Charge transfer in DNA: Effects of humidity and molecular vibrations on detection and rate of hole transport

Aspects of the mechanism and experimental detection of charge transfer in DNA are studied both theoretically and computationally. The first portion of this thesis is dedicated to the development of an electrostatic model to explain the unique experimental data that shows with increasing humidity there is an increase in conductance of several orders of magnitude. The binding energy of the ions formed in the water self-dissociation process dictates the amount of conductance and is dependent on the thickness of the water layer due to the contribution of polarization from the DNA strands. This polarization causes an electric field to be confined within the water surrounding DNA and results in an increase in binding energy that reduces the amount of ionic conduction. The second portion discusses the role of molecular vibrations in inhibiting charge transfer in DNA. Normal mode analysis was performed to determine the contribution of each mode to the reorganization energy and electronic coupling terms that dictate the rate of electron transfer in Marcus Theory. The key development is that certain modes occur via thermal activation and others through quantum tunneling at room temperature, which results in the rate of charge transfer being highly temperature dependent. The final portion of this disseration is dedicated to the suggestion of using transient infrared absorption spectroscopy to monitor charge transfer opposed to the currently used methods. Through density functional methods it is shown that oxidation of the guanine-cytosine base pair shows a unique change in the infrared spectrum upon oxidation, and this change is in regards to amide vibrations. There is a relatively mysterious reduction in intensity upon oxidation for amide scissor modes, and a mysterious increase in intensity for amide stretching modes. Even though the nature of this mode is unknown, it is shown to still be an effective marker for charge transfer detection in organic systems.