Search

Crystal structure refinement and analysis is a powerful method for determination of crystal structures and finds widespread application in determination of structures of crystals of small molecules and frameworks at atomic resolution. The independent atom model is used to describe atomic scattering for routine use, while more accurate aspherical scattering factors are increasingly available. The structure factor is presented as the Fourier transform of convolutions of scattering and probability densities in the crystal structure to clarify how aspherical scattering factors and alternative displacement probabilities can be introduced into refinement methods. Non-linear least squares fitting of the crystal structure parameters in the structure factor equations is described using matrix algebra notation which enables simple derivation of the extensions required for discussion of crystallographic restraints and leverage analysis. Finally, combined analysis of multiple single-crystal experiments is discussed highlighting the potential of refinement tools to extract useful information from joint X-ray and neutron data and from mixed ground-state and excited-state X-ray data from pump-probe experiments. [ABSTRACT FROM AUTHOR]

Transition-metal complexes are widely used in the physical and biological sciences. They have essential roles in catalysis, synthesis, materials science, photophysics and bioinorganic chemistry. Our understanding of transition-metal complexes originates from Alfred Werner's realization that their three-dimensional shape influences their properties and reactivity1, and the intrinsic link between shape and electronic structure is now firmly underpinned by molecular-orbital theory2–5. Despite more than a century of advances in this field, the geometries of transition-metal complexes remain limited to a few well-understood examples. The archetypal geometries of six-coordinate transition metals are octahedral and trigonal prismatic, and although deviations from ideal bond angles and bond lengths are frequent6, alternative parent geometries are extremely rare7. The hexagonal planar coordination environment is known, but it is restricted to condensed metallic phases8, the hexagonal pores of coordination polymers9, or clusters that contain more than one transition metal in close proximity10,11. Such a geometry had been considered12,13 for [Ni(PtBu)6]; however, an analysis of the molecular orbitals suggested that this complex is best described as a 16-electron species with a trigonal planar geometry14. Here we report the isolation and structural characterization of a simple coordination complex in which six ligands form bonds with a central transition metal in a hexagonal planar arrangement. The structure contains a central palladium atom surrounded by three hydride and three magnesium-based ligands. This finding has the potential to introduce additional design principles for transition-metal complexes, with implications for several scientific fields. A six-coordinate transition-metal complex with a hexagonal planar geometry is isolated and characterized. [ABSTRACT FROM AUTHOR]

Background: The size and complexity of molecules being studied by single crystal diffraction is growing year by year, resulting in an increase in the difficulties encountered during structure determination. From the crystallisation itself and sample handling, to structure solution and refinement, specific problems due to larger molecules are discussed. Results: During refinement, several methods are available to deal with the problems encountered with large structures within the software CRYSTALS. Hydrogens atoms can neither be found easily nor refined freely, but restraints can be applied automatically. Special scattering factors can be used to model complex disorder. Finally chemical information can be included in the form of restraints in order to help the determination of a good model. Multicollinearity problems are more likely in the refinement of large structures; to some extent more precise and accurate algorithms can help. Also, if the global minimum is less well defined, faster refinement enables more cycles to be carried out, a necessity for good convergence. The efficiency of the algorithms in CRYSTALS have been increased to help address these issues. Conclusions: Thus, crystal structures are getting larger and their complexity is increasing. Recent developments in precision and speed during the least squares in CRYSTALS is helping the structural scientist to deal with larger structures more efficiently. [ABSTRACT FROM AUTHOR]

We present ElectroShape, a novel ligand-based virtual screening method, that combines shape and electrostatic information into a single, unified framework. Building on the ultra-fast shape recognition (USR) approach for fast non-superpositional shape-based virtual screening, it extends the method by representing partial charge information as a fourth dimension. It also incorporates the chiral shape recognition (CSR) method, which distinguishes enantiomers. It has been validated using release 2 of the Directory of useful decoys (DUD), and shows a near doubling in enrichment ratio at 1% over USR and CSR, and improvements as measured by Receiver Operating Characteristic curves. These improvements persisted even after taking into account the chemotype redundancy in the sets of active ligands in DUD. During the course of its development, ElectroShape revealed a difference in the charge allocation of the DUD ligand and decoy sets, leading to several new versions of DUD being generated as a result. ElectroShape provides a significant addition to the family of ultra-fast ligand-based virtual screening methods, and its higher-dimensional shape recognition approach has great potential for extension and generalisation. [ABSTRACT FROM AUTHOR]