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Many philosophers of science and physicists take it for granted that "physics" determines "chemistry". Or in terms of the theory of supervenience, it is commonly supposed that the domain of chemistry supervenes upon the domain of fundamental physics. This is the thesis of physicalism: the idea that all causation ultimately depends on the causal powers of the phenomena described by fundamental physics.

R. F. Hendry takes up this issue in his contribution to Davis Baird, Eric Scerri, and Lee McIntyre's very interesting volume, Philosophy of Chemistry. Hendry takes the position that this relation of supervenience does not obtain; chemistry does not supervene upon fundamental physics.

Hendry points out that the dependence claim depends crucially on two things: what aspects of physics are to be considered? And second, what kind of dependency do we have in mind between higher and lower levels? For the first question, he proposes that we think about fundamental physics -- quantum mechanics and relativity theory (174). For the second question, he enumerates several different kinds of dependency: supervenience, realization, token identity, reducibility, and derivability (175). In discussing the macro-property of transparency in glass, he cites Jaegwon Kim in maintaining that transparency in glass is "nothing more" than the features of the microstructure of glass that permit it to transmit light. But here is a crucial qualification:
But as Kim admits, this last implication only follows if it is accepted that “the microstructure of a system determines its causal/nomic properties” (283), for the functional role is specified causally, and so the realizer’s realizing the functional property that it does (i.e., the realizer–role relation itself) depends on how things in fact go in a particular kind of system. For a microstructure to determine the possession of a functional property, it must completely determine the causal/nomic properties of that system. (175) Hendry argues that the key issue underlying claims of dependence of B upon A is whether there is downward causation from the level of chemistry (B) to the physical level (A); or, on the contrary, is physics "causally complete". If the causal properties of the higher level are fully fixed by the causal properties of the underlying level, then supervenience is possible; but if the higher level has causal properties that permit influence on the lower level, then supervenience is not possible.

In order to gain insight into the specific issues arising concerning chemistry and physics, Hendry makes use of the "emergentist" thinking associated with C.D. Broad. He finds that Broad offers convincing arguments against "Pure Mechanism", the view that all material things are determined by the micro-physical level (177). Here are Broad's two contrasting possibilities for understanding the relations between higher levels and the physical micro-level:
(i) On the first form of the theory the characteristic behavior of the whole could not, even in theory, be deduced from the most complete knowledge of the behavior of its components, taken separately or in other combinations, and of their proportions and arrangements in this whole . . .
(ii) On the second form of the theory the characteristic behavior of the whole is not only completely determined by the nature and arrangements of its components; in addition to this it is held that the behavior of the whole could, in theory at least, be deduced from a sufficient knowledge of how the components behave in isolation or in other wholes of a simpler kind (1925, 59). [Hendry, 178] The first formulation describes "emergence", whereas the second is "mechanism". In order to give more contemporary expression to the two views Hendry introduces the key concept of quantum chemistry, the Hamiltonian for a molecule. A Hamiltonian is an operator describing the total energy of a system. A "resultant" Hamiltonian is the operator that results from identifying and summing up all forces within a system; a configurational Hamiltonian is one that has been observationally adjusted to represent the observed energies of the system. The first version is "fundamental", whereas the second version is descriptive.

Now we can pose the question of whether chemistry (behavior of molecules) is fixed by the resultant Hamiltonian for the components of the atoms involved (electrons, protons, neutrons) and the forces that they exert on each other. Or, on the other hand, does quantum chemistry achieve its goals by arriving at configurational Hamiltonians for molecules, and deriving properties from these descriptive operators? Hendry finds that the latter is the case for existing derivations; and this means that quantum chemistry (as it is currently practiced) does not derive chemical properties from fundamental quantum theory. Moreover, the configuration of the Hamiltonians used requires abstractive description of the hypothesized geometry of the molecule and the assumption of the relatively slow motion of the nucleus. But this is information at the level of chemistry, not fundamental physics. And it implies downward causation from the level of chemical structure to the level of fundamental physics.
Furthermore, to the extent that the behavior of any subsystem is affected by the supersystems in which it participates, the emergent behavior of complex systems must be viewed as determining, but not being fully determined by, the behavior of their constituent parts. And that is downward causation. (180) So chemistry does not derive from fundamental physics. Here is Hendry's conclusion, supporting pluralism and anti-reductionism in the case of chemistry and physics:
On the other hand is the pluralist version, in which physical law does not fully determine the behavior of the kinds of systems studied by the special sciences. On this view, although the very abstractness of the physical theories seems to indicate that they could, in principle, be regarded as applying to special science systems, their applicability is either trivial (and correspondingly uninformative), or if non-trivial, the nature of scientific inquiry is such that there is no particular reason to expect the relevant applications to be accurate in their predictions.... The burden of my argument has been that strict physicalism fails, because it misrepresents the details of physical explanation (187) Hendry's argument has a lot in common with Herbert Simon's arguments about system complexity (link) and with Nancy Cartwright's arguments about the limitations of (real) physics' capability of representing and calculating the behavior of complex physical systems based on first principles (link). In each case we get a pragmatic argument against reductionism, and a weakened basis for assuming a strict supervenience relation between higher-level structures and a limited set of supposedly fundamental building blocks. What is striking is that Hendry's arguments undercut the reductionist impulse at what looks like its most persuasive juncture -- the relationship between quantum physics and quantum chemistry.