Rosanna Rizzi

EXPO: a program for full powder pattern decomposition and crystal structure solution

EXPO is the integration of two programs, EXTRA and SIRPOW.92, the first devoted to full powder pattern decomposition and the second to the solution and refinement of crystal structures. The program is able to exploit the prior information obtained during the crystal structure solution process for improving the classical decomposition. EXPO also allows preliminary cycles of Rietveld refinement.

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.

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.

New techniques for indexing: N-TREOR in EXPO

Indexing of a powder diffraction pattern is still a critical point in procedures aiming at solving crystal structures from powder data. New code has been associated to the program TREOR90 in order to define an efficient peak search procedure, to modify the crystallographic decisions coded into TREOR90 to make it more exhaustive, to refine the selected unit cell automatically, and to make the entire procedure user friendly, via a graphical interface. The new program, called N-TREOR, has been integrated into the package EXPO to create a suite of programs able to provide a structural model from the analysis of the experimental pattern. N-TREOR is also available as a stand-alone program.

Quanto: a Rietveld program for quantitative phase analysis of polycrystalline mixtures

Quantitative determination of phase abundance in a multicomponent polycrystalline mixture is a basic goal in materials characterization. Because of several advantages compared with traditional techniques, the Rietveld method has been increasingly applied to this task. Further progress in this direction would be to carry out the analysis automatically. The new Rietveld package Quanto is devoted to the automatic estimation of the weight fraction of each crystalline phase in a mixture. The amorphous content can be estimated by means of the internal-standard method. Corrections for preferred orientation and microabsorption effects are available. A user-friendly graphical interface facilitates interaction. A data bank including several organic and inorganic phases is supplied with the program.

Diarylheterocycle core ring features effect in selective COX-1 inhibition.

The COX‐1 isoenzyme plays a significant role in a variety of diseases, as it catalyzes the bioprocesses behind many health problems. Among the diarylheterocycle class of COX inhibitors, the isoxazole ring has been widely used as a central heterocycle for the preparation of potent and selective COX‐1 inhibitors such as P6 [3‐(5‐chlorofuran‐2‐yl)‐5‐methyl‐4‐phenylisoxazole]. The role of the isoxazole nucleus in COX‐1 inhibitor selectivity has been clarified by preparing a set of new diarylheterocycles with various heterocycle cores. Replacement of isoxazole with isothiazole or pyrazole gave a drastic decrease in COX‐1 inhibitory activity, whereas the introduction of an electron‐donating group (EDG) on the N‐aryl pyrazole allowed recovery of COX‐1 inhibitory activity and selectivity. The EDG‐equipped 5‐(furan‐2‐yl)‐1‐(4‐methoxyphenyl)‐3‐(trifluoromethyl)‐1H‐pyrazole (17) selectively inhibits COX‐1 activity (IC50=3.4 μM; 28 % COX‐2 inhibition at 50 μM), in contrast to its inactive analogue, 3‐(furan‐2‐yl)‐1‐phenyl‐5‐(trifluoromethyl)‐1H‐pyrazole, which does not bear the methoxy EDG. Molecular docking studies of compound 17 into the binding site of COX‐1 shed light on its binding mode.

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.