  In this thesis, I investigate the molecular electronic properties of
molecular junctions formed from single molecules. I started my thesis by
discusses the main theoretical methods using in this work density functional
theory and the green function formalism of electron transport. These two
techniques are used to study the charge transport through dicarboxylic acid
terminated alkanes in chapter 4, with graphene gold nanogap electrodes. The
results are then compared with those using symmetric gold electrodes and reveal
that there is a difference between the two situations due to the difference in
Fermi energies relative to the frontier orbitals of the molecules. Furthermore,
the electrical conductance in the asymmetric junction is higher than that in
the symmetric junction, which suggests that graphene offers superior electrode
performance when utilizing carboxylic acid anchor groups. In chapter 5, I study
affected of the saturated chain conductance by adding oxygen to the chain.
Comparisons between my electronic structure calculations on oligoether chains
and previous work on alkanes show that the conductance of oligoether is lower
than that of alkane chains with the same length. I found that the beta
tunneling factor per methyl unit of the alkanes is lower than the beta factor
of oligoether. In the final chapter, molecular dynamic simulations are used to
examine the molecular assembly of two candidate molecules for graphene-based
molecular electronics, one with one pyrene anchor, Pyrene PEGn exTTF, PPT, and
the other with three pyrene anchors, tri pyrene derivative, TPPT, on a
disordered graphene surface. PPT is seen to form flat structures whilst TPPT is
seen to form semicircular cone like micelle structures on the graphene surface.
In the presence of water, the PPT tends to aggregate whereas the TPPT micelle
expands.
