Quantum physics is the foundation for chemistry, but the concept of chemical bonding is not easily reconciled with quantum mechanical models of molecular systems. The quantum theory of atoms in molecules, developed by Richard F.W. Bader and colleagues, seeks to define bonding using a topological analysis of the electron density distribution. The “bond paths” identified by the analysis are posited as indicators of a special pairwise physical relationship between atoms. While elements of the theory remain subject to debate, I argue (...) that QTAIM embodies a distinctive interactive conception of bonding that is an attractive alternative to others previously discussed. (shrink)

In this paper I briefly reply to Shant Shahbazian’s comments on my paper “Austere quantum mechanics as a reductive basis for chemistry” and argue that quantum theory of atoms in molecules can be characterised as a research programme in the theories of chemistry. I also explore the areas in which Shahbazian and me agree and disagree.

Recently, the author of this paper and his research team have extended the orthodox quantum theory of atoms in molecules (QTAIM) to a novel paradigm called the two-component QTAIM (TC-QTAIM). This extended framework enables one to incorporate nuclear dynamics into the AIM analysis as well as performing AIM analysis of the exotic species; positronic and muonic species are a few examples. In present paper, this framework has been reviewed, providing some computational examples with particular emphasis on origins (...) and applications, in a non-technical language. The main questions, enigmas and basic ideas that finally yielded the TC-QTAIM are considered in chronological order to help the reader comprehend the intuition behind the math. Finally, it is demonstrated that the TC-QTAIM and its more refined versions are able to tackle problems inaccessible to the orthodox QTAIM. (shrink)

It is with great delight that I have accepted the unexpected invitation to edit this two part special issue of Foundations of Chemistry dedicated to the philosophical aspects and implications of the quantum theory of atoms in molecules (QTAIM) (Bader 1990). This theory has been primarily the oeuvre of Richard F. W. Bader (1931–2012), one of his most significant (but not the only significant) contributions to chemistry. Bader’s contributions have been summarized in a tribute (Matta et al. 2011) that (...) appeared in a recent Festschrift of The Journal of Physical Chemistry A (2011). This special issue of Foundations is neither a duplication, a complement, or an afterthought to that Festchrift, nor is it intended as another tribute to this great scientist, as deserving as he may be, instead it serves an entirely different purpose. This issue is focused principally on the epistemology and ontology of the science of QTAIM. The sort of questions that are addressed in, or that should emerge from. (shrink)

This treatise presents thoughts on the divide that exists in chemistry between those who seek their understanding within a universe wherein the laws of physics apply and those who prefer alternative universes wherein the laws are suspended or ‘bent’ to suit preconceived ideas. The former approach is embodied in the quantum theory of atoms in molecules (QTAIM), a theory based upon the properties of a system’s observable distribution of charge. Science is experimental observation followed by appeal to theory that, (...) upon occasion, leads to new experiments. This is the path that led to the development of the molecular structure hypothesis—that a molecule is a collection atoms with characteristic properties linked by a network of bonds that impart a structure—a concept forged in the crucible of nineteenth century experimental chemistry. One hundred and fifty years of experimental chemistry underlie the realization that the properties of some total system are the sum of its atomic contributions. The concept of a functional group, consisting of a single atom or a linked set of atoms, with characteristic additive properties forms the cornerstone of chemical thinking of both molecules and crystals and Dalton’s atomic hypothesis has emerged as the operational theory of chemistry. We recognize the presence of a functional group in a given system and predict its effect upon the static, reactive and spectroscopic properties of the system in terms of the characteristic properties assigned to that group. QTAM gives physical substance to the concept of a functional group. (shrink)

The quantum theory of atoms in molecules (QTAIM) uses physics to define an atom and its contribution to observable properties in a given system. It does so using the electron density and its flow in a magnetic field, the current density. These are the two fields that Schrödinger said should be used to explain and understand the properties of matter. It is the purpose of this paper to show how QTAIM bridges the conceptual gulf that separates the observations (...) of chemistry from the realm of physics and do so in a manner that is both rigorous and conceptually simple. Since QTAIM employs real measurable fields, it enables one to present the findings of complex quantum mechanical calculations in a pictorial manner that isolates the essential physics. The time has arrived for a sea change in our attempts to predict and classify the observations of chemistry, time to replace the use of simplified and arbitrary models with the full predictive power of physics, as applied to an atom in a molecule. (shrink)

By moving away from the traditional reductionist reading of the quantum theory of atoms in molecules, in this paper we analyze the role played by QTAIM in the relationship between molecular chemistry and quantum mechanics from an emergentist perspective. In particular, we show that such a relationship involves two steps: an intra-domain emergence and an inter-domain emergence. Intra-domain emergence, internal to quantum mechanics, results from the fact that the electron density, from which all the other QTAIM’s concepts are (...) defined, arises from the wavefunction as a coarse-grained magnitude. Inter-domain emergence involves an analogical link, a mapping, between QTAIM’s entities, such as topological atoms and bond paths, and the entities that populate the molecular-chemistry domain, such as chemical atoms and chemical bonds. (shrink)

In this pedagogical communication after demonstrating the legitimacy for using the quantum theory of atoms in molecules (QTAIM) to non-Coulombic systems, Hookean H2 +/H3 2+ species are used for AIM analysis. In these systems, in contrast to their Coulombic counterparts, electron density is atom-like and instead of expected two/three topological atoms, just a single topological atom emerges. This observation is used to demonstrate that what is really “seen” by the topological analysis of electron densities is the clustering of electrons. (...) The very trait of monotonic decay of electron density around the “centers” of clustering guarantees the appearance of topological atoms as basin of attraction of the gradient vector field of the electron density. Although observations with Hookean molecules may seem disappointing at first glance, a careful reasoning points to the fact that the QTAIM methodology is extendable to novel domains, by a knowledge of the morphology of underlying densities, beyond the typical Coulombic systems. (shrink)

This paper analyses Richard Bader’s ‘operational’ view of quantum mechanics and the role it plays in the the explanation of chemistry. I argue that QTAIM can partially be reconstructed as an ‘austere’ form of quantum mechanics, which is in turn committed to an eliminative concept of reduction that stems from Kemeny and Oppenheim. As a reductive theory in this sense, the theory fails. I conclude that QTAIM has both a regulatory and constructive function in the theories of chemistry.

A novel non-classical mereological concept built up by blending the Metaphysics of Xavier Zubiri and the Quantum Theory of Atoms in Molecules of R. F. W. Bader is proposed. It is argued that this philosophical concept is necessary to properly account for what happens in a chemical reaction. From the topology of the gradient of the laplacian of the electronic charge density, \\) within the QTAIM framework, different “atomic graphs” are found for each atom depending on the molecular context, (...) reflecting how the whole molecule affects each atom. In this way, the whole molecular system imposes certain geometry onto each atom, and every atom exhibits different ontological modality. On the Metaphysical side, for X. Zubiri real things are system of different notes. The physical essence is the subsystem of essential notes with a coherence unity. Every note is grounded on the essence. The unity of the system is present somehow in every note-of beforehand, and every essential note-of turns towards the other. The essence determines the position of each note within the system, and hence is the grounding for modality of the notes. By conflating both “theories” and taking the atoms as essential notes, we propose the concept of “Molecule in atoms-of” or “atoms-of in Molecules”. Within the course of a chemical reaction the atoms-of modified their “of” as required by the new molecular unity being formed, and eventually change their modality. The validity to the Zubiri’s statements, is attained by evaluating necessity and possibility in a set-up of finite accessible “possible worlds”. (shrink)

The problem of the reduction of chemistry to physics has been traditionally addressed in terms of classical structural chemistry and standard quantum mechanics. In this work, we will study the problem from the perspective of the Quantum Theory of Atoms in Molecules, proposed by Richard Bader in the nineties. The purpose of this article is to unveil the role of QTAIM in the inter-theoretical relations between chemistry and physics. We argue that, although the QTAIM solves two relevant obstacles (...) to reduction by providing a rigorous definition of chemical bond and of atoms in a molecule, it appeals to concepts that are unacceptable in the quantum–mechanical context. Therefore, the QTAIM fails to provide the desired reduction. On the other hand, we will show that the QTAIM is more similar to Bohmian mechanics and that the basic elements of both theories are closely related. (shrink)