Solvation effect might have a tremendous influence on chemical reactions. However, precise quantum chemistry calculations are most often done either in vacuum neglecting the role of the solvent or using continuum solvent model ignoring its molecular nature. We propose a new method coupling a quantum description of the solute using electronic density functional theory with a classical grand-canonical treatment of the solvent using molecular density functional theory. Unlike previous work, both densities are minimized self consistently, accounting for mutual polarization of the molecular solvent and the solute. The electrostatic interaction is accounted using the full electron density of the solute rather than fitted point charges. The introduced methodology represents a good compromise between the two main strategies to tackle solvation effect in quantum calculation. It is computationally more effective than a direct quantum-mechanics/molecular mechanics coupling, requiring the exploration of many solvent configurations. Compared to continuum methods it retains the full molecular-level description of the solvent. We validate this new framework onto two usual benchmark systems: a water solvated in water and the symmetrical nucleophilic substitution between chloromethane and chloride in water. The prediction for the free energy profiles are not yet fully quantitative compared to experimental data but the most important features are qualitatively recovered. The method provides a detailed molecular picture of the evolution of the solvent structure along the reaction pathway.
The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent configuration, explicit solute-solvent interactions are key to understanding solution-phase reactivity and spectroscopy, simulating accurate inhomogeneous broadening, and predicting absorption spectra. In this tutorial review, we give an overview of factors to consider when modeling excited states of molecules interacting with explicit solvent. We provide practic…
The problem of a solute described by Quantum Chemistry within a solvent represented as a polarizable continuum model (PCM) is here reformulated in terms of the open quantum systems (OQS) theory. Using its stochastic Schrödinger Equation formulation, we are able to provide a more comprehensive picture of the electronic energies and of the coupling between solute and solvent electronic dynamics. In particular, OQS-PCM proves to be a unifying theoretical framework naturally including polarization and dispersion interactions, the effect of solvent fluctuations, and the non-Markovian solvent respon…
Coupled cluster Green's function (GFCC) calculation has drawn much attention in the recent years for targeting the molecular and material electronic structure problems from a many body perspective in a systematically improvable way. However, GFCC calculations on scientific computing clusters usually suffer from expensive higher dimensional tensor contractions in the complex space, expensive interprocess communication, and severe load imbalance, which limits it's routine use for tackling electronic structure problems. Here we present a numerical library prototype that is specifically designed f…
Molecular excitations in the liquid-phase environment are renormalized by the surrounding solvent molecules. Herein, we employ the GW approximation to investigate the solvation effects on the ionization energy of phenol in various solvent environments. The electronic effects differ by up to 0.4 eV among the five investigated solvents. This difference depends on both the macroscopic solvent polarizability and the spatial decay of the solvation effects. The latter is probed by separating the electronic subspace and the GW correlation self-energy into fragments. The fragment correlation energy de…
Experimental measurements of electron transport properties of molecular junctions are often performed in solvents. Solvent-molecule coupling and physical properties of the solvent can be used as the external stimulus to control electric current through a molecule. In this paper, we propose a model, which includes dynamical effects of solvent-molecule interaction in the non-equilibrium Green's function calculations of electric current. The solvent is considered as a macroscopic dipole moment that reorients stochastically and interacts with the electrons tunnelling through the molecular junction…
We develop an extension of the time-dependent equation-of-motion formulation of the polarizable continuum model (EOM-TDPCM) to introduce nonequilibrium cavity field effects in quantum mechanical calculations of solvated molecules subject to time-dependent electric fields. This method has been implemented in Octopus, a state-of-the-art code for real-space, real-time time-dependent density functional theory (RT-TDDFT) calculations. To show the potential of our methodology, we perform EOM-TDPCM/RT-TDDFT calculations of trans-azobenzene in water and in other model solvents with shorter relaxation …
We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersion-repulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules…
We investigate the ability of mechanical and electronic density functional theory (DFT)-based embedding approaches to describe the solvent effects on nuclear magnetic resonance (NMR) shielding constants of the $^{95}$Mo nucleus in the molybdate ion in aqueous solution. From the description obtained from calculations with two- and four-component relativistic Hamiltonians, we find that for such systems spin-orbit coupling effects are clearly important for absolute shielding values, but for relative quantities a scalar relativistic treatment provides a sufficient estimation of the solvent effects…
We investigate the solvent shift of phthalocyanine (Pc) doped into superfluid helium droplets and probed by optical spectroscopy at the electronic origin. Our present work complements extant studies and provides results that in part contradict previous conclusions. In particular, the solvent shift does not increase monotonously with droplet radius all the way up to the bulk limit, but exhibits a turnaround instead. Moreover, a substructure is resolved, whose characteristics depend on the droplet size. This behavior can hardly be reconciled with that of a freely rotating Pc-helium complex.
Molecular conduction operating in dielectric solvent environments are often described using kinetic rates based on Marcus theory of electron transfer at a molecule-metal electrode interface. However, the successive nature of charge transfer in such system implies that the solvent does not necessarily reach equilibrium in such process. Here we generalize the theory to account for solvent nonequilibrium and consider a molecular junction consisting of an electronic donor-acceptor system coupled to two metallic electrodes and placed in a polarizable solvent. We determine the nonequilbrium distribu…
A method for study of charge-transfer interactions between solute molecules and solvent based on the comparison of the ratios of spectral shifts of different electronic transitions in solute molecules in chemically inert solvent is proposed. The method is applicable to molecules that do not change their dipole moment on excitation. As an example, a presence of charge transfer interactions in higher electronic states of aromatic hydrocarbons (benzene, phenanthrene, and naphthalene) dissolved in water and alcohols was demonstrated.
Self-consistency based Kohn-Sham density functional theory (KS-DFT) electronic structure calculations with Gaussian basis sets are reported for a set of 17 protein-like molecules with geometries obtained from the protein data bank. It is found that in many cases such calculations do not converge due to vanishing HOMO-LUMO gaps. A sequence of polyproline I helix molecules is also studied, and it is found that self-consistency calculations using pure functionals fail to converge for helices longer than six proline units. Since the computed gap is strongly correlated to the fraction of Hartree-Fo…
Due to solvation, excess charge carriers on 1d semiconductor nanostructures immersed in polar solvents undergo self-localization into polaronic states. Using a simplified theoretical model for small-diameter structures, we study low-frequency properties of resulting 1d adiabatic polarons. The combined microscopic dynamics of the electronic charge density and the solvent leads to macroscopic Langevin dynamics of a polaron and to the appearance of local dielectric relaxation modes. Polaron mobility is evaluated as a function of system parameters. Numerical estimates indicate that the solvated ca…
The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion (EOM) for the apparent solvent polarization charges that generate the reaction field in the Polarizable Continuum Model (PCM) for solvation and we have coupled them to a real-time time-dependent density functional theory (RT TDDFT) description of the solute [Corni et al. J. Phys. Chem. A 119, 5405 (2014)]. Here we present an extension of the EOM-PCM approach to…
We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of arbitrary complexity immersed in a molecular solvent, both represented by molecules with interacting atomic sites and classical force fields. The molecular solvent density $ρ(\mathbf{r},\mathbfΩ)$ around the solute is a function of the position $\mathbf{r}\equiv(x,y,z)$ and of the three Euler angles $\mathbfΩ\equiv(θ,ϕ,ψ)$ describing the solvent orientation.…
Understanding the formation of lead halide (LH) perovskite solution precursors is crucial to gain insight into the evolution of these materials to thin films for solar cells. Using density-functional theory in conjunction with the polarizable continuum model, we investigate 18 complexes with chemical formula PbX$_2$M$_4$, where X = Cl, Br, I and M are common solvent molecules. Through the analysis of structural properties, binding energies, and charge distributions, we clarify the role of halogen species and solvent molecules in the formation of LH perovskite precursors. We find that interatom…
In this manuscript we present a computational study on the photoluminescence properties of several heteroleptic [Ru(H)(CO)(N^N)(tpp)2]+ complexes (tpp = triphenylphosphine). A special focus is set on disentangling the temperature-dependent emissive properties. Experimentally, when cooling a solution of [Ru(H)(CO)(dmphen)(tpp)2]+ (dmphen = 5,6-dimethyl-1,10-phenanthroline) from room to cryogenic temperature, a partial emission switch from metal-to-ligand charge transfer (3MLCT) to ligand-centered (3LC) phosphorescence is observed, resulting in dual photoluminescence. Two different origins of th…
Electrochemical Electron Transfer: Key Concepts, Theories, and Parameterization via Atomistic Simulations
University of Science and Technology of China（中国科学技术大学）；Forschungszentrum Jülich GmbH（于利希研究中心有限公司）；University of Jyväskylä（约恩苏大学）；RWTH Aachen University（亚琛工业大学）
Electronic excitations in dilute solutions of poly para phenylene ethynylene (poly-PPE) are studied using a QM/MM approach combining many-body Green's functions theory within the $GW$ approximation and the Bethe-Salpeter equation with polarizable force field models. Oligomers up to a length of 7.5\,nm (10 repeat units) functionalized with nonyl side chains are solvated in toluene and water, respectively. After equilibration using atomistic molecular dynamics (MD), the system is partitioned into a quantum region (backbone) embedded into a classical (side chains and solvent) environment. Optical…
Lead halide perovskites (LHPs) are promising materials for opto-electronics and photovoltaics, thanks to favorable characteristics and low manufacturing costs enabled by solution processing. In light of this, it is crucial to assess the impact of solvent-solute interactions on the electronic and optical properties of LHPs and of their solution precursors. In a first-principles work based on time-dependent density-functional theory coupled with the polarizable continuum model, we investigate the electronic and optical properties of a set of charge-neutral compounds with chemical formula, PbX$_2…
The Angular Localization Function (ALF): a practical tool to measure solvent angular order with Molecular Density Functional Theory
Sorbonne Université（索邦大学）；CNRS（法国国家科学研究中心）；Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX（界面电解质与纳米系统物理化学 PHENIX）；Réseau sur le Stockage Électrochimique de l’Énergie (RS2E)（电化学储能网络 RS2E）
Many important applications of electronic structure methods involve molecules or solid surfaces in a solvent medium. Since explicit treatment of the solvent in such methods is usually not practical, calculations often employ continuum solvation models to approximate the effect of the solvent. Previous solvation models either involve a parametrization based on atomic radii, which limits the class of applicable solutes, or based on solute electron density, which is more general but less accurate, especially for charged systems. We develop an accurate and general solvation model that includes a c…
Molecular systems containing donor-bridge-acceptor sites or molecular antennas constitute promising candidates for organic photovoltaic device implementation. Photo-induced electron transfer in multi-chromophore molecular systems is defined by a subtle interaction between the donor and the molecular bridge, and by the system-solvent coupling. Here, we address the computation of quantum properties such as population inversion and electron transfer in molecular photo-systems composed of fulleroisoxazoline, fulleropyrrolidine, BODIPY and Zn-porphyrin, as well as their system-solvent ultrafast dyn…
Non-radiative decay channels in the L-edge fluorescence spectra from transition metal-aqueous solutions give rise to spectral dips in X-ray transmission spectra. Their origin is unraveled here using partial and inverse partial fluorescence yields on the micro-jet combined with multi-reference ab initio electronic structure calculations. Comparing Fe2+, Fe3+, and Co2+ systems we demonstrate unequivocally that spectral dips are due to a state-dependent electron delocalization within the manifold of d-orbitals.
Imidazoline-based nitroxide radicals are often used as spin probes for medium acidity and polarity in different systems. In this work, using the density functional theory (DFT) approach, we have studied how physico-chemical characteristics (geometry, atomic charges and electron spin density distribution) of pH-sensitive spin label 4-amino-2,2,5,5-tetramethyl-3-imidazoline-N-oxyl (ATI) depend on protonation and aqueous surroundings. Our calculations demonstrate that ATI protonation should occur at the nitrogen atom of the imidazoline ring rather than at the amino group. Protonation of ATI leads…
We describe a parallel linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM. Forces are obtained using the Hellman-Feynmann relationship, giving continuous gradients, and excellent energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to CCSD(T)-F12 electronic structure theory, we built a 64-state MS-EVB model designed to study the F + CD3CN -> DF + CD2CN reaction in CD3CN solvent. This approach allows us to build a reactive potential energy surface (PES) whose balanced a…
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a DFT framework, using plane-waves basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [J. Chem. Phys. 124, 74103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the so…
Excited-state nonadiabatic dynamics in explicit solvent using machine learned interatomic potentials
Research Platform on Accelerating Photoreaction Discovery (ViRAPID), University of Vienna（维也纳大学加速光反应发现研究平台（ViRAPID））；Vienna Doctoral School in Chemistry, University of Vienna（维也纳大学维也纳化学博士学院）；Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna（维也纳大学化学学院理论化学研究所）；Department of Chemistry, Sapienza University of Rome（罗马大学化学系）；Wilhelm-Ostwald Institute, University of Leipzig（莱比锡大学威廉·奥斯特瓦尔德研究所）
Push-Pull functional compounds consisting of dicyanorhodanine derivatives have attracted a lot of interest because their optical, electronic, and charge transport properties make them useful as building blocks for organic photovoltaic implementations. The analysis of the frontier molecular orbitals shows that the vertical transitions of electronic absorption are characterized as intramolecular charge transfer; furthermore, we show that the analyzed compounds exhibit bathochromic displacements when comparing the presence (or absence) of solvent as an interacting medium. In comparison with mater…
Fast and accurate simulation of complex chemical systems in environments such as solutions is a long standing challenge in theoretical chemistry. In recent years, machine learning has extended the boundaries of quantum chemistry by providing highly accurate and efficient surrogate models of electronic structure theory, which previously have been out of reach for conventional approaches. Those models have long been restricted to closed molecular systems without accounting for environmental influences, such as external electric and magnetic fields or solvent effects. Here, we introduce the deep …
Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key ingredient of continuum models is the choice of the solute cavity, i.e. the definition of the sharp or smooth boundary between the regions of space occupied by the quantum-mechanical (QM) system and the continuum embedding environment. Although most of the solute-based approaches developed lead to models with comparable and high accuracy when applied to smal…
It is a promising extension of the quantum mechanical/molecular mechanical (QM/MM) approach to incorporate the solvent molecules surrounding the QM solute into the QM region to ensure the adequate description of the electronic polarization of the solute. However, the solvent molecules in the QM region inevitably diffuse into the MM bulk during the QM/MM simulation. In this article we developed a simple and efficient method, referred to as boundary constraint with correction (BCC), to prevent the diffusion of the solvent water molecules by means of a constraint po- tential. The point of the BCC…
A combined high-resolution Fourier transform infrared (FTIR) spectra of ferrocene (Fc) and density functional theory (DFT) based quantum mechanical calculations confirmed the dominance of the eclipsed Fc conformer in the fingerprint region of 400-500 cm-1. The IR spectra of Fc were measured in solutions with a number of non-polar solvents such as acetonitrile, dichloromethane, tetrahydrofuran and dioxane. The measurements agree well with the earlier IR spectra of Lippincott and Nelson (1958) as well as the most recent IR spectral measurement in dichloromethane solution of Duhovic and Diaconesc…
The benzene radical anion is a molecular ion pertinent to several organic reactions, including the Birch reduction of benzene in liquid ammonia. The species exhibits a dynamic Jahn-Teller effect due to its open-shell nature and undergoes pseudorotation of its geometry. Here we characterize the complex electronic structure of this condensed-phase system based on ab initio molecular dynamics simulations and GW calculations of the benzene radical anion solvated in liquid ammonia. Using detailed analysis of molecular and electronic structure, we find that the spatial character of the excess electr…
Molecular fragment or embedding methods are powerful techniques for overcoming scalability limitations in electronic structure theory by dividing large molecular systems into individual units that are small enough to be treated using standard techniques. Our group has developed a linear-scaling coupled-cluster based fragment effective field method, molecular cluster perturbation theory (MCPT), that provides a systematically improvable description of the electronic wavefunction and is scalable to thousands of atoms using the Aces4 massively parallel software package. We will present a systemati…
Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on Density Functional Theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications…
The solvation model proposed by Fattebert and Gygi [Journal of Computational Chemistry 23, 662 (2002)] and Scherlis et al. [Journal of Chemical Physics 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations encountered and extending its range of applicability. We first recast the problem in terms of induced polarization charges that act as a direct mapping of the self-consistent continuum dielectric; this allows to define a functional form for the dielectric that is well behaved both in the high-density region of the nuclear charges and in the low-density region wher…
We study the relaxation dynamics of photoexcited Fe-II complexes dissolved in water and identify the relaxation pathway which the molecular complex follows in presence of a hydration shell of bound water at the interface between the complex and the solvent. Starting from a low-spin state, the photoexcited complex can reach the high-spin state via a cascade of different possible transitions involving electronic as well as vibrational relaxation processes. By numerically exact path integral calculations for the relaxational dynamics of a continuous solvent model, we find that the vibrational lif…
The first-principles simulation of the electronic structure of organic semiconductors in solution poses a number of challenges that are not trivial to address simultaneously. In this work, we investigate the effects and the mutual interplay of solvation, alkylization, and doping on the structural, electronic, and optical properties of sexithiophene, a representative organic semiconductor molecule. To this end, we employ (time-dependent) density functional theory in conjunction with the polarizable-continuum model. We find that the torsion between adjacent monomer units plays a key role, as it …
We investigate the coupling of different quantum-embedding approaches with a third molecular-mechanics layer, which can be either polarizable or non-polarizable. In particular, such a coupling is discussed for the multilevel families of methods, in which the system is divided into an active and an inactive orbital spaces. The computational cost of the resulting three layers approaches is reduced by treating the long-range interactions at the classical level.The methods developed are tested against the calculation of the excitation energies of molecular systems in aqueous solution, for which an…
In this work, we extend the quantum optimal control theory of molecules subject to ultrashort laser pulses to the case of solvated systems, explicitly including the solvent dielectric properties in the system Hamiltonian. A reliable description of the solvent polarization is accounted for within the Polarizable Continuum Model (PCM). The electronic dynamics for the molecule in solution is coupled with the dynamics of the surrounding polarizable environment, that affects the features of the optimized light pulse. Examples on test molecules are presented and discussed to illustrate such effects.
Nowadays, hydrogen activation by frustrated Lewis pairs (FLPs) and their applications have been demonstrated to be one of emerge research topics in the field of catalysis. Previous studies have shown that the thermodynamics of these reaction is determined by electronic structures of FLPs and solvents. Herein, we investigated the systems consisting of typical FLPs and ionic liquids (ILs), which are well known by their large number of types and excellent solvent effects. The density functional theory (DFT) calculations were performed to study the thermodynamics for H2 activation by both inter- a…
A subsystem approach for obtaining electron binding energies in the valence region and apply it to the case of halide ions (X$^-$, X = F-At) in water. This approach is based on electronic structure calculations combining the relativistic equation of motion coupled-cluster method for electron detachment (EOM-IP-CCSD) and density functional theory via the frozen density embedding (FDE) approach, using structures from classical molecular dynamics with polarizable force fields for discrete systems (in the present study, droplets containing the anion and 50 water molecules). Our results indicate on…
Downsizing microswimmers to the nanoscale, and using light as an externally controlled fuel, are two important goals within the field of active matter. Here we demonstrate using all-atom molecular dynamics simulations that solvation relaxation, the solvent dynamics induced after visible light electronic excitation of a fluorophore, can be used to propel nanoparticles immersed in polar solvents. We show that fullerenes functionalized with fluorophore molecules in liquid water exhibit substantial enhanced mobility under external excitation, with a propulsion speed proportional to the power dissi…
