Simulating the aggregation of DNA oligonucleotides

In this work we have studied, by means of Molecular Dynamics simulations, the process of denaturation and self-assembly of short oligonucleotides. Supramolecular ordering of DNA short strands is a promising field which is constantly enriched with new findings. Examples are provided by micellar and fibrils formations and due to the selectivity of DNA bindings, "intelligent" devices have been developed to perform simple logic operations. It is worth to notice that computer simulations of these DNA nanosystems would complement experiments with detailed insight into processes involved in self-assembly. In order to obtain an accurate description of the interactions involved in the complex structure of DNA we used oxDNA, a coarse-grained model developed by Ouldridge. We simulated the melting transition of 4, 6, and 8 base pair sequences. Sequence and length dependence were analyzed, specifically we compared thermodynamic parameters DeltaH, DeltaS and the melting temperature with literature results. Moreover, we have attempted to reproduce liquid crystal ordering of the ultrashort sequence GCCG at relatively high saline concentration, until now only experimentally observed in Bellini's works. We found that our simple model successfully reproduces the experimental phase sequence (isotropic, nematic, columnar) at T= 5 °C as a function of oligonucleotide concentration, and we fully characterized the microscopic structure of the three phases.

Photoactive (supra)molecular devices in double layer membranes

Biological systems are complex and highly organized architectures governed by non-covalent interactions responsible for the regulation of essential tasks in all living organisms. These systems are a constant source of inspiration for supramolecular chemists aiming to design multicomponent molecular assemblies able to perform elaborated tasks, thanks to the role and action of the components that constitute them. Artificial supramolecular systems exploit non-covalent interactions to mimic naturally occurring events. In this context, stimuli-responsive supramolecular systems have attracted attention due to the possibility to control macroscopic effects through modifications at the nanoscale. This thesis is divided in three experimental chapters, characterized by a progressive increase in molecular complexity. Initially, the preparation and studies of liposomes functionalized with a photoactive guest such as azobenzene in the bilayer were tackled, in order to evaluate the effect of such photochrome on the vesicle properties. Subsequently, the synthesis and studies of thread-like molecules comprising an azobenzene functionality was reported. Such molecules were conceived to be intercalated in the bilayer membrane of liposomes with the aim to be used as components for photoresponsive transmembrane molecular pumps. Finally, a [3]rotaxane was developed and studied in solution. This system is composed of two crown ether rings interlocked with an axle containing three recognition sites for the macrocycles, i.e. two pH-switchable ammonium stations and a permanent triazolium station. Such molecule was designed to achieve a change in the ratio between the recognition sites and the crown ethers as a consequence of acid-base inputs. This leads to the formation of rotaxanes containing a number of recognition sites respectively larger, equal or lower than the number of interlocked rings and connected by a network of acid-base reactions.

Electrospun hierarchical artificial muscle for soft robotics applications

Nowadays, one of the most ambitious challenges in soft robotics is the development of actuators capable to achieve performance comparable to skeletal muscles. Scientists have been working for decades, inspired by Nature, to mimic both their complex structure and their perfectly balanced features in terms of linear contraction, force-to-weight ratio, scalability and flexibility. The present Thesis, contextualized within the FET open Horizon 2020 project MAGNIFY, aims to develop a new family of innovative flexible actuators in the field of soft-robotics. For the realization of this actuator, a biomimetic approach has been chosen, drawing inspiration from skeletal muscle. Their hierarchical fibrous structure was mimicked employing the electrospinning technique, while the contraction of sarcomeres was designed employing chains of molecular machines, supramolecular systems capable of performing movements useful to execute specific tasks. The first part deals with the design and production of the basic unit of the artificial muscle, the artificial myofibril, consisting in a novel electrospun core-shell nanofiber, with elastomeric shell and electrically conductive core, coupled with a conductive coating, for the realization of which numerous strategies have been investigated. The second part deals instead with the integration of molecular machines (provided by the project partners) inside these artificial myofibrils, preceded by the study of several model molecules, aimed at simulating the presence of these molecular machines during the initial phases of the project. The last part concerns the realization of an electrospun multiscale hierarchical structure, aimed at reproducing the entire muscle morphology and fibrous organization. These research will be joined together in the near future like the pieces of a puzzle, recreating the artificial actuator most similar to biological muscle ever made, composed of millions of artificial myofibrils, electrically activated in which the nano-scale movement of molecular machines will be incrementally amplified to the macro-scale contraction of the artificial muscle.

Diazene photoswitches in artificial molecular machines and light-effected materials

The research developed in this thesis focused on the spectroscopic and photochemical characterization of molecular diazene photoswitches, both as individual species and as functional components of mechanically interlocked molecules, molecular-based materials and artificial molecular machines and motors. Among the plethora of photochromes reported so far, azobenzene is the most versatile photoswitch due to its reproducible and well-established photochemical properties. Part I of this thesis work focuses on the characterization of light-responsive supramolecular systems based on azobenzene: a photochemically-driven rotary motor, a light-responsive supramolecular polymeric material and a supramolecular system capable of photoinduced entantiodiscrimination. Despite the wide success of azobenzene photoswitches, the tunability of their photochemical properties as a function of the diversified substitution pattern on its aryl ring presents intrinsic limitations. To overcome this issue, in the last decade heteroaryl azoswitches (i.e., azobenzene having heterocyclic rings in place of one or both phenyl groups) have attracted a great deal of attention. Hence, Part II of this thesis work treats the photochemical characterization of two different families of azoheteroarenes embedding imidazolium and thienyl functionalities in their structures. Their potential implementation in water-soluble artificial molecular machines and light-effected semiconductor materials is also assessed.