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.

SIR97: a new 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.

SIR2004: an improved tool for crystal structure determination and refinement

A series of novel hexafluorophosphate salts, based on N,N′-dialkylimidazolium and substituted N-alkylpyridinium cations, display liquid crystalline behaviour at temperatures above their melting point. The temperature range over which liquid crystalline behaviour is observed increases markedly with increasing alkyl chain length. Alkyl substitution at the 3- and 4-positions on the pyridinium ring results in a decrease in the melting point compared with the equivalent unsubstituted salt, but also leads to a large decrease in the tendency towards liquid crystalline behaviour (or mesogenicity). The salts prepared are fully characterised using a wide variety of techniques, including NMR and IR spectroscopy, DSC, and single crystal X-ray diffraction in the case of 1-dodecyl-3-methylimidazolium hexafluorophosphate. The effect of preparing mixtures containing different proportions of two cations is also reported.

Ionic liquid crystals: hexafluorophosphate salts

SIR2011, the successor of SIR2004, is the latest program of the SIR suite. It can solve ab initio crystal structures of small- and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data. With respect to the predecessor the program has several new abilities: e.g. a new phasing method (VLD) has been implemented, it is able to exploit prior knowledge of the molecular geometry via simulated annealing techniques, it can use molecular replacement methods for solving proteins, it includes new tools like free lunch and new approaches for electron diffraction data, and it visualizes three-dimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.

SIR2011: a new package for crystal structure determination and refinement

An unusual luminescent inorganic oxide, Sr2CeO4, was identified by parallel screening techniques from within a combinatorial library of more than 25,000 members prepared by automated thin-film synthesis. A bulk sample of single-phase Sr2CeO4 was prepared, and its structure, determined from powder x-ray diffraction data, reveals one-dimensional chains of edge-sharing CeO6 octahedra, with two terminal oxygen atoms per cerium center, that are isolated from one another by Sr2+ cations. The emission maximum at 485 nanometers appears blue-white and has a quantum yield of 0.48 +/- 0.02. The excited-state lifetime, electron spin resonance, magnetic susceptibility, and structural data all suggest that luminescence originates from a ligand-to-metal Ce4+ charge transfer.

https://science.sciencemag.org/content/sci/279/5352/837.full.pdf

A rare-earth phosphor containing one-dimensional chains identified through combinatorial methods

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.

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

The quality of an E map is usually affected by systematic and/or random phase errors, by amplitude truncation effects in the series representation of the electron density, by the experimental uncertainty in the estimation of |E| and by the intrinsic nature of the Fourier coefficients used (i.e. the E's). It is shown that simple supplemental calculations can improve the quality of an E map. Large molecular fragments can often be localized in the new map even when the original one is not easily interpretable.

E-map improvement in direct procedures

The probabilistic approach has been extensively used for analysing the statistical meanings of some traditional figures of merit. New figures of merit have also been introduced; some exploit one-phase and two-phase structure seminvariants of the first rank, the expected negative and/or enantiomorph-sensitive triplet invariants, and the expected negative and/or enantiomorph-sensitive quartets. Other figures of merit exploit the distribution of statistical parameters connected with PSI(0) and active triplets. A new combined figure of merit is shown to be a powerful tool for selecting the correct solutions among the various sets output by multisolution methods.

Figures of merit in direct methods: a new point of view

New faster and more accurate procedures for the evaluation of two-phase seminvariants by means of the representation theory are described. Some special relationships are also considered and specific methods for their estimation are proposed. The use of the generalized first representation is discussed and detailed examples are given. These ideas for the evaluation of two-phase seminvariants have been introduced in the SIR program and examples of actual applications are given.

The SIR program. II. The evaluation and use of two-phase seminvariants

The present paper deals with the finding and the estimation of negative quartets. The use of symmetry is also discussed and the results obtained for four structures of increasing size are reported. Conditional probability distributions using magnitudes contained in the second representation of the quartets provides improved estimates of their phases.

D. Viterbo

Papers

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

E-map improvement in direct procedures

Figures of merit in direct methods: a new point of view

The SIR program. II. The evaluation and use of two-phase seminvariants

The SIR program. I. Use of negative quartets