110 research outputs found
Electron density of a benzoylated tetrafructopyranose
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
Redetermination and invariom refinement of 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-4-ium-1-yl)-1,4-dihydroquinoline-3-carboxylate hexahydrate at 120 K
The structure of the title compound, C17H18FN3O3·6H2O, has been redetermined at 120 K. An invariom refinement, a structural refinement using aspherical scattering factors from theoretically predicted multipole population parameters, yields accurate geometry and anisotropic displacement parameters, including hydrogen-bonding parameters. All potential hydrogen-bond donors and acceptors are involved in hydrogen bonding, forming an intricate three-dimensional network of N—H⋯O and O—H⋯O bonds
Enhanced rigid-bond restraints
An extension is proposed to the rigid-bond description of atomic thermal motion in crystals
Redetermination and invariom refinement of 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-4-ium-1-yl)-1,4-dihydroquinoline-3-carboxylate hexahydrate at 120 K
Charge density analysis of two polymorphs of antimony(III) oxide
High-resolution X-ray diffraction data have been collected on the cubic polymorph of antimony(III) oxide (senarmontite) to determine the charge distribution in the crystal. The results are in quantitative agreement with crystal Hartree–Fock calculations for this polymorph, and have been compared with theoretical calculations on the orthorhombic polymorph (valentinite). Information about the nature of bonding and relative bond strengths in the two polymorphs has been extracted in a straightforward manner via topological analysis of the electron density. All the close contacts in both polymorphs are found to be similar in nature based on the value of the Laplacian, the magnitude of the electron density and the local energy density at the bond critical points, and these characterise the observed interactions as substantially polar covalent, similar to molecular calculation results on Si–O and Ge–O. Electrostatic potential isosurfaces reveal the octopolar nature of this function for senarmontite, and shed light on the observed packing arrangement of Sb4O6 molecules in the crystal
Analysis of two [2]catenanes based on electron densities from invariom refinement and results from DFT calculations
The authors are grateful to the Deutsche Forschungsgemeinschaft (DFG) for financial support by project DI 921/6-1.Catenanes are of considerable interest as potential building blocks for molecular machines. The simplest [2]catenanes, Hopf links, consist of two macrocycles that are mechanically interlocked. This unusual architecture cannot be opened without breaking at least one covalent bond. Based on these structural characteristics, unusual properties on Hirshfeld or electrostatic potential surfaces could be expected. For a comparison of their structural and electronic properties, the electron densities (EDs) of two [2]catenanes, coded H22 and H4L7 in the original papers, were examined after application of the invariom formalism, relying on X-ray diffraction data collected earlier. The obtained electron density distributions were subjected to an analysis using the QTAIM formalism to yield bond and atomic properties. Moreover, molecular Hirshfeld surfaces and electrostatic potentials (ESP) were calculated. There are different types of intra- and intermolecular interactions in these two [2]catenanes. In addition to classical N-H···N and C-H···O hydrogen bonds, various types of π···π interactions in H22 and in H4L7 exist. Most of them are verified by local ED concentrations visible on the corresponding Hirshfeld surfaces, except for the parallel π···π interactions in H22, which are either too weak or too diffuse to generate an ED signal on the Hirshfeld surface between the contributing aromatic rings. The electrostatic potentials (ESPs) were calculated and displayed on molecular surfaces. The interaction in the cavity of one macrocycle with the penetrated fragment of the second one was examined and it was found that corresponding to the above-mentioned contacts attractive and repulsive interactions exist. Additionally the ED was examined using results of density functional calculations, including non-covalent interaction index (NCI) and electron localizability indicator (ELI-D) surface analysis, complementing experimental findings.Publisher PDFPeer reviewe
Larvicidal activity of metabolites from the endophytic Podospora sp. against the malaria vector Anopheles gambiae
In a screening for natural products with mosquito larvicidal activities, the endophytic fungus Podospora sp. isolated from the plant Laggera alata (Asteraceae) was conspicuous. Two xanthones, sterigmatocystin (1) and secosterigmatocystin (2), and an anthraquinone derivative (3) 13-hydroxyversicolorin B were isolated after fermentation on M2 medium. These compounds were characterised using spectroscopic and X-ray analysis and examined against third instar larvae of Anopheles gambiae. The results demonstrated that compound 1 was the most potent one with LC50 and LC90 values of 13.3 and 73.5 ppm, respectively. Over 95% mortality was observed at a concentration 100 ppm after 24 h. These results compared farvourably with the commercial larvicide pylarvex® that showed 100% mortality at the same concentration. Compound 3 was less potent and had an LC50 of 294.5 ppm and over 95% mortality was achieved at a concentration of 1,000 ppm. Secosterigmatocystin (2) revealed relatively weak activity and therefore LC values were not determined
On modelling disordered crystal structures through restraints from molecule-in-cluster computations,and distinguishing static and dynamic disorder
Distinguishing disorder into static and dynamic based on multi-temperature
X-ray or neutron diffraction experiments is the current state of the art, but is
only descriptive, not predictive. Here, several disordered structures are revisited
from the Cambridge Crystallographic Data Center ‘drug subset’, the Cambridge
Structural Database and own earlier work, where experimental intensities of
Bragg diffraction data were available. Using the molecule-in-cluster approach,
structures with distinguishable conformations were optimized separately, as
extracted from available or generated disorder models of the respective
disordered crystal structures. Re-combining these ‘archetype structures’ by
restraining positional and constraining displacement parameters for conventional
least-squares refinement, based on the optimized geometries, then often
achieves a superior fit to the experimental diffraction data compared with
relying on experimental information alone. It also simplifies and standardizes
disorder refinement. Ten example structures were analysed. It is observed
that energy differences between separate disorder conformations are usually
within a small energy window of RT (T = crystallization temperature). Further
computations classify disorder into static or dynamic, using single experiments
performed at one single temperature, and this was achieved for propionamide
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