Scanning tunneling microscopy (STM) is used to study large, organometallic complexes with multiple metal centers. These complexes are capable of forming stable mixed-valence (MV) states and are typically characterized using ensemble measurements according to the Robin-Day classification. Neutral and MV molecules are studied with the STM after pulse deposition onto an Au(111) substrate in ultra-high-vacuum and low-temperature conditions. Pulse deposition of molecules on a substrate removes bulk solvent and the charge-transfer properties of the molecules of interest can be studied. The STM tip is a sensitive probe for the visualization of the electronic properties of both neutral and MV molecules. Generally, neutral molecules show a symmetric electronic charge distribution whereas MV molecules show an asymmetric charge distribution in STM images. Factors such as geometry of the metal centers and molecule-surface interactions also play a role in charge transfer capabilities within a molecule. Electronic structure calculations from density functional theory (DFT) and constrained density functional theory (CDFT) are also used to study MV characteristics of molecules.
STM was also used to study self-assembly of carboxylic acid monolayers. In most cases, the formation of two strong hydrogen bonds results in dimer formation; in some others, linear catemer chains are formed. Observation of a five-membered catemer ring, stabilized by additional CH$cdots$O interactions available in the cyclic structure is reported. The existence of CH$cdots$O hydrogen bonding is confirmed with DFT calculations and by observing the disappearance of pentamers when molecules without suitable CH donors are used. Long range assembly of pentamers results in a two-dimensional quasicrystalline lattice, the first observation of such structure from small-molecule self assembly.