Dissertations / Theses on the topic 'Nonadiabatic molecular dynamics'

The field of femtochemistry seeks to comprehend the fundamental underlying mechanisms of the interaction between light and molecules and to study the ultrafast timescales on which these processes occur. In particular, the photoresistance of biologically relevant molecules to potential damage caused by absorption of ultraviolet radiation is of great interest. The so called 'building blocks' of life use ultrafast non-radiative relaxation pathways for the dissipation of the high excess UV energy as vibrational energy into the surroundings, which is the key of their photoprotective function. The use of a 'bottom-up' methodology for such investigations is applied to understand basic model UV chromophores, which are molecular sub-units of various bio-molecules such as, for example, the DNA bases and the melanin pigmentation system. The photophysics of the basic model chromophores, indole and the aniline derivatives N,N-dimethylaniline and 3,5-dimethylaniline, were investigated in the gas phase to understand the link between their molecular structure, the ultrafast non-adiabatic dynamics and thus their potential photoprotection function. This study was done with the powerful time-resolved photoelectron imaging (TRPEI) technique, which provides temporal, energy- and angle-resolved information related to the non-adiabatic relaxation dynamics operating within each molecular system. TRPEI is a highly differential pump-probe spectroscopic technique providing a detailed picture of the underlying processes, since it is sensitive to both electronic and nuclear motion within the molecule. The observation of the complete dynamical process using the TRPEI method is however restricted by the energy of the utilised probe pulse. For this reason the spectroscopic technique was improved with the integration of a newly built femtosecond vacuum ultraviolet (VUV) light source. The VUV laser pulses are generated in a four wave frequency mixing process in third order nonlinear media, such as noble gases. First results from this instrument are presented for the butadiene molecule. The combination of the new VUV laser light and the already powerful spectroscopic technique enables, in principle, the detection of the complete non-radiative relaxation process of a large variety of molecular systems.

Photoinduced excitation and relaxation of organic molecules (C2H4 and CH2NH+2) are investigated by means of nonadiabatic quantum molecular dynamics with hopping (NA-QMD-H), developed recently [Fischer, Handt, and Schmidt, paper I of this series, Phys. Rev. A 90, 012525 (2014)]. This method is first applied to molecules assumed to be initially ad hoc excited to an electronic surface. Special attention is drawn to elaborate the role of electron-nuclear correlations, i.e., of quantum effects in the nuclear dynamics. It is found that they are essential for a realistic description of the long-time behavior of the electronic relaxation process, but only of minor importance to portray the short-time scenario of the nuclear dynamics. Migration of a hydrogen atom, however, is identified as a quantum effect in the nuclear motion. Results obtained with explicit inclusion of an fs-laser field are presented as well. It is shown that the laser-induced excitation process generally leads to qualitatively different gross features of the relaxation dynamics, as compared to the field-free case. Nevertheless, the nuclear wave packet contains all subtleties of the cis-trans isomerization mechanism as observed without a laser field.

An extension of the nonadiabatic quantum molecular dynamics approach is presented to account for electron-nuclear correlations in the dynamics of atomic many-body systems. The method combines electron dynamics described within time-dependent density-functional or Hartree-Fock theory with trajectory-surface-hopping dynamics for the nuclei, allowing us to take into account explicitly a possible external laser field. As a case study, a model system of H++H collisions is considered where full quantum-mechanical calculations are available for comparison. For this benchmark system the extended surface-hopping scheme exactly reproduces the full quantum results. Future applications are briefly outlined.

An extension of the nonadiabatic quantum molecular dynamics approach is presented to account for electron-nuclear correlations in the dynamics of atomic many-body systems. The method combines electron dynamics described within time-dependent density-functional or Hartree-Fock theory with trajectory-surface-hopping dynamics for the nuclei, allowing us to take into account explicitly a possible external laser field. As a case study, a model system of H++H collisions is considered where full quantum-mechanical calculations are available for comparison. For this benchmark system the extended surface-hopping scheme exactly reproduces the full quantum results. Future applications are briefly outlined.

La conversion interne (CI) est fondamentale pour les mécanismes de photoprotection dans l'ADN, le développement de matériaux photothermiques et de radiateurs moléculaires plus efficaces. Cette thèse se concentre sur les petites molécules hétéro-bicycliques azotées, en particulier les fragments d'acide nucléique et l'azaindole dont plusieurs aspects de la conversion interne sont encore inconnus. L'adénine et son nucléoside adénosine sont de bons exemples pour étudier ces caractéristiques. Pour évaluer comment la température affecte la durée de vie à l'état excité, nous avons simulé la dynamique non adiabatique des deux molécules à 0 K et 400 K. Nous montrons que la redistribution de l'énergie vibrationnelle est la clé derrière le taux de CI plus lent pour l'adénosine à 0 K, tandis que l'adénine est à peine affectée par les changements de température. Nous avons étudié de manière comparative comment la liaison hydrogène intramoléculaire impacte la désactivation à l'état excité de l'adénosine en phase gazeuse en simulant la dynamique moléculaire non adiabatique pour deux conformères, avec et sans une telle liaison hydrogène. Les résultats montrent que la liaison hydrogène accélère le taux de CI, toujours dominé par les croisements d'états plissés S1/S0. Enfin, nous avons considéré l'azaindole protoné et comment la tautomérisation affecte sa conversion interne. Nos simulations dynamiques ont révélé pourquoi la durée de vie S3 expérimentale du 7-azaindole protoné est environ dix fois plus longue que son isomère, le 6-azaindole protoné
Internal conversion (IC) is fundamental for photoprotection mechanisms in DNA and the development of more efficient photothermal materials and molecular heaters. This thesis focuses on small nitrogenated hetero-bicyclic molecules, particularly nucleic acid fragments and azaindole, whose several aspects of their internal conversion are still unclear. Adenine and its nucleoside adenosine are good examples to investigate those features. To assess how temperature affects their excited-state lifetime, we simulated the nonadiabatic dynamics of both molecules at 0 K and 400 K. We show that vibrational energy redistribution is the key behind the slower IC rate for adenosine at 0 K, while adenine is barely affected by changes in the temperature. We comparatively investigated how the intramolecular hydrogen bond impacts the excited-state deactivation of adenosine in the gas phase by simulating the nonadiabatic molecular dynamics for two conformers, with and without such a hydrogen bond. The results show that the hydrogen bond accelerates the IC rate, still dominated by puckered S1/S0 state crossings. Finally, we investigate how tautomerization affects the internal conversion of protonated azaindole. Our dynamics simulations revealed why the experimental S3 lifetime of protonated 7-azaindole is about ten times longer than its isomer, protonated 6-azaindole

Two complementary experiments were used to study the ultrafast dynamics of large molecules in the gas phase. Both experiments used time-resolved pump-probe velocity map imaging to monitor energetically dispersed spectra of isolated systems on a femtosecond timescale. A ‘bottom-up’ methodology is applied, whereby initially simple, small, systems are studied in a high level of detail, and then the complexity of system studied is gradually increased. The overall goal was to explore the concept of photostability, the mechanism whereby molecules can withstand bombardment by visible and ultraviolet light, especially in biomolecules. In the first set of experiments, based in Warwick University, the dissociation of hydrogen atoms from neutral phenol and 2-hydroxy phenol (catechol) following ultraviolet excitation was measured with femtosecond resolution. These experiments give unprecedented insight into the electronic structure of phenolic systems, and in particular hydrogen atom tunnelling underneath a conical intersection was directly observed. Varying the excitation energy allowed the transition from tunnelling dynamics to direct dissociation dynamics to be observed. The second set of experiments, completed at Durham University, performed timeresolved photoelectron spectroscopy on large gaseous anions from an electrospray source. The electrospray technique allows very large ions to be introduced into the gas phase, so the bottom-up methodology can be continued. First, the dynamics of the common dye indigo carmine were explored, demonstrating that excited state proton transfer accounts for its photostability. Secondly, the dynamics of the nucleotides making up DNA were explored. The dynamics of nucleobase chromophores were shown to map onto larger nucleotide and oligonucleotide systems, retaining ultrafast photostable properties. Finally, a new instrument was designed and constructed in Warwick. This machine will use laser desorption techniques to help further extend the size range isolated dynamics can be studied in, this time for neutrals. Overall, the bottom-up methodology grants insight into the excited state dynamics of real-world relevant molecules, at an extremely high level of detail.

A fundamental understanding of ultrafast nonequilibrium dynamical processes in molecular aggregates is crucially important for the design of nanodevices that utilize quantum mechanical effects. However, understanding the coupled electron-phonon dynamics of such high-dimensional systems remains a challenging issue. As a result of the ever-growing computational power that is available, realistic parameterization of model Hamiltonians and implementation of sophisticated quantum dynamics algorithms have become indispensable tools for gaining insight into these processes. The focus of this dissertation is the development and implementation of approximate path integral-based methods to compute the time-evolution as well as linear and nonlinear spectroscopic signals of molecular aggregates following photo-excitation. The developments and applications presented here are geared toward gaining a better understanding of the role that electron-phonon coupling plays in framing ultrafast excitation energy transfer networks in photosynthetic light-harvesting complexes. The ultrafast excitation energy transfer dynamics that occurs upon photo-excitation of a network of electronically coupled chromophores is remarkably sensitive to the strength of electronic coupling as well as the frequencies and coupling strengths that characterize electron-phonon interactions. Based on approximations to the diabatic representation of molecular Hamiltonians, energetic models of condensed phase molecular aggregates can be parameterized from a first principles description. Often times, computational parameterization of these models reveals comparable magnitudes for intermolecular electronic couplings and electron-phonon couplings, negating the applicability of popular perturbative algorithms (such as those based on Forster or Redfield theory) for describing their time-evolution. Moreover, non-perturbative exact methods (e.g. stochastic Schrodinger equations and the Hierarchical Equations of Motion) are generally inefficient for all but a few specific limiting forms of electron-phonon coupling, or make assumptions about autocorrelation timescales of the vibrational environment. Because of the failure of the energetic parameters determined through recent ab initio studies of natural molecular aggregates to abide by the rather restrictive requirements for efficient application of the above-mentioned methods, the development of approximate non-perturbative algorithms for predicting nonequilibrium dynamical properties of such systems is a central theme in this dissertation. Following a general introductory section describing the basic concepts that are fundamental to the remainder of the thesis, the derivation of path integral dynamics methods is presented. These include a cartesian phase space path integral derivation of the truncated Wigner approximation as applied to the Meyer-Miller-Stock-Thoss mapping model for describing vibronic systems as well as a novel derivation of the Partially Linearized Density Matrix algorithm, highlighting its emergence as a leading order approximation to an, in principle, exact expression for the density matrix. An algorithm for computing the nonlinear response function for higher-order optical spectroscopy signals is presented within the framework of the partially linearized density matrix formalism. Time-resolved two-dimensional electronic spectra are computed and compared with exact results as well as standard perturbation theory-based results, highlighting the accuracy and efficiency of the developed method. Additionally, the recently popularized symmetrical quasi-classical method for computing the reduced density matrix dynamics is extended for computing linear optical spectroscopy signals, and compared with results from the partially linearized density matrix treatment. A generalization of the model Hamiltonian form utilized in recent ab initio studies is presented, allowing for direct vibrational energy relaxation due to coupling between intramolecular normal modes and their environment. The consequences of including these interactions within a model Hamiltonian that is inspired by energetic parameters found in studies of a photosynthetic light-harvesting complex are highlighted in the context of density matrix dynamics and time-resolved two-dimensional electronic spectroscopy. The results indicate that this physical process can be utilized as a means of optimizing the efficiency of excitation energy transfer and localization. Inspired by ab initio characterization of model Hamiltonians for molecular aggregates, a new approximate semiclassical propagator for describing the time-evolution of a system consisting of discrete electronic states in the presence of both high-frequency harmonic vibrational modes as well as slow environmental DOFs with arbitrary potentials is presented. Results indicate that this algorithm provides a more accurate description in this parameter regime than standard linearized path integral methods such as the partially linearized density matrix algorithm and the truncated Wigner approximation. Finally, preliminary results of dynamics involving non-perturbative field-matter interactions is presented with emphasis on strategically shaped pulses, field design through optimal control, and non-perturbative pump-probe spectroscopy.

Simulation of quantum dynamics for many-body systems is an open area of research. For interacting many-body quantum systems, the computer memory necessary to perform calculations has an astronomical value, so that approximated models are needed to reduce the required computational resources. A useful approximation that can often be made is that of quantum-classical dynamics, where the majority of the degrees are treated classically, while a few of them must be treated quantum mechanically. When energy is exchanged very quickly between the quantum subsystem and classical environment, the dynamics is nonadiabatic. Most theories for nonadiabatic dynamics are unsatisfactory, as they fail to properly describe the quantum backreaction of the subsystem on the environment. However, an approach based on the quantum-classical Liouville equation solves this problem. Even so, nonadiabatic dynamics is di cult to implement on a computer, and longer simulation times are often inaccessible due to statistical error. There is thus a need for improved algorithms for nonadiabatic dynamics. In this thesis, two algorithms that utilise the quantum-classical Liouville equation will be qualitatively and quantitatively compared. In addition, stochastic sampling schemes for nonadiabatic transitions will be studied, and a new sampling scheme is introduced [D. A. Uken et al., Phys. Rev. E. 88, 033301 (2013)] which proves to have a dramatic advantage over existing techniques, allowing far longer simulation times to be calculated reliably.
Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

In this thesis quantum-classical dynamics is applied to the study of quantum condensed phase processes. This approach is based on the quantum-classical Liouville equation where the dynamics of a small subset of the degrees of freedom are treated quantum mechanically while the remaining degrees of freedom are treated by classical mechanics to a good approximation. We use this approach as it is computationally tractable, and the resulting equation of motion accurately accounts for the quantum and classical dynamics, as well as the coupling between these two components of the system. By recasting the quantum-classical Liouville equation into the form of a generalized master equation we investigate connections to surface-hopping. The link between these approaches is decoherence arising from interaction of the subsystem with the environment. We derive an evolution equation for the subsystem which contains terms accounting for the effects of the environment. One of these terms involves a memory kernel that accounts for the coherent dynamics. If this term decays rapidly, a Markovian approximation can be made. By lifting the resulting subsystem master equation into the full phase space, we obtain a Markovian master equation that prescribes surface-hopping-like dynamics. Our analysis outlines the conditions under which such a description is valid. Next, we consider the calculation of the rate constant for a quantum mechanical barrier crossing process. Starting from the reactive-flux autocorrelation function, we derive a quantum-classical expression for the rate kernel. This expression involves quantum-classical evolution of a species operator averaged over the initial quantum equilibrium structure of the system making it possible to compute the rate constant via computer simulation. Using a simple model for a proton transfer reaction we compare the results of the rate calculation obtained by quantum-classical Liouville dynamics with that of master equation dynamics. The master equation provides a good approximation to the full quantum-classical Liouville calculation for our model and a more stable algorithm results due to the elimination of oscillating phase factors in the simulation. Finally, we make use of the theoretical framework established in this thesis to analyze some aspects of decoherence used in popular surface-hopping techniques.