Assessing the persistence of chalcogen bonds in solution with neural network potentials

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 have centered on solid-state materials or fairly simple molecules made of a limited number of elements. Herein, we focus on the persistence and strength of chalcogen bonds involving a benzotelluradiazole in condensed phase. While the tellurium-containing heteroaromatic molecules are known to exhibit pronounced interactions with anions and lone pairs of different atoms, the relevance of competing intermolecular interactions, notably with the solvent, is complicated to monitor experimentally but also challenging to model at an accurate electronic structure level. Here, we train direct and baselined NNPs to reproduce hybrid DFT energies and forces in order to identify what the most prevalent non-covalent interactions occurring in a solute-Cl−–THF mixture are. The simulations in explicit solvent highlight the clear competition with chalcogen bonds formed with the solvent and the short-range directionality of the interaction with direct consequences for the molecular properties in the solution. The comparison with other potentials (e.g., AMOEBA, direct NNP, and continuum solvent model) also demonstrates that baselined NNPs offer a reliable picture of the non-covalent interaction interplay occurring in solution.

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

Capturing Non-local Effects in Kohn-Sham Density Functional Theory

Andrey Laktionov

Density Functional Theory (DFT) and its time-dependent extension (TDDFT) have become two of the most popular approaches for computer simulations of the electronic structure and response properties of quantum systems. A reasonable compromise between accuracy and computational cost allows to apply DFT to a wide range of systems from small molecules to biological complexes. Despite the in principle exact nature of DFT and TDDFT, practical calculations require the use of approximate DFT exchange-correlation (XC) functionals and TDDFT kernels and the accuracy of the obtained results is determined by the accuracy of the chosen XC description. These approximations inevitably introduce some limitations in the use of DFT-based methods.The inability of the local spin density approximation, generalized gradient approximations (GGA) and even some hybrid functionals to properly describe charge transfer (CT) excitations and predict intermolecular interaction energies of weakly bound complexes are two major drawbacks of current XC descriptions. This thesis is therefore devoted to the improvement of XC functionals for the special cases of weak interactions and charge-transfer excitations. Many original strategies have been suggested to cure DFT calculations from these failures. In particular, the Dispersion-Corrected Atom-Centered Potentials (DCACP) approach provides an accurate description of dispersion forces within generalized gradient approximations for the exchange-correlation functional. The DCACP method has been extensively used for the last seven years and has shown an excellent performance for a large class of applications. However, one of the drawbacks of the current implementation of DCACP is that the correct R-6 asymptotics of dispersion interaction is not reproduced. A first goal of this thesis was to enable DCACP to recover the R-6 asymptotic limit. To this end, we have designed a new 2-channel version of DCACP and carried out test calculations on both small molecules and large macromolecular complexes. The obtained results demonstrate the excellent performance and transferability of the DCACP approach. Moreover, for large macromolecular complexes, in which the binding energy is dominated by dispersion, [pi]-stacking, or hydrogen bonding, 2-channels DCACP were found to be the best method overall for correcting the popular BLYP functional. Our study clearly shows that account of R-6 asymptotics is crucial for the description of large complexes and that 2-channels DCACP are fully able to capture these effects. On the contrary, an account of R-6 asymptotics is of little importance for small molecules since the remaining errors of the underlying GGA functional are dominating. With the aim of deepening our understanding of the DCACP concept and the reasons for its excellent performance, we explored the properties of the two DCACP parameters and were able to establish some systematic trends. It turned out that variational tuning of the DCACP can be done in an analytical manner that enables the easy generation of DCACP potentials for the full periodic table. Furthermore, since DCACP have little but crucial impact on the electronic density, dispersion energies can be obtained from non-self-consistent electron densities. These empirical findings suggest that the high transferability of DCACP is due to their atom-centered form and the intrinsically weak nature of dispersion interactions. [...]

EPFL2014

Nonadiabatic Molecular Dynamics Simulations: Synergies between Theory and Experiments

Ivano Tavernelli

CONSPECTUS: Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular mechanics (QM/MM) approach has the advantage of providing an atomistic (even though approximated) description of the solvent molecules, which is crucial for the characterization of all ultrafast relaxation phenomena that depend on the geometrical arrangement at the interface between a molecule and the solvent, for example, the hydrogen bond network. After a short description of the TDDFT-based implementation of Ehrenfest and trajectory surface hopping dynamics, I will present applications in different domains of molecular chemistry and physics: the analysis and the understanding of (time-resolved) X-ray absorption spectra, the interpretation of the ultrafast relaxation dynamics of photoexcited dyes in solution, and the design of specific laser pulses (capable of inducing desired chemical reactions) using local control theory.

Amer Chemical Soc2015