Investigations into Two-Dimensional Self-Assembly of Small Molecules

Scanning tunneling microscopy is an experimental methodology which provides the unique opportunity to observe two dimensional structures at the molecular level. By using a low-temperature and ultra-high-vacuum scanning tunneling microscope (STM), the local clustering of molecules in two dimensions can be directly observed over significant periods of time without risk of sample degradation.

These investigations come with challenges both instrumental and experimental. Of the instrumental challenges, the construction of the preamplifier used to boost the incredibly small tunneling currents produced by the instrument is one of the most important. Two major circuit architectures for the preamplifier exist, the feedback transimpedance amplifier (TIA) and the shunt electrometer, each with their own benefits. Balancing the importance of current gain, the frequency at which the instrument is operating at, and the noise inherent to the preamplifier is of peak importance to the performance of the instrument.

Beyond the instrument itself, the creation of a monolayer of small molecules upon a metallic surface is necessary. Pulse deposition is used to prepare samples for study, a non-equilibrium process by which numerous structures are formed, including many metastable structures. Of these metastable structures, pentamers are a commonly observed motif. These pentamers are stabilized by the presence of minor secondary interactions, most notably of which are C–H・・・ O hydrogen bonds.

Density functional theory (DFT) is employed in tandem with STM to provide additional insight into the mechanisms by which molecules cluster in two dimensions. By geometrically and energetically optimizing both individual molecules and clusters of molecules, the binding energy of specific hydrogen bonds can be determined, giving rise to a quantitative understanding of the clusters.

The works presented within this thesis aim to further develop the study of crystal growth in two dimensions, by presenting a variety of small molecules, and derivatives of these molecules intentionally chosen to probe individual hydrogen-bonding sites.