CoreChem:Organic Nitrogen Compounds
There is a tremendous variety of organic compounds which can be derived from carbon, hydrogen, and oxygen which is evident from the numerous previous sections discussing these compounds. If we include nitrogen as a possible constituent of these molecular structures, many more possibilities arise. Most of the nitrogen-containing compounds are less important commercially, however, and we will only discuss a few of them here.
Amines may be derived from ammonia by replacing one, two, or all three hydrogens with alkyl groups. Some examples are
|Task: Is this a place where replacing the 3 classes of amines with Jmol woudld make sense, or would that just be overuse of the tool, without actually enhancing the usefulness of the material? I'm on the fence, but leaning towards it not being necessary, and that showing the amino acids down the page is more useful. Twendorff 14:56, 10 June 2009 (UTC) Tim: Add the Lewis Structures from the chemeddl-jmol - at some point we will have them branded with a logo that can be clicked on to show the corresponding 3d applet when they are desired. I think that the Lewis Structure would be good. Same down the page (I deleted the Task) Xavier, just delete your name when you read this - I just was sending along an example of where the branding would be useful. Jshorb 03:16, 28 June 2009 (UTC) Since both the secondary and tertiary amine are in the jmol2 library, I don't think we can do this at the moment. Same holds for the amino acids I think.Twendorff 22:41, 19 January 2010 (UTC) ( Tim Wendorff, Xavier Prat-Resina )|
The terms primary (one), secondary (two), and tertiary (three) refer to the number of hydrogens that have been replaced. Both primary and secondary amines are capable of hydrogen bonding with themselves, but tertiary amines have no hydrogens on the electronegative nitrogen atom.
Amines usually have unpleasant odors, smelling “fishy“. The three methylamines listed above can all be isolated from herring brine. Amines, as well as ammonia, are produced by decomposition of nitrogen-containing compounds when a living organism dies. The methylamines are obtained commercially by condensation of methanol with ammonia over an aluminum oxide catalyst:
Dimethylamine is the most important, being used in the preparation of herbicides, in rubber vulcanization, and to synthesize dimethylformamide, an important solvent.
Amides are another important nitrogen containing organic compound. The key feature of an amine is a nitrogen atom bonded to a carbonyl carbon atom. Like esters, amides are formed in a condensation reaction. While esters are formed from the condensation reaction of an alcohol and a carboxylic acid, amides are formed from the condensation of an amine and a carboxylic acid:
This general reaction is usually unfavorable, because the hydroxyl group acts as a bad leaving group. Organic chemists have devised methods to work around this by using certain chemicals to activate the carboxylic acid and allow for the addition of the amine.
As amides are formed by condensation reactions, many important condensation polymers involve amide linkages. Nylon, for instance, is formed from the amide condensation of hexamethylenediamine and adipic acid.
A second set of condensation polymers formed from amide linkages are the proteins and peptides found in your body and in all organisms. These polymers are formed from another organic nitrogen compound, the amino acid. These molecules contain both an amine group and a carboxyl group. Examples of such amino acids are glycine and lysine:
Amino acids are the constituents from which proteins are made. Some, like glycine, can be synthesized in the human body, but others cannot. Lysine is an example of an essential amino acid—one which must be present in the human diet because it cannot be synthesized within the body. As mentioned, the condensation of amino acids into peptides forms amide linkages. For this reason, scientists sometimes refer to the amide backbone of a protein or peptide. A protein has a long series of amide bonds, as can be seen in the following figure showing the synthesis of a tri-peptide from three amino acids:
The intermolecular forces and boiling points of nitrogen-containing organic compounds may be explained according to the same principles used for oxygen-containing substances.
EXAMPLE Rationalize the following boiling points: (a) 0°C for CH3CH2CH2CH3; (b) 11°C for CH3CH2OCH3; (c) 97°C for CH3CH2CH2OH; and (d) 170°C for NH2CH2CH2OH.
Solution All four molecules have very similar geometries and the same number of electrons (26 valence electrons plus 8 core electrons), and so their London forces should be about the same. Compound (a) is an alkane and is nonpolar. By contrast compound (b) is an ether and should be slightly polar. This slight polarity results in a slightly higher boiling point. Compound (c) is isomeric with compound (b) but is an alcohol. There is hydrogen bonding between molecules of (c), and its boiling point is much higher. Molecule (d) has both an amino group and a hydroxyl group, each of which can participate in hydrogen bonding. Consequently it has the highest boiling point of all.