title: Chiral organisations expressed by biomolecules at the Cu(110) surface
Creators: name: Sgrilli, Tommaso
Publisher: name: University of Liverpool Repository
Year: 2016

description: This thesis aims at understanding the manifestations of chirality that are expressed by selected organic molecules of biochemical relevance when adsorbed on a copper single-crystal exposing the (110) face. All the experiments described in this thesis are carried out in Ultra High Vacuum (UHV) environment by means of complementary surface science techniques. In some circumstances, the experimental results are interpreted on the basis of theoretical calculations that have been performed by collaborators. The adsorption of enantiopure amino acid R-serine on Cu(110), previously reported to give rise to a symmetry-breaking organisational arrangement, is studied with the aim of establishing the geometry of the single conformers populating the organic adlayer. While theoretical calculations on this system indicate two energetically preferred geometries, on the basis of a direct comparison between experimental and simulated Scanning Tunneling Microscopy (STM) investigations a single geometry is proposed. This features homochirality at the footprint level, with the stereo-distribution of the molecular atoms coordinated with the surface possessing uniform chirality. Furthermore, the hydrogen bonds that give stability to the proposed molecular assembly are discussed, and are suggested to play a symmetry-breaking role in the characteristic chiral direction of elongation of R-serine islands on Cu(110). The behaviour of serine in racemic proportion on Cu(110) is characterised by two main phenomena. The tendency of the two enantiomers to segregate into domains with homogeneous chirality is accompanied by a second effect, which sees interactions between molecules with differing chirality. The latter phenomenon takes place principally when the surface coverage is high and tends to disappear once the sample is annealed, thus is proposed to possess a metastable nature. By means of high-resolution STM images, the metastable state is investigated and the chirality of the single molecules can be tracked. As a result, the occurrence of serine trimers, constituted by a homochiral serine dimer and a serine molecule with opposite chirality, is revealed. These trimers represent a recurrent manifestation of heterochiral recognition when racemic serine is adsorbed on Cu(110). The study of enantiopure S-valine on Cu(110) reveals a temperature-dependent chiral-achiral phase transition at the organisational level. The achiral high-temperature phase is found, by means of STM and Low Energy Electron Diffraction (LEED) to possess a (3x2) periodicity with alternating footprint chirality, as corroborated by theoretical calculations. The interruptions and irregularities that occur within the (3x2) structure are discussed on the basis of previous studies conducted on the alanine/Cu(110) system, and are proposed to be originated by the presence of rotational domains, by the local occurrence of different molecular conformations or a bigger unit cell. Finally, the adsorption of the achiral nucleobase adenine on Cu(110) is investigated exclusively with STM. Given the characteristics of the probing technique, the complete understanding of the molecular geometry of the adsorbed molecules is not attempted. However, the nucleation of chirality at the supramolecular level is followed and a proposed mechanism of formation of the previously reported long-range chiral assembly on Cu(110) is presented. It is shown in fact that, despite the formation of diverse temperature-dependent molecular phases, a key role in the break of the surface symmetry is played by the on-surface formation of chiral adenine dimers, which can interact laterally to give rise to chiral 1D chains and 2D domains when the sample is annealed further.