This thesis investigates the epistemological and metaphysical relations between chemistry and quantum mechanics. These relations are examined with respect to how chemistry and quantum mechanics each describe a single inert molecule. A review of how these relations are understood in the literature shows that there is a proliferation of positions which focus on how chemistry is separate from quantum mechanics. This proliferation is accompanied by a tendency within the philosophy of chemistry community to connect the legitimacy of the field with (...) the autonomy of chemistry. First, it is argued that this connection should not be made. Secondly, it is argued that chemistry and quantum mechanics are unified in accordance with Harold Kincaid’s model of non-reductive unity because the two theories exhibit particular epistemic and metaphysical interconnections. Thirdly, a metaphysical account is examined which is incompatible with Kincaid’s model of unity; namely strong emergence as understood by Robin Hendry. According to Hendry, the structure of a single inert molecule strongly emerges from its quantum mechanical entities in the sense that there is downward causation. However, Hendry’s defense of this account faces certain problems. Moreover, the putative empirical evidence for his understanding of strong emergence can be explained without invoking strong emergence. This is shown by considering how quantum mechanics assumes an idealized understanding of a molecule’s stability and structure. In the light of the philosophical literature on idealizations, this idealization can be interpreted in two different ways, both of which explain why quantum mechanics describes the structure of a single molecule the way it does, without assuming strong emergence in Hendry’s sense. Each interpretation has philosophical implications regarding the nature of chemical properties, and the relation of chemistry and quantum mechanics. These implications are consistent with Kincaid’s model of unity and thus further support chemistry’s unity with quantum mechanics (as per Kincaid). (shrink)