Linear Catenanes: a Computational Study

In recent years, significant effort has been dedicated to realizing and characterizing mechanically interlocked molecules, supra-molecular constructs in which distinct molecular strands are topologically linked. Arguably, the most fundamental instance of such topologically-complex meta-materials are linear catenanes, made of a linear succession of interlocked ring polymers. These constructs, which have long remained elusive for synthetic chemistry, have recently been obtained with high yield and for large molecular weights, i.e. for numerous repeats of linked rings. These experimental breakthrough have, in turned, fostered numerous theoretical and computational studies aimed at predicting the properties of such systems, and at guiding the design of their desirable features. In this Thesis, as part of this ongoing theoretical effort, I will present a series of studies where I characterized the statics and dynamics of linear catenanes in a variety of still unexplored physical contexts. The results that I present have been mostly obtained using coarse-grained models and molecular dynamics simulations. The driving questions that I addressed ranged from how the rigidity of the constitutive rings reflects on the emerging physical properties of the entire catenane to how spatial confinement in nano-channels impacts the relaxation dynamics and metric scaling properties of the catenanes. I will further discuss the influence of poor solvent conditions on the unique self-entanglement properties of catenanes, and present preliminary results for equilibrated catenanes made of block co-polyelectrolyte rings. Finally, I will extend considerations to a further type of topologically-complex molecules, namely viral RNA, and use nanopore translocation simulations to illuminate their unique biological functional properties.