Biscarbene-ruthenium complexes in catalysis: novel stereoselective synthesis of (1E,3E)-1,4-disubstituted-1,3-dienes via head-to-head coupling of terminal alkynes and addition of carboxylic acids

The reaction of a variety of alkynes RCtbd1;CH with a variety of carboxylic acids R(1)CO(2)H, in the presence of 5% of RuCl(COD)C(5)Me(5), selectively leads to the dienylesters (1E,3E)-RCH(1)=CH(2)-CH(3)=C(R)(O(2)CR(1)). The reaction also applies to amino acid and dicarboxylic acid derivatives. It is shown that the first step of the reaction consists of the head-to-head alkyne coupling and of the formation of the metallacyclic biscarbene-ruthenium complex isolated for R = Ph and catalyzing the formation of dienylester. D-labeled reactions show that the alkyne protons remain at the alkyne terminal carbon atoms and carboxylic acid protonates the C(1) carbon atom. QM/MM (ONIOM) calculations, supporting a mixed Fischer-Schrock-type biscarbene complex, show that protonation occurs preferentially at the carbene carbon C(1) adjacent to Ru, in the relative cis position with respect to the Ru-Cl bond, to give a mixed C(1)alkyl-C(4)carbene complex in which the C(4) carbene is conjugated with the noncoordinated C(2)=C(3) double bond. This 16-electron intermediate has a weak stabilizing alpha agostic C-H bond. This most stable isomer appears to have a C(4) center more accessible to the nucleophilic addition which accounts for the experimentally observed product.     

Computer-Assisted Solution of Chemical Problems—The Historical Development and the Present State of the Art of a New Discipline of Chemistry

The topic of this article is the development and the present state of the art of computer chemistry, the computer-assisted solution of chemical problems. Initially the problems in computer chemistry were confined to structure elucidation on the basis of spectroscopic data, then programs for synthesis design based on libraries of reaction data for relatively narrow classes of target compounds were developed, and now computer programs for the solution of a great variety of chemical problems are available or are under development. Previously it was an achievement when any solution of a chemical problem could be generated by computer assistance. Today, the main task is the efficient, transparent, and non-arbitrary selection of meaningful results from the immense set of potential solutions—that also may contain innovative proposals. Chemistry has two aspects, constitutional chemistry and stereochemistry, which are interrelated, but still require different approaches. As a result, about twenty years ago, an algebraic model of the logical structure of chemistry was presented that consisted of two parts: the constitution-oriented algebra of be- and r-matrices, and the theory of the stereochemistry of the chemical identity group. New chemical definitions, concepts, and perspectives are characteristic of this logic-oriented model, as well as the direct mathematical representation of chemical processes. This model enables the implementation of formal reaction generators that can produce conceivable solutions to chemical problems—including unprecedented solutions—without detailed empirical chemical information. New formal selection procedures for computer-generated chemical information are also possible through the above model. It is expedient to combine these with interactive methods of selection. In this review, the Munich project is presented and discussed in detail. It encompasses the further development and implementation of the mathematical model of the logical structure of chemistry as well as the experimental verification of the computer-generated results. The article concludes with a review of new reactions, reagents, and reaction mechanisms that have been found with the PC-programs IGOR and RAIN.     

Computation of LCAO wave functions for ground states of polymers and solids

The LCAO form of the Hartree–Fock method is discussed in its application to crystals. General formulae are given for obtaining Fourier coefficient of electronic density (in direct space) as well as of the band structure (in momentum space). Finally, it is shown that in its LCAO form, Slater–Hartree–Fock equations are very simple and that this method is of interest for numerical applications. Special integrals occurring in this formalism are evaluated for a Gaussian basis in the last part of this paper.     

Experimental and theoretical study of the V → T,R relaxation of CD4 between 300 and 100 K

Rate constants for the vibrational deactivation of CD₄ by the collision partners CD₄, He, Ne, Ar, Kr, D₂ and O₂ have been measured using a laser-fluorescence technique. The results are compared with those for the deactivation of CH₄ by the same collision partners and with a modified SSH type theoretical treatment.     

Controllable growth of chains and grids from polyoxomolybdate building blocks linked by silver(I) dimers

Molecular growth processes utilizing a beta-octamolybdate synthon and {Ag2} dimers are described and the directing influence of "encapsulating" cations and coordinating solvent is also demonstrated. The growth of two 1D chains, (nBu4N)2n[Ag2Mo8O26]n (1) and (nBu4N)2n[Ag2Mo8O26(CH3CN)2]n (2), is achieved when nBu4N+ ions are used, and the diameter of the chains can be expanded by the coordination of CH3CN solvent (2). The formation of a type of gridlike structure in which 1D chains are crossed-over each other in alternatively packed layers is achieved in DMSO as the solvent; DMSO acts as a linking group to give (nBu4N)2n[Ag2Mo8O26(dmso)2]n (3), which, similar to 1 and 2, still incorporates the Bu4N+ ions that exert an "encapsulating" influence. However, in (HDMF)n[Ag3(Mo8O26)(dmf)4]n (4) the relatively bulky Bu4N+ ions are exchanged for protonated DMF cations, thereby allowing the chains to condense to a 2D array. The building block concept is further enforced by the isolation of a "monomeric" unit (Ph4P)2[Ag2Mo8O26(dmso)4] (5), which is isolated when the Ph4P+ ions are so "encapsulating" as to prevent aggregation of the {Ag-Mo8-Ag} building blocks. The nature of the AgAg dimers in each of the compounds 1-4 is examined by DFT calculations and the interplay between these Ag-Ag interactions and the structure types is described.     

Ferromagnetic resonance investigation of dispersed Ni catalysts: epitaxial and textural effects from the support

Catalysts consisting of dispersed Ni particles supported on silica and alumina, with sizes ranging from 6 to 20 nm, have been studied by ferromagnetic resonance. For the Ni on Al₂O₃ catalyst, a textural promotion effect is shown to be present and it is attributed to the possible presence of NiAl₂O₄. The FMR data confirm the epitaxial growth of Ni on SiO₂ when Ni antigorite is reduced and show that some anisotropy is still present after sintering of the catalyst at about 1200K.     

Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.     

Tuning cell adhesion on gradient poly(2-hydroxyethyl methacrylate)-grafted surfaces

A simple yet versatile method was developed to prepare a low-density polymerization initiator gradient, which was combined with surface-initiated atom transfer radical polymerization (ATRP) to produce a well-defined poly(2-hydroxyethyl methacrylate) (HEMA) gradient substrate. A smooth variation in film thickness was measured across the gradient, ranging from 20 A to over 80 A, but we observed a nonmonotonic variation in water contact angle. Fits of X-ray reflectivity profiles suggested that at the low graft density end, the polymer chain structure was in a "mushroom" regime, while the polymer chains at high graft density were in a "brush" regime. It was found that the "mushroom" region of the gradient could be made adhesive to cells by adsorbing adhesion proteins, and cell adhesion could be tuned by controlling the density of the polymer grafts. Fibroblasts were seeded on gradients precoated with fibronectin to test cellular responses to this novel substrate, but it was found that cell adhesion did not follow the expected trend; instead, saturated cell adhesion and spreading was found at the low grafting density region.     

Solution conformation by NMR and molecular modeling of three sulfide-free somatostatin octapeptide analogs compared to angiopeptin

Summary The conformation in dimethylsulfoxide of the somatostatin derivative angiopeptin and of three disulfide-free analogs was estimated by two-dimensional nuclear magnetic resonance spectroscopy at room temperature. The resulting 3D molecular graphics were compared and shown to reflect the observed differences in the inhibition of restenosis after rat aorta balloon injury by these octapeptide inhibitors. Angiopeptin and its active analog 2 displayed a relatively rigid conformation of the cyclic hexapeptide backbone due to the presence of two well-defined hydrogen bonds, further stabilized by a third hydrogen bond outside the ring. No such constraints were detected for the two biologically inactive analogs, which, compared to 2, had a two-atom longer or shorter hexapeptide ring. The well-defined structure of compound 2 may serve as an improved pharmacophore for this new class of drugs.