandeite is studied and a rich set of mechanical properties are determined. The Raman spectrum is recorded from the natural sample and determined theoretically. Since both spectra have a high-degree of consistence, all spectral bands are rigorously assigned using a theoretical normal-coordinate analysis. Two bands in the Raman spectra, located at 2327 and 1604 cm, are recognized as overtones and a band at 1554 cm is identified as a combination band. The fundamental thermodynamic functions of vandenbrandeite are computed as a function of temperature using phonon calculations. These properties, unknown so far, are key-parameters for the performance-assessment of geological repositories for storage of radioactive nuclear waste and for understanding the paragenetic sequence of minerals arising from the corrosion of uranium deposits. The thermodynamic functions are used here to determine the thermodynamic properties of formation of vandenbrandeite in terms of the elements and the Gibbs free-energies and reaction constants for a series of reactions involving vandenbrandeite and a representative subset of the most important secondary phases of spent nuclear fuel. Finally, from the thermodynamic data of these reactions, the relative stability of vandenbrandeite with respect to these phases as a function of temperature and in the presence of hydrogen peroxide is evaluated. Vandenbrandeite is shown to be highly stable under the simultaneous presence of water and hydrogen peroxide., The supercomputer time provided by the CTI-CSIC center is greatly acknowledged. This work has been carried out in the context of a CSIC-CIEMAT collaboration agreement: “Caracterizaci´on experimental y te´orica de fases secundarias y ´oxidos de uranio formados en condiciones de almacenamiento de combustible nuclear”. JP acknowledges the support through the project no. LO1603 of the Ministry of Education, Youth and Sports National Sustainability Program I of the Czech Republic. JS and JC were supported by the Ministry of Culture of the Czech Republic (long-term project DKRVO 2019-2023/1.II.a and 1.II.b; National Museum, 00023272). VT was supported by the Ministry of Science, Innovation and Universities within the Project FIS2016-77726-C3-1-P. VP thanks the support from the Czech Science Foundation (project 18-10504S).

We provide an exhaustive characterization of structural properties and nuclear dynamics in tungstic acid (WO3·H2O). To this end, we employ neutron and X-ray diffraction (ND and XRD) combined with inelastic neutron scattering (INS) and neutron Compton scattering (NCS) experiments, and we corroborate the analysis with extensive ab initio modeling. The first step in our analysis is the elucidation of the crystal structure based on the refinement of low-temperature powder ND data, extending the knowledge gained from XRD analysis of a mineral specimen of tungstite. These results are confronted with low-temperature INS experiments and zero-temperature phonon calculations. The analysis reveals an inconsistency in the definition of the structure of confined water with respect to crystallographic data, also showing a concomitant failure of the phonon calculations due to a strongly anharmonic confining potential. Extending the computational route toward ab initio MD (AIMD) simulations allows us to probe different structural configurations and provides an improved description of the vibrational dynamics as compared to high-resolution INS experiments, nevertheless, requiring the use of effective classical temperatures. The analysis of both INS and the NCS data reveals a remarkable similarity to the nuclear dynamics earlier reported for water confined in single-wall carbon nanotubes (SWNT), which has been qualitatively described as a new phase of ice. Our analysis reveals a strong two-dimensional hydrogen-bonding network, similar to the shell model for water in SWNT. The reported NCS data show narrowing of the hydrogen momentum distribution with respect to the reference ab initio calculations, indicating a great deal of conformational freedom due to spatial delocalization of protons in the ground state of the system, a clear signature of the quantum character of the nuclei., The authors gratefully acknowledge the financial support from the U.K. Science and Technologies Facilities Council (STFC), granting the beamtime on WISH, TOSCA, and VESUVIO. The authors also acknowledge the computing resources provided by the STFC Scientific Computing Department’s SCARF cluster. K.D. gratefully acknowledges financial support from the Gipuzkoako Foru Aldundia under Grant Number 2020-CIEN-000009-01. This work has been gratefully supported by PL-Grid Infrastructure and the PROMETHEUS facility.

The experimental electron-density distribution in two isostructural complexes, tetra­kis(μ2-acetato)di­aquadicopper(II) [H2OCu(ac)2Cu(ac)2H2O] and tetra­kis(μ2-acetato)di­aquadichromium(II) [H2OCr(ac)2Cr(ac)2H2O], has been studied and compared., The experimental electron density distribution in two isostructural and isomorphous complexes, tetra­kis(μ2-acetato)di­aquadicopper(II) [H2OCu(ac)2Cu(ac)2H2O] (I) and tetra­kis(μ2-acetato)diaquadichromium(II), [H2OCr(ac)2Cr(ac)2H2O] (II), has been obtained from high-resolution X-ray diffraction data in order to shed light on the bonding properties in the compounds studied. It has been shown that from accurate X-ray data it is possible to discuss the bonding capability of the metal atom (Cu/Cr) and the ligands in these complexes. A comparison of results obtained from averaged and non-averaged X-ray data demonstrates that using the non-averaged data and introducing an anisotropic correction for secondary extinction errors provides a more detailed distribution of the electron density in the area of the metal atoms. In both complexes studied, the bonding of the acetate oxygen atom to the central metal atom is significantly affected by the formation of hydrogen bonds. The electron density and its Laplacian at the bond critical point of metal–oxygen coordination bonds for those oxygen atoms not involved in the intermolecular hydrogen bonds are approximately 10% larger compared with the case when oxygen atoms take part in hydrogen bonds with the neighboring water molecules. It is shown that metal–oxygen bonds in a quasi-equatorial plane are typical coordination bonds and differ significantly from the apical metal–oxygen bond. Metal–metal inter­action with a small positive value of the electron density Laplacian at this bond critical point is mainly of electrostatic character. The metal–metal inter­action is definitely not a bond according to the classical definition. Based on a search of the Cambridge Structural Database, it can be argued that there are four typical coordination bonds in the [CuO6] chromophore, similar to the four Cu—O coordination bonds in the basal plane of the CuO5 pyramid in one of the complexes under study.

We describe here the case of twinning by reticular (pseudo)merohedry in case of natural zippeite crystal from Cap Garonne, France. The twin is by two-fold rotation in [100] and it is a first document of this type of twinning in zippeite-related minerals and compounds. Zippeite crystals from Cap Garonne mine, France, were studied by single-crystal X-ray diffraction [a=8.7243(4), b=13.9337(7), c=8.8741(4) Å, β=104.243(5) and V=1045.59(9) Å3, Z=2, in C2/m]; refinement taking into account of the twinning resulted in R=2.81% for 1596 reflections with [I>3σ(I)] and refined twin fraction 0.7773(9):0.2227(9).

The uranyl mineral swamboite has been redefined to swamboite-(Nd) and its structure has been solved and refined as a commensurate structure in six-dimensional superspace. The structure is monoclinic, superspace group P21 /m(a1,b1,g1)00(−a1,b1,g1)00 (a2,0,g2)0s, cell parameters a=6.6560(3), b=6.9881(5), c=8.8059(6), c=11.3361(16) Å, β=102.591(5)°, modulation wave-vectors q 1 =1/3 1/3 0; q 2 =−1/3 1/3 0; q 3 =1/2 0 1/2. The structure was refined from 8717 reflections to a final R=0.0610. The model includes modulation both of atomic positions and displacement parameters, as well as occupancy waves. The structure is based upon uranyl-silicate sheets of uranophane topology alternating with an interlayer of partly occupied Nd3+ sites and H2O molecules. The strong (3+3) dimensional modulation of the structure originates from the distribution of the Nd-dominated sites and further accommodation of the suitable geometry within the sheets and charge distribution within the structure. The separation distances between the corresponding occupied Nd sites are rationals of the super-cell vectors corresponding to the modulation vectors of the structure. The case of swamboite-(Nd) is the first example of a modulated structure within the oxysalts of U6+.

Parabutlerite, orthorhombic FeIIISO4(OH)·2H2O, has been reinvestigated using single-crystal X-ray diffraction. The structure of parabutlerite is commensurately modulated, witha= 20.0789 (8),b= 7.4024 (7),c= 7.2294 (15) Å andq= 0.4b*. The superstructure has been determined, using a superspace approach, as having the superspace groupPnma(0β0)s0sandt0= 1/20, and refined toR= 0.0295 for 2392 main reflections withI> 3σ(I). The structure consists of infinite chains of Fe octahedra that are linkedviavertices (OH groups); these chains are encased from both sides by SO4tetrahedra. The displacive modulation of atoms in parabutlerite is connected with a tilt of the chains around thebaxis towards the adjacent chains due to the accommodation of an energetically more favorable hydrogen-bond geometry.

Morpholinium tetrafluoroborate, [C4H10NO]+[BF4]−, belongs to a class of ferroelectric compounds ABX 4. However, [C4H10NO]+[BF4]− does not develop ferroelectric properties because the incommensurate phase below T c,I = 153 K is centrosymmetric with superspace group Pnam(σ100)00s and σ1 = 0.42193 (12) at T = 130 K; the threefold superstructure below T c,II = 117–118 K possesses the acentric but non-ferroelectric space group P212121. At ambient conditions, [C4H10NO]+[BF4]− comprises orientationally disordered [BF4]− anions accommodated in cavities between four morpholinium cations. A structure model for the incommensurately modulated phase, which involves modulated orientational ordering of [BF4]− together with modulated distortions and displacements of the morpholinium ions is reported. A mechanism is proposed for the phase transitions, whereby at low temperatures morpholinium cations are shaped around the tetrafluoroborate anion in order to optimize the interactions with one orientation of this anion and, thus, forcing [BF4]− into this orientation. This mechanism is essentially different from a pure order–disorder phase transition. It is supported by consideration of the transition entropy. The difference in configurational entropy between the disordered and incommensurate phases has been computed from the structure models. It is shown to be much smaller than the experimental transition entropy reported by Owczarek et al. [Chem. Phys. (2011), 381, 11–20]. These features show that the order–disorder contribution is only a minor contribution to the transition entropy and that other factors, such as conformational changes, play a larger role in the phase transitions.

The ambient temperature structure of Cu4SnS4 has been revisited and the recently reported low temperature structure has been confirmed from single-crystal X-ray diffraction data. A structural phase transition from a large monoclinic unit cell at low temperature to a smaller orthorhombic unit cell at high temperature has been observed. The room temperature phase exhibited disorder in the two copper sites, which is a different finding from earlier reports. The low temperature monoclinic form crystallizes in P21/c space group, which is isostructural with Cu4GeS4. The phase transition has also been studied with variable temperature powder X-ray diffraction and 119Sn Mossbauer spectroscopy. The Seebeck coefficients and electrical resistivity of polycrystalline Cu4SnS4 are reported from 16 to 400 K on hot pressed pellets. Thermal conductivity measurements at high temperatures, 350 – 750 K exhibited very low thermal conductivities in the range 0.28 – 0.35 W K–1 m–1. In all the transport measurements the phase transition has been observed at around 232 K. Resistivity decreases, while Seebeck coefficient increases after the phase transition during warming up from low to high temperatures. This change in resistivity has been correlated with the results of first-principles electronic band structure calculations using highly-accurate screened-exchange local density approximation. It was found that both the low hole effective mass of 0.63 me for the Γ→Y crystallographic direction and small band gap, 0.49 eV, are likely to contribute to the observed higher conductivity of the orthorhombic phase. Cu4SnS4 is also electrochemically active and shows reversible reaction with lithium between 1.7 and 3.5 volts.

Kamotoite-(Y) is a rare supergene product of uraninite hydration–oxidation weathering and its structure is unknown. Based on single-crystal X-ray diffraction data collected with high-redundancy using a microfocus source, kamotoite-(Y) is monoclinic, has space group P21/n,with a = 12.3525(5), b = 12.9432(5), c = 19.4409(7) Å, β = 99.857(3)°, V = 3069.8(2) Å3 and Z = 4. Crystals are pervasively twinned (two-fold rotation around [0.75 0 0.75]), giving a strongly pseudo-orthorhombic diffractionpattern. The pseudoorthorhombic pattern can be described with an orthorhombic super-cell (transformation matrix 0,1,0/1,0,1/3,0,1), approximately four times larger in volume then a true monoclinic unit cell. This unit-cell is the same as the cell given elsewhere for the structure of bijvoetite-(Y),another (REE)-containing uranyl carbonate. The successful structure solution and refinement (R = 0.044 for 6294 unique observed reflections), carried out using our choice of unit cell, as well as the superstructure refinement and comparison of the original structure data forbijvoetite-(Y) reveal that these two crystal structures are identical. The crystal structure of kamotoite-(Y) consists of electroneutral sheets of the bijvoetite-(Y) uranylanion topology and an interlayer with H2O molecules not-coordinated directly to any metal cation. Despite determinationof the kamotoite-(Y) structure and demonstration that bijvoetite-(Y) has the same structure, the identity of these two minerals cannot be proved without additional study of the holotype material.

Strain engineering via epitaxial thin-film synthesis is an efficient way to modify the crystal structure of a material in order to induce new features or improve existing properties. One of the challenges in this approach is to quantify structural changes occurring in these films. While X-ray diffraction is the most widely used technique for obtaining accurate structural information from bulk materials, severe limitations appear in the case of epitaxial thin films. This past decade, precession electron diffraction tomography has emerged as a relevant technique for the structural characterization of nano-sized materials. While its usefulness has already been demonstrated for solving the unknown structure of materials deposited in the form of thin films, the frequent existence of orientation variants within the film introduces a severe bias in the structure refinement, even when using the dynamical diffraction theory to calculate diffracted intensities. This is illustrated here using CaTiO3films deposited on SrTiO3substrates as a case study. By taking into account twinning in the structural analysis, it is shown that the structure of the CaTiO3films can be refined with an accuracy comparable to that obtained by dynamical refinement from non-twinned data. The introduction of the possibility to handle twin data sets is undoubtedly a valuable add-on and, notably, paves the way for a successful use of precession electron diffraction tomography for accurate structural analyses of thin films.

We report on x-ray magnetic circular dichroism experiments in pulsed fields up to 30 T to follow the rotations of individual magnetic moments through the field-induced phase transition in the ferrimagnet ${\mathrm{HoFe}}_{5}{\mathrm{Al}}_{7}$. Near the ground state, we observe simultaneous stepwise rotations of the Ho and Fe moments and explain them using a two-sublattice model for an anisotropic ferrimagnet with weak intersublattice exchange interactions. Near the compensation point, we find two phase transitions. The additional magnetization jump reflects the fact that the Ho moment is no longer rigid as the applied field acts against the intersublattice exchange field.

The high-pressure silicate K1.5Mg2Si2O7H0.5, synthesized and characterized by Welchet al.[(2012),Am. Mineral.97, 1849–1857], has been re-examined with the aim of determining the nature of the superstructure noted in their study. The composition corresponds to a 1:1 combination of KMg2Si2O7H and K2Mg2Si2O7end-members, but it is not a solid solution. Single-crystal X-ray diffraction data for one of the original K1.5Mg2Si2O7H0.5crystals synthesized at 16 GPa/1573 K, has been collected using a much longer exposure time in order to improve the intensity statistics of weak superlattice reflections identified by Welchet al.(2012). The superstructure has been determined using a superspace approach as having the superspace groupCmcm(0,β,0)00sandt0= 1/16 with refined parametersa= 8.7623 (10),b= 5.0703 (7),c= 13.2505 (11) Å,V= 588.69 (12) Å3. This structure corresponds to one with the conventional space groupPbnmand unit-cell parametersa= 8.7623 (10),b= 20.281 (3),c= 13.2505 (11) Å,V= 2354.7 (5) Å3and is based upon a super-sheet motif in which ordering involves rows of pairs of vacant interlayer K sites. This is the third topologically distinct structure type for the KMg2Si2O7H−K2Mg2Si2O7join and suggests that there is very limited solid solution, and so it can be expected that each of the three structures (P63cm, P\bar 3 1m andPbnm) has its own stability field, rather than being part of a continuous compositional series based upon a single structure type. As such, K1.5Mg2Si2O7H0.5should be considered as a potentially significant host of K in the Earth's mantle.

We devised and synthesized a series of electron-rich compounds featuring diphenylamine, carbazole or dibenzo[c,g]carbazole connected via phenylacetylene linkers to an aromatic central unit. The key synthetic step was a high yielding cross coupling reaction between halogenated (bi)naphthalene and organometallic reagents prepared in situ from terminal alkynes (side-arms). By masking one of the iodo functions with a diethyltriazenyl group in the side-arm precursors, we efficiently circumvented the formation of doubly aminated by-products. Although one step longer, this approach led to higher yields of terminal alkynes than the direct coupling route. Spectroscopic and electrochemical measurements supported by computational evidence revealed that conjugation in the 1,4-disubstituted naphthalene backbone is superior to the 1,5 or 2,6 substituted cores. The diphenylamine derivative gets oxidized more readily when compared to its carbazole analogs. Expanding the core to binaphthalene did not alter electronic properties, but influenced the physical characteristics significantly.

Twinning is a phenomenon complicating structure analysis of single crystals of standard as well as modulated structures. Jana2006 as a software for advanced structure analysis contains tools for recognition and refinement of twins including most complicated cases of modulated and magnetic structures. In order to efficiently use the tools of Jana2006 related to twinning, we explain the basic terminology and the underlying theory, especially the symmetry of the diffraction patterns affected by twinning. We present typical diffraction patterns of twins and show how twinning can be recognized or detected by various tools and described with twinning matrices. Data processing of twins and ways of how they can be imported to Jana2006 are also discussed. Two examples demonstrate the solution of typical twins: twinning by metric merohedry and twinning by reticular merohedry, followed by the third example demonstrating twinning in a commensurately modulated structure. The relationship between the dimensionality of the structure and twinning is discussed, too.

Four amino acids with linear, hydrophobic side chains display an unprecedented series of solid-state phase transitions between 100 and 470 K. These involve hydrogen-bond rearrangements, sliding of molecular bilayers in one or two dimensions and development of side-chain disorder. The first modulated structures of amino acids are reported., The solid-state phase transitions and intermediate structures of S-2-amino­butanoic acid (l-2-aminobutyric acid), S-2-aminopentanoic acid (l-norvaline), S-2-aminohexanoic acid (l-norleucine) and l-methionine between 100 and 470 K, identified by differential scanning calorimetry, have been characterized in a comprehensive single-crystal X-ray diffraction investigation. Unlike other enantiomeric amino acids investigated until now, this group featuring linear side chains displays up to five distinct phases. The multiple transitions between them involve a number of different processes: alteration of the hydrogen-bond pattern, to our knowledge the first example of this observed for an amino acid, sliding of molecular bilayers, seen previously only for racemates and quasiracemates, concerted side-chain rearrangements and abrupt as well as gradual modifications of the side-chain disorder. Ordering of l-norleucine upon cooling even proceeds via an incommensurately modulated structure. l-Methionine has previously been described as being fully ordered at room temperature. An accurate refinement now reveals extensive disorder for both molecules in the asymmetric unit, while two previously unknown phases occur above room temperature.

The incommensurate modulated crystal structure of Bi2.27Sr1.73CuO6 + δ(2201) phase [a= 5.3874 (5),b= 5.3869 (4),c= 24.579 (3) Å; β = 90.01 (1)°,q= 0.2105 (3)a* + 0.538 (4)c*,Z= 4, the (3 + 1)-dimensional monoclinicA2/a(α0γ) group] has been refined withR= 0.041,wR= 0.052 from X-ray single-crystal data including up to third-order satellite reflections. The same structure has also been considered as incommensurate composite witha2= 2.437,b2= 5.387,c2= 24.614, β2= 93.06,q2= 0.4524a2*−0.243c2*and the (3 + 1)-dimensionalA2/m(α0γ)0sgroup for the second component. Both approaches give quite similar results. The structure possesses oxygen disorder in the oxygen-rich region of the BiO layer. An extra O atom is determined in the bridging position shifted ∼ 0.6 Å from BiO towards the SrO layer. Its presence is the cause of the tremendous increase of the bismuthU11atomic displacement parameter in ∼ 20% of the unit cells (t= −0.05–0.15). Vacancies are determined in the oxygen site of the SrO layer, which may result in the oxygen content variation with annealing at different oxygen pressures. The total refined oxygen content 6.18 (1) corresponds to the results of chemical analysis.

Discontinuous modulation functions called crenel and saw-tooth have been developed for description and refinement of strongly modulated crystal structures with abrupt changes of modulation parameters. Although used for refinement of many modulated structures and mentioned in books on aperiodic crystals, technical details of such refinements have never been published and remained hidden in the source code of the refinement program Jana2006. In this article we explain how to recognize discontinuous modulations in a Fourier map and how to refine structures where crenel or saw-tooth functions are combined with additional secondary modulation. Three sets of functions suitable for such combination are presented: the traditional ortho-harmonics, and newly developed sets of Legendre polynomials and x-harmonics. Tiny differences between refinements based on particular function sets are demonstrated using simulated as well as existing modulated structures.

Spin ices are exotic phases of matter characterized by frustrated spins obeying local ice rules, in analogy with the electric dipoles in water ice. In two dimensions, one can similarly define ice rules for in-plane Ising-like spins arranged on a kagome lattice. These ice rules require each triangle plaquette to have a single monopole, and can lead to various unique orders and excitations. Using experimental and theoretical approaches including magnetometry, thermodynamic measurements, neutron scattering and Monte Carlo simulations, we establish HoAgGe as a crystalline (i.e. non-artificial) system that realizes the kagome spin ice state. The system features a variety of partially and fully ordered states and a sequence of field-induced phases at low temperatures, all consistent with the kagome ice rule., 4 figures and 2 tables, with the figures slightly different from the formal online version

Due to the long-range oscillatory character of RKKY exchange interactions, for ${\mathrm{Dy}}_{2}{\mathrm{Co}}_{3}{\mathrm{Al}}_{9}$ there exist positive and negative couplings between the Dy magnetic moments that lead to magnetic frustration. As a result, the ground state can be easily perturbed, and the system displays a number of spontaneous and field-induced phase transitions. We performed magnetization, magnetic-susceptibility, specific-heat, and electrical-resistivity measurements as well as neutron-diffraction experiments on a single crystal. We find two transitions to distinct incommensurate antiferromagnetic phases at 6.2 and 5.2 K that evolve to a commensurate phase at 3.7 K. In applied magnetic field, new phases emerge. Field-dependent magnetization exhibits a multistep metamagnetic process with sharp transitions accompanied by pronounced magnetoresistance changes. The large number of phases and their complex magnetic structures suggest that the physical properties of ${\mathrm{Dy}}_{2}{\mathrm{Co}}_{3}{\mathrm{Al}}_{9}$ are ruled by exchange frustration in the presence of a large magnetocrystalline anisotropy.

The crystal structure of caesium neodymium(III) sulfate, CsNd(SO4)2, was determined from intensity data collected on a Rigaku tabletop XtaLAB mini II diffractometer at the International Union of Crystallography Congress 2017, in Hyderabad, India. CsNd(SO4)2is the fourth crystal structure to be reported in the CsPr(SO4)2family: the Cs and Nd atoms have site symmetries of 2.. and ..2, respectively. In the extended structure, NdO8square antiprisms and SO4tetrahedra are connected into layers, which propagate in the (101) plane and CsO14polyhedra connect the layers into a three-dimensional network.

In the hexagonal crystal structure of ${\mathrm{Pr}}_{3}{\mathrm{Ru}}_{4}{\mathrm{Al}}_{12}$, the Pr atoms form a distorted kagome lattice, and their magnetic moments, are subject to competing exchange and anisotropy interactions. We performed magnetization, magnetic-susceptibility, specific-heat, electrical-resistivity, and neutron-scattering measurements. ${\mathrm{Pr}}_{3}{\mathrm{Ru}}_{4}{\mathrm{Al}}_{12}$ is a uniaxial ferromagnet with ${T}_{\text{C}}=39$ K that displays a collinear magnetic structure (in the high-temperature range of the magnetically ordered state) for which the only crystallographic position of Pr is split into two sites carrying different magnetic moments. A spin-reorientation phase transition is found at 7 K. Below this temperature, part of the Pr moments rotate towards the basal plane, resulting in a noncollinear magnetic state with a lower magnetic symmetry. We argue that unequal RKKY exchange interactions competing with the crystal electric field lead to a moment instability and qualitatively explain the observed magnetic phases in ${\mathrm{Pr}}_{3}{\mathrm{Ru}}_{4}{\mathrm{Al}}_{12}$.

Homogeneous and inclusion-free single crystals of 2:1 mullite (Al4.8Si1.2O9.6) grown by the Czochralski technique were examined by X-ray and neutron diffraction methods. The observed diffuse scattering together with the pattern of satellite reflections confirm previously published data and are thus inherent features of the mullite structure. The ideal composition was closely met as confirmed by microprobe analysis (Al4.82 (3)Si1.18 (1)O9.59 (5)) and by average structure refinements. 8 (5) to 20 (13)% of the available Si was found in theT* position of the tetrahedra triclusters. The strong tendencey for disorder in mullite may be understood from considerations of hypothetical superstructures which would have to ben-fivefold with respect to the three-dimensional average unit cell of 2:1 mullite andn-fourfold in case of 3:2 mullite. In any of these the possible arrangements of the vacancies and of the tetrahedral units would inevitably be unfavorable. Three directions of incommensurate modulations were determined:q1= [0.3137 (2) 0 ½],q2= [0 0.4021 (5) 0.1834 (2)] andq3= [0 0.4009 (5) −0.1834 (2)]. The one-dimensional incommensurately modulated crystal structure associated withq1was refined for the first time using the superspace approach. The modulation is dominated by harmonic occupational modulations of the atoms in the di- and the triclusters of the tetrahedral units in mullite. The modulation amplitudes are small and the harmonic character implies that the modulated structure still represents an average structure in the overall disordered arrangement of the vacancies and of the tetrahedral structural units. In other words, when projecting the local assemblies at the scale of a few tens of average mullite cells into cells determined by either one of the modulation vectorsq1,q2orq3a weak average modulation results with slightly varying average occupation factors for the tetrahedral units. As a result, the real structure of mullite is locally ordered (as previously known), but on the long-range its average is not completely disordered, the modulated structure of mullite may be denoted the true `average structure of mullite'.

Accurate structure refinement from electron-diffraction data is not possible without taking the dynamical-diffraction effects into account. A complete three-dimensional model of the structure can be obtained only from a sufficiently complete three-dimensional data set. In this work a method is presented for crystal structure refinement from the data obtained by electron diffraction tomography, possibly combined with precession electron diffraction. The principle of the method is identical to that used in X-ray crystallography: data are collected in a series of small tilt steps around a rotation axis, then intensities are integrated and the structure is optimized by least-squares refinement against the integrated intensities. In the dynamical theory of diffraction, the reflection intensities exhibit a complicated relationship to the orientation and thickness of the crystal as well as to structure factors of other reflections. This complication requires the introduction of several special parameters in the procedure. The method was implemented in the freely available crystallographic computing systemJana2006.

Parabutlerite, orthorhombic Fe

The structure of meneghinite (CuPb13Sb7S24), from the Bottino mine in the Apuan Alps (Italy), has been solved and refined as an incommensurate structure in four-dimensional superspace. The structure is orthorhombic, superspace groupPnma(0β0)00s, cell parametersa =24.0549 (3),b =4.1291 (6),c =11.3361 (16) Å, modulation vectorq= 0.5433 (4)b*. The structure was refined from 6604 reflections to a finalR= 0.0479. The model includes modulation of both atomic positions and displacement parameters, as well as occupational waves. The driving forces stabilizing the modulated structure of meneghinite are linked to the occupation modulation of Cu and some of the Pb atoms. As a consequence of the Cu/[] and Pb/Sb modulations, three- to sevenfold coordinations of theMcations (Pb/Sb) occur in different parts of the structure. The almost bimodal distribution of the occupation of Cu/[] and Pb/Sb atM5 conforms with the coupled substitution Sb3++ [] → Pb2++ Cu+, thus corroborating the hypothesis deduced previously for the incorporation of copper in the meneghinite structure. The very small departure (∼0.54versus0.50) from the commensurate value of the modulation raises the question of whether other sulfosalts considered superstructures have been properly described, and, in this light, if incommensurate modulation in sulfosalts could be much more common than thought.

JANA2006 is a freely available program for structure determination of standard, modulated and magnetic samples based on X-ray or neutron single crystal/ powder diffraction or on electron diffraction. The system has been developed for 30 years from specialized tool for refinement of modulated structures to a universal program covering standard as well as advanced crystallography. The aim of this article is to describe the basic features of JANA2006 and explain its scope and philosophy. It will also serve as a basis for future publications detailing tools and methods of JANA.

In the ionic structure of the title compound, [Fe(C12H8N2)3](C9H5N4O2)2·H2O, the octahedral tris-chelate [Fe(phen)3]2+dications [Fe—N = 1.9647 (14)–1.9769 (14) Å; phen is 1,10-phenathroline] afford one-dimensional chains by a series of slipped π–π stacking interactions [centroid-to-centroid distances = 3.792 (3) and 3.939 (3) Å]. The 1,1,3,3-tetracyano-2-(2-hydroxyethyl)propenide anions, denoted tcnoetOH−, reveal an appreciable delocalization of π-electron density, involving the central propenide [C—C = 1.383 (3)–1.401 (2) Å] fragment and four nitrile groups, and this is also supported by density functional theory (DFT) calculations at the B97D/6-311+G(2d,2p) level. Primary noncovalent inter-moiety interactions comprise conventional O—H...O(N) and weak C—H...O(N) hydrogen bonding [O...O(N) = 2.833 (2)–3.289 (5) Å and C...O(N) = 3.132 (2)–3.439 (2) Å]. The double anion...π interaction involving a nitrile group of tcnoetOH−and twocis-positioned pyridine rings (`π-pocket') of [Fe(phen)3]2+[N...centroid = 3.212 (2) and 3.418 (2) Å] suggest the relevance of anion...π stackings for charge-diffuse polycyanoanions and commonM-chelate species.

The pavonites is a homologous series of sulfosalts with galena-like modules of variable size. A survey of their unit cells reveals that they are severely constrained by the metrics of an underlying common average sublattice. The unit cell of any compound of the series accommodates with high precision an integer number of approximately equal subcells. This explains a peculiar non-uniform variation of the unit cell parameters within the series and evidences that the interface between the galena-like modules, despite having a very different topology, approximately maintains the subperiodicity of the modules, and must therefore be subject to strong steric restrictions. It also implies that cations and anions occupy the nodes of the observed common underlying average sublattice according to a striking alternate cation/anion occupational modulation. This is the starting point for a description of these materials as modulated structures, which can make a proficient use of the approximate atomic positional non-crystallographic correlations caused by their modular character. Under this approach only four parameters suffice to define a realistic approximate model of any member of the series. A full structural characterization of any of the compounds only requires the determination of additional small/smooth modulations. As an example, the case of the P 7 pavonite Ag3Bi6.2Pb0.8S12, is analyzed.

The toolbox for computational protein crystallography is full of easy-to-use applications for the routine solution and refinement of periodic diffraction data sets and protein structures. There is a gap in the available software when it comes to aperiodic crystallographic data. Current protein crystallography software cannot handle modulated data, and small-molecule software for aperiodic crystallography cannot work with protein structures. To adapt software for modulated protein data requires training data to test and debug the changed software. Thus, a comprehensive training data set consisting of atomic positions with associated modulation functions and the modulated structure factors packaged as both a three-dimensional supercell and as a modulated structure in (3+1)D superspace has been created. The (3+1)D data were imported into Jana2006; this is the first time that this has been performed for protein data.

The structure of meneghinite (CuPb

This paper addresses the electronic properties of $\mathrm{N}{\mathrm{d}}_{3}\mathrm{R}{\mathrm{u}}_{4}\mathrm{A}{\mathrm{l}}_{12}$ (hexagonal crystal structure) with focus on its magnetic anisotropy that allows a comparison between single-ion and two-ion mechanisms when comparing to ${\mathrm{U}}_{3}\mathrm{R}{\mathrm{u}}_{4}\mathrm{A}{\mathrm{l}}_{12}$. We performed magnetization measurements on a single crystal in static and pulsed magnetic fields as well as neutron-diffraction experiments. $\mathrm{N}{\mathrm{d}}_{3}\mathrm{R}{\mathrm{u}}_{4}\mathrm{A}{\mathrm{l}}_{12}$ is a strongly anisotropic uniaxial ferromagnet with a Curie temperature of 39 K. The magnetic moments are aligned collinearly along the [001] axis. The magnetic structure of $\mathrm{N}{\mathrm{d}}_{3}\mathrm{R}{\mathrm{u}}_{4}\mathrm{A}{\mathrm{l}}_{12}$ has orthorhombic symmetry for which the crystallographic Nd site is split into two magnetically inequivalent positions, Nd1 and Nd2. The Nd1 and Nd2 atoms exhibit reduced magnetic moments, 0.95 and $2.66\phantom{\rule{0.28em}{0ex}}{\ensuremath{\mu}}_{\mathrm{B}}$, as compared to the free $\mathrm{N}{\mathrm{d}}^{3+}$-ion value ($3.28\phantom{\rule{0.28em}{0ex}}{\ensuremath{\mu}}_{\mathrm{B}}$). We discuss this finding in terms of crystal-field effects and competing exchange and anisotropy interactions. Since the single-ion mechanism in $\mathrm{N}{\mathrm{d}}_{3}\mathrm{R}{\mathrm{u}}_{4}\mathrm{A}{\mathrm{l}}_{12}$ leads to uniaxial anisotropy and the two-ion mechanism of the actinide analog ${\mathrm{U}}_{3}\mathrm{R}{\mathrm{u}}_{4}\mathrm{A}{\mathrm{l}}_{12}$ is known to lead to planar anisotropy, this paper demonstrates the decisive influence of these different mechanisms on the magnetic anisotropy.