Theoretical modeling of organic molecules and reactions is a powerful tool and can lead to further insight into these chemical systems. Modeling allows portions of the potential energy surface that cannot be examined experimentally, such as transition states. These transition states can lend themselves to better understanding of the system's reactivity. Modeling can also be used to perform analysis that would time-consuming and tedious experimentally or clarify ambiguous experimental results. In this thesis, the use of theoretical modeling to examine the structure, spectra, and reactivity of organic systems will be explored. In this thesis modeling is used to examine the regioselectivity of indole aryne cycloadditions and kinetic isotope effects of substituted anilines. The use of proton nucleomers to calculate linear free energy relationships to reduce both experimental and computational time is examined. A significant portion of this thesis is dedicated to the use of calculated nuclear magnetic resonance chemical shifts and coupling constants to differentiate between stereo- and structural isomers; something that can be very difficult to do using experimental spectra.