MODELLING THE SELF-ASSEMBLY OF SUPRAMOLECULAR NANOSTRUCTURES ADSORBED ON METALLIC SUBSTRATES

The term Nanotechnology is used to describe a variety of techniques to fabricate materials and devices at the nanoscale. Nano-techniques include those used for fabrication of nanowires, those used in semiconductor fabrication such as deep ultraviolet and electron beam lithography, focused ion beam machining, nanoimprint lithography, atomic layer deposition, molecular vapor deposition, and the ones including molecular self-assembly techniques. All these methods are still being developed and not all of them were devised with the sole purpose of creating devices for nanotechnology. A number of physical phenomena become noticeably pronounced as the system size decreases. These include statistical effects, as well as quantum effects, where the electronic properties of solids are altered if the particle size is greatly reduced. There are also effects which never come into play by going from macro to micro dimensions, while they become dominant when the nanometer scale is reached. Furthermore nanotechnology can be thought of as extensions of traditional disciplines towards the explicit consideration of all these effects. Traditional disciplines can be re-interpreted as specific applications of nanotechnology. Broadly speaking, nanotechnology is the synthesis and application of ideas from science and engineering towards the understanding and production of novel materials and devices with atomicscale control. Modern synthetic chemistry has reached the point where it is possible to prepare small molecules of almost any (stable) structure. Methods exist today to produce a wide variety of useful chemicals. A branch of nanotechnology, relevant to the present thesis work, is looking for methods to assemble single molecules into supramolecular assemblies arranged in a well defined manner. These approaches use molecular self-assembly and supramolecular chemistry to automatically arrange the single molecules into interesting and potentially useful structures. The scanning tunneling microscope (STM) is a non-optical microscope that scans an electrical probe (the tip) over a conductive surface to be imaged. It allows scientists to visualize regions of high electron density at the atomic scale, and hence infer the position of individual atoms and molecules on a material surface. STM is specially suited for the study of the self-assembly of molecules deposited on conductive substrates because it provides direct insight into the assembled structures. However, the STM images are often insufficient for a complete description of the phenomena, and computer simulations offer a complementary approach that can effectively integrate the experiments . The theoretical investigation of the molecular self-assembly aims at the understanding of the mechanisms that are involved in the assemblies formatiom. In particular the atomistic simulation can provide information on the geometry of the stable structures, the nature and the intensity of the interactions as well as on the dynamical processes. In this thesis, a combination of first principles and classical molecular dynamics simulations is used to shed light on the self-assembly of some organic molecules deposited on noble metal substrates. Three cases are discussed, the self-assembly of TMA and BTA molecules on Ag(111) and the self-assembly of an oxalic amide derivative on Au(111). When TMA and BTA molecules are deposited onto a silver surface at a temperature lower than room temperature they form a regular 2D honeycomb network featuring double hydrogen bonds between carboxylic groups. Even if this bonding makes the network very stable, when these systems are annealed to higher temperatures they undergo some irreversible phase transition into closer-packed supramolecular arrangements. Namely, the TMA has a transition from honeycomb to a high coverage “quartet” structure and the BTA has two transtions: from honeycomb to unidimensional stripes and from here to a closed-packed monolayer. A combination of experimental and theoretical techniques allowed us to identify the stepwise deprotonation of the carboxylic acid groups as the driving force driving the phase transitions. Our theoretical investigation targeted the electrostatic interaction involved in the formation of the various phases revealing that a depolarisation of the molecular ions occurs as a consequence of the deprotonation process. Therefore, the repulsive contribution arising from the interaction of negatively charged molecules can be overcome by the attractive hydrogen bond interaction involving the deprotonated carboxylic groups, thus resulting in a stable closed-packed arrangement. Rather remarkably, this exemplifies how higher-coverage phases can be obtained at each step of a series of phase transitions in a supramolecular assembled system, despite the increasing temperature and the increasing electrostatic repulsive energy cost accompanying deprotonation. The oxalic amide derivative molecules arranges themselves in linear chains both in the molecular solid and when adsorbed on a gold surface. However the intermolecular distance and the geometry of the chains are different in these two cases. Various relaxed bonding structure between molecules in the chains have been calculated from first principles in the present work. The rationale of the different linkage behaviour between molecules in the two situations described have also been investigated: the interaction with the substrate appears to be the main cause for the particular rearrangement observed in the chains. Both experimental observations and theoretical predictions indicate that a conformational change involving the rotation of the phenyl rings of the monomers is necessary for chain formation.