Corrado Cuocci

EXPO2009: structure solution by powder data in direct and reciprocal space

The program EXPO2009 is the evolution of EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst. 37, 1025–1028]. EXPO2009 performs all the steps of ab initio structure solution by powder data: indexing, space-group determination, estimation of the reflection integrated intensities, structure solution by direct/Patterson methods and/or by a direct-space/hybrid approach, and model refinement by the Rietveld technique. New procedures have been introduced in EXPO2009 for enhancing the structure solution process, particularly in the case of low-resolution data and/or organic compounds, when traditional approaches like direct methods may fail. The EXPO2009 graphical interface has been optimized and made very user friendly.

Crystal structure determination and refinement via SIR2014

SIR2014 is the latest program of the SIR suite for crystal structure solution of small, medium and large structures. A variety of phasing algorithms have been implemented, both ab initio (standard or modern direct methods, Patterson techniques, Vive la Difference) and non-ab initio (simulated annealing, molecular replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density maps via suitable viewers.

EXPO2013: a kit of tools for phasing crystal structures from powder data

EXPO2013, the heir of EXPO2009, has been enriched by a variety of new algorithms and graphical tools aiming at strengthening the individual steps of the powder structure solution pathway. Particular attention has been addressed to the procedures devoted to improving structural models provided by direct methods in ab initio approaches. In addition, a new procedure has been implemented, working in direct space, which may be chosen by the user as an alternative to the traditional simulated annealing algorithm.

Automatic structure determination from powder data with EXPO2004

EXPO2004 is the updated version of the EXPO program [Altomare et al. (1999). J. Appl. Cryst. 32, 339–340]. The traditional steps of the ab initio powder solution process are performed automatically: indexing, space-group determination, decomposition of the pattern for extracting the observed structure-factor moduli, structure solution by direct methods, model refinement by Rietveld technique. Special strategies may be applied to improve both the estimates of the extracted structure-factor moduli and the quality of the structure model. In addition, the use of special procedures exploiting available supplementary information on molecular geometry can be successfully adopted. The graphical interface has also been improved.

Third structure determination by powder diffractometry round robin "SDPDRR-3…

The results from a third structure determination by powder diffractometry (SDPD) round robin are discussed. From the 175 potential participants having downloaded the powder data, nine sent a total of 12 solutions (8 and 4 for samples 1 and 2, respectively, a tetrahydrated calcium tartrate and a lanthanum tungstate). Participants used seven different computer programs for structure solution (ESPOIR, EXPO, FOX, PSSP, SHELXS, SUPERFLIP, and TOPAS), applying Patterson, direct methods, direct space methods, and charge flipping approach. It is concluded that solving a structure from powder data remains a challenge, at least one order of magnitude more difficult than solving a problem with similar complexity from single-crystal data. Nevertheless, a few more steps in the direction of increasing the SDPD rate of success were accomplished since the two previous round robins: this time, not only the computer program developers were successful but also some users. No result was obtained from crystal structure prediction experts.

Space-group determination from powder diffraction data: a probabilistic approach

Experimental powder diffraction diagrams, once indexed and decomposed into single diffraction intensities, can be submitted to statistical analysis for the determination of space-group symmetry. A new algorithm is illustrated, which is able to provide, on a quantitative basis, a probability value for each extinction symbol compatible with the previously established lattice symmetry. The algorithm has been implemented in EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst. 37, 1025–1028] and has been successfully tested using a large set of experimental data.

Direct methods and simulated annealing: a hybrid approach for powder diffraction data

The solution of crystal structures from powder data using direct methods can be very difficult if the quality of the diffraction pattern is low and if no heavy atoms are present in the molecule. On the contrary, the use of direct-space methods does not require good quality diffraction data, but if a molecular model is available, the structure solution is limited principally by the number of degrees of freedom used to describe the model. The combination of the information contained in the electron density map (direct methods) with the Monte Carlo method, which uses simulated annealing as a global minimization algorithm (direct-space techniques), can be a useful tool for crystal structure solution, especially for organic structures. A modified and improved version of this approach [Altomare et al. (2003), J. Appl. Cryst. 36, 230–238] has been implemented in the EXPO2004 program and is described here.

Minimally resolution biased electron-density maps.

Electron-density maps are calculated by Fourier syntheses with coefficients based on structure factors. Diffraction experiments provide intensities up to a limited resolution; as a consequence, the Fourier syntheses always show series-termination errors. The worse the resolution, the less accurate is the Fourier representation of the electron density. In general, each atomic peak is shifted from the correct position, shows a deformed (with respect to the true distribution of the electrons in the atomic domain) profile, and is surrounded by a series of negative and positive ripples of gradually decreasing amplitude. An algorithm is described which is able to reduce the resolution bias by relocating the peaks in more correct positions and by modifying the peak profile to better fit the real atomic electron densities. Some experimental tests are performed showing the usefulness of the procedure.

QUALX2.0: a qualitative phase analysis software using the freely available database POW_COD

QUALX2.0 is the new version of QUALX, a computer program for qualitative phase analysis by powder diffraction data. The previous version of QUALX was able to carry out phase identification by querying the PDF-2 commercial database. The main novelty of QUALX2.0 is the possibility of querying also a freely available database, POW_COD. POW_COD has been built up by starting from the structure information contained in the Crystallography Open Database (COD). The latter is a growing collection of diffraction data, freely downloadable from the web, corresponding to inorganic, metal–organic, organic and mineral structures. QUALX2.0 retains the main capabilities of the previous version: (a) automatically estimating and subtracting the background; (b) locating the experimental diffraction peaks; (c) searching the database for single-phase pattern(s) best matching to the experimental powder diffraction data; (d) taking into account suitable restraints in the search; (e) performing a semi-quantitative analysis; (f) enabling the change of default choices and strategies via a user-friendly graphic interface. The advances of QUALX2.0 with respect to QUALX include (i) a wider variety of types of importable ASCII file containing the experimental diffraction pattern and (ii) new search–match options. The program, written in Fortran and C++, runs on PCs under the Windows operating system. The POW_COD database is exported in SQLite3 format.

Correcting resolution bias in electron density maps of organic molecules derived by direct methods from powder data

Fourier syntheses providing electron density maps are usually affected by truncation effects due to the limited data resolution. A recent theoretical approach [Altomare, Cuocci, Giacovazzo, Kamel, Moliterni & Rizzi (2008). Acta Cryst. A64, 326–336] suggests that the resolution bias may be reduced by correcting the current electron density maps in accordance with the physics of the diffraction experiment. We have implemented the approach in EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst. 37, 1025–1028], a program devoted to the solution of crystal structures from powder data. The new algorithm was applied at the end of the direct methods modulus, to verify if the reduction of the resolution bias is able to improve the electron density maps and to provide additional power to direct methods. Application of this method to a large set of test structures indicates that resolution-bias correction often makes the difference between success and failure, and thus constitutes a new tool for reducing the dependence of modern crystallography on resolution effects. The chances of failure are expected to depend on the quality of the experimental data (e.g. the accuracy of the full-pattern decomposition procedure and the data resolution), on the size of the structure and on its chemical composition.