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Foundations of Science

On the Ontological Status of Molecular Structure: Is it Possible to Reconcile Molecular Chemistry with Quantum Mechanics?

Sebastián Fortín, Martín Labarca, Olímpia Lombardi

Published Mar 3, 2022• 7 citations
Publisher
DOI
10.1007/s10699-022-09834-4

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Abstract In this article I examine several related views expressed by Robin Hendry concerning molecular structure, emergence and chemical bonding. There is a long-standing problem in the philosophy of chemistry arising from the fact that molecular structure cannot be strictly derived from quantum mechanics. Two or more compounds which share a molecular formula, but which differ with respect to their structures, have identical Hamiltonian operators within the quantum mechanical formalism. As a consequence, the properties of all such isomers yield precisely the same calculated quantities such as their energies, dipole moments etc. The only means through which the difference between the isomers can be recovered is to build their structures into the quantum mechanical calculations, something that is carried out by the application of the Born-Oppenheimer approximation. Consequently, it has been argued by many authors that molecular structure is written in ‘by hand’ rather than derived. Robin Hendry is one such author, but he goes a great deal further by proposing that this situation implies the existence of emergence and downward causation. In the current article I argue that there are alternative explanations which render emergence and downward causation redundant. Such an alternative lies in the notion of quantum decoherence and the appeal to work in the foundations of physics, which posits that the various isomers exist as a superposition until their wavefunctions are collapsed either by observation or by interacting with their environment. Hendry also alludes to a debate among chemists as to whether chemical bonds are real or not, in the sense of directional connections between two or more nuclei in any given molecule. I reject this view and propose that the structural and energetic views of chemical bonding, that have been discussed by some philosophers of chemistry including Hendry, do not refer to any essential ontological differences. I agree that chemists view bonding in a more realistic fashion and may consider bonds to be in some senses real, while physicists may consider bonding in more abstract energetic terms. However, I do not believe that such differences in scientific practice and attitudes should be considered to offer a window as to the ontological status of bonding or whether bonding is real. Finally, I discuss the kinetic energy school of chemical bonding which would seem to challenge any notion of bonds as directional entities, since bonding is no longer regarded as being primarily due to the build-up of electron density between nuclei.

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Abstract: Reconciling the probabilistic framework of quantum mechanics with the deterministic, stereochemical reality of macroscopic chemistry remains a central objective in the philosophy of science. Standard continuous quantum chemistry often views localized molecular structure as an asymptotic pattern or a secondary byproduct of environmental decoherence---an epistemological tension formally known as the Problem of Molecular Structure. To secure localized spatial geometry within the continuous formalism, standard models traditionally invoke the Born-Oppenheimer approximation (BOA), mathematically clamping nuclei at discontinuous parametric boundaries. To bridge this ontological gap and explore alternatives to claims of strong emergence, this manuscript introduces the Topological Lattice Configuration (TLC) framework. Grounded in a moderate Ontic Structural Realism, the TLC models the fundamental spatial manifold as a strictly orthogonal, piecewise linear square lattice (Q-net) constrained by immense Föppl-von Kármán stretching limits. Classical chemical ontology---electrostatic charge, discrete rest mass, and molecular chirality---is reimagined as the deterministic kinematic states and topological defects of this highly constrained grid. By integrating KTHNY defect dynamics, the discrete Laplace-Beltrami operator, and rigid origami kinematics (isothermal-conjugate geodesic nets), this analysis seeks to map topological semimetals, covalent networks, and the exotic fractional corner charges of the f-block directly to the Q-net, aiming to provide a unified, computable, geometric framework for the foundations of chemistry.
The concept of atomic and molecular orbitals has been a fundamental pillar in modern chemistry, shedding light on the structures and reactivity of chemical compounds. This article examines the evolution and significance of orbital theory, its applications in chemistry, and the ongoing debate about the existence of orbitals from both physics and chemistry perspectives. Philosophical aspects related to the ontology of orbitals are explored, emphasizing the complex interplay between mathematical abstractions and tangible reality. The multifaceted nature of orbitals, their role in quantum mechanics, and their implications for understanding the quantum realm are discussed. While the debate surrounding the ontological status of orbitals remains ongoing, it highlights the profound nature of inquiries into the fundamental essence of reality. This exploration underscores the significance of continuous research and discourse in advancing our understanding of these fundamental constituents of the quantum world.
Abstract In this article I examine several related views expressed by Robin Hendry concerning molecular structure, emergence and chemical bonding. There is a long-standing problem in the philosophy of chemistry arising from the fact that molecular structure cannot be strictly derived from quantum mechanics. Two or more compounds which share a molecular formula, but which differ with respect to their structures, have identical Hamiltonian operators within the quantum mechanical formalism. As a consequence, the properties of all such isomers yield precisely the same calculated quantities such as their energies, dipole moments etc. The only means through which the difference between the isomers can be recovered is to build their structures into the quantum mechanical calculations, something that is carried out by the application of the Born-Oppenheimer approximation. Consequently, it has been argued by many authors that molecular structure is written in ‘by hand’ rather than derived. Robin Hendry is one such author, but he goes a great deal further by proposing that this situation implies the existence of emergence and downward causation. In the current article I argue that there are alternative explanations which render emergence and downward causation redundant. Such an alternative lies in the notion of quantum decoherence and the appeal to work in the foundations of physics, which posits that the various isomers exist as a superposition until their wavefunctions are collapsed either by observation or by interacting with their environment. Hendry also alludes to a debate among chemists as to whether chemical bonds are real or not, in the sense of directional connections between two or more nuclei in any given molecule. I reject this view and propose that the structural and energetic views of chemical bonding, that have been discussed by some philosophers of chemistry including Hendry, do not refer to any essential ontological differences. I agree that chemists view bonding in a more realistic fashion and may consider bonds to be in some senses real, while physicists may consider bonding in more abstract energetic terms. However, I do not believe that such differences in scientific practice and attitudes should be considered to offer a window as to the ontological status of bonding or whether bonding is real. Finally, I discuss the kinetic energy school of chemical bonding which would seem to challenge any notion of bonds as directional entities, since bonding is no longer regarded as being primarily due to the build-up of electron density between nuclei.