Development of RT-TDDFT for the Interaction with the Explicit Solvent and for Correct Description of Excitation Process

The electronic energy transfer processes in natural systems, such as the light harvesting pigment protein complexes, and semiconductors, such as photovoltaic devices, occur via electron dynamics in complex systems. Understanding the excited state dynamics is important in designing the biological or nanostructured materials. The computational simulation of electron dynamics in an accurate and affordable manner is crucial for making progress in this area. The time dependent open system self consistent field at second order (OSCF2) is a real-time time-dependent density functional theory (RT-TDDFT) method. The block orthogonalized partitioning method eliminates unphysical errors of the embedded mean field theory at no additional cost. This thesis focuses on the application of OSCF2 to the simulation of transient absorption spectroscopy. OSCF2 accurately reproduced transient absorption spectra and non-radiative relaxation rates of green fluorescent protein chromophore derivative 3 (GFP-3). The implementation of an embedded mean-field theory using block-orthogonolized partitioning to real-time time dependent density functional theory (RT-TDDFT) and its effect of accuracy and affordability are discussed. The block orthogonalized partitioning in RT-TDDFT accurately describes the interactions between the regions while maintaining computational affordability. The method development for the excitation process for RT-TDDFT using the Tamm- Dancoff approximation is discussed. The effort to describe the excitation process in RT-TDDFT leads to partial success. Studies using neural networks on molecular dynamics using bullvalene and mechanistic studies on formation of oxindole derivative from squaraine dyes are discussed. The neural network force field was not successful to reproduce the conformer search through molecular dynamics simulations, presumably due to insufficient simulation times. The free energy barriers of ring opening step of squaraine ring are in line with the experimental observations. Lastly, the software implementations to PySCF, Q2MM, and automated CatVS are discussed.