ИСТИНА

Nowadays implementing multiscale approaches is one the most powerful and effective computational strategy to describe complex systems. The largely used approach is a combination of a quantum- mechanical description for a specific part of the whole system, whose properties are important to study, and a classical approach for a remainder that is indicated as “environment” (QM/MM). It can be applied in the development of a new generation of nanoscale computing devises based on parallel and multivalued logic operations at the molecular scale1. One of the promising candidates to be implemented in such devices is sulforodamine-rhodamine B (Tamra) dimer (RHO_TAMRA) mounted on a short DNA duplex of 28 base pairs in a water solution. Two approaches to study RHO_TAMRA on DNA system are performed in our work. One is using time-dependent density functional theory (TD DFT) with variety of functionals for snapshots from the molecular dynamic (MD) trajectory that includes both the DNA scaffold and the water environment explicitly. It gives us the information of the vertical transition distribution and molecular orbital excitations for the ensemble of snapshots considered. In this case we study the RHO_TAMRA dimer with the polarizable continuum model (PCM) to describe the environment (DNA in water solution). The second approach is based on QM/MM DFT (ONIOM scheme) optimization of the whole system starting from different points of MD trajectory where RHO_TAMRA is included in QM part and DNA with a water solution are treated with MM. Water is represented both as implicit solvent (PCM) and as an explicit one. Electronic embedding is used for a better description of the electrostatic interaction of the RHO_TAMRA dimer with the environment and to include MM polarization.