At the energy-chemistry nexus, key molecules include carbon dioxide (CO2), hydrogen (H2), methane (CH4), and ammonia (NH3). The position of these four molecules and that of the more general family of synthetic macromolecular polymer blends (found in plastics) were cross-analyzed with the Planetary Boundary framework, and as part of five scientific policy roadmaps for the energy transition. According to the scenarios considered, the use of some of these molecules will be drastically modified in the coming years. Ammonia, which is currently almost exclusively synthesized as feedstock for the fertilizer industry, is envisioned as a future carbon-free energy vector. ‘Green hydrogen’ is central to many projected decarbonized chemical processes. Carbon dioxide is forecast to shift from an unavoidable byproduct to a valuable feedstock for the production of carbon-based compounds. In this context, we believe that interdisciplinary elements from history, economics and anthropology are relevant to any attempted cross-analysis. Distinctive and crucial insights drawn from elements of humanities and social sciences have led us to formulate or re-raise open questions and possible blind-spots in main roadmaps, which were developed to guide, inter alia, chemical research toward the energy transition. We consider that these open questions are not sufficiently addressed in the academic arena around chemical research. Nevertheless, they are relevant to our understanding of the current planetary crisis, and to our capacity to properly assess the potential and limitations of chemical research addressing it. This academic perspective was written to share this understanding with the broader academic community. This work is intended not only as a call for a larger interdisciplinary method, to develop a sounder scientific approach to broader scenarios, but also – and perhaps mostly – as a call for the development of radically transdisciplinary routes of research. As scientists with different backgrounds, specialized in different disciplines and actively involved in providing solutions by means of our research, we bear ethical responsibility for the consequences of our acts, which often lead to consequences well beyond our discipline. Do our research and the knowledge it produces respond, perpetuate or even aggravate the problems encountered by society?