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I am wondering why it is not mentioned at all in basic text books such as Lehninger?

Books are not flawless.

Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, then why is histidine such a weak base?

Pyrolles have a weak basicity because of delocalization of the electron lone pair of nitrogen. It is the lone pair of nitrogen, in amines, which gives it basicity (Check Lewis bases and acids) .

In imidazole, the other nitrogen (N-2) has a free lone pair and does contribute to its basicity. As you pointed out before, imidazolium is a stable moiety and imidazole is much stronger base than pyridine.

But compared to lysine (pKb ≃ 10.5) and arginine (pKb ≃ 12.48) it is a weaker base (pKb ≃ 7). Imines are generally weaker bases than amines because the sp2 hybridization of the former gives them a more s-like character; this makes the lone pair to be held more tightly to the nucleus thereby reducing the basicity. Also, the angle C-N(2)-C angle is constrained (small) because of the planar ring. This again leads to a higher s-like character.

The strong basicity of arginine is because of the guanidium group.

I am wondering why it is not mentioned at all in basic text books such as Lehninger?

Books are not flawless.

Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, then why is histidine such a weak base?

Pyrroles have a weak basicity because of delocalization of the electron lone pair of nitrogen. It is the lone pair of nitrogen, in amines, which gives it basicity (Check Lewis bases and acids) .

In imidazole, the other nitrogen (N-2) has a free lone pair and does contribute to its basicity. As you pointed out before, imidazolium is a stable moiety and imidazole is a much stronger base than pyridine, although it is a weaker (pKb ≃ 7) base than lysine (pKb ≃ 10.5) and arginine (pKb ≃ 12.48). 

Imines are generally weaker bases than amines because the sp2 hybridization of the former gives them a more s-like character; this causes the lone pair to be held more tightly to the nucleus thereby reducing the basicity. Also, the C-N(2)-C angle is constrained (small) because of the planar ring. This again leads to a more s-like character.

The strong basicity of arginine is because of the guanidium group.

I am wondering why it is not mentioned at all in basic text books such as Lehninger?

Books are not flawless.

Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, > then why is histidine such a weak base?

Pyrolles have a weak basicity because of delocalization of the electron lone pair of nitrogen. It is the lone pair of nitrogen, in amines, which gives it basicity (Check Lewis bases and acids) .

In imidazole, the other nitrogen (N-2) has a free lone pair and does contribute to its basicity. As you pointed out before, imidazolium is a stable moiety and imidazole is much stronger base than pyridine.

But compared to lysine (pKb ≃ 10.5) and arginine (pKb ≃ 12.48) it is a weaker base (pKb ≃ 7). Imines are generally weaker bases than amines because the sp2 hybridization of the former gives them a more s-like character; this makes the lone pair to be held more tightly to the nucleus thereby reducing the basicity. Also, the angle C-N(2)-C angle is constrained (small) because of the planar ring. This again leads to a higher s-like character.

The strong basicity of arginine is because of the guanidium group.

I am wondering why it is not mentioned at all in basic text books such as Lehninger?

Books are not flawless.

Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, then why is histidine such a weak base?

Pyrolles have a weak basicity because of delocalization of the electron lone pair of nitrogen. It is the lone pair of nitrogen, in amines, which gives it basicity (Check Lewis bases and acids) .

In imidazole, the other nitrogen (N-2) has a free lone pair and does contribute to its basicity. As you pointed out before, imidazolium is a stable moiety and imidazole is much stronger base than pyridine.

But compared to lysine (pKb ≃ 10.5) and arginine (pKb ≃ 12.48) it is a weaker base (pKb ≃ 7). Imines are generally weaker bases than amines because the sp2 hybridization of the former gives them a more s-like character; this makes the lone pair to be held more tightly to the nucleus thereby reducing the basicity. Also, the angle C-N(2)-C angle is constrained (small) because of the planar ring. This again leads to a higher s-like character.

The strong basicity of arginine is because of the guanidium group.

I am wondering why it is not mentioned at all in basic text books such as Lehninger?

Books are not flawless.

Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, > then why is histidine such a weak base?

Pyrolles have a weak basicity because of delocalization of the electron lone pair of nitrogen. It is the lone pair of nitrogen, in amines, which gives it basicity (Check Lewis bases and acids) .

In imidazole, the other nitrogen (sp2) has a free lone pair and does contribute to its basicity. As you pointed out before, imidazolium is a stable moiety and imidazole is much stronger base than pyridine.

But compared to lysine (pKb ≃ 10.5) and arginine (pKb ≃ 12.48) it is a weaker base (pKb ≃ 7). Imines are generally weaker bases than amines because the sp2 hybridization of the former gives them a more s-like character; this makes the lone pair to be held more tightly to the nucleus thereby reducing the basicity.

The strong basicity of arginine is because of the guanidium group.

I am wondering why it is not mentioned at all in basic text books such as Lehninger?

Books are not flawless.

Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, > then why is histidine such a weak base?

Pyrolles have a weak basicity because of delocalization of the electron lone pair of nitrogen. It is the lone pair of nitrogen, in amines, which gives it basicity (Check Lewis bases and acids) .

In imidazole, the other nitrogen (N-2) has a free lone pair and does contribute to its basicity. As you pointed out before, imidazolium is a stable moiety and imidazole is much stronger base than pyridine.

But compared to lysine (pKb ≃ 10.5) and arginine (pKb ≃ 12.48) it is a weaker base (pKb ≃ 7). Imines are generally weaker bases than amines because the sp2 hybridization of the former gives them a more s-like character; this makes the lone pair to be held more tightly to the nucleus thereby reducing the basicity. Also, the angle C-N(2)-C angle is constrained (small) because of the planar ring. This again leads to a higher s-like character.

The strong basicity of arginine is because of the guanidium group.