Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture.

Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each C(α) effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around hydrogen bonds, which can be non-local along the backbone and are of major importance for protein structure. Here, we introduce the spatial rotation between hydrogen bonded peptide planes as a new descriptor for protein structure locally around a hydrogen bond. Strikingly, this rotational descriptor sampled over high-quality structures from the protein data base (PDB) concentrates into 30 localized clusters, some of which correlate to the common secondary structures and others to more special motifs, yet generally providing a unifying systematic classification of local structure around protein hydrogen bonds. It further provides a uniform vocabulary for comparison of protein structure near hydrogen bonds even between bonds in different proteins without alignment.

Stereodirection of an α-ketoester at sub-molecular sites on chirally modified Pt(111): heterogeneous asymmetric catalysis.

Chirally modified Pt catalysts are used in the heterogeneous asymmetric hydrogenation of α-ketoesters. Stereoinduction is believed to occur through the formation of chemisorbed modifier-substrate complexes. In this study, the formation of diastereomeric complexes by coadsorbed methyl 3,3,3-trifluoropyruvate, MTFP, and (R)-(+)-1-(1-naphthyl)ethylamine, (R)-NEA, on Pt(111) was studied using scanning tunneling microscopy and density functional theory methods. Individual complexes were imaged with sub-molecular resolution at 260 K and at room temperature. The calculations find that the most stable complex isolated in room-temperature experiments is formed by the minority rotamer of (R)-NEA and pro-S MTFP. The stereodirecting forces in this complex are identified as a combination of site-specific chemisorption of MTFP and multiple non-covalent attractive interactions between the carbonyl groups of MTFP and the amine and aromatic groups of (R)-NEA.

Adsorption, mobility, and dimerization of benzaldehyde on Pt(111).

Building on results for the adsorption of benzene on Pt(111), the adsorption of benzaldehyde is investigated using density functional theory. Benzaldehyde is found to chemisorb preferentially with its aromatic ring in the flat-lying bridge geometry that is also preferred for benzene. Across the investigated geometries, adsorption is homogeneously weakened compared to corresponding benzene geometries. This is found to be true for very different adsorption modes, namely, η(6) and η(8) modes, the latter having metal atoms inserted in the carbonyl bond. Reorientation and diffusion of benzaldehyde is found to have low energy barriers. Aggregation of molecules in dimers bound by aryl C-H···O hydrogen bonds is investigated, and specific configurations are found to be up to 0.15 eV more favorable than optimally configured, separated adsorbates. The binding is significantly stronger than what is found for gas phase dimers, suggesting an enhancing effect of the metal interaction.

Scanning Tunneling Microscopy Measurements of the Full Cycle of a Heterogeneous Asymmetric Hydrogenation Reaction on Chirally Modified Pt(111).

The hydrogenation of a prochiral substrate, 2,2,2-trifluoroacetophenone (TFAP), on Pt(111) was studied using room-temperature scanning tunneling microscopy (STM) measurements. The experiments were carried out both on a clean surface and on a chirally modified surface, using chemisorbed (R)-(+)-1-(1-naphthyl)ethylamine, ((R)-NEA), as the modifier. On the nonmodified surface, introduction of H2 at a background pressure of ∼1 × 10(-6) mbar leads to the rapid break-up of TFAP dimer structures followed by the gradual removal of all TFAP-related images. During the latter step, some monomers display an extra protrusion compared to TFAP in dimer structures. They are attributed to a half-hydrogenated intermediate. The introduction of H2 to a mixture of (R)-NEA and TFAP on Pt(111) leads to the removal of TFAP without any change in the population of the modifier, as required for an efficient chirally modified catalyst.

Direct observation of molecular preorganization for chirality transfer on a catalyst surface.

The chemisorption of specific optically active compounds on metal surfaces can create catalytically active chirality transfer sites. However, the mechanism through which these sites bias the stereoselectivity of reactions (typically hydrogenations) is generally assumed to be so complex that continued progress in the area is uncertain. We show that the investigation of heterogeneous asymmetric induction with single-site resolution sufficient to distinguish stereochemical conformations at the submolecular level is finally accessible. A combination of scanning tunneling microscopy and density functional theory calculations reveals the stereodirecting forces governing preorganization into precise chiral modifier-substrate bimolecular surface complexes. The study shows that the chiral modifier induces prochiral switching on the surface and that different prochiral ratios prevail at different submolecular binding sites on the modifier at the reaction temperature.