Sanders, BarrySalahub, DennisJohannes, Jonathan2016-01-292016-01-292016-01-292016Johannes, J. (2016). Bridging the Gap Between the Theoretical and Empirical Reorganization Energy (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca. doi:10.11575/PRISM/25165http://hdl.handle.net/11023/2801Biological electron transfer (ET) reactions are fundamental to the production of energy in all living cells. Efficient, site-selective ET is crucial for effective metabolic processes to sustain life. An accurate description of the ET process through a protein complex is lacking. In particular, with the methylamine dehydrogenase (MADH) and amicyanin protein complex there is a discrepancy between the theoretical and the empirical reorganization energy. Attempts at better understanding the reorganization energy of reaction involve adapting Marcus theory, the standard for simple ET reactions, by describing the reorganization energy with a two-parameter model. In this thesis I apply the two-parameter model to the MADH-amicyanin system. It does not reconcile the discrepancy between the theoretical and empirical reorganization energy. The results of this work provide insight, consistent with other systems onto which the two-parameter has been applied, into why Marcus theory breaks down.engUniversity of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.Physics--Molecularelectron transfermarcus theoryprotein complexmolecular simulationsmaster thesis10.11575/PRISM/25165