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CIS electronic structure calculations have been employed to derive the fluctuation in the ground to excited state energy gap of dihydroNicotinamide Adenine Dinucleotide (NADH) embedded in the Horse Liver Alcohol Dehyrogenase (LADH figure 1.) protein matrix as a function of time. Classical molecular dynamics trajectories of 130 ps in length have been generated for an LADH+NADH dimer in water to elucidate the dynamics of equilibrated LADH over a 5ps timescale. Steady-state absorption and emission spectra have then been calculated to an accuracy within 10 % of experiment (figure 2) by utilising ca. 10,000 CIS QM/MM calculations per simulation coupled to our framework for predicting optical spectra based on linear response theory. 1,2,3 It has been found that the accuracy of the results obtained are very dependent on the quality of the molecular dynamics trajectory, especially in the parameterisation of the nicotinamide moiety. This can be explained by considering the orbitals involved in the excitation leading to the observed emission. Figure 3 shows a snapshot from one of the CIS calculations. The orbitals are localised on the nicotinamide moiety and so it is fluctuations in this section of the NADH that are responsible for the emission spectra of LADH. The results have shown that applications of linear response theory can work for systems, such as NADH, which have very large reorganisation energies (Stokes Shift ≈ 1 eV) yielding predicted spectra that are within 10 % of experiment. Previous work with different NADH parameters yielded poor results implying that the method employed in this work provides an independent method for validating certain force field parameters.

Large and Fast Relaxations inside a Protein: Calculation and Measurement of Reorganization Energies in Alcohol Dehydrogenase