(a) Write the structures of nucleosides and nucleotides, and discuss the primary structures of DNA and RNA. (10 marks) (b) Write…

(a) Structures of nucleosides and nucleotides; primary structures of DNA and RNA

A nucleoside is a molecule consisting of a nitrogenous base (purine or pyrimidine) covalently linked to a pentose sugar via an N-glycosidic bond at the C1' position. A nucleotide is formed when one or more phosphate groups are esterified to the 5′-hydroxyl group of the nucleoside, creating a phosphoester linkage. Examples: adenosine (adenine + ribose) and 2′-deoxythymidine are nucleosides, and adenosine 5′-monophosphate (AMP) and dTMP are nucleotides. Purines bond through N-9 and pyrimidines through N-1 to C-1′ of the sugar, in the β-configuration.

The primary structure of DNA is a linear polymer of deoxyribonucleotides connected by 3',5'-phosphodiester linkages, creating a sugar-phosphate backbone with 5' to 3' polarity. It contains the bases Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). The primary structure of RNA is similar but utilizes ribose (containing a 2'-OH group) and Uracil (U) in place of Thymine. This 2'-OH group makes RNA more chemically labile than DNA. The 5' to 3' polarity is maintained in both, but the presence of the 2'-OH in RNA allows for different secondary structures and catalytic functions.

(b) Products of photolysis of 2-methylcyclohexanone in solution phase

Upon n→π* excitation, 2-methylcyclohexanone undergoes Norrish Type I α-cleavage. The bond between the carbonyl carbon and the more substituted α-carbon (C2) breaks preferentially to generate a 1,5-biradical, as this yields a more stable secondary alkyl radical. In the solution phase, this biradical does not fragment to release CO.

The major products arise from intramolecular hydrogen transfer. Transfer of a hydrogen atom from the carbon adjacent to the alkyl radical to the acyl radical yields unsaturated aldehydes, specifically hept-5-enal and hept-6-enal. Alternatively, hydrogen transfer in the reverse direction (from C-6 to the alkyl radical) produces a ketene, pentylketene, which is trapped by the solvent to form a heptanoate ester or heptanoic acid. Recombination of the biradical also regenerates the ketone, resulting in epimerization at C-2. This mechanism is distinct from gas-phase photolysis, where decarbonylation is the primary pathway.

(c) Synthesis and product identification

(i) The target is 1-ethynylcyclopentan-1-ol, a tertiary propargylic alcohol, so it is made by adding acetylide to cyclopentanone (ethynylation).

1. HC≡CH + NaNH₂ in liquid NH₃ (−33 °C) gives sodium acetylide, HC≡C⁻ Na⁺. One equivalent of base is used so that only one C–H is removed.
2. Cyclopentanone is added. The acetylide carbon attacks the carbonyl carbon, and the C=O π electrons move onto oxygen to give the sodium alkoxide.
3. Aqueous NH₄Cl (or dilute acid) work-up protonates the alkoxide to give 1-ethynylcyclopentan-1-ol.

The same addition can be run industrially with KOH and acetylene under pressure (Favorskii ethynylation).

(ii) The products are identified as follows:

• W: Benzyl bromide (formed by benzylic bromination with NBS).
• X: Benzaldehyde. CrO₃ in Ac₂O traps the aldehyde as benzylidene diacetate, PhCH(OAc)₂, which prevents over-oxidation, and H₃O⁺ then hydrolyses it to PhCHO.
• Y: Cinnamic acid (formed by the Perkin reaction of benzaldehyde with acetic anhydride).
• Z: 3-phenylpropan-1-ol (excess LiAlH₄ reduces the COOH to CH₂OH and, through the allylic alkoxide, also saturates the conjugated C=C. With limited hydride, cinnamyl alcohol would result).

(d) Distinguishing amines by IR and alcohols by PMR

(i) In IR spectroscopy, primary amines exhibit two distinct N-H stretching bands (symmetric and asymmetric) in the 3500-3300 cm⁻¹ region. In contrast, secondary amines show only a single N-H stretching band in this region. Tertiary amines show no N-H stretching absorption. This difference in the number of N-H bonds is the primary diagnostic feature for distinguishing between these amine classes using IR spectroscopy.

(ii) In PMR spectroscopy, the splitting of the hydroxyl proton (OH) allows for distinction. Primary alcohols (R-CH2-OH) show the OH as a triplet due to coupling with two adjacent protons. Secondary alcohols (R-CH-OH) show the OH as a doublet due to coupling with one adjacent proton. Tertiary alcohols (R3C-OH) show the OH as a singlet because there are no adjacent protons on the carbinol carbon. This works when OH exchange is slow, in DMSO-d₆ or very dry CDCl₃. In ordinary CDCl₃ the OH is a broad singlet, and the carbinol protons then decide: RCH₂OH near δ 3.6 (2H), R₂CHOH near δ 3.9 (1H), and no carbinol H for R₃COH. Shaking with D₂O removes the OH signal and confirms it.

(e) Matching spectral data to structures

• Data (i) matches Structure (4) (Benzyl acetate). The IR peak at 1750 cm⁻¹ indicates an ester. The NMR signal at δ 2.0 (s, 3H) corresponds to the acetate methyl group, and δ 5.1 (s, 2H) is the benzylic OCH₂ group. The aromatic protons appear as a singlet at δ 7.3.
• Data (ii) matches Structure (2) (methyl phenylacetate, PhCH₂CO₂CH₃). The IR peak at 1740 cm⁻¹ indicates an ester. The NMR signal at δ 3.6 (s, 2H) is the benzylic CH2, and δ 3.5 (s, 3H) is the ester OCH₃ group. The aromatic protons appear as a singlet at δ 7.4.
• Data (iii) matches Structure (5) (3-phenylpropanoic acid). The broad IR band at 3200-2800 cm⁻¹ and peak at 1700 cm⁻¹ indicate a carboxylic acid. The NMR shows two triplets (δ 2.75 and 2.95) for the two CH2 groups and a broad singlet at δ 12.0 for the acidic proton.