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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 this paper, we discuss the impact of using a frequency-dependent embedding potential in quantum chemical embedding calculations of response properties. We show that the introduction of a frequency-dependent embedding potential leads to further model complications upon solving the central equations defining specific molecular properties. On the other hand, we also show from a numerical point of view that the consequences of using such a frequency-dependent embedding potential is almost negligible. Thus, for the kind of systems and processes studied in this paper the general recommendation is to use frequency-independent embedding potentials since this leads to less complicated model issues. However, larger effects are expected if the absorption bands of the environment are closer to that of the region treated using quantum mechanics.

Source at https://doi.org/10.1002/qua.25717. The polarizable embedding (PE) model is a fragment‐based quantum‐classical approach aimed at accurate inclusion of environment effects in quantum‐mechanical response property calculations. The aim of this tutorial review is to give insight into the practical use of the PE model. Starting from a set of molecular structures and until you arrive at the final property, there are many crucial details to consider in order to obtain trustworthy results in an efficient manner. To lower the threshold for new users wanting to explore the use of the PE model, we describe and discuss important aspects related to its practical use. This includes directions on how to generate input files and how to run a calculation.

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.

The magnetic compass sense utilized by migratory birds for long-distance navigation functions only once light of a certain wavelength is present. This piece of evidence fits partially with the popular hypothesis of chemical magnetoreception in cryptochrome proteins, located in the bird retina. According to this hypothesis a magnetosensitive radical pair is produced after photoexcitation of an FAD cofactor inside cryptochrome, and as such the absorption properties of FAD are of crucial importance for cryptochrome activation. However, we reveal that absorption spectra of FAD show very little variation between six different cryptochromes, suggesting that the electronic transitions are barely affected by the chemical differences in the proteins. This conclusion hints on the presence of a secondary photoreceptor or cofactor that could be necessary to explain green-light-activated magnetoreception in birds.

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.

Magnetic circular dichroism (MCD) is defined as the differential absorption of left and right circularly polarized light in a sample subjected to an external magnetic field. In order to interpret the results of MCD measurements, theoretical predictions of key MCD parameters can be of utmost importance. From an experimental point of view, MCD spectra of molecules are often measured in an environment and most notably in a solution. Thus, it may be very important that the method used to predict the MCD parameters is able to correctly account for medium effects. In this paper, we investigate the quality of MCD calculations within the polarizable embedding approach, which represents a fully atomistic and polarizable representation of an environment surrounding a smaller region treated using quantum mechanics. Furthermore, we compare the performance of the polarizable embedding scheme to the use of the more conventional dielectric continuum approach. Results are presented for cytosine and hypoxanthine solvated in water.

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.

Polarizable quantum mechanical (QM)/molecular mechanics (MM)-embedding methods are currently among the most promising methods for computationally feasible, yet reliable, production calculations of localized excitations and molecular response properties of large molecular complexes, such as proteins and RNA/DNA, and of molecules in solution. Our aim is to develop a computational methodology for distributed multipole moments and their associated multipole polarizabilities which is accurate, computationally efficient, and with smooth convergence with respect to multipole order. As the first step toward this goal, we herein investigate different ways of obtaining distributed atom-centered multipole moments that are used in the construction of the electrostatic part of the embedding potential. Our objective is methods that not only are accurate and computationally efficient, but which can be consistently extended with site polarizabilities including internal charge transfer terms. We present a new way of dealing with well-known problems in relation to the use of basis sets with diffuse functions in conventional atomic allocation algorithms, avoiding numerical integration schemes. Using this approach, we show that the classical embedding potential can be systematically improved, also when using basis sets with diffuse functions, and that very accurate embedding potentials suitable for QM/MM embedding calculations can be acquired. © 2016 Wiley Periodicals, Inc.