Chemistry Fundamental concepts in organic reaction mechanism

### Topics to be covered

=> Fundamental concepts in organic reaction mechanism
=> Fission of a covalent bond
=> Nucleophiles and electrophiles
=> Electron movement in organic reactions
=> Electron displacement effects in covalent bond
=> Inductive effect

### FUNDAMENTAL CONCEPTS IN ORGANIC REACTION MECHANISM

In an organic reaction, the organic molecule (also referred as a substrate) reacts with an appropriate attacking reagent and leads to the formation of one or more intermediate(s) and finally product(s).

The general reaction is depicted as follows :

Substrate is that reactant which supplies carbon to the new bond and the other reactant is called color{green}("reagent"). If both the reactants supply carbon to the new bond then choice is arbitrary and in that case the molecule on which attention is focused is called color{green}("substrate").

𝐀 𝐬𝐞𝐪𝐮𝐞𝐧𝐭𝐢𝐚𝐥 𝐚𝐜𝐜𝐨𝐮𝐧𝐭 𝐨𝐟 𝐞𝐚𝐜𝐡 𝐬𝐭𝐞𝐩, 𝐝𝐞𝐬𝐜𝐫𝐢𝐛𝐢𝐧𝐠 𝐝𝐞𝐭𝐚𝐢𝐥𝐬 𝐨𝐟 𝐞𝐥𝐞𝐜𝐭𝐫𝐨𝐧 𝐦𝐨𝐯𝐞𝐦𝐞𝐧𝐭, 𝐞𝐧𝐞𝐫𝐠𝐞𝐭𝐢𝐜𝐬 𝐝𝐮𝐫𝐢𝐧𝐠 𝐛𝐨𝐧𝐝 𝐜𝐥𝐞𝐚𝐯𝐚𝐠𝐞 𝐚𝐧𝐝 𝐛𝐨𝐧𝐝 𝐟𝐨𝐫𝐦𝐚𝐭𝐢𝐨𝐧, 𝐚𝐧𝐝 𝐭𝐡𝐞 𝐫𝐚𝐭𝐞𝐬 𝐨𝐟 𝐭𝐫𝐚𝐧𝐬𝐟𝐨𝐫𝐦𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐫𝐞𝐚𝐜𝐭𝐚𝐧𝐭𝐬 𝐢𝐧𝐭𝐨 𝐩𝐫𝐨𝐝𝐮𝐜𝐭𝐬 (𝐤𝐢𝐧𝐞𝐭𝐢𝐜𝐬) 𝐢𝐬 𝐫𝐞𝐟𝐞𝐫𝐫𝐞𝐝 𝐭𝐨 𝐚𝐬 𝐫𝐞𝐚𝐜𝐭𝐢𝐨𝐧 𝐦𝐞𝐜𝐡𝐚𝐧𝐢𝐬𝐦.

### Fission of a Covalent Bond

A covalent bond can get cleaved either by : (i) 𝐡𝐞𝐭𝐞𝐫𝐨𝐥𝐲𝐭𝐢𝐜 𝐜𝐥𝐞𝐚𝐯𝐚𝐠𝐞, or by (ii) 𝐡𝐨𝐦𝐨𝐥𝐲𝐭𝐢𝐜 𝐜𝐥𝐞𝐚𝐯𝐚𝐠𝐞.

In 𝐡𝐞𝐭𝐞𝐫𝐨𝐥𝐲𝐭𝐢𝐜 𝐜𝐥𝐞𝐚𝐯𝐚𝐠𝐞, the bond breaks in such a fashion that the shared pair of electrons remains with one of the fragments.

After heterolysis, one atom has a sextet electronic structure and a positive charge and the other, a valence octet with at least one lone pair and a negative charge. Thus, heterolytic cleavage of bromomethane will give :
color{red}(overset(+)CH_3) and color{red}(Br^-) as shown below.

A species having a carbon atom possessing sextext of electrons and a positive charge is called a carbocation (earlier called carbonium ion). The methyl ion is known as a methyl cation or methyl carbonium ion.

Carbocations are classified as primary, secondary or tertiary depending on whether one, two or three carbons are directly attached to the positively charged carbon. Some other examples of carbocations are:

Carbocations are highly unstable and reactive species. Alkyl groups directly attached to the positively charged carbon stabilise the carbocations due to inductive and hyperconjugation effects.

The observed order of carbocation stability is:

color{red}(overset(+)(C)H_3 < CH_3 overset(+)(C)H_2 < ( CH_3)_2 overset(+)(C)H < ( CH_3)_3 overset(+)C)

These carbocations have trigonal planar shape with positively charged carbon being color{red}(sp^2) hybridised.

Thus, the shape of color{red}(overset(+)CH_(3)) may be considered as being derived from the overlap of three equivalent color{red}(C(sp^2)) hybridised orbitals with 1s orbital of each of the three hydrogen atoms. Each bond may be represented as color{red}(C(sp^2)–H(1s)) sigma bond. The remaining carbon orbital is perpendicular to the molecular plane and contains no electrons.

The heterolytic cleavage can also give a species in which carbon gets the shared pair of electrons. For example, when group Z attached to the carbon leaves without electron pair, the methyl anion is formed. Such a carbon species carrying a negative charge on carbon atom is called carbanion. Carbanions are also unstable and reactive species. The organic reactions which proceed through heterolytic bond cleavage are called 𝐢𝐨𝐧𝐢𝐜 𝐨𝐫 𝐡𝐞𝐭𝐞𝐫𝐨𝐩𝐨𝐥𝐚𝐫 or just polar reactions.

In 𝐡𝐨𝐦𝐨𝐥𝐲𝐭𝐢𝐜 𝐜𝐥𝐞𝐚𝐯𝐚𝐠𝐞, one of the electrons of the shared pair in a covalent bond goes with each of the bonded atoms. Thus, in homolytic cleavage, the movement of a single electron takes place instead of an electron pair. The single electron movement is shown by ‘half-headed’ (fish hook : ) curved arrow. Such cleavage results in the formation of neutral species (atom or group) which contains an unpaired electron. These species are called free radicals. Like carbocations and carbanions, free radicals are also very reactive. A homolytic cleavage can be shown as:

Alkyl radicals are classified as primary, secondary, or tertiary. Alkyl radical stability increases as we proceed from primary to tertiary:

Organic reactions, which proceed by homolytic fission are called free radical or homopolar or nonpolar reactions.

### Nucleophiles and Electrophiles

A reagent that brings an electron pair is called a 𝐧𝐮𝐜𝐥𝐞𝐨𝐩𝐡𝐢𝐥𝐞 color{red}(("Nu:")) i.e., nucleus seeking and the reaction is then called 𝐧𝐮𝐜𝐥𝐞𝐨𝐩𝐡𝐢𝐥𝐢𝐜. A reagent that takes away an electron pair is called 𝐞𝐥𝐞𝐜𝐭𝐫𝐨𝐩𝐡𝐢𝐥𝐞 color{red}((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 electrophile that 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 nucleophile 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 color{red}((HO^– )), cyanide color{red}((CN^–)) ions and carbanions color{red}((R_3C: text()^–)).

Neutral molecules can also act as nucleophiles due to the presence of lone pair of electrons.

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 color{red}(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.
Q 3264234155

Using curved-arrow notation, show the formation of reactive intermediates when the following covalent bonds undergo heterolytic cleavage.

(a) CH_3–SCH_3,
(b) CH_3–CN,
(c) CH_3–Cu

Solution:

Q 3214234159

Giving justification, categorise the following molecules/ions as nucleophile or electrophile:

HS^(-) , BF_3 , C_2H_5O^(-) , (CH_3)_3N : , Coverset(+)(l) , CH_3 - overset(+)(C) =O , H_2 N :^(-) , overset(+)(N) O_2

Solution:

Nucleophiles : HS^(-) , C_2H_5O^(-) , (CH_3)_3 N : , H_2N :^(-)

These species have unshared pair of electrons, which can be donated and shared with an electrophile.

Electrophiles: BF_3 , Coverset(+)(l) , CH_3 - overset(+)(C) = O , overset(+)(N) O_2.

Reactive sites have only six valence electrons; can accept electron pair from a nucleophile.
Q 3234334252

Identify electrophilic centre in the following: CH_3CH=O, CH_3CN, CH_3I.

Solution:

Among CH_3 H overset(star)(C) = O , H_3 C overset(star)(C) equiv N and H_3 overset(star)(C) - I the starred carbon atoms are electrophilic centers as they will have partial positive charge due to polarity of the bond.

### Electron Movement in Organic Reactions

The movement of electrons in organic reactions can be shown by curved-arrow notation. It shows how changes in bonding occur due to electronic redistribution during the reaction. To show the change in position of a pair of electrons, curved arrow starts from the point from where an electron pair is shifted and it ends at a location to which the pair of electron may move.

Presentation of shifting of electron pair is given below :

Movement of single electron is indicated by a single barbed ‘fish hooks’ (i.e. half headed curved arrow). For example, in transfer ohydroxide ion giving ethanol and in the dissociation of chloromethane, the movement of electron using curved arrows can be depicted as follows:

### Electron Displacement Effects in Covalent Bonds

The electron displacement in an organic molecule may take place either in the ground state under the influence of an atom or a substituent group or in the presence of an appropriate attacking reagent.

The electron displacements due to the influence of an atom or a substituent group present in the molecule cause permanent polarlisation of the bond. Inductive effect and resonance effects are examples of this type of electron displacements.

Temporary electron displacement effects are seen in a molecule when a reagent approaches to attack it. This type of electron displacement is called electromeric effect or polarisability effect.

### Inductive Effect

When a covalent bond is formed between atoms of different electronegativity, the electron density is more towards the more electronegative atom of the bond. Such a shift of electron density results in a polar covalent bond.

Let us consider cholorethane (color{red}(CH_3CH_2Cl)) in which the color{red}(C–Cl) bond is a polar covalent bond. It is polarised in such a way that the carbon-1 gains some positive charge (color{red}(delta^+)) and the chlorine some negative charge (color{red}(delta^– )). The fractional electronic charges on the two atoms in a polar covalent bond are denoted by symbol color{red}(delta) (delta) and the shift of electron density is shown by an arrow that points from color{red}(delta^+) to color{red}(delta^–) end of the polar bond.

In turn carbon-1, which has developed partial positive charge (color{red}(delta^+) ) draws some electron density towards it from the adjacent color{red}(C-C) bond. Consequently, some positive charge (color{red}(delta delta^+)) develops on carbon-2 also, where color{red}(delta delta^+) symbolises relatively smaller positive charge as compared to that on carbon – 1. In other words, the polar color{red}(C – Cl) bond induces polarity in the adjacent bonds. Such polarisation of color{red}(sigma)-bond caused by the polarisation of adjacent color{red}(sigma)-bond is referred to as the inductive effect. This effect is passed on to the subsequent bonds also but the effect decreases rapidly as the number of intervening bonds increases and becomes vanishingly small after three bonds.

The substitutents can be classified as electron-withdrawing or electron donating groups relative to hydrogen. Halogens and many other groups such as nitro (color{red}(- NO_2)), cyano (color{red}(- CN)), carboxy (color{red}(- COOH)), ester (color{red}(-COOR)), aryloxy (color{red}(-OAr), e.g. color{red}(– OC_6H_5)), etc. are electron-withdrawing groups. On the other hand, the alkyl groups like methyl (color{red}(–CH_3)) and ethyl (color{red}(–CH_2–CH_3)) are usually considered as electron donating groups.

Q 3254334254

Which bond is more polar in the following pairs of molecules:
(a) H_3C-H, H_3C-Br
(b) H_3C-NH_2, H_3C-OH
(c) H_3C-OH, H_3C-SH

Solution:

(a) C–Br, since Br is more electronegative than H,
(b) C–O,
(c) C–O
Q 3264334255

In which C–C bond of CH_3CH_2CH_2Br, the inductive effect is expected to be the
least?

Solution:

Magnitude of inductive effect diminishes as the number of intervening bonds increases. Hence, the effect is least in the bond between carbon-3 and hydrogen.