The work presented in the following chapters was undertaken with the goal of understanding and improving education in organic chemistry. Initial work, described in Chapters 1 and 2, focuses on students' ability to explain and rationalize the outcomes of organic chemistry reactions. Chapter 1 explores the relationship between assessment emphasis and the structure-energy connections students made when asked to explain the outcome of a hydrobromination reaction. Using a mixed methods study design, an association was found between the kinds of tasks students were given on assessments and the ideas they utilized in their written explanations on a separate researcher-authored assessment. The relationship between assessment emphasis and conceptual ideas was probed qualitatively in Chapter 2. Students were interviewed as they proposed electron-pushing mechanisms and predicted the products for familiar and unfamiliar reactions. The ideas they drew on in their reasoning were found to be similar to the core ideas around which their course was designed, indicating that the students had internalized the utility of these ideas for problem-solving. More recently, the focus of the work has shifted toward understanding the epistemic aspect of organic chemistry education. Chapter 2 describes our first foray into epistemology; in addition to characterizing the conceptual resources students invoked, we characterized some of the epistemic resources they utilized. This allowed us to differentiate between moments when students were recalling explanations versus moments when they were constructing them in the moment by connecting different bits of prior knowledge. Chapter 3 presents a critical review of how the field of chemistry education has studied and modeled undergraduate students' epistemic cognition and in particular, draws attention to the implications of evaluating students' epistemic cognition in a hierarchical manner that does not attend to context. In Chapter 4, we compare two ways of modeling epistemic cognition and discuss their affordances and limitations with regard to interpreting interview data on organic chemistry instructor's thinking for teaching and learning chemistry. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com.bibliotheek.ehb.be/en-US/products/dissertations/individuals.shtml.]