Chemistry Kit Model Organic
Chemistry Kit Model Organic
In chemistry, a molecular model is a geometric or topological representation of a molecule or of the arrangement of molecules in a solid substance, with the purpose of visualizing some of its properties, such as the nature and relative positions of its atoms, the chemical bonds between them, the three-dimensional shape of the molecule, and how its shape can change by bending or rotation of the bonds. The electronic structure of the atoms is usually omitted or represented in a highly simplified way.
There is a great variety of molecular models, including two-dimensional diagrams, physical artifacts, and three-dimensional computer models. The creation of such models is the discipline of molecular modelling, and their visual presentation is the topic of molecular graphics.
Overview
Physical models of molecules and other multi-atom assemblies 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 (e.g., the structure of DNA);
- as analogue computers (e.g., for measuring distances and angles in flexible systems);
- 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 modelling, and this article lists only the most common or historically important. The main strategies are:
- bespoke construction of a single model;
- use of common materials (plasticine, matchsticks) or children's toys (Tinkertoy(TM), Meccano, Lego, etc.);
- re-use of generic components in kits (ca. 1930s to present).
Models encompass a wide range of degrees of precision and engineering: some models such as J.D. Bernal's water are conceptual, while the macromodels of Pauling and Crick and Watson were created with much greater precision.
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 (e.g., conformational analysis and pseudorotation).
History
In the 1600s, Johannes Kepler speculated on the symmetry of snowflakes and also on the close packing of spherical objects such as fruit (this problem remained unsolved until very recently). 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 Loschmidt did not create physical models, his diagrams based on circles are two-dimensional analogues of later models.
Hofmann is credited with the first physical molecular model around 1860. The importance of the 3D geometry of molecules was not then recognised, so his models were still essentially topological.
J.H. van 't Hoff and J. 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.
Bernal built water molecule models with plasticine and spokes to illustrate the structure of liquid water.
In 1952, R. Corey, L. Pauling built accurate space-filling models of proteins and other biomolecules, where atoms were faceted hardwood spheres and bonds were realized by metallic pins held by screws.
They also produced less accurate models with plastic balls held together by snap fasteners. An improved version of their models wasdeveloped and patented by W. Koltun in 1965. Their assignment of colors to the four main elements of organic chemistry — black for carbon, red for oxygen, blue for nitrogen, etc. — became the basis for the coloring schemes used in modern chemical modeling software.
Francis Crick and James D. Watson built skeletal models of the DNA molecle using spikes, flat templates, and conectors with screws.
The use of computers for molecular modeling began around 1960.
Kinds of models
Models based on balls
Robert Hooke proposed a relationship between crystals and the packing of spheres . R. Haüy argued that the structures of crystals involved regular lattices of repeating units with shapes similar to the macroscopic crystal. Barlow, who jointly developed the theories of space groups, proposed models of crystals based on sphere packings ( ca. 1890).
Ball models are often used to depict the structure of crystalline solids. Such models became popular after the advent of X-ray crystallography, which normally reveals the positions of atoms but not the bonds between them. In these models, each ball usually represents an atom or monoatomic ion, but may also stand for a molecule or polyatomic ion. The size of each ball may be arbitrary, or proportional to the atomic or ionic radius. The balls may be large enough to touch or overlap their neighbors, or may be small enough to allow the entire model to be seen from the outside. Physical ball models are often constructed with polystyrene parts.
Such ball models may be used, for example, to illustrate the various crystallographic groups, or show why the difference in cation sizes results in different structured for sodium chloride (NaCl) and caesium chloride (CsCl)
An important class of ball models are the space-filling models developed by Corey and Pauling (1952) and perfected by Koltun (1965).
Models based on balls and sticks
In a ball-and-stick model, each atom is represented by a ball, and chemical (usually covalent) bonds are represented by rods. Each ball is drilled with multiple holes, placed so that the rods can match the atom's bonding patterns typically seen in chemical compounds. Thus, for example, a sphere representing a carbon atom will have at least four holes directed towards the vertices of a tetrahedron, separated by angles of about 109 degrees; and possibly more holes to allow for other bonding patterns, such as the flat trivalent pattern seen in graphite. The holes are sized and shaped so that they hold the rods firmly but allow rotation around single bonds (as may happen in real molecules). The rods are usually flexible, to allow for deviations from the nominal bond angles (as seen, for examle, in cyclopropene and cubane) and to imitate the flexibility of bonds in the real molecule. Double and triple bonds may be represented by two or three curved rods, which restrict rotation (as in real molecules), and allow the demonstration of phenomena such as cis/trans isomerism.
Ball-and-stick models clearly display the relative positions of the atoms and the chemical bonds between them. This type of model became popular with the advent of stereochemistry and is still widely used today. In earlier models, the atoms were represented by wooden balls, while the bonds could be wood sticks, metal rods, or metal springs. Today the balls are generally made of plastic, and the rods are either plastic or metal rods.
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.
Andre Dreiding introduced a molecular modelling kit (ca. 1975) 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 (such as Orbit) 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 (e.g. PO 4 tetrahedra, TiO 6 octahedra). Structures can be modelled by gluing together polyhedra made of paper or plastic.
Composite models
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