Exploring coordination-driven self-assembly with autonomous chemical robots

The work presented herein focused on the automation of coordination-driven self assembly, exploring methods that allow syntheses to be followed more closely while forming new ligands, as part of the fundamental study of the digitization of chemical synthesis and discovery. Whilst the control and understanding of the principle of pre-organization and self-sorting under non-equilibrium conditions remains a key goal, a clear gap has been identified in the absence of approaches that can permit fast screening and real-time observation of the reaction process under different conditions. A firm emphasis was thus placed on the realization of an autonomous chemical robot, which can not only monitor and manipulate coordination chemistry in real-time, but can also allow the exploration of a large chemical parameter space defined by the ligand building blocks and the metal to coordinate. The self-assembly of imine ligands with copper and nickel cations has been studied in a multi-step approach using a self-built flow system capable of automatically controlling the liquid-handling and collecting data in real-time using a benchtop MS and NMR spectrometer. This study led to the identification of a transient Cu(I) species in situ which allows for the formation of dimeric and trimeric carbonato bridged Cu(II) assemblies. Furthermore, new Ni(II) complexes and more remarkably also a new binuclear Cu(I) complex, which usually requires long and laborious inert conditions, could be isolated. The study was then expanded to the autonomous optimization of the ligand synthesis by enabling feedback control on the chemical system via benchtop NMR. The synthesis of new polydentate ligands has emerged as a result of the study aiming to enhance the complexity of the chemical system to accelerate the discovery of new complexes. This type of ligand consists of 1-pyridinyl-4-imino-1,2,3-triazole units, which can coordinate with different metal salts. The studies to test for the CuAAC synthesis via microwave lead to the discovery of four new Cu complexes, one of them being a coordination polymer obtained from a solvent dependent crystallization technique. With the goal of easier integration into an automated system, copper tubing has been exploited as the chemical reactor for the synthesis of this ligand, as it efficiently enhances the rate of the triazole formation and consequently promotes the formation of the full ligand in high yields within two hours. Lastly, the digitization of coordination-driven self-assembly has been realized for the first time using an in-house autonomous chemical robot, herein named the ‘Finder’. The chemical parameter space to explore was defined by the selection of six variables, which consist of the ligand precursors necessary to form complex ligands (aldehydes, alkineamines and azides), of the metal salt solutions and of other reaction parameters – duration, temperature and reagent volumes. The platform was assembled using rounded bottom flasks, flow syringe pumps, copper tubing, as an active reactor, and in-line analytics – a pH meter probe, a UV-vis flow cell and a benchtop MS. The control over the system was then obtained with an algorithm capable of autonomously focusing the experiments on the most reactive region (by avoiding areas of low interest) of the chemical parameter space to explore. This study led to interesting observations, such as metal exchange phenomena, and also to the autonomous discovery of self assembled structures in solution and solid state – such as 1-pyridinyl-4-imino-1,2,3-triazole based Fe complexes and two helicates based on the same ligand coordination motif.

Investigating automated chemical evolution of oil-in-water droplets

One of the main unresolved questions in science is how non-living matter became alive in a process known as abiognesis, which aims to explain how from a primordial soup scenario containing simple molecules, by following a ``bottom up'' approach, complex biomolecules emerged forming the first living system, known as a protocell. A protocell is defined by the interplay of three sub-systems which are considered requirements for life: information molecules, metabolism, and compartmentalization. This thesis investigates the role of compartmentalization during the emergence of life, and how simple membrane aggregates could evolve into entities that were able to develop ``life-like'' behaviours, and in particular how such evolution could happen without the presence of information molecules. Our ultimate objective is to create an autonomous evolvable system, and in order tp do so we will try to engineer life following a ``top-down'' approach, where an initial platform capable of evolving chemistry will be constructed, but the chemistry being dependent on the robotic adjunct, and how then this platform can be de-constructed in iterative operations until it is fully disconnected from the evolvable system, the system then being inherently autonomous. The first project of this thesis describes how the initial platform was designed and built. The platform was based on the model of a standard liquid handling robot, with the main difference with respect to other similar robots being that we used a 3D-printer in order to prototype the robot and build its main equipment, like a liquid dispensing system, tool movement mechanism, and washing procedures. The robot was able to mix different components and create populations of droplets in a Petri dish filled with aqueous phase. The Petri dish was then observed by a camera, which analysed the behaviours described by the droplets and fed this information back to the robot. Using this loop, the robot was then able to implement an evolutionary algorithm, where populations of droplets were evolved towards defined life-like behaviours. The second project of this thesis aimed to remove as many mechanical parts as possible from the robot while keeping the evolvable chemistry intact. In order to do so, we encapsulated the functionalities of the previous liquid handling robot into a single monolithic 3D-printed device. This device was able to mix different components, generate populations of droplets in an aqueous phase, and was also equipped with a camera in order to analyse the experiments. Moreover, because the full fabrication process of the devices happened in a 3D-printer, we were also able to alter its experimental arena by adding different obstacles where to evolve the droplets, enabling us to study how environmental changes can shape evolution. By doing so, we were able to embody evolutionary characteristics into our device, removing constraints from the physical platform, and taking one step forward to a possible autonomous evolvable system.