We extend the model of exciton-plasmon materials to include a ro-vibrational structure of molecules using wave-packet propagations on electronic potential energy surfaces. The new model replaces conventional two-level emitters with more complex molecules allowing to examine the influence of alignment and vibrational dynamics on strong coupling with surface plasmon-polaritons. We apply the model to a hybrid system comprising a thin layer of molecules placed on top of a periodic array of slits. Rigorous simulations are performed for two types of molecular systems described by vibrational bound-bound and bound-continuum electronic transitions. Calculations reveal new features in transmission, reflection and absorption spectra including the observation of significantly higher values of the Rabi splitting and vibrational patterns clearly seen in the corresponding spectra. We also examine the influence of anisotropic initial conditions on optical properties of hybrid materials demonstrating that the optical response of the system is significantly affected by an initial pre-alignment of the molecules. Our work demonstrates that pre-aligned molecules could serve as an efficient probe for the sub-diffraction characterization of the near-field near metal interfaces.
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