Theoretical Study of the Mechanism of Exemestane Hydroxylation Catalyzed by Human Aromatase Enzyme

Human aromatase (CYP19A1) aromatizes the androgens to form estrogens via a three-step oxidative process. The estrogens are necessary in humans, mainly in women, because of the role they play in sexual and reproductive development. However, these also are involved in the development and growth of hormone-dependent breast cancer. Therefore, inhibition of the enzyme aromatase, by means of drugs known as aromatase inhibitors, is the frontline therapy for these types of cancers. Exemestane is a suicidal third-generation inhibitor of aromatase, currently used in breast cancer treatment. In this study, the hydroxylation of exemestane catalyzed by aromatase has been studied by means of hybrid QM/MM methods. The Free Energy Perturbation calculations provided a free energy of activation for the hydrogen abstraction step (rate-limiting step) of 17 kcal/ mol. The results reveal that the hydroxylation of exemestane is not the inhibition stage, suggesting a possible competitive mechanism between the inhibitor and the natural substrate androstenedione in the first catalytic subcycle of the enzyme. Furthermore, the analysis of the interaction energy for the substrate and the cofactor in the active site shows that the role of the enzymatic environment during this reaction consists of a transition state stabilization by means of electrostatic effects

Development of Reaction Discovery Tools in Photochemistry and Condensed Phases

Photochemistry obeys different rules than ground-state chemistry and by doing so opens avenues for synthesis and materials properties. However, the different rules of photochemistry make understanding the fine details of photochemical reactions difficult. Computational chemistry can provide the details for understanding photochemical reactions, but the field of computational photochemistry is still new, and many techniques developed for ground-state reactions are not directly applicable to photochemical reactions. As a result, many photochemical mechanisms are not understood, and this hinders the rational design and synthesis of new photochemistry. To address this need, this thesis develops techniques to search for and study photochemical reactions. Chapter 2 and 3 develop methods to calculate photochemical reactions in gas- and condensed-phases via minimum energy reaction paths. First, Chapter 2 develops a method to search the molecular 3N-6 space for photochemical reactions. This space, although vast, is not chaotic and can be efficiently searched using a concept familiar to chemists: breaking and adding bonds and driving angles and torsions. Furthermore, this procedure can be automated to predict new chemistry not previously identified by experiments. Chapter 3 furthers this research by leveraging the concept of molecules to enable the computational study of reactions in large multi-molecular systems like crystals. Specifically, the use of a new coordinate system involving translational and rotational coordinates allows decoupling of the coordinate systems of the individual molecules, which is necessary for the efficient algebra. Importantly, these methods are general, they can be used to study single molecules and crystals, and much in between. These methods are demonstrated on complex chemical problems including the isomerization pathways of ethylene and stilbene (Chapter 2), the photocycloaddition of butadiene (Chapter 2), the rotation of a crystalline gyroscope (Chapter 3), the bicycle pedal rotation of cis,cis-diphenylbutadiene (Chapter 4), and the mechanism of a reversible photoacid (Chapter 5). These problems have value in understanding the processes of vision, optomechanics, and high-energy materials, and through their xx study much needed insight is gained that can be useful for designing new syntheses and materials. Furthermore, the new computational methods open the possibility for many future investigations. The results of Chapter 2 find a novel roaming-atom and hula-twist isomerization pathway and use automated reaction discovery tools to identify a missing butadiene photoproduct and why the [4+2] cycloaddition is forbidden. The results of Chapter 3 and 4 build on Chapter 2 by including the influence of a steric environment. Chapter 3 demonstrates by application to a molecular gyroscope that extreme long-range correlated motion can be captured with GSM, and Chapter 4 details how the one-bond flip and hula-twist mechanisms are suppressed by the crystal cavity, the nature of the seam space in steric environments, and the features of the bicycle pedal mechanism. For example, the bicycle pedals rotate through the passageway in the adjacent monomers. However, the models do not capture the quantitative activation barriers and more work is needed. Finally, Chapter 5 provides the ultrafast details of how the photoacid isomerizes and ring-closes with experimental and computational evidence. Unfortunately, quantitative calculation of pKa cannot be provided with the computations employed herein. In summary, this thesis provides an advancement in the knowledge of photochemical mechanisms that can be used for the development of new syntheses and offers new tools with capacity to study complex photochemical problems.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/163005/1/craldaz_1.pd

Exploring potential energy surfaces in ground- and excited states

Chemical reactivity of atoms, molecules and ions is governed by their underlying potential energy surface. Calculating the whole potential energy surface within reasonable bounds, is impossible for all but the smallest molecules. Usually, only parts of the full potential energy surface can be studied, namely stationary points and the minimum energy paths connecting them. By comparing energies of stationary points and their separating barriers, conclusions regarding possible reactions mechanism, or their infeasibility, can be drawn. Taking excited states into account leads to further complications, as now multiple potential energy surfaces have to be considered and root flips between different excited states may occur, requiring effective state-tracking. Part II of this thesis describes the required methods to locate stationary points and minimum energy paths on potential energy surfaces, by using surface-walking, chain-of-states optimization and intrinsic reaction coordinate integration. Several approaches to state-tracking are presented in chapter 4. Results of this thesis are presented in Part III, containing two contributions to the field of photochemistry: chapter 12 provides a possible excited-state reaction mechanism for a biaryl cross-coupling reaction and offers a plausible explanation for its high regioselectivity. The second contribution is the development pysisyphus (chapter 13), an external optimizer implemented in python, aware of excited states and thus the core of this thesis. By implementing the state-tracking algorithms outlined in chapter 4 it allows effective and efficient optimizations of stationary points in ground- and excited-states. The performance of pysisyphus is verified for several established benchmark sets. Results for several excited-state optimizations are presented in section 13.3, where pysisyphus shows good performance for the optimization of sizeable transition-metal complexes