(a) (i) Draw the structure of 2'-deoxycytidine-3'-monophosphate. (ii) Why nucleotides and nucleic acids are acidic ? Mention the…

(a) Nucleotides and nucleic acids

(i) 2′-Deoxycytidine-3′-monophosphate: cytosine is joined through N-1 to C-1′ of β-D-2-deoxyribofuranose by a β-N-glycosidic bond. C-2′ carries two hydrogens (no OH), C-5′ carries a free CH₂OH, and the phosphate is esterified to the 3′-OH.

(ii) Nucleotides and nucleic acids are acidic because of their phosphate groups. A phosphomonoester has pKₐ values of about 1 and 6, and the single remaining P–OH of each phosphodiester link in DNA or RNA has pKₐ near 1. At physiological pH the backbone is therefore fully ionised, a polyanion with one negative charge per nucleotide, and the conjugate base is resonance-stabilised over the P–O bonds.

The DNA duplex is stabilised by four factors. Watson–Crick hydrogen bonding (A=T two bonds, G≡C three) gives specificity. Base stacking, through van der Waals and π–π interactions between the planar bases, is the largest contribution. The hydrophobic effect buries the bases inside and exposes the sugar-phosphate backbone to water. Counter-ions (Na⁺, Mg²⁺, polyamines) screen the repulsion between the phosphates of the two strands.

(iii) Cytosine–guanine pairing has three hydrogen bonds: cytosine N4–H to guanine O6, guanine N1–H to cytosine N3, and guanine N2–H to cytosine O2.

(b)(i) Vapour-phase photolysis of cyclopentanone

Excitation (n→π*) is followed by Norrish Type I α-cleavage of a C(=O)–Cα bond, which gives the acyl–alkyl 1,5-biradical •C(=O)–CH₂CH₂CH₂CH₂•. This biradical can follow three paths. Recombination regenerates cyclopentanone. Intramolecular H-transfer, in which the acyl radical takes an H from the CH₂ next to the alkyl radical, gives pent-4-enal, CH₂=CH–CH₂CH₂–CHO. Loss of CO from the acyl radical gives the tetramethylene 1,4-biradical •CH₂CH₂CH₂CH₂•, which either closes to cyclobutane or fragments at its central C–C bond to two molecules of ethylene.

The products are therefore CO, ethylene, cyclobutane and pent-4-enal. In the vapour phase no solvent cage holds the radicals together, so decarbonylation (CO + ethylene + cyclobutane) is especially important.

(b)(ii) Direct versus sensitised photolysis of 1,3-butadiene

Path I, direct irradiation: butadiene absorbs only at short wavelength (π→π*, near 217 nm) and reacts from its singlet excited state. The s-cis conformer undergoes photochemically allowed disrotatory 4π electrocyclisation to cyclobutene, and the s-trans conformer gives bicyclo[1.1.0]butane. Both are unimolecular reactions of the singlet.

Path II, benzophenone at 366 nm: butadiene does not absorb at 366 nm, but benzophenone does (n→π*). It crosses to its triplet by fast intersystem crossing (E_T about 69 kcal mol⁻¹) and transfers energy to butadiene (E_T about 60 kcal mol⁻¹), which is triplet sensitisation. Triplet butadiene lives long enough to meet a ground-state molecule and adds to it stepwise through a 1,4-biradical, giving 1,2-divinylcyclobutane and 4-vinylcyclohexene. The triplet state therefore gives bimolecular dimerisation instead of unimolecular electrocyclisation.

(c)(i) Structures of A–E

Compound A is the S-methyl xanthate of 2-methylpentan-3-ol: CS₂/NaOH forms the sodium xanthate and MeI S-methylates it, giving (CH₃)₂CH–CH(C₂H₅)–O–C(=S)–SCH₃.

Compound B: SeO₂ does not act on a xanthate, and the scheme shows no heating, so the Chugaev pyrolysis of A (a syn, six-membered cyclic elimination that releases COS and CH₃SH) is taken as implied before the SeO₂ step. Of the two β-carbons, the CH₂ with two hydrogens gives 4-methylpent-2-ene (E) as the main alkene, and the single tertiary H gives a little 2-methylpent-2-ene. SeO₂ then effects Riley allylic oxidation (ene reaction, [2,3]-shift, hydrolysis), attacking the allylic CH₃ in preference to the tertiary CH. B is 4-methylpent-2-en-1-ol (E); further oxidation to the enal is possible.

Compound C: m-CPBA epoxidises the more electron-rich, tetrasubstituted ring-fusion C=C selectively at 0 °C. The disubstituted C=C and the dimethoxy-arene survive. C is the racemic epoxide at that double bond.

Compound D: Pb(OAc)₄ causes oxidative bis-decarboxylation of the vicinal diacid 2,2,3,3-tetramethylsuccinic acid, losing two CO₂ and forming a C=C. D is 2,3-dimethylbut-2-ene, (CH₃)₂C=C(CH₃)₂.

Compound E: CrO₃·pyridine oxidises the allylic CH₂ (C-6) of (R)-3-methylcyclohexene to the enone. E is 4-methylcyclohex-2-en-1-one (R); the stereocentre is not touched and remains R.

(c)(ii) OsO₄ dihydroxylation of cyclohexene

(I) OsO₄ adds to the C=C in a concerted syn [3+2] cycloaddition. With pyridine, A is the cyclic osmate(VI) ester (the pyridine adduct of the five-membered Os–O–C–C–O ring). B is the reagent that cleaves the Os–O bonds, aqueous NaHSO₃ (or H₂S). It releases cis-cyclohexane-1,2-diol; both C–O bonds keep the syn stereochemistry of the addition.

(II) Osmium is in the +6 oxidation state in A (two oxo, −4, and the diolate, −2, balance Os⁺⁶). The osmate ester itself is four-coordinate, distorted tetrahedral; pyridine coordinates to give a five- or six-coordinate (pseudo-octahedral) adduct.

(c)(iii) Hexitol with cyclohexanone and then HIO₄

The hexitol drawn is D-mannitol, (2R,3R,4R,5R)-hexane-1,2,3,4,5,6-hexol. Compound A: cyclohexanone with BF₃·Et₂O, with HC(OMe)₃ removing the water, protects the two terminal 1,2-diols as five-membered cyclohexylidene ketals. A is 1,2:5,6-di-O-cyclohexylidene-D-mannitol, leaving the C-3/C-4 vicinal diol free.

Compound B: HIO₄ cleaves the free vicinal diol through a cyclic periodate ester, breaking the C3–C4 bond. B is two molecules of 2,3-O-cyclohexylidene-D-glyceraldehyde, (R)-1,4-dioxaspiro[4.5]decane-2-carbaldehyde.