FAD1018 W12 — Amine & Amino Acids
Week 12 lecture covering amines and amino acids. Lecture 3 on amino acids presented by Dr Syazreen Nadia Sulaiman. Source files: W12 (1).pdf, W12 (2).pdf, W12 (3).pdf from lecture notes folders.
Summary
Study of amines (classification, properties, reactions) and amino acids as building blocks of proteins.
Key Concepts
- Amines & Amino Acids — Nitrogen-containing organic compounds
- Primary, Secondary, Tertiary Amines — Classification
- Quaternary Ammonium Salts — R₄N⁺
- Amino Acids — Building blocks of proteins
- Fischer Projection — D- and L-amino acid configuration
- Essential Amino Acids — Must be obtained from diet
- Zwitterions — Dipolar ions
- Isoelectric Point (pI) — pH of zero net charge
- pKa Values — Ionizable groups in amino acids
- Electrophoresis — Separation based on pI
- Peptide Bond — Amide linkage between amino acids
W12 (2) — Amine Lecture 2: Preparation & Chemical Reactions
Lecturer: Dr Syazreen Nadia Sulaiman
Scope: Preparation methods of amines and their chemical reactions with acyl chlorides, acid anhydrides, esters, nitrous acid, and bromine water.
Learning Outcomes
- Categorize amines as primary, secondary, or tertiary
- Draw and name amines according to IUPAC nomenclature
- Explain physical properties (boiling points, solubility)
- Compare basicity of ammonia, aliphatic amines, and aromatic amines
- Explain preparation of aromatic amines, primary aliphatic amines (via nitriles), and primary/secondary/tertiary amines (via amides, Hoffmann degradation)
- Explain chemical properties with reference to reactions with acyl chloride, acid anhydrides, nitrous acid, bromine water
Preparation of Amines
1. Reduction of Nitro Compounds
Nitro compounds can be reduced to primary amines using one of the following reagents:
- H₂ with Ni, Pt, or Pd catalyst
- Zn, Fe, or Sn with HCl
- SnCl₂ + HCl
- LiAlH₄ followed by hydrolysis
General reaction:
Specific examples:
CC[N+](=O)[O-]>>CCN
Ethylnitrobenzene → Ethanamine (catalytic hydrogenation with H₂/Ni)
N(=O)(=O)c1ccccc1>>Nc1ccccc1
Nitrobenzene → Aniline (Fe/HCl or Sn/HCl)
[!note] Aromatic nitro compounds Nitrobenzene (C₆H₅NO₂) reduced with Sn/HCl gives aniline (C₆H₅NH₂).
2. Reduction of Amides
Converting amides to amines. The carbonyl carbon is reduced to CH₂.
Key reagents:
- H₂ with Ni, Pt, or Pd catalyst
- LiAlH₄ followed by hydrolysis
General reactions:
| Starting amide | Product |
|---|---|
| 1° amide (R-CONH₂) | 1° amine (R-CH₂-NH₂) |
| 2° amide (R-CONHR') | 2° amine (R-CH₂-NHR') |
| 3° amide (R-CONR'R'') | 3° amine (R-CH₂-NR'R'') |
Specific examples:
CC(N)=O>>CCN
Ethanamide → Ethanamine (LiAlH₄ / H₃O⁺)
CC(=O)N(C)C>>CCN(C)C
N,N-dimethylethanamide → N,N-dimethylethanamine (LiAlH₄ / H₃O⁺)
[!tip] Carbon count Reduction of amides does not change the carbon count. R-C(=O)-NH₂ → R-CH₂-NH₂
3. Reduction of Nitriles
Reduction of nitriles produces primary amines only.
Key reagents:
- H₂ with Ni, Pt, or Pd catalyst
- LiAlH₄ followed by hydrolysis
General reaction:
Specific examples:
CC(C)C#N>>CC(C)CN
2-methylpropanenitrile → 2-methylpropan-1-amine
CC(C)CC#N>>CC(C)CCN
3-methylbutanenitrile → 3-methylbutan-1-amine
[!note] Carbon count increases by 1 R-C≡N → R-CH₂-NH₂. The nitrile carbon becomes the extra carbon in the amine.
4. Hoffmann's Degradation of Amides
In the presence of a strong base, a primary amide reacts with halogen (Cl₂ or Br₂) to form a primary amine with the loss of its carbonyl group (one carbon is removed).
Key reagents: Br₂ + NaOH (strong base & halogen)
General reaction:
Specific examples:
NC(=O)c1ccccc1>>Nc1ccccc1
Benzamide → Aniline (Cl₂/KOH or Br₂/KOH)
CC(C)C(N)=O>>CC(C)N
2-methylpropanamide → propan-2-amine (Br₂/KOH)
[!important] Carbon chain shortening Hoffmann degradation converts primary amides to primary amines while removing one carbon atom.
Summary: Starting from 2-methylpropan-1-ol
Depending on the method chosen, three different primary amines can be prepared:
| Method | Carbon count | Product |
|---|---|---|
| Reduction of amide (same C) | Same as starting alcohol | 2-methylpropan-1-amine |
| Hoffmann degradation (lose 1 C) | Less by one C | propan-2-amine |
| Reduction of nitrile (gain 1 C) | Greater by one C | 3-methylbutan-1-amine |
5. Alkylation of Ammonia or Alkylamines
Ammonia and amines are good nucleophiles, thus react with haloalkanes to give the appropriate amines.
General reaction:
However, this is a poor method of amine preparation since 1°, 2°, and 3° amines have similar reactivity. Multiple alkylations occur, giving a mixture of 1°, 2°, 3° amines and quaternary ammonium salts.
Chemical Reactions of Amines
Due to their lone pair, amines react as nucleophiles.
| Reagent | Product | Mechanism |
|---|---|---|
| haloalkane | substituted amine | nucleophilic substitution |
| acyl chloride | N-substituted amide | addition elimination |
1. Acylation
Amines react with acid derivatives (acid chlorides, acid anhydrides, and esters) to produce amides.
a) Reaction with Acid Chlorides
General reactions:
- 1° amine + acid chloride → 2° amide + ammonium chloride salt
- 2° amine + acid chloride → 3° amide + ammonium chloride salt
- 3° amine + acid chloride → no reaction (no H on nitrogen to attach to Cl)
Specific examples:
CC(=O)Cl.CN>>CC(=O)NC
Acetyl chloride + methanamine → N-methylacetamide
CC(=O)Cl.CNC>>CC(=O)N(C)C
Acetyl chloride + dimethylamine → N,N-dimethylacetamide
b) Reaction with Acid Anhydrides
General reactions:
- 1° amine + acid anhydride → 2° amide + carboxylic acid
- 2° amine + acid anhydride → 3° amide + carboxylic acid
Specific examples:
CC(=O)OC(C)=O.CN>>CC(=O)NC
Acetic anhydride + methanamine → N-methylacetamide + acetic acid
CC(=O)OC(C)=O.CNC>>CC(=O)N(C)C
Acetic anhydride + dimethylamine → N,N-dimethylacetamide + acetic acid
c) Reaction with Esters
General reactions:
- 1° amine + ester → 2° amide + alcohol
- 2° amine + ester → 3° amide + alcohol
Specific examples:
COC(C)=O.CCN>>CCNC(C)=O
Methyl acetate + ethanamine → N-ethylacetamide + methanol
CCOC(C)=O.CN(C)CC>>CCN(C)C(C)=O
Ethyl acetate + N-methylethanamine → N-ethyl-N-methylacetamide + ethanol
2. Reaction with Nitrous Acid (HNO₂)
Nitrous acid is a weak acid. It is unstable and always prepared in situ:
- HCl + NaNO₂(aq) → HO-NO(aq) + NaCl(aq)
- H₂SO₄ + NaNO₂(aq) → 2 HO-NO(aq) + Na₂SO₄(aq)
Nitrous acid reacts with all amines. However, amines of different classes yield different products. This reaction is used as a laboratory test to differentiate amines.
a) Primary Aliphatic Amines
The reaction yields highly unstable aliphatic diazonium salts which decompose spontaneously, even at low temperature (0-5 °C), to form carbocations by evolving N₂ gas.
The carbocation stabilizes by losing a proton to form alkenes, and reacts with nucleophiles in the mixture (water to form alcohols, X⁻ to form haloalkanes).
General reaction:
Specific example:
CCCN.O=N[O-].[Na+].[Cl-].[Na+].Cl>>C=CC.CC(C)O.CC(C)Cl
Propan-1-amine + NaNO₂/HCl (0-5 °C) → propene + propan-2-ol + 2-chloropropane + N₂
[!note] Products are a mixture Primary aliphatic amines give a mixture of alkene, alcohol, and haloalkane due to carbocation rearrangement and nucleophilic attack.
b) Primary Aromatic Amines
Reactions of nitrous acid with primary aromatic amines yield arenediazonium salts which are stable at temperatures < 5 °C.
Formation:
Nc1ccccc1.O=N[O-].[Na+].[Cl-].[Na+].Cl>>[N+]#Nc1ccccc1.[Cl-]
Aniline + NaNO₂/HCl (0-5 °C) → benzenediazonium chloride + NaCl + 2H₂O
Substitutions of the diazonium group:
Arenediazonium salts are highly useful intermediates. The diazonium group can be substituted by almost any nucleophile:
| Reagent | Product | Name |
|---|---|---|
| H₃O⁺ | Ph-OH | Phenol |
| CuCl | Ph-Cl | Chlorobenzene |
| CuBr | Ph-Br | Bromobenzene |
| CuCN | Ph-CN | Benzonitrile |
| KI | Ph-I | Iodobenzene |
[!tip] Temperature sensitivity Arenediazonium salts are unstable at temperatures above 5-10 °C. Most substitution reactions do not require their isolation — reagents are added directly and warmed gently with evolution of N₂ gas.
Azo coupling reactions:
Arenediazonium ions are weak electrophiles and undergo coupling reactions with aromatic compounds containing strong electron-donating groups (-OH, -NR₂) at the para position to yield azo compounds.
[Cl-].[N+]#Nc1ccccc1.Oc1ccccc1>>O=S(=O)([O-])c1ccc(N=Nc2ccccc2O)cc1
Benzenediazonium salt + phenol → orange azo dye
[Cl-].[N+]#Nc1ccccc1.CN(C)c1ccccc1>>CN(C)c1ccc(N=Nc2ccccc2)cc1
Benzenediazonium salt + N,N-dimethylaniline → yellow azo dye
[!note] Azo dyes Azo compounds are usually intensely colored and relatively inexpensive, used extensively as dyes.
c) Secondary Amines (Aliphatic & Aromatic)
Secondary aliphatic amines and aromatic amines react with nitrous acid to form N-nitroso-N-alkylalkanamine and N-nitroso-N-alkylaniline respectively as an oily yellow liquid.
General reaction:
Specific examples:
CNC.O=N[O-].[Na+].[Cl-].[Na+].Cl>>CN(C)N=O
Dimethylamine + NaNO₂/HCl → N,N-dimethylnitrous amide (yellow oil)
CNc1ccccc1.O=N[O-].[Na+].[Cl-].[Na+].Cl>>CN(c1ccccc1)N=O
N-methylaniline + HNO₂ → N-methyl-N-phenylnitrous amide
d) Tertiary Aliphatic Amines
Tertiary aliphatic amines react with nitrous acid to form a mixture of salts:
- The amine reacts as a base and accepts a proton from HCl to form trialkylammonium chloride
- The amine can also react as a Lewis base by donating the lone pair to a nitroso ion (NO⁺) to form trialkylnitrosoammonium chloride
These salts are soluble in water (clear solution).
Specific example:
CCN(C)C.O=N[O-].[Na+].[Cl-].[Na+].Cl>>CC[NH+](C)C.[Cl-].CC[N+](C)(C)N=O.[Cl-]
N,N-dimethylethanamine + NaNO₂/HCl → N,N-dimethylethanammonium chloride + N,N-dimethyl-N-nitrosoethanammonium chloride
e) Tertiary Aromatic Amines
Tertiary aromatic amines react with nitrous acid to form solid products with a nitroso group attached to the para position in the benzene ring. If the para position is not available, the nitroso group attaches to the ortho position.
Specific example:
CN(CC)c1ccccc1.O=N[O-].[Na+].[Cl-].[Na+].Cl>>CN(CC)c1ccc(N=O)cc1
N-ethyl-N-methylaniline + NaNO₂/HCl → N-ethyl-N-methyl-4-nitrosoaniline (solid)
Summary Table: Reaction with Nitrous Acid
| Amine | Observation |
|---|---|
| 1° aliphatic | Bubbles of N₂ gas |
| 1° aromatic | No bubble of gas at < 5 °C |
| 2° aliphatic & aromatic | Yellow oil |
| 3° aliphatic | Clear solution |
| 3° aromatic | Precipitate (solid) |
3. Reaction of Aniline with Bromine Water
The amino group (-NH₂) is an activating group and an ortho-para director, just like the -OH group in phenol.
Aniline reacts easily with aqueous bromine to give a high yield of 2,4,6-tribromoaniline as a white precipitate.
Nc1ccccc1.[Br-].[Br-].[Br-].[K+].[K+].[K+]>>Nc1c(Br)cc(Br)cc1Br
Aniline + 3 Br₂(aq) → 2,4,6-tribromoaniline (white precipitate) + 3 HBr
The bromine decolorizes and hydrogen bromide is given off.
[!important] Preliminary test Due to the readiness of the reaction which gives a very clear observation, this reaction is used as a preliminary test to identify the presence of aniline.
Amino Acids — Lecture 3 Details (Dr Syazreen Nadia Sulaiman)
Learning Outcomes
- Identify the general structure of amino acids
- Identify the structures of 20 standard amino acids
- Name amino acids according to IUPAC rules
- Define zwitterion and isoelectric point
- Draw amino acid structures in acidic, basic, and at pI media
- Explain reactions of amino acids
- Describe peptide bond formation in polypeptides
- Explain protein structure and importance
Structure & Chirality
-
Amino acids are carboxylic acids containing an amino (-NH₂) group attached to the α-carbon
-
General structure: H₂N-CHR-COOH
-
Simplest amino acid: Glycine (NH₂-CH₂-COOH), IUPAC: 2-aminoethanoic acid
NCC(=O)O
- All α-amino acids except glycine contain a stereocenter/chiral center → optically active
- Exist in L- and D-forms based on molecular configuration (Fischer projection)
- L-amino acid: amino group on the left in Fischer projection (natural form in proteins)
- D-amino acid: amino group on the right in Fischer projection
The 20 Common (Standard) α-Amino Acids
Non-polar Side Chain (H or Alkyl)
- Glycine (Gly, G): H — none — non-essential
- Alanine (Ala, A): -CH₃ — alkyl — non-essential
- Valine (Val, V)*: -CH(CH₃)₂ — alkyl — essential
- Leucine (Leu, L)*: -CH₂-CH(CH₃)₂ — alkyl — essential
- Isoleucine (Ile, I)*: -CH(CH₃)-CH₂-CH₃ — alkyl — essential
- Phenylalanine (Phe, F)*: -CH₂-C₆H₅ — aromatic — essential
- Proline (Pro, P): cyclic — rigid cyclic — non-essential
- Methionine (Met, M)*: -CH₂-CH₂-S-CH₃ — sulfide — essential
- Tryptophan (Trp, W)*: -CH₂-indole — indole — essential
N[C@@H](C)C(=O)O
Alanine (Ala)
CC(C)[C@@H](N)C(=O)O
Valine (Val)
CC(C)C[C@@H](N)C(=O)O
Leucine (Leu)
CC[C@H](C)[C@@H](N)C(=O)O
Isoleucine (Ile)
N[C@@H](Cc1ccccc1)C(=O)O
Phenylalanine (Phe)
OC(=O)[C@@H]1CCCN1
Proline (Pro)
CSCC[C@@H](N)C(=O)O
Methionine (Met)
N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O
Tryptophan (Trp)
Polar Side Chain (contains -OH or non-basic nitrogen)
- Serine (Ser, S): -CH₂-OH — hydroxyl — non-essential
- Threonine (Thr, T)*: -CH(OH)-CH₃ — hydroxyl — essential
- Tyrosine (Tyr, Y): -CH₂-C₆H₄-OH — phenolic-OH — non-essential
- Cysteine (Cys, C): -CH₂-SH — thiol — non-essential
- Asparagine (Asn, N): -CH₂-CONH₂ — amide — non-essential
- Glutamine (Gln, Q): -CH₂-CH₂-CONH₂ — amide — non-essential
OC[C@@H](N)C(=O)O
Serine (Ser)
C[C@H](O)[C@@H](N)C(=O)O
Threonine (Thr)
N[C@@H](Cc1ccc(O)cc1)C(=O)O
Tyrosine (Tyr)
SC[C@@H](N)C(=O)O
Cysteine (Cys)
NC(=O)C[C@@H](N)C(=O)O
Asparagine (Asn)
NC(=O)CC[C@@H](N)C(=O)O
Glutamine (Gln)
Acidic Side Chain
- Aspartic acid (Asp, D): -CH₂-COOH — carboxylic acid — negatively charged at pH 7
- Glutamic acid (Glu, E): -CH₂-CH₂-COOH — carboxylic acid — negatively charged at pH 7
N[C@@H](CC(=O)O)C(=O)O
Aspartic acid (Asp)
N[C@@H](CCC(=O)O)C(=O)O
Glutamic acid (Glu)
Basic Side Chain
- Lysine (Lys, K)*: -(CH₂)₄-NH₂ — amino — positively charged at pH 7 — essential
- Arginine (Arg, R)*: -(CH₂)₃-NH-C(=NH)-NH₂ — guanidino — positively charged at pH 7 — essential
- Histidine (His, H)*: -CH₂-imidazole — imidazole — positively charged at pH 7 — essential
NCCCC[C@@H](N)C(=O)O
Lysine (Lys)
NC(=N)NCCC[C@@H](N)C(=O)O
Arginine (Arg)
N[C@@H](Cc1c[nH]cn1)C(=O)O
Histidine (His)
[!note] Essential Amino Acids Ten amino acids marked with * must be obtained from diet: Val, Leu, Ile, Phe, Met, Trp, Thr, Lys, Arg, His
[!note] Abbreviations Most abbreviations are the first three letters. Exceptions: Ile, Trp, Asn, Gln. One-letter symbols are usually the first letter, with exceptions: Phe (F), Trp (W), Asn (N), Gln (Q), Tyr (Y), Asp (D), Glu (E), Lys (K), Arg (R).
Rare Amino Acids
- 4-Hydroxyproline & 5-Hydroxylysine — found in collagen
- D-Glutamic Acid — present in bacterial cell walls
- D-Serine — found in earthworms, neurological signaling
- GABA — neurotransmitter, regulates brain activity
- Beta-Alanine — component of pantothenic acid (Vitamin B5)
OC(=O)[C@@H]1C[C@H](O)CN1
4-Hydroxyproline
N[C@@H](CCCC(CN)O)C(=O)O
5-Hydroxylysine
N[C@H](CCC(=O)O)C(=O)O
D-Glutamic acid
N[C@H](CO)C(=O)O
D-Serine
NCCCC(=O)O
GABA
NCCC(=O)O
Beta-Alanine
Classification
- By structure: Based on functional group location (α, β, γ, etc.)
- By polarity: Grouped by side chain functional groups
- By pH level: Acidic (Asp, Glu), Basic (Lys, Arg, His), Neutral (Gly, Ala, etc.)
- By nutritional importance: Essential, Semi-essential, Non-essential
Nomenclature
- Named as derivatives of carboxylic acids
- The carboxyl (-COOH) group is the parent chain
- All other groups are named as substituents
- Examples: Methionine = 2-amino-4-methylthiobutanoic acid; Asparagine = 2,4-diamino-4-oxobutanoic acid
Physical Properties
- Crystalline solids with high melting points — strong ionic attractions between zwitterions
- Solubility in water — generally soluble; insoluble in non-polar solvents; varies with R-group
- Highly polar molecules — large dipole moment; high dielectric constant
- Zwitterion formation — dominant form in solution (no net charge, but dipolar)
General amino acid zwitterion
[NH3+]CC(=O)[O-]
Glycine zwitterion, pI = 6.0
Chemical Properties
Reactions of the Carboxylic Acid Group
- With NaOH: Neutralization → salt + water
- With alcohol (Esterification): Ester formed with alcohol in presence of acid (HCl/H⁺)
[NH3+]CC(=O)[O-].[Na+].[OH-]>>[NH3+]CC(=O)[O-].[Na+].[OH-]
Glycine zwitterion + NaOH → sodium glycinate + H₂O
[NH3+]CC(=O)[O-].CO.[H+].[Cl-]>>[NH3+]CC(=O)OC.[Cl-]
Glycine + methanol (H⁺) → glycine methyl ester
Reactions of the Amino Group
- With HCl: Forms aminium salt
- With acid chlorides: Formation of acyl derivatives
- With nitrous acid (HNO₂) at 0°C: Formation of α-hydroxy carboxylic acids; products include alcohols, haloalkanes, and alkenes
[NH3+]CC(=O)[O-].[H+].[Cl-]>>[NH3+]CC(=O)O.[Cl-]
Glycine zwitterion + HCl → glycinium chloride
N[C@@H](C)C(=O)O.O=N[O-].[Na+].[Cl-].[Na+].Cl>>CC(O)C(=O)O
Alanine + HNO₂ → 2-hydroxypropanoic acid + N₂
Peptide Bond Formation
Amino acids link together through amide bonds (peptide bonds) between the α-COOH of one amino acid and the α-NH₂ of another, with elimination of water.
NCC(=O)O.N[C@@H](C)C(=O)O>>NCC(=O)N[C@@H](C)C(=O)O
Glycine + Alanine → glycylalanine (dipeptide) + H₂O
[!note] Peptide bond The peptide bond (-CO-NH-) is an amide linkage. Polypeptides are chains of amino acids; proteins consist of one or more polypeptide chains.
Acid-Base Properties
Amphoteric Nature
- Can act as both acids and bases
- -NH₂ group → base (accepts protons)
- -COOH group → acid (donates protons)
pH-Dependent Forms
- Low pH (Acidic): Ammonium Carboxylic Acid — fully protonated cation (+ charge)
- Neutral pH (pI): Zwitterion — no net charge
- High pH (Basic): Amino Carboxylate Ion — fully deprotonated anion (- charge)
Low pH (acidic) — fully protonated cation
Neutral pH (pI) — zwitterion, no net charge
High pH (basic) — fully deprotonated anion
pKa Values
- Carboxyl group (-COOH): pKa ≈ 2
- Amino group (-NH₃⁺): pKa ≈ 9–10
- Example: glycine pKa₁ ≈ 2.3, pKa₂ ≈ 9.6, pI = 6.0
Isoelectric Point (pI)
- Neutral side chains: pI = ½(pKa₁ + pKa₂)
- Acidic side chains: average of two most acidic pKa values
- Basic side chains: average of two least acidic pKa values
- Example: Lysine pI = (10.53 + 8.95)/2 = 9.74
- Neutral amino acids: isoelectric pH slightly acidic (5–6)
- Least soluble at pI
Separation by Electrophoresis
- pI > solution pH → +ve charge → moves toward cathode (-)
- pI < solution pH → -ve charge → moves toward anode (+)
- pI = solution pH → no movement
Related Topics
- Carboxylic Acids & Derivatives — Amide formation
- Polymer Chemistry — Proteins as natural polymers
Study Notes
[!important] Key biomolecular topic Amino acids and proteins are fundamental to biochemistry. Know the 20 common amino acids and their classifications.