Theoretical and Experimental Explorations of Charge Transfer in Small Molecules and Peptide Nucleic Acids

Non-adiabatic charge transfer (CT) is one of the simplest but very important (if not the most important) chemical reactions. As a model system, alkanedithiols are among the most popular ones for short- or medium-range CT. Peptide nucleic acids (PNAs), which consist of nucleobases but with peptide backbones instead of the phosphate backbones in DNA, is another promising model system for long-range CT. Various models and computational methods have been developed to describe three major experimental configurations: electrochemical measurement with self-assembled monolayer films (SAMs), single-molecule conductance measurement and photoinduced electron transfer (PET).\ud \ud This dissertation have employed above experimental techniques and computational methods to study the two model systems. The first work focuses on electrochemical models. Single-step models are widely used for analyzing CT through SAMs. However, long-range CT can occur in a “hopping” regime that involves multiple events. This study describes a three-step kinetic scheme to model CT in this regime. It is corroborated by the experimental results of a 10-mer peptide nucleic acid SAM. The second study compares single molecule conductances of alkanedithiols and alkoxydithiols. Both molecular junction measurements and theoretical simulations by non-equilibrium Green’s function (NEGF) method show that the conductance is lower for alkoxydithiols and the difference is length dependent. A pathway analysis of the electronic coupling is used to explain the results. The last two studies address the importance of conformational distributions on charge transfer in PNAs: The third study compares the electrochemical charge transfer rates of normal aeg-PNA and γ-PNA which has a less flexible backbone. Molecular dynamics and NEGF calculations show that the greater flexibility of the aeg-PNA gives rise to a more frequent appearance of high-CT rate conformations. In the last study a new PNA scaffold with a [Ru(Bpy)3]2+ donor and a bis(8-hydroxyquinolinate)2 copper acceptor for PET is described. Experiments show that whether the [Ru(Bpy)3]2+ is terminally or centrally situated affects PET. Molecular dynamics simulations reveal that the difference in conformational distributions is a possible explanation. The findings in these studies provide a deeper understanding of CT in molecules, and may facilitate the development of non-adiabatic dynamics in a bigger picture.\u