The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

/pdf/crystal-structure-refinement-with-shelxl-1jual428j8.pdf

Crystal structure refinement with SHELXL

J. Appl. Cryst.の発刊に際して

The quality of diffraction data obtained using silver and molybdenum microsources has been compared for six model compounds with a wide range of absorption factors. The experiments were performed on two 30 W air-cooled Incoatec IµS microfocus sources with multilayer optics mounted on a Bruker D8 goniometer with a SMART APEX II CCD detector. All data were analysed, processed and refined using standard Bruker software. The results show that Ag Kα radiation can be beneficial when heavy elements are involved. A numerical absorption correction based on the positions and indices of the crystal faces is shown to be of limited use for the highly focused microsource beams, presumably because the assumption that the crystal is completely bathed in a (top-hat profile) beam of uniform intensity is no longer valid. Fortunately the empirical corrections implemented in SADABS, although originally intended as a correction for absorption, also correct rather well for the variations in the effective volume of the crystal irradiated. In three of the cases studied (two Ag and one Mo) the final SHELXL R1 against all data after application of empirical corrections implemented in SADABS was below 1%. Since such corrections are designed to optimize the agreement of the intensities of equivalent reflections with different paths through the crystal but the same Bragg 2θ angles, a further correction is required for the 2θ dependence of the absorption. For this, SADABS uses the transmission factor of a spherical crystal with a user-defined value of μr (where μ is the linear absorption coefficient and r is the effective radius of the crystal); the best results are obtained when r is biased towards the smallest crystal dimension. The results presented here suggest that the IUCr publication requirement that a numerical absorption correction must be applied for strongly absorbing crystals is in need of revision.

/pdf/comparison-of-silver-and-molybdenum-microfocus-x-ray-sources-39mmpb4n7o.pdf

Comparison of silver and molybdenum microfocus X-ray sources for single-crystal structure determination

ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

/pdf/shelxle-a-qt-graphical-user-interface-for-shelxl-9wh4ewtajc.pdf

ShelXle: a Qt graphical user interface for SHELXL

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Determining the structures of nanoparticles at atomic resolution is vital to understand their structure–property correlations. Large metal nanoparticles with core diameter beyond 2 nm have, to date, eluded characterization by single-crystal X-ray analysis. Here we report the chemical syntheses and structures of two giant thiolated Ag nanoparticles containing 136 and 374 Ag atoms (that is, up to 3 nm core diameter). As the largest thiolated metal nanoparticles crystallographically determined so far, these Ag nanoparticles enter the truly metallic regime with the emergence of surface plasmon resonance. As miniatures of fivefold twinned nanostructures, these structures demonstrate a subtle distortion within fivefold twinned nanostructures of face-centred cubic metals. The Ag nanoparticles reported in this work serve as excellent models to understand the detailed structure distortion within twinned metal nanostructures and also how silver nanoparticles can span from the molecular to the metallic regime. The structure of nanoparticles strongly influences their properties. Here, the authors use single crystal X-ray diffraction to resolve the crystal structures of Ag136 and Ag374nanoparticles, enabling the observation of local structure distortion and the lower size limit of surface plasmon resonance.

/pdf/plasmonic-twinned-silver-nanoparticles-with-molecular-2vtpu0wpi4.pdf

Plasmonic twinned silver nanoparticles with molecular precision

A simple approach to nonspherical electron densities by using invarioms.

A simple self-assembled [Pd2 L4 ] coordination cage consisting of four carbazole-based ligands was found to dimerize into the interpenetrated double cage [3 X@Pd4 L8 ] upon the addition of 1.5 equivalents of halide anions (X=Cl(-) , Br(-) ). The halide anions serve as templates, as they are sandwiched by four Pd(II) cations and occupy the three pockets of the entangled cage structure. The subsequent addition of larger amounts of the same halide triggers another structural conversion, now yielding a triply catenated link structure in which each Pd(II) node is trans-coordinated by two pyridine donors and two halide ligands. This simple system demonstrates how molecular complexity can increase upon a gradual change of the relative concentrations of reaction partners that are able to serve different structural roles.

Stepwise Halide-Triggered Double and Triple Catenation of Self-Assembled Coordination Cages

https://journals.iucr.org/m/issues/2014/05/00/fc5002/fc5002.pdf

Birger Dittrich

Papers

ShelXle: a Qt graphical user interface for SHELXL

Plasmonic twinned silver nanoparticles with molecular precision

A simple approach to nonspherical electron densities by using invarioms.

Stepwise Halide-Triggered Double and Triple Catenation of Self-Assembled Coordination Cages

Hirshfeld atom refinement