Chemical structure

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.

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.

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).

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 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).

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

Chemfig and tikz are package add-ons for LaTeX for chemical structures.

References

References

1. Haaland, Arne. (2008). "Molecules and Models: The Molecular Structures of Main Group Element Compounds". Oxford University Press.
2. (2005). "Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective". Cambridge University Press.
3. (2001). "Chemical Bonding and Molecular Geometry: From Lewis to Electron Densities". Oxford University Press.
4. Rankin, David W. H.. (2013). "Structural methods in molecular inorganic chemistry". Wiley.
5. Wells, A. F.. (July 12, 2012). "Structural inorganic chemistry". Clarendon Press.
6. Rankin, David W. H.. (January 2, 2013). "Structural methods in molecular inorganic chemistry". Wiley.
7. Glusker, Jenny Pickworth. (1994). "Crystal structure analysis for chemists and biologists". VCH.
8. "Helpful LaTeX Packages for Chemistry | Computational Chemistry Resources".