| Summary: | The main focus of this thesis is the theoretical investigations of a nanogap platform used for molecular electronics measurements under ambient conditions. The nanogap is about 20 nm wide, while the molecules investigated here (octanethiol(OT) and octanedithiol(ODT)) are about 1-1.5 nm long making it impossible to bridge the gap with one molecule. Two different approaches are investigated. In the first approach the electrodes of the nanogap are coated with a layer of OT molecules, and large gold nanoparticles (diameter of about 30 nm) are trapped in the gap creating two molecular junctions with assemblies of molecules. In the second approach the electrodes are kept clean, but instead the gold nanoparticles are coated with doubly functionalized molecules (ODT) and trapped in the gap. Here the nanoparticles are limited in size to about 5 nm, hence it is necessary to consider nanoparticle-molecule chains or small networks to bridge the gap. The first principles modeling of the structure of the metal-molecule junctions combined with elastic and inelastic transport properties is performed using the density functional theory (DFT) combined with the non-equilibrium Green’s functions (DFT-NEGF) method. In the first approach with the coated electrodes and the large nanoparticles, simulations show that structural irregularities at the electrode interface can lead to a significant variation of the conductance through the molecular film. Due to the size of the nanoparticles, the shape and orientation of the facets will have great influence on how many molecules are connected, affecting the measured resistance of the device. With the second approach utilizing the functionalized nanoparticles, more stable junctions are obtained since the nanogap is bridged by molecular junctions chemisorbed in both ends. To make chemical bonds to both sides of the junctions, the outer functional group needs to be protected before the trapping of nanoparticles in the gap. Deprotected nanoparticles agglomerate and cannot be trapped. We have inves- tigated the most probable configurations of the molecules in these junctions. During deprotection of the functional group in the gap, a conduction increase have been observed. We have found that the removal of the protection group is not responsible for the increased conduction. Instead, since the deprotected molecule is shorter and the nanoparticles are mobile during deprotection, a reorganization of the nanopar- ticles in the gap occurs. This reorganization leads to decreasing of the tunneling length for the electrons, hence increasing the conduction. We also demonstrate, that we can obtain the inelastic electron tunneling spectroscopy (IETS) signature of an octanedithiol molecule in this platform. This is done on the network of chemisorbed ODT junctions, where we are able to relate the low-bias Au-S and C-S stretch modes of the molecule to observed peaks in IETS. From this we estimate that the main contribution in the signal comes from chains containing 5, 6 and 7 molecular junctions. To identify the peaks, we have calculated the theoretical spectra for one molecule, from which we are able to extract the important vibrational modes, and their couplings to the electrons. This we then use in a model, including the Coulomb blockade observed in the nanoparticles, to fit the theoretical spectra to the measured one.
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