Volume 229, Issue 5

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.

The atomic structure of the incommensurate Pd 5 B 1-z phase has been analysed in detail by selected area electron diffraction and neutron-powder diffraction. That structure is based on a close-packed cubic arrangement of Pd atoms with the B atoms occupying the octahedral sites in a long-range ordered fashion. The ordering pattern of B is an incommensurately modulated one with a modulation vector of a length which changes with the B content ( ~ PdB 0.18-0.19 ) to adapt the ordering pattern continuously to the actual composition. The structure can be conceived to be constituted from “isolated” BPd 6 units (also occurring in the previously reported Pd 6 B phase) and edge-sharing B 2 Pd 10 octahedra units, which occur in a ratio reflecting the actual B content. As predicted on the basis of elastic interactions between B atoms, nearest neighbour B-B pairs occur (the B 2 Pd 10 double octahedra units) in the structure of the Pd 5 B 1-z phase, whereas occurrence of second-nearest neighbour B-B pairs is avoided. For the ideal composition Pd 5 B the crystal structure of the Pd 5 B 1-z phase corresponds to that of monoclinic UCl 5 with U playing the role of B and Cl that of Pd.

Single crystals of the new guanidinium uranyl selenate, [CH 6 N 3 ] 2 [(UO 2 ) 2 (SeO 4 ) 3 ] (1), and methylammonium uranyl sulfate, [CH 3 NH 3 ] 2 [(UO 2 ) 2 (SO 4 ) 3 ] (2) have been prepared by isothermal evaporation from aqueous solutions under room-temperature conditions. The crystal structure of 1 has been solved by direct methods [monoclinic, P2, a = 9.9448(15), b = 9.727(2), c = 10.1508(15) Å, β = 90.213(12)°, V = 981.9(3) Å 3 , Z = 2] and refined to R 1 = 0.0696 (wR 2 = 0.1611) for 2511 reflections with |F 0 | ≥ 4σ F using least square techniques. The crystal structure of 2 has been solved by direct methods [triclinic, P1, a = 8.4784(6), b = 9.7873(8), c = 9.8121(7) Å, α = 90.170(2), β = 95.744(2), γ = 90.136(2)°, V = 810.12(10) Å3, Z = 1] and refined to R1 = 0.0146 (wR 2 = 0.0336) for 5378 reflections with |F 0 | ≥ 4σ F using least square techniques. The structures of 1 and 2 are based upon the [(UO 2 ) 2 (TO 4 ) 3 ] 2 - (T = Se, S) twodimensional uranyl layers formed by linkage of U pentagonal bipyramids and TO 4 tetrahedra via common O atoms. The layers consist of two types of 4-membered rings; this topology has previously been observed in the structures of several actinyl compounds that crystallize in tetragonal or orthorhombic space groups. Violation of the higher symmetry is caused by tiltings of the TO 4 tetrahedra, associated with displacement of bridging oxygen atoms from their ideal position induced by the formation of moderate hydrogen bonds with the organic cations.

The crystal structure of 9,9′-(1,3,4-oxadiazole- 2,5-diyldi(1,1′-biphenyl)-2′,4-diyl)bis[9H-carbazole] [Pna2 1 , Z = 4, a = 17.9874 (4) Å, b = 9.2989 (8) Å, c = 21.5822 (9) Å, R obs = 0.0395, 9239 F data, 496 parameters] features a pseudo-centre of inversion strictly valid only for isolated layers of the structure. It is an order-disorder (OD) structure made up of one kind of non-polar layers composed of (I) molecules connected to polar layer pairs. The major polytype is of a maximum degree of order. The magnitude of the intrinsic translation vectors of the glides and screws relating adjacent layers is a convenient quantification of the deviation from perfect centrosymmetry.

This work presents a method for solving the crystal structure of an organic thin-film prepared on an isotropic surface. Combining specular X-ray diffraction and grazing incidence X-ray diffraction, a full structure solution is exemplarily derived for crystals of the molecule ternaphthalene (NNN). The data are analysed following a classic approach, first, by indexing the Bragg peak pattern and, second, by solving the structure using the experimentally observed intensities. Direct space methods with a rigid-body refinement are applied. The result shows that the NNN crystallizes in a layered herringbone structure. The calculated peak intensities based on this structure are in excellent agreement with the experimentally observed intensities. Overall, following this approach, the crystal structure of the molecule NNN grown in a preferred orientation within thin-films could be unambigously solved providing a general pathway for future thin-film structure solutions.

The crystal and molecular structures of 1:1 cocrystals formed between sulfadimidine and each of three bipyridine-type molecules, namely 4,4′-bipyridine (1), 4- [(E)-2-(pyridin-4-yl)ethenyl]pyridine (2) and 4-[2-(pyridin- 4-yl)ethyl]pyridine (3), are described; 1 and 2 were characterised as acetone hemi-solvates. A common feature of the sulfadimidine molecules is the adoption of a shape approximating the letter L. Conformational variability of sulfadimidine as well as in the bipyridine-type molecules is highlighted. The common feature of the crystal packing is the formation of non-linear supramolecular chains sustained by amino- and amide-H…N(pyridyl) hydrogen bonds

The relationship between linear elasticity theory of solids and their equations of state (EoS) is reviewed, along with the commonly-used types of isothermal EoS, thermal expansion models, and P-V-T EoS. A new console program, EosFit7c, is presented. It performs EoS calculations and fitting for both volume and linear isothermal data, isobaric data and P-T data. Linear data is handled by cubing the quantities and treating them as volumes in all EoS formulations. Least-squares fitting of EoS to data incorporates the option to weight the fit with the measurement uncertainties in P, V and T simultaneously. The EosFit7c program is built with a new library of subroutines for EoS calculations and manipulation, written in Fortran. The library has been incorporated as a module, cfml_eos, in the publicly-available CrysFML library. The module handles Murnaghan, Tait, Birch-Murnaghan, Vinet, and Natural Strain EoS. For P-V-T calculations any of these isothermal EoS can be combined with a variety of published thermal expansion models, including a model of thermal pressure. The entire library has been revalidated against other software and against an ab-initio re-derivation of the EoS, which identified a number of small errors in published formulae for some EoS.