Molecular graphics

Molecular graphics (MG) is the discipline and philosophy of studying molecules and their properties through graphical representation.IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. This article concentrates on the use of computers to create molecular graphics. Note, however, that many molecular graphics programs and systems have close coupling between the graphics and editing commands or calculations such as in molecular modelling.

There has been a long tradition of creating molecular models from physical materials. Perhaps the best known is Crick and Watson's model of DNA built from rods and planar sheets, but the most widely used approach is to represent all atoms and bonds explicitly using the "ball and stick" approach. This can demonstrate a wide range of properties, such as shape, relative size, and flexibility. Many chemistry courses expect that students will have access to ball and stick models. One goal of mainstream molecular graphics has been to represent the "ball and stick" model as realistically as possible and to couple this with calculations of molecular properties.

Figure 1 shows a small molecule (NH
3CH
2CH
2C(OH)(PO
3H)(PO
3H)-), as drawn by the Jmol program. It is important to realize that the colors and shapes are purely a convention, as individual atoms are not colored, nor do they have hard surfaces. Bonds between atoms are also not rod-shaped.

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