and aligned to the amide atoms of each unit. This strategy removes the dependence of the site energies on the internal chromophore geometries sampled from MD, and has proven successful for the calculation of CD spectra of nucleic acids and proteins. The elements of the exciton Hamiltonian (S3), E a i and V ab ij , as well as the transition dipole moments µ ia and m ia , are directly obtained by multiscale quantum mechanics/molecular mechanics (QM/MM) calculations with polarizable embedding. The site energies E a i and all the other site properties are obtained from TD-DFT calculations of each chromophoric unit at the ωB97X-D 21 /6-31+G(d) level of theory, including the first 6 excited states in the calculations. The effect of all the other chromophoric units, as well as of the side chains and the solvent, is accounted for by a polarizable QM/MM embedding (QM/MMPol) .