This thesis has investigated the electronic properties of organic molecular junctions, which form gold|single-molecule|gold structures, using a combination of density functional theory (DFT) and the equilibrium Green’s function formalism of transport theory. The first project considers the role of symmetric and asymmetric anchor groups for controlling charge transfer in molecular junctions, and how that relates to the position of the electrode Fermi level relative to the molecular resonances through various molecules. The results indicated that symmetric anchors such as thiol and pyridyl yield pinning of the electrode Fermi level to the resonances, whereas this pinning behaviour does not appear with asymmetric anchors such as pyridyl and SMe. It is found that changing the basis set has no effect on the transmission curves, when the pinning occurs, and that is likely due to the shape of the gold surface. This behaviour does not occur in the absence of the tip gold with using SAMs approach, which clarifies that the shape of the electrode plays a role in controlling the relative position of its Fermi energy.
The second project concentrates on studying the effect of vibrations of the molecule on electron transport, and how it controls the value of the Seebeck coefficient. Different side groups are investigated for a series of fluorene-based molecules. The results indicated that the Seebeck coefficient of meta-connected molecules is more sensitive to the fluctuations of the side groups compared to the para case, which means that varying the pendant groups in molecular junctions can be exploited to control quantum interference (QI) and enhance the thermoelectric properties. Although C≡C and C≡N pendant groups behave similarly at room temperature, the transmission behaviour of the whole molecules different, where most of the curves in the C≡N case have this parallel shape (i.e., the anti-resonance is alleviated), leading to more enhancement in the Seebeck. In contrast, a less rigid pendant group such as C_13 (F_5 )_2 results in a large shift of the resonances causing broader conductance and Seebeck distributions. It is believed that the charge distribution of fluorine atoms could produce a gating environment on the backbone of the molecule leading to this large shift.
The final project investigates the electron transport behaviour of para and meta connected molecules with and without the metal atoms, due to the presence of PdCl_2. Introducing a metal atom into the path of the molecule creates another transmission path, which may play a role in disrupting or changing the QI. The complex structure of these molecules leads to multiple binding locations for attachment to gold electrodes and therefore multiple junction configurations can be formed. The results showed that the addition of the palladium with the chlorine atoms to the ligand molecules enhanced the conductance for both connectivities through the SMe anchor group due to the shift of the LUMO resonance to the Fermi energy. However, the different junction geometries do not enhance the Seebeck value.