Intermolecular forces (IMFs), or more broadly, noncovalent interactions either within or between molecules, are central to an understanding of a wide range of chemical and biological phenomena. In this study, we present a multiyear, multi-institutional, longitudinal comparison of how students enrolled in traditional general chemistry courses and those in a transformed general chemistry course (Chemistry, Life, the Universe and Everything, or CLUE) represent intermolecular forces in the context of small molecules. For multiple cohorts of students at two different universities, we found that students who participate in the CLUE curriculum were significantly more likely than those in a traditional curriculum to indicate (correctly) that intermolecular forces occur between, rather than within small molecules. In a longitudinal study, we followed the students from one cohort through the subsequent year of organic chemistry and found that the differences between the CLUE and traditional students persisted over the course of two years of chemistry instruction. In general, students who are enrolled in the transformed general chemistry curriculum have a more scientifically correct and more coherent understanding of IMFs. The finding that a majority of students leave general chemistry without a coherent understanding of the difference between covalent and noncovalent interactions must certainly impact their subsequent understanding of chemical and biological phenomena.