Molecular model

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.

Jacobus Henricus van 't Hoff and Joseph Le Bel introduced the concept of chemistry in three dimensions of space, that is, stereochemistry.

After the development of X-ray crystallography as a tool for determining crystal structures, many laboratories built models based on spheres.

Initially atoms were made of spherical wooden balls with specially drilled holes for rods.

The balls have colours: black represents carbon (C); red, oxygen (O); blue, nitrogen (N); and white, hydrogen (H).

However, most molecules require holes at other angles and specialist companies manufacture kits and bespoke models.

Arnold Beevers in Edinburgh created small models using PMMA balls and stainless steel rods.

Many of these atoms are directly moulded into the template, and fit together by pushing plastic stubs into small holes.

The plastic grips well and makes bonds difficult to rotate, so that arbitrary torsion angles can be set and retain their value.

The conformations of the backbone and side chains are determined by pre-computing the torsion angles and then adjusting the model with a protractor.

It has also recently become possible to create accurate molecular models inside glass blocks using a technique known as subsurface laser engraving.

The image at right shows the 3D structure of an E. coli protein (DNA polymerase beta-subunit, PDB code 1MMI) etched inside a block of glass by British company Luminorum Ltd. Computers can also model molecules mathematically.

Programs such as Avogadro can run on typical desktops and can predict bond lengths and angles, molecular polarity and charge distribution, and even quantum mechanical properties such as absorption and emission spectra.

For most practical purposes, such as drug design or protein folding, the calculations of a model require supercomputing or cannot be done on classical computers at all in a reasonable amount of time.