Chemical structure

Phosphorus pentoxide chemical structure in 2D

A chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together and can be represented using structural formulae and by molecular models; ^[1] complete electronic structure descriptions include specifying the occupation of a molecule's molecular orbitals. ^{[2] [3]} Structure determination can be applied to a range of targets from very simple molecules (e.g., diatomic oxygen or nitrogen) to very complex ones (e.g., such as protein or DNA).

History

Theories of chemical structure were first developed by August Kekulé, Archibald Scott Couper, and Aleksandr Butlerov, among others, from about 1858. Kekulé proposed the earliest ideas about valency by suggesting the elements had a prefered number of chemical bonds. Couper developed the first chemical structure diagrams, ways of representing structure on paper. Butlerov was the first to use 'structure' in chemistry and to recognize that chemical compounds are not a random cluster of atoms and functional groups, but rather had a definite order defined by the valency of the elements composing the molecule. ^[4]

In 1883 Alexander Crum Brown deduced the crystal structure of NaCl and built a model of it using knitting needles and wool balls. He also proposed a structure for ethanoic acid that matches modern models well before experimental structural analysis techniques were developed. ^[4]

Background

Concerning chemical structure, one has to distinguish between pure connectivity of the atoms within a molecule (chemical constitution), a description of a three-dimensional arrangement (molecular configuration, includes e.g. information on chirality) and the precise determination of bond lengths, angles, and torsion angles, i.e. a full representation of the (relative) atomic coordinates.

In determining structures of chemical compounds, one generally aims to obtain, first and minimally, the pattern and degree of bonding between all atoms in the molecule; when possible, one seeks the three dimensional spatial coordinates of the atoms in the molecule (or other solid). ^[5]

Structural elucidation

The methods by which one can determine the structure of a molecule is called structural elucidation. These methods include:

• concerning only connectivity of the atoms: spectroscopies such as nuclear magnetic resonance (proton and carbon-13 NMR), and various methods of mass spectrometry (to give overall molecular mass, as well as fragment masses). Techniques such as absorption spectroscopy and the vibrational spectroscopies, infrared, and Raman, provide, respectively, important supporting information about the numbers and adjacencies of multiple bonds, and about the types of functional groups (whose internal bonding gives vibrational signatures); further inferential studies that give insight into the contributing electronic structure of molecules include cyclic voltammetry and X-ray photoelectron spectroscopy.
• concerning precise metric three-dimensional information: can be obtained for gases by gas electron diffraction and microwave (rotational) spectroscopy (and other rotationally resolved spectroscopy) and for the crystalline solid state by X-ray crystallography ^[6] or neutron diffraction. These technique can produce three-dimensional models at atomic-scale resolution, typically to a precision of 0.001 Å for distances and 0.1° for angles (in unusual cases even better). ^{[7] [6]}

Additional sources of information are: When a molecule has an unpaired electron spin in a functional group of its structure, ENDOR and electron-spin resonance spectroscopes may also be performed. These latter techniques become all the more important when the molecules contain metal atoms, and when the crystals required by crystallography or the specific atom types that are required by NMR are unavailable to exploit in the structure determination. Finally, more specialized methods such as electron microscopy are also applicable in some cases.

TeX for chemical structures

See also: Comparison of TeX editors

Chemfig and tikz are package add-ons for LaTeX for chemical structures. ^[8]

See also

• ChemDraw - software for chemical structure diagrams
• Chemical graph generator
• Crystallographic database
• Pauli exclusion principle
• Structural chemistry
• Structural formula

References

1. Haaland, Arne (2008). Molecules and Models: The Molecular Structures of Main Group Element Compounds. Oxford: Oxford University Press. ISBN   978-0-19-923535-3. OCLC   173809048.
2. Weinhold, Frank; Landis, Clark R. (2005). Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective. Cambridge, UK: Cambridge University Press. ISBN   0-521-83128-8. OCLC   59712377.
3. Gillespie, Ronald J.; Popelier, Paul L. A. (2001). Chemical Bonding and Molecular Geometry: From Lewis to Electron Densities. New York: Oxford University Press. ISBN   0-19-510495-1. OCLC   43552798.
4. Rankin, David W. H.; Morrison, Carole A.; Mitzel, Norbert W. (2013). Structural methods in molecular inorganic chemistry. A Wiley series of advanced textbooks. Chichester, West Sussex, United Kingdom: Wiley. ISBN   978-1-118-46288-1.
5. Wells, A. F. (July 12, 2012). Structural inorganic chemistry (Fifth ed.). Oxford: Clarendon Press. ISBN   978-0-19-965763-6. OCLC   801026482.
6. Rankin, David W. H. (January 2, 2013). Structural methods in molecular inorganic chemistry. Morrison, Carole A., 1972-, Mitzel, Norbert W., 1966-. Chichester, West Sussex, United Kingdom: Wiley. ISBN   978-1-118-46288-1. OCLC   810442747.
7. Glusker, Jenny Pickworth (1994). Crystal structure analysis for chemists and biologists. Lewis, Mitchell; Rossi, Miriam. New York: VCH. ISBN   0-89573-273-4. OCLC   25412161.
8. "Helpful LaTeX Packages for Chemistry | Computational Chemistry Resources".

Further reading

• Gallagher, Warren (2006). "Lecture 7: Structure Determination by X-ray Crystallography". Chem 406: Biophysical Chemistry (PDF) (self-published course notes). Eau Claire, WI, USA: University of Wisconsin-Eau Claire, Department of Chemistry. Retrieved July 2, 2014.
• Ward, S. C.; Lightfoot, M. P.; Bruno, I. J.; Groom, C. R. (April 1, 2016). "The Cambridge Structural Database". Acta Crystallographica Section B. 72 (2): 171–179. Bibcode:2016AcCrB..72..171G. doi: 10.1107/S2052520616003954 . ISSN   2052-5206. PMC   4822653 . PMID   27048719.