Many-Body Perturbation Theory (MBPT) and Time-Dependent Density-Functional Theory (TD-DFT): MBPT Insights About What is Missing in, and Corrections to, the TD-DFT Adiabatic Approximation

In their famous paper Kohn and Sham formulated a formally exact density-functional theory (DFT) for the ground-state energy and density of a system of $N$ interacting electrons, albeit limited at the time by certain troubling representability questions. As no practical exact form of the exchange-correlation (xc) energy functional was known, the xc-functional had to be approximated, ideally by a local or semilocal functional. Nowadays however the realization that Nature is not always so nearsighted has driven us up Perdew's Jacob's ladder to find increasingly nonlocal density/wavefunction hybrid functionals. Time-dependent (TD-) DFT is a younger development which allows DFT concepts to be used to describe the temporal evolution of the density in the presence of a perturbing field. Linear response (LR) theory then allows spectra and other information about excited states to be extracted from TD-DFT. Once again the exact TD-DFT xc-functional must be approximated in practical calculations and this has historically been done using the TD-DFT adiabatic approximation (AA) which is to TD-DFT very much like what the local density approximation (LDA) is to conventional ground-state DFT. While some of the recent advances in TD-DFT focus on what can be done within the AA, others explore ways around the AA. After giving an overview of DFT, TD-DFT, and LR-TD-DFT, this article will focus on many-body corrections to LR-TD-DFT as one way to building hybrid density-functional/wavefunction methodology for incorporating aspects of nonlocality in time not present in the AA.Comment: 56 pages, 17 figure

Theoretical insights into the formation and stability of radical oxygen species in cryptochrome

International audienceCryptochrome is a blue-light absorbing flavoprotein containing a flavin adenine dinucleotide (FAD) cofactor. FAD can accept up to two electrons and two protons, which can be subsequently transferred to substrates present in the binding pocket. It is well known that reactive oxygen species are generated when triplet molecular oxygen is present in the cavity. Here, we investigate the formation and stability of radical oxygen species in Drosophila melanogaster cryptochrome using molecular dynamics simulations and electronic structure calculations. We find that superoxide and hydroxyl radicals in doublet spin states are stabilized in the pocket due to attractive electrostatic interactions and hydrogen bonding with partially reduced FAD. These finding validate from a molecular dynamics perspective that [FAD •−-HO • 2 ] or [FADH •-O •− 2 ] can be alternative radical pairs at the origin of magnetoreception

An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators

Hybrid quantum mechanics / molecular mechanics (QM/MM) models successfully describe the properties of biological macromolecules. However, most QM/MM methodologies are constrained to unrealistic gas phase models, thus limiting their applicability. In the literature, several works have attempted to define a QM/MM model in periodic boundary conditions (PBC) but frequently the models are too time-consuming for general applicability to biological systems in solution. Here, we define a simple and efficient electrostatic embedding QM/MM model in PBC combining the benefits of electrostatic potential fitted (ESPF) atomic charges and particle-mesh Ewald sums, that can efficiently treat systems of arbitrary size at a reasonable computational cost. To illustrate this, we apply our scheme to extract the lowest singlet excitation energies from a model for arabidopsis thaliana cryptochrome 1 containing circa 93000 atoms, reproducing accurately the experimental absorption maximum.Comment: 4 pages, 2 figure

Assessment Of Density Functional Theory For Describing The Correlation Effects On The Ground And Excited State Potential Energy Surfaces Of A Retinal Chromophore Model

In the quest for a cost-effective level of theory able to describe a large portion of the ground and excited potential energy surfaces of large chromophores, promising approaches are rooted in various approximations to the exact density functional theory (DFT). In the present work, we investigate how generalized Kohn-Sham DFT (GKS-DFT), time-dependent DFT (TDDFT), and spin-restricted ensemble-DFT (REKS) methods perform along three important paths characterizing a model retinal chromophore (the penta-2,4-dieniminium cation) in a region of near-degeneracy (close to a conical intersection) with respect to reference high-level multiconfigurational wave function methods. If GKS-DFT correctly describes the closed-shell charge transfer state, only TDDFT and REKS approaches give access to the open-shell diradical, one which sometimes corresponds to the electronic ground state. It is demonstrated that the main drawback of the usual DFT-based methods lies in the absence of interactions between the charge transfer and the diradicaloid configurations. Hence, we test a new computational scheme based on the State-averaged REKS (SA-REKS) approach, which explicitly includes these interactions into account. The State-Interaction SA-REKS (SI-SA-REKS) method significantly improves on the REKS and the SA-REKS results for the target system. The similarities and differences between DFT and wave function-based approaches are analyzed according to (1) the active space dimensions of the wave function-based methods and (2) the relative electronegativities of the allyl and protonated Schiff base moieties

Impact of the Dynamic Electron Correlation on the Unusually Long Excited-State Lifetime of Thymine

Non-radiative relaxation of the photoexcited thymine in the gas phase shows an unusually long excited-state lifetime, and, over the years, a number of models, i.e., S₁-trapping, S₂-trapping, and S₁&S₂-trapping, have been put forward to explain its mechanism. Here, we investigate this mechanism using non-adiabatic molecular dynamics (NAMD) simulations in connection with the recently developed mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. We show that the previously predicted S₂-trapping model was due to an artifact caused by an insufficient account of the dynamic electron correlation. The current work supports the S₁-trapping mechanism with two lifetimes, τ₁ = 30 ± 1 fs and τ₂ = 6.1 ± 0.035 ps, quantitatively consistent with the recent time-resolved experiments. Upon excitation to the S₂ (ππ*) state, thymine undergoes an ultrafast (ca. 30 fs) S₂→S₁ internal conversion and resides around the minimum on the S₁ (n₀π*) surface, slowly decaying to the ground state (ca. 6.1 ps). While the S₂→S₁ internal conversion is mediated by fast bond length alternation distortion, the subsequent S₁→S₀ occurs through several conical intersections, involving a slow puckering motion

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations

Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM

International audienceThymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S2 to S1. In the S1 state, it gets trapped for several picoseconds until returning to the ground-state S0. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S0/S1 intersection and have a negligible effect on the S1/S2 intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets

Improved correlation kernels for linear-response time-dependent density-functional theory

La théorie de la fonctionnelle de la densité dépendante du temps (TDDFT) est une méthode basée sur la densité pour calculer les états excités. Bien que la TDDFT soit une théorie exacte, on doit en pratique partir d'une approximation de la fonctionnelle d'échange-corrélation, qui reste inconnue. L'approximation adiabatique est l'approximation de la fonctionnelle la plus courante. Cette approximation donne de très bons résultats pour les propriétés spectroscopiques, mais elle est inexacte pour les simulations en photochimie. Dans cette thèse, on montre que l'origine du problème réside dans l'approximation de la fonctionnelle de corrélation. Le résultat principal de la thèse consiste en un noyau de corrélation, qui peut être utilisé dans la formulation de la réponse linéaire, noyau dérivée à partir de la théorie des perturbations à plusieurs corps. Le noyau inclut de façon générale les excitations doubles qui donnent l'effet principal à la corrélation dans les états excités. La comparaison de ce noyau avec la fonctionnelle adiabatique nous a permis d'identifier les termes manquants à ce dernier. Nous avons testé la possibilité d'ajouter ces termes comme une correction à l'approximation adiabatique. Le noyau pourrait potentiellement être appliqué à des systèmes de grosse taille.Time-dependent density-functional theory (TDDFT) is a density-functional method for calculating excited states. TDDFT is formally exact, though in practice one has to approximate the unknown exchange-correlation functional, which contains all the unknown many-body effects. The adiabatic functionals are the most commonly used. Although they are very successful for spectroscopy, the adiabatic functionals are too inaccurate to be applied to photochemistry. In this thesis, we show that the main problem is due to the approximations in the correlation functional. The main result of the thesis is a correlation kernel for linear-response TDDFT, derived using many-body perturbation theory techniques, which generally includes double excitations, thus introducing the leading correlation effects in the excited states. The comparison of this kernel with the adiabatic functionals allowed us to identify which correlation effects are missing in these approximation. We tested the possibility of improving the description of correlation by adding the missing terms from many-body theory to the adiabatic functionals. This mixed kernel is more efficient than the full many-body kernel, and can potentially be applied to systems of medium to large size

Noyau de corrélation amélioré pour la réponse linéaire de la théorie de la fonctionnelle de la densité dépendante du temps

Time-dependent density-functional theory (TDDFT) is a density-functional method for calculating excited states. TDDFT is formally exact, though in practice one has to approximate the unknown exchange-correlation functional, which contains all the unknown many-body effects. The adiabatic functionals are the most commonly used. Although they are very successful for spectroscopy, the adiabatic functionals are too inaccurate to be applied to photochemistry. In this thesis, we show that the main problem is due to the approximations in the correlation functional. The main result of the thesis is a correlation kernel for linear-response TDDFT, derived using many-body perturbation theory techniques, which generally includes double excitations, thus introducing the leading correlation effects in the excited states. The comparison of this kernel with the adiabatic functionals allowed us to identify which correlation effects are missing in these approximation. We tested the possibility of improving the description of correlation by adding the missing terms from many-body theory to the adiabatic functionals. This mixed kernel is more efficient than the full many-body kernel, and can potentially be applied to systems of medium to large size.La théorie de la fonctionnelle de la densité dépendante du temps (TDDFT) est une méthode basée sur la densité pour calculer les états excités. Bien que la TDDFT soit une théorie exacte, on doit en pratique partir d'une approximation de la fonctionnelle d'échange-corrélation, qui reste inconnue. L'approximation adiabatique est l'approximation de la fonctionnelle la plus courante. Cette approximation donne de très bons résultats pour les propriétés spectroscopiques, mais elle est inexacte pour les simulations en photochimie. Dans cette thèse, on montre que l'origine du problème réside dans l'approximation de la fonctionnelle de corrélation. Le résultat principal de la thèse consiste en un noyau de corrélation, qui peut être utilisé dans la formulation de la réponse linéaire, noyau dérivée à partir de la théorie des perturbations à plusieurs corps. Le noyau inclut de façon générale les excitations doubles qui donnent l'effet principal à la corrélation dans les états excités. La comparaison de ce noyau avec la fonctionnelle adiabatique nous a permis d'identifier les termes manquants à ce dernier. Nous avons testé la possibilité d'ajouter ces termes comme une correction à l'approximation adiabatique. Le noyau pourrait potentiellement être appliqué à des systèmes de grosse taille