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Do Molecules Have Structure in Isolation? How Models Can Provide the Answer

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Molecules may not have structure in isolation. I support this by investigating how quantum models identify structure for isolated molecules. Specifically, I distinguish between two sets of models: those that identify structure in isolation and those that do not. The former identify structure because they presuppose structural information about the target system via the Born-Oppenheimer approximation. However, it is an idealization to assume structure in isolation because there is no empirical evidence of this. In fact, whenever structure is empirically examined it is always partially determined by factors that are absent in isolation. Together with the growing empirical evidence that isolated molecules behave in non-classical ways, this shows that the quantum models that do not identify structure are more faithful representations of isolated molecules.


  • Models
  • Molecular structure
  • Born-Oppenheimer approximation
  • Isolated molecules
  • Idealisation
  • Reduction
  • Emergence

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  1. 1.

    ‘Molecular structure’ refers to the spatial arrangement of the particles that constitute the molecule. This definition is in line with how molecular structure is understood in the relevant literature (such as Chang, 2015; Fortin et al., 2016; Hendry, 2010a; Lombardi, 2014; Lombardi & Castagnino, 2008; Primas, 1981; Woolley, 1978; Woolley & Sutcliffe, 1977). I do not consider conceptual issues regarding molecular structure (see for example Hendry, 2016).

  2. 2.

    I do not claim that this is the only correct way of expressing this issue; existing analyses have contributed greatly to understanding molecular structure and its quantum mechanical description.

  3. 3.

    The other questions are pertinent to this discussion, so they will also be investigated to some extent.

  4. 4.

    I do not claim that my claim implies the in toto rejection of anti-reduction or strong emergence. I only point out that to the extent that any philosophical account is contingent on the assumption that isolated molecules have structure, such accounts face a problem that needs to be addressed.

  5. 5.

    Such as the debate around the different interpretations of quantum mechanics, the measurement problem, and the issue of the classical-quantum divide.

  6. 6.

    This implies that I do not offer an explanation as to why (and in what way) molecules do not have structure in isolation. That is, I do not provide ontological grounds for believing this claim. Nevertheless, I take accounts that provide such explanations to further enforce my claim that there is no structure in isolation (though I leave it open about which particular explanation is the right one − see Sects. 6.4 and 6.5).

  7. 7.

    Note that there are also other means of representation that are not always understood as models. Also, there is debate about whether models are a specific kind of scientific representation and whether all scientific representations are models (see Frigg & Nguyen, 2020). Given that it makes no substantial difference to the current discussion, I assume for simplicity that models are at least a kind of scientific representation. In this context, the above definition of models suffices to broadly characterize models (this definition is largely based on Suarez’s (2003) definition of scientific representations).

  8. 8.

    Gavroglu and Simões call quantum chemistry “a sub-discipline that is not quite physics, not quite chemistry, and not quite applied mathematics” (2012: viii). More precisely, it is the “branch of theoretical chemistry in which the methods of quantum mechanics are applied to chemical problems” (Palgrave Macmillan Ltd, 2004: 1845).

  9. 9.

    Some philosophers have identified specific types of models in quantum chemistry (see Weisberg, 2007). This is outside the scope of this contribution.

  10. 10.

    These models include the Valence Bond Approach, the Molecular Orbital Approach, and the Hartree-Fock Method.

  11. 11.

    This question may also involve investigating the structure of scientific theories (in terms of −say− the syntactic or semantic view; see Winther, 2016, for an overview). This issue is not investigated here.

  12. 12.

    According to Thomson’s model (also known as the plum pudding model), atoms are uniform spheres of positive charge where electrons are embedded. On the other hand, Bohr’s model takes positive charge to be concentrated in the nucleus and electrons to move in dynamically stable orbits around the nucleus. Bohr’s model was very much based on Rutherford’s model of the atom (for an overview of the different models of the atom, see Cushing, 1998; Pullman, 2001).

  13. 13.

    This does not mean that Bohr’s model of the atom is the most faithful representation of atomic structure. In fact, scientists have identified various respects in which this model is not a faithful representation.

  14. 14.

    Interestingly, Hendry also identifies the assumption of structure in isolation as an idealisation. He states: “the Hamiltonians are usually relevant only to isolated molecules, of which there are none in the real word” (1998: 125). However, in his analysis of quantum models he does not further consider whether the application of this idealisation has any effect on the faithfulness of the relevant models.

  15. 15.

    Quantum mechanics is characterised as ‘ab initio’ when the description is formulated from first principles, without appeal to ad hoc assumptions (including chemical facts), and by taking into account only the number and types of physical entities that make up the examined system (see, for example, Scerri, 2004, and IUPAC, 2014, under the term ‘ab initio’). Moreover, a molecule is in isolation when (i) it is far removed from any other system and thus doesn't interact with other entities; and, (ii) the total energy of the molecule is conserved (Seifert, 2020: 21).

  16. 16.

    Of course quantum chemists apply a number of additional assumptions and approximations in order to arrive at a computationally tractable and useful description of the target system. Nevertheless, it seems incontestable in the literature that in practice the BO approximation is always applied in order to identify structure.

  17. 17.

    The issue of classicality and Heisenberg’s uncertainty principle is another problem in defending chemistry’s reduction (see also Chang, 2015, and Sect. 6.4).

  18. 18.

    My proposed distinction of quantum models is an oversimplification as there are differences and similarities between those two sets of models, as well as alternative categorisations of quantum models, that are completely disregarded here. For example, scientists standardly distinguish models in terms of whether they apply the Valence Bond or the Molecular Orbital approach (for an overview, see Weisberg, 2008). Nevertheless, I believe this is a useful way to rephrase the debate about molecular structure as it illuminates previously unexplored epistemic features of quantum mechanics that are closely relevant to the discussion of molecular structure.

  19. 19.

    In the next section I show that it is because of the BO approximation that models can identify structure.

  20. 20.

    It seems to me that ‘exact’ is just an alternative term for ‘ab initio’ −though I leave it open that there is an alternative definition of ‘exact’ that I am not aware of.

  21. 21.

    See footnote above for a definition of isolation.

  22. 22.

    Obviously this analogy can be philosophically challenged and debated. Nevertheless, this doesn’t undermine the possibility of understanding such properties in this manner.

  23. 23.

    Specifically, scientific programs are currently under way whose goal is to “explore, to test, and to control the ‘strange’ quantum properties of non-locality, entanglement, and decoherence, and to apply these features to complex systems including large molecules” (Chatzidimitriou-Dreismann & Arndt, 2004: 144; see also Arndt et al., 1999; Wang & Kais, 2007).

  24. 24.

    Note that the abductive argument just sketched is an example of an Inference to the Best Explanation. I do not examine here the validity of abduction nor consider possible objections that have been made against such arguments, including objections within the debate about scientific realism (see for example Douven, 2017; Psillos, 2005).

  25. 25.

    Whether the BO approximation is a necessary step to identifying structure through quantum mechanics is not examined here; it may be that the BO is used just because scientists have not yet developed other computational means to describe molecules without it. As things stand however, there is no model which identifies molecular structure without applying this approximation . So I will only draw conclusions based on the present situation in quantum chemistry, and not on how they could potentially be in the future.

  26. 26.

    In light of the previous paragraph, it is evident that one needs to investigate whether relational properties can be consistently regarded as essences, propensities, or potencies. For example, Molnar argues that relational properties cannot be regarded as potencies (2003: 158–162). Bird examines how such a position can be challenged (2007: 166–167).


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Special thanks to James Ladyman, Alexander Franklin, Francesca Belazzi, Toby Friend, Samuel Kimpton-Nye and Tuomas Tahko. This paper was supported by the European Research Council Project ‘The Metaphysical Unity of Science’, grant no. 771509.

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Seifert, V.A. (2022). Do Molecules Have Structure in Isolation? How Models Can Provide the Answer. In: Lombardi, O., Martínez González, J.C., Fortin, S. (eds) Philosophical Perspectives in Quantum Chemistry. Synthese Library, vol 461. Springer, Cham.

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