A molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an important role in understanding chemistry and generating and testing hypotheses. The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their graphical depiction is referred to as molecular graphics. The term, "molecular model" refer to systems that contain one or more explicit atoms (although solvent atoms may be represented implicitly) and where nuclear structure is neglected. The electronic structure is often also omitted unless it is necessary in illustrating the function of the molecule being modeled. Molecular models may be created for several reasons – as pedagogic tools for students or those unfamiliar with atomistic structures; as objects to generate or test theories (e.g., the structure of DNA); as analogue computers (e.g., for measuring distances and angles in flexible systems); or as aesthetically pleasing objects on the boundary of art and science. The construction of physical models is often a creative act, and many bespoke examples have been carefully created in the workshops of science departments. There is a very wide range of approaches to physical modeling, including ball-and-stick models available for purchase commercially, to molecular models created using 3D printers. The main strategy, initially in textbooks and research articles and more recently on computers. Molecular graphics has made the visualization of molecular models on computer hardware easier, more accessible, and inexpensive, although physical models are widely used to enhance the tactile and visual message being portrayed.
History In the 1600s, Johannes Kepler speculated on the symmetry of snowflakes and the close packing of spherical objects such as fruit. The symmetrical arrangement of closely packed spheres informed theories of molecular structure in the late 1800s, and many theories of crystallography and solid state inorganic structure used collections of equal and unequal spheres to simulate packing and predict structure. John Dalton represented compounds as aggregations of circular atoms, and although Johann Josef Loschmidt did not create physical models, his diagrams based on circles are two-dimensional analogues of later models.
August Wilhelm von Hofmann is credited with the first physical molecular model around 1860. The surviving model of methane is from his Friday Evening Discourse on 7th April 1865 at the Royal Institution, where he used croquet balls to illustrate different chemical structures: Thus we distinguish the chlorine atom as univalent, the atom of oxygen as bivalent, that of nitrogen as trivalent, and lastly the carbon atom as quadrivalent. - this I believe I can show you by a very simple contrivance. I will on this occasion, with your permission, select my illustration from that most delightful of games croquet. Let the croquet balls represent our atoms, and let us distinguish the atoms of different elements by different colours. The white balls are hydrogen, the green ones chlorine atoms; the atoms of fiery oxygen are red, those of nitrogen, blue; the carbons atoms, lastly, are naturally represented by black balls. But we have, in addition, to exhibit the different combining powers of these atoms. This we accomplish by screwing into the balls a number of metallic arms (tubes and pins), which correspond respectively to the combining powers of the atoms represented, and which, while constituting an additional feature of distinction, enable us at the same time to join the balls and to rear in this manner a kind of mechanical structures in imitation of the atomic edifices to be illustrated." Hofmann used this as a illustrative model, rather than a representation of reality: the sticks do not represent physical bonds, nor the actual molecule being planar. The importance of stereochemistry was not then recognised and the model is essentially topological (it should be a 3-dimensional tetrahedron). Jacobus Henricus van 't Hoff and Joseph Le Bel introduced the concept of chemistry in three dimensions of space, that is, stereochemistry. Van 't Hoff built tetrahedral molecules representing the three-dimensional properties of carbon.
Models based on spheres
Repeating units will help to show how easy it is and clear it is to represent molecules through balls that represent atoms. The binary compounds sodium chloride (NaCl) and caesium chloride (CsCl) have cubic structures but have different space groups. This can be rationalised in terms of close packing of spheres of different sizes. For example, NaCl can be described as close-packed chloride ions (in a face-centered cubic lattice) with sodium ions in the octahedral holes. After the development of X-ray crystallography as a tool for determining crystal structures, many laboratories built models based on spheres. With the development of plastic or polystyrene balls it is now easy to create such models.
Models based on ball-and-stick The concept of the chemical bond as a direct link between atoms can be modelled by linking balls (atoms) with sticks/rods (bonds). This has been extremely popular and is still widely used today. Initially atoms were made of spherical wooden balls with specially drilled holes for rods. Thus carbon can be represented as a sphere with four holes at the tetrahedral angles cos−1(−1⁄3) ≈ 109.47°. A problem with rigid bonds and holes is that systems with arbitrary angles could not be built. This can be overcome with flexible bonds, originally helical springs but now usually plastic. This also allows double and triple bonds to be approximated by multiple single bonds.
The model shown above represents a ball-and-stick model of proline. The balls have colours: black represents carbon (C); red, oxygen (O); blue, nitrogen (N); and white, hydrogen (H). Each ball is drilled with as many holes as its conventional valence (C: 4; N: 3; O: 2; H: 1) directed towards the vertices of a tetrahedron. Single bonds are represented by (fairly) rigid grey rods. Double and triple bonds use two longer flexible bonds which restrict rotation and support conventional cis/trans stereochemistry.
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