Abstract

Kristallklar: Die experimentelle Ladungsdichte einer Vitamin-B₁₂-Modifikation bestehend aus mehr als 250 Atomen (siehe Struktur) wurde aus den Daten einer hochauflösenden Röntgenbeugung mit ca. 660 000 Bragg-Reflexen bestimmt, wobei eine Kombination des Pseudoatomformalismus mit quantenchemischen Modellen zur Anwendung kam.

Crystal clear: The experimental charge density of a new solvate of vitamin B₁₂ with more than 250 atoms in the asymmetric unit is determined by high-resolution X-ray diffraction. A data set of approximately 660 000 Bragg reflections is interpreted using a combination of the pseudoatom formalism and quantum-chemical models.

The experimental charge densities of the halogenated C₆₀ fullerenes C₆₀F₁₈ and C₆₀Cl₃₀ were determined from high-resolution X-ray data sets measured with conventional Mo_Kα radiation at 20 K for C₆₀Cl₃₀ and with synchrotron radiation at 92 K for the fluorine compound. Bond topological and atomic properties were analyzed by using Bader's AIM theory. For the different CC bonds, which vary in lengths between 1.35 and 1.70 Å bond orders n between n=2 and significantly below n=1 were calculated from the bond topological properties at the bond critical points (BCP's). The low bond orders are seen for 5/6 bonds with each contributing carbon carrying a halogen atom. By integration over Bader's zero flux basins in the electron density gradient vector field atomic properties were also obtained. In contrast to free C₆₀, in which all carbon atoms have a uniform volume of 11 ų and zero charge, atomic volumes vary roughly between 5 and 10 ų in the halogenated compounds. Almost zero atomic charges are also found in the Cl derivative but a charge separation up to ±0.8 e exists between C and F in C₆₀F₁₈ due to the higher fluorine electronegativity, which is also seen in the electrostatic potential for which the electronegativity difference between carbon and fluorine, and the addition to one hemisphere of the fullerene cage leads to a strong potential gradient along the C₆₀F₁₈ molecule. From the summation over all atomic volumes it follows that the halogen addition does not only lead to a dramatic distortion of the C₆₀ cage but also to a significant shrinkage of its volume.

Ein hochaufgelöstes Synchrotron-Beugungsexperiment ermöglichte die Bestimmung der Elektronendichte eines [1.1.1]Propellanderivates und die Analyse ihrer Topologie. Es wurde ein Bindungspfad mit einem bindungskritischen Punkt von signifikanter Elektronendichte zwischen den „invertierten“ Brückenkopfatomen C4⋅⋅⋅C4a (siehe Bild) gefunden, was charakteristisch für eine kovalente Bindung ist; dagegen wurde am bindungskritischen Punkt keine Ladungskonzentration festgestellt.

Synchrotron radiation was required for high-resolution diffraction experiments to determine the electron density and analyze the topology of a new [1.1.1]propellane derivative. A bond path with a bond critical point of significant electron density was found between the “inverted” bridgehead atoms C4⋅⋅⋅C4a (see picture), which is characteristic for a covalent bond; however, no charge accumulation at the bond critical point was seen.

The crystal structure of pure DL-tryptophan has been determined at 173 K, using large but thin plate formed crystals of C₁₁H₁₂N₂O₂, which were grown by cooling down a saturated solution of DL-tryptophan in isopropanole / formic acid. The crystals are monoclinic, space group P 2₁/c, with the unit cell constants: a = 18.899(2), b = 5.7445(6), c = 9.309(1) Å, β = 101.776(2), V = 989.4(4) , D_calc = 1.371, Z = 4, F(000) = 432, λ(MoKα) = 0.71073 Å, μ = 0.096 mm^-1. The crystal structure was solved by direct methods and refined by full-matrix least squares to a final R-factor = 4.03 % with 3343 unique reflections of which 2104 were observed. The molecule is zwitterionic in the crystal with the protonated amino group and the carboxylate group in unusual conformations with respect to the indole ring system compared to other tryptophan derivatives. A D- and L- molecular pair forms a dimer by N – H … O hydrogen bonds via a crystallographic inversion center. The dimers are linked by further N – H … O hydrogen bonds to form a head to head bilayer arrangement of the molecules in the crystal lattice. Except for weak van der Waals contacts there is no relation between indole tails of neighboured bilayers. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Two penicillin derivatives, the active penamecillin and the inactive penamecillin-1β-sulfoxide, were used to study the relationship between their charge density and their activity. Single crystals of both compounds were measured at the synchrotron beamline F1 at the HASYLAB/DESY, at 100 K and up to resolutions of around 0.4 Å. Experimental charge densities were obtained by using the Hansen–Coppens multipole formalism. The cleavage of the amide bond in the β-lactam ring is of paramount importance in the mechanism of action of penicillins. Topological analysis of this bond in terms of Bader's AIM theory showed that its strength is equal in both compounds; therefore a direct influence of bond strength on the activity can be ruled out. However, the two derivatives differ significantly in their experimental electrostatic potentials. These differences are discussed and provide further insight into the chemistry and activity of penicillins.

C₁₄H₁₅NO₂ (293 K): monoclinic space group P2₁/n, a = 24.580(10), b = 5.536(2), c = 9.037(3) Å, β = 91.18(4)°, V = 1229.4(8) ų, D_x = 1.239 g · cm^-3, Z = 4, F(000) = 488, λ(CuKα) = 1.5418 Å, μ = 0.667 mm^-1. The title compound which was isolated from the rhizomes of Piper lolot C.DC has antibacterial activity. Its chemical identity was established by this X-ray analysis. The molecule consists of a planar propanoyl pyrrole and a methoxyphenyl fragment with an interplanar angle of 93.8(3)° which is by 30° larger than the corresponding angle reported in the literature for the comparable dimethoxy derivative, which was also derived from Piper species.

Despite its high instability, the cumulene 1,1,4,4-tetrafluorobutatriene was obtained in a crystalline form. Its X-ray structure characterization revealed the presence of a herring-bone motif in the solid state (see picture). Experimental and calculated charge desity distributions show, as expected, that the central double bond is shorter and displays a higher charge density than the two outer double bonds.

Trotz seiner hohen Instabilität gelang die Kristallzüchtung und die röntgenographische Charakterisierung des Cumulens 1,1,4,4-Tetrafluorbutatrien, das im festen Zustand eine Fischgrätenanordnung einnimmt (siehe Bild). Aus experimentellen und berechneten Ladungsdichteverteilungen ergibt sich erwartungsgemäß, dass die zentrale Doppelbindung kürzer ist und eine höhere Ladungsdichte aufweist als die beiden äußeren Bindungen.

The charge density of glycyl-L-threonine dihydrate is extracted from a synchrotron data set of 98 405 reflections collected at 100 K with a Bruker CCD area detector up to a resolution of d=0.38 Å (sinθ/λ=1.32 Å⁻¹). The data are interpreted in terms of the “rigid pseudoatom” model. The topology of the experimental density is analyzed and compared with the topology obtained experimentally for the constituting amino acids and to that derived from Hartree-Fock calculations for the isolated molecule. All critical points of the electron density at the covalent and hydrogen bonds, as well as those of the Laplacian, were located, thereby deriving quantitative topological data for the peptide and side chain bonds. Bond topological indices in the dipeptide compare well with those of the corresponding bonds in the building amino acids, thus suggesting transferability of electronic properties of atoms and functional groups when these are derived by Bader's partitioning. Discrepancies between theoretical and experimental results could be attributed to crystal field effects.

Die Ladungsdichteverteilung von Glycyl-L-threonin Dihydrat wurde aus einem Synchrotrondatensatz von 98 405 Reflexen bestimmt, der bei 100 K mit einem Bruker CCD Flächendetektor bis zu einer Auflösung von d=0.38 Å (bzw. sinθ/λ= 1.32 Å⁻¹) gemessen wurde. Der Datensatz wurde mit Hilfe des “Pseudoatom”-Formalismus interpretiert. Eine topologische Analyse der experimentellen Ladungsdichte wurde durchgeführt und die Ergebnisse wurden einerseits mit der Topologie der entsprechenden Monoaminosäuren Gly und L-Thr verglichen, andererseits mit Befunden von Hartree-Fock-Rechnungen an dem isolierten Molekül des Dipeptids. Alle kritischen Punkte auf den kovalenten Bindungen und den Wasserstoffbrücken wurden sowohl für die Ladungsdichte als auch für die Laplacefunktion bestimmt, so daß quantitative topologische Daten für die Peptidbindung und die Bindungen in den Seitengruppen zur Verfügung stehen. Letztere stimmen gut mit den entsprechenden Bindungen in den beitragenden Aminosäuren Gly und L-Thr überein, was für die Übertragbarkeit elektronischer Eigenschaften von Atomen oder funktionellen Gruppen spricht, wenn diese nach dem Bader'schen Partitionierungskonzept behandelt werden. Abweichungen zwischen theoretischen und experimentellen Ergebnissen konnten intermolekularen Wechselwirkungen im Kristall zugeordnet werden.

Synchrotron radiation and CCD detection give the possibility for fast diffraction experiments, which were employed to deduce the exact charge-density distributions of some amino acids. Their topological analysis (the figure shows the negative Laplacian function of dl-serine in the plane of the carboxylate group) yields not only comparable information about intramolecular but also about weak intermolecular interactions.

The electron density distribution of diisocyanomethane (see picture) is obtained from single-crystal X-ray diffraction data and by ab initio calculations. Multipole models with different restraints are applied to judge the physical significance of the parametrization of the experimental density. Topological indices as well as the electrostatic potential indicate crystal field effects.

Synchrotronstrahlung und CCD-Detektion ermöglichten schnelle Beugungsexperimente, mit denen genaue Ladungsdichteverteilungen von Aminosäuren hergeleitet werden konnten. Ihre topologische Analyse (das Bild zeigt die negative Laplace-Funktion von DL-Serin in der Ebene der Carboxylatgruppe) liefert für die Aminosäuren nicht nur vergleichbare Informationen über intramolekulare, sondern auch über schwache intermolekulare Wechselwirkungen.

The synthesis of the AB-type Diels-Alder (DA) monomer 12 is reported whose self-condensation leads to the formation of the linear ladder oligomer 17 and its cyclic congener 18. 18 is the largest [n]cyclacene derivative known (n = 18) and can be obtained by thermal treatment of 17 in yields of up to 45% utilizing the reversibility of the DA cyclization involved. 17 can be considered a “storage form” for 18.

Traditional direct methods alone are not potent enough to solve the crystal structures of mid-sized molecules (over 200 non-hydrogen atoms). Considerably more efficient are the new methods such as shake-and-bake and SHELXD. Even the 1000-atom barrier has now been overcome, so the gap between small and large molecules is closing.

Traditionelle Direkte Methoden allein sind kaum geeignet, um die Strukturen mittelgroßer Moleküle mit über 200 Nichtwasserstoffatomen kristallographisch zu lösen. Wesentlich leistungsfähiger sind die neuen Methoden Shake-and-Bake und SHELXD. Inzwischen kann sogar die 1000-Atome-Grenze überschritten und damit die Lücke in der Strukturaufklärung zwischen kleinen und großen Molekülen geschlossen werden.