Molecular model
Encyclopedia
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 simplified way.
and generating and testing hypotheses. Most commonly there is an explicit representation of atoms, though other approaches such as soap film
s and other continuous media have been useful. There are several motivations for creating physical models:
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:
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:
speculated on the symmetry
of snowflake
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
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 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 (Fig. 1). 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 (it should be a 3-dimensional tetrahedron
).
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
.
proposed a relationship between crystal
s and the packing of spheres
. René Just Haüy
argued that the structures of crystals involved regular lattice
s of repeating units with shapes similar to the macroscopic crystal. Barlow, who jointly developed the theories of space group
s, proposed models of crystals based on sphere packings ( ca. 1890).
The binary compound
s sodium chloride
(NaCl) and caesium chloride
(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 ion
s (in a face-centered cubic lattice) 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.
can be represented as a sphere with four holes at the tetrahedral angles cos−1(-1/3) ≈ 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 (Fig. 3).
Figure 3 represents a ball-and-stick model
of proline
. The balls have colours: black represents carbon
(C); red, oxygen
(O); blue, nitrogen
(N); and white, hydrogen
(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 stereochemistry.
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 (showing molecular flexibility) and a disadvantage (models are floppy). The approximate scale was 5 cm per ångström
(0.5 m/nm or 500,000,000:1), 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.
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.
of electronegative atoms (e.g. PO4 tetrahedra, TiO6 octahedra). Structures can be modelled by gluing together polyhedra made of paper or plastic.
A good example of composite models is the Nicholson approach, widely used from the late 1970s for building models of biological macromolecule
s. The components are primarily amino acid
s and nucleic acid
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
s 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.
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 (at a scale of approximately 20 Å/cm or 1:5,000,000) and green fluorescent protein
, 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
. The image at right (Fig. 7) 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.
{| class="wikitable"
|{|Hydrogen
|{|White
|-
|{|Alkali Metals
|{|Violet
|-
|{|Alkaline-Earth Metals
|{|Dark Green
|-
|{|Boron, Most Transition Metals
|{|Pink
|-
|{|Carbon
|{|Black
|-
|{|Nitrogen
|{|Dark Blue
|-
|{|Oxygen
|{|Red
|-
|{|Fluorine, Chlorine
|{|Green
|-
|{|Bromine
|{|Dark Red
|-
|{|Iodine
|{|Dark Violet
|-
|{|Noble Gases
|{|Cyan
|-
|{|Phosphorus
|{|Orange
|-
|{|Sulfur
|{|Yellow
|-
|{|Titanium
|{|Gray
|}
{| class="wikitable"
|-
! Developer(s)
! Approximate date
! Technology
! Comments
|-
| Kepler
|
|
| sphere packing, symmetry of snowflakes.
|-
| Loschmidt
|
| 2-D graphics
| representation of atoms and bonds by touching circles
|-
| Hofmann
|
| ball-and-stick
| first recognisable physical molecular model
|-
| van't Hoff
|
| paper?
| representation of atoms as tetrahedra supported the development of stereochemistry
|-
| Bernal
|
| Plasticine and spokes
| model of liquid water
|-
| Corey, Pauling
, Koltun (CPK coloring
)
|
| Space-filling model
s of alpha-helix, etc.
| Pauling's "Nature of the Chemical Bond" covered all aspects of molecular structure and influenced many aspects of models
|-
| Crick
and Watson
|
| spikes, flat templates and connectors with screws
| model of DNA
|-
| Molecular graphics
| ca 1960
| display on computer screens
| complements rather than replaces physical models
|}
Molecular modelling
Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...
, and their graphical depiction is molecular graphics
Molecular graphics
Molecular graphics 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"...
, 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 simplified way.
Overview
Physical models of atomistic systems have played an important role in understanding chemistryChemistry
Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
and generating and testing hypotheses. Most commonly there is an explicit representation of atoms, though other approaches such as soap film
Soap film
Soap films are thin layers of liquid surrounded by air. For example, if two soap bubbles enters in contact, they merged and a thin film is created in between. Thus, foams are composed of a network of films connected by Plateau borders...
s 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
Bespoke
Bespoke is a term employed in a variety of applications to mean an item custom-made to the buyer's specification...
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 (plasticinePlasticinePlasticine, a brand of modelling clay, is a putty-like modelling material made from calcium salts, petroleum jelly and aliphatic acids. The name is a registered trademark of Flair Leisure Products plc...
, matchsticks) or children's toys (TinkertoyTinkertoyThe Tinkertoy Construction Set was created in 1914—one year after the A. C. Gilbert Company's Erector Set—by Charles H. Pajeau and Robert Pettit in Evanston, Illinois. Pajeau, a stonemason, designed the toy after seeing children play with pencils and empty spools of thread. He and...
(TM), MeccanoMeccanoMeccano is a model construction system comprising re-usable metal strips, plates, angle girders, wheels, axles and gears, with nuts and bolts to connect the pieces. It enables the building of working models and mechanical devices....
, LegoLegoLego is a line of construction toys manufactured by the Lego Group, a privately held company based in Billund, Denmark. The company's flagship product, Lego, consists of colorful interlocking plastic bricks and an accompanying array of gears, minifigures and various other parts...
, 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
Linus Pauling
Linus Carl Pauling was an American chemist, biochemist, peace activist, author, and educator. He was one of the most influential chemists in history and ranks among the most important scientists of the 20th century...
and Crick and Watson were created with much greater precision.
Molecular models have inspired molecular graphics
Molecular graphics
Molecular graphics 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"...
, 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 pseudorotationPseudorotationThe IUPAC defines pseudorotation as "a conformational change resulting in a structure that appears to have been produced by rotation of the entire initial molecule and is superimposable on the initial one, unless different positions are distinguished by substitution or isotopic labeling...
).
History
In the 1600s, Johannes KeplerJohannes Kepler
Johannes Kepler was a German mathematician, astronomer and astrologer. A key figure in the 17th century scientific revolution, he is best known for his eponymous laws of planetary motion, codified by later astronomers, based on his works Astronomia nova, Harmonices Mundi, and Epitome of Copernican...
speculated on the symmetry
Symmetry
Symmetry generally conveys two primary meanings. The first is an imprecise sense of harmonious or aesthetically pleasing proportionality and balance; such that it reflects beauty or perfection...
of snowflake
Snowflake
Snowflakes are conglomerations of frozen ice crystals which fall through the Earth's atmosphere. They begin as snow crystals which develop when microscopic supercooled cloud droplets freeze. Snowflakes come in a variety of sizes and shapes. Complex shapes emerge as the flake moves through...
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
Crystallography is the experimental science of the arrangement of atoms in solids. The word "crystallography" derives from the Greek words crystallon = cold drop / frozen drop, with its meaning extending to all solids with some degree of transparency, and grapho = write.Before the development of...
and solid state
Solid
Solid is one of the three classical states of matter . It is characterized by structural rigidity and resistance to changes of shape or volume. Unlike a liquid, a solid object does not flow to take on the shape of its container, nor does it expand to fill the entire volume available to it like a...
inorganic structure used collections of equal and unequal spheres to simulate packing and predict structure.
John Dalton
John Dalton
John Dalton FRS was an English chemist, meteorologist and physicist. He is best known for his pioneering work in the development of modern atomic theory, and his research into colour blindness .-Early life:John Dalton was born into a Quaker family at Eaglesfield, near Cockermouth, Cumberland,...
represented compounds as aggregations of circular atoms, and although Loschmidt did not create physical models, his diagrams based on circles are two-dimensional analogues of later models. Hofmann
August Wilhelm von Hofmann
August Wilhelm von Hofmann was a German chemist.-Biography:Hofmann was born at Gießen, Grand Duchy of Hesse. Not intending originally to devote himself to physical science, he first took up the study of law and philology at Göttingen. But he then turned to chemistry, and studied under Justus von...
is credited with the first physical molecular model around 1860 (Fig. 1). Note how the size of the carbon appears smaller than the hydrogen. The importance of stereochemistry
Stereochemistry
Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms within molecules. An important branch of stereochemistry is the study of chiral molecules....
was not then recognised and the model is essentially topological (it should be a 3-dimensional tetrahedron
Tetrahedron
In geometry, a tetrahedron is a polyhedron composed of four triangular faces, three of which meet at each vertex. A regular tetrahedron is one in which the four triangles are regular, or "equilateral", and is one of the Platonic solids...
).
J.H. van 't Hoff
Jacobus Henricus van 't Hoff
Jacobus Henricus van 't Hoff, Jr. was a Dutch physical and organic chemist and the first winner of the Nobel Prize in chemistry. He is best known for his discoveries in chemical kinetics, chemical equilibrium, osmotic pressure, and stereochemistry...
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
Carbon
Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...
.
Models based on spheres
Robert HookeRobert Hooke
Robert Hooke FRS was an English natural philosopher, architect and polymath.His adult life comprised three distinct periods: as a scientific inquirer lacking money; achieving great wealth and standing through his reputation for hard work and scrupulous honesty following the great fire of 1666, but...
proposed a relationship between crystal
Crystal
A crystal or crystalline solid is a solid material whose constituent atoms, molecules, or ions are arranged in an orderly repeating pattern extending in all three spatial dimensions. The scientific study of crystals and crystal formation is known as crystallography...
s and the packing of spheres
Sphere packing
In geometry, a sphere packing is an arrangement of non-overlapping spheres within a containing space. The spheres considered are usually all of identical size, and the space is usually three-dimensional Euclidean space...
. René Just Haüy
René Just Haüy
René Just Haüy – 3 June 1822 in Paris) was a French mineralogist, commonly styled the Abbé Haüy after he was made an honorary canon of Notre Dame. He is often referred to as the "Father of Modern Crystallography." -Biography:...
argued that the structures of crystals involved regular lattice
Crystal structure
In mineralogy and crystallography, crystal structure is a unique arrangement of atoms or molecules in a crystalline liquid or solid. A crystal structure is composed of a pattern, a set of atoms arranged in a particular way, and a lattice exhibiting long-range order and symmetry...
s of repeating units with shapes similar to the macroscopic crystal. Barlow, who jointly developed the theories of space group
Space group
In mathematics and geometry, a space group is a symmetry group, usually for three dimensions, that divides space into discrete repeatable domains.In three dimensions, there are 219 unique types, or counted as 230 if chiral copies are considered distinct...
s, proposed models of crystals based on sphere packings ( ca. 1890).
Binary compound
A binary compound is a chemical compound that contains exactly two different elements. Examples of binary ionic compounds include calcium chloride , sodium fluoride , and magnesium oxide , whilst examples of binary covalent compounds include water , carbon monoxide , and sulfur hexafluoride...
s sodium chloride
Sodium chloride
Sodium chloride, also known as salt, common salt, table salt or halite, is an inorganic compound with the formula NaCl. Sodium chloride is the salt most responsible for the salinity of the ocean and of the extracellular fluid of many multicellular organisms...
(NaCl) and caesium chloride
Caesium chloride
Caesium chloride is the inorganic compound with the formula CsCl. This colorless solid is an important source of caesium ions in a variety of applications. Its crystal structure forms a major structural type where each caesium ion is coordinated by 8 chlorine ions...
(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 ion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...
s (in a face-centered cubic lattice) with sodium ions in the octahedral holes. After the development of X-ray crystallography
X-ray crystallography
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
as a tool for determining crystal structures, many laboratories built models based on spheres. With the development of plastic or polystyrene
Polystyrene
Polystyrene ) also known as Thermocole, abbreviated following ISO Standard PS, is an aromatic polymer made from the monomer styrene, a liquid hydrocarbon that is manufactured from petroleum by the chemical industry...
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 carbonCarbon
Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...
can be represented as a sphere with four holes at the tetrahedral angles cos−1(-1/3) ≈ 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 (Fig. 3).
Ball-and-stick model
In chemistry, the ball-and-stick model is a molecular model of a chemical substance which is to display both the three-dimensional position of the atoms and the bonds between them...
of proline
Proline
Proline is an α-amino acid, one of the twenty DNA-encoded amino acids. Its codons are CCU, CCC, CCA, and CCG. It is not an essential amino acid, which means that the human body can synthesize it. It is unique among the 20 protein-forming amino acids in that the α-amino group is secondary...
. The balls have colours: black represents carbon
Carbon
Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...
(C); red, oxygen
Oxygen
Oxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
(O); blue, nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
(N); and white, hydrogen
Hydrogen
Hydrogen is the chemical element with atomic number 1. It is represented by the symbol H. With an average atomic weight of , hydrogen is the lightest and most abundant chemical element, constituting roughly 75% of the Universe's chemical elemental mass. Stars in the main sequence are mainly...
(H). Each ball is drilled with as many holes as its conventional valence
Valence (chemistry)
In chemistry, valence, also known as valency or valence number, is a measure of the number of bonds formed by an atom of a given element. "Valence" can be defined as the number of valence bonds...
(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 stereochemistry.
Ångström
The angstrom or ångström, is a unit of length equal to 1/10,000,000,000 of a meter . Its symbol is the Swedish letter Å....
(0.5 m/nm or 500,000,000:1), but was not consistent over all elements.
Arnold Beevers in Edinburgh
Edinburgh
Edinburgh is the capital city of Scotland, the second largest city in Scotland, and the eighth most populous in the United Kingdom. The City of Edinburgh Council governs one of Scotland's 32 local government council areas. The council area includes urban Edinburgh and a rural area...
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
Ruby
A ruby is a pink to blood-red colored gemstone, a variety of the mineral corundum . The red color is caused mainly by the presence of the element chromium. Its name comes from ruber, Latin for red. Other varieties of gem-quality corundum are called sapphires...
in this style.
Skeletal models
Crick and Watson's DNADNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
model and the protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
-building kits of Kendrew
John Kendrew
Sir John Cowdery Kendrew, CBE, FRS was an English biochemist and crystallographer who shared the 1962 Nobel Prize in Chemistry with Max Perutz; their group in the Cavendish Laboratory investigated the structure of heme-containing proteins.-Biography:He was born in Oxford, son of Wilford George...
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 sphereCoordination sphere
In coordination chemistry, the coordination sphere refers to a central atom or ion and an array of molecules or anions, the ligands, around.Molecules that are attached noncovalently to the ligands are called the second coordination sphere....
of electronegative atoms (e.g. PO4 tetrahedra, TiO6 octahedra). Structures can be modelled by gluing together polyhedra made of paper or plastic.
Composite models
Macromolecule
A macromolecule is a very large molecule commonly created by some form of polymerization. In biochemistry, the term is applied to the four conventional biopolymers , as well as non-polymeric molecules with large molecular mass such as macrocycles...
s. The components are primarily amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
s and nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
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
Backbone chain
In polymer science, the backbone chain or main chain of a polymer is the series of covalently bonded atoms that together create the continuous chain of the molecule....
and side chain
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 "main chain" or backbone. The placeholder R is often used as a generic placeholder for alkyl group side chains in chemical structure diagrams. To indicate other non-carbon...
s are determined by pre-computing the torsion angles and then adjusting the model with a protractor
Protractor
In geometry, a protractor is a circular or semicircular tool for measuring an angle or a circle. The units of measurement utilized are usually degrees.Some protractors are simple half-discs; these have existed since ancient times...
.
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
Anthrax
Anthrax is an acute disease caused by the bacterium Bacillus anthracis. Most forms of the disease are lethal, and it affects both humans and other animals...
toxin, left (at a scale of approximately 20 Å/cm or 1:5,000,000) and green fluorescent protein
Green fluorescent protein
The green fluorescent protein is a protein composed of 238 amino acid residues that exhibits bright green fluorescence when exposed to blue light. Although many other marine organisms have similar green fluorescent proteins, GFP traditionally refers to the protein first isolated from the...
, 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
Laser engraving, or laser marking, is the practice of using lasers to engrave or mark an object. The technique does not involve the use of inks, nor does it involve tool bits which contact the engraving surface and wear out...
. The image at right (Fig. 7) shows the 3D structure of an E. coli protein (DNA polymerase beta-subunit, PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
code 1MMI) 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:{| class="wikitable"
|{|Hydrogen
|{|White
|-
|{|Alkali Metals
|{|Violet
|-
|{|Alkaline-Earth Metals
|{|Dark Green
|-
|{|Boron, Most Transition Metals
|{|Pink
|-
|{|Carbon
|{|Black
|-
|{|Nitrogen
|{|Dark Blue
|-
|{|Oxygen
|{|Red
|-
|{|Fluorine, Chlorine
|{|Green
|-
|{|Bromine
|{|Dark Red
|-
|{|Iodine
|{|Dark Violet
|-
|{|Noble Gases
|{|Cyan
|-
|{|Phosphorus
|{|Orange
|-
|{|Sulfur
|{|Yellow
|-
|{|Titanium
|{|Gray
|}
Chronology
This table is an incomplete chronology of events where physical molecular models provided major scientific insights.{| class="wikitable"
|-
! Developer(s)
! Approximate date
! Technology
! Comments
|-
| Kepler
|
|
| sphere packing, symmetry of snowflakes.
|-
| Loschmidt
|
| 2-D graphics
| representation of atoms and bonds by touching circles
|-
| Hofmann
August Wilhelm von Hofmann
August Wilhelm von Hofmann was a German chemist.-Biography:Hofmann was born at Gießen, Grand Duchy of Hesse. Not intending originally to devote himself to physical science, he first took up the study of law and philology at Göttingen. But he then turned to chemistry, and studied under Justus von...
|
| ball-and-stick
| first recognisable physical molecular model
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| van't Hoff
Jacobus Henricus van 't Hoff
Jacobus Henricus van 't Hoff, Jr. was a Dutch physical and organic chemist and the first winner of the Nobel Prize in chemistry. He is best known for his discoveries in chemical kinetics, chemical equilibrium, osmotic pressure, and stereochemistry...
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| paper?
| representation of atoms as tetrahedra supported the development of stereochemistry
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| Bernal
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| Plasticine and spokes
| model of liquid water
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| Corey, Pauling
Pauling
Pauling is a surname. People with this surname include:*Linus Pauling**Paulingite**Pauling's rules**4674 Pauling**Linus Pauling Institute**Linus Pauling Library**Linus Pauling Award**Pauling Field*Ava Helen Pauling, wife of Linus*Tom Pauling...
, Koltun (CPK coloring
CPK coloring
In chemistry, the CPK coloring is a popular color convention for distinguishing atoms of different chemical elements in molecular models. The scheme is named after the CPK molecular models designed by chemists Robert Corey and Linus Pauling, and improved by Walter Koltun.-History:In 1952, Corey...
)
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| Space-filling model
Space-filling model
In chemistry a space-filling model, also known as calotte model, is a type of three-dimensional molecular model where the atoms are represented by spheres whose radii are proportional to the radii of the atoms and whose center-to-center distances are proportional to the distances between the atomic...
s of alpha-helix, etc.
| Pauling's "Nature of the Chemical Bond" covered all aspects of molecular structure and influenced many aspects of models
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| Crick
Francis Crick
Francis Harry Compton Crick OM FRS was an English molecular biologist, biophysicist, and neuroscientist, and most noted for being one of two co-discoverers of the structure of the DNA molecule in 1953, together with James D. Watson...
and Watson
James D. Watson
James Dewey Watson is an American molecular biologist, geneticist, and zoologist, best known as one of the co-discoverers of the structure of DNA in 1953 with Francis Crick...
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| spikes, flat templates and connectors with screws
| model of DNA
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| Molecular graphics
Molecular graphics
Molecular graphics 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"...
| ca 1960
| display on computer screens
| complements rather than replaces physical models
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See also
- Space-filling (Calotte) modelSpace-filling modelIn chemistry a space-filling model, also known as calotte model, is a type of three-dimensional molecular model where the atoms are represented by spheres whose radii are proportional to the radii of the atoms and whose center-to-center distances are proportional to the distances between the atomic...
- Molecular modellingMolecular modellingMolecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...
- Molecular graphicsMolecular graphicsMolecular graphics 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"...
- Software for molecular mechanics modeling
- Molecular design softwareMolecular Design softwareMolecular design software is software for molecular modeling, that provides special support for developing molecular models de novo.In contrast to the usual molecular modeling programs such as the molecular dynamics and quantum chemistry programs, such software directly supports the aspects related...