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[
{
"name": "IChO-2025_2",
"background": {
"image": "images/2/2_bg.png",
"context": "Rapamycin was isolated from the bacterium Streptomyces hygroscopicus in 1972. It acts as a molecular glue and inhibits the activity of the protein mTOR through binding to another protein. It has been used to treat various diseases. The stereochemical complexity of rapamycin makes its total synthesis challenging. The figure shows part of the first total synthesis by the Nicolaou group.",
"parsing_note": "The molecular structure has been converted to SMILES format.",
"molecular_name": "Rapamycin",
"smiles": "C[C@@H]1CCC2C[C@@H](/C(=C/C=C/C=C/[C@H](C[C@H](C(=O)[C@@H]([C@@H](/C(=C/[C@H](C(=O)C[C@H](OC(=O)[C@@H]3CCCCN3C(=O)C(=O)[C@@]1(O2)O)[C@H](C)C[C@@H]4CC[C@H]([C@@H](C4)OC)O)C)/C)O)OC)C)C)/C)OC"
},
"points": 67
},
{
"name": "IChO-2025_2.1",
"modality": "image + text",
"type": "Structure Construction",
"evaluation": "Structure Match",
"points": 12,
"field": "",
"source": "IChO-2025",
"question": {
"context": "The major stereoisomer C is formed from the chromium-mediated coupling reaction of aldehyde A and vinyl iodide B and can be predicted using the Felkin-Anh model without chelation. Draw a Newman projection showing the best approach of the nucleophile in this reaction. Use the labels =O, -H, -R^{1}, -OMe,and Nu. Draw the full structure of the major diastereomer C showing all stereochemistry.",
"image": "images/2/2.1_ques.png",
"parsing_note": "The reaction diagram has been converted to reaction_scheme.",
"requirement": "Draw a Newman projection showing the best approach of the nucleophile in this reaction. Use the labels =O, –H, –R¹, –OMe, and Nu. The projection should be viewed along the C(α)-C(carbonyl) bond. Draw the structure of compound C formed in the Nozaki-Hiyama-Kishi coupling reaction. Show all stereochemistry clearly, particularly at the newly formed chiral centers.",
"reaction_scheme": [
{
"reactant_name": "A, B",
"reactant_formula": "C=C[C@@H](C)C[C@@H](C)[C@@H](OCC1=CC=C(OC)C=C1)[C@H](OC)C([H])=O, I/C(C)=C/[C@@H](C)[C@@H](OCC1=CC=C(OC)C=C1)CCO[Si](C)(C)C(C)(C)C",
"conditions": "CrCl_{2}, NiCl_{2} (cat.)",
"product_name": "C, C'",
"product_formula": "C_{41}H_{66}O_{7}Si",
"product_ratio": "2:1"
},
{
"reactant_name": "C",
"conditions": "multiple steps",
"product_name": "D + E",
"product_formula": "[R2]CC([H])=O, O=C1O[C@@H](C2=CC=CC=C2)[C@@H](C)N1C(CC[C@@H]3CC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](C)C3)=O"
},
{
"reactant_name": "D + E",
"reactant_formula": "[R2]CC([H])=O, O=C1O[C@@H](C2=CC=CC=C2)[C@@H](C)N1C(CC[C@@H]3CC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](C)C3)=O",
"conditions": "nBu_{2}BOTf, Et_{3}N",
"product_name": "F"
},
{
"reactant_name": "F",
"conditions": "multiple steps",
"product_name": "rapamycin",
"product_formula": "C[C@@H]1CCC2C[C@@H](/C(=C/C=C/C=C/[C@H](C[C@H](C(=O)[C@@H]([C@@H](/C(=C/[C@H](C(=O)C[C@H](OC(=O)[C@@H]3CCCCN3C(=O)C(=O)[C@@]1(O2)O)[C@H](C)C[C@@H]4CC[C@H]([C@@H](C4)OC)O)C)/C)O)OC)C)C)/C)OC"
}
]
},
"answer": [
{
"image": "images/2/2.1_ans_1.png",
"projection_type": "Newman projection",
"viewing_direction": "along C(α)-C(carbonyl) bond",
"front_carbon": {
"substituents": [
{
"position": "top",
"group": "R^{1}"
},
{
"position": "bottom-left",
"group": "H"
},
{
"position": "bottom-right",
"group": "OMe"
}
]
},
"back_carbon": {
"substituents": [
{
"position": "top",
"group": "=O"
},
{
"position": "bottom-left",
"group": "H"
},
{
"position": "bottom-right",
"group": "attacking group (Nu)"
}
]
},
"nucleophile_approach": {
"direction": "from bottom-right",
"angle_to_carbonyl": "~107°",
"anti_to": "R^{1}",
"explanation": "Nucleophile approaches anti to the largest group (R¹) following Felkin-Anh model"
},
"grading": {
"partial_credit": [
{
"condition": "If nucleophile approach not shown or incorrect",
"deduction": -2
},
{
"condition": "If chirality at rear carbon is wrong, but OMe placed perpendicular",
"deduction": -4
},
{
"condition": "If chirality at rear carbon is correct, but OMe not placed perpendicular",
"deduction": -4
}
],
"notes": "Need to use Felkin-Anh model without chelation and put electronegative group OMe perpendicular to aldehyde."
},
"points": 8
},
{
"name": "C and C'",
"image": "images/2/2.1_ans_2.png",
"C_smiles": "C=C[C@@H](C)C[C@@H](C)[C@@H](OCC1=CC=C(OC)C=C1)[C@H](OC)[C@H](O)/C(C)=C/[C@@H](C)[C@@H](OCC2=CC=C(OC)C=C2)CCO[Si](C)(C)C(C)(C)C",
"C'_smiles": "C=C[C@@H](C)C[C@@H](C)[C@@H](OCC1=CC=C(OC)C=C1)[C@H](OC)[C@@H](O)/C(C)=C/[C@@H](C)[C@@H](OCC2=CC=C(OC)C=C2)CCO[Si](C)(C)C(C)(C)C",
"points": 4,
"grading": {
"full_credit": {
"condition": "Structure of C fully correct"
},
"partial_credit": [
{
"condition": "If C' is given instead of C"
},
{
"condition": "Absolute stereochemistry of OH and OMe is correct",
"additional_note": "If incorrect, but the relative stereochemistry is correct",
"additional_points": 1
},
{
"condition": "For each error in each molecule in functional groups not undergoing reaction",
"deduction": -1
}
],
"notes": "No error carried forward awarded even if part a is incorrect as stereochemistry can be inferred from the final structure of rapamycin. PMBO refers to para-methoxybenzyl ether protecting group, OPMB refers to para-methoxybenzyl group, OTBS refers to tert-butyldimethylsilyl ether protecting group."
}
}
]
},
{
"name": "IChO-2025_2.2",
"modality": "image + text",
"type": "Structure Construction",
"evaluation": "Structure Match",
"points": 19,
"field": "",
"source": "IChO-2025",
"question": {
"context": "After a few transformations, C can be converted into an aldehyde D which reacts with E to form F. F can be further transformed into rapamycin. Using the Zimmerman-Traxler model, predict the arrangement of the reactants as they come together to form the six-membered ring transition state in the reaction to form F. Draw the substituents at positions labelled with numbers. If a position does not have a substituent, put an X in the box. Boxes 1 and 2 have been filled in as an example. You may use the abbreviation R^{2} as given in the scheme above. Draw the structure of F showing all stereochemistry. You may use the abbreviation R^{2} as given in the scheme above.",
"image": "images/2/2.2_ques.png",
"requirement": "Using the Zimmerman-Traxler six-membered ring transition state model, fill in the boxes (3-8) to show the arrangement of groups in the transition state that leads to the formation of product F. Draw the structure of compound F with correct stereochemistry, including the newly formed stereocenters from the aldol reaction."
},
"answer": [
{
"model": "Six-membered ring Zimmerman-Traxler Model",
"transition_state_positions": {
"position_3": {
"group": "Evans auxiliary with Ph and Me groups",
"description": "Phenyl group on nitrogen-containing oxazolidinone auxiliary with Me substituent"
},
"position_4": {
"group": "X",
"description": "Position marker or variable group"
},
"position_5": {
"group": "—H",
"description": "Hydrogen on the enolate carbon"
},
"position_6": {
"group": "Cyclohexyl fragment with OMe and OTBS",
"description": "Six-membered ring with methoxy and tert-butyldimethylsilyl ether substituents"
},
"position_7": {
"group": "R²",
"description": "Alkyl chain from aldehyde (polyene fragment)"
},
"position_8": {
"group": "—H",
"description": "Hydrogen on the aldehyde carbon"
}
},
"key_features": {
"chair_conformation": "Six-membered ring chair",
"boron_coordination": "Boron center coordinates enolate oxygen and aldehyde oxygen",
"Z_enolate": "Z-configuration of enolate (positions 5/6)",
"aldehyde_orientation": "Aldehyde at back with R² group (position 7/8)"
},
"points": 15,
"grading": {
"full_credit": [
{
"condition": "Aldehyde approach (aldehyde is at the back instead of the front)",
"points": 5
},
{
"condition": "Z enolate (flip 5/6)",
"points": 5
},
{
"condition": "Aldehyde conformation (flip 7/8)",
"points": 5
}
],
"partial_credit": [
{
"condition": "For swapping positions 3 and 4",
"deduction": -2
},
{
"condition": "For each trivial mistake",
"deduction": -1
}
]
}
},
{
"structure_description": "Aldol product with Evans auxiliary still attached",
"key_features": {
"auxiliary": "Phenyl oxazolidinone with Me group remains attached",
"new_stereocenters": "Two newly formed stereocenters from aldol reaction",
"polyene_chain": "R² represents the polyene chain from compound C",
"protected_groups": "OMe and OTBS groups on cyclohexyl fragment",
"hydroxyl_group": "New OH group formed at aldol position"
},
"smiles": "[Complex structure with Evans auxiliary, new stereocenters, and polyene chain - exact SMILES depends on R² definition]",
"points": 4,
"grading": {
"full_credit": {
"condition": "Structure of F with stereochemistry fully correct",
"points": 4
},
"partial_credit": [
{
"condition": "Absolute stereochemistry of newly formed stereocenters is correct",
"points": 2,
"additional_note": "If incorrect, but the relative stereochemistry is correct",
"additional_points": 1
},
{
"condition": "For each error of functional groups not undergoing reaction (trivial error)",
"deduction": -1
}
],
"notes": "No error carried forward awarded even if part 2.2a is incorrect as stereochemistry can be inferred from the final structure of rapamycin."
}
}
]
},
{
"name": "IChO-2025_2.3",
"modality": "image + text",
"type": "Structure Construction",
"evaluation": "Structure Match",
"points": 18,
"field": "",
"source": "IChO-2025",
"question": {
"context": "Whilst stereochemical control is challenging synthetically, the biological synthesis controls stereochemistry elegantly through an assembly line of various enzymes. The carbon chain is built up through the addition of monomers. These units are connected via a thioester to Coenzyme A (CoA). The functions of the various enzymes and proteins are shown in the table. The first part of the assembly line is shown with blanks. The enzymes are shown in circles and act in the order of the arrow. Draw in the hexagons the structure of the monomer needed by the enzyme AT at each of the points numbered 1-4. Carbon dioxide is released when the monomers are incorporated. The monomers have the following general structure where the R group is anionic. Fill in each circle with the abbreviations of enzyme(s) needed. Write X if no additional enzyme is needed. Complete the rectangles with the structure of the growing molecule attached to the enzyme.",
"image": [
"images/2/2.3_ques_1.png",
"images/2/2.3_ques_2.png"
],
"requirement": "Identify the building blocks (in hexagons) and the enzymes (in circles) involved in the polyketide synthesis pathway. Also draw the structures (in rectangles) corresponding to each stage of the synthesis.",
"table": [
{
"Abbreviation": "ACP",
"Name": "Acyl-carrier protein",
"Function": "Carries growing chain between domains"
},
{
"Abbreviation": "CoL",
"Name": "CoA-Ligase",
"Function": "Activates a carboxylic acid substrate to be loaded onto the ACP"
},
{
"Abbreviation": "AT",
"Name": "Acyltransferase",
"Function": "Selects monomer and transfers to ACP"
},
{
"Abbreviation": "KS",
"Name": "Ketosynthase",
"Function": "Accepts growing chain from previous ACP and activates it for Claisen condensation with next monomer-loaded ACP"
},
{
"Abbreviation": "KR",
"Name": "Ketoreductase",
"Function": "Reduces carbonyl of a previous monomer to a hydroxyl"
},
{
"Abbreviation": "DH",
"Name": "Dehydratase",
"Function": "Forms α, β-unsaturated thioester via elimination on the previous monomer"
},
{
"Abbreviation": "ER",
"Name": "Enoylreductase",
"Function": "Reduces α, β-unsaturated thioester to saturated chain on the previous monomer"
}
],
"answer": {
"question_id": "building_blocks_and_enzymes",
"answer": {
"building_blocks": {
"hexagon_1": {
"name": "Me Malonyl CoA",
"structure": "Methylmalonyl-CoA",
"smiles": "CC(C(=O)SCoA)C(=O)[O-]",
"points": 1
},
"hexagon_2": {
"name": "Malonyl CoA",
"structure": "Malonyl-CoA",
"smiles": "[O-]C(=O)CC(=O)SCoA",
"points": 1
},
"hexagon_3": {
"name": "Malonyl CoA",
"structure": "Malonyl-CoA (with methyl branch)",
"smiles": "[O-]C(=O)C(C)C(=O)SCoA",
"points": 1
},
"hexagon_4": {
"name": "Malonyl CoA",
"structure": "Malonyl-CoA (with methyl branch)",
"smiles": "[O-]C(=O)C(C)C(=O)SCoA",
"points": 1
}
},
"enzymes": {
"circle_module_1": {
"enzymes": [
"KR",
"DH",
"ER"
],
"description": "Ketoreductase, Dehydratase, Enoyl reductase",
"points": 2
},
"circle_module_2": {
"enzymes": [
"KR"
],
"description": "Ketoreductase",
"points": 2
},
"circle_module_3": {
"enzymes": [
"X"
],
"description": "Unknown or no additional enzyme beyond KS, AT, ACP",
"points": 2
},
"circle_module_4": {
"enzymes": [
"KR",
"DH"
],
"description": "Ketoreductase, Dehydratase",
"points": 2
}
},
"structures": {
"rectangle_1": {
"description": "Structure after Module 1 processing",
"features": [
"Thioester attached to enzyme (S bond)",
"Fully reduced chain (no ketone)",
"Cyclohexane ring with two OH groups",
"Saturated carbon chain"
],
"smiles": "CC(C)CC(O)C1CCC(O)C(O)C1",
"stereochemistry": "Shows specific stereochemistry with wedge/dash bonds",
"points": 2
},
"rectangle_2": {
"description": "Structure after Module 2 processing",
"features": [
"Thioester attached to enzyme (S bond)",
"Beta-hydroxy ketone (ketone reduced to OH)",
"Cyclohexane ring with two OH groups",
"Extended carbon chain"
],
"smiles": "CC(C(=O)CC(O)C)CC1CCC(O)C(O)C1",
"stereochemistry": "Shows specific stereochemistry with wedge/dash bonds",
"points": 2
},
"rectangle_3": {
"description": "Structure after Module 3 processing",
"features": [
"Thioester attached to enzyme (S bond)",
"Beta-keto ester (ketone not reduced)",
"Two carbonyl groups present",
"Two OH groups on cyclohexane ring",
"Further extended carbon chain"
],
"smiles": "CC(C(=O)CC(=O)C(C)CC(O)C)CC1CCC(O)C(O)C1",
"stereochemistry": "Shows specific stereochemistry with wedge/dash bonds",
"points": 2
},
"rectangle_4": {
"description": "Structure after Module 4 processing",
"features": [
"Thioester attached to enzyme (S bond)",
"Alpha,beta-unsaturated ketone (dehydrated)",
"Double bond present",
"Multiple OH groups",
"Fully extended carbon chain",
"Cyclohexane ring with two OH groups"
],
"smiles": "CC(C(=O)C=C(C)C(C(=O)CC(=O)C(C)CC(O)C)C)CC1CCC(O)C(O)C1",
"stereochemistry": "Shows specific stereochemistry with wedge/dash bonds",
"points": 2
}
}
},
"points": {
"total": 18,
"breakdown": {
"hexagons": 4,
"enzymes": 8,
"structures": 8
}
},
"grading": {
"building_blocks": "Hexagons for building blocks are worth 1 pt each. Total = 4 pts",
"enzymes_and_structures": "Circles for enzymes and rectangles for structures worth 2 pts each. Total 14 pts.",
"partial_credit": "No partial credit for this part. The order of the enzymes in the circles is not graded.",
"error_carried_forward": "Error carried forward can be implemented for the structures in the rectangles."
}
}
}
},
{
"name": "IChO-2025_2.4",
"modality": "image + text",
"type": "Qualitative Identification",
"evaluation": "Selection Check",
"points": 18,
"field": "",
"source": "IChO-2025",
"question": {
"context": "The final steps of the enzymatic synthesis are shown below. The building blocks involved were determined by feeding the bacterium with three different ^{13}C -labelled starting materials which are incorporated into the monomers ^{13}C are circled as shown below: Circle the carbons in rapamycin that will be ^{13}C -labelled when the bacterium is fed with each of the three starting materials a-c in turn, following the guidelines on the next page. Incorrect circles will be penalised but there is no negative scoring. Guidelines for circling carbon atoms: Do not include multiple carbon atoms in the same circle. Do not circle any bonds.",
"image": "images/2/2.4_ques.png",
"requirement": "",
"reaction_scheme": [
{
"reactant_smiles": "O=C(CC([C@H](C)CC[C@H](O)C[C@H](O)/C(C)=C/C=C/C=C/C(C)CC(C)C(C[C@H](O)/C(C)=C/C(C)C(C[C@H](O)[C@H](C)C[C@]1([H])CC[C@@H](O)[C@H](O)C1)=O)=O)=O)S[ACP]",
"conditions": "O=C([C@H]1NCCCC1)O",
"product_formula": "O[C@@]1(C(C(N2[C@]([H])(C(O[C@H]([C@H](C)C[C@@]3([H])C[C@@H](O)[C@H](O)CC3)CC([C@H](C)/C=C(C)/[C@@H](O)C4)=O)=O)CCCC2)=O)=O)O[C@@](C[C@H](O)/C(C)=C/C=C/C=C/[C@@H](C)C[C@@H](C)C4=O)([H])CC[C@H]1C"
},
{
"reactant_name": "O[C@@]1(C(C(N2[C@]([H])(C(O[C@H]([C@H](C)C[C@@]3([H])C[C@@H](O)[C@H](O)CC3)CC([C@H](C)/C=C(C)/[C@@H](O)C4)=O)=O)CCCC2)=O)=O)O[C@@](C[C@H](O)/C(C)=C/C=C/C=C/[C@@H](C)C[C@@H](C)C4=O)([H])CC[C@H]1C",
"conditions": "multiple steps",
"product_name": "rapamycin",
"product_formula": "C[C@@H]1CCC2C[C@@H](/C(=C/C=C/C=C/[C@H](C[C@H](C(=O)[C@@H]([C@@H](/C(=C/[C@H](C(=O)C[C@H](OC(=O)[C@@H]3CCCCN3C(=O)C(=O)[C@@]1(O2)O)[C@H](C)C[C@@H]4CC[C@H]([C@@H](C4)OC)O)C)/C)O)OC)C)C)/C)OC"
}
],
"^{13}C-labelled starting materials a": {
"smiles": "CCC(O[Na])=O",
"notes": "From left to right, C-1 and C-2 are circled."
},
"^{13}C-labelled starting materials b": {
"smiles": "CC(O[Na])=O",
"notes": "From left to right, C-2 are circled."
},
"^{13}C-labelled starting materials c": {
"smiles": "CC(O[Na])=O",
"notes": "From left to right, C-1 are circled."
}
},
"answer": [
{
"name": "C-11, C-12, C-23, C-24, C-26, C-27, C-35, C-36, C-41, C-42, C-44, C-45, C-49, C-50"
},
{
"name": "C-3, C-22, C-32, C-37, C-38, C-47, C-49"
},
{
"name": "C-2, C-22, C-30, C-32, C-37, C-38, C-48"
}
]
}
]
|