ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122], currently the most widely used program for smallmolecule 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 (F o ) and difference density (F o -F c ) 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.

The new automated iterative Hirshfeld atom refinement method is explained and validated through comparison of structural models of Gly–l-Ala obtained from synchrotron X-ray and neutron diffraction data at 12, 50, 150 and 295 K. Structural parameters involving hydrogen atoms are determined with comparable precision from both experiments and agree mostly to within two combined standard uncertainties.

An approach is outlined for X-ray structure refinement using atomic density fragments obtained by Hirshfeld partitioning of quantum-mechanical density fragments. Results are presented for crystal structure refinements of urea and benzene using these 'Hirshfeld atoms'. Using this procedure, the quantum-mechanical non-spherical electron density is taken into account in the structural model based on the conformation found in the crystal. Contrary to current consensus in structure refinement, the anisotropic displacement parameters of H atoms can be reproduced from neutron diffraction measurements simply from a least-squares fit using the Hirshfeld atoms derived from the BLYP level of theory and including a simple point-charge model to treat the crystal environment.

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 Hohenberg-Kohn theorem [1] highlights the importance of the electron density 1(r) as a fundamental physical property that uniquely characterizes an electronic system. It states that the ground-state energy of a nondegenerate quantum chemical system is a function of the electron density. The electron density of a crystalline state can, in principle, be measured by high-resolution X-ray diffraction. In spite of the significantly improved experimental conditions (availability of area detectors, synchrotron radiation, and low-temperature devices), the collection of high-resolution data (d 0.5 or sin ql À1 ! 1.0 À1 )-prerequisite for X-ray charge density

Invarioms are aspherical atomic scattering factors that enable structure refinement of more accurate and more precise geometries than refinements with the conventional independent atom model (IAM). The use of single-crystal X-ray diffraction data of a resolution better than sin / = 0.6 Å À1 (or d = 0.83 Å ) is recommended. The invariom scatteringfactor database contains transferable pseudoatom parameters of the Hansen-Coppens multipole model and associated local atomic coordinate systems. Parameters were derived from geometry optimizations of suitable model compounds, whose IUPAC names are also contained in the database. Correct scattering-factor assignment and orientation reproduces molecular electron density to a good approximation. Molecular properties can hence be derived directly from the electron-density model. Coverage of chemical environments in the invariom database has been extended from the original amino acids, proteins and nucleic acid structures to many other environments encountered in organic chemistry. With over 2750 entries it now covers a wide sample of general organic chemistry involving the elements H, C, N and O, and to a lesser extent F, Si, S, P and Cl. With respect to the earlier version of the database, the main modification concerns scattering-factor notation. Modifications improve ease of use and success rates of automatic geometry-based scatteringfactor assignment, especially in condensed hetero-aromatic ring systems, making the approach well suited to replace the IAM for structures of organic molecules.

Due to the inherent difficulties in achieving a defined and exclusive formation of multicomponent assemblies against entropic predisposition, we present the rational assembly of a heteroleptic [PdLL] coordination cage achieved through the geometric complementarity of two carefully designed ligands, L and L. With Pd(II) cations as rigid nodes, the pure distinctly angular components readily form homoleptic cages, a [PdL] strained helical assembly and a [PdL] box-like structure, both of which were characterized by X-ray analysis. Combined, however, the two ligands could be used to cleanly assemble a cis-[PdLL] cage with a bent architecture. The same self-sorted product was also obtained by a quantitative cage-to-cage transformation upon mixing of the two homoleptic cages revealing the [PdLL] assembly as the thermodynamic minimum. The structure of the heteroleptic cage was examined by ESI-MS, COSY, DOSY, and NOESY methods, the latter of which pointed toward a cis-conformation of ligands in the assembly. Indeed, DFT calculations revealed that the angular ligands and strict Pd(II) geometry strongly favor the cis-[PdLL] species. The robust nature of the cis-[PdLL] cage allowed us to probe the accessibility of its cavity, which could be utilized for shape recognition toward stereoisomeric guests. The ability to directly combine two different backbones in a controlled manner provides a powerful strategy for increasing complexity in the family of [PdL] cages and opens up possibilities of introducing multiple functionalities into a single self-assembled architecture.

Three X-ray data sets of the same D,L-serine crystal were measured at temperatures of 298, 100 and 20 K. These data were then evaluated using invarioms and the Hansen & Coppens aspherical-atom model. Multipole populations for invarioms, which are pseudoatoms that remain approximately invariant in an intermolecular transfer, were theoretically predicted using different density functional theorem (DFT) basis sets. The invariom parameters were kept fixed and positional and thermal parameters were refined to compare the fitting against the multi-temperature data at different resolutions. The deconvolution of thermal motion and electron density with respect to data resolution was studied by application of the Hirshfeld test. Above a resolution of sin theta/lambda approximately 0.55 A-1, or d approximately 0.9 A, this test was fulfilled. When the Hirshfeld test is fulfilled, a successful modeling of the aspherical electron density with invarioms is achieved, which was proven by Fourier methods. Molecular geometry improves, especially for H atoms, when using the invariom method compared to the independent-atom model, as a comparison with neutron data shows. Based on this example, the general applicability of the invariom concept to organic molecules is proven and the aspherical density modeling of a larger biomacromolecule is within reach.