On-the-fly ab initio semiclassical evaluation of absorption spectra of polyatomic molecules beyond the Condon approximation

To evaluate vibronic spectra beyond the Condon approximation, we extend the on-the-fly ab initio thawed Gaussian approximation by considering the Herzberg-Teller contribution due to the dependence of the electronic transition dipole moment on nuclear coordinates. The extended thawed Gaussian approximation is tested on electronic absorption spectra of phenyl radical and benzene: Calculated spectra reproduce experimental data and are much more accurate than standard global harmonic approaches, confirming the significance of anharmonicity. Moreover, the extended method provides a tool to quantify the Herzberg-Teller contribution: we show that in phenyl radical, anharmonicity outweighs the Herzberg-Teller contribution, whereas in benzene, the Herzberg-Teller contribution is essential, since the transition is electronically forbidden and Condon approximation yields a zero spectrum. Surprisingly, both adiabatic harmonic spectra outperform those of the vertical harmonic model, which describes the Franck-Condon region better. Finally, we provide a simple recipe for orientationally averaging spectra, valid beyond Condon approximation, and a relation among the transition dipole, its gradient, and nonadiabatic coupling vectors.Comment: Final form available via open access in J. Phys. Chem. Lett.: https://pubs.acs.org/doi/10.1021/acs.jpclett.8b00827. Last 11 pages contain the Supporting Informatio

From low dimensions to full configuration space: Generalising models for nonadiabatic molecular dynamics

This thesis aims to bridge the development of nonadiabatic dynamics methods and their application for studies of real molecular systems. First, this work explores fundamental concepts of photochemistry by investigating two different pictures, arising from the Born-Oppenheimer and the exact factorisation representation. Based on a simplistic model, a photochemical experiment from the excitation up to the formation of photoproducts is simulated. This study then compares the Born-Oppenheimer and exact factorisation representations of the processes. Subsequently, the influence of the Born-Oppenheimer picture for approximate nonadiabatic dynamics is investigated on two-dimensional model systems around conical intersections. The effects of neglected couplings and geometric phase are evaluated for ab initio multiple spawning (AIMS), a method for nonadiabatic molecular dynamics based on classically moving Gaussians. Afterwards, this work introduces a standardised test set of molecules to connect between tests of newly developed nonadiabatic dynamics methods on one-dimensional model systems and their intended application to full-dimensional molecules. Inspired by the widely used one-dimensional Tully models, three molecules are selected to form the molecular Tully models, which undergo similar photophysical processes, but in a high-dimensional space. In addition, the recently proposed stochastic-selection AIMS framework is also tested on two molecules undergoing ring-opening reactions to explore the strengths and limitations of the method. Finally, a direct comparison between experimental and computational results is presented. The photochemistry of 2(5H)-thiophenone is probed during and after the initial ring opening using time-resolved photoelectron spectroscopy. Static and dynamic calculations unravel the photoprocesses and identify a variety of photoproducts. Using the computational results, the experimental signal can be translated to insights into the ongoing photochemistry. Overall, this thesis aims to bring models in nonadiabatic dynamics in a real-world context. This work contributes to facilitating the transfer of new nonadiabatic dynamics methods towards the study of molecules in their full dimensionality

Photochemistry and photophysics of chemical and biologically relevant systems: mechanisms, dynamics and methodologies

El proyecto presentado en esta Tesis se basa en la aplicación y desarrollo de métodos teóricos y computacionales con el fin de describir la fotoquímica y la fotofísica de compuestos moleculares químicos y de relevancia biológica. Más detalladamente, se lograron los siguientes objetivos: i.Aplicación de la metodología CASPT2//CASSCF al estudio de un modelo de la conformación giro-beta, formado por dos glicinas enlazadas a través de un enlace de hidrógeno. Se consiguieron calcular los caminos de mínima energía encontrados a partir de la irradiación UV que permiten finalmente, la disipación de la energía de excitación como energía vibracional. ii.Aplicación de la metodología CASPT2//CASSCF/AMBER al estudio de mecanismos de fotoestabilidad en la proteína gamma-B-cristalina, que forma (junto con otras proteínas cristalinas) el cristalino del ojo humano. Especialmente, se destaca el papel que puede jugar el elemento denominado "Tyrosine corner", una parte seleccionada de la cadena proteica que permite un giro de aproximadamente 180? a través de un enlace de hidrógeno entre la cadena principal y el grupo lateral de una tirosina. iii.Desarrollo de un método de determinación cuantitativa de la energía de excitación de un cromóforo con diferente sustitución, en el caso de que la sustitución química afecte al cromóforo solo a nivel estructural y no a la naturaleza electrónica del estado excitado considerado. iv.Tratamiento de los efectos del entorno sobre un interruptor molecular inducido por luz, como fuerzas externas que actúan en los dos extremos del cromóforo. En el caso del azobenceno (uno de los interruptores moleculares inducidos por luz más empleado), los isómeros cis y trans muestran una fotosensibilidad considerable respecto a las fuerzas aplicadas, permitiendo la modulación de la longitud de onda del máximo de absorción

Photochemistry and photophysics of chemical and biologically relevant systems: mechanisms, dynamics and methodologies

El proyecto presentado en esta Tesis se basa en la aplicación y desarrollo de métodos teóricos y computacionales con el fin de describir la fotoquímica y la fotofísica de compuestos moleculares químicos y de relevancia biológica. Más detalladamente, se lograron los siguientes objetivos: i.Aplicación de la metodología CASPT2//CASSCF al estudio de un modelo de la conformación giro-beta, formado por dos glicinas enlazadas a través de un enlace de hidrógeno. Se consiguieron calcular los caminos de mínima energía encontrados a partir de la irradiación UV que permiten finalmente, la disipación de la energía de excitación como energía vibracional. ii.Aplicación de la metodología CASPT2//CASSCF/AMBER al estudio de mecanismos de fotoestabilidad en la proteína gamma-B-cristalina, que forma (junto con otras proteínas cristalinas) el cristalino del ojo humano. Especialmente, se destaca el papel que puede jugar el elemento denominado "Tyrosine corner", una parte seleccionada de la cadena proteica que permite un giro de aproximadamente 180? a través de un enlace de hidrógeno entre la cadena principal y el grupo lateral de una tirosina. iii.Desarrollo de un método de determinación cuantitativa de la energía de excitación de un cromóforo con diferente sustitución, en el caso de que la sustitución química afecte al cromóforo solo a nivel estructural y no a la naturaleza electrónica del estado excitado considerado. iv.Tratamiento de los efectos del entorno sobre un interruptor molecular inducido por luz, como fuerzas externas que actúan en los dos extremos del cromóforo. En el caso del azobenceno (uno de los interruptores moleculares inducidos por luz más empleado), los isómeros cis y trans muestran una fotosensibilidad considerable respecto a las fuerzas aplicadas, permitiendo la modulación de la longitud de onda del máximo de absorción

Computational mechanistic photochemistry: The central role of conical intersections

In this thesis, I review my own contributions in the field of computational photochemistry. This manuscript is written as an introduction to this field of research. It is not intended to be a textbook, as more emphasis has been made on illustrations rather than on methodologies and technical guidelines. In this way, I hope that it will be accessible to a large audience, from undergraduate students to more experienced scientists who would be interested in learning about this fascinating and relatively young field of research

Challenges in simulating light-induced processes in DNA

© 2016 by the authors; licensee MDPI, Basel, Switzerland. In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments

Ab initio studies on photorelaxation

This work addresses relaxation mechanisms of photoexcited organic molecules of small and medium size, up to 62 atoms. For most systems it is investigated theoretically, how modifications, often in the form of substituents, influence the decay processes. The research in large parts is done in close collaboration with groups providing experimental data, which allows to formulate robust hypotheses and models. Four systems are discussed in this context. We find the formation of the dewar lesion in deoxyribonucleic acid (DNA) to only occur, when the nucleobase is embedded in the DNA backbone, which sterically hinders accessing alternative channels. Substituting hydroxy groups at certain points of thioindigo is shown to open up an efficient deactivation channel via excited state intramolecular proton transfer, and greatly enhance the photostability of the molecule. By substituting electron donating groups to the stilbene moiety of the hemithioindigo photoswitch and correlating their effect to their Hammett parameters, the isomerization speed of hemithioindigo is optimized. And lastly, when adding an aldehyde group to furan, an additional pathway is found for its derivatives furfural and β-furfural. Their relaxation is slowed down regardless. The effects on the excited state potential energy surfaces are described as general means, by which the surfaces can be influenced, and likely can be translated to other molecules as well. This eventually allows to predict properties and tailor molecules to yield desired behavior. In this context, for example for furan, furfural and β-furfural the structural implications of the aldehyde substituent on one conical intersection are deducted from the extended two-electron two-orbital model prior to any calculations or experiments. Alongside the system specific investigations, an interface for the on-the-fly dynamics package NewtonX to the quantum chemistry package Molpro was programmed. Non-adiabatic semiclassical on-the-fly dynamics are a powerful tool to simulate complete relaxation processes without constraints in the dimensionality. For the interface, which in its primary setup uses complete active space self consistent field theory calculations, a number of features has been implemented. Most notably, it enables non-adiabtatic dynamics on complete active space perturbation and ONIOM level of theory

Quantum/classical simulation of molecular excited state dynamics and spectroscopy

The ability of modern quantum chemistry to answer ever more complex questions rises steadily. In this thesis, a comprehensive exploration of molecular photochemistry using high-level electronic structure methods for quantum-classical dynamics is presented. The first chapter introduces theoretical methods for simulating photodynamical processes, focussing on the relaxation of molecules in explicit atomistic environments. These approaches include nuclear wavepacket dynamics embedded within classical molecular dynamics. The presented Ehrenfest and multi-configurational Ehrenfest approaches are applied to small molecules surrounded by noble gas atoms. Furthermore, trajectory surface hopping is discussed, as, in later chapters, the program SHARC is used to perform such simulations. During this thesis, adaptive time-stepping and two new interfaces to electronic structure codes were implemented. These methods facilitate efficient and accurate dynamics calculations on a variety of photochemically relevant systems ranging from simulations in the gas phase with high-level XMS-CASPT2 electronic structure (including spin-orbit couplings) to QM/MM simulations in the condensed phase. The second chapter focuses on the energy transfer between an infrared laser and solvated molecules, combining the traditional harmonic approximation to calculate infrared spectra with methods based on \textit{ab initio} molecular dynamics. This methodology is used to elucidate the coherent energy transfer dynamics from the field to the molecule in field-resolved spectroscopic measurements. The third chapter of this thesis surveys the intricate world of 2-enone photochemistry. By exploring $\pi\pi^*$ and $n\pi^*$ reactivity using high-level electronic structure methods, insights are gained into the \textit{Z}/\textit{E} isomerization of cyclohept-2-enone and the photoinduced rearrangement of 5,5-dimethylcyclopent-2-enone to a ketene. In the final chapter, mechanistic investigations are extended to Lewis acid\hyp coordinated enones, uncovering the impact of coordination on the electronic states, UV-Vis spectra, and reactivity. Trajectory surface hopping calculations are used in combination with ultrafast transient absorption spectroscopy to uncover the dynamics of the relaxation of cyclohex-2-enone-BF$_3$ to the reactive triplet states and the photo-induced B\textendash Cl bond dissociation in benzaldehyde-BCl$_3$. Collectively, this work exemplifies the potent synergy of computational and spectroscopic techniques in unraveling photochemical mechanisms. From explicit solvent relaxation to multi-step organic reactions and from spectroscopic signatures to intricate electronic transitions, this thesis advances our understanding of photochemical processes across a spectrum of molecular examples. The findings have implications for the design and understanding of photochemical reactions and spectroscopic studies in complex environments