hopelessly complicated universe preventing chemists to ever discover the right tools
to give them solid insight in this universe? Interpretative methods urgently need to
make predictions that are falsifiable: one method is wrong and the other is right. Or
is asking for such binary resolution naïve? Or is calling for this binary clarity a step
towards doing better science? This chapter will give a few examples of interpretations disagreeing and thereby setting the scene for falsification.
2.2 The Topological Atom
Surely everyone can agree that there are atoms inside molecules, in the same way
that there are living cells inside an animal or a plant. Molecules are not novel
aggregates of electrons and nuclei but are rather constructions based on
pre-organised entities called atoms. Similarly, an animal is not a totally new form of
life but instead built from specialised cells that each represent pre-organised (more
elementary) matter such as proteins, lipids, carbohydrates and nucleotides. Several
energy production mechanisms inside a unicellular creature are the same as in the
cell of an animal. In a loosely similar vein, atoms largely retain their energy in
going from an isolated state in the gas phase to an existence inside a molecule. The
near-preservation of atoms is exactly what chemistry is about as a science: the study
of how atoms change when interacting with other atoms. Therefore it is important
that an atom inside a molecule is defined and calculated such that it does a good job
in not changing too much while going from the gas phase to the molecule. It is then
that one recovers a truly chemical atom rather than a physical atom. The chemist
recovers an atom that allows her, or more modernly him, to insulate how the atom
interacts with other atoms rather than being distracted by how that atom was built
from scratch (i.e. electrons and the nucleus). Only physics is interested in building
the atom from its constituents. Chemistry focuses on the small changes an atom
undergoes as it interacts with other atoms, small compared to the energy changes
involved in building an atom from electrons and a nucleus (all brought together
from infinity).
The question is now how to define an atom inside a molecular system and this is
where opinions differ, perhaps unfortunately. No experiment helps in settling the
contentious question of how to define an atom, and even if there was such an
experiment then the interpretation of its measured signal would probably be equally
contentious. Hence, it appears that an answer to a prime question of chemistry—
what is an atom in a molecule?—can only be tackled theoretically. An important
guide to value the theoretical proposals on what an atom inside a molecule actually
is, is the energetic transferability of that atom. In other words, how much does the
energy of a given atom change as it is transferred from one atomic environment to
another one? We will come back to energy transferability in Sect. 2.3.
In this section we focus on the molecular electron density and its shape. We seek
a theoretical proposal to define an atom inside a molecule, based on the internal
differences in the molecular density. In doing so, we avoid introducing a reference
2 On Quantum Chemical Topology
25
to give them solid insight in this universe? Interpretative methods urgently need to
make predictions that are falsifiable: one method is wrong and the other is right. Or
is asking for such binary resolution naïve? Or is calling for this binary clarity a step
towards doing better science? This chapter will give a few examples of interpretations disagreeing and thereby setting the scene for falsification.
2.2 The Topological Atom
Surely everyone can agree that there are atoms inside molecules, in the same way
that there are living cells inside an animal or a plant. Molecules are not novel
aggregates of electrons and nuclei but are rather constructions based on
pre-organised entities called atoms. Similarly, an animal is not a totally new form of
life but instead built from specialised cells that each represent pre-organised (more
elementary) matter such as proteins, lipids, carbohydrates and nucleotides. Several
energy production mechanisms inside a unicellular creature are the same as in the
cell of an animal. In a loosely similar vein, atoms largely retain their energy in
going from an isolated state in the gas phase to an existence inside a molecule. The
near-preservation of atoms is exactly what chemistry is about as a science: the study
of how atoms change when interacting with other atoms. Therefore it is important
that an atom inside a molecule is defined and calculated such that it does a good job
in not changing too much while going from the gas phase to the molecule. It is then
that one recovers a truly chemical atom rather than a physical atom. The chemist
recovers an atom that allows her, or more modernly him, to insulate how the atom
interacts with other atoms rather than being distracted by how that atom was built
from scratch (i.e. electrons and the nucleus). Only physics is interested in building
the atom from its constituents. Chemistry focuses on the small changes an atom
undergoes as it interacts with other atoms, small compared to the energy changes
involved in building an atom from electrons and a nucleus (all brought together
from infinity).
The question is now how to define an atom inside a molecular system and this is
where opinions differ, perhaps unfortunately. No experiment helps in settling the
contentious question of how to define an atom, and even if there was such an
experiment then the interpretation of its measured signal would probably be equally
contentious. Hence, it appears that an answer to a prime question of chemistry—
what is an atom in a molecule?—can only be tackled theoretically. An important
guide to value the theoretical proposals on what an atom inside a molecule actually
is, is the energetic transferability of that atom. In other words, how much does the
energy of a given atom change as it is transferred from one atomic environment to
another one? We will come back to energy transferability in Sect. 2.3.
In this section we focus on the molecular electron density and its shape. We seek
a theoretical proposal to define an atom inside a molecule, based on the internal
differences in the molecular density. In doing so, we avoid introducing a reference
2 On Quantum Chemical Topology
25