Laboratory photo-chemistry of covalently bonded fluorene clusters: observation of an interesting PAH bowl-forming mechanism

The fullerene C$_{60}$, one of the largest molecules identified in the interstellar medium (ISM), has been proposed to form top-down through the photo-chemical processing of large (more than 60 C-atoms) polycyclic aromatic hydrocarbon (PAH) molecules. In this article, we focus on the opposite process, investigating the possibility that fullerenes form from small PAHs, in which bowl-forming plays a central role. We combine laboratory experiments and quantum chemical calculations to study the formation of larger PAHs from charged fluorene clusters. The experiments show that with visible laser irradiation, the fluorene dimer cation - [C$_{13}$H$_{9}$$-$C$_{13}$H$_{9}$]$^+$ - and the fluorene trimer cation - [C$_{13}$H$_{9}$$-$C$_{13}$H$_{8}$$-$C$_{13}$H$_{9}$]$^+$ - undergo photo-dehydrogenation and photo-isomerization resulting in bowl structured aromatic cluster-ions, C$_{26}$H$_{12}$$^+$ and C$_{39}$H$_{20}$$^+$, respectively. To study the details of this chemical process, we employ quantum chemistry that allows us to determine the structures of the newly formed cluster-ions, to calculate the hydrogen loss dissociation energies, and to derive the underlying reaction pathways. These results demonstrate that smaller PAH clusters (with less than 60 C-atoms) can convert to larger bowled geometries that might act as building blocks for fullerenes, as the bowl-forming mechanism greatly facilitates the conversion from dehydrogenated PAHs to cages. Moreover, the bowl-forming induces a permanent dipole moment that - in principle - allows to search for such species using radio astronomy.Comment: 8 pages, 7 figures, accepte

Mimicking Intermolecular Interactions of Tight Protein–Protein Complexes for Small-Molecule Antagonists

Tight protein–protein interactions (Kd1000 Å2) are highly challenging to disrupt with small molecules. Historically, the design of small molecules to inhibit protein–protein interactions has focused on mimicking the position of interface protein ligand side chains. Here, we explore mimicry of the pairwise intermolecular interactions of the native protein ligand with residues of the protein receptor to enrich commercial libraries for small-molecule inhibitors of tight protein–protein interactions. We use the high-affinity interaction (Kd=1 nm) between the urokinase receptor (uPAR) and its ligand urokinase (uPA) to test our methods. We introduce three methods for rank-ordering small molecules docked to uPAR: 1) a new fingerprint approach that represents uPA′s pairwise interaction energies with uPAR residues; 2) a pharmacophore approach to identify small molecules that mimic the position of uPA interface residues; and 3) a combined fingerprint and pharmacophore approach. Our work led to small molecules with novel chemotypes that inhibited a tight uPAR⋅uPA protein–protein interaction with single-digit micromolar IC50 values. We also report the extensive work that identified several of the hits as either lacking stability, thiol reactive, or redox active. This work suggests that mimicking the binding profile of the native ligand and the position of interface residues can be an effective strategy to enrich commercial libraries for small-molecule inhibitors of tight protein–protein interactions