A molecular model is a
physical model
A model is an informative representation of an object, person or system. The term originally denoted the plans of a building in late 16th-century English, and derived via French and Italian ultimately from Latin ''modulus'', a measure.
Models c ...
of an atomistic system that represents
molecules
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bio ...
and their processes. They play an important role in understanding
chemistry
Chemistry is the scientific study of the properties and behavior of matter. It is a natural science that covers the elements that make up matter to the compounds made of atoms, molecules and ions: their composition, structure, proper ...
and generating and testing
hypotheses
A hypothesis (plural hypotheses) is a proposed explanation for a phenomenon. For a hypothesis to be a scientific hypothesis, the scientific method requires that one can test it. Scientists generally base scientific hypotheses on previous obse ...
. 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
atom
Every atom is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Only the most common variety of hydrogen has no neutrons.
Every solid, liquid, gas, a ...
s (although
solvent
A solvent (s) (from the Latin '' solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for ...
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
The word ''bespoke'' () has evolved from a verb meaning 'to speak for something', to its contemporary usage as an adjective. Originally, the adjective ''bespoke'' described tailor-made suits and shoes. Later, it described anything commissioned t ...
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 model
In chemistry, the ball-and-stick model is a molecular model of a chemical substance which displays both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by rods ...
s 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
Johannes Kepler (; ; 27 December 1571 – 15 November 1630) was a German astronomer, mathematician, astrologer, natural philosopher and writer on music. He is a key figure in the 17th-century Scientific Revolution, best known for his laws ...
speculated on the
symmetry
Symmetry (from grc, συμμετρία "agreement in dimensions, due proportion, arrangement") in everyday language refers to a sense of harmonious and beautiful proportion and balance. In mathematics, "symmetry" has a more precise definiti ...
of
snowflake
A snowflake is a single ice crystal that has achieved a sufficient size, and may have amalgamated with others, which falls through the Earth's atmosphere as snow.Knight, C.; Knight, N. (1973). Snow crystals. Scientific American, vol. 228, no. ...
s 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
Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics ( condensed matter physics). The wor ...
and
solid state inorganic structure used collections of equal and unequal spheres to simulate packing and predict structure.
John Dalton
John Dalton (; 5 or 6 September 1766 – 27 July 1844) was an English chemist, physicist and meteorologist. He is best known for introducing the atomic theory into chemistry, and for his research into Color blindness, colour blindness, which ...
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
August Wilhelm von Hofmann (8 April 18185 May 1892) was a German chemist who made considerable contributions to organic chemistry. His research on aniline helped lay the basis of the aniline-dye industry, and his research on coal tar laid the g ...
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
Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation. The study of stereochemistry focuses on the relationships between stereoi ...
was not then recognised and the model is essentially topological (it should be a 3-dimensional
tetrahedron
In geometry, a tetrahedron (plural: tetrahedra or tetrahedrons), also known as a triangular pyramid, is a polyhedron composed of four triangular faces, six straight edges, and four vertex corners. The tetrahedron is the simplest of all ...
).
Jacobus Henricus van 't Hoff and
Joseph Le Bel
Joseph Achille Le Bel (21 January 1847 in Pechelbronn – 6 August 1930, in Paris, France) was a French chemist. He is best known for his work in stereochemistry. Le Bel was educated at the École Polytechnique in Paris. In 1874 he announced his ...
introduced the concept of chemistry in space—stereochemistry in three dimensions. van 't Hoff built
tetrahedral molecules representing the three-dimensional properties of
carbon
Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon ma ...
.
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
Sodium chloride , commonly known as salt (although sea salt also contains other chemical salts), is an ionic compound with the chemical formula NaCl, representing a 1:1 ratio of sodium and chloride ions. With molar masses of 22.99 and 35. ...
(NaCl) and
caesium chloride
Caesium chloride or cesium chloride is the inorganic compound with the formula Cs Cl. This colorless salt is an important source of caesium ions in a variety of niche applications. Its crystal structure forms a major structural type where each ca ...
(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
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
as a tool for determining crystal structures, many laboratories built models based on spheres. With the development of plastic or
polystyrene
Polystyrene (PS) is a synthetic polymer made from monomers of the Aromatic hydrocarbon, aromatic hydrocarbon styrene. Polystyrene can be solid or foamed. General-purpose polystyrene is clear, hard, and brittle. It is an inexpensive resin pe ...
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
Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon ma ...
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.
The model shown to the left represents a
ball-and-stick model
In chemistry, the ball-and-stick model is a molecular model of a chemical substance which displays both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by rods ...
of
proline
Proline (symbol Pro or P) is an organic acid classed as a proteinogenic amino acid (used in the biosynthesis of proteins), although it does not contain the amino group but is rather a secondary amine. The secondary amine nitrogen is in the p ...
. The balls have colours: black represents
carbon
Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon ma ...
(C);
red,
oxygen
Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements ...
(O);
blue,
nitrogen
Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
(N); and white,
hydrogen
Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-to ...
(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
Trans- is a Latin prefix meaning "across", "beyond", or "on the other side of".
Used alone, trans may refer to:
Arts, entertainment, and media
* Trans (festival), a former festival in Belfast, Northern Ireland, United Kingdom
* ''Trans'' (fil ...
stereochemistry.
However, most molecules require holes at other angles and specialist companies manufacture kits and bespoke models. Besides tetrahedral,
trigonal
In crystallography, the hexagonal crystal family is one of the six crystal families, which includes two crystal systems (hexagonal and trigonal) and two lattice systems (hexagonal and rhombohedral). While commonly confused, the trigonal crystal ...
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 (showing molecular flexibility) and a disadvantage (models are floppy). The approximate scale was 5 cm per
ångström
The angstromEntry "angstrom" in the Oxford online dictionary. Retrieved on 2019-03-02 from https://en.oxforddictionaries.com/definition/angstrom.Entry "angstrom" in the Merriam-Webster online dictionary. Retrieved on 2019-03-02 from https://www.m ...
(0.5 m/nm or 500,000,000:1), but was not consistent over all elements.
Arnold Beevers in
Edinburgh
Edinburgh ( ; gd, Dùn Èideann ) is the capital city of Scotland and one of its 32 Council areas of Scotland, council areas. Historically part of the county of Midlothian (interchangeably Edinburghshire before 1921), it is located in Lothian ...
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
A ruby is a pinkish red to blood-red colored gemstone, a variety of the mineral corundum ( aluminium oxide). Ruby is one of the most popular traditional jewelry gems and is very durable. Other varieties of gem-quality corundum are called ...
in this style.
Skeletal models
Crick and Watson's
DNA model and the
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
-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
André S. Dreiding (22 June 1919 in Zürich – 24 December 2013 in Herrliberg near Zurich) was a Swiss chemist.40 years, many researchers and departments still maintain and use their collections. In order to ease the general supply problem for ...
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 (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
In chemistry, an inorganic compound is typically a chemical compound that lacks carbon–hydrogen bonds, that is, a compound that is not an organic compound. The study of inorganic compounds is a subfield of chemistry known as ''inorganic chemist ...
solids consist of atoms surrounded by a
coordination sphere of
electronegative
Electronegativity, symbolized as , is the tendency for an atom of a given chemical element to attract shared electrons (or electron density) when forming a chemical bond. An atom's electronegativity is affected by both its atomic number and the ...
atoms (e.g. PO
4 tetrahedra, TiO
6 octahedra). 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
macromolecule
A macromolecule is a very large molecule important to biophysical processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The ...
s. The components are primarily
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...
s and
nucleic acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main ...
s 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 chain
In organic chemistry and biochemistry, a side chain is a chemical group that is attached to a core part of the molecule called the "main chain" or backbone. The side chain is a hydrocarbon branching element of a molecule that is attached to a ...
s are determined by pre-computing the torsion angles and then adjusting the model with a
protractor
A protractor is a measuring instrument, typically made of transparent plastic or glass, for measuring angles.
Some protractors are simple half-discs or full circles. More advanced protractors, such as the bevel protractor, have one or two sw ...
.
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
Anthrax is an infection caused by the bacterium '' Bacillus anthracis''. It can occur in four forms: skin, lungs, intestinal, and injection. Symptom onset occurs between one day and more than two months after the infection is contracted. The s ...
toxin, left (at a scale of approximately 20 Å/cm or 1:5,000,000) and
green fluorescent protein
The green fluorescent protein (GFP) is a protein that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish '' Aequore ...
, right (5 cm high, at a scale of about 4 Å/cm or 1:25,000,000) 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
Laser engraving is the practice of using lasers to engrave an object. Laser marking, on the other hand, is a broader category of methods to leave marks on an object, which in some cases, also includes color change due to chemical/molecular alt ...
. 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.
Computational Models
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. However, these sorts of programs cannot model molecules as more atoms are added, because the number of calculations is quadratic in the number of atoms involved; if four times as many atoms are used in a molecule, the calculations with take 16 times as long. 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. Quantum computers can model molecules with fewer calculations because the type of calculations performed in each cycle by a quantum computer are well-suited to molecular modelling.
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.
See also
*
Molecular design software
*
Molecular graphics
*
Molecular modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials sci ...
*
Ribbon diagram
Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon shows the overall path and organization of the protein ...
*
Software for molecular mechanics modeling
*
Space-filling (Calotte) model
References
Further reading
*
*
*
history of molecular modelsPaper presented at the
EuroScience Open Forum (ESOF), Stockholm on August 25, 2004 W. Gerhard Pohl, Austrian Chemical Society. Photo of van't Hoff's tetrahedral models, and Loschmidt's organic formulae (only 2-dimensional).
*
Wooster's biographical notesincluding setting up of Crystal Structure Ltd.
External links
by Eric Martz and Eric Francoeur. Contains a mixture of physical models and
molecular graphics.
{{DEFAULTSORT:Molecular Model
Model