This paper discusses factors limiting the development of a modern, quantum-based chemistry in Nazi Germany. The first part presents a case study of industrial research in Nazi Germany that suggests the delayed introduction of space-filling molecular models into structural analysis and synthesis in industrial organic chemistry, almost a decade after their invention by a German physicist. Was this symptomatic of a broader pattern of neglect of quantum chemistry in Nazi Germany? To answer this question this paper examines the origins of such models, and their appearance (or not) in selected textbooks and monographs dealing with problems in the interdisciplinary borderland between the physical and organic dimensions of chemistry. While it appears that those on the physical side were more comfortable with such models than those on the organic side, it is also clear that even a theoretically unsophisticated organic chemist could learn to use these models effectively, without necessarily understanding the intricacies of the quantum chemistry on which they were based. Why then were they not better integrated into mainstream chemical education? To this end the second part discusses three phases (pre-1933, 1933–38, 1939–43) of the broader scientific, institutional, and political contexts of efforts to reform or “modernize” chemical education among many groups in Germany, particularly through the Association of Laboratory Directors in German Universities and Colleges, the autonomous group that administered the predoctoral qualifying examination (Association Examination) for chemistry students until its dissolution in 1939 by the Education Ministry and the establishment of the first official certifying examination and associated title for chemists, the Diplom-Chemiker (certified chemist). Continuing debates modified the examination in 1942–43, but given the limitations imposed by the political and wartime contexts, and the need to accelerate chemical training for the purposes of industrial and military mobilization, the resulting chemical education could not produce students adequately trained in the modern physical science emerging elsewhere in the world. Quantum chemists remained missing in action in Nazi Germany.