Module 09: Nitrogen Functional Groups

Amines: Structure, Nomenclature, and Properties

• Definition & Classification: Organic derivatives of ammonia ($\text{NH}_3$) classified by the number of carbons directly bonded to nitrogen:

  • Primary ($1^\circ$): One $R$ group ($R\text{-NH}_2$).

  • Secondary ($2^\circ$): Two $R$ groups ($R_1\text{-NH-}R_2$).

  • Tertiary ($3^\circ$): Three $R$ groups ($R_1\text{-N}(R_2)\text{-}R_3$). The nitrogen in $1^\circ$, $2^\circ$, and $3^\circ$ amines contains a lone pair of non-bonding electrons fulfilling an octet.

  • Quaternary ($4^\circ$): Four $R$ groups ($R_4\text{N}^+ X^-$); nitrogen utilizes its lone pair to bond to the fourth group, carrying a formal positive charge.

• Aromatic & Heterocyclic Amines:

  • Aromatic amines: Aniline ($1^\circ$ aromatic amine), N-Methylaniline ($2^\circ$ aromatic amine), Benzyldimethylamine ($3^\circ$ aliphatic amine).

  • Heterocyclic aliphatic amines: Pyrrolidine, Piperidine.

  • Heterocyclic aromatic amines: Pyridine, Pyrimidine, Imidazole, Purine.

• Nomenclature:

  • Common system: List attached alkyl groups in alphabetical order followed by the suffix -amine (e.g., methylamine, dimethylamine, ethylmethylamine).

  • IUPAC system: The functional group becomes the suffix -amine if primary, or prefix amino- if a higher priority functional group is present (e.g., 2-pentanamine, 2-amino-1-propanol).

  • Aromatic amines: Named as derivatives of aniline; substituents located on the nitrogen atom are designated using the italicized prefix N- (e.g., 2-methylaniline, N-ethyl-N-propyl-aniline).

  • Quaternary salts: Named as ionic compounds; name alkyl groups with -ammonium followed by the anion name (e.g., ethyl trimethyl ammonium bromide).

• Physical Properties:

  • Odor: Low-molecular-weight amines exhibit sharp, penetrating odors (e.g., trimethylamine causes the characteristic rotten fish odor).

  • Hydrogen Bonding & Boiling Points: The polar $\text{N-H}$ bond allows intermolecular hydrogen bonding ($\text{N-H}\cdots\text{N}$). Because nitrogen is less electronegative than oxygen ($\Delta\text{EN} = 3.0 - 2.1 = 0.9$ versus $3.5 - 2.1 = 1.4$), amine hydrogen bonding is weaker than alcohol hydrogen bonding.

  • Boiling Point Comparison (similar molecular weight): Ethane ($\text{MW} = 30.1\,\text{amu}$, $\text{bp} = -88.6\,^\circ\text{C}$) < Methanamine ($\text{MW} = 31.1\,\text{amu}$, $\text{bp} = -6.3\,^\circ\text{C}$) < Methanol ($\text{MW} = 32.0\,\text{amu}$, $\text{bp} = 65.0\,^\circ\text{C}$).

  • Solubility: Low-molecular-weight amines are completely water-soluble via hydrogen bonding with water molecules. Water solubility diminishes as hydrocarbon chain length increases; long hydrocarbon chains confer solubility in non-polar solvents.

Chemical Reactions of Amines

• Basicity & Salt Formation:

  • Nitrogen lone pairs accept protons from acids to form amine salts:     $R\text{-NH}_2 + HX \rightarrow R\text{-NH}_3^+ + X^-$

  • Example: $\text{CH}_3\text{-NH}_2 + \text{HCl} \rightarrow \text{CH}_3\text{NH}_3^+ + \text{Cl}^-$

  • Pharmaceuticals containing amine groups are formulated as hydrochloride salts to maximize solubility in aqueous media and the bloodstream.

  • Reaction with carboxylic acids forms carboxylate salts via acid-base neutralization rather than amides:     $\text{CH}_3\text{COOH} + \text{CH}_3\text{NH}_2 \rightarrow \text{CH}_3\text{NH}_3^+ + \text{CH}_3\text{COO}^-$

• Amide Synthesis:

  • Direct mixtures of carboxylic acids and amines do not yield amides under mild conditions.

  • Reactive carboxylic acid derivatives (acid chlorides or acid anhydrides) react with primary or secondary amines to produce amides:     $\text{CH}_3\text{CH}_2\text{COCl} + \text{CH}_3\text{NH}_2 \rightarrow \text{CH}_3\text{CH}_2\text{CONHCH}_3 + \text{HCl}$

  • Tertiary ($3^\circ$) amines lack a removable hydrogen atom on nitrogen and cannot form amides.

  • Polyamides (nylons, Kevlar) form via condensation between diamines and diacyl chlorides (dionyl chlorides).

Amides: Structure, Properties, and Reactions

• Structure & Nomenclature:

  • Characterized by a carbonyl group bonded directly to an amine nitrogen ($R\text{-CO-NR}'R''$).

  • Simple amides: Suffix -amide added to parent alkane root (e.g., ethanamide, 3-methylbutanamide).

  • Substituted amides: Alkyl groups attached to nitrogen are designated by prefix N- (e.g., N-ethylethanamide, N-ethyl-N-methylbutanamide).

• Physical Properties:

  • Except for liquid methanamide, all simple amides are solids at room temperature due to extensive intermolecular hydrogen bonding.

  • Alkyl substitution on the nitrogen reduces hydrogen-bonding capability, lowering melting and boiling points.

  • Amides containing $6$ or fewer carbons are water-soluble due to hydrogen bonding with the carbonyl oxygen ($\text{C=O}^{\delta-}\cdots\text{H}^{\delta+}\text{-O-H}$.

  • Amides are neutral and non-basic in comparison to amines.

• Amide Hydrolysis:

  • Hydrolysis requires heat alongside strong acid or base catalysis:

  • Acid hydrolysis: Produces a carboxylic acid and an amine/ammonium salt ($R\text{-COOH} + R'\text{NH}_3^+$).

  • Base hydrolysis: Produces a carboxylate salt and a free amine ($R\text{-COO}^- + R'\text{NH}_2$).

  • Biological hydrolysis of polyamides and proteins is enzymatically catalyzed to digest peptide bonds into smaller fragments or free amino acids.

Amino Acids and Zwitterions

• Structure & Stereochemistry:

  • Composed of a central $\alpha$-carbon bonded to an amino group ($\text{-NH}_2$), a carboxyl group ($\text{-COOH}$), a hydrogen atom, and a variable side chain ($R$): $\text{H}_2\text{N-CH}(R)\text{-COOH}$.

  • With the exception of glycine ($R = \text{H}$), all standard $\alpha$-amino acids contain at least one stereocenter, are chiral, and occur naturally in proteins as L-enantiomers.

• Zwitterionic States and Isoelectric Point ($pI$):

  • Zwitterion: Dipolar ionic form with no net electrical charge ($\text{H}_3\text{N}^+\text{-CH}(R)\text{-COO}^-$).

  • Isoelectric Point ($pI$): The specific pH at which an amino acid possesses a net charge of zero.

• pH-Dependent Protonation:

  • Low pH (e.g., pH $2$): High $[\text{H}^+]$; carboxylate ion protonates to form neutral $\text{-COOH}$; molecule possesses a net positive charge ($\text{H}_3\text{N}^+\text{-CH}(R)\text{-COOH}$, overall charge $+1$).

  • High pH (e.g., pH $10$): High $[\text{OH}^-]$; ammonium group deprotonates to neutral $\text{-NH}_2$; molecule possesses a net negative charge ($\text{H}_2\text{N-CH}(R)\text{-COO}^-$, overall charge $-1$).

• Classification of Standard Amino Acid Side Chains:

  • Non-polar: Alanine (Ala, A), Glycine (Gly, G), Isoleucine (Ile, I), Leucine (Leu, L), Methionine (Met, M), Phenylalanine (Phe, F), Proline (Pro, P), Tryptophan (Trp, W), Valine (Val, V).

  • Polar, Neutral: Asparagine (Asn, N), Glutamine (Gln, Q), Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Tyrosine (Tyr, Y).

  • Acidic (net negative charge at pH $7.0$):

  • Aspartic acid (Asp, D): $\alpha\text{-COOH } pK_a = 2.10$, $\alpha\text{-NH}_3^+ pK_a = 9.82$, side chain $pK_a = 3.86$, $pI = 2.98$.

  • Glutamic acid (Glu, E): $\alpha\text{-COOH } pK_a = 2.10$, $\alpha\text{-NH}_3^+ pK_a = 9.47$, side chain $pK_a = 4.07$, $pI = 3.08$.

  • Basic (net positive charge at pH $7.0$):

  • Histidine (His, H): $\alpha\text{-COOH } pK_a = 1.77$, $\alpha\text{-NH}_3^+ pK_a = 9.18$, side chain $pK_a = 6.10$, $pI = 7.64$.

  • Lysine (Lys, K): $\alpha\text{-COOH } pK_a = 2.18$, $\alpha\text{-NH}_3^+ pK_a = 8.95$, side chain $pK_a = 10.53$, $pI = 9.74$.

  • Arginine (Arg, R): $\alpha\text{-COOH } pK_a = 2.01$, $\alpha\text{-NH}_3^+ pK_a = 9.04$, side chain $pK_a = 12.48$, $pI = 10.76$.

Peptides and Levels of Protein Structure

• Peptide Bond Formation & Chain Conventions:

  • A peptide bond is an amide linkage formed by condensation between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another.

  • Written left-to-right from the unbonded N-terminal ($\text{-NH}_3^+$) to the unbonded C-terminal ($\text{-COO}^-$).

  • Peptide: Short polymer of amino acids; dipeptide has $2$ units; polypeptide contains many units; protein comprises at least $30\text{ to }50$ amino acid residues.

• Primary ($1^\circ$) Structure:

  • The linear sequence of amino acids held entirely by covalent peptide bonds.

  • Resistant to hydrolysis; cleavage requires boiling in $6\,\text{mol}\,\text{L}^{-1}\text{ HCl}$ at $110\,^\circ\text{C}$ for $24\text{ to }72\,\text{hours}$.

  • Dictates all higher structural tiers (e.g., insulin contains an A-chain and B-chain held by interchain and intrachain disulfide bonds).

• Secondary ($2^\circ$) Structure:

  • Localized spatial arrangements stabilized by hydrogen bonds between backbone amide $\text{N-H}$ and carbonyl $\text{C=O}$ groups:

  • $\alpha$-Helix: Right-handed spiral coil; side-chain $R$ groups project outwards; intrachain hydrogen bonds run parallel to the helical axis.

  • $\beta$-Pleated Sheet: Parallel or antiparallel polypeptide backbones aligned side-by-side; $R$ groups alternate strictly above and below the sheet plane; held by inter-strand hydrogen bonds.

• Tertiary ($3^\circ$) Structure:

  • The overall three-dimensional folding of a single polypeptide chain driven by side-chain interactions:

  • Disulfide bonds: Covalent links formed by oxidation between pairs of cysteine thiol groups ($-\text{CH}_2\text{-S-S-CH}_2-$).

  • Salt bridges: Electrostatic attractions between ionized acidic side chains ($-\text{COO}^-$) and basic side chains ($-\text{NH}_3^+$).

  • Hydrogen bonds: Dipole-dipole interactions between polar side chains (e.g., Ser, Asn, Thr).

  • Hydrophobic interactions: Association of non-polar side chains forced inward away from aqueous solvent.

• Quaternary ($4^\circ$) Structure:

  • Aggregation of two or more independent polypeptide subunits held together via non-covalent interactions (and occasional disulfide bridges).

  • Example: Adult hemoglobin consists of two $\alpha$-chains ($141$ amino acids each) and two $\beta$-chains ($146$ amino acids each), each bound to an iron-containing heme prosthetic unit.

Protein Denaturation

• Concept: Disruption of secondary, tertiary, and quaternary structures resulting in complete loss of native biological function without cleaving covalent primary peptide bonds.

• Denaturing Agents & Modes of Action:

  • Heavy-metal ions ($\text{Hg}^{2+}, \text{Ag}^+, \text{Cd}^{2+}, \text{Pb}^{2+}$): Bind tightly to cysteine $-\text{SH}$ groups, disrupting covalent disulfide bonds and forming insoluble heavy-metal protein precipitates.

  • Heat and UV light: Increase molecular kinetic energy and vibrations, disrupting hydrogen bonds and electrostatic interactions; leads to unfolding and coagulation.

  • Detergents: Amphiphilic molecules disrupt native hydrophobic and ionic associations by associating with non-polar cores via micelle-like structures.

  • Organic solvents (e.g., ethanol, methanol): Polar solvents disrupt native intramolecular hydrogen bonds by forming new competing solute-solvent hydrogen bonds.

  • Strong acids and bases: Disrupt side-chain ionization states, severing salt bridges and hydrogen bonds; prolonged heating leads to complete chemical hydrolysis of peptide bonds.