IChO 2024 · Theory problem 6

Penicillin

Penicillins are a group of antibiotics that have played a crucial role in medicine since their discovery.

Figure 1

Penicillin VK

6.1. Mark the stereogenic carbon centers on the structure of Penicillin VK on the answer sheet. Write the corresponding \(R/S\) stereodescriptors next to the centers on the answer sheet. 6 pt

6.2. Give the total number of possible stereoisomers of Penicillin VK. 2 pt

One of the many synthetic methods to obtain Penicillin VK starts from the amino acid valine, as shown in the scheme on the next page of this problem.

Hints:

  • Among other signals, the \({}^{1}\mathrm{H}\)NMR spectrum of compound A contains two signals that each integrate to 3H. Both of these signals are doublets.
  • Compounds A and D are open-chain compounds, while B and E each have a five membered ring (in addition to any rings in the PhthN-group).
  • Brucine is used for chiral resolution.
Figure 2

*Please note that in the formation of (+)-C, the word "Separation" means separation.

**Conc. HCl means concentrated HCl.

6.3. Choose the suitable reagent for the numbered steps \((1–4)\) on the answer sheet. 8 pt

a) \(2\,\mathrm{M}\) \(\ce{HCl_{(aq)}}\)

b) \(\ce{SO3, H2SO4}\)

c) \(\ce{NaOH_{(aq)}}\)

d) \(\ce{HCO2H, Ac2O}\)

e) i) \(\ce{N2H4}\) ii) \(\ce{HCl_{(aq)}, AcOH}\)

f) i) \(\ce{H2S, Na, CH3OH}\) ii) \(\ce{H2O}\)

6.4. Draw the structures of A, B, (+)-C, D, E and F on the answer sheet. Show the stereostructure using wedge–dash notation (

Figure 3

) when relevant. 18 pt

6.5. Select the role of acetone in the step leading to B on the answer sheet. 2 pt

a) solvent

b) catalyst

c) electrophile

d) nucleophile

6.6. Select the role of DCC in the step leading from F to Penicillin VK on the answer sheet. 2 pt

a) oxidizing reagent

b) catalyst

c) coupling reagent

d) radical initiator

Official English text of the problem.

Answers

  • 6.1. There are three stereogenic carbon centers, with configuration \((2S,5R,6R)\) in standard penam numbering:
  • Carboxylate-bearing carbon: \(S\).
  • Fused-ring carbon bearing the explicitly drawn hydrogen: \(R\).
  • β-Lactam carbon bearing the phenoxyacetamido substituent: \(R\).

  • 6.2. \(8\) stereoisomers.

  • 6.3. 1 → f; 2 → d; 3 → a; 4 → e.

  • 6.4. The structures are given below. A and B are racemates; their SMILES specify connectivity without selecting one enantiomer.

Compound Name SMILES
A \((\pm)\)-\(N\)-(2-Chloroacetyl)valine CC(C)C(NC(=O)CCl)C(=O)O
B \((\pm)\)-2,2,5,5-Tetramethyl-1,3-thiazolidine-4-carboxylic acid CC1(C)NC(C(=O)O)C(C)(C)S1
(+)-C \((4S)\)-3-Formyl-2,2,5,5-tetramethyl-1,3-thiazolidine-4-carboxylic acid CC1(C)N(C=O)[C@@H](C(=O)O)C(C)(C)S1
D \((2S)\)-2-Amino-3-methyl-3-sulfanylbutanoic acid, D-penicillamine CC(C)(S)[C@@H](N)C(=O)O
E \((2R,4S)\)-2-[(\(1R\))-2-tert-butoxy-1-(1,3-dioxoisoindolin-2-yl)-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid CC(C)(C)OC(=O)[C@@H](N1C(=O)c2ccccc2C1=O)[C@H]1SC(C)(C)[C@H](C(=O)O)N1
F Penicilloic acid V: \((2R,4S)\)-2-[(\(R\))-carboxy(2-phenoxyacetamido)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid O=C(O)[C@@H](NC(=O)COc1ccccc1)[C@H]1SC(C)(C)[C@H](C(=O)O)N1

D is shown above as its neutral parent. In the acidic mixture from step 3, it is D-penicillamine hydrochloride, CC(C)(S)[C@@H]([NH3+])C(=O)O.[Cl-].

  • 6.5. c) electrophile.

  • 6.6. c) coupling reagent.

Solution

6.1. Stereogenic centers and absolute configurations

Penicillin VK is potassium \((2S,5R,6R)\)-6-(2-phenoxyacetamido)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate:

CC1(C)S[C@@H]2[C@H](NC(=O)COc3ccccc3)C(=O)N2[C@H]1C(=O)[O-].[K+]

The three stereogenic carbons and their CIP priorities are:

Center Position in the supplied drawing Priorities, highest to lowest Configuration
\(C_2\) Upper-right carbon bearing the carboxylate Ring nitrogen; gem-dimethyl carbon; carboxylate carbon; hydrogen \(S\)
\(C_5\) Fused-ring carbon bearing the solid-wedge hydrogen Sulfur; ring nitrogen; \(C_6\); hydrogen \(R\)
\(C_6\) β-Lactam carbon bearing the dashed-bond amide substituent Side-chain nitrogen; \(C_5\); β-lactam carbonyl carbon; hydrogen \(R\)

Two carbon-versus-carbon comparisons deserve attention:

  • At \(C_2\), the gem-dimethyl carbon has the next-layer atoms \((\ce{S},\ce{C},\ce{C})\), whereas the carboxylate carbon has oxygen atoms. Sulfur gives the former higher priority.
  • At \(C_6\), the \(C_5\) branch presents \((\ce{S},\ce{N},\ce{H})\), whereas the carbonyl branch presents \((\ce{O},\ce{O},\ce{N})\). Again, the sulfur-containing branch has higher priority.

Applying these priorities to the shown wedges and dashes gives \((2S,5R,6R)\). The carbon bearing two methyl groups is not stereogenic because those two substituents are identical.

6.2. Number of stereoisomers

There are three stereogenic carbon centers and no internal symmetry that produces a meso form. Therefore,

\[ N_{\text{stereoisomers}}=2^3=\boxed{8}. \]

These comprise four enantiomeric pairs.

6.3. Identification of reagents

Step Choice and reagents, with SMILES Reason
1 f: hydrogen sulfide S, sodium [Na], methanol CO; then water O Introduces the thiol group at the carbon bearing two methyl groups; subsequent hydrolysis opens the oxazolone.
2 d: formic acid O=CO, acetic anhydride CC(=O)OC(C)=O Formylates the thiazolidine nitrogen, producing the shown \(N\)-formyl compound C.
3 a: \(2\,\mathrm{M}\) aqueous hydrochloric acid; hydrogen chloride Cl Hydrolyzes the \(N\)-formyl group and the acetone-derived cyclic \(N,S\)-acetal, releasing open-chain penicillamine.
4 e: hydrazine NN; then hydrochloric acid Cl and acetic acid CC(=O)O Removes the phthaloyl protecting group by hydrazinolysis and gives the amino ester hydrochloride.

The molecular SMILES Cl denotes hydrogen chloride. Its aqueous ionized representation is hydronium chloride, [OH3+].[Cl-].

6.4. Structures and reaction sequence

The equations below are balanced net equations. Neutral parent structures are used unless a hydrochloride is explicitly indicated.

Formation of A and the oxazolone. Racemic valine, 2-amino-3-methylbutanoic acid, CC(C)C(N)C(=O)O, undergoes nitrogen acylation with chloroacetyl chloride, O=C(Cl)CCl:

\[ \ce{(CH3)2CHCH(NH2)COOH + ClCH2COCl -> A + HCl}. \]

The supplied base traps the hydrogen chloride. Thus A is \(N\)-(2-chloroacetyl)valine.

The isopropyl group remains intact. Each methyl group couples to the adjacent methine proton, giving a doublet integrating to three hydrogens. The two methyl groups can have different chemical shifts because the molecule contains the neighboring stereogenic α-carbon. This agrees with the NMR hint.

Let U denote the drawn oxazolone, 2-methyl-4-(propan-2-ylidene)-1,3-oxazol-5(4H)-one:

CC1=NC(=C(C)C)C(=O)O1

Its formation involves cyclodehydration and loss of hydrogen chloride. Including acetic anhydride as the dehydrating reagent gives the net balance

\[ \ce{A + (CH3CO)2O -> U + 2CH3COOH + HCl}. \]

Sulfur introduction and formation of B. In step 1, hydrosulfide, [SH-], adds to the exocyclic double bond at the carbon bearing the two methyl groups. Hydrolysis then opens the oxazolone, giving X, \(N\)-acetyl-DL-penicillamine:

CC(=O)NC(C(=O)O)C(C)(C)S

The net reaction is

\[ \ce{U + H2S + H2O -> X}. \]

Hot aqueous hydrochloric acid hydrolyzes the acetyl protecting group. Calling the resulting racemic penicillamine P, CC(C)(S)C(N)C(=O)O, the neutral-parent balance is

\[ \ce{X + H2O -> P + CH3COOH}. \]

The amino and thiol groups of P then condense with acetone, propan-2-one, CC(=O)C:

\[ \ce{P + (CH3)2CO -> B + H2O}. \]

The resulting five-membered ring has the sequence

\[ \text{S}- \text{acetone-derived carbon}- \text{N}- \text{carboxyl-bearing carbon}- \text{gem-dimethyl carbon}. \]

Consequently, B is racemic 2,2,5,5-tetramethyl-1,3-thiazolidine-4-carboxylic acid. The acetone-derived carbon is not stereogenic because it bears two identical methyl groups.

Formation and resolution of C. Formic acid activated by acetic anhydride formylates the secondary ring nitrogen:

\[ \ce{B + HCOOH + (CH3CO)2O -> C + 2CH3COOH}. \]

At this stage C is racemic. Brucine forms diastereomeric salts with its two enantiomers, allowing physical separation. The subsequent dilute-acid treatment releases (+)-C.

The sign of optical rotation does not determine an \(R/S\) descriptor. The required configuration follows from the synthesis: this carboxyl-bearing stereocenter becomes the \(S\) carboxyl-bearing center of Penicillin VK. Accordingly, (+)-C has configuration \(4S\).

Formation of D. Step 3 hydrolyzes both the formamide and the acetone-derived \(N,S\)-acetal:

\[ \ce{C + 2H2O + HCl -> D*HCl + (CH3)2CO + HCOOH}. \]

Thus D is \((S)\)-penicillamine, obtained under these conditions as its hydrochloride. Its stereogenic carbon retains its configuration.

Formation of E. Let G denote the aldehyde supplied in the scheme: tert-butyl \((2S)\)-2-(1,3-dioxoisoindolin-2-yl)-3-oxopropanoate:

CC(C)(C)OC(=O)[C@@H](N1C(=O)c2ccccc2C1=O)C=O

The amine of D condenses with the aldehyde, and intramolecular thiol addition closes a five-membered thiazolidine ring. Sodium acetate, CC(=O)[O-].[Na+], enables condensation of the hydrochloride salt. A balanced net equation is

\[ \ce{D*HCl + G + CH3COONa -> E + H2O + CH3COOH + NaCl}. \]

Here sodium chloride is [Na+].[Cl-].

In E:

  • The penicillamine stereocenter becomes thiazolidine \(C_4\), with configuration \(S\).
  • The former aldehyde carbon becomes the new thiazolidine \(C_2\), with configuration \(R\) for the product carried through the shown synthesis.
  • The external phthalimido-bearing carbon has configuration \(R\).

The last assignment involves a change of descriptor without inversion. In G, the ester carbon outranks the aldehyde carbon because their next-layer atoms are respectively \((\ce{O},\ce{O},\ce{O})\) and \((\ce{O},\ce{O},\ce{H})\). After cyclization, the former aldehyde carbon is bonded to sulfur, nitrogen and hydrogen. That branch now outranks the ester branch, changing the retained stereocenter’s descriptor from \(S\) to \(R\).

Removal of the phthaloyl group. Let \(\ce{Q*HCl}\) denote the amino ester hydrochloride drawn after step 4: the hydrochloride of \((2R,4S)\)-2-[(\(1R\))-1-amino-2-tert-butoxy-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid:

CC(C)(C)OC(=O)[C@@H]([NH3+])[C@H]1SC(C)(C)[C@H](C(=O)O)N1.[Cl-]

Hydrazine removes the phthaloyl group, producing phthalhydrazide, O=C1NNC(=O)c2ccccc21, with formula \(\ce{C8H6N2O2}\). Including hydrochloride formation,

\[ \ce{E + N2H4 + HCl -> Q*HCl + C8H6N2O2}. \]

The tert-butyl ester remains present.

Formation of F. Phenoxyacetyl chloride, O=C(Cl)COc1ccccc1, acylates the newly exposed amino group. Triethylamine, CCN(CC)CC, accepts the acid.

Let R be the resulting side-chain tert-butyl ester of penicilloic acid V:

CC(C)(C)OC(=O)[C@@H](NC(=O)COc1ccccc1)[C@H]1SC(C)(C)[C@H](C(=O)O)N1

Accounting for the initial hydrochloride and the acid generated during acylation,

\[ \ce{Q*HCl + PhOCH2COCl + 2Et3N -> R + 2Et3NHCl}. \]

Triethylammonium chloride is CC[NH+](CC)CC.[Cl-].

Concentrated hydrochloric acid removes the tert-butyl ester; pyridine, n1ccccc1, provides the subsequent basic work-up. Written as net ester hydrolysis,

\[ \ce{R + H2O -> F + (CH3)3COH}. \]

The alcohol in this balance is tert-butanol, CC(C)(C)O. F therefore contains two free carboxylic acid groups, a free thiazolidine nitrogen, and the installed phenoxyacetamido side chain.

Precise wedge–dash descriptions for the answer sheet:

  • A and B: show racemic structures, using unspecified stereobonds or depicting both enantiomers.
  • (+)-C: retain the orientation of the drawn racemic C. Make the bond from its stereogenic ring carbon to the right-hand carboxyl group a hashed wedge, with the corresponding hydrogen toward the viewer. This gives \(4S\).
  • D: draw the backbone with the gem-dimethyl thiol-bearing carbon to the left and the carboxyl carbon to the right. Draw the amino group below the stereocenter on a hashed wedge, with hydrogen toward the viewer. This gives \(2S\).
  • E and F: use the orientation of the amino ester shown after step 4. Keep the ring \(C_4\)–carboxyl bond as a solid wedge, the ring \(C_2\)–hydrogen bond as a solid wedge, and the external stereocenter’s bond to its nitrogen substituent as a hashed wedge. In E, that nitrogen belongs to the phthalimide group; in F, it belongs to the phenoxyacetamido group. E has the tert-butyl ester, whereas F has the corresponding free carboxylic acid.

6.5. Role of acetone

Acetone, CC(=O)C, acts as an electrophile.

Its carbonyl carbon accepts nucleophilic attack from the amino group. Condensation and intramolecular sulfur attack then produce the cyclic \(N,S\)-acetal. The carbonyl carbon of acetone becomes the ring carbon between nitrogen and sulfur, retaining both methyl groups.

Thus the correct choice is c).

6.6. Role of DCC

DCC is \(N,N'\)-dicyclohexylcarbodiimide:

C1CCC(CC1)N=C=NC2CCCCC2

It acts as a coupling reagent, activating the side-chain carboxyl group of F for intramolecular attack by the thiazolidine nitrogen. Formation of this amide bond closes the four-membered β-lactam ring.

DCC is consumed, forming \(N,N'\)-dicyclohexylurea, DCU:

O=C(NC1CCCCC1)NC2CCCCC2

Including potassium hydroxide, [K+].[OH-], the overall atom-balanced reaction is

\[ \ce{ C16H20N2O6S + KOH + C13H22N2 -> C16H17KN2O5S + C13H24N2O + H2O }. \]

The organic reactants are F and DCC; the organic products are Penicillin VK and DCU. The carboxyl group not incorporated into the β-lactam remains as the potassium carboxylate.

Thus the correct choice is c).

The solution was checked against the official solution.