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As covered in previous tutorials (Drawing Curved Arrows – Part 1 and Part 2), organic reaction mechanisms involve the movement of electrons, which often results in changes to the formal charges of the atoms involved. The charge of an atom depends on its number of valence electrons, bonds and lone pairs (see Formal Charges and Mechanisms – Part 1).
In intro organic chemistry, the most common elements are hydrogen (H), carbon (C), nitrogen (N), and oxygen (O). It’s worth familiarizing yourself with the typical numbers of bonds and lone pairs on these atoms, and how this relates to their formal charge.
Formal Charges and Mechanisms
Hydrogen, as a first-row element, is easy: in an organic structure, it will only ever have one bond, no lone pairs, and a neutral charge. You will sometimes see positively charged (H+, proton) and negatively charged (H–, hydride) hydrogen ions listed as reagents (although this is not necessarily accurate), but if a hydrogen atom is part of an organic molecule, it will have a neutral charge.
Carbon, nitrogen, and oxygen, as second-row elements, are bit more complicated. You will often see positively and negative charged forms of these elements in reaction mechanisms.
To begin with, it’s a good idea to memorize the number of lone pairs and bonds found on neutral carbon, nitrogen, and oxygen atoms in an organic molecule.
One way of remembering this: the order of these elements in the periodic table, from left to right, is carbon, nitrogen, then oxygen. Neutral carbon has four bonds and no lone pairs. Going right, for the neutral species, the number of bonds decreases, and the number of lone pairs increases:
Building off of this, by changing the number of lone pairs and bonds on carbon, nitrogen, and oxygen, you can get the charged species in the following chart:
Note the names given to the positively and negatively charged carbon, nitrogen, and oxygen species. These names generally apply if the central atom is bonded to alkyl groups and/or hydrogen atoms. The name alkoxide assumes that the oxygen is bonded to an alkyl group; if it is bonded to a hydrogen atom, it is a hydroxide ion.
These charged forms of carbon, nitrogen, and oxygen often come up in reaction mechanisms as Brønsted acids and bases. Recall that Brønsted acids donate protons, and Brønsted bases accept protons.
Carbanions, amides, and alkoxides are all strong Brønsted bases, accepting protons from Brønsted acids. Ammonium ions and oxonium ions can act as strong Brønsted acids (if there is a hydrogen bonded to the nitrogen or oxygen).
In addition to being Brønsted acids and bases, molecules containing charged carbons, nitrogens and oxygens are very important Lewis acids and bases.
The next tutorial, Lewis Acids/Bases and Mechanisms, will introduce the importance of Lewis acids and bases in organic reaction mechanisms, with a focus on positively and negatively charged carbon, nitrogen, and oxygen species.