For electron-phonon Hamiltonians with the couplings linear in the phonon operators we construct a class of unitary transformations that separate the normal modes into two groups. The modes in the first group interact with the electronic degrees of freedom directly. The modes in the second group interact directly only with the modes in the first group but not with the electronic system. We show that for the $n$-level electronic system the minimum number of modes in the first group is $n_s=(n^2+n-2)/2$. The separation of the normal modes into two groups allows one to develop new approximation schemes. We apply one of such schemes to study exitonic relaxation in a model semiconducting molecular heterojuction.
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