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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. 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. [ABSTRACT FROM AUTHOR]

Abstract: Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

X-ray crystallographic characterization of products derived from natural and fully synthetic trioxacarcins, molecules with potent antiproliferative effects, illuminates aspects of their reactivity and mechanism of action. Incubation of the fully synthetic trioxacarcin analog 3 , which lacks one of the carbohydrate residues present in the natural product trioxacarcin A ( 1 ) as well as oxygenation at C2 and C4 yet retains potent antiproliferative effects, with the self-complimentary duplex oligonucleotide d(AACCGGTT) led to production of a crystalline covalent guanine adduct ( 6 ). Adduct 6 is closely analogous to gutingimycin ( 2 ), the previously reported guanine adduct derived from incubation of natural trioxacarcin A ( 1 ) with duplex DNA, suggesting that 3 and 1 likely share a common basis of cytotoxicity. In addition, we isolated a novel, dark-red crystalline guanine adduct ( 7 ) from incubation of trioxacarcin A itself with the self-complimentary duplex oligonucleotide d(CGTATACG). Crystallographic analysis suggests that 7 is an anthraquinone derivative, which we propose arises by a sequence of guanosine alkylation within duplex DNA, depurination, base-catalyzed elimination of the trioxacarcinose A carbohydrate residue, and oxidative rearrangement to form an anthraquinone. We believe that this heretofore unrecognized chemical instability of natural trioxacarcins may explain why trioxacarcin analogs lacking C4 oxygenation exhibit superior chemical stabilities yet, as evidenced by structure 3 , retain a capacity to form lesions with duplex DNA. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The rigid-bond model [Hirshfeld (1976). Acta Cryst. A 32, 239-244] states that the mean-square displacements of two atoms are equal in the direction of the bond joining them. This criterion is widely used for verification (as intended by Hirshfeld) and also as a restraint in structure refinement as suggested by Rollett [ Crystallographic Computing (1970), edited by F. R. Ahmed et al., pp. 167-181. Copenhagen: Munksgaard]. By reformulating this condition, so that the relative motion of the two atoms is required to be perpendicular to the bond, the number of restraints that can be applied per anisotropic atom is increased from about one to about three. Application of this condition to 1,3-distances in addition to the 1,2-distances means that on average just over six restraints can be applied to the six anisotropic displacement parameters of each atom. This concept is tested against very high resolution data of a small peptide and employed as a restraint for protein refinement at more modest resolution ( e.g. 1.7 Å). [ABSTRACT FROM AUTHOR]

The article examines the crystal structure of ciprofloxacin-2,2-difluoroethanol (2/3) and ciprofloxacin-water (3/14.5). The first compound contains two zwitterionic ciprofloxacin molecules and three difluorethanol solvent molecules, while the other has three zwitterionic ciprofloxacin molecules and a mixture of ordered and disordered water molecules. The intermolecular interactions of these compounds were also analyzed using fingerprint plots from Hirshfield surfaces.

Two new polymorphs of the phase-change material sodium acetate were characterized by single-crystal X-ray diffraction. A tetragonal form was found first. It converted to a orthorhombic form after measurement of a single crystal of the tetragonal form at 100 K and subsequent warming to ambient temperature. Hirshfeld surface fingerprint plots show the different packing environments of the two new compared to the two known orthorhombic polymorphs Forms I and II. The accuracy and precision of the structures were improved compared to conventional independent atom model refinement through the use of aspherical scattering factors of the invariom database. We think that the layered nature of all sodium acetate forms, and the thereby limited (“quantized”) availability of vibrational modes, is related to the phenomenon of supersaturation, which is connected to its phase-change properties. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]