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 the x-axis of the reaction coordinate diagrams, while largely ignoring the energies of the species encoded along the y-axis. Implications for teaching organic chemistry are discussed.