This dissertation covers a range of computational explorations of different theoretical, synthetically relevant, and biosynthetically relevant systems. Chapter 1 introduces the quantum mechanical concepts behind computational organic chemistry, as well as common practices for applying these methods to mechanistic studies. Specifically, the chapter discusses the different types of calculations used in later chapters, such as stationary point analyses, calculation of different types of energies, and quasiclassical downhill molecular dynamics simulations. All chapters examine various organic reaction mechanisms and their nuances, with Section I discussing systems that contain post-transition state bifurcations. Chapter 2 is based on a Rh-catalyzed C-H insertion reaction that bifurcates following the insertion transition state structure, producing either a [beta]-lactone (the desired product, in the case of the experimental study used as a point of comparison) or a fragmented product. The specific reaction was taken from a previously published study, which actually reported production of one of the products along the fragmentation pathway, giving experimental evidence that this pathway is accessible. It was found that subtle changes in the structure, and even the conformation, of the transition state structure would lead to large changes in product distributions seen in downhill molecular dynamics simulations. As Rh-catalyzed C-H insertion reactions are common in synthetic organic chemistry, the principles uncovered in this study are the first steps to predict design elements that would manipulate product outcomes for these and other reactions containing bifurcations. Chapter 3 covers a theoretical reaction dubbed the “Hiscotropic Rearrangement” that exhibits a post-transition state bifurcation. The two possible products in this case are generated based on the torquoselectivity of a cyclopropyl ring opening. This torquoselectivity could be modulated based on the presence of a benzene ring near to the reacting transition state structure (the benzene acting as a “theozyme”). With no additional barriers to overcome on the way to the two products, reactions with post-transition state bifurcations are sensitive to their local environment, and this study shows the ability of intermolecular electrostatic interactions to influence selectivity. Chapter 4 then discusses an example of a system where implicit solvent models manipulate the products following a post-transition state bifurcation (i.e., a continuum solvent with no explicit solvent molecules in the calculations). The Pummerer-like rearrangement reaction examined could lead to either a formal [2,3]- or [3,3]-rearrangement product. Transition state structures were optimized in various implicit solvents, and the distances of the two possible forming bonds (i.e., for formation of either the [2,3] or [3,3] product) were strongly correlated to solvent dielectric constant. Additionally, these distances could be correlated to the product distributions observed in molecular dynamics trajectories initiated from the transition state structures. While work to pin down the origins of this effect is ongoing, it appears an intramolecular interaction is likely to blame for reaction steering in this case. Section II contains chapters that are collaborations with synthetic chemists, as well as computational data generated in reference to experiments that have already been published. Chapter 5 discusses a collaboration with the Dina Merrer group at Barnard college. The Merrer group discovered unexpected rearrangement products after reacting carbene precursors with polycyclic compounds containing bridgehead alkenes (adamantene and homoadamantene). The computational studies shed light on the most probable mechanisms for formation of these products, whittling down an initial seven proposed mechanisms to the two most likely pathways. Chapter 6 was a project conducted in large part by my undergraduate mentee, Jessica Farnham, and examines the proposed mechanism of a published synthesis of the natural product (+)-chatancin. By calculating the energies of the stationary points along the proposed pathway and also a slightly altered pathway, it was found that a cycloaddition involving a pyrylium ion would have a lower energetic barrier than said previously proposed cycloadditions involving a 2H-pyran or furan. Lastly, chapter 7 details an ongoing collaboration with the Ang Li group at the Shanghai Institute of Organic Chemistry. Along the way to their total syntheses of the natural products daphnilongeranin B and hybridaphniphylline B, several questions arose about the selectivity they were seeing. In the case of the synthesis of daphnilongeranin B, the questions were (1) how a methyl ester group on the reactant and (2) the polarity of the solvent affect the relative barriers for a Claisen and a Cope rearrangement. The total synthesis of hybridaphniphylline B involved a step that interconverted three different structures via [1,5]-hydride shifts under thermodynamic conditions, and it was unclear what caused the experimental ratio of these structures. The calculations thus far do not conclusively resolve these questions, but the collaboration will continue with more back-and-forth between calculations and experiment until a consistent picture is drawn.