In this thesis the hybrid method ONIOM is applied to computing the reaction pathways and vibrational modes of molecules embedded within complex environments. ONIOM combines different levels of theory in order to treat the most chemically important regions of the molecule at a sufficiently high level of theory, while simultaneously including the steric and electronic effects of the remainder of the molecule such that the calculation remains affordable. Normal mode analysis also allows characterisation of critical points located on the Potential Energy Surface (PES). While the ONIOM PES is well defined for a given combination of theories, this does not ensure that the PESs for each individual level of theory are qualitatively the same. In cases where they differ this may cause the curvature of the ONIOM PES to be sensitive to method combinations and ONIOM partitioning. We present a method for analysing the ONIOM Hessian to indicate where such situations occur. The ONIOM method is then applied to computing vibrational modes of the Green Fluorescent Protein (GFP). This enhances interpretation of spectra
obtained from time-resolved femtosecond spectroscopy. ONIOM(QM:MM) reduces the cost associated with assembly of the Hessian matrix and reformulation of the CPHF equations enables inclusion of the environment electronic effect in the normal mode analysis. This has been used to understand how chromophore vibrational modes are modified through covalent and hydrogen bonding, transition dipole coupling, accidental degeneracy and the vibrational Stark effect. In the final application, ONIOM(CAS:MM) models how the protein environment of the Photoactive Yellow Protein (PYP) modifies reaction pathways.
The protein enhances trans-cis isomerization compared to vacuum. ONIOM allows separate analysis of the steric and electronic roles of the protein environment and reveals that the steric effect disfavoured the gas-phase pathway while the electronic environment allows the alternative pathway to directly access the
intersection crossing seam.