Aromatic interactions in proteins, DNA and synthetic receptors

Abstract

Non-covalent interactions between aromatic molecules ($\pi $-$\pi $ interactions) play a major role in biological molecular recognition. A simple theoretical model which accounts for the geometric properties of $\pi $-$\pi $ interactions is described. The key feature of this model is that it specifically allows for out-of-plane $\pi $-electron density in the calculation of electrostatic interactions. Experimental evidence for the validity of the model comes from studies of the geometric distribution of phenylalanine-phenylalanine interactions in protein X-ray crystal structures. The model has also been used to design a synthetic molecular receptor which recognizes p-benzoquinone using H-bonds and edge-to-face $\pi $-$\pi $ interactions. Aromatic stacking interactions provide the crucial link between sequence and three-dimensional structure in double-helical DNA. The $\pi $-$\pi $ interaction model has been used to calculate the conformational preferences of all ten DNA base-pair steps and the results provide new insight into the molecular basis of sequence-dependent DNA structure.