In a world facing complex global issues, citizens need to be able to make and justify decisions, an important aspect of scientific argumentation skills. Building from previous work in chemistry education and philosophy of science, we have developed an argumentation framework focused on reasoning, granularity, and comparisons, and we have used this framework to characterize students' arguments in organic chemistry. We found that students' arguments appropriately varied between tasks and contexts, including the reasoning, granularity, and comparisons within those arguments. We propose using constructive alignment, where outcomes for students are determined before instruction and used to guide teaching and assessment, as a potential tool for educators to support students' argumentation in chemistry.