Electronic absorption spectra from MM and ab initio QM/MM molecular dynamics: Environmental effects on the absorption spectrum of photoactive yellow protein

Citation:

Isborn, C. M., Götz, A. W., a. Clark, M., Walker, R. C., & Martinez, T. J. (2012). Electronic absorption spectra from MM and ab initio QM/MM molecular dynamics: Environmental effects on the absorption spectrum of photoactive yellow protein. Journal of Chemical Theory and Computation, 8, 5092–5106.

Abstract:

We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.