Almutib, Eman and Lambert, Colin (2016) Quantum and classical dynamics of molecular scale structures. PhD thesis, Lancaster University.
Thesis13_12_2016_EA.pdf - Published Version
Available under License Creative Commons Attribution-NoDerivs.
Download (4MB)
Abstract
In this thesis, I investigate the electronic properties of molecular junctions formed from single molecules. Most of my work uses the saturated alkane chain as my reference molecule to study some problems of charge transfer in nanoscale devices. Chapters 2 and 3 present a brief introduction to Density Functional Theory using the SIESTA implementation, and the Green’s function formalism of electron transport as implemented in the GOLLUM code, which is a nextgeneration equilibrium transport code, born out of the non-equilibrium transport code SMEAGOL. These two techniques are used to study the charge transport through dicarboxylic-acid-terminated alkanes in chapter 4, which are bound to 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 graphene–molecule–Au junction leading to an increase in the electrical conductance compared with Au–molecule–Au junctions, which suggests that graphene offers superior electrode performance when utilizing carboxylic acid anchor groups. In chapter 5, I show that the conductance of the saturated chain is affected by adding oxygen to the chain. Comparisons between my electronic structure calculations on oligoethers such as poly ethylene glycol (PEG) chains and previous work on alkanes shows that the conductance of oligoethers is lower than that of alkane chains with the same length. The calculation of the length dependence of the electrical conductance of alkanes and oligoethers, shows that the beta tunnelling factor 훽푁 per methyl unit of the alkanes is lower than the beta factor of oligoethers. In the final chapter, molecular dynamic (MD) simulations using the DLPOLY_4 code, are used to examine the molecular assembly of two candidate molecules for graphene based molecular electronics, one with one pyrene anchor, Pyrene-PEGn-ex-TTF (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 semi-circular cone like micelle structures on the graphene surface. In the presence of water, the PPT tends to aggregate whereas the TPPT micelle expands. The hydrophobic pyrene anchors are firmly attached to the graphene surface in both cases while the hydrophilic dithiol heads groups which allow the water to disperse the micelles.