The purpose of this study was to elucidate and describe students’ thinking when making connections between substitution and elimination reactions and their corresponding reaction coordinate diagrams. Thirty-six students enrolled in organic chemistry II participated in individual, semi-structured interviews. Three major themes were identified that characterize students’ difficulties with integrating the information from the reactions and the reaction coordinate diagrams: incorrect ideas about the meanings of the reaction coordinate diagrams’ features, errors when examining reaction mechanisms, and an inability to assess the relative energies of reaction species. These findings suggest that students need support for coherence formation between reactions and reaction coordinate diagrams. Implications for teaching to address these student difficulties are suggested.

Organic chemistry students struggle with understanding the energetics of chemical reactions. Reaction coordinate diagrams are one tool that is widely used in organic chemistry classrooms to assist students with visualizing and explaining the energy changes that take place throughout a reaction. Thirty-six students enrolled in organic chemistry II participated in a qualitative study that used semi-structured interviews to investigate the extent to which students meaningfully extract and integrate information encoded in reaction coordinate diagrams. Results show that students have difficulties explaining the meanings of surface features such as peaks, valleys, peak height, and peak width. Analysis of students’ explanations resulted in four themes that describe students’ challenges with correctly interpreting the features of reaction coordinate diagrams. Students conflated transition states and intermediates, despite being able to recite definitions. Students described the chemical species encoded at points along thex-axis of the reaction coordinate diagrams, while largely ignoring the energies of the species encoded along they-axis. Implications for teaching organic chemistry are discussed.