Theoretical Investigations of Cycloadditions and Subsequent Transformations Involving Allenes and Arenes to Form Complex Polycycles

This dissertation is a culmination of research projects that combine the utility of computational methods with the practicality of experiments in order to investigate a variety of chemical phenomena. The theoretical molecular models and quantum chemical calculations reported herein provide explanations of selectivity, elucidations of mechanisms, and predictions of reactivity that will continually advance the scientific community in future endeavors, especially in the field of organic chemistry and complex polycycle synthesis. Section I describes investigations centering upon the 4+2 cycloaddition between benzene and allene, a reaction developed by Gerhard Himbert in the 1980s. In collaboration with Chris Vanderwal at UC Irvine, we study the mechanisms of intramolecular Diels–Alder cycloadditions of various N-phenyl-allenamides to uncover the competing concerted and stepwise diradical pathways that bring about intriguing experimental observations. Additionally, the reaction optimization of carbon analogues is aided and explained through computations, providing access to novel cycloadducts. With growing interest in the mechanistic intricacy of the 4+2 reaction, a theoretical study of the Diels–Alder reaction of allene with butadiene and with benzene elucidates the complexity of each cycloaddition, revealing an ambimodal transition state along the butadiene/allene pathway and the importance of preserving aromaticity in the reaction with benzene. To gain insight into the importance of intramolecularity in the original Himbert systems, we conducted a systematic investigation of various tether moieties and their effects on the thermodynamics of the reaction. Finally, in our quest to efficiently synthesize a library of complex polycyclic scaffolds, we looked into subsequent transformations of the bicyclo[2.2.2]octadiene cycloadducts, namely ring-rearrangement metathesis to form fused tricycles and an interesting dyotropic shift that occurs in a stepwise manner, resulting in isomerized bicyclo[3.2.1]octadiene skeletons. Section II compiles research pertaining to other pericyclic reactions as well as collaborative projects with different research groups. Intramolecular Diels–Alder reactions with tryptamine-derived Zincke aldehydes and diene-tethered cycloalkenones, in conjunction with Chris Vanderwal and Samuel Danishefsky, respectively, are studied computationally to explain stereoselectivities and influences from external reagents. Collaborative efforts with the Barrio and Petric groups provide a deeper understanding of the noncovalent binding modes of a class of positron emission tomography probes used for diagnosing and treating neurodegenerative conditions. Additionally, the utilization of computations to further synthetic efforts is exemplified in the molecular modeling of Vanderwal’s tetracyclic exiguaquinol core and Jung’s palladium-catalyzed alkene isomerizations. The thermodynamic properties of Rebek’s host–guest systems were examined, using molecular mechanics and implicit solvent to understand the binding of adamantyl guests in resorcinarene-based cavitands. Finally, a review analyzes hydrocarbon-bound protein structures and other properties in order to identify potential de novo enzyme templates for the cleavage of C–C single bonds