Coupled nuclear and electron dynamics in molecules

The interaction of light with a molecular system is the fundamental step of various chemical, physical and biological phenomena. Investigating the nuclear and electron dynamics initiated by light-matter interaction is important to understand, optimize and control the underlying processes. In this thesis two theoretical methods describing the coupled nuclear and electron dynamics in molecular systems are addressed. In the presented studies the coupled dynamics induced by photoexcitation, the subsequent relaxation processes and the possibility to control the dynamics in the vicinity of conical intersections (CoIns) are investigated for different molecular systems. In the first part of this work the photorelaxation pathways of a group of molecules commonly used in organic-based optoelectronic devices are characterized with the help of semiclassical ab intio molecular dynamics simulations. The relaxation pathways starting from the first excited singlet state of thiophene and of small oligothiophenes containing up to three rings is characterized by the interplay of internal conversion (IC) and intersystem crossing (ISC). Especially the ISC is mediated by ring-opening via a carbon-sulfur bond cleavage. The resulting entropically favored open-ring structures trap the molecules in a complex equilibrium between singlet and triplet states and a fast ring closure in the ground state is hindered. The extension of the π-system going from the monomer to the trimer weakens and slows down the ring opening process. Consequently the ISC is reduced for longer thiophene chains. The following two chapters are centered around the topics of controlling the molecular dynamics near a CoIn and monitoring the coherent electron dynamics induced by CoIns and laser interactions in the nucleobase uracil and the symmetric molecule NO2. In order to investigate the coherent electron dynamics, the ansatz used in this work allows a full-quantum description of the electron and nuclear motion and is called nuclear and electron dynamics in molecular systems (NEMol). As part of this work NEMol was extended to capture the coupled dynamics in complex high dimensional molecular systems. The observed electron dynamics both in NO2 and uracil reflects coherence, decoherence and reappearance which are all determined by the associated nuclear dynamics. The control of the molecular dynamics at a CoIn is realized with the help of a few-cycle infrared (IR) pulse. The applied control schema utilizes the carrierenvelope phase (CEP) of the pulse and allows to control the population distribution after the CoIn, the nuclear dynamics as well as the coherent electron dynamics. Depending on the chosen laser parameters and the molecular properties around the CoIn given by nature, two different mechanisms enable the control of the system. Both depend on the CEP but one is based on interference, which is generated by the interaction with the CoIn, and the other one is solely due to the few-cycle waveform of the pulse. As demonstrated for NO2 and uracil, the CEP control scheme even works for quite challenging boundary conditions. Therefore, it seems to be a general concept which can be used also in different molecules

Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment

Little is known about the biochemical environment in phagosomes harboring an infectious agent. To assess the state of this organelle we captured the transcriptional responses of Mycobacterium tuberculosis (MTB) in macrophages from wild-type and nitric oxide (NO) synthase 2–deficient mice before and after immunologic activation. The intraphagosomal transcriptome was compared with the transcriptome of MTB in standard broth culture and during growth in diverse conditions designed to simulate features of the phagosomal environment. Genes expressed differentially as a consequence of intraphagosomal residence included an interferon � – and NO-induced response that intensifies an iron-scavenging program, converts the microbe from aerobic to anaerobic respiration, and induces a dormancy regulon. Induction of genes involved in the activation and �-oxidation of fatty acids indicated that fatty acids furnish carbon and energy. Induction of �E-dependent, sodium dodecyl sulfate–regulated genes and genes involved in mycolic acid modification pointed to damage and repair of the cell envelope. Sentinel genes within the intraphagosomal transcriptome were induced similarly by MTB in the lungs of mice. The microbial transcriptome thus served as a bioprobe of the MTB phagosomal environment

Visualizing Conical Intersection Passages via Vibronic Coherence Maps Generated by Stimulated Ultrafast X--Ray Raman Signals

The rates and outcomes of virtually all photophysical and photochemical processes are determined by Conical Intersections. These are regions of degeneracy between electronic states on the nuclear landscape of molecules where electrons and nuclei evolve on comparable timescales and become strongly coupled, enabling radiationless relaxation channels upon optical excitation. Due to their ultrafast nature and vast complexity, monitoring Conical Intersections experimentally is an open challenge. We present a simulation study on the ultrafast photorelaxation of uracil, which demonstrates a new window into Conical Intersections obtained by recording the transient wavepacket coherence during this passage with an x-ray free electron laser pulse. We report two major findings. First, we find that the vibronic coherence at the conical intersection lives for several hundred femtoseconds and can be measured during this entire time. Second, the time-dependent energy splitting landscape of the participating vibrational and electronic states is directly extracted from Wigner spectrograms of the signal. These offer a novel physical picture of the quantum Conical Intersection pathways through visualizing their transient vibronic coherence distributions. The path of a nuclear wavepacket around the Conical Intersection is directly mapped by the proposed experiment.Comment: 7 pages, 5 Figures, to be published in PNA

Cavity-Born-Oppenheimer Hartree-Fock Ansatz: Light-matter Properties of Strongly Coupled Molecular Ensembles

Experimental studies indicate that optical cavities can affect chemical reactions, through either vibrational or electronic strong coupling and the quantized cavity modes. However, the current understanding of the interplay between molecules and confined light modes is incomplete. Accurate theoretical models, that take into account inter-molecular interactions to describe ensembles, are therefore essential to understand the mechanisms governing polaritonic chemistry. We present an ab-initio Hartree-Fock ansatz in the framework of the cavity Born-Oppenheimer approximation and study molecules strongly interacting with an optical cavity. This ansatz provides a non-perturbative, self-consistent description of strongly coupled molecular ensembles taking into account the cavity-mediated dipole self-energy contributions. To demonstrate the capability of the cavity Born-Oppenheimer Hartree-Fock ansatz, we study the collective effects in ensembles of strongly coupled diatomic hydrogen fluoride molecules. Our results highlight the importance of the cavity-mediated inter-molecular dipole-dipole interactions, which lead to energetic changes of individual molecules in the coupled ensemble

Unraveling a cavity induced molecular polarization mechanism from collective vibrational strong coupling

We demonstrate that collective vibrational strong coupling of molecules in thermal equilibrium can give rise to significant local electronic polarization effects in the thermodynamic limit. We do so by first showing that the full non-relativistic Pauli-Fierz problem of an ensemble of strongly-coupled molecules in the dilute-gas limit reduces in the cavity Born-Oppenheimer to a cavity-Hartree equation. Consequently, each molecule experiences a self-consistent coupling to the dipoles of all other molecules. In the thermodynamic limit, the sum of all molecular dipoles constitutes the macroscopic polarization field and the self-consistency then accounts for the delicate back-action on its heterogeneous microscopic constituents. The here derived cavity-Hartree equations allow for a computationally efficient implementation in an ab-initio molecular dynamics setting. For a randomly oriented ensemble of slowly rotating model molecules, we observe a red shift of the cavity resonance due to the polarization field, which is in agreement with experiments. We then demonstrate that the back-action on the local polarization takes a non-negligible value in the thermodynamic limit and hence the collective vibrational strong coupling can modify individual molecular properties locally. This is not the case, however, for dilute atomic ensembles, where room temperature does not induce any disorder and local polarization effects are absent. Our findings suggest that the thorough understanding of polaritonic chemistry, e.g. modified chemical reactions, requires self-consistent treatment of the cavity induced polarization and the usually applied restrictions to the displacement field effects may be insufficient

Photoprotecting uracil by coupling with lossy nanocavities

We analyze how the photorelaxation dynamics of a molecule can be controlled by modifying its electromagnetic environment using a nanocavity mode. In particular, we consider the photorelaxation of the RNA nucleobase uracil, which is the natural mechanism to prevent photodamage. In our theoretical work, we identify the operative conditions in which strong coupling with the cavity mode can open an efficient photoprotective channel, resulting in a relaxation dynamics twice as fast as the natural one. We rely on a state-of-the-art chemically detailed molecular model and a non-Hermitian Hamiltonian propagation approach to perform full-quantum simulations of the system dissipative dynamics. By focusing on the photon decay, our analysis unveils the active role played by cavity-induced dissipative processes in modifying chemical reaction rates, in the context of molecular polaritonics. Remarkably, we find that the photorelaxation efficiency is maximized when an optimal trade-off between light-matter coupling strength and photon decay rate is satisfied. This result is in contrast with the common intuition that increasing the quality factor of nanocavities and plasmonic devices improves their performance. Finally, we use a detailed model of a metal nanoparticle to show that the speedup of the uracil relaxation could be observed via coupling with a nanosphere pseudomode, without requiring the implementation of complex nanophotonic structuresThis work has been funded by the European Research Council through Grants ERC-2016-StG- 714870 (S. Felicetti, J. Feist, and J. Fregoni) and ERC-2015- CoG-681285 (J. Fregoni, PI Stefano Corni) and by the Spanish Ministry for Science, Innovation, and Universities - Agencia Estatal de Investigación through Grants RTI2018- 099737-B-I00, PCI2018-093145 (through the QuantERA program of the European Commission), and MDM-2014- 0377 (through the Marıá de Maeztu program for Units of Excellence in R&D). T. Schnappinger and R. de Vivie-Riedle gratefully acknowledge the DFG Normalverfahren. S. Reiter gratefully acknowledges financial support by the International Max Planck Research School of Advanced Photon Science (IMPRS-APS