Modelling Molecules for Shape-Driven Aggregation
: Three Case Studies

Student thesis: Doctoral ThesisDoctor of Philosophy


The exploitation of self-assembling for the development of reliable technological platforms de-pends on the characterisation of the interactions between molecules. The possibility of tuning these interactions in order to create complex aggregates bearing specific chemical/physical prop-erties at the macroscopic level, is of crucial importance for the development of nanotechnology. In this framework, atomistic simulations constitute a powerful tool capable of providing fun-damental contributions. Following this line, the present work combines three distinct studies carried out on as many molecular systems, where the use of a common set of computational techniques, based on classical potentials and Density Functional Theory (DFT ), was addressed to understand the aggregation mechanisms displayed by poly-aromatic gelators, poly-aromatic hydrocarbons and nucleic acids. This thesis is structured as follows.
In the first chapter, a review of the main computational techniques used throughout this study is presented. The foundations of Molecular Dynamics (MD) are introduced first, with particular attention to the atomistic classical potentials and the main algorithms used for the integration of the equation of motions, the generation of the correct ensemble and for the solvation energies. An overview of DFT is also presented, completing the overview of the investigation methods adopted.
In the second chapter, the results of the research carried out to characterise the interactions between a particular type of poly-aromatic gelators, is presented. In particular, the study focuses on the individuation of a set of binding configurations able to provide a rationale for the sensitivity of gel formation to the enantiopurity of the solution.
The third chapter focuses on the work conducted in collaboration with the British Petroleum. Over the course of three years, in the framework of two consecutive research projects, the design and development of fuel additives was supported by a series of computational studies aimed at assessing the e˙ectiveness of di˙erent molecular structures and functional groups for the interaction with aromatic substrates. Here, the results of DFT calculations carried out on a series of polycyclic aromatic compound are presented, together with a correction scheme applied to a widely used classical potential for π − π interactions; a model dendritic structure with multiple phenyl terminations is proposed and tested with a molecular model, demonstrating the e˙ectiveness of a multivalent structure for the binding with highly defective polyaromatic substrates.
In the fourth chapter, the work conducted for the characterisation of DNA Self-Assembled mono-layer is presented. MD simulations of DNA high-density monolayers of increasing hybridisation states have been carried out for the characterisation of the energetics of the nanostructure in the framework of surface hybridisation; this allowed to highlight the intrinsic hybridisation limit reported by several independent experimental works.
In the conclusive section, the results presented in the previous three chapters are summarised, highlighting the major achievements and element of novelty of the research. The critical review of the work is combined with some considerations on the expected developments and future experimental outcomes.
Date of Award2016
Original languageEnglish
Awarding Institution
  • King's College London
SupervisorAlessandro De Vita (Supervisor) & Franca Fraternali (Supervisor)

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