It is important to be clear what the system is. Most of chemistry is not really about isolated molecules. A significant amount of chemistry occurs in an environment, often within a solvent. Then the system is the chemicals of interest and the solvent. For example, when it is stated that HCl is an acid, this is not a reference to isolated HCl molecules but a solution of HCl in water, and then the HCl dissociates into H+ and Cl- ions. Chemical properties such as reactivity can change significantly depending on whether a compound is in the solid, liquid, or gas state, or on the properties of the solvent in which it is dissolved.
Scales
The time scales for processes, which range from molecular vibrations to chemical reactions, can vary from femtoseconds to days. Relevant energy scales, corresponding to different effective interactions, can vary from tens of eV (strong covalent bonds) to microwave energies of 0.1 meV (quantum tunnelling in an ammonia maser).
Other scales are the total number of atoms in a compound, which can range from two to millions, the total number of electrons, and the number of different chemical elements in the compound. As the number of atoms and electrons increases, so does the dimensionality of the Hilbert space of the corresponding quantum system.
Novelty
All chemical compounds are composed of a discrete number of atoms, usually of different type. For example, acetic acid, denoted CH3COOH, is composed of carbon, oxygen, and hydrogen atoms. The compound usually has chemical and physical properties that the individual atoms do not have.
Chemistry is all about transformation. Reactants combine to produce products, e.g. A + B -> C. C may have chemical or physical properties that A and B did not have.
Chemistry involves concepts that do not appear in physics. Roald Hoffmann argued that concepts such as acidity and basicity, aromaticity, functional groups, and substituent effects have great utility and are lost in a reductionist perspective that tries to define them precisely and mathematicise them.
Diversity
Chemistry is a wonderland of diversity, as it arranges chemical elements in a multitude of different ways that produce a plethora of phenomena. Much of organic chemistry just involves three different atoms: carbon, oxygen, and hydrogen.
Molecular structure
Simple molecules (such as water, ammonia, carbon dioxide, methane, benzene) have a unique structure defined by fixed bond lengths and angles. In other words, there is a well-defined geometric structure that gives the locations of the centres of atomic nuclei. This is a classical entity. This emerges from the interactions between the electrons and nuclei of the constituent atoms.
In philosophical discussions of emergence in chemistry, molecular structure has received significant attention. Some claim it provides evidence of strong emergence. The arguments centre around the fact that the molecular structure is a classical entity and concept that is imposed, whereas a logically self-consistent approach would treat both electrons and nuclei quantum mechanically.
The molecular structure of ammonia (NH3) illustrates the issue. It has an umbrella structure which can be inverted. Classically, there are two possible degenerate structures. For an isolated molecule, quantum tunnelling back and forth between the two structures can occur. The ground state is a quantum superposition of two molecular structures. This tunnelling does occur in a dilute gas of ammonia at low temperature, and the associated quantum transition is the basis of the maser, the forerunner of the laser. This example of ammonia was discussed by Anderson at the beginning of his seminal More is Different article to illustrate how symmetry breaking leads to well-defined molecular structures in large molecules.
Born-Oppenheimer approximation
Without this concept, much of theoretical chemistry and condensed matter would be incredibly difficult. It is based on the separation of time and energy scales associated with electronic and nuclear motion. It is used to describe and understand the dynamics of nuclei and electronic transitions in solids and molecules. The potential energy surfaces for different electronic states define effective theory for the nuclei. Without this concept, much of theoretical chemistry and condensed matter would be incredibly difficult.
Singularity. The Born-Oppenheimer approximation is justified by an asymptotic expansion in powers of (m/M)^1/4, where m is the mass of an electron and M the mass of an atomic nucleus in the molecule. This has been discussed by Primas and Bishop.
The rotational and vibrational degrees of freedom of molecules also involve a separation of time and energy scales. Consequently, one can derive separate effective Hamiltonians for the vibrational and rotational degrees of freedom.
Qualitative difference with increase in molecular size
Consider the following series with varying chemical properties: formic acid (CH2O2), acetic acid (C2H4O2), propionic acid (C3H6O2), butyric acid (C4H8O2), and valerianic acid (C5H10O2), whose members involve the successive addition of a CH2 radical. The Marxist Friedrich Engels used these examples as evidence for Hegel’s law: “The law of transformation of quantity into quality and vice versa”.
In 1961, Platt discussed properties of large molecules that “might not have been anticipated” from properties of their chemical subgroups. Table 1 in Platt’s paper lists “Properties of molecules in the 5- to 50-range that have no counterpart in diatomics and many triatomics.” Table 2 lists “Properties of molecules in the 50- to 500-atom range and up that go beyond the properties of their chemical sub-groups.” The properties listed included internal conversion (i.e., non-radiative decay of excited electronic states), formation of micelles for hydrocarbon chains with more than ten carbons, the helix-coil transition in polymers, chromatographic or molecular sorting properties of polyelectrolytes such as those in ion-exchange resins, and the contractility of long chains.
Platt also discussed the problem of molecular self-replication. Until 1951, it was assumed that a machine could not reproduce itself,f and this was the fundamental difference between machines and living systems. However, von Neumann showed that a machine with a sufficient number of parts and a sufficiently long list of instructions can reproduce itself. Platt pointed out that this suggested there is a threshold for autocatalysis: “this threshold marks an essentially discontinuous change in properties, and that fully-complex molecules larger than this size differ from all smaller ones in a property of central importance for biology.” Thus, self-replication is an emergent property. A modification of this idea has been pursued by Stuart Kauffman with regard to the origin of life, that when a network of chemical reactions is sufficiently large, it becomes self-replicating.
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