Molecules assembling and reacting under the constraint of weak and strong surface interactions

On surface chemistry and physics of nanoscale molecular self-assemblies manufactured in a “bottom-up” approach is the base on which this thesis is established. The formation of the mentioned self-assemblies is dependent on the interactions between their organic molecular building blocks and building blocks-substrate interaction. These organic molecules are synthesized for specific purposes by modifying molecular topology, structure and functional groups. The substrates employed are predominantly single crystals composed of coinage metals or single crystals with deposited adlayers. Chemical modification of these compounds via different bonding motifs (i.e. Hydrogen bonding, coordination, Van der Waals interaction, etc) in their self-assemblies is studied after their in-situ deposition using Scanning Tunneling Microscopy (STM), X-ray photoelectron spectroscopy (XPS) and Density Functional Theory (DFT). In chapter [[1]] direct comparison between in-solution and on-surface behavior of the same compounds is presented. Synthesis and surface assembly of the higher pyrazinacenes and their oxidized analogues using PbO2 in solution and annealing on Cu(111) substrate is studied. Upon thermal deposition of these compounds on single Cu(111) crystal, the molecules arrange in a chiral conformation. Subsequent annealing at 150 °C causes the dehydrogenation of the molecules and consequently the formation of linear arrays. Further annealing to 300 °C breaks the linear chains and the molecules appear to adopt a “double-lobe” or “two dark satellite” morphology which we attribute to further oxidation (cyclodehydrogenation). In chapter [[2]] the unprecedented ‘out-of-plane’ oriented, hydrogen-bonded assemblies of a planar module, the perylene derivative DPDI on a specifically-chosen weakly interacting substrate is studied. A single atomic layer of semi-metallic Bi in p(10x10) phase is selected as the substrate as it is known to be electronically decoupled from the underlying metallic Cu(100) single crystal thus can be used to study mainly intermolecular interactions. Extended, hexagonal networks containing “windmill-shaped” nodes with unique bi-chirality features, together with a compact assembly of zigzag structures are the two spontaneously formed supramolecular structures which are of great chemical importance since direct deposition of DPDI on Cu(100) does not lead to any sort of assembly. In chapter [[3]] the self-assembly of functionalized tetraphenylporphyrins in different architectures is presented. Trifluoromethyl and methoxy- functionalized tetraphenylporphyrins were synthesized and used to reveal polymorphism, driven by F…F interactions and C-F…H-C hydrogen bonds. The on-surface behavior of the symmetric and asymmetric functionalized compounds (trans and mono, respectively) is compared with tetrakis(3,4,5-trimethoxyphenyl)- and tetrakis(3,5-trifluoromethylphenyl)-porphyrins