Birger Dittrich

ShelXle: a Qt graphical user interface for SHELXL

ShelXle is a user-friendly graphical user interface for SHELXL. It combines an editor with syntax highlighting for SHELXL-associated files with an interactive graphical display for visualization of a three-dimensional structure.

The invariom model and its application: refinement of d,l-serine at different temperatures and resolution

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.

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

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.

MoleCoolQt – a molecule viewer for charge-density research

MoleCoolQt is a molecule viewer designed for experimental charge density studies with a user-friendly graphical user interface.

Automation of invariom and of experimental charge density modelling of organic molecules with the preprocessor program InvariomTool

The program InvariomTool can be used to obtain high-quality X-ray structures of organic molecules by automating both invariom modelling and the modelling process employed in experimental charge density studies. InvariomTool is a preprocessor program for the XD package [Koritsanszky et al. (2003), Technical Report, Freie Universitat Berlin] and allows the analysis of a structure in terms of the local atomic bonding environment in order to assign Hansen–Coppens pseudoatoms that are transferable from one molecule to another (invarioms). It relies on a database of invariom entries, each containing the invariom name, local atomic site symmetry, coordinate system, model-compound name and theoretically predicted multipole population parameters. The information on chemical equivalence and local atomic site symmetry determines which multipole parameters are to be refined in the least-squares procedure of an experimental charge density study. InvariomTool allows the user to generate input files either for invariom refinement, where parameters are fixed and taken from the database, or for an experimental refinement of multipole parameters.

Enhanced rigid-bond restraints

An extension is proposed to the rigid-bond description of atomic thermal motion in crystals.

Donor-acceptor-stabilized silicon analogue of an acid anhydride.

A stable silicon analogue of an acid anhydride {PhC(Bu(t)N)(2)}Si{═O·B(C(6)F(5))(3)}O-Si(H){═O·B(C(6)F(5))(3)}{(NBu(t))(HNBu(t))CPh} (4) with a O═Si-O-Si═O core has been prepared by treating monochlorosilylene PhC(Bu(t)N)(2)SiCl (1) with H(2)O·B(C(6)F(5))(3) in the presence of NHC (NHC = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene). Compound 4 has been characterized by elemental analysis and multinuclear NMR spectroscopic investigations. The molecular structure of 4 has been established by single-crystal X-ray diffraction studies, and DFT calculations support the experimental results.

Triggered exchange of anionic for neutral guests inside a cationic coordination cage.

Molecular encapsulation processes under the control of an external trigger play a major role in biological signal transduction processes and enzyme catalysis. Here, we present an artificial mimic of a controllable host system that forms via self-assembly from a simple bis-monodentate ligand and Pd(II) cations. The resulting interpenetrated double cage features three consecutive pockets which initially contain one tetrafluoroborate anion, each. Activation of this host system with two halide anions triggers a conformational change that renders the central pocket susceptible to the uptake of small neutral guest molecules. Thereby, the pentacationic cage expels the central anion and replaces it with a neutral molecule to give a hexacationic species. The cage structures prior and after the halide triggered binding of benzene were examined by X-ray crystallography, ESI MS, and NMR techniques. The kinetics and thermodynamics of the encapsulation of benzene, cyclohexane, and norbornadiene are compared.

anti-Oligoannelated THF Moieties: Synthesis via Push−Pull-Substituted Cyclopropanes‡

The first synthesis of anti-fused oligoannelated THF moieties is reported. The key transformation of the synthetic sequence, consisting of cyclopropanation, reduction and oxidation, is the expansion of a push-pull-substituted three-membered ring into a five-membered enol ether system. A repetition of the sequence allows the creation of oligoacetals up to a nonacyclic system.

Synthesis of [n,5]-Spiroketals by Ring Enlargement of Donor-Acceptor-Substituted Cyclopropane Derivatives

Exocyclic enol ethers served as starting materials for the synthesis of [n,5]-spiroketals (n = 5, 6). A metal-mediated cyclopropanation using ethyl diazoacetate afforded spiroannelated cyclopropane derivatives bearing an ester group. A reduction of the corresponding ester by LiAlH(4), followed by subsequent oxidation using hypervalent iodine reagents, produced [n,5]-spiroketals in moderate to good yields. The key step within this three-step sequence is the ring enlargement of the three-membered ring with an oxygen donor and a carbonyl acceptor group into the five-membered enol ether system. Catalytic amounts of the Lewis acid Yb(OTf)(3) facilitate the ring enlargement and increase the yield of the corresponding spiroketal in many cases. When Yb(OTf)(3) was used, our experiments revealed an open transition state rather than a concerted mechanism because the stereochemistry of the spirocenter was not conserved during the ring enlargement. As a result, the thermodynamically more favored anomeric [n,5]-spiroketal was observed as the major product. All the structures were established unambiguously by NOESY experiments.