Molecular structure elucidation

 

     Organic compounds consist of carbon atoms, hydrogen atoms, and functional groups. The valence of carbon is 4, and hydrogen is 1, functional groups are generally 1. From the number of carbon atoms and hydrogen atoms in a molecule the degree of unsaturation can be obtained. Many, but not all structures can be envisioned by the simple valence rule that there will be one bond for each valence number. The knowledge of the chemical formula for an organic compound is not sufficient information because many isomers can exist. Organic compounds often exist as mixtures. Because many organic compounds have relatively low boiling points and/or dissolve easily in organic solvents there exist many methods for separating mixtures into pure constituents that are specific to organic chemistry such as distillation, crystallization and chromatography techniques. There exist several methods for deducing the structure an organic compound. In general usage are (in alphabetical order):

     Crystallography: This is the most precise method for determining molecular geometry; however, it is very difficult to grow crystals of sufficient size and high quality to get a clear picture, so it remains a secondary form of analysis. Crystallography has seen especially extensive use in biochemistry (for protein structure determination) and in the characterization of organometallic catalysts, which often possess significant symmetry.

     Elemental analysis: A destructive method used to determine the elemental composition of a molecule. See also mass spectrometry, below.

     Infrared spectroscopy: Chiefly used to determine the presence (or absence) of certain functional groups.

     Mass spectrometry: Used to determine the molecular weight of a compound and from the fragmentation pattern of its structure. High resolution mass spectrometry can often identify the precise formula of a compound through knowledge of isotopic masses and abundances; it is thus sometimes used in lieu of elemental analysis.

     Nuclear magnetic resonance (NMR) spectrometry identifies different nuclei based on their chemical environment. This is the most important and commonly used spectroscopic technique for organic chemists, often permitting complete assignment of atom connectivity and even stereochemistry given the proper set of spectroscopy experiments (e.g. correlation spectroscopy).

     Optical rotation: Distinguishes between two enantiomers of a chiral compound based on the sign of rotation of plane polarized light. If the specific rotation of an enantiomer is known, the magnitude of rotation also gives the ratio of enantiomers in a mixed sample, though HPLC with a chiral column also can supply this information.

     UV/VIS spectroscopy: Used to determine degree of conjugation in the system. While still sometimes used to characterize molecules, UV/VIS is more commonly used to quantitate how much of a known compound is present in a (typically liquid) sample.

Additional methods are provided by analytical chemistry.