Multiscale atomistic simulation methods are applied to studying excited molecules in organic nanomaterials and their interaction with neighboring molecules. The formation of exciplexes at the interface between layers of organic molecules in multilayer structures, typical for organic light-emitting diodes, for organic solar cells, and for other devices of organic electronics and photonics, makes an important contribution to the emission energies and to the shape of the emission band. Adequate models of a complex system containing excited components and suitable methods for the description of charge and/or excitation transfer are considered. The following steps are briefly discussed: (1) the construction and use of the library of parameters of the EFP (Effective Fragment Potentials) approximation for the simulation of environment of luminescent dopants and transport molecules in the layers; (2) the estimation of the accuracy of the obtained results; (3) the creation of a program complex for the construction of the polarized environment using the library of parameters in the EFP approximation; (4) the investigation of the effect of the polarized environment on the positions of triplet and singlet levels of luminescent dopants; (5) the development and improvement of approaches to the calculation and interpretation of absorption spectra of supramolecular systems using hybrid QM/MM methods; (6) studying the formation of exciplexes forming at the interface between two organic semiconducting layers by molecular dynamics and the calculation of their properties by quantum chemical methods; (7) selection and development of force fields for metal-organic complexes, molecular dynamics simulation of such system using these force fields; (8) the development and improvement of the computational approach based on multiconfigurational quantum-chemical calculations of radiative and intersystem crossing constants; (9) studying spin-mixed states of phosphorescent iridium(III) complexes, the calculation of radiative phosphorescence constants, and analysis of channels of nonradiative phosphorescence quenching. Computational methods and programs that can be used for efficient realization of these steps are briefly discussed.