This project will develop a new method for spatial manipulation of light by designing and validating assemblies of plasmonic nanostructures and fluorophores to advance visualization of densely packed biological structures and their dynamics. The visualization of densely packed biological structures is extremely challenging, yet crucial for understanding dynamic biological processes in virtually any context; light manipulation at the nanoscale using plasmonic nanoparticles has the potential to magnify nanoscopic sample structure while simultaneously enhancing the optical response beyond the capabilities of current super-resolution microscopy techniques. While the ability of metal nanostructures to enhance the response of fluorophores has been utilized for decades, we are still far from understanding the underlying mechanisms of plasmonic enhancement. To fully exploit the potential of this approach, we need to know how spectral overlap between the plasmonic nanoparticle and the absorption and emission channels of the fluorophore affects the coupling efficiency and spatial projection. To translate these effect into applications, we have to understand how the fluorophore-particle distance affects the far-field projection of the fluorophore. We will use self-assembled DNA, single-molecule localization microscopy, and finite difference time domain electromagnetic simulations to measure, describe and reconstruct sub-diffraction limited shifts in the projection of plasmon-coupled fluorophores. This will let us pave the way to the design of a magnifying device aimed at visualizing densely packed biological structures. Fundamental understanding of plasmonic coupling obtained in this project will be directly applicable in various fields of research by providing a tool for high-resolution visualization of molecular structures and their dynamics in the form of plasmonic assemblies, and enabling precise control over enhancement in fluorescence and Raman systems.

Computational modelling of molecules and materials has had a great impact on understanding experimental observations and suggesting new routes for development. A prominent example are chemical reactions where modelling allows one to follow the motion of atoms and to obtain a detailed insight into the process. To model chemical reactions, quantum mechanics for electrons is needed and currently the most widely used method for this task is Kohn-Sham density functional theory (DFT). DFT is exact in principle, but in practice, different approximations are made. These approximations affect the accuracy of description of both strong intramolecular forces (chemical bonds) and weaker intermolecular interactions (e.g., van der Waals forces). If the errors are significant, one can obtain misleading results. Systems where an accurate description of both strong and weak forces is crucial are molecules in porous materials, such as zeolites. Zeolites are important industrial catalysts and also perspective materials for gas separation. During the catalytic process, molecules interact first weakly with the zeolite before chemical reaction takes place. Therefore, if we want to further improve the function of porous materials or develop new ones with desired chemical activity, we need to be able to model reliably both strong and weak forces. It is the goal of this project to develop new reliable methods that will enable the development of new materials. This goal will be accomplished by combining state-of-the-art DFT approximations for modelling strong and weak interactions and implementing promising schemes recently proposed. Using the expertise of the host group, we will use data available for zeolites and molecules in zeolites to validate the methods and understand their accuracy. The ability to model reliably processes in porous materials will have a large impact on the development of materials in a range of fields, including materials for solving future energy needs.

The crucial step for selective cleavage and formation of C-H bonds is a concerted transfer of proton (PT) and electron(s) (ET): hydrogen atom abstraction (HAA) or hydride transfer (HT). The HAA and HT processes can be employed to various chemical transformations: from activation of inert bonds to reduction of CO2. This approach, however, requires a strict control of the regioselectivity of the reaction. Notably, enzymes - catalysts developed by Nature, are characterised by high activity and selectivity. In this project, we would like to provide insight into the interplay of reaction thermodynamics and sterics given by the microenvironment of prototypical enzymatic active sites (employing HAA or HT as a key step in catalysis) and to decipher which of these effects is more important in enzymatic selectivity. The focal point of the project is the novel three component thermodynamic-based model for reactivity, developed for concerted H+/e− abstraction. The model captures the coupled nature of PT and ET by the relative magnitutes of redox potentials and acidity constants of the reactants - their values determine not only the the reaction driving force but also the two novel contributions: asynchronicity and frustration with opposing effects on the barrier for the reaction. An asynchronous process, featuring a large disparity in ET and PT components of the reaction driving force, is more efficient. In contrast, a common large size of these ET and PT components makes HAA more frustrated and hence less effective. Based on this model we would like to look into systems capable of CO2 reduction and C-H bond activation to assess to what extent their reactivity is tweaked by the local conditions given by the enzymatic microenvironment versus the “canonical” factors affecting enzymatic activity, such as sterics and specific interactions. The studies may serve as a guide for design for systems capable of effective reduction of CO2 and rational redesign of C-H activating enzymes.