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The electron density distribution (EDD) of a tetrasaccharide composed of four benzoylated fructopyranosyl units was obtained by refinement with scattering factors from the invariom library. X-ray diffraction data was downloaded from the Cambridge Structural Database (CSD). Bond topological and atomic properties were obtained by application of Bader’s QTAIM formalism. From a large number of 105 C–C bonds in the molecule average bond orders for 33 single and 72 aromatic bonds were calculated yielding values of 1.33 and 1.61. Molecular Hirshfeld and electrostatic potential (ESP) surfaces show that only weak non-covalent interactions exist. The phenyl rings of the benzoyl fragments in the outer regions of the molecule generate a positive ESP shell with repulsive properties between adjacent molecules. Weak surface interactions result in a rather unusual low density around 1.3 g cm−3, which is understandable when compared to other carbohydrates where strong O–H⋯O hydrogen bonds allow a 20% more dense packing with densities >1.5 g cm−3 as determined by single crystal X-ray diffraction.

Despite its cramped interior, a [Pd2L4] coordination cage consisting of bulky adamantyl ligands shows impressive motility and a rich encapsulation chemistry., Substituent control in self-assembled host systems allows for a fine-tuning of structure, dynamics and guest preference. Flat banana-shaped ligands L1 assemble with Pd(ii) cations into the interpenetrated coordination cage dimer [3BF4@Pd4L18], capable of sequential guest uptake. In contrast, the introduction of bulky adamantyl groups in ligand L2 prevents dimerization and results in the clean formation of monomeric cage species [Pd2L24]. Owing to steric crowding, the adamantyl substituent is considerably bent sideways with respect to the ligand backbone, and is rapidly flipping between both faces of the free ligand giving rise to two energetically degenerate conformers. Surprisingly, the flipping is preserved in the cage, albeit at a lower rate due to entropic reasons. Despite the very dense packing within the self-assembled structure, the cage is able to encapsulate a series of bis-anionic guests in an induced-fit fashion. Electronic structure calculations revealed a substantial contribution from dispersion interactions between the guest and the surrounding adamantyl groups that stabilize the host–guest complex. Guest exchange kinetics were quantified and the influence that encapsulated guests imparted on the ligand flipping dynamics was examined by a series of 2D NMR experiments. Four synchrotron X-ray structures of the cage and its host–guest complexes are presented, allowing for unprecedented insight into the host–guest interactions of a sterically overcrowded host and its guest-induced distortion.

The self‐assembly of eight PdII cations and sixteen phenanthrene‐derived bridging ligands with 60° bite angles yielded a novel M8L16 metallosupramolecular architecture composed of two interlocked D4h‐symmetric barrel‐shaped containers. Mass spectrometry, NMR spectroscopy, and X‐ray analysis revealed this self‐assembled structure to be a very large “Hopf link” catenane featuring channel‐like cavities, which are occupied by NO3− anions. The importance of the anions as catenation templates became imminent when we observed the nitrate‐triggered structural rearrangement of a mixture of M3L6 and M4L8 assemblies formed in the presence of BF4− anions into the same interlocked molecule. Furthermore, the densely packed structure of the M8L16 catenane was exploited in the preparation of a hexyloxy‐functionalized analogue, which further self‐assembled into vesicle‐like aggregates in a reversible manner.

Angewandte Chemie / International edition 57(19), 5534 - 5538 (2018). doi:10.1002/anie.201800490, The self‐assembly of eight Pd$^{II}$ cations and sixteen phenanthrene‐derived bridging ligands with 60° bite angles yielded a novel M$_8$L$_{16}$ metallosupramolecular architecture composed of two interlocked D$_{4h}$‐symmetric barrel‐shaped containers. Mass spectrometry, NMR spectroscopy, and X‐ray analysis revealed this self‐assembled structure to be a very large “Hopf link” catenane featuring channel‐like cavities, which are occupied by NO$_{3}$$^{−}$ anions. The importance of the anions as catenation templates became imminent when we observed the nitrate‐triggered structural rearrangement of a mixture of M$_3$L$_6$ and M$_4$L$_8$ assemblies formed in the presence of BF$_{4}$$^{−}$ anions into the same interlocked molecule. Furthermore, the densely packed structure of the M$_8$L$_{16}$ catenane was exploited in the preparation of a hexyloxy‐functionalized analogue, which further self‐assembled into vesicle‐like aggregates in a reversible manner., Published by Wiley-VCH, Weinheim

Silicondiselenide is a semiconductor and exists as an insoluble polymer (SiSe2)n which is prepared by reacting elemental silicon with selenium powder in the temperature range of 400–850 °C., Silicondiselenide is a semiconductor and exists as an insoluble polymer (SiSe2)n which is prepared by reacting elemental silicon with selenium powder in the temperature range of 400–850 °C. Herein, we report on the synthesis, isolation, and characterization of carbene stabilized molecular silicondiselenide in the form of (cAAC)2Si2Se4 (3) [cAAC = cyclic alkyl(amino)carbene]. 3 is synthesized via reaction of diatomic silicon(0) compound (cAAC)2Si2 (2) with black selenium powder at –78 °C to room temperature. The intensely orange colored compound 3 is soluble in polar organic solvents and stable at room temperature for a month under an inert atmosphere. 3 decomposes above 245 °C. The molecular structure of 3 has been confirmed by X-ray single crystal diffraction. It is also characterized by UV-vis, IR, Raman spectroscopy and mass spectrometry. The stability, bonding, and electron density distributions of 3 have been studied by theoretical calculations.

The trans‐epoxysuccinyl amide group as a biologically active moiety in cysteine protease inhibitors such as loxistatin acid E64c has been used as a benchmark system for theoretical studies of environmental effects on the electron density of small active ingredients in relation to their biological activity. Here, the synthesis and the electronic properties of the smallest possible active site model compound are reported to close the gap between the unknown experimental electron density of trans‐epoxysuccinyl amides and the well‐known function of related drugs. Intramolecular substituent effects are separated from intermolecular crystal packing effects on the electron density, which allows us to predict the conditions under which an experimental electron density investigation on trans‐epoxysuccinyl amides will be possible. In this context, the special importance of the carboxylic acid function in the model compound for both crystal packing and biological activity is revealed through the novel tool of model energy analysis.

Modelling coordination compounds has been shown to be feasible using the invariom method; for the best fit to a given set of diffraction data, additional steps other than using lookup tables of scattering factors need to be carried out. Here such procedures are applied to a number of `duplicate structures', where structures of two or more supposedly different coordination complexes with identical ligand environments, but with different 3d metal ions, were published. However, only one metal atom can be plausibly correct in these structures, and other spectroscopic data are unavailable. Using aspherical scattering factors, a structure can be identified as correct from the deposited Bragg intensities alone and modelling only the ligand environment often suffices to make this distinction. This is not possible in classical refinements using the independent atom model. Quantum-chemical computations of the better model obtained after aspherical-atom refinement further confirm the assignment of the element in the respective figures of merit. peerReviewed

The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described., Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.