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


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")`.

๐€ ๐ฌ๐ž๐ช๐ฎ๐ž๐ง๐ญ๐ข๐š๐ฅ ๐š๐œ๐œ๐จ๐ฎ๐ง๐ญ ๐จ๐Ÿ ๐ž๐š๐œ๐ก ๐ฌ๐ญ๐ž๐ฉ, ๐๐ž๐ฌ๐œ๐ซ๐ข๐›๐ข๐ง๐  ๐๐ž๐ญ๐š๐ข๐ฅ๐ฌ ๐จ๐Ÿ ๐ž๐ฅ๐ž๐œ๐ญ๐ซ๐จ๐ง ๐ฆ๐จ๐ฏ๐ž๐ฆ๐ž๐ง๐ญ, ๐ž๐ง๐ž๐ซ๐ ๐ž๐ญ๐ข๐œ๐ฌ ๐๐ฎ๐ซ๐ข๐ง๐  ๐›๐จ๐ง๐ ๐œ๐ฅ๐ž๐š๐ฏ๐š๐ ๐ž ๐š๐ง๐ ๐›๐จ๐ง๐ ๐Ÿ๐จ๐ซ๐ฆ๐š๐ญ๐ข๐จ๐ง, ๐š๐ง๐ ๐ญ๐ก๐ž ๐ซ๐š๐ญ๐ž๐ฌ ๐จ๐Ÿ ๐ญ๐ซ๐š๐ง๐ฌ๐Ÿ๐จ๐ซ๐ฆ๐š๐ญ๐ข๐จ๐ง ๐จ๐Ÿ ๐ซ๐ž๐š๐œ๐ญ๐š๐ง๐ญ๐ฌ ๐ข๐ง๐ญ๐จ ๐ฉ๐ซ๐จ๐๐ฎ๐œ๐ญ๐ฌ (๐ค๐ข๐ง๐ž๐ญ๐ข๐œ๐ฌ) ๐ข๐ฌ ๐ซ๐ž๐Ÿ๐ž๐ซ๐ซ๐ž๐ ๐ญ๐จ ๐š๐ฌ ๐ซ๐ž๐š๐œ๐ญ๐ข๐จ๐ง ๐ฆ๐ž๐œ๐ก๐š๐ง๐ข๐ฌ๐ฆ.

Fission of a Covalent Bond

A covalent bond can get cleaved either by : (i) ๐ก๐ž๐ญ๐ž๐ซ๐จ๐ฅ๐ฒ๐ญ๐ข๐œ ๐œ๐ฅ๐ž๐š๐ฏ๐š๐ ๐ž, or by (ii) ๐ก๐จ๐ฆ๐จ๐ฅ๐ฒ๐ญ๐ข๐œ ๐œ๐ฅ๐ž๐š๐ฏ๐š๐ ๐ž.

In ๐ก๐ž๐ญ๐ž๐ซ๐จ๐ฅ๐ฒ๐ญ๐ข๐œ ๐œ๐ฅ๐ž๐š๐ฏ๐š๐ ๐ž, 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)โ€“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 ๐ข๐จ๐ง๐ข๐œ ๐จ๐ซ ๐ก๐ž๐ญ๐ž๐ซ๐จ๐ฉ๐จ๐ฅ๐š๐ซ or just polar reactions.

In ๐ก๐จ๐ฆ๐จ๐ฅ๐ฒ๐ญ๐ข๐œ ๐œ๐ฅ๐ž๐š๐ฏ๐š๐ ๐ž, 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 โ€˜half-headedโ€™ (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 ๐ง๐ฎ๐œ๐ฅ๐ž๐จ๐ฉ๐ก๐ข๐ฅ๐ž `color{red}(("Nu:"))` i.e., nucleus seeking and the reaction is then called ๐ง๐ฎ๐œ๐ฅ๐ž๐จ๐ฉ๐ก๐ข๐ฅ๐ข๐œ. A reagent that takes away an electron pair is called ๐ž๐ฅ๐ž๐œ๐ญ๐ซ๐จ๐ฉ๐ก๐ข๐ฅ๐ž `color{red}((E^+))` i.e., electron seeking and the reaction is called ๐ž๐ฅ๐ž๐œ๐ญ๐ซ๐จ๐ฉ๐ก๐ข๐ฅ๐ข๐œ.

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^โ€“ ))`, cyanide `color{red}((CN^โ€“))` ions and carbanions `color{red}((R_3C: text()^โ€“))`.

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_3โ€“SCH_3,`
(b) `CH_3โ€“CN,`
(c) `CH_3โ€“Cu`


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`


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`.


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 โ€˜fish hooksโ€™ (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}(Cโ€“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^โ€“ ))`. 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^โ€“)` 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 โ€“ 1. In other words, the polar `color{red}(C โ€“ 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}(โ€“ OC_6H_5)`), etc. are electron-withdrawing groups. On the other hand, the alkyl groups like methyl (`color{red}(โ€“CH_3)`) and ethyl (`color{red}(โ€“CH_2โ€“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`


(a) `Cโ€“Br`, since` Br` is more electronegative than `H`,
(b) `Cโ€“O`,
(c) `Cโ€“O`
Q 3264334255

In which `Cโ€“C` bond of `CH_3CH_2CH_2Br`, the inductive effect is expected to be the


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.