Molecular model
A molecular model, in this article, is a physical model that represents molecules and their processes. The creation of mathematical models of molecular properties and behaviour is molecular modelling, and their graphical depiction is molecular graphics, but these topics are closely linked and each uses techniques from the others. In this article, "molecular model" will primarily refer to systems containing more than one atom and where nuclear structure is neglected. The electronic structure is often also omitted or represented in a highly sophisticated way.
Overview
Physical models of atomistic systems have played an important role in understanding chemistry and generating and testing hypotheses. Most commonly there is an explicit representation of atoms, though other approaches such as soap films and other continuous media have been useful. There are several motivations for creating physical models:- as pedagogic tools for students or those unfamiliar with atomistic structures;
- as objects to generate or test theories ;
- as analogue computers ;
- as aesthetically pleasing objects on the boundary of art and science.
- bespoke construction of a single model;
- use of common materials or children's toys ;
- re-use of generic components in kits.
Molecular models have inspired molecular graphics, initially in textbooks and research articles and more recently on computers. Molecular graphics has replaced some functions of physical molecular models, but physical kits continue to be very popular and are sold in large numbers. Their unique strengths include:
- cheapness and portability;
- immediate tactile and visual messages;
- easy interactivity for many processes.
History
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. Note how the size of the carbon appears smaller than the hydrogen. The importance of stereochemistry was not then recognised and the model is essentially topological.
Jacobus Henricus van 't Hoff and Joseph Le Bel introduced the concept of chemistry in space—stereochemistry in three dimensions. 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.lattice, showing close-packed spheres representing a face-centered cubic AB lattice similar to that of NaCl and most other alkali halides. In this model the spheres are equal sizes whereas more "realistic" models would have different radii for cations and anions.
The binary compounds sodium chloride and caesium chloride 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 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 with sticks/rods. 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 ≈ 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.
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Figure 3 represents a ball-and-stick model of proline. The balls have colours: black represents carbon ; red, oxygen ; blue, nitrogen ; and white, hydrogen. Each ball is drilled with as many holes as its conventional valence directed towards the vertices of a tetrahedron. Single bonds are represented by rigid grey rods. Double and triple bonds use two longer flexible bonds which restrict rotation and support conventional cis/trans stereochemistry.
made with acrylic balls and stainless steel rods by Miramodus Ltd..
However, most molecules require holes at other angles and specialist companies manufacture kits and bespoke models. Besides tetrahedral, trigonal and octahedral holes, there were all-purpose balls with 24 holes. These models allowed rotation about the single rod bonds, which could be both an advantage and a disadvantage. The approximate scale was 5 cm per ångström, but was not consistent over all elements.
Arnold Beevers in Edinburgh created small models using PMMA balls and stainless steel rods. By using individually drilled balls with precise bond angles and bond lengths in these models, large crystal structures to be accurately created, but with light and rigid form. Figure 4 shows a unit cell of ruby in this style.
Skeletal models
Crick and Watson's DNA model and the protein-building kits of Kendrew were among the first skeletal models. These were based on atomic components where the valences were represented by rods; the atoms were points at the intersections. Bonds were created by linking components with tubular connectors with locking screws.André Dreiding introduced a molecular modelling kit in the late 1950s which dispensed with the connectors. A given atom would have solid and hollow valence spikes. The solid rods clicked into the tubes forming a bond, usually with free rotation. These were and are very widely used in organic chemistry departments and were made so accurately that interatomic measurements could be made by ruler.
More recently, inexpensive plastic models use a similar principle. A small plastic sphere has protuberances onto which plastic tubes can be fitted. The flexibility of the plastic means that distorted geometries can be made.
Polyhedral models
Many inorganic solids consist of atoms surrounded by a coordination sphere of electronegative atoms. Structures can be modelled by gluing together polyhedra made of paper or plastic.Composite models
A good example of composite models is the Nicholson approach, widely used from the late 1970s for building models of biological macromolecules. The components are primarily amino acids and nucleic acids with preformed residues representing groups of atoms. 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.The plastic is white and can be painted to distinguish between O and N atoms. Hydrogen atoms are normally implicit and modelled by snipping off the spokes. A model of a typical protein with approximately 300 residues could take a month to build. It was common for laboratories to build a model for each protein solved. By 2005, so many protein structures were being determined that relatively few models were made.
Computer-based models
With the development of computer-based physical modelling, it is now possible to create complete single-piece models by feeding the coordinates of a surface into the computer. Figure 6 shows models of anthrax toxin, left and green fluorescent protein, right from 3D Molecular Design. Models are made of plaster or starch, using a rapid prototyping process.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 etched inside a block of glass by British company Luminorum Ltd.
Common colors
Some of the most common colors used in molecular models are as follows:Chronology
This table is an incomplete chronology of events where physical molecular models provided major scientific insights.| Developer | Date | Technology | Comments |
| Johannes Kepler | c. 1600 | sphere packing, symmetry of snowflakes. | |
| Johann Josef Loschmidt | 1861 | 2-D graphics | representation of atoms and bonds by touching circles |
| August Wilhelm von Hofmann | 1860 | ball-and-stick | first recognisable physical molecular model |
| Jacobus Henricus van 't Hoff | 1874 | paper? | representation of atoms as tetrahedra supported the development of stereochemistry |
| John Desmond Bernal | c. 1930 | Plasticine and spokes | model of liquid water |
| Robert Corey, Linus Pauling, Walter Koltun | 1951 | Space-filling models of alpha-helix, etc. | Pauling's "Nature of the Chemical Bond" covered all aspects of molecular structure and influenced many aspects of models |
| Francis Crick and James D. Watson | 1953 | spikes, flat templates and connectors with screws | model of DNA |
| Molecular graphics | c. 1960 | display on computer screens | complements rather than replaces physical models |