Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins

The PhD thesis entitled "<em>Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins</em>" by Jógvan Magnus Haugaard Olsen was handed in on October 1st 2012 and defended on October 29th 2012 at the University of Southern Denmark. The PhD degree was obtained on November 8th 2012. The evaluation committee consisted of: Assoc. Prof. Hans Jørgen Aagard Jensen, Dept. of Physics, Chemistry and Pharmacy, University of Southern Denmark, Denmark Prof. Benedetta Mennucci, Dept. of Chemistry, Univeristy of Pisa, Italy Assoc. Prof. Stephan P. A. Sauer, Dept. of Chemistry, University of Copenhagen, Denmark Abstract: In this thesis we present new developments in the pursuit of computationally efficient methods that can be used rationalize the processes that occur in photoactive proteins. We formulate an advanced polarizable embedding model rooted in so-called multilevel methods that takes advantage of the fact that the photonic processes that occur in photoactive proteins can often be localized in well-defined regions of the protein. In this model we employ the expensive but accurate quantum chemical methods only on the parts of the system that partake directly in the electronic process. The effects of the environment are incorporated by adding them to the quantum mechanical equations in an effective manner. We outline the theoretical basis of the model as well as the equations that need to be incorporated in the quantum chemical methods. The work presented here is an advancement of conventional multilevel methods in that we introduce an additional layer around the important part of the system where the interactions are described at a higher level of theory thereby allowing more accurate calculations to be performed. Furthermore, we describe some of essential elements of the implementation of the model which is an important part of the development of computationally efficient methods. Finally, we also demonstrate the model by performing numerical calculations on large molecular systems such as solute-solvent systems and photoactive proteins.