Abstract Chemistry occupies a distinctive explanatory position: quantum mechanics governs electronic behaviour, yet molecular structure is definite, stable, and causally efficacious. This paper argues that the apparent tension between quantum indeterminacy and chemical definiteness dissolves once molecular identity is understood as constraint localised at finite scale. Drawing on the Triaxial Existential Field (TEF) framework, the analysis reinterprets the potential energy surface as R-register constraint operating at molecular scale, molecular identity as C-locus persistence under that constraint, and chemical reactions as constraint reconfiguration rather than mere rearrangement of substance. The Born-Oppenheimer approximation is reinterpreted not as a substance distinction between classical nuclei and quantum electrons but as a register distinction between constraint and participation. Chirality is analysed as topological asymmetry in the constraint landscape, with homochirality identified as a candidate threshold condition for biological admissibility. The paper concludes that chemistry is the regime where constraint first localises at finite scale, providing the template for all subsequent levels of structural organisation and bridging the foundational physics treated elsewhere in the TEF programme with the biological domain addressed in a companion paper.
Abstract Chemistry occupies a distinctive explanatory position: quantum mechanics governs electronic behaviour, yet molecular structure is definite, stable, and causally efficacious. This paper argues that the apparent tension between quantum indeterminacy and chemical definiteness dissolves once molecular identity is understood as constraint localised at finite scale. Drawing on the Triaxial Existential Field (TEF) framework, the analysis reinterprets the potential energy surface as R-register constraint operating at molecular scale, molecular identity as C-locus persistence under that constraint, and chemical reactions as constraint reconfiguration rather than mere rearrangement of substance. The Born-Oppenheimer approximation is reinterpreted not as a substance distinction between classical nuclei and quantum electrons but as a register distinction between constraint and participation. Chirality is analysed as topological asymmetry in the constraint landscape, with homochirality identified as a candidate threshold condition for biological admissibility. The paper concludes that chemistry is the regime where constraint first localises at finite scale, providing the template for all subsequent levels of structural organisation and bridging the foundational physics treated elsewhere in the TEF programme with the biological domain addressed in a companion paper.
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.
Abstract The question of whether chemical structure is reducible to Everettian Quantum Mechanics (EQM) should be of interest to philosophers of chemistry and philosophers of physics alike. Among the three realist interpretations of quantum mechanics, EQM resolves the measurement problem by claiming that measurements (now interpreted as instances of decoherence) have indeterminate outcomes absolutely speaking, but determinate outcomes relative to emergent worlds—Maudlin (Topoi, 14:7-15, 1995). Philosophers who wish to be sensitive to the practice of quantum chemistry e.g. Scerri (The changing views of a philosopher of chemistry on the question of reduction, 2016) should be interested in EQM because Franklin and Seifert (J. Philos. Sci, 2020) claim that resolving the measurement problem also resolves the reducibility of chemical structure, and EQM is the interpretation which involves no mathematical structure beyond that used by practicing scientists. Philosophers interested in the quantum interpretation debate should be interested in the reducibility of chemistry because chemical structure is precisely the kind of determinate three-dimensional fact which EQM should be able to ground if it is to be empirically coherent—see Allori (Quantum Rep, 5:80-101, 2023). The prospects for reduction of chemical structure are poor if it cannot succeed in EQM; the prospects for EQM as a guide to ontology are poor if it cannot reduce chemical structure. Unfortunately for proponents of chemical reduction and EQM, there are three serious barriers to the reduction of chemistry to EQM. The first concern is that quantum treatments of chemical structure rely on the Born-Oppenheimer approximation, which holds nuclear locations fixed while minimizing the energy of the electronic configuration—Hendry (Philosophical Perspectives in Quantum Chemistry, 147-172, 2022), but this approximation is not licensed by EQM. The Born-Oppenheimer approximation relies on nuclei and molecular orbitals being simultaneously present, but in the three-dimensional ontology following from the Everett interpretation these only emerge at different energy scales and are not simultaneously present—Miller (Found. Chem, 25:405-417, 2023). The second concern is that the emergent worlds of EQM are supposed to be decoherent at the macro-scale—Wilson (The Nature of Contingency: Quantum Physics as Modal Realism 2020), but the recent development of superchemistry suggests that chemical reactions can occur in coherent states—Zhang et al. (Nat. Phys, 1-5, 2023). The third concern is that emergent worlds are only pragmatic pseudo-processes—Wallace (The Emergent Multiverse: Quantum Theory According to the Everett Interpretation, 2012b), but this means EQM trades realist physics for mere instrumentalism about chemistry. Absent a commitment to chemical realism, reduction is an empty promise. The prospects for reduction of chemical structure to EQM are therefore poor.
This paper provides a rigorous epistemological analysis of the boundaries between quantum chemistry and nuclear physics, focusing on the conceptual "isolation of the nucleus" from its chemical environment. It argues that the computational success of the Born–Oppenheimer approximation has inadvertently led to a rigid ontological commitment, treating the nucleus as effectively independent of surrounding chemical structures. Drawing upon Nancy Cartwright’s account of nomological machines, Quine's criterion of ontological commitment, and anti-reductionist philosophy of chemistry, the author affirms the relative autonomy of chemistry against physical imperialism. Through a historical re-reading of Ida Noddack’s 1934 intervention and the introduction of a novel thought experiment "Topological Nuclear Strain" (TNS) the paper demonstrates how mathematical approximations can morph into epistemological constraints. It challenges linear energy-scale assumptions by exploring how non-linear quantum tunneling could, in principle, be influenced by complex, asymmetric chemical articulation.
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.
Modern quantum chemistry is built on a conceptual picture of atoms and molecules developed over the past century, yet key elements of this picture especially the structure of the nucleus and the nature of the electron were never fully reconciled with the wave‑based formalism of quantum mechanics. The author’s previous work on quantum chemistry (https://doi.org/10.5281/zenodo.13336683) revisited these foundations, showing that many conceptual inconsistencies arise from treating electrons as particles rather than as extended wavefields. That reconstruction begins with the nucleus. Rather than a point charge orbited by discrete electrons, the nucleus defines a field environment in which the electron exists as an extended wave. Its spatial distribution, energy levels, and interactions follow from this field structure, not from the motion of a particle. This field‑centric view allows neutrality, shielding, and core–valence structure to be understood as continuous wave effects rather than as discrete electron “occupancy.” From this basis, the earlier work introduced a distinction between two operational modes of electronic behavior. In stable atomic and molecular settings, electrons appear as extended wave‑like configurations shaped by the surrounding nuclei; these determine bonding, structure, and charge distribution. The familiar particle‑like electron arises only during interaction events measurement, scattering, ionization, or chemical reaction when the extended wave becomes localized. These are not two kinds of electrons but two manifestations of the same quantum object. The original exposition presented this distinction clearly but without a formal mathematical framework. The insights were qualitative and chemically motivated, yet lacked the Hilbert‑space and field‑operator machinery needed to integrate them into mainstream quantum theory. The present paper provides the rigorous foundation that this conceptual distinction requires.
The accurate computational determination of chemical, materials, biological, and atmospheric properties has a critical impact on a wide range of health and environmental problems, but is deeply limited by the computational scaling of quantum mechanical methods. The complexity of quantum chemical studies arises from the steep algebraic scaling of electron correlation methods and the exponential scaling in studying nuclear dynamics and molecular flexibility. To date, efforts to apply quantum hardware to such quantum chemistry problems have focused primarily on electron correlation. Here, we provide a framework that allows for the solution of quantum chemical nuclear dynamics by mapping these to quantum spin-lattice simulators. Using the example case of a short-strong hydrogen-bonded system, we construct the Hamiltonian for the nuclear degrees of freedom on a single Born-Oppenheimer surface and show how it can be transformed to a generalized Ising model Hamiltonian. We then demonstrate a method to determine the local fields and spin-spin couplings needed to identically match the molecular and spin-lattice Hamiltonians. We describe a protocol to determine the on-site and intersite coupling parameters of this Ising Hamiltonian from the Born-Oppenheimer potential and nuclear kinetic energy operator. Our approach represents a paradigm shift in the methods used to study quantum nuclear dynamics, opening the possibility to solve both electronic structure and nuclear dynamics problems using quantum computing systems.