Response properties of embedded molecules through the polarizable embedding model

Abstract

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. K E Y W O R D S computational spectroscopy, molecular properties, polarizable embedding, QM/MM, response properties 1 | INTRODUCTION Hybrid quantum-classical approaches for modeling of chemical or biological systems have in recent years gained considerable interest. The reasonfor such popularity of these models relies, to a large degree, on their efficiency and the fact that such models enable calculations on systems of sizes that are otherwise impossible using pure quantum-mechanical methods. The dielectric continuum models belong to the simplest of the quantum-classical approaches, [1,2] and models like the polarizable continuum model [3,4] are today implemented in many of the available electronic-structure programs. In addition, such models are very easy to use: based on a predefined set of atomic radii and the dielectric constant of the solvent, the user can include solvation effects based only on a single calculation. Only one calculation is needed because the dielectric continuum models implicitly include sampling of solvent configurations. On the other hand, it is well-known that the dielectric continuum models possess several drawbacks, such as the inability to model the directionality of specific intermolecular interactions like hydrogen bonding or π-π stacking. Because of this, modeling of environment anisotropies, as found in, for example, protein matrices is lost.Another class of quantum-classical approaches consists of discrete models where the atomistic detail of the environment is kept, that is, models based on the concept of combined quantum mechanics and molecular mechanics (QM/MM). [5][6][7][8] Discrete models, compared to the dielectric continuum models, realistically describe the environment, but at an increased level of both complexity and computational requirements.Regarding the latter point, the increase in computational time is not linked to the discrete nature of the environment as such but rather that

Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM

“…The distributed multipoles and polarizabilities were computed using the LoProp approach (Gagliardi et al, 2004) employing the CAM-B3LYP functional and the ANO-form of the 6-31+G * basis set [named loprop-6-31+G(d) in Dalton]. We refer to the work by Steinmann et al (2019) for a tutorial review on the setup, use, and capabilities of the PE model (Olsen et al, 2010). A commented Python script employing PyFraME used in the present work is included in the repository (Rossano-Tapia et al, 2020).…”

Combining polarizable embedding with the Frenkel exciton model: applications to absorption spectra with overlapping solute–solvent bands

“…s,el , provides the kth order derivative of the electronic electric potential at site s. 19 k is a three-dimensional multi-index notation of multipoles implying that k = 0 is the notation for a monopole (point charge), k = 1 is a dipole and so forth.…”

“…This discrepancy is most likely due to over-polarization effects which could probably be ameliorated by including some form of damping when solving for the induced moments. 19 When computing the deviations of the spectra to the reference spectrum for solute 1 one obtains 0.38, 0.27 and 0.24 for W1, W2 and W3, respectively. This is, for W1 and W2 almost an improvement by a factor of two.…”

Interfacing CRYSTAL/AMBER to Optimize QM/MM Lennard–Jones Parameters for Water and to Study Solvation of TiO2 Nanoparticles

“…After the pioneering work of M. Levitt and A. Warshel [ 1 ], the fundamental QM/MM methodology of joining explicit electronic structure to classical potential functions is constantly being both applied and expanded upon [ 2 , 3 , 4 , 5 , 6 , 7 ]. While much work is being put into methods that go beyond the electrostatic embedding-type of additive QM/MM, which explicitly couples the two subsystems via a Coloumb term but leaves the MM charges fixed, this form of coupling still seems prevalent within additive QM/MM applications [ 8 ], most likely due to its generally accepted trade-off between accuracy and efficiency.…”