Molecular model
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A molecular model is a physical model of an atomistic system that represents
molecules A molecule is a group of two or more atoms that are held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemistry ...
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 physical science within the natural sciences that studies the chemical elements that make up matter and chemical compound, compounds made of atoms, molecules a ...
and generating and testing
hypotheses A hypothesis (: hypotheses) is a proposed explanation for a phenomenon. A scientific method, scientific hypothesis must be based on observations and make a testable and reproducible prediction about reality, in a process beginning with an educ ...
. 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 Atoms are the basic particles of the chemical elements. An atom consists of a atomic nucleus, nucleus of protons and generally neutrons, surrounded by an electromagnetically bound swarm of electrons. The chemical elements are distinguished fr ...
s (although
solvent A solvent (from the Latin language, Latin ''wikt:solvo#Latin, solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a Solution (chemistry), solution. A solvent is usually a liquid but can also be a solid, a gas ...
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 ''Bespoke'' () describes anything commissioned to a particular specification, altered or tailored to the customs, tastes, or usage of an individual purchaser. In contemporary usage, ''bespoke'' has become a general marketing and branding concep ...
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 Molecular geometry, three-dimensional position of the atoms and the chemical bond, bonds between them. The atoms are typically represente ...
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 philosophy, natural philosopher and writer on music. He is a key figure in the 17th-century Scientific Revolution, best know ...
speculated on the
symmetry Symmetry () in everyday life refers to a sense of harmonious and beautiful proportion and balance. In mathematics, the term has a more precise definition and is usually used to refer to an object that is Invariant (mathematics), invariant und ...
of snowflakes and the close packing of spherical objects such as fruit. The symmetrical arrangement of closely packed spheres informed theories of molecular structure in the late 1800s, and many theories of
crystallography Crystallography is the branch of science devoted to the study of molecular and crystalline structure and properties. The word ''crystallography'' is derived from the Ancient Greek word (; "clear ice, rock-crystal"), and (; "to write"). In J ...
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 introduced the atomic theory into chemistry. He also researched Color blindness, colour blindness; as a result, the umbrella term ...
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 Stereochemistry, a subdiscipline of chemistry, studies the spatial arrangement of atoms that form the structure of molecules and their manipulation. The study of stereochemistry focuses on the relationships between stereoisomers, which are defined ...
was not then recognised and the model is essentially topological (it should be a 3-dimensional
tetrahedron In geometry, a tetrahedron (: tetrahedra or tetrahedrons), also known as a triangular pyramid, is a polyhedron composed of four triangular Face (geometry), faces, six straight Edge (geometry), edges, and four vertex (geometry), vertices. The tet ...
).
Jacobus Henricus van 't Hoff Jacobus Henricus van 't Hoff Jr. (; 30 August 1852 – 1 March 1911) was a Dutch physical chemistry, physical chemist. A highly influential theoretical chemistry, theoretical chemist of his time, Van 't Hoff was the first winner of the Nobe ...
and Joseph Le Bel introduced the concept of chemistry in three dimensions of space, that is, stereochemistry. Van 't Hoff built tetrahedral molecules representing the three-dimensional properties of
carbon Carbon () is a chemical element; it has chemical symbol, symbol C and atomic number 6. It is nonmetallic and tetravalence, tetravalent—meaning that its atoms are able to form up to four covalent bonds due to its valence shell exhibiting 4 ...
.


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#Edible salt, edible salt, is an ionic compound with the chemical formula NaCl, representing a 1:1 ratio of sodium and chloride ions. It is transparent or translucent, brittle, hygroscopic, and occurs a ...
(NaCl) and
caesium chloride Caesium chloride or cesium chloride is the inorganic compound with the formula Caesium, CsChloride, Cl. This colorless salt is an important source of caesium ions in a variety of niche applications. Its crystal structure forms a major structural ...
(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 of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring th ...
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 styrene. Polystyrene can be solid or foamed. General-purpose polystyrene is clear, hard, and brittle. It is an inexpensive resin per unit weight. It i ...
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; it has chemical symbol, symbol C and atomic number 6. It is nonmetallic and tetravalence, tetravalent—meaning that its atoms are able to form up to four covalent bonds due to its valence shell exhibiting 4 ...
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 Molecular geometry, three-dimensional position of the atoms and the chemical bond, bonds between them. The atoms are typically represente ...
of proline. The balls have colours: black represents
carbon Carbon () is a chemical element; it has chemical symbol, symbol C and atomic number 6. It is nonmetallic and tetravalence, tetravalent—meaning that its atoms are able to form up to four covalent bonds due to its valence shell exhibiting 4 ...
(C); red,
oxygen Oxygen is a chemical element; it has chemical symbol, symbol O and atomic number 8. It is a member of the chalcogen group (periodic table), group in the periodic table, a highly reactivity (chemistry), reactive nonmetal (chemistry), non ...
(O); blue,
nitrogen Nitrogen is a chemical element; it has Symbol (chemistry), symbol N and atomic number 7. Nitrogen is a Nonmetal (chemistry), nonmetal and the lightest member of pnictogen, group 15 of the periodic table, often called the Pnictogen, pnictogens. ...
(N); and white,
hydrogen Hydrogen is a chemical element; it has chemical symbol, symbol H and atomic number 1. It is the lightest and abundance of the chemical elements, most abundant chemical element in the universe, constituting about 75% of all baryon, normal matter ...
(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 In crystallography, the hexagonal crystal family is one of the six crystal family, crystal families, which includes two crystal systems (hexagonal and trigonal) and two lattice systems (hexagonal and rhombohedral). While commonly confused, the tr ...
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 Edinburgh is the capital city of Scotland and one of its 32 Council areas of Scotland, council areas. The city is located in southeast Scotland and is bounded to the north by the Firth of Forth and to the south by the Pentland Hills. 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 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 sapph ...
in this style.


Skeletal models

Crick and Watson's
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
model and the
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
-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 (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 An inorganic compound is typically a chemical compound that lacks carbon–hydrogen bonds⁠that is, a compound that is not an organic compound. The study of inorganic compounds is a subfield of chemistry known as '' inorganic chemistry''. Inor ...
solids consist of atoms surrounded by a 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

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 "molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." Polymers are physi ...
s. The components are primarily
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...
s and
nucleic acid Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...
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 substituent, chemical group that is attached to a core part of the molecule called the "main chain" or backbone chain, backbone. The side chain is a hydrocarbon branching element of a mo ...
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.


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 (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 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 *
Ribbon diagram Ribbon diagrams, also known as Richardson diagrams, are three-dimensional space, 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and o ...
* Software for molecular mechanics modeling * Space-filling (Calotte) model


References


Further reading

* * *


history of molecular models
Paper 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 notes
including 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 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 , . Models can be divided in ...