Invariom refinement of a new monoclinic solvate of thiostrepton at 0.64†Šresolution.

A new monoclinic solvate containing two molecules of the thiopeptide antibiotic thiostrepton in the asymmetric unit has been crystallized in space group P2(1). Single-crystal diffraction data to a resolution of 0.64 Šwere collected at the SLS synchrotron, allowing structure solution by direct methods and resolution of the disorder present. Valence electron density can be observed in the Fourier residual density from refinement with the independent-atom model, which is a prerequisite for successful application of more sophisticated aspherical-atom scattering factors such as the invariom model when aiming to improve the structural model. Invariom refinement improves quality indicators such as R1(F) for thiostrepton, as previously demonstrated for small molecules. The nonspherical electron-density model also allows the direct derivation of a dipole moment and an electrostatic potential for the whole molecule, which is discussed in the context of antibiotic activity and molecular recognition.

Isolation and reactivity of an elusive diazoalkene.

Most functional groups, especially those consisting of the abundant elements of organic matter-carbon, nitrogen and oxygen-have been extensively studied and only very few remain speculative due to their high intrinsic reactivity. In contrast to the well-explored chemistry of diazoalkanes (R2C=N2), diazoalkenes (R2C=C=N2) have been postulated in several organic transformations, but remain elusive long-sought intermediates. Here, we present a room-temperature stable diazoalkene, utilizing a dinitrogen transfer from nitrous oxide. This functional group shows dual-site nucleophilicity (C and N atoms) and features a bent C-C-N entity (124°) and a long N-N bond together with a remarkable low infrared absorption (1,944 cm-1). Substitution of N2 by an isocyanide leads to a vinylidene ketenimine. Furthermore, photochemically triggered loss of dinitrogen might proceed through a transient triplet vinylidene. We anticipate the existence of a stable diazoalkene functional group to pave an exciting avenue into the chemistry of low-valent carbon and unsaturated carbenes.

Validation of experimental charge densities: refinement of the macrolide antibiotic roxithromycin.

Multipole refinements of larger organic molecules have so far been limited to a few exceptional cases. We report an investigation of the detailed experimental electron-density distribution (EDD) of roxithromycin, a macrolide antibiotic consisting of 134 atoms. Although the experimental multipole refinement on high-resolution synchrotron data converged smoothly, validation of the electron density by calculation of an `experiment minus invariom' difference density revealed conformational disorder of the H atoms. Hydrogen disorder is shown to affect the EDD, the electrostatic potential and atomic properties as defined by Bader's quantum theory of atoms in molecules. A procedure to obtain the electron density distribution in the presence of disorder is proposed.

The generalized invariom database (GID).

Invarioms are aspherical atomic scattering factors that enable structure refinement of more accurate and more precise geometries than refinements with the conventional independent atom model (IAM). The use of single-crystal X-ray diffraction data of a resolution better than sin θ/λ = 0.6 Å(-1) (or d = 0.83 Å) is recommended. The invariom scattering-factor database contains transferable pseudoatom parameters of the Hansen-Coppens multipole model and associated local atomic coordinate systems. Parameters were derived from geometry optimizations of suitable model compounds, whose IUPAC names are also contained in the database. Correct scattering-factor assignment and orientation reproduces molecular electron density to a good approximation. Molecular properties can hence be derived directly from the electron-density model. Coverage of chemical environments in the invariom database has been extended from the original amino acids, proteins and nucleic acid structures to many other environments encountered in organic chemistry. With over 2750 entries it now covers a wide sample of general organic chemistry involving the elements H, C, N and O, and to a lesser extent F, Si, S, P and Cl. With respect to the earlier version of the database, the main modification concerns scattering-factor notation. Modifications improve ease of use and success rates of automatic geometry-based scattering-factor assignment, especially in condensed hetero-aromatic ring systems, making the approach well suited to replace the IAM for structures of organic molecules.