New software, OLEX2, has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-oriented and fully comprehensive graphical user interface for structure solution, refinement and report generation, as well as novel tools for structure analysis. OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.

OLEX2: a complete structure solution, refinement and analysis program

The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.

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SHELXT - Integrated space-group and crystal- structure determination

The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as the SIR and SHELX suites of programs. The program ORTEP for Windows provides a graphical user interface (GUI) for the classic ORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray-traced outputs. The programs WinGX and ORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.

/pdf/wingx-and-ortep-for-windows-an-update-2x46kgdygv.pdf

WinGX and ORTEP for Windows: an update

J. Appl. Cryst.の発刊に際して

SUPERFLIP is a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from X-ray and neutron diffraction data. Structure solution from powder diffraction data is supported by combining the charge-flipping algorithm with a histogram-matching procedure. SUPERFLIP is written in Fortran90 and is distributed as a source code and as precompiled binaries. It has been successfully compiled and tested on a variety of operating systems.

/pdf/superflip-a-computer-program-for-the-solution-of-crystal-4rhmh61d41.pdf

SUPERFLIP– a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions

In this paper, an extremely simple structure solution method termed charge flipping is presented. It works ab initio on high-resolution X-ray diffraction data in the manner of Fourier recycling. The real-space modification simply changes the sign of charge density below a threshold, while in reciprocal space the moduli Fobs are retained resulting in an Fobs map without weighting. The algorithm is tested using synthetic data for a wide range of structures, the solution statistics are analysed and the quality of reconstruction is checked. Finally, mathematical aspects of the algorithm are considered in detail, and these show that in this chaotic iteration process the solution is a limit cycle and not a fixed point.

Ab initio structure solution by charge flipping.

NEARLY all of the molecular crystals containing C60, formed at ambient pressure1,2 have inter-fullerene separations of the order of 10 A — the expected distance based on the molecular van der Waals radii. The sole exceptions are the room-temperature phases of AC60 (where A denotes K, Rb or Cs), which are formed by reversible solid-state transformation from high-temperature (>150 °C) phases3. These phases have lattice parameters about 9% shorter in one direction, and in addition RbC60 has magnetic properties suggestive of a one-dimensional metal4. We suggested in ref. 4 that this short distance may be due to covalent bonding between neighbouring C60 molecules. Here we provide direct evidence for such bonding from powder X-ray diffraction studies of RbC60 and KC60 . The linkage is through a [2+2] cycloaddition, which has been hypothesized to take place during photopolymerization of solid C60 (ref. 5), and which has also been proposed6 for RbC60. Such inter-fullerene linkages are calculated7,8 to be the preferred mode of dimerization of C60. The AC60 phases thus provide an example of a thermal phase transition driven by the reversible formation and breaking of covalent bonds.

Polymeric fullerene chains in RbC60 and KC60

X-ray diffraction studies show that the stable phase of the alkali fullerene RbC[sub 60] is orthorhombic ([ital o]-RbC[sub 60]) below 350 K. C[sub 60] molecules form chains along [bold a] with an unusually short spacing of 9.12 A and magnetic properties suggest that [ital o]-RbC[sub 60] is a quasi-1D metal with a transition to a spin density wave ground state at 50 K. The high temperature fcc phase of RbC[sub 60] may be stabilized below 300 K by quenching from 500 K; it is paramagnetic above 300 K and transforms into a nonmagnetic ground state beween 300 and 250 K.

Quasi-one-dimensional electronic structure in orthorhombic RbC60.

The original charge flipping algorithm [Oszlanyi & Sutő (2004). Acta Cryst. A60, 34–141] is an amazingly simple structure solution method which works ab initio on high-resolution X-ray diffraction data. In this paper, a new version of the algorithm is presented that complements the phase exploration in reciprocal space. Instead of prescribing observed moduli of all structure factors, weak reflections are treated separately. For these reflections, calculated moduli are accepted unchanged and calculated phases are shifted by a constant Δφ = π/2. This means that the observed data of weak reflections are not used in the iteration, except for the knowledge that they are indeed weak. The improvement is drastic, in some cases the success rate is increased by a factor of ten, in other cases a previously unsolvable structure becomes solvable by the modified algorithm.

Ab initio structure solution by charge flipping. II. Use of weak reflections

This paper summarizes the current state of charge flipping, a recently developed algorithm of ab initio structure determination. Its operation is based on the perturbation of large plateaus of low electron density but not directly on atomicity. Such a working principle radically differs from that of classical direct methods and offers complementary applications. The list of successful structure-solution cases includes periodic and aperiodic crystals using single-crystal and powder diffraction data measured with X-ray and neutron radiation. Apart from counting applications, the paper mainly deals with algorithmic issues: it describes and compares new variants of the iteration scheme, helps to identify and improve solutions, discusses the required data and the use of known information. Finally, it tries to foretell the future of such an alternative among well established direct methods.

https://journals.iucr.org/a/issues/2008/01/00/sc5009/sc5009.pdf

G. Oszlányi

Papers

Ab initio structure solution by charge flipping.

Polymeric fullerene chains in RbC60 and KC60

Quasi-one-dimensional electronic structure in orthorhombic RbC60.

Ab initio structure solution by charge flipping. II. Use of weak reflections

The charge flipping algorithm