Analysis of magnetic structures in JANA2020.

JANA2020 is a program developed for the solution and refinement of regular, twinned, modulated, and composite crystal structures. In addition, JANA2020 also includes a magnetic option for solving magnetic structures from powder and single-crystal neutron diffraction data. This tool uses magnetic space and superspace symmetry to describe commensurate and incommensurate magnetic structures. The basics of the underlying formulation of magnetic structure factors and the use of magnetic symmetry for handling modulated and non-modulated magnetic structures are presented here, together with the general features of the magnetic tool. Examples of structures solved in the magnetic option of JANA2020 are given to illustrate the operation and capabilities of the program.

Guidelines for communicating commensurate magnetic structures. A report of the International Union of Crystallography Commission on Magnetic Structures.

A report from the International Union of Crystallography Commission on Magnetic Structures outlining the recommendations for communicating commensurate magnetic structures.

Microscopic Nature of the First-Order Field-Induced Phase Transition in the Strongly Anisotropic Ferrimagnet HoFe_{5}Al_{7}.

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 HoFe_{5}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.

Vacancy pairing and superstructure in the high-pressure silicate K1.5Mg2Si2O7H0.5: a new potential host for potassium in the deep Earth.

The high-pressure silicate K1.5Mg2Si2O7H0.5, synthesized and characterized by Welch et 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 K2Mg2Si2O7 end-members, but it is not a solid solution. Single-crystal X-ray diffraction data for one of the original K1.5Mg2Si2O7H0.5 crystals 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 Welch et al. (2012). The superstructure has been determined using a superspace approach as having the superspace group Cmcm(0,ß,0)00s and t0 = 1/16 with refined parameters a = 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 group Pbnm and unit-cell parameters a = 8.7623 (10), b = 20.281 (3), c = 13.2505 (11) Å, V = 2354.7 (5) Å3 and 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-K2Mg2Si2O7 join 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 and Pbnm) has its own stability field, rather than being part of a continuous compositional series based upon a single structure type. As such, K1.5Mg2Si2O7H0.5 should be considered as a potentially significant host of K in the Earth's mantle.

Room-temperature tetragonal non-collinear Heusler antiferromagnet Pt2MnGa.

Antiferromagnetic spintronics is a rapidly growing field, which actively introduces new principles of magnetic storage. Despite that, most applications have been suggested for collinear antiferromagnets. In this study, we consider an alternative mechanism based on long-range helical order, which allows for direct manipulation of the helicity vector. As the helicity of long-range homogeneous spirals is typically fixed by the Dzyaloshinskii-Moriya interactions, bi-stable spirals (left- and right-handed) are rare. Here, we report a non-collinear room-temperature antiferromagnet in the tetragonal Heusler group. Neutron diffraction reveals a long-period helix propagating along its tetragonal axis. Ab-initio analysis suggests its pure exchange origin and explains its helical character resulting from a large basal plane magnetocrystalline anisotropy. The actual energy barrier between the left- and right-handed spirals is relatively small and might be easily overcome by magnetic pulse, suggesting Pt2MnGa as a potential candidate for non-volatile magnetic memory.

(3 + 1)-dimensional crystal and antiferromagnetic structures in CeRuSn.

At 320 K, the crystal structure of CeRuSn is commensurate with the related CeCoAl-type of structure by the doubling of the c lattice parameter. However, with lowering the temperature it becomes incommensurate with x and z position parameters at all three elemental sites being modulated as one moves along the c-axis. The resulting crystal structure can be conveniently described within the superspace formalism in (3 + 1) dimensions. The modulation vector, after initially strong temperature dependence, approaches a value close to qnuc = (0 0 0.35). Below TN = 2.8 (1) K, CeRuSn orders antiferromagnetically with a propagation vector qmag = (0 0 0.175), i.e. with the magnetic unit cell doubled along the c-axis direction with respect to the incommensurate crystal structure. Ce moments appear to be nearly collinear, confined to the a-c plane, forming ferromagnetically coupled pairs. Their magnitudes are modulated between 0.11 and 0.95 µB as one moves along the c-axis.

Structure refinement and superspace description of the system Bi(2(n + 2))Mo(n)O(6(n + 1)) (n = 3, 4, 5 and 6).

The system Bi(2(n + 2))Mo(n)O(6(n + 1)) is described within the superspace formalism. Two superspace models are proposed for the different members of this family, depending on the parity of the parameter n. The superspace model for the odd members is constructed through the embedding of the cationic distribution of the member with n = 3, and the modification of a superspace model previously proposed for the compound Bi(2)MoO(6). However, this model cannot be applied to the even members of the family. Performing the appropriate transformations, a suitable superspace model for the even members is obtained. The atomic structure of the different compounds of the family have been refined through the Rietveld method combining synchrotron X-ray and neutron powder diffraction data.

Helical screw type magnetic structure of the multiferroic CaMn7O12 with low Cu-doping.

The modulated crystal structure and modulated magnetic ordering of the multiferroic CaCu(x)Mn(7-x)O(12) is studied by analysing neutron and synchrotron-radiation (SR) powder diffraction data with a model based on the magnetic superspace group R31'(00γ)ts. Both atomic position modulations and magnetic modulations are described with the modulation vector (0, 0, q). The magnetic ordering is a screw-type circular helix where the magnetic moments are perpendicular to the c direction. The temperature dependence of the modulation vector length and the ordered magnetic moments of Mn(3+) and Mn(4+) ions is given between T = 50 K and the Néel temperature T(N) is approximately equal to 90 K. The atomic position modulation length L(p) and the magnetic modulation length L(m) fulfil the relation L(m) = 2L(p) at all temperatures between 50 K and T(N).

Magnetic superspace groups and symmetry constraints in incommensurate magnetic phases.

Superspace symmetry has been for many years the standard approach for the analysis of non-magnetic modulated crystals because of its robust and efficient treatment of the structural constraints present in incommensurate phases. For incommensurate magnetic phases, this generalized symmetry formalism can play a similar role. In this context we review from a practical viewpoint the superspace formalism particularized to magnetic incommensurate phases. We analyse in detail the relation between the description using superspace symmetry and the representation method. Important general rules on the symmetry of magnetic incommensurate modulations with a single propagation vector are derived. The power and efficiency of the method is illustrated with various examples, including some multiferroic materials. We show that the concept of superspace symmetry provides a simple, efficient and systematic way to characterize the symmetry and rationalize the structural and physical properties of incommensurate magnetic materials. This is especially relevant when the properties of incommensurate multiferroics are investigated.

Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution.

Flash-freezing is a technique that is commonly used nowadays to collect diffraction data for X-ray structural analysis. It can affect both the crystal and molecular structure and the molecule's surface, as well as the internal cavities. X-ray structural data often serve as a template for the protein receptor in docking calculations. Thus, the size and shape of the binding site determines which small molecules could be found as potential ligands in silico, especially during high-throughput rigid docking. Data were analyzed for wild soybean lipoxygenase-3 (MW 97 kDa) at 293 and 93 K and compared with the results from studies of its molecular complexes with known inhibitors, structures published by others for a derivative of the same enzyme (98 K) or a topologically close isozyme lipoxygenase-1 (at ambient temperature and 100 K). Analysis of these data allows the following conclusions. (i) Very small changes in the relative orientation of the molecules in the crystal can cause major changes in the crystal reciprocal lattice. (ii) The volume of the internal cavities can ;shrink' by several percent upon freezing even when the unit-cell and the protein molecular volume show changes of only 1-2%. (iii) Using a receptor structure determined based on cryogenic data as a target for computational screening requires flexible docking to enable the expansion of the binding-site cavity and sampling of the alternative conformations of the crucial residues.

Five-dimensional structure refinement of natural melilite, (Ca(1.89)Sr(0.01)Na(0.08)K(0.02))(Mg(0.92)Al(0.08)-(Si(1.98)Al(0.02))O(7).

The structure of a crystal of natural melilite from San Venanzo, Umbria (Italy) of the general formula X(2)T1(T2)(2)O(7), where X = Ca(0.945)Sr(0.005)Na(0.04)K(0.01), T1 = Mg(0.92)Al(0.08) and T2 = Si(0.99)Al(0.01), has been solved and refined as an incommensurate structure in five-dimensional superspace. The structure is tetragonal, superspace group P(-)42(1)m:p4mg, cell parameters a = 7.860 (1), c = 5.024 (1) A, modulation vectors q(1) = 0.2815 (3)(a* + b*), q(2) = 0.2815 (3)(-a* + b*). The data collection was performed on a KumaCCD diffractometer. The structure was refined from 7606 reflections to final R = 0.0481. A special modification of the refinement program Jana2000 was necessary to take into account overlapping of satellite reflections m x n = +/-1, which could not be properly separated in the integration procedure. The final model includes modulations of the atomic positions as well as modulations of the thermal parameters. The latter are induced by strong differences in the neighbourhood of the actual modulated positions. The occupational modulation was neither significant for X nor for T1 sites and the sites were supposed to be occupied only by Ca and Mg, respectively. As a consequence of the Ca and O positional modulations six-, seven- and eightfold Ca coordination occur throughout the structure and the thermal ellipsoid changes its shape correspondingly. The positional modulation of the atoms causes variations in the interatomic distances which, however, do not affect bond-valence sums considerably, but induce flattening and rotation in T1 and T2 tetrahedra, respectively.

X-ray diffraction study of the phase transition of K2Mn2(BeF4)3: a new type of low-temperature structure for langbeinites.

The potassium manganese tetrafluoroberyllate langbeinite compound has been studied in the temperature range 100-300 K. Using DSC measurements, a phase transition has been detected at 213 K. The space group of the low-temperature phase was determined to be P112(1) using X-ray diffraction experiments and optical observations of the domain structure. The b axis is doubled with respect to the prototypic P2(1)3 cubic phase. Lattice parameters were determined by powder diffraction data [a = 10.0690 (8), b = 20.136 (2), c = 10.0329 (4) A, gamma = 90.01 (1) degrees ]. A precise analysis of the BeF(4) tetrahedra in the low-temperature phase shows that two independent tetrahedra rotate in opposite directions along the doubled crystallographic axis. A symmetry mode analysis of the monoclinic distortion is also reported. This is the first report of the existence of such a phase transition in K(2)Mn(2)(BeF(4))(3) and also of a new type of low-temperature structure for langbeinite compounds.

Superspace description of the structure of the composite crystal urea/n-octane at room temperature.

A structural model for the composite crystal urea/n-octane is proposed. Despite the lack of information from the largely disordered guest substructure, the final model is consistent with the collected diffraction pattern. The use of the superspace approach stresses the composite character of the inclusion compounds and makes easier a unified view of the whole urea/n-alkane family. In particular, a comparison between the octane and heptadecane derivatives shows a common pattern for the origin of the modulation of the guest chains based on the distribution of the NH(2) groups within each tunnel wall.

Average structure of the composite crystal urea/octanedioic acid at room temperature within the superspace formalism.

The average structure of the composite urea/octanedioic acid has been refined using the superspace formalism [superspace group H'3(1)21(00gamma)001;]. Modulation effects seem to be almost negligible. The guest substructure appears to be largely disordered and has been modelled using rigid units occupying 12 equiprobable different orientations inside the urea tunnels. Guest molecules are slightly tilted with respect to the tunnel axis favouring a stronger guest-guest intratunnel interaction.

Modulated structure of La2Co1.7 from neutron and X-ray diffraction data

An La(2)Co(1.7) crystal was investigated by single-crystal neutron and X-ray diffraction. The neutron measurement was performed with a Laue white-beam technique at 15 K and room temperature, using a large position-sensitive detector. The X-ray measurements were obtained at room temperature from a CCD detector. The average structure of La(2)Co(1.7) is hexagonal with cell parameters a = 4. 885 (1), c = 4.273 (2) A and space group P6(3)/mmc. The satellites are located at the vertices of small hexagons perpendicular to the c axis. The modulated crystal was indexed assuming a sixfold twinned 3 + 1 dimensional structure with q = (alpha, 0, gamma). The structure was solved in the pseudoorthorhombic cell, with a = 8.461 (1), b = 4. 885 (1), c = 4.273 (2) A, in the superspace group C2/m(alpha, 0, gamma). Owing to space requirements, the Co atoms cannot fit precisely into the octahedral sites of the La h.c.p. (hexagonal close packing). Instead, the Co atoms adopt a different periodicity, which is not commensurate with the periodicity of the La atoms. Two structure models have been refined in order to describe this behaviour, one using the sawtooth function for the positional modulation of cobalt and the other describing the structure as a composite system. The chemical composition calculated from the composite model is La(2)Co(1.8 (1)) with the estimated standard deviation arising from the variation of q for different samples. In both models lanthanum is incommensurately modulated, while the position of cobalt seems not to be affected by any relative periodic displacement.

Structures and phase transitions of the A7PSe6 (A = ag, Cu) argyrodite-type ionic conductors. III. alpha-Cu7PSe6

The crystal structure of the third polymorph of the Cu(7)PSe(6) argyrodite compound, alpha-Cu(7)PSe(6), heptacopper phosphorus hexaselenide, is determined by means of single-crystal diffraction from twinned crystals and X-ray powder diffraction, with the help of extensive NMR measurements. In the low-temperature form, i.e. below the last phase transition, alpha-Cu(7)PSe(6) crystallizes in orthorhombic symmetry, space group Pna2(1), with a = 14.3179 (4), b = 7.1112 (2), c = 10.1023 (3) A, V = 1028.590 (9) A(3) (deduced from powder data, T = 173 K) and Z = 4. Taking into account a twinning by reticular merohedry, the refinement of the alpha-Cu(7)PSe(6) structure leads to the residual factors R = 0.0466 and wR = 0.0486 for 127 parameters and 3714 observed, independent reflections (single-crystal data, T = 173 K). A full localization of the Cu(+)d(10) element is reached with one twofold-, one threefold- and five fourfold-coordinated Cu atoms. The observation of two phase transitions for Cu(7)PSe(6), to be compared with only one for Ag(7)PSe(6), is attributed to the d(10) element stability in a low coordination environment, copper being less prone to lower coordination sites than silver, especially at low temperature.

Ferroelastic structures of n-pentyl-, n- hexyl- and n-nonylammonium dihydrogenphosphate crystals.

This study reports the structure redeterminations of C(5)H(11)NH(3)(+).H(2)PO(4)(-) (n-pentylammonium dihydrogenphosphate, C5ADP), C(6)H(13)NH(3)(+).H(2)PO(4)(-) (n-hexylammonium dihydrogenphosphate, C6ADP) and C(9)H(19)NH(3)(+).H(2)PO(4)(-) (n-nonylammonium dihydrogenphosphate, C9ADP). The structures are monoclinic (P2(1)/n), belonging to the series of previously studied structures C2ADP-C8ADP and C10ADP. The structures exhibit reproducible ferroelastic switching. There are hydrogen bonds between the dihydrogenphosphates and the n-alkylammonium groups. Among them there are two hydrogen bonds with hydrogens which hop from the donor to the acceptor oxygens during the ferroelastic switching. C5ADP as well as C3ADP differ from the other members of the series by packing of the double layers of the dihydrogenphosphates. Moreover, the packing of n-alkylammonium molecules in all these structures depends on the parity of the number of atoms in the n-alkylammonium chains. All the samples contained two domains and their structures were refined as twins.

Silver niobium trioxide, AgNbO3

The present structure determination of silver niobium trioxide at 291 K was performed on a twinned single crystal with a predominant presence [about 93 (1)%] of one twin domain. The sample contained traces of V (about 1 atomic %). This study confirms that the room-temperature phase of AgNbO(3) is isostructural with the room-temperature phase of NaNbO(3), i.e. it is a tilted perovskite. Structural deviation in AgNbO(3) from centrosymmetry was not detected in this study and its structure was refined in Pbcm, though a previous study indicated ferroelectricity below 350 K, in contrast with NaNbO(3).

Structures and phase transitions of the A7PSe6 (A = Ag, Cu) argyrodite-type ionic conductors. II. Beta- and gamma-Cu7PSe6

The crystal structures of two of the three polymorphic forms of the Cu7PSe6 argyrodite compound are determined by means of single-crystal X-ray diffraction. In the high-temperature form, at 353 K, i.e. 33 K above the first phase transition, gamma-Cu7PSe6 crystallizes in cubic symmetry, space group F43m. The full-matrix least-squares refinement of the structure leads to the residual factors R = 0.0201 and wR = 0.0245 for 31 parameters and 300 observed independent reflections. In the intermediate form, at room temperature, beta-Cu7PSe6 crystallizes again in cubic symmetry, but with space group P2(1)3. Taking into account a merohedric twinning, the refinement of the beta-Cu7PSe6 structure leads to the residual factors R = 0.0297 and wR = 0.0317 for 70 parameters and 874 observed, independent reflections. The combination of a Gram-Charlier development of the Debye-Waller factor and a split model for copper cations reveals the possible diffusion paths of the d10 species in the gamma-Cu7PSe6 ionic conducting phase. The partial ordering of the Cu+ d10 element at the phase transition is found in concordance with the highest probability density sites of the high-temperature phase diffusion paths. A comparison between the two Cu7PSe6 and Ag7PSe6 analogues is carried out, stressing the different mobility of Cu+ and Ag+ and their relative stability in low-coordination chalcogenide environments.

A new structure type in the hexagonal perovskite family; structure determination of the modulated misfit compound Sr(9/8)TiS3

Sr(9/8)TiS3, strontium titanium sulfide, a new phase in the hexagonal perovskite-like Sr(x)TiS3 system, has been prepared and its structure solved from single-crystal X-ray data within the (3 + 1)-dimensional [(3 + 1)D] formalism. Sr(9/8)TiS3 crystallizes with trigonal symmetry [R3m(00gamma)0s superspace group], with the following lattice parameters: a(s) = 11.482 (3), c(s) = 2.9843 (8) A, q = 0.56247 (7)c* and Vs = 340.7 (3) A3. The structure was considered as commensurate [R3c three-dimensional (3D) space group], but refined within the (3 + 1)D formalism to a residual factor R = 2.79% for 64 parameters and 1084 independent reflections. Original crenel functions were used for the sulfur and strontium description. The structure is different from that of the hexagonal perovskite-like oxide counterparts. The main difference is related to the presence of a new type of polyhedron in the [MS3] transition metal chains, intermediate between the octahedra classically found in such chains and the trigonal prismatic sites encountered in the oxides.