Fluorine substituents have become a widespread and important drug component, their introduction facilitated by the development of safe and selective fluorinating agents. Organofluorine affects nearly all physical and adsorption, distribution, metabolism, and excretion properties of a lead compound. Its inductive effects are relatively well understood, enhancing bioavailability, for example, by reducing the basicity of neighboring amines. In contrast, exploration of the specific influence of carbon-fluorine single bonds on docking interactions, whether through direct contact with the protein or through stereoelectronic effects on molecular conformation of the drug, has only recently begun. Here, we review experimental progress in this vein and add complementary analysis based on comprehensive searches in the Cambridge Structural Database and the Protein Data Bank.

Intermolecular interactions involving aromatic rings are key processes in both chemical and biological recognition. Their understanding is essential for rational drug design and lead optimization in medicinal chemistry. Different approaches-biological studies, molecular recognition studies with artificial receptors, crystallographic database mining, gas-phase studies, and theoretical calculations-are pursued to generate a profound understanding of the structural and energetic parameters of individual recognition modes involving aromatic rings. This review attempts to combine and summarize the knowledge gained from these investigations. The review focuses mainly on examples with biological relevance since one of its aims it to enhance the knowledge of molecular recognition forces that is essential for drug development.

This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

Acetylenic coupling is currently experiencing some of the most intensive study of its long history. Rigid and sterically undemanding di- and oligoacetylene moieties, which are frequently encountered in natural products, are finding increasing application as key structural elements in synthetic receptors for molecular recognition. Interesting electronic and optical properties of extensively pi-conjugated systems have spurred research into new linear oligoalkynes and acetylenic carbon allotropes. The synthetic challenges associated with these efforts have in turn spawned new methods. While classical Glaser conditions are still frequently used for homocoupling, the demand for increasingly selective heterocoupling conditions has provided the focus of research over the past decades. These efforts have undoubtedly been hampered by a relatively poor mechanistic understanding of these processes. More recently, palladium-catalyzed coupling methods have led to improvements in both the selectivity and reliability of acetylenic homo- and heterocouplings and paved the way for their application to ever more complicated systems. The variety of acetylenic coupling protocols, the current mechanistic understanding, and their application in natural product and targeted synthesis are discussed comprehensively for the first time in this review, with an emphasis on the most recently developed methods, and their application to the synthesis of complex macromolecular structures.

The development of structure-property relationships for monodisperse oligomers has been extremely useful to rationalize the properties of high molecular weight linear π-conjugated polymers. A great variety of spectacular molecular architecture has been generated, culminating in the recent preparation of molecular wires such as 1 with lengths exceeding 10 nm that have potential applications in molecular electronics.

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Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.