Ions are generally not formed in the reactions of organic compounds. Molecules as such participate in the reaction. It is convenient to name one reagent as substrate and other as reagent. In general, a molecule whose carbon is involved in new bond formation is called substrate and the other one is called reagent. When carbon-carbon bond is formed, the choice of naming the reactants as substrate and reagent is arbitrary and depends on molecule under observation. Example:
Nucleophiles and Electrophiles
Reagents attack the reactive site of the substrate. The reactive site may be electron deficient portion of the molecule (a positive reactive site) e.g., an atom with incomplete electron shell or the positive end of the dipole in the molecule. If the attacking species is electron rich, it attacks these sites. If attacking species is electron deficient, the reactive site for it is that part of the substrate molecule which can supply electrons, e.g., electrons in a double bond.
A reagent that brings an electron pair to the reactive site is called a nucleophile (Nu:) i.e., nucleus seeking and the reaction is then called nucleophilic. A reagent that takes away an electron pair from reactive site is called electrophile (E+) i.e., electron seeking and the reaction is called electrophilic. During a polar organic reaction, a nucleophile attacks an electrophilic centre of the substrate which is that specific atom or part of the substrate which is electron deficient.
Similarly, the electrophiles attack at nucleophilic centre, which is the electron rich centre of the substrate. Thus, the electrophiles receive electron pair from the substrate when the two undergo bonding interaction. A curved-arrow notation is used to show the movement of an electron pair from the nucleophile to the electrophile.
Some examples of nucleophiles are the negatively charged ions with lone pair of electrons such as hydroxide (HO–), cyanide (NC–) ions and carbanions (R3C:–). Neutral molecules such as H2O, R3N, R2NH etc., can also act as nucleophiles due to the presence of lone pair of electrons.
Examples of electrophiles include carbocations ( 3CH+ ) and neutral molecules having functional groups like carbonyl group (>C=O) or alkyl halides (R3C-X, where X is a halogen atom). The carbon atom in carbocations has sextet configuration; hence, it is electron deficient and can receive a pair of electrons from the nucleophiles.
In neutral molecules such as alkyl halides, due to the polarity of the C-X bond a partial positive charge is generated on the carbon atom and hence the carbon atom becomes an electrophilic centre at which a nucleophile can attack.