Mercedes Camalli

SIR97: a new tool for crystal structure determination and refinement

SIR97 is the integration of two programs, SIR92 and CAOS, the first devoted to the solution of crystal structures by direct methods, the second to refinement via least-squares–Fourier procedures. Several new features have been introduced in SIR97 with respect to the previous version, SIR92: greater automatization, increased efficiency of the direct methods section, and a powerful graphics interface. The program also provides publication tables and CIF files.

SIR2004: an improved tool for crystal structure determination and refinement

SIR2004 is the evolution of the SIR2002 program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003). J. Appl. Cryst. 36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented in SIR2004 make this program efficient: it is able to solve ab initio both small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 A, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

SIR2002: the program

Dipartimento di Scienze della Terra Piazza UniversitaÁ, 06100 Perugia, Italy, Istituto di Cristallografia, CNR, Sezione di Monterotondo, CP 10, Monterotondo Stazione, 00016 Roma, Italy, Istituto di Cristallografia, CNR, c/o Dipartimento Geomineralogico, UniversitaÁ di Bari, Campus Universitario, Via Orabona 4, 70125 Bari, Italy, and CNR, Istituto di Cristallografia c/o Dipartimento Geomineralogico, UniversitaÁ di Bari, Campus Universitario, Via Orabona 4, 70125 Bari, Italy. Correspondence e-mail: carmelo.giacovazzo@ic.cnr.it

SIR88 – a direct-methods program for the automatic solution of crystal structures

SIR88 is an integrated package of computer programs for the solution of crystal structures. The package is based on the estimation of one- and two-phase structure seminvariants and three- and four-phase structure invariants according to the theory of representations [Giacovazzo (1977). Acta Cryst. A33, 933–944; (1980). Acta Cryst. A36, 362–372]. The program works in all the space groups and in most cases it is able to provide the correct solution without user intervention. Some prior information like the availability of a partial structure or of pseudotranslational symmetry is easily exploited to obtain the structure solution.

IL MILIONE: a suite of computer programs for crystal structure solution of proteins

IL MILIONEIl Milione is the title of the book by Marco Polo, dictated to Rustichello da Pisa in 1298 in the Genova prison where Marco was imprisoned after a naval battle between Genova and Venezia. Il Milione is a travel report: the name suggests the millions of marvels seen during the travel. Most contemporaries thought that they were a million tales. Our program is also a travel report, but in the world of crystallography. is a suite of computer programs devoted to protein crystal structure determination by X-ray crystallography. It may be used in the following key activities. (a) Ab initio phasing, via Patterson or direct methods. The program may succeed even with structures with up to 6000 non-H atoms in the asymmetric unit, provided that atomic resolution is available, and with data at quasi-atomic resolution (1.4–1.5 A). (b) Single or multiple isomorphous replacement, single- or multiple-wavelength anomalous diffraction, and single or multiple isomorphous replacement with anomalous scattering techniques. In the first step the program finds the heavy-atom/anomalous scatterer substructure, then automatically uses the above information to phase protein reflections. Phase extension and refinement are performed by electron density modification techniques. (c) Molecular replacement. The orientation and the location of the protein molecules are found via reciprocal space methods. Phase extension and refinement are performed by electron density modification techniques. All the programs integrated into IL MILIONE are controlled by means of a user-friendly graphical user interface, which is used to input data and to monitor intermediate and final results by means of real-time updated messages, diagrams and histograms.

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.

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.

Synthesis, characterization and antioxidant activity of new copper(I) complexes of scorpionate and water soluble phosphane ligands

New copper(I) complexes have been synthesised from the reaction of CuCl with potassium hydrotris(4-bromo-1H-pyrazol-1-yl)borate, KTp4Br or lithium bis(3,5-dimethylpyrazol-1-yl)acetate, Li[L2CO2] ligands and 4- or 2-(diphenylphosphane)benzoic acid or tris(m-sulfonatophenyl)posphine trisodium salt (TPPTS) coligands. The complexes obtained have been characterized by elemental analyses and FT-IR in the solid state, and by NMR (1H and 31P[1H]) and electrospray mass spectrometry (ESI-MS) in solution. Single crystal structural characterisation was undertaken for the [Cu[PPh2(4-C6H4COOH)](Tp4Br)] derivative, an interesting dimeric supramolecular assembly. A chemiluminescence study has demonstrated the superoxide scavenging activity of these new copper complexes. The Comet assay was used to evaluate the impairment of DNA in rat epithelial cells exposed to different reactive nitrogen species. In addition, the same complexes were included in this study to determine their efficacy as antioxidants in mitigating oxidative DNA damage. The parameter tail moment, used as an index of DNA damage, showed that the complex [Cu[PPh2(4-C6H4COOH)](Tp4Br)] remarkably inhibited DNA strand breaks induced by the different nitrogen oxide species. The other copper complexes under study showed a different ability to reduce tail moment values depending on the type of RNOS donor used.

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.