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In this paper we present a study of the methodological aspects regarding calculations of optical properties for DNA systems in solution. Our computational approach will be built upon a fully polarizable QM/MM/Continuum model within a damped linear response theory framework. In this approach the environment is given a highly advanced description in terms of the electrostatic potential through the polarizable embedding model. Furthermore, bulk solvent effects are included in an efficient manner through a conductor-like screening model. With the aim of reducing the computational cost we develop a set of averaged partial charges and distributed isotropic dipole-dipole polarizabilities for DNA suitable for describing the classical region in ground-state and excited-state calculations. Calculations of the UV-spectrum of the 2-aminopurine optical probe embedded in a DNA double helical structure are presented. We show that inclusion of polarizabilities in the embedding potential stemming from the DNA double helix is of crucial importance, while the water cluster surrounding the DNA system is well represented using a continuum approach.

In recent years computational methods based on embedding have become of increasing popularity when the aim is to introduce environmental effects into quantum chemistry calculations of molecular properties. This is due in particular to the efficiency of such methods while still retaining a high degree of accuracy compared to full quantum chemistry treatments. In the present paper we compare two popular embedding methods - fluctuating charges (FQ) and polarizable embedding (PE) - highlighting their similar mathematical structure. Furthermore, based on a unified formulation of the two embedding methods, we present theory and implementation of these embedding methods within resonant-convergent response theory up to the level of quadratic response. A numerical comparison between FQ and PE is presented for a set of solute-solvent systems based on calculations of UV/vis and magnetic circular dichroism spectra. Overall, we find in the cases considered the FQ and PE models to perform rather similarly, especially upon introducing effects of explicit conformational sampling into the theoretical predictions.

We present a study of mobility field and temperature dependence for C60 with Kinetic Monte Carlo simulations. We propose a new scheme to take into account polarization effects in organic materials through atomic induced dipoles on nearby molecules. This leads to an energy correction for the single site energies and to an external reorganization happening after each hopping. The inclusion of polarization allows us to obtain a good agreement with experiments for both mobility field and temperature dependence.

We present a formulation of the polarizable density embedding (PDE) method in combination with the complex polarization propagator (CPP) method for the calculation of absorption spectra of molecules in solutions. The method is particularly useful for the calculation of near-edge X-ray absorption fine structure (NEXAFS) spectra. We compare the performance of PDE-CPP with the previously formulated polarizable embedding (PE)-CPP model for the calculation of the NEXAFS spectra of adenine, formamide, glycine, and adenosine triphosphate (ATP) in water at the carbon and nitrogen K-edges, as well as of formamide and glycine at the oxygen K-edge. In general, we find only minor differences between the performance of PDE and PE for the targeted parts of the spectra, except in the case of transitions involving Rydberg states, for which nonelectrostatic effects are found to be important.

We present a systematic investigation of the key components needed to model single chromophore electronic circular dichroism (ECD) within the polarizable embedding (PE) approach. By relying on accurate forms of the embedding potential, where especially the inclusion of local field effects are in focus, we show that qualitative agreement between rotatory strength parameters calculated by full quantum mechanical calculations and the more efficient embedding calculations can be obtained. An important aspect in the computation of reliable absorption parameters is the need for conformational sampling. We show that a significant number of snapshots are needed to avoid artifacts in the calculated electronic circular dichroism parameters due to insufficient configurational sampling, thus highlighting the efficiency of the PE model.