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Disorder in crystal structures can disappear, depending on the circumstances, as shown by multi-temperature measurements, aspherical-atom refinement and computational analyses.

The quality of various approximation methods for modelling anisotropic displacement parameters (ADPs) for hydrogen atoms was investigated in a comparative study. A multipole refinement was performed against high-resolution single crystal X-ray data of 9-diphenylthiophosphoranylanthracene (SPAnH) and 9,10-bis-diphenylthiophosphoranylanthracene·toluene (SPAnPS). Hydrogen-atom parameters and structural properties derived from our collected neutron data sets were compared with those obtained from the SHADE-server, the software APD-Toolkit based on the invariom database, the results from Hirshfeld atom refinement conducted in the OLEX2 GUI (HARt), and the results of anisotropic hydrogen refinement within XD2016. Additionally, a free refinement of H-atom positions against X-ray data was performed with fixed ADPs from various methods. The resulting C—H bond distances were compared with distances from neutron diffraction experiments and the HARt results. Surprisingly, the refinement of anisotropic hydrogen displacement parameters against the X-ray data yielded the smallest deviations from the neutron values. However, the refinement of bond-directed quadrupole parameters turned out to be vital for the quality of the resulting ADPs. In both model structures, SHADE and, to a lesser extent, APD-Toolkit showed problems in dealing with atoms bonded to carbon atoms with refined Gram-Charlier parameters for anharmonic motion. The HARt method yields the most accurate C—H bond distances compared to neutron data results. Unconstrained refinement of hydrogen atom positions using ADPs derived from all other used approximation methods showed that even with well approximated hydrogen ADPs, the resulting distances were still significantly underestimated.

A new series of [Pd2(L)4] cages based on photochromic dithienylethene (DTE) ligands allowed us to gain insight into the successive photoswitching of multiple DTE moieties in a confined metallo‐supramolecular assembly. Three new X‐ray structures of [Pd2(o‐L4)4], [Pd2(o‐L1)2(c‐L1)2] and [Pd2(c‐L1)4] (o‐L and c‐L = open and closed forms of DTE ligands, respectively) were obtained. The structures deliver snapshots of three different combinations of DTE photoisomeric states within the cage, facilitating a comparison of the all‐open with the all‐closed, and most notably, an intermediate form where open and closed switches co‐exist in the same cage. Moreover, a series of spherical anionic borate clusters was introduced in order to study their roles in the light‐controllable host–guest chemistry. The binding guests show higher affinities with the flexible open cage [Pd2(o‐L1)4] than with the rigid closed cage [Pd2(c‐L1)4]. For the [B12F12]2− guest, thermodynamic data obtained from NMR experiments was compared to results from isothermal titration calorimetry (ITC).

The angucyclines form the largest family of polycyclic aromatic polyketides, and have been studied extensively. Herein, we report the discovery of lugdunomycin, an angucycline‐derived polyketide, produced by Streptomyces species QL37. Lugdunomycin has unique structural characteristics, including a heptacyclic ring system, a spiroatom, two all‐carbon stereocenters, and a benzaza‐[4,3,3]propellane motif. Considering the structural novelty, we propose that lugdunomycin represents a novel subclass of aromatic polyketides. Metabolomics, combined with MS‐based molecular networking analysis of Streptomyces sp. QL37, elucidated 24 other rearranged and non‐rearranged angucyclines, 11 of which were previously undescribed. A biosynthetic route for the lugdunomycin and limamycins is also proposed. This work demonstrates that revisiting well‐known compound families and their producer strains still is a promising approach for drug discovery.

A new aspherical scattering factor formalism was implemented in SHELXL. It relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. The automated atom-type assignment was derived from the invariom formalism., A new aspherical scattering factor formalism has been implemented in the crystallographic least-squares refinement program SHELXL. The formalism relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. Asphericity contributions were derived from the electron density obtained from quantum-chemical density functional theory computations of suitable model compounds that contain particular chemical environments, as defined by the invariom formalism. Thanks to a new algorithm, invariom assignment for refinement in SHELXL is automated. A suitable parameterization for each chemical environment within the new model was achieved by metaheuristics. Figures of merit, precision and accuracy of crystallographic least-squares refinements improve significantly upon using the new model.

Amino acid structures are an ideal test set for method‐development studies in crystallography. High‐resolution X‐ray diffraction data for eight previously studied genetically encoding amino acids are provided, complemented by a non‐standard amino acid. Structures were re‐investigated to study a widely applicable treatment that permits accurate X−H bond lengths to hydrogen atoms to be obtained: this treatment combines refinement of positional hydrogen‐atom parameters with aspherical scattering factors with constrained “TLS+INV” estimated hydrogen anisotropic displacement parameters (H‐ADPs). Tabulated invariom scattering factors allow rapid modeling without further computations, and unconstrained Hirshfeld atom refinement provides a computationally demanding alternative when database entries are missing. Both should incorporate estimated H‐ADPs, as free refinement frequently leads to over‐parameterization and non‐positive definite H‐ADPs irrespective of the aspherical scattering model used. Using estimated H‐ADPs, both methods yield accurate and precise X−H distances in best quantitative agreement with neutron diffraction data (available for five of the test‐set molecules). This work thus solves the last remaining problem to obtain such results more frequently. Density functional theoretical QM/MM computations are able to play the role of an alternative benchmark to neutron diffraction.

A set of look-up point charges for generating molecular electrostatic potentials is provided. The set relies on atom classification of the invariom database, which has already been applied to assign aspherical scattering factors in single-crystal X-ray diffraction. The focus of the investigation is on improving the accuracy of electrostatic potentials calculated by using tabulated point charges. In this respect, the performance of invariom point charges is compared with 1) those from a restrained fit to the electrostatic potential directly following quantum-chemical DFT computations, 2) semi-empirical AM1-bcc charges, and 3) conceptually similar TPACM4 look-up charges. Invariom classification gives charges that perform better than those from TPACM4, although tabulated charges remain inferior to those from molecule-specific computations. Point-charge electrostatic potentials also agree favorably with those from charge-density studies on the basis of X-ray experiments, without requiring the considerable effort of the latter.

A novel method and a new program for estimating anisotropic displacement parameters for H atoms are presented. Results are validated against molecular orbital computations and neutron diffraction data., Invariom partitioning and notation are used to estimate anisotropic hydrogen displacements for incorporation in crystallographic refinement models. Optimized structures of the generalized invariom database and their frequency computations provide the information required: frequencies are converted to internal atomic displacements and combined with the results of a TLS (translation–libration–screw) fit of experimental non-hydrogen anisotropic displacement parameters to estimate those of H atoms. Comparison with TLS+ONIOM and neutron diffraction results for four example structures where high-resolution X-ray and neutron data are available show that electron density transferability rules established in the invariom approach are also suitable for streamlining the transfer of atomic vibrations. A new segmented-body TLS analysis program called APD-Toolkit has been coded to overcome technical limitations of the established program THMA. The influence of incorporating hydrogen anisotropic displacement parameters on conventional refinement is assessed.

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.

Ein einfacher selbstorganisierter [Pd2L4]-Koordinationskafig bestehend aus vier Carbazol-basierten Liganden dimerisiert nach Zugabe von 1.5 Aquivalenten eines Halogenidions (X=Cl−, Br−) zu einem verflochtenen Doppelkafig [3 X@Pd4L8]. Die Halogenidionen agieren als Template, eingelagert in den drei Taschen der verschlungenen Kafigstruktur und umgeben von vier PdII Kationen. Zugabe hoherer Mengen desselben Halogenidions bewirkt eine weitere strukturelle Umwandlung, die in einer dreifach verschlungenen Verbindung resultiert. Letztere enthalt trans-koordinierte PdII-Zentren, die von zwei Pyridin-Donor- und zwei Halogenidliganden umgeben sind. Dieses einfache System zeigt eindrucksvoll, wie molekulare Komplexitat aus der graduellen Anderung der relativen Konzentrationen einer geringen Zahl an Reaktionspartnern erwachsen kann, insbesondere, wenn diese unterschiedliche strukturelle Rollen einnehmen konnen.

The temperature dependence of hydrogen U iso and parent U eq in the riding hydrogen model is investigated by neutron diffraction, aspherical-atom refinements and QM/MM and MO/MO cluster calculations. Fixed values of 1.2 or 1.5 appear to be underestimated, especially at temperatures below 100 K., The temperature dependence of H-U iso in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-U iso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.

(cAAC)Ge(GeL)2 (1) (cAAC = cyclic alkyl(amino) carbene; L = PhC(tBuN)2), a functionalized Ge3-compound was prepared. Quantum mechanical studies on 1 show a reciprocal relationship between the electronic state of the central tri-coordinated Ge atom and its reactivity towards protons, viz. tetravalent Ge(0) in terms of bonding and divalent Ge(0) in terms of reactivity. Thus the central Ge atom can be considered as having a hidden but highly reactive lone pair of electrons. However, the terminal Ge atoms can be considered as tri-coordinated divalent Ge(I) with an active lone pair of electrons.

The quality of various approximation methods for modelling anisotropic displacement parameters (ADPs) for hydrogen atoms was investigated in a comparative study. A multipole refinement was performed against high-resolution single crystal X-ray data of 9-diphenylthiophosphoranylanthracene (SPAnH) and 9,10-bis-diphenylthiophosphoranylanthracene·toluene (SPAnPS). Hydrogen-atom parameters and structural properties derived from our collected neutron data sets were compared with those obtained from the SHADE-server, the software APD-Toolkit based on the invariom database, the results from Hirshfeld atom refinement conducted in the OLEX2 GUI (HARt), and the results of anisotropic hydrogen refinement within XD2016. Additionally, a free refinement of H-atom positions against X-ray data was performed with fixed ADPs from various methods. The resulting C-H bond distances were compared with distances from neutron diffraction experiments and the HARt results. Surprisingly, the refinement of anisotropic hydrogen displacement parameters against the X-ray data yielded the smallest deviations from the neutron values. However, the refinement of bond-directed quadrupole parameters turned out to be vital for the quality of the resulting ADPs. In both model structures, SHADE and, to a lesser extent, APD-Toolkit showed problems in dealing with atoms bonded to carbon atoms with refined Gram-Charlier parameters for anharmonic motion. The HARt method yields the most accurate C-H bond distances compared to neutron data results. Unconstrained refinement of hydrogen atom positions using ADPs derived from all other used approximation methods showed that even with well approximated hydrogen ADPs, the resulting distances were still significantly underestimated.

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@Pd4L1 8], 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 [Pd2L2 4]. 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. peerReviewed

A disiladicarbene, (Cy-cAAC)2Si2 (2), was synthesized by reduction of Cy-cAAC:SiCl4 adduct with KC8. The dark-colored compound 2 is stable at room temperature for a year under an inert atmosphere. Moreover, it is stable up to 190 °C and also can be characterized by electron ionization mass spectrometry. Theoretical and Raman studies reveal the existence of a Si═Si double bond with a partial double bond between each carbene carbon atom and silicon atom. Cyclic voltammetry suggests that 2 can quasi-reversibly accept an electron to produce a very reactive radical anion, 2(•-), as an intermediate species. Thus, reduction of 2 with potassium metal at room temperature led to the isolation of an isomeric neutral rearranged product and an anionic dimer of a potassium salt via the formation of 2(•-).