Julian J. Holstein

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.

N-Heterocyclic Carbene Stabilized Dichlorosilylene Transition-Metal Complexes of V(I), Co(I), and Fe(0)

Reactions of N-heterocyclic carbene stabilized dichlorosilylene IPr·SiCl(2) (1) (IPr = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) with (η(5)-C(5)H(5))V(CO)(4), (η(5)-C(5)H(5))Co(CO)(2), and Fe(2)(CO)(9) afford dichlorosilylene complexes IPr·SiCl(2)·V(CO)(3)(η(5)-C(5)H(5)) (2), IPr·SiCl(2)·Co(CO)(η(5)-C(5)H(5)) (3), and IPr·SiCl(2)·Fe(CO)(4) (4), respectively. Complexes 2-4 are stable under an inert atmosphere, are soluble in common organic solvents, and have been characterized by elemental analysis and multinuclear ((1)H, (13)C, and (29)Si) NMR spectroscopy. Molecular structures of 2-4 have been determined by single crystal X-ray crystallographic studies and refined with nonspherical scattering factors.

Geometric Complementarity in Assembly and Guest Recognition of a Bent Heteroleptic cis-[Pd2LA2LB2] Coordination Cage

Due to the inherent difficulties in achieving a defined and exclusive formation of multicomponent assemblies against entropic predisposition, we present the rational assembly of a heteroleptic [Pd2LA2LB2]4+ coordination cage achieved through the geometric complementarity of two carefully designed ligands, LA and LB. With Pd(II) cations as rigid nodes, the pure distinctly angular components readily form homoleptic cages, a [Pd2LA4]4+ strained helical assembly and a [Pd4LB8]8+ box-like structure, both of which were characterized by X-ray analysis. Combined, however, the two ligands could be used to cleanly assemble a cis-[Pd2LA2LB2]4+ cage with a bent architecture. The same self-sorted product was also obtained by a quantitative cage-to-cage transformation upon mixing of the two homoleptic cages revealing the [Pd2LA2LB2]4+ assembly as the thermodynamic minimum. The structure of the heteroleptic cage was examined by ESI-MS, COSY, DOSY, and NOESY methods, the latter of which pointed toward a cis-conformation of ligands in the assembly. Indeed, DFT calculations revealed that the angular ligands and strict Pd(II) geometry strongly favor the cis-[Pd2LA2LB2]4+ species. The robust nature of the cis-[Pd2LA2LB2]4+ cage allowed us to probe the accessibility of its cavity, which could be utilized for shape recognition toward stereoisomeric guests. The ability to directly combine two different backbones in a controlled manner provides a powerful strategy for increasing complexity in the family of [Pd2L4] cages and opens up possibilities of introducing multiple functionalities into a single self-assembled architecture.

Anharmonic Motion in Experimental Charge Density Investigations

In the charge density study of 9-diphenylthiophosphinoylanthracene the thermal motion of several atoms needed an anharmonic description via Gram-Charlier coefficients even for data collected at 15 K. As several data sets at different temperatures were measured, this anharmonic model could be proved to be superior to a disorder model. Refinements against theoretical data showed the resemblance of an anharmonic model and a disorder model with two positions very close to each other (~0.2 Å), whereas these two models could be clearly distinguished if the second position is 0.5 Å apart. The refined multipole parameters were distorted when the anharmonic motion was not properly refined. Therefore, this study reveals the importance of detecting and properly handling anharmonic motion. Unrefined anharmonic motion leads to typical shashlik-like residual density patterns. Therefore, careful analysis of the residual density and the derived probability density function after the refinement of the Gram-Charlier coefficients proved to be the most useful tools to indicate the presence of anharmonic motion.

An experimental charge density study of two isomers of hexasilabenzene.

The similarities and differences between carbon and its heavier congener silicon generate challenging synthetic targets, especially when multiply bonded systems are concerned. The first stable compound with a Si=Si bond goes back to West et al. in 1981, and conjugated systems with Si= Si double bonds were pioneered in 1997 by Weidenbruch et al. Whether silicon analogues of benzene can show aromatic character is still a point of constant debate. The aromatic nature of silabenzenes has been predicted theoretically, but the synthesis of a stable silabenzene was not accomplished until Tokitoh et al. reported the sterically encumbered 2,4,6-tris[bis(trimethylsilyl)methyl]phenyl-substituted monosila derivative. At the same time, Ando et al. independently reported the synthesis of 1,4-disila Dewar benzene. Only two years later, Sekiguchi et al. accomplished the synthesis of 1,2-disilabenzene by reacting RSi SiR (R = Si(CH(SiMe3)2iPr) with PhC CH in a formal [2+2+2] cycloaddition reaction. Recently, in a cooperative effort with the Roesky group, we reported the synthesis of a 1,4-disilabenzene by reacting [{PhC(NtBu)2}Si]2 with diphenyl alkyne. [8] With regards to homonuclear systems, the Scheschkewitz group recently made groundbreaking progress with the isolation of ring and cage isomers of hexasilabenzene (Scheme 1), which prompted the present experimental charge-density study. The dark-green-colored six-membered ring system 1 rearranges upon heating or UV irradiation to the red silicon cage compound 2 with a bridged propellane structure. An analogous transformation for fully saturated silicon compounds under irradiative conditions has been described by Kira and co-workers. We propose a transition of 1 to 2 by the reaction pathway in Scheme 1 (bottom). The transformation proceeds by the breaking of the Si1 Si3 and Si2 Si4 bonds in 1, followed by a twist of the four-membered silicon ring and the formation of the new Si1 Si2 and Si3 Si4 bonds (see Scheme 1 and video in the Supporting Information). In the following, we analyze the bonding situation in the ring (1) and cage (2) isomer of hexasilabenzene (TipSi)6 on the basis of experimental charge-density investigations (Figure 1). High-resolution X-ray data with (sinq/l)max =

DSR: enhanced modelling and refinement of disordered structures with SHELXL

The new computer program DSR enables semi-automatic modelling of disordered or well ordered moieties in crystal structures via a placement procedure of molecular fragments and corresponding stereochemical restraints from a database.

The group 7 metal carbonyl complexes from a stable heteroleptic silylene PhC(NtBu)2SiNPh2

Two silylene transition metal complexes were prepared by reacting stable N-heterocyclic silylene L {L = PhC(NtBu)(2)SiNPh(2)}with Mn(2)(CO)(10) and Re(2)(CO)(10) respectively in a 2 : 1 ratio to yield [L(2)Mn(CO)(4)](+)[Mn(CO)(5)](-) (1) and [L(2)Re(CO)(4)](+)[Re(CO)(5)](-) (2). Both complexes and were characterized by NMR spectroscopy, EI-MS spectrometry and elemental analysis. The molecular structures of complexes 1 and 2 were established by single crystal X-ray analysis.

Electrostatic properties of nine fluoroquinolone antibiotics derived directly from their crystal structure refinements

This article discusses the relevance of the similarity of the molecular electrostatic potential for rational drug design and optimization of lead structures on the basis of a comparison of nine fluoroquinolone antibiotics. Molecular electrostatic potentials and dipole moments were calculated directly from the electron-density distribution after crystal structure refinement with invarioms, theoretical non-spherical scattering factors. Deposited, newly determined and re-measured single-crystal diffraction data of varying quality were evaluated in this manner. An in silico validation procedure for invariom database entries is presented. Despite differences in their substitution pattern, molecular electrostatic potentials for molecules with the same protonation states show a striking degree of similarity for the whole group of compounds studied. The rapid calculation of electrostatic potentials directly from the invariom database makes the procedure suitable for high-throughput screening.

Carboxylic Acid Functionalized Clathrochelate Complexes:Large, Robust, and Easy-to-Access Metalloligands

Polycarboxylate ligands are among the most important building blocks for the synthesis of metal-organic frameworks (MOFs). The ability to access these ligands in an efficient way is of key importance for future applications of MOFs. Here, we demonstrate that mono- and dinuclear clathrochelate complexes are versatile scaffolds for the preparation of polytopic carboxylate ligands. The largely inert clathrochelate complexes have a trigonal-bipyramidal shape. The synthesis of functionalized clathrochelates with two, three, four, or five carboxylic acid groups in the ligand periphery can be achieved in a few steps from simple starting materials. Apart from being easily accessible, the metalloligands display interesting characteristics for applications in metallasupramolecular chemistry and materials science: they are rigid, large (up to 2.2 nm), and robust and they can show additional functions (e.g., fluorescence or extra charge) depending on the metal ion that is present in the clathrochelate core. The utility of these new metalloligands in MOF chemistry is demonstrated by the synthesis of zinc- and zirconium-based coordination polymers. The combination of Zn(NO3)2 with clathrochelates having two or three carboxylic acid groups gives MOFs in which the clathrochelate ligands are connected by Zn4O clusters or zinc paddlewheel links. The structures of the resulting two- and three-dimensional networks could be established by single-crystal X-ray crystallography. The reaction of carboxylic acid functionalized clathrochelates with ZrCl4 gives amorphous powders that display permanent porosity after solvent removal.

Desymmetrization of an Octahedral Coordination Complex Inside a Self-Assembled Exoskeleton

The synthesis of a centrally functionalized, ribbon-shaped [6]polynorbornane ligand L that self-assembles with Pd(II) cations into a {Pd2 L4 } coordination cage is reported. The shape-persistent {Pd2 L4 } cage contains two axial cationic centers and an array of four equatorial H-bond donors pointing directly towards the center of the cavity. This precisely defined supramolecular environment is complementary to the geometry of classic octahedral complexes [M(XY)6 ] with six diatomic ligands. Very strong binding of [Pt(CN)6 ](2-) to the cage was observed, with the structure of the host-guest complex {[Pt(CN)6 ]@Pd2 L4 } supported by NMR spectroscopy, MS, and X-ray data. The self-assembled shell imprints its geometry on the encapsulated guest, and desymmetrization of the octahedral platinum species by the influence of the D4h -symmetric second coordination sphere was evidenced by IR spectroscopy. [Fe(CN)6 ](3-) and square-planar [Pt(CN)4 ](2-) were strongly bound. Smaller octahedral anions such as [SiF6 ](2-) , neutral carbonyl complexes ([M(CO)6 ]; M=Cr, Mo, W) and the linear [Ag(CN)2 ](-) anion were only weakly bound, showing that both size and charge match are key factors for high-affinity binding.