Maximum common binding modes (MCBM): consensus docking scoring using multiple ligand information and interaction fingerprints

Improving the scoring functions for small molecule-protein docking is a highly challenging task in current computational drug design. Here we present a novel consensus scoring concept for the prediction of binding modes for multiple known active ligands. Similar ligands are generally believed to bind to their receptor in a similar fashion. The presumption of our approach was that the true binding modes of similar ligands should be more similar to each other compared to false positive binding modes. The number of conserved (consensus) interactions between similar ligands was used as a docking score. Patterns of interactions were modeled using ligand receptor interaction fingerprints. Our approach was evaluated for four different data sets of known cocrystal structures (CDK-2, dihydrofolate reductase, HIV-1 protease, and thrombin). Docking poses were generated with FlexX and rescored by our approach. For comparison the CScore scoring functions from Sybyl were used, and consensus scores were calculated thereof. Our approach performed better than individual scoring functions and was comparable to consensus scoring. Analysis of the distribution of docking poses by self-organizing maps (SOM) and interaction fingerprints confirmed that clusters of docking poses composed of multiple ligands were preferentially observed near the native binding mode. Being conceptually unrelated to commonly used docking scoring functions our approach provides a powerful method to complement and improve computational docking experiments.     

Vibrational spectra of monolayer islands on single crystal faces. Island size and shape effects on infrared frequencies,intensities and bandwidths

A method for theoretical analysis spectra of rectangular segments (islands) of two-dimensional ordered overlayers of adsorbed species has been proposed. The simple formulae for frequencies, absorption coefficients and bandwidths as functions of island size and shape have been deduced. If frequencies and bandwidths of appropriate bands in infrared spectra of chemisorbed monolayers are measured simultaneously, the size and shape of the islands can be estimated.     

Selective Hydrogenation of Acrolein Over Pd Model Catalysts: Temperature and Particle‐Size Effects

The selectivity in the hydrogenation of acrolein over Fe₃O₄‐supported Pd nanoparticles has been investigated as a function of nanoparticle size in the 220–270 K temperature range. While Pd(111) shows nearly 100 % selectivity towards the desired hydrogenation of the C=O bond to produce propenol, Pd nanoparticles were found to be much less selective towards this product. In situ detection of surface species by using IR‐reflection absorption spectroscopy shows that the selectivity towards propenol critically depends on the formation of an oxopropyl spectator species. While an overlayer of oxopropyl species is effectively formed on Pd(111) turning the surface highly selective for propenol formation, this process is strongly hindered on Pd nanoparticles by acrolein decomposition resulting in CO formation. We show that the extent of acrolein decomposition can be tuned by varying the particle size and the reaction temperature. As a result, significant production of propenol is observed over 12 nm Pd nanoparticles at 250 K, while smaller (4 and 7 nm) nanoparticles did not produce propenol at any of the temperatures investigated. The possible origin of particle‐size dependence of propenol formation is discussed. This work demonstrates that the selectivity in the hydrogenation of acrolein is controlled by the relative rates of acrolein partial hydrogenation to oxopropyl surface species and of acrolein decomposition, which has significant implications for rational catalyst design.     

Model studies in heterogeneous catalysis at the microscopic level: from the structure and composition of surfaces to reaction kinetics

Heterogeneous catalysis is one of the fields of modern technology, in which a characterization of structural and chemical properties of solid surfaces at the microscopic level is of enormous importance. For a long time, such insights have been precluded by the complexity of most catalytically active materials. Recently, substantial progress has been made, however, toward a microscopic-level understanding of complex catalyst surfaces. We discuss the driving factors for these advancements, which are based on the development of new well-defined model systems as well as on advances in experimental technology and theory. Scrutinizing the example of planar model catalysts, we identify the process of linking structural and chemical information to microscopic reaction kinetics as a particular challenging aspect of today’s work. We review the kinetic effects which may have an influence on the reaction kinetics on complex surfaces. As an example how structural and kinetic information can be correlated at the microscopic level we discuss the case of surface oxidation and oxygen induced restructuring of Pd nanoparticles as studied by molecular beam methods.     

Model Studies in Heterogeneous Catalysis. From Structure to Kinetics

Summary. Heterogeneous catalysis is one of the fields of modern technology, where the application of complex inorganic materials is of enormous economical importance. For a long time, the chemical and structural complexity of catalyst materials has precluded detailed insights into chemical processes on catalyst surfaces. In the last decades, however, substantial progress has been made toward a microscopic-level understanding of reaction mechanisms and kinetics, mainly based on the development of new well-defined model systems and on advances in experimental technology and theory. Scrutinizing the example of supported model catalysts, we review some of these innovations in model catalysis. As a particular challenging aspect of todays work, we discuss the question how detailed structural information on the model systems can be linked to catalytic reaction kinetics at the microscopic level.This revised version was published online in February 2005. In the previous version the issue was not marked as a special issue, and the issue title and the editor was missing