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

Gervais Chapuis
2007
Journal paper

Abstract

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.

Official source

https://infoscience.epfl.ch/record/115184?ln=en

About this result

This page is automatically generated and may contain information that is not correct, complete, up-to-date, or relevant to your search query. The same applies to every other page on this website. Please make sure to verify the information with EPFL's official sources.

Related concepts

Related publications

The comparable order of magnitude between interatomic distances in a crystal and the wavelength of X-rays make X-ray crystallography the ideal analytical tool to gain insight into the structure of crystalline material, including biomolecules. Nevertheless, biomolecular crystallography has until now relied on the successful growth of single crystals of suitable size and quality. These remain the exception rather than the rule, since biomolecules often produce polycrystalline precipitate instead. Yet, an interest in making use of the once-discarded polycrystalline material, through the technique of powder diffraction, has only recently emerged. This can be accounted for by the information deficit which powder diffraction data suffers from in comparison with that of single crystal. The paucity of information in powder data stems from the compression of the three-dimensional reciprocal space onto the one-dimension of a powder pattern. In spite of this, powder diffraction holds the potential for application in biomolecular crystallography as is shown in the two different studies presented herein. Both studies were carried out with methods which do not rely on employing previously determined crystal-structures as molecular models. This therefore allowed the objective assessment of the quality of information that powder diffraction data can contribute to the structural investigation of biomolecules. In the first project, the traditional single-crystal structure-solution process is applied to data extracted from protein powder diffraction patterns measured on a synchrotron source. The use of models is avoided by employing the de novo phasing method of isomorphous replacement. With two protein test-cases, namely hen egg white lysozyme and porcine pancreatic elastase, it is demonstrated that protein powder diffraction data can afford structural information up to medium resolution. Indeed, a single isomorphous replacement analysis generated molecular envelopes accurately describing the crystal packing of both protein systems, while a multiple isomorphous replacement experiment, carried out only on lysozyme, revealed an electron density map in which elements of the secondary structure could be located. In fact, the resolution of the latter was discovered to be sufficient to determine the chirality of the protein molecule it represented. In addition to being encouraging, these results do not reflect the full potential of biomolecular powder diffraction, due, in large part, to the ultimately unsuitable nature of one type of phasing method, single crystal, being applied to another type of data, powder. An alternative approach to extract information from protein powder diffraction data is to employ powder-specific structure-solution techniques, such as global optimization methods. Although these methods make use of a starting "model", it is a molecular description of the system under study based on known chemical quantities rather than a related molecular configuration based on a previously determined crystal structure. Since their conception, global optimization methods have continuously been developed to enable the tackling of increasingly complex crystal structures. However, the immense complexity of biomacromolecules has kept proteins well out of reach of such methods. In an attempt to further reduce the gap separating the two levels of complexity, the second study reported herein puts forth the implementation of Ramachandran plot restraints into the algorithm of a global optimization method, i.e. that of simulated annealing. More specifically, the Ramachandran plot was approximated using a two-dimensional Fourier series which was subsequently expressed as a penalty function and incorporated into the search algorithm.

EPFL2011

Structure of the Orthorhombic gamma-Phase and Phase Transitions of Ca(BD4)(2)

Philippe Mauron

We have solved and refined the crystal structure of the orthorhombic gamma-phase of Ca(BD4)(2) by combined synchrotron X-ray powder diffraction, neutron powder diffraction, and ab initio calculations. Among five structural candidates giving the same quality of the fit of the diffraction data, the structural model with the highest symmetry and space group Pbca is the most appropriate. This is supported by the implicit presence of the Pbca symmetry operations in the low-symmetry space groups in both experimental and DFT calculated structures. The Ca atoms are surrounded by six BD4 groups that have similar distortions as reported for the beta-phase of Ca(BD4)(2). On the basis of the experimental structures, free energies of the alpha-, beta-, and gamma-phases are calculated in the range 300 K < T < 620 K. The phase transitions are observed in the same temperature range by means of X-ray diffraction on Ca(BD4)(2) + MgD2 and pure Ca(BD4)(2) samples. According to the ab initio calculations, the alpha-phase is the ground state at 0 K. At room temperature, the calculated free energies of the alpha-phase, beta-phase, and gamma-phase were found to be within similar to 0.13 eV/f.u., in agreement with the observed coexistence of these phases. Moreover, calculations provide insight into trends for relative stabilities of alpha-, beta-, and gamma-phases. That is, with increasing temperature, the beta-phase becomes more stable, while the metastable gamma-phase becomes more destabilized with respect to the alpha-phase.

2009

Synthesis, crystal growth and physical properties of the frustrated spin ladder material BiCu2PO6

Shuang Wang

In recent years quantum antiferromagnets with an intrinsically disordered (“spin liquid”) ground state and an energy gap in the spin excitation spectrum have received a great deal of attention. In search for new experimental realizations of spin-ladder and related models, we have embarked upon a new interesting family of low-dimensional materials with the general formula BiCu2AO6 (A = P, V and As). Among them, BiCu2PO6 shows a structure where Cu spins appear to form a two-leg zigzag ladder, which is believed to be a valuable model of a quantum magnet. However, for detailed studies of quantum magnetism, single crystals are indispensible. Therefore, in this thesis, synthesis and characterization of the newly-discovered spin ladder material BiCu2PO6 (BCPO) and its derivatives in the form of powder and single crystal are presented. Polycrystalline samples of Bi(Cu1-xZnx)2PO6 (x= 0.01, 0.02, 0.03, 0.04, 0.05 and 1), Bi1-y(Ca, Sr, La )yCu2PO6 (y = 0.15, 0.5 and 1) and BiCu2(P1-zVz)O6 (z = 1) were synthesized in this work. The solid state synthesis reactions, phase purity and thermal properties of the samples, substitution solubility, and preliminary magnetic susceptibility have been studied by thermal analysis (TG-DTA), X-ray powder diffraction (XRD), and Scanning Electron Microscope (SEM) as well as DC magnetization measurements, respectively. The BiCu2PO6 structure shows a remarkable chemical flexibility and interesting substitution effects. For detailed studies of the magnetic properties, well characterized large single crystals are indispensable. Thus in this thesis, a number of single crystal growth experiments have been performed using the Travelling Solvent Floating Zone method (TSFZ). Under the elaborated crystal growth conditions (growth rate of ~1 mm/h, gas mixture of 20% O2 in Argon, total 3 pressure (6~6.5 bar), high quality cm -size single crystals of Bi(Cu1-xZnx)2PO6 (x = 0, 0.01, 0.03, 0.05) have been successfully grown for the first time. For these crystals phase purity, crystal morphology/orientation, defect density, chemical composition distribution, crystal structure (room temperature and 1.5 K) and single crystal quality were thoroughly studied based on X-ray and neutron powder diffraction, optical and scanning electron microscopy, X-ray/neutron Laue diffraction, ICP-OES/X-ray fluorescence and two-axis neutron diffraction. Moreover, the specific heat Cp (H,T), AC susceptibility χ(H,T) and DC magnetization M(H,T) measurements on well-characterized single crystal samples of the undoped BCPO and 5% Zn-doped BCPO with the field applied along main crystallographic axes were performed in order to study the unique low temperature magnetic behaviour exhibited in this system, such as anisotropy of the magnetic properties, impurity-induced magnetism by the substitution of non-2+ magnetic cations (e.g. Zn ) and frustration. The magnetic phase diagram (H-T) under low field has been constructed. Further results obtained by close collaborators, based on the measurements made on single crystal samples grown in this thesis, including field-induced quantum phase transitions, NMR, Raman studies are attached directly at the end of this thesis.

EPFL2013

Synthesis, crystal growth and physical properties of the frustrated spin ladder material BiCu2PO6

Shuang Wang

EPFL2013

EPFL2011