The Molecular Model

carbonClearly, we have left the discussion of the structure of the atom with some seemingly key questions unanswered. In part, these questions will require an introduction to quantum theory that was to develop after Bohr introduced his initial model in 1913. However, history shows that Bohr himself was to become a major contributor to quantum theory along with many others, i.e. deBroglie, Heisenberg, Schrodinger, Dirac, which led to what has become known, by the end of the 1930’s, as the `Copenhagen Interpretation'. However, this interpretation was not without its own ambiguities, which will also need to be considered, but for now, there is some advantage in progressing up the dimension scale towards the molecular and organic models.

As already suggested, the transition from alchemy to the science of molecular chemistry can be linked to the publication of Boyle’s work in 1661. However, it can also be argued that without any real understanding of the composition of the atomic elements, as suggested by the periodic table, the science of chemistry remained in its infancy until the late 19th century.  By this time, some 60 elements were known, but by the 1930’s, this number was converging towards the 92 elements that were known to exist in nature. However, in the light of subsequent developments in nuclear physics, science is now much more circumspect about the exact number of elements that can be created. Today, web sites such as WebElements list 118 elements, although some of these may only have transitory and somewhat artificial existence.

Atomic Shells

The aggregation of sub-atomic particles into specific elements and their subsequent combination into molecules continues the transition from the sub-atomic universe. Within this process, the ambiguity of matter particles solidifies, literally, first into molecular particles and finally into tangible objects visible in the human domain. Therefore, even some basic insight of this transition process may be useful to the general understanding of the structure of matter. Traditionally, chemistry defines the atom as the smallest particle that can take part in a chemical reaction, but recognises that the key to understanding these reactions lies within its sub-atomic structure. In this context, our initial starting point was Bohr’s model, as it provides a frame of reference in which to introduce some of the basic ideas that ultimately signalled the transition from the classical particle model to the quantum wave model. However, the diagram above reflects the more classical idea of fundamental particles to describe the basic make-up of a carbon atom, i.e. a central nucleus of 6 positively charged protons and 6 neutrons being 'orbited' by negatively charged electrons. Classically, the electron orbits were assigned to shells K, L, M, N, O, P and Q, although subsequently referenced by numbers, i.e. 1, 2, 3, 4, 5, 6 and 7. In addition, each shell can have a number of sub-shells, denoted as s, p, d and f, but now also referenced numerically.

One of the main issues with the Bohr model is that it continues to suggest that the electron exists as a distinct particle with a definite radius and velocity, whereas it is possibly more accurate, but not necessarily absolutely correct, to described the nucleus of an atom as surrounded by a `cloud of electrons`. Within quantum theory, this cloud is organised into separate probability distributions, each of which can contain up to two electrons. These probability distributions are still referred to as orbitals, which broadly align to the concept of shells and sub-shells. The orbitals are grouped into sets by their symmetry and there are 4 known sets of orbitals, which are called s, p, d, and f. The number of orbitals increases for each type, so while there is only one `s` orbital per shell, there is seven `f` orbitals. Each orbital holds 2 electrons.

s orbital 1 per shell sharp
p orbital 3 per shell principal
d orbital 5 per shell diffuse
f orbital 7 per shell fundamental

The letters come from names given to the appearance of spectral lines from the orbitals. There are shells of orbitals that increase in energy at the higher shells. Shell 1 only contains an `s` orbital and each shell adds to  the next orbital type, so shell 2 has `s` and `p` orbitals etc. The energies of the shells overlap so that eventually the 4s shell has a lower energy than the 3d shell. The actual filling is shown below.

1s       2 electrons 2 total
2s     2p 8 electrons 10 total
3s     3p 8 electrons 18 total
4s   3d 4p 18 electrons 36 total
5s   4d 5p 18 electrons 54 total
6s 4f 5d 6p 32 electrons 86 total
7s 5f 6d 7p 32 electrons 118 total

This filling order, while generally correct, does have slight irregularities due to the closeness (energy-wise) of certain orbital groups during partial filling.  At this point, it is worth just mentioning the `Aufbau Principle` that describes the rules for filling orbitals:

  • Lower-energy orbitals fill first.
  • An orbital can hold only 2 electrons with opposite spins in-line with the Pauli Exclusion Principle.
  • If there are 2 or more degenerate orbitals, i.e. have the same energy level, 1 electron goes in each, until all are half-full. This is also known as Hund's Rule.

Theoretically, electrons in the same shell possess the same energy, but this is not really true for multi-electron atoms due to a process called shielding. Shielding results from repulsion of electrons either in the same shell or inner shell. While we have barely begun to scratch the surface of this model, it is clear that the visual aspect of this model is quickly losing its value.

The Periodic Table

However, in terms of chemistry, it is the ability of the outer electrons to interact with other atomic structures that determines the general properties of an element. In this context, the shells and orbitals can be used to explain the order of the elements and the size of the various rows in the periodic table.


The name 'periodic table' became about as it was recognised that many properties of the elements are periodic functions of their atomic number, i.e. the number of protons within the element's atomic nucleus. Therefore, the periodic table is an arrangement of the chemical elements, ordered by atomic number in columns or groups against rows so as to emphasize their periodic properties. Again, there are already many websites that explain the detailed classification of the elements.

Chemical Bonding

As indicated, a chemical bond between atoms is typically based on an interaction of the outer electrons of the respective elements. Within the context of this general introduction, we shall describe two basic types of bonds:  Ionic & Covalent.

  • Ionic Bonds
    These bonds arise when elements with almost empty outer shells react with elements with near full outer shells. Typically, within this type of bonding, one atom loses an electron, while another gains an electron and therefore the charge neutrality of the original atoms is converted to either a negative or positive ion. Thus the new compound is bonded via charge attraction, although the new molecules, as a whole, can still remain charge neutral. Table salt, i.e. sodium chloride, is a good example, where sodium gives up its one outer shell electron to chlorine, which needs only one electron to fill its shell.

  • Covalent Bonds
    These bonds involve a sharing of electrons and occur between atoms that have partially filled outer shells. A diamond is a well-known example of a molecular structure, which involves a network of covalent bonds between carbon atoms.

So, it is through such processes, that sub-atomic structures combine to form molecules, which eventually aids the transition from the quantum world into the `touch and see` world of humanity. So, to summarise:

  • An atom is the smallest particle that can take part in a chemical reaction.
  • Chemistry requires energy to create interaction between atoms.
  • Too much energy, i.e. as in stars, tears apart molecular bonds.
  • Too little energy, i.e. near zero temperature of space, prevents interaction.

As such, planets may provide an important, and possibly unique, environment for molecular chemistry to take place, which is a prerequisite of organic chemistry, which is the topic of the next page.