The United Nations General Assembly has designated 2025 as the “International Year of Quantum Science and Technology”. Quantum science, in fact, provides the foundation for basic research and the interpretation of the atomic/molecular world, and its beginning can be dated back to the works of Heisenberg and Pauli in 1925. The study of the molecular world, however, did not begin that year. Nineteenth-century chemists, in fact, developed useful concepts in this world and connected them to the macroscopic properties of chemical substances. In this educational paper, we intend to discuss the conceptual aspects and “open issues” of the relationship between quantum mechanics and the historical concepts of chemistry. Although this physical theory represented a revolutionary change in the study of the atomic/molecular world, it still struggles to gain traction in the educational and general/cultural contexts, both for “objective” reasons and due to the current lack of attention to the analysis of the conceptual/philosophical problems of this theory and their educational treatment.