jablonkagroup/corral-environment-tasks huggingface dataset:
Task: make_1_lvl2-template_search-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: In a carbonyl-ene reaction, an alkene reacts with an allylic hydrogen and a carbonyl group to form a new carbon-carbon bondm. This reaction can take place between parts of the same molecule. The reaction typically requires a Lewis acid catalyst and proceeds via a concerted mechanism. The stereochemistry of the product is influenced by the geometry of the alkene and the carbonyl group. The result of the reaction is the formation of a new carbon-carbon bond and a new stereocenter at the site of the allylic hydrogen, in which one of the substituents is going to be a hydroxyl group. Additionally, the reaction involves the change in the order of a C=C bond to a C-C bond, and a C=O bond to a C-O bond. 'ketones' and 'C-C double bonds' are gone, while a 'aliphatic hydroxyl' and a 'five-membered rings' are formed. A Carbon-Carbon bond is formed.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_1_lvl2-apply_template-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_1_lvl2-template_search-1 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_1_lvl2-build_complete_route
Environment: retrosynthesis (level_2 subtask)
Description: Can you build and return the complete route of chemicals based on the inputs?
Allowed tools: verify_step, verify_route, search_catalog_by_smiles, is_buyable
Submission format: Submit a JSON object representing the retrosynthesis route. It must follow the same JSON format as the next example: `{
  "type": "mol",
  "smiles": "CO",
  "children": [
    {
      "type": "reaction",
      "template_id": 1234,
      "children": [
        {
          "type": "mol",
          "smiles": "BrC"
        },
        {
          "type": "mol",
          "smiles": "[OH-]"
        }
      ]
    }
  ]
}`.
Task: make_2_lvl2-template_search-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: A Dies-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, resulting generally in the formation of a six-membered ring. The reaction is stereospecific, meaning that the stereochemistry of the reactants is preserved in the product. The reaction typically proceeds via a concerted mechanism, where the pi electrons of the diene and dienophile interact to form new sigma bonds. The reaction can be catalyzed by heat or Lewis acids, and the regioselectivity of the product can be influenced by substituents on the diene and dienophile. As a result of the reaction, a new carbon-carbon bond is formed, and the order changes from C=C to C-C, and from C=C to C-C as well.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_2_lvl2-apply_template-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_2_lvl2-template_search-1 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_2_lvl2-build_complete_route
Environment: retrosynthesis (level_2 subtask)
Description: Can you build and return the complete route of chemicals based on the inputs?
Allowed tools: verify_step, verify_route, search_catalog_by_smiles, is_buyable
Submission format: Submit a JSON object representing the retrosynthesis route. It must follow the same JSON format as the next example: `{
  "type": "mol",
  "smiles": "CO",
  "children": [
    {
      "type": "reaction",
      "template_id": 1234,
      "children": [
        {
          "type": "mol",
          "smiles": "BrC"
        },
        {
          "type": "mol",
          "smiles": "[OH-]"
        }
      ]
    }
  ]
}`.
Task: make_3_lvl2-template_search-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: In a cycloaddition reaction, two unsaturated molecules (or parts of the same molecule) combine to form a cyclic product. The reaction typically involves the formation of new sigma bonds between the reacting species, resulting in the creation of a ring structure. During the reaction a carbon-carbon bond is formed, while a carbon-oxygen is broken. As a result of these transformations, a 'ketones' and 'C-C triple bonds' functional groups are lost.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_3_lvl2-apply_template-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_3_lvl2-template_search-1 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_3_lvl2-build_complete_route
Environment: retrosynthesis (level_2 subtask)
Description: Can you build and return the complete route of chemicals based on the inputs?
Allowed tools: verify_step, verify_route, search_catalog_by_smiles, is_buyable
Submission format: Submit a JSON object representing the retrosynthesis route. It must follow the same JSON format as the next example: `{
  "type": "mol",
  "smiles": "CO",
  "children": [
    {
      "type": "reaction",
      "template_id": 1234,
      "children": [
        {
          "type": "mol",
          "smiles": "BrC"
        },
        {
          "type": "mol",
          "smiles": "[OH-]"
        }
      ]
    }
  ]
}`.
Task: make_4_lvl2-template_search-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: The Peterson Reaction allows the preparation of alkenes from alpha-silylcarbanions. An intermediate beta-hydroxy silane is formed, following an elimination step to yield the alkene. Thus, a new carbon-carbon double bond is formed, while a carbon-silicon bond and a carbon-oxygen bond are broken. As a result, a 'C-C double bonds' functional group is formed, while 'ketones' and 'trimethylsilyl' groups are lost.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_4_lvl2-apply_template-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_4_lvl2-template_search-1 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_4_lvl2-build_complete_route
Environment: retrosynthesis (level_2 subtask)
Description: Can you build and return the complete route of chemicals based on the inputs?
Allowed tools: verify_step, verify_route, search_catalog_by_smiles, is_buyable
Submission format: Submit a JSON object representing the retrosynthesis route. It must follow the same JSON format as the next example: `{
  "type": "mol",
  "smiles": "CO",
  "children": [
    {
      "type": "reaction",
      "template_id": 1234,
      "children": [
        {
          "type": "mol",
          "smiles": "BrC"
        },
        {
          "type": "mol",
          "smiles": "[OH-]"
        }
      ]
    }
  ]
}`.
Task: make_5_lvl2-template_search-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: tert-Butyldimethylsilyl (TBS or TBDMS) is a common protecting group for alcohols in organic synthesis. It is introduced using reagents such as tert-butyldimethylsilyl chloride (TBDMSCl) or tert-butyldimethylsilyl trifluoromethanesulfonate (TBDMSOTf) in the presence of a base like imidazole or pyridine. The TBS group is stable under a variety of reaction conditions, including acidic and basic environments, making it useful for multi-step syntheses. It can be removed (deprotected) using fluoride sources such as tetrabutylammonium fluoride (TBAF) or by acidic hydrolysis, regenerating the free alcohol. As a result of this reaction, a bond between oxygen and silicon is broken, and a 'aliphatic hydroxyls' functional group is formed, and a 't-butyldimethylsilyl' gone.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_5_lvl2-apply_template-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_5_lvl2-template_search-1 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_5_lvl2-template_search-2
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: In the Horner-Wadsworth-Emmons reaction, the reaction of aldehydes or ketones with stabilized phosphorus ylides (phosphonate carbanions) leads to olefins with excellent E-selectivity. The overall of the reaction is a carbon-carbon bond formed, while a carbon-phosphorus bond and a carbon-oxygen are broken. As a result, an 'aliphatic carboxylic acid', and  'C-C double bonds' groups are formed.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_5_lvl2-apply_template-2
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_5_lvl2-template_search-2 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_5_lvl2-template_search-3
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: DIBAL-H is a reducing agent used in organic synthesis, particularly for the selective reduction of esters and nitriles to aldehydes. It is a complex of diisobutylaluminum hydride and is typically used in low temperatures to minimize side reactions. Overall a carbon-oxygen bond is broken, and a another carbon-oxygen bond order changes from 2 to 1, forming a 'aliphatic hydroxyls' functional group.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_5_lvl2-apply_template-3
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_5_lvl2-template_search-3 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_5_lvl2-template_search-4
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: TMSOTf can be used to protect alcohols by converting them into their corresponding trimethylsilyl (TMS) ethers. The reaction typically involves the treatment of the alcohol with TMSOTf in the presence of a base, such as triethylamine or pyridine. During the reaction a oxygen-silicon bond is broken and another one (O-Si) is formed. No functional groups are formed in the transformation, but the most notable broken is 'aliphatic hydroxyls'.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_5_lvl2-apply_template-4
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_5_lvl2-template_search-4 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_5_lvl2-template_search-5
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: The Still-Gennari reaction is a modification of the Horner-Wadsworth-Emmons (HWE) reaction that allows for the selective formation of (Z)-alkenes from aldehydes and phosphonate esters. The reaction typically involves the use of a phosphonate ester with electron-withdrawing groups, such as bis(trifluoroethyl) or bis(2,2,2-trifluoroethyl) groups, which helps to stabilize the carbanion intermediate formed during the reaction. Thus, a carbon-carbon double bond, and a carbon-oxygen are formed, while a carbon-phosphorus bond, a carbon-carbon bond and a carbon-oxygen bond are broken. Additionally, the triple bond of an alkyne is changed to a single bond. As a result 'C-C double bonds' and  'carboxylic esters' functional groups are formed.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_5_lvl2-apply_template-5
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_5_lvl2-template_search-5 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_5_lvl2-build_complete_route
Environment: retrosynthesis (level_2 subtask)
Description: Can you build and return the complete route of chemicals based on the inputs?
Allowed tools: verify_step, verify_route, search_catalog_by_smiles, is_buyable
Submission format: Submit a JSON object representing the retrosynthesis route. It must follow the same JSON format as the next example: `{
  "type": "mol",
  "smiles": "CO",
  "children": [
    {
      "type": "reaction",
      "template_id": 1234,
      "children": [
        {
          "type": "mol",
          "smiles": "BrC"
        },
        {
          "type": "mol",
          "smiles": "[OH-]"
        }
      ]
    }
  ]
}`.
Task: make_6_lvl2-template_search-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: The Sn2 reaction is a bimolecular nucleophilic substitution reaction where a nucleophile attacks an electrophilic carbon atom, leading to the displacement of a leaving group. The reaction proceeds via a single transition state, resulting in the inversion of stereochemistry at the carbon center. Common nucleophiles used in Sn2 reactions include hydroxide ions (OH-), alkoxide ions (RO-), and cyanide ions (CN-). The reaction typically occurs in polar aprotic solvents, which help to stabilize the transition state and enhance the nucleophilicity of the attacking species. As a result of the reaction, a new carbon-nucleophile bond is formed while a carbon-leaving group bond is broken, e.g. C-N formed and C-Cl gone breaking an 'halide' functional group.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.
Task: make_6_lvl2-apply_template-1
Environment: retrosynthesis (level_2 subtask)
Description: Can you return all possible precursors of applying the template as the result of the task make_6_lvl2-template_search-1 to the molecule below?
Allowed tools: get_template, apply_template, verify_step
Submission format: Return a list of lists where each inner list contain each possible combination in which each item of the inner list corresponds to the SMILES of each of the precursors as a string. For example, `[['CCO', 'O'], ['CC=O', 'CCO']]`.
Task: make_6_lvl2-template_search-2
Environment: retrosynthesis (level_2 subtask)
Description: Can you return the `mapped_rxn` associated with the template that, when applied to the molecule below (provided as available input data), reproduces the reaction: The Friedel-Crafts acylation is a type of electrophilic aromatic substitution reaction that introduces an acyl group onto an aromatic ring. The reaction typically involves the use of an acyl chloride (RCOCl) in the presence of a Lewis acid catalyst, such as aluminum chloride (AlCl3) or ferric chloride (FeCl3). The Lewis acid activates the acylating agent, generating a more electrophilic species that can attack the aromatic ring, leading to the formation of a new carbon-carbon bond and breaking a carbon-chlorine bond. An 'halide' functional group is gone during the transformation.. Note that the hints are describing the forward reaction, but you have to perform the retrosynthetic step.
Allowed tools: check_smiles_reaction_template_matching, search_template_catalog_by_criteria, get_template, get_available_functional_groups, deprotect_molecule, detect_functional_groups, detect_protection_groups
Submission format: Return a dict with the `mapped_rxn` as a string and the `template_id` (the one used to search the database not the hash) as an integer in JSON format, e.g., {'mapped_rxn': 'Cc1ccccc1.Br>>Cc1ccccc1Br', 'template_id': 12345}.