Chemical structure

A chemical structure determination includes a chemist’sspecifying the molecular geometry and, when feasi-ble and necessary, the electronic structure of the tar-get molecule or other solid. Molecular geometry refersto the spatial arrangement of atoms in a molecule andthe chemical bonds that hold the atoms together, andcan be represented using structural formulae and bymolecular models; complete electronic structure descrip-tions include specifying the occupation of a molecule’smolecular orbitals. Structure determination can be ap-plied to a range of targets from very simple molecules(e.g., diatomic oxygen or nitrogen), to very complex ones(e.g., such as of protein or DNA).Theories of chemical structure were first developed byAugust Kekule, Archibald Scott Couper, and AleksandrButlerov, among others, from about 1858. These theo-ries were first to state that chemical compounds are not arandom cluster of atoms and functional groups, but ratherhad a definite order defined by the valency of the atomscomposing the molecule, giving the molecules a three di-mensional structure that could be determined or solved.In determining structures of chemical compounds, onegenerally aims to obtain, minimally, the pattern and mul-tiplicity of bonding between all atoms in the molecule;when possible, one seeks the three dimensional spatialcoordinates of the atoms in the molecule (or other solid).The methods by which one can elucidate the structure ofa molecule include spectroscopies such as nuclear mag-netic resonance (proton and carbon-13 NMR), variousmethods of mass spectrometry (to give overall molecularmass, as well as fragment masses), and x-ray crystallog-raphy when applicable. The last technique can producethree-dimensional models at atomic-scale resolution, aslong as crystals are available. When a molecule has an un-paired electron spin in a functional group of its structure,ENDOR and electron-spin resonance spectroscopes mayalso be performed. Techniques such as absorption spec-troscopy and the vibrational spectroscopies, infrared andRaman, provide, respectively, important supporting in-formation about the numbers and adjacencies of multiplebonds, and about the types of functional groups (whoseinternal bonding gives vibrational signatures); further in-ferential studies that give insight into the contributingelectronic structure of molecules include cyclic voltam-metry and X-ray photoelectron spectroscopy. These lat-ter techniques become all the more important when themolecules contain metal atoms, and when the crystals re-quired by crystallography or the specific atom types thatare required by NMR are unavailable to exploit in the

structure determination. Finally, more specialized meth-ods such as electron microscopy are also applicable insome cases.

1 See also• Chemical structure diagram

• Pauli exclusion principle

• Crystallographic database

2 References

3 Further reading• Warren Gallagher, 2006, “Lecture 7: Struc-ture Determination by X-ray Crystallography,” inChem 406: Biophysical Chemistry, self-publishedcourse notes, Eau Claire, WI, USA:University ofWisconsin-Eau Claire, Department of Chemistry,see , accessed 2 July 2014.

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