How Important is Self-Consistency for the dDsC Density Dependent Dispersion Correction?

The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations.These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical point of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging test.

Characterization at the Atomistic Level of Defective Structures in Complex Materials

Piyush Agrawal

Defects are key to enhance or deploy particular materials properties. In this thesis I present analyses of the impact of defects on the electronic structure of materials using combined experimental and theoretical Electron energy loss spectroscopy (EELS) in (Scanning) Transmission Electron Microscopy. The energy loss near-edge structure (ELNES) in EELS reflects the element-specific electronic structure providing insights into bonding characteristics of individual atomic species. New electron optical devices have boosted the analytical capabilities by which materials can be investigated with atomic resolution and single atom sensitivity using (scanning) transmission electron spectroscopy (STEM/TEM).With the help of aberration correctors for forming small electron probes, high intensity electron beams can nowadays be focused to clearly less than 100 pm which has enhanced the resolution and sensitivity in analytical scanning transmission electron microscopy (STEM). Various kinds of defects in different complex oxides were studied: point defects like oxygen vacancies in BiVO4 and SrMnO3, edge-dislocations in BiFeO3, and planar defects in GaAs. By comparison with experimental data, structures for these systems were proposed based on all-electron density functional theory (DFT) code Wien2k. By comparing theoretical calculations and experimental data, a pronounced surface reduction in the oxidation state of vanadium in BiVO4 from +5 to +4 was unveiled, which is due to a high density of oxygen vacancies, and its importance in potential application of BiVO4 in photoelectrochemical energy conversion. A similar study was performed on a series of SrMnO3 thin films with different epitaxial strain where theoretical investigations revealed the impact of oxygen non-stoichiometry and strain on the O-K ELNES. In the next study, molecular dynamics simulations were combined with FEFF-based EELS calculations and its comparison with experiments was helpful for the correct prediction of the edge dislocation core structure in BiFeO3. This study also confirmed the presence of Fe atoms in the core of the edge dislocation which possibly makes these defects ferromagnetic whereas the bulk structure is known to be antiferromagnetic. This thesis has established methodologies for utilizing different codes, illustrating how links between experimental and theoretical ELNES can be used in revealing structural information around defects and how defects affect materials properties. This tandem methodology of theory and experiments is applicable to various future materials where the reliable interpretation of EELS data is pivotal in unfolding mysteries of such technologically important materials.

EPFL2017

Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

Pablo Campomanes Ramos, Ursula Röthlisberger, Ivano Tavernelli

Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of the protein matrix in modulating the absorption of retinal chromophore in rhodopsin, but, while generally agreeing in predicting the correct location of the absorption maximum, they often reached contradicting conclusions on how the environment tunes the spectrum. To address this controversial issue, we combine here a thorough structural and dynamical characterization of rhodopsin with a careful validation of its excited-state properties via the use of a wide range of state-of-the-art quantum chemical approaches including various flavors of time-dependent density functional theory (TDDFT), different multireference perturbative schemes (CASPT2 and NEVPT2), and quantum Monte Carlo (QMC) methods. Through extensive quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, we obtain a comprehensive structural description of the chromophoreprotein system and sample a wide range of thermally accessible configurations. We show that, in order to obtain reliable excitation properties, it is crucial to employ a sufficient number of representative configurations of the system. In fact, the common use of a single, ad hoc structure can easily lead to an incorrect model and an agreement with experimental absorption spectra due to cancelation of errors. Finally, we show that, to properly account for polarization effects on the chromophore and to quench the large blue-shift induced by the counterion on the excitation energies, it is necessary to adopt an enhanced description of the protein environment as given by a large quantum region including as many as 250 atoms.

Amer Chemical Soc2013

A Classical and Quantum Trajectory Description of Nonadiabatic Dynamics within Time-Dependent Density Functional Theory

Basile Curchod

Characterizing and predicting the nuclear dynamics of electronically excited molecules is of paramount importance to the understanding of photochemical and photophysical processes in molecules and to the development of new technologies in domains like solar energy conversion, efficient illumination devices, and medicine. However, the theoretical description of such phenomena remains a challenge for theoretical chemists. The most notable difficulty comes from the breakdown of the widely used Born-Oppenheimer approximation, which considers the time evolution of the nuclei fully decoupled from the one of the electrons. Moving beyond this approximation requires the inclusion of nonadiabatic effects, which induces an entangled electron-nuclear dynamics. Additionally, the convenient approximation that the motion of the nuclear degrees of freedom can be described with classical mechanics is likely to fail in the case of nonadiabatic events. While several theoretical techniques have been proposed to treat both the electronic structure and the nonadiabatic dynamics problems, they all rely on a compromise between accuracy and efficiency. The principal goal of this thesis is to improve the description of molecular nonadiabatic phenomena using classical and quantum trajectories, combined with linear-response time-dependent density functional theory (LR-TDDFT) for the calculation of the electronic structure properties. In the first part of this work, we review several methods used to solve exactly or in an approximate way the nuclear time-dependent Schrödinger equation with quantum or classical trajectories. We then move on to show how the molecular time-dependent Schrödinger equation can be reformulated exactly in terms of quantum trajectories evolving in coupled adiabatic electronic states. This nonadiabatic Bohmian dynamics (NABDY) scheme allows for the description of all nuclear quantum effects like decoherence and tunneling, and is compatible with a nuclear wavepacket dynamics in which the electronic structure information is computed on-the-fly. Furthermore, we discuss how NABDY can be related, through several approximations, to the trajectory surface hopping (TSH) method, which is one of the most commonly applied on-the-fly trajectory-based techniques to describe the dynamics of molecular systems beyond the Born-Oppenheimer approximation in (the unconstrained) configuration space of molecules. The TSH method describes the nuclear wavepacket dynamics with a swarm of uncorrelated classical trajectories, consequently banishing all nuclear quantum effects. Understanding the underlying limitations of TSH is of foremost importance for the improvement of the theory. In this thesis, several one dimensional model systems are used to assess the accuracy of TSH through a comparison with the correlated NABDY dynamics. In the second part, we focus on the electronic structure problem and discuss how LR-TDDFT can be used in the implementation of an efficient on-the-fly nonadiabatic molecular dynamics scheme. Within this theory, all the electronic information needed, namely excitation energies, excited state nuclear forces, nonadiabatic couplings, and other electronic matrix elements, have to be represented as a functional of the electronic density. We show how the concept of auxiliary many-electron wavefunction can be used to compute the matrix elements of any one-body operators. In the third and last part, we discuss two extensions of the TSH method based on LR-TDDFT, aimed at describing the effects of the environment on a molecular system in the most possible realistic way. First, the effects of an explicit solvent on a photoactive solute is described within a QM/MM formalism. The resulting TSH/LR-TDDFT/MM scheme is applied to the nonradiative relaxation of the inorganic compound ruthenium (II) trisbipyridine in water. This application further highlights the need for the inclusion of relativistic effects in the TSH algorithm such as spin-orbit coupling to describe intersystem crossing processes. Second, the TSH equations are coupled with an external time-dependent electric field, such that photoexcitation processes can be naturally described within this mixed quantum/classical method. The electric field can be either parametrized or shaped to selectively maximize the population of a given target electronic state. TSH dynamics coupled to an electric field is first applied to the study of the photodissociation dynamics of a diatomic molecule (lithium fluoride) and then used for the investigation of the photoinduced proton transfer reaction in an organic compound (4-hydroxyacridine). This thesis presents several possibilities to describe the nonadiabatic dynamics of molecules. In addition, it also highlights some current limitations of both electronic structure and nonadiabatic dynamics methods, proposing new potential solutions to these problems.

EPFL2013