Graduation Year

2012

Document Type

Dissertation

Degree

Ph.D.

Degree Granting Department

Electrical Engineering

Major Professor

Rudy Schlaf

Keywords

charge injection barrier, interface dipole, peptide nucleic acid, tetraphenylporphyrin, work function, XPS

Abstract

The studies presented here address the characterization of the electronic structure of various self-assembled monolayers (SAMs) of peptide nucleic acid (PNA) and tetraphenylporphyrin (TPP) SAMs and arrays, formed on gold substrates.

PNA is a promising alternative to DNA for bio-sensing applications, as well as for strategies for self-assembly based on nucleic acid hybridization. In recent years charge transfer through PNA molecules was a focus of research due to possible applications in self-assembled molecular circuits and molecular tools. In light of this research it is interesting to investigate the electronic structure of PNA interfaces to gold, a potential electrode material.

TPP is, due to its electronic structure, an organic p-type molecular semiconductor. Such a material can provide an alternative to standard micro- and optoelectronic devices and in recent years more attention was paid to semiconducting polymers and organic compounds offering these low-cost and flexible alternatives. Therefore, it is of high importance to investigate the prospect of using modified TPP molecules for the formation of interconnected molecular networks on metallic surfaces.

All investigated monolayers were formed from solution in a nitrogen atmosphere inside a homemade glove box. This process allowed for PNA SAM and TPP SAM and array formation on clean Au substrates without the exposure to the ambient atmosphere. Ultraviolet and X-ray photoemission spectroscopy (UPS and XPS) measurements on the resulting PNA SAMs and TPP SAMs and arrays, which were performed in a to the glove box attached vacuum chamber containing a photoemission spectrometer, revealed the hole injection barriers at the interfaces and the interface dipoles.

In addition to the UPS and XPS measurements on PNA, electronic structure calculations based on molecular dynamics sampling of the PNA structure were obtained, yielding the HOMO-LUMO gap and the electronic density of states for PNA. Combined with the UPS data, the theoretical calculations enabled estimation of the charge injection barriers for the PNA SAMs at the interface, as well as the assignment of individual UP-spectral features to specific molecular orbitals.

The orbital line-up at the interface between the Au substrate and the PNA indicated a significant interface dipole resulting in the alignment of the Au Fermi level near the center of the PNA HOMO-LUMO gap. This alignment causes large charge injection barriers for both holes and electrons, and thus impedes charge transfer from Au into the PNA SAM. The study of PNA molecules with ferrocene termini showed that this hole injection barrier is shifted to lower energies at the PNA/ferrocene interface. This shift was explained with a molecular orbital reconfiguration through the presence of the ferrocene terminus. The further investigation of the dependence of the electronic structure of PNA SAMs, based on their orientation, showed that incomplete films containing flat lying molecules can have a significant impact on the charge injection barriers. The close proximity of the nucleobases to the Au surface offers new ways for charge transfer between the substrate and the PNA molecule through its nitrogen sites, leading to a lowering of the hole injection barrier at the interface.

The TPP arrays were formed by depositing AgNO3 on the Au substrate prior to TPP incubation using the electrospray technique. The interaction of AgNO3 with the TPP promoted the formation of an interconnected thin film forming a network on the Au substrate. The line-up at the Au/TPP interface without AgNO3 exposure showed an interface dipole formation with injection barriers that would potentially obstruct charge injection into the molecule. However, the addition of AgNO3 to the process resulted in the formation of fine structures, and lead to a lower hole injection barrier due to an induced dipole, which would ultimately improve charge transfer between the substrate and the thin film. A separate thiolated TPP derivative was used to form SAMs on a gold substrate. The SAM exhibited an even lower injection barrier than the mentioned TPP thin film with AgNO3 exposure, leading to the conclusion that a mix of both TPP derivatives could potentially lead to a SAM with long range interconnectivity and a low hole injection barrier towards the substrate.

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