Datasets:
id int64 | problem_number string | title string | statement string | plain_statement string | specialist_statement string | background string | category dict | secondary_categories list | difficulty dict | status string | consensus_state string | status_confidence float64 | primary_question_type string | question_types list | chemical_entities list | chemical_processes list | reaction_classes list | phases_and_media list | regimes list | conditions dict | scales list | why_open string | what_would_settle_it string | resolution_modes list | investigation_modes list | evidence_state list | source_type string | source_support_level string | source_url string | source_citation string | source_identifiers dict | source_license string | reuse_mode string | sets list | tags list | year_proposed int64 | proposed_by list | statement_status string | literature_checked_at timestamp[s] | research_classification string | duplicate_of string | archive_reason string | is_gold_seed bool | published bool | created_at timestamp[s] | updated_at timestamp[s] |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | UCHEM-000001 | Molecular interactions determining the transfer of chirality | What are the molecular interactions determining the transfer of chirality? | When controlling three-dimensional stereochemistry in transfer of chirality (organic mechanisms and synthesis science), what chiral induction factors answer: What are the molecular interactions determining the transfer of chirality? | With respect to bond formation, bond cleavage in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for transfer of chirality), what are the molecular interactions determining the transfer of chirality? | Context from Communications Chemistry (2021): The geometries and energies of TSs that lead to competing products are defined by noncovalent interactions (NCIs) which are expressed in several different forms (CH−π, π−π, electrostatic, etc.) and are energetically weak (the energy increments associated with these interact... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 5,
"level": 5,
"name": "L5: Foundational or Grand"
} | open | established_open_question | 0.95 | stereocontrol | [
"stereocontrol",
"bonding",
"mechanism",
"selectivity"
] | [
{
"name": "chemical system in transfer of chirality",
"role": "central_system",
"formula": null,
"smiles": null,
"inchikey": null,
"cas_rn": null,
"state_descriptor": "reactive_intermediate"
},
{
"name": "urea / hydrogen-bonding motif (CH4N2O)",
"role": "central_system",
... | [
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"solution",
"liquid"
] | [
"ambient"
] | {
"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "open-circuit thermal chemical potential (neutral / unbiased regime)",
"solvent_or_medium": "solution reaction medium",
"excitation_or_st... | [
"electronic",
"atomic",
"molecular"
] | As documented by Jolene P Reid (2021) in Communications Chemistry: "The geometries and energies of TSs that lead to competing products are defined by noncovalent interactions (NCIs) which are expressed in several different forms (CH−π, π−π, electrostatic, etc.) and are energetically weak (the energy increments associat... | Direct kinetics, isotopic labeling of transfer of chirality under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | open_questions_commentary | explicit_question | https://doi.org/10.1038/s42004-021-00614-y | Jolene P Reid (2021), "Open questions on the transfer of chirality", Communications Chemistry, doi:10.1038/s42004-021-00614-y | {
"source_id": "SRC-CHEM-00013",
"doi": "10.1038/s42004-021-00614-y",
"pmid": "36697611",
"pmcid": "PMC9814639"
} | CC BY 4.0 | verbatim_allowed | [
{
"id": 1,
"name": "comm_chem_open_questions",
"display_name": "Communications Chemistry — Open Questions in Chemistry",
"slug": "comm-chem-open-questions"
},
{
"id": 2,
"name": "trends_in_chemistry_big_questions",
"display_name": "Trends in Chemistry — Big Questions in Chemistry",
... | [
"organic_mechanisms_and_synthesis_science",
"stereocontrol",
"physical_organic_chemistry",
"reactive_intermediates"
] | 2,021 | [
"Jolene P Reid"
] | exact | 2026-10-14T19:45:00 | OPEN-VERIFIED | null | null | true | true | 2026-10-14T19:45:00 | 2026-10-14T19:45:00 |
2 | UCHEM-000002 | Driving forces that pivot a polypeptide chain to a specific conformation | What are the driving forces that pivot a polypeptide chain to a specific conformation amongst the vast conformation space? | For Structural determinants of protein folding (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What are the driving forces that pivot a polypeptide chain to a specific conformation amongst the vast conformation space? | With respect to bond formation, bond cleavage in surface reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Structural determinants of protein folding), what are the driving forces that pivot a polypeptide chain to a specific conformation amongst the vast conformati... | Context from Cellular and Molecular Life Sciences : CMLS (2009): The last several decades have seen an explosion of knowledge in the field of structural biology. With critical advances in spectroscopic techniques in examining structures of biomacromolecules, in maturation of molecular biology techniques, as well as vas... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | conformation | [
"conformation",
"mechanism",
"stereocontrol",
"selectivity"
] | [
{
"name": "chemical system in Structural determinants of protein folding",
"role": "central_system",
"formula": null,
"smiles": null,
"inchikey": null,
"cas_rn": null,
"state_descriptor": "reactive_intermediate"
},
{
"name": "N,N-dimethylformamide / amide (C3H7NO)",
"role": "... | [
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"surface",
"biological_milieu",
"solution"
] | [
"ambient"
] | {
"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "buffered physiological pH (7.0–7.4) and cellular redox potential",
"solvent_or_medium": "surface reaction medium",
"excitation_or_stimul... | [
"electronic",
"atomic",
"molecular"
] | As documented by Kang TS, Kini RM (2009) in Cellular and Molecular Life Sciences : CMLS: "The last several decades have seen an explosion of knowledge in the field of structural biology. With critical advances in spectroscopic techniques in examining structures of biomacromolecules, in maturation of molecular biology t... | Direct kinetics, isotopic labeling of Structural determinants of protein folding under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_question | https://doi.org/10.1007/s00018-009-0023-5 | Kang TS, Kini RM (2009), "Structural determinants of protein folding", Cellular and Molecular Life Sciences : CMLS, doi:10.1007/s00018-009-0023-5 | {
"source_id": "SRC-CHEM-00014",
"doi": "10.1007/s00018-009-0023-5",
"pmid": "19367367",
"pmcid": "PMC11115868"
} | Publisher Standard License | paraphrase_only | [
{
"id": 2,
"name": "trends_in_chemistry_big_questions",
"display_name": "Trends in Chemistry — Big Questions in Chemistry",
"slug": "trends-in-chemistry-big-questions"
}
] | [
"organic_mechanisms_and_synthesis_science",
"conformation",
"physical_organic_chemistry",
"reactive_intermediates"
] | 2,009 | [
"Kang TS",
"Kini RM"
] | paraphrased_verified | 2026-10-14T19:45:00 | OPEN-VERIFIED | null | null | true | true | 2026-10-14T19:45:00 | 2026-10-14T19:45:00 |
3 | UCHEM-000003 | After the ribosome structures | Do any components of the site enhance the rate of peptide-bond formation chemically? | For After the ribosome structures (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: Do any components of the site enhance the rate of peptide-bond formation chemically? | With respect to bond formation, bond cleavage in solid-state lattice or crystalline solid interface (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for After the ribosome structures), do any components of the site enhance the rate of peptide-bond formation chemically? | Context from RNA (2003): Atomic resolution crystal structures of the large subunit published since the middle of August 2000 prove that the peptidyl transferase center of the ribosome, which is the site of peptide-bond formation, is composed entirely of RNA; the ribosome is a ribozyme. They also demonstrate that alignm... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | structure | [
"structure",
"mechanism",
"stereocontrol",
"selectivity"
] | [
{
"name": "chemical system in After the ribosome structures",
"role": "central_system",
"formula": null,
"smiles": null,
"inchikey": null,
"cas_rn": null,
"state_descriptor": "reactive_intermediate"
},
{
"name": "N,N-dimethylformamide / amide (C3H7NO)",
"role": "solvent_or_me... | [
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"crystalline_solid",
"solution",
"liquid"
] | [
"ambient"
] | {
"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "open-circuit thermal chemical potential (neutral / unbiased regime)",
"solvent_or_medium": "solid-state lattice or crystalline solid inter... | [
"electronic",
"atomic",
"molecular"
] | As documented by Moore PB, Steitz TA (2003) in RNA: "Atomic resolution crystal structures of the large subunit published since the middle of August 2000 prove that the peptidyl transferase center of the ribosome, which is the site of peptide-bond formation, is composed entirely of RNA; the ribosome is a ribozyme. They ... | Direct kinetics, isotopic labeling of After the ribosome structures under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_question | https://doi.org/10.1261/rna.2127103 | Moore PB, Steitz TA (2003), "After the ribosome structures: how does peptidyl transferase work?", RNA, doi:10.1261/rna.2127103 | {
"source_id": "SRC-CHEM-00015",
"doi": "10.1261/rna.2127103",
"pmid": "12554855",
"pmcid": "PMC1370378"
} | Publisher Standard License | paraphrase_only | [
{
"id": 2,
"name": "trends_in_chemistry_big_questions",
"display_name": "Trends in Chemistry — Big Questions in Chemistry",
"slug": "trends-in-chemistry-big-questions"
}
] | [
"organic_mechanisms_and_synthesis_science",
"structure",
"physical_organic_chemistry",
"reactive_intermediates"
] | 2,003 | [
"Moore PB",
"Steitz TA"
] | paraphrased_verified | 2026-10-14T19:45:00 | OPEN-VERIFIED | null | null | true | true | 2026-10-14T19:45:00 | 2026-10-14T19:45:00 |
4 | UCHEM-000004 | Capability of Oxidovanadium(IV) Derivatives to Act as All-Around Catalytic Promoters | What functions could vanadium or its very stable oxidovanadium(IV) derivatives have had in the prebiotic world and in the origins of life in Capability of Oxidovanadium(IV) Derivatives to Act as All-Around Catalytic Promoters? | For Capability of Oxidovanadium(IV) Derivatives to Act as All-Around Catalytic Promoters (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What functions could vanadium or its very stable oxidovanadium(IV) derivatives have had in the prebiotic wo... | With respect to network emergence, bond formation in aqueous solution or buffered electrolyte (H2O) (thermal activation under biological conditions; probed via kinetics, isotopic labeling for Capability of Oxidovanadium(IV) Derivatives to Act as All-Around Catalytic Promoters), what functions could vanadium or its very... | Context from Molecules (2020): For a long time the biological role of vanadium was not known, while now the possibility of using its derivatives as potential therapeutic agents has given rise to investigations on their probable side effects. Vanadium compounds may inhibit different biochemical processes and lead to a v... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | emergence | [
"emergence",
"mechanism",
"stereocontrol",
"selectivity"
] | [
{
"name": "chemical system in Capability of Oxidovanadium(IV) Derivatives to Act as All-Around Catalytic Promoters",
"role": "central_system",
"formula": null,
"smiles": null,
"inchikey": null,
"cas_rn": null,
"state_descriptor": "reactive_intermediate"
},
{
"name": "adenosine mo... | [
"network_emergence",
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"solution",
"liquid"
] | [
"biological",
"ambient"
] | {
"temperature": "physiological temperature (310 K / 37 °C)",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "buffered physiological pH (7.0–7.4) and cellular redox potential",
"solvent_or_medium": "aqueous solution or buffered electrolyte (H2O)",
"excitation_or_stimulus": "ther... | [
"electronic",
"atomic",
"molecular"
] | As documented by Campitelli P, Crucianelli M (2020) in Molecules: "For a long time the biological role of vanadium was not known, while now the possibility of using its derivatives as potential therapeutic agents has given rise to investigations on their probable side effects. Vanadium compounds may inhibit different b... | Direct kinetics, isotopic labeling of Capability of Oxidovanadium(IV) Derivatives to Act under biological conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_question | https://doi.org/10.3390/molecules25133073 | Campitelli P, Crucianelli M (2020), "On the Capability of Oxidovanadium(IV) Derivatives to Act as All-Around Catalytic Promoters Since the Prebiotic World", Molecules, doi:10.3390/molecules25133073 | {
"source_id": "SRC-CHEM-00016",
"doi": "10.3390/molecules25133073",
"pmid": "32640541",
"pmcid": "PMC7412518"
} | cc by | verbatim_allowed | [
{
"id": 2,
"name": "trends_in_chemistry_big_questions",
"display_name": "Trends in Chemistry — Big Questions in Chemistry",
"slug": "trends-in-chemistry-big-questions"
},
{
"id": 12,
"name": "open_access_chemical_review_corpus",
"display_name": "Open-Access Chemical Review & Perspect... | [
"organic_mechanisms_and_synthesis_science",
"emergence",
"physical_organic_chemistry",
"reactive_intermediates"
] | 2,020 | [
"Campitelli P",
"Crucianelli M"
] | exact | 2026-10-14T19:45:00 | OPEN-VERIFIED | null | null | true | true | 2026-10-14T19:45:00 | 2026-10-14T19:45:00 |
5 | UCHEM-000005 | Chemistry of Spiroindolenines by Mechanistically-Driven Reaction Development | Can the spiroindolenine species be formed effectively under Pictet-Spengler conditions? | When controlling three-dimensional stereochemistry in Chemistry of Spiroindolenines by Mechanistically-Driven Reaction Development (organic mechanisms and synthesis science), what chiral induction factors answer: Can the spiroindolenine species be formed effectively under Pictet-Spengler conditions? | With respect to bond formation, bond cleavage in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Chemistry of Spiroindolenines by Mechanistically-Driven Reaction Development), can the spiroindolenine species be formed effectively under Pictet-Spengler co... | Context from Accounts of Chemical Research (2020): The Pictet-Spengler reaction is a fundamental named reaction in organic chemistry, and it is the most straightforward method for the synthesis of tetrahydro-β-carbolines, a core structure embedded in numerous alkaloids. Spiroindolenines are often proposed as possible i... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | stereocontrol | [
"stereocontrol",
"mechanism",
"selectivity"
] | [
{
"name": "chemical system in Chemistry of Spiroindolenines by Mechanistically-Driven Reaction Development",
"role": "central_system",
"formula": null,
"smiles": null,
"inchikey": null,
"cas_rn": null,
"state_descriptor": "reactive_intermediate"
},
{
"name": "tetrahydrofuran (THF... | [
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"solution",
"liquid"
] | [
"ambient"
] | {
"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "open-circuit thermal chemical potential (neutral / unbiased regime)",
"solvent_or_medium": "solution reaction medium",
"excitation_or_st... | [
"electronic",
"atomic",
"molecular"
] | As documented by Zheng C, You SL (2020) in Accounts of Chemical Research: "The Pictet-Spengler reaction is a fundamental named reaction in organic chemistry, and it is the most straightforward method for the synthesis of tetrahydro-β-carbolines, a core structure embedded in numerous alkaloids. Spiroindolenines are ofte... | Direct kinetics, isotopic labeling of Chemistry of Spiroindolenines by Mechanistically-Driven Reaction Development under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_question | https://doi.org/10.1021/acs.accounts.0c00074 | Zheng C, You SL (2020), "Exploring the Chemistry of Spiroindolenines by Mechanistically-Driven Reaction Development: Asymmetric Pictet-Spengler-type Reactions and Beyond", Accounts of Chemical Research, doi:10.1021/acs.accounts.0c00074 | {
"source_id": "SRC-CHEM-00017",
"doi": "10.1021/acs.accounts.0c00074",
"pmid": "32275392",
"pmcid": null
} | Publisher Standard License | paraphrase_only | [
{
"id": 2,
"name": "trends_in_chemistry_big_questions",
"display_name": "Trends in Chemistry — Big Questions in Chemistry",
"slug": "trends-in-chemistry-big-questions"
}
] | [
"organic_mechanisms_and_synthesis_science",
"stereocontrol",
"physical_organic_chemistry",
"reactive_intermediates"
] | 2,020 | [
"Zheng C",
"You SL"
] | paraphrased_verified | 2026-10-14T19:45:00 | OPEN-VERIFIED | null | null | true | true | 2026-10-14T19:45:00 | 2026-10-14T19:45:00 |
6 | UCHEM-000006 | Kynurenic Acid Strategies for Next-Generation Therapeutics via Rational Drug Design | What causes minor structural alterations to induce significant changes in disease outcomes? | For Kynurenic Acid Strategies for Next-Generation Therapeutics via Rational Drug (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What causes minor structural alterations to induce significant changes in disease outcomes? | With respect to bond formation, bond cleavage in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Kynurenic Acid Strategies for Next-Generation Therapeutics via Rational Drug), what causes minor structural alterations to induce significant changes in dise... | Context from Pharmaceuticals (2025): Background Quinoline-derived metabolites exhibit notable chemical complexity. What causes minor structural alterations to induce significant changes in disease outcomes? Historically, eclipsed by more straightforward scaffolds, these chemicals serve as a dynamic hub in tryptophan me... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | mechanism | [
"mechanism",
"stereocontrol",
"selectivity"
] | [
{
"name": "chemical system in Kynurenic Acid Strategies for Next-Generation Therapeutics via Rational Drug Design",
"role": "central_system",
"formula": null,
"smiles": null,
"inchikey": null,
"cas_rn": null,
"state_descriptor": "reactive_intermediate"
},
{
"name": "acetic acid /... | [
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"solution",
"liquid"
] | [
"ambient"
] | {
"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "open-circuit thermal chemical potential (neutral / unbiased regime)",
"solvent_or_medium": "solution reaction medium",
"excitation_or_st... | [
"electronic",
"atomic",
"molecular"
] | As documented by Tanaka M, Szatmári I, Vécsei L (2025) in Pharmaceuticals: "Background Quinoline-derived metabolites exhibit notable chemical complexity. What causes minor structural alterations to induce significant changes in disease outcomes?" Resolving this mechanism question is challenged by competing bond formati... | Direct kinetics, isotopic labeling of Kynurenic Acid Strategies for Next-Generation Therapeutics under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_question | https://doi.org/10.3390/ph18050607 | Tanaka M, Szatmári I, Vécsei L (2025), "Quinoline Quest: Kynurenic Acid Strategies for Next-Generation Therapeutics via Rational Drug Design", Pharmaceuticals, doi:10.3390/ph18050607 | {
"source_id": "SRC-CHEM-00018",
"doi": "10.3390/ph18050607",
"pmid": "40430428",
"pmcid": "PMC12114834"
} | cc by | verbatim_allowed | [
{
"id": 2,
"name": "trends_in_chemistry_big_questions",
"display_name": "Trends in Chemistry — Big Questions in Chemistry",
"slug": "trends-in-chemistry-big-questions"
},
{
"id": 12,
"name": "open_access_chemical_review_corpus",
"display_name": "Open-Access Chemical Review & Perspect... | [
"organic_mechanisms_and_synthesis_science",
"mechanism",
"physical_organic_chemistry",
"reactive_intermediates"
] | 2,025 | [
"Tanaka M",
"Szatmári I",
"Vécsei L"
] | exact | 2026-10-14T19:45:00 | OPEN-VERIFIED | null | null | true | true | 2026-10-14T19:45:00 | 2026-10-14T19:45:00 |
7 | UCHEM-000007 | Mechanism of Anomeric effect, hyperconjugation and electro | Why are such questions inherently controversial in Anomeric effect, hyperconjugation and electrostatics? | For Anomeric effect, hyperconjugation and electrostatics (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: Why are such questions inherently controversial in Anomeric effect, hyperconjugation and electrostatics? | With respect to bond formation, bond cleavage in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Anomeric effect, hyperconjugation and electrostatics), why are such questions inherently controversial in Anomeric effect, hyperconjugation and electrostatic... | Context from Chemical Society Reviews (2021): Understanding the interplay of multiple components (steric, electrostatic, stereoelectronic, dispersive, etc. ) that define the overall energy, structure, and reactivity of organic molecules can be a daunting task. The task becomes even more difficult when multiple approach... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
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} | open | active_debate | 0.92 | conformation | [
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{
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8 | UCHEM-000008 | Mechanism of Psychrophily and catalysis | How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered in Psychrophily and catalysis? | For Psychrophily and catalysis (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered in Psychrophily and catalysis? | With respect to bond formation, bond cleavage in biological milieu reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Psychrophily and catalysis), how do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered in Psychrop... | Context from Biology (2013): Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect ... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
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"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
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"solvent_or_medium": "biological milieu reaction medium",
"excitation... | [
"electronic",
"atomic",
"molecular"
] | As documented by Gerday C (2013) in Biology: "Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since... | Direct kinetics, isotopic labeling of Psychrophily and catalysis under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
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"kinetics",
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] | review_article | explicit_question | https://doi.org/10.3390/biology2020719 | Gerday C (2013), "Psychrophily and catalysis", Biology, doi:10.3390/biology2020719 | {
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"doi": "10.3390/biology2020719",
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"id": 12,
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9 | UCHEM-000009 | Conformational selection or induced fit? 50 years of debate resolved | Do the different conformations involved already exist spontaneously in the absence of the regulatory ligands (Monod-Wyman-Changeux), such that the complementary protein conformation would be selected to mediate signal transduction, or do particular ligands induce the receptor to adopt the conformation best suited to th... | During catalytic or functional operation of Conformational selection or induced fit? 50 years of debate (organic mechanisms and synthesis science), what is the true resting or turnover-limiting active chemical species: Do the different conformations involved already exist spontaneously in the absence of the regulatory ... | With respect to bond formation, bond cleavage in biological milieu reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Conformational selection or induced fit? 50 years of debate), do the different conformations involved already exist spontaneously in the absence of ... | Context from F1000 Biology Reports (2011): Exactly 50 years ago, biochemists raised the question of the mechanism of the conformational change that mediates "allosteric" interactions between regulatory sites and biologically active sites in regulatory/receptor proteins. Do the different conformations involved already e... | {
"id": 1,
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"physical_organic_chemistry",
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{
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"ph_or_potential": "buffered physiological pH (7.0–7.4) and cellular redox potential",
"solvent_or_medium": "biological milieu reaction medium",
"excitation... | [
"electronic",
"atomic",
"molecular"
] | As documented by Changeux JP, Edelstein S (2011) in F1000 Biology Reports: "Exactly 50 years ago, biochemists raised the question of the mechanism of the conformational change that mediates "allosteric" interactions between regulatory sites and biologically active sites in regulatory/receptor proteins. Do the different... | Direct kinetics, isotopic labeling of Conformational selection or induced fit? 50 years under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
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10 | UCHEM-000010 | Oxygen reduction reaction is coupled to proton translocation in Structural and functional mechanisms | What is the mechanism by which the oxygen reduction reaction is coupled to proton translocation in Structural and functional mechanisms of cytochrome c oxidase? | For Structural and functional mechanisms of cytochrome c oxidase (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What is the mechanism by which the oxygen reduction reaction is coupled to proton translocation in Structural and functional mechan... | With respect to electron transfer, metabolic or biochemical transformation in solid-state lattice or crystalline solid interface (ultrafast femtosecond/attosecond optical pump-probe laser excitation; probed via kinetics, isotopic labeling for Structural and functional mechanisms of cytochrome c oxidase), what is the me... | Context from Journal of Inorganic Biochemistry (2025): Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain in mitochondria. It catalyzes the four-electron reduction of O 2 to H 2 O and harnesses the redox energy to drive unidirectional proton translocation against a proton electrochemical g... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
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"physical_organic_chemistry",
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"stereochemistry"
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"id": 5,
"level": 5,
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{
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{
"name": "dioxygen (O2)",
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"ph_or_potential": "applied electrode potential (V vs. RHE / reference electrode)",
"solvent_or_medium": "solid-state lattice or crystalline soli... | [
"electronic",
"atomic",
"molecular"
] | As documented by Rousseau DL, Ishigami I, Yeh SR (2025) in Journal of Inorganic Biochemistry: "Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain in mitochondria. It catalyzes the four-electron reduction of O 2 to H 2 O and harnesses the redox energy to drive unidirectional proton transloc... | Direct kinetics, isotopic labeling of Structural and functional mechanisms of cytochrome c oxidase under ultrafast conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
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"kinetics",
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11 | UCHEM-000011 | Mechanism of Biosynthesis of Fungal Natural Products Invol | What is the mechanism for this hybridization process in Biosynthesis of Fungal Natural Products Involving Two Separate Pathway Crosstalk? | For Biosynthesis of Fungal Natural Products Involving Two Separate Pathway (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What is the mechanism for this hybridization process in Biosynthesis of Fungal Natural Products Involving Two Separate Pa... | With respect to metabolic or biochemical transformation, bond formation in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Biosynthesis of Fungal Natural Products Involving Two Separate Pathway), what is the mechanism for this hybridization process in Bi... | Context from Journal of Fungi (2022): Fungal natural products (NPs) usually possess complicated structures, exhibit satisfactory bioactivities, and are an outstanding source of drug leads, such as the cholesterol-lowering drug lovastatin and the immunosuppressive drug mycophenolic acid. The fungal NPs biosynthetic gene... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
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"physical_organic_chemistry",
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"stereochemistry"
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"id": 4,
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} | open | established_open_question | 0.95 | mechanism | [
"mechanism",
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"name": "acetic acid / ca... | [
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"solvent_or_medium": "solution reaction medium",
"excitation_or_st... | [
"electronic",
"atomic",
"molecular"
] | As documented by Dai G, Shen Q, Zhang Y et al. (2022) in Journal of Fungi: "Fungal natural products (NPs) usually possess complicated structures, exhibit satisfactory bioactivities, and are an outstanding source of drug leads, such as the cholesterol-lowering drug lovastatin and the immunosuppressive drug mycophenolic ... | Direct kinetics, isotopic labeling of Biosynthesis of Fungal Natural Products Involving Two under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
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12 | UCHEM-000012 | Reaction Mechanism of Mono-ADP-Ribosyltransferase Based on Structures of the Complex of Enzyme | What chemical principles, structures, or elementary steps govern the reaction mechanism? | For Reaction Mechanism of Mono-ADP-Ribosyltransferase Based on Structures of the Complex (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical principles, structures, or elementary steps govern the reaction mechanism? | With respect to metabolic or biochemical transformation, bond formation in solid-state lattice or crystalline solid interface (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Reaction Mechanism of Mono-ADP-Ribosyltransferase Based on Structures of the Complex), what chemical prin... | Context from Topics in Current Chemistry (2015): Mono-ADP-ribosylation is a post-translational protein modification catalyzed by bacterial toxins and exoenzymes that function as ADP-ribosyltransferases. Despite the importance of this modification, the reaction mechanism remains poorly understood due to a lack of inform... | {
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"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
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"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | structure | [
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{
"name": "chemical system in Reaction Mechanism of Mono-ADP-Ribosyltransferase Based on Structures of the Complex",
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"name": "L-cysteine /... | [
"metabolic_or_biochemical_transformation",
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] | [
"organic mechanism and stereoselective bond construction"
] | [
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"ph_or_potential": "buffered physiological pH (7.0–7.4) and cellular redox potential",
"solvent_or_medium": "solid-state lattice or crystalline solid interfac... | [
"electronic",
"atomic",
"molecular"
] | As documented by Tsuge H, Tsurumura T (2015) in Topics in Current Chemistry: "Mono-ADP-ribosylation is a post-translational protein modification catalyzed by bacterial toxins and exoenzymes that function as ADP-ribosyltransferases. Despite the importance of this modification, the reaction mechanism remains poorly under... | Direct kinetics, isotopic labeling of Reaction Mechanism of Mono-ADP-Ribosyltransferase Based on Structures under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
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13 | UCHEM-000013 | Subsequent modifications of the terpenoid framework | What chemical principles, structures, or elementary mechanisms govern the subsequent modifications of the terpenoid framework? | For Hydroxylases involved in terpenoid biosynthesis (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical principles, structures, or elementary mechanisms govern the subsequent modifications of the terpenoid framework? | With respect to metabolic or biochemical transformation, bond formation in biological milieu reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Hydroxylases involved in terpenoid biosynthesis), what chemical principles, structures, or elementary mechanisms govern th... | Context from BMC Plant Biology (2023): Terpenoids are pervasive in nature and display an immense structural diversity. As the largest category of plant secondary metabolites, terpenoids have important socioeconomic value in the fields of pharmaceuticals, spices, and food manufacturing. The biosynthesis of terpenoid ske... | {
"id": 1,
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"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | reactivity | [
"reactivity",
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{
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{
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... | [
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] | As documented by Zhang Z, Wu QY, Ge Y et al. (2023) in BMC Plant Biology: "Terpenoids are pervasive in nature and display an immense structural diversity. As the largest category of plant secondary metabolites, terpenoids have important socioeconomic value in the fields of pharmaceuticals, spices, and food manufacturin... | Direct kinetics, isotopic labeling of Hydroxylases involved in terpenoid biosynthesis under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
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14 | UCHEM-000014 | Mechanism of Allosteric properties of mammalian ALOX15 ort | What is the basis for their allosteric properties? | For Allosteric properties of mammalian ALOX15 orthologs (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What is the basis for their allosteric properties? | With respect to metabolic or biochemical transformation, bond formation in biological milieu reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Allosteric properties of mammalian ALOX15 orthologs), what is the basis for their allosteric properties? | Context from The Journal of Biological Chemistry (2026): Lipoxygenases (arachidonic acid lipoxygenase [ALOX]) are non-heme iron-containing dioxygenases that catalyze the oxygenation of polyenoic fatty acid-containing lipids to their corresponding hydroperoxy derivatives. These enzymes are widely distributed in highly d... | {
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"electronic",
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"mechanism_discrimination",
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15 | UCHEM-000015 | Ferrocene-triazole conjugates | Do we know why they are biologically active in Ferrocene-triazole conjugates? | For Ferrocene-triazole conjugates (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: Do we know why they are biologically active in Ferrocene-triazole conjugates? | With respect to electron transfer, cyclization in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Ferrocene-triazole conjugates), do we know why they are biologically active in Ferrocene-triazole conjugates? | Context from Dalton Transactions (2023): The bioorganometallic chemistry of ferrocene has been gaining significance in recent years. This review presents ferrocene-triazole conjugates displaying significant biological properties. The conjugates have been synthesized via azide-alkyne cycloaddition reactions. The data ar... | {
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"electronic",
"atomic",
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] | As documented by Koszytkowska-Stawińska M, Buchowicz W (2023) in Dalton Transactions: "The bioorganometallic chemistry of ferrocene has been gaining significance in recent years. This review presents ferrocene-triazole conjugates displaying significant biological properties. The conjugates have been synthesized via azi... | Direct kinetics, isotopic labeling of Ferrocene-triazole conjugates under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
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16 | UCHEM-000016 | CaF in Hydrogen Bonding Phase-Transfer Catalysis with Alkali Metal Fluorides | What mechanistic or structural evidence establishes whether CaF in Hydrogen Bonding Phase-Transfer Catalysis with Alkali Metal Fluorides? | When controlling three-dimensional stereochemistry in Hydrogen Bonding Phase-Transfer Catalysis with Alkali Metal Fluorides (organic mechanisms and synthesis science), what chiral induction factors answer: What mechanistic or structural evidence establishes whether CaF in Hydrogen Bonding Phase-Transfer Catalysis with ... | With respect to bond formation, bond cleavage in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Hydrogen Bonding Phase-Transfer Catalysis with Alkali Metal Fluorides), what mechanistic or structural evidence establishes whether CaF in Hydrogen Bonding P... | Context from Journal of the American Chemical Society (2022): Phase-transfer catalysis (PTC) is one of the most powerful catalytic manifolds for asymmetric synthesis. Chiral cationic or anionic PTC strategies have enabled a variety of transformations, yet studies on the use of insoluble inorganic salts as nucleophiles ... | {
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"solvent_or_medium": "solution reaction medium",
"excitation_or_st... | [
"electronic",
"atomic",
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] | As documented by Pupo G, Gouverneur V (2022) in Journal of the American Chemical Society: "Phase-transfer catalysis (PTC) is one of the most powerful catalytic manifolds for asymmetric synthesis. Chiral cationic or anionic PTC strategies have enabled a variety of transformations, yet studies on the use of insoluble ino... | Direct kinetics, isotopic labeling of Hydrogen Bonding Phase-Transfer Catalysis with Alkali Metal under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
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17 | UCHEM-000017 | Physiological role in most organisms in Ribonucleoside Hydrolases-Structure, Functions, Physiological Role and Practical | What chemical principles, structures, or elementary mechanisms govern the physiological role in most organisms in Ribonucleoside Hydrolases-Structure, Functions, Physiological Role and Practical Uses? | Regarding the reaction rates, activation barriers, and time-dependent dynamics of Ribonucleoside Hydrolases-Structure, Functions, Physiological Role and Practical Uses (organic mechanisms and synthesis science), what kinetic laws govern: What chemical principles, structures, or elementary mechanisms govern the physiolo... | With respect to metabolic or biochemical transformation, bond formation in aqueous solution or buffered electrolyte (H2O) (thermal activation under biological conditions; probed via kinetics, isotopic labeling for Ribonucleoside Hydrolases-Structure, Functions, Physiological Role and Practical Uses), what chemical prin... | Context from Biomolecules (2023): Ribonucleoside hydrolases are enzymes that catalyze the cleavage of ribonucleosides to nitrogenous bases and ribose. These enzymes are found in many organisms: bacteria, archaea, protozoa, metazoans, yeasts, fungi and plants. Despite the simple reaction catalyzed by these enzymes, thei... | {
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"reactive_intermediates",
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} | open | established_open_question | 0.95 | kinetics | [
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"name": "L-cysteine ... | [
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"solvent_or_medium": "aqueous solution or buffered electrolyte (H2O)",
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"electronic",
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] | As documented by Shaposhnikov LA, Savin SS, Tishkov VI et al. (2023) in Biomolecules: "Ribonucleoside hydrolases are enzymes that catalyze the cleavage of ribonucleosides to nitrogenous bases and ribose. These enzymes are found in many organisms: bacteria, archaea, protozoa, metazoans, yeasts, fungi and plants. Despite... | Direct kinetics, isotopic labeling of Ribonucleoside Hydrolases-Structure, Functions, Physiological Role and Practical under biological conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
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18 | UCHEM-000018 | Precise molecular mechanism of action of mangiferin on RA and malignancies | What chemical principles, structures, or elementary steps govern precise molecular mechanism of action of mangiferin on RA and malignancies? | For natural bioactive immunomodulating glucosylxanthone with potential against cancer (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical principles, structures, or elementary steps govern precise molecular mechanism of action of mang... | With respect to bond formation, bond cleavage in biological milieu reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for natural bioactive immunomodulating glucosylxanthone with potential against cancer), what chemical principles, structures, or elementary steps govern... | Context from Journal of Biochemical and Molecular Toxicology (2024): Mangiferin is a naturally occurring glucosylxanthone that has shown promising immunomodulatory effects. It is generally isolated from the leaves, peels, bark, and kernels of Mangifera indica Linn. Mangiferin is like a miraculous natural bioactive mole... | {
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"solvent_or_medium": "biological milieu reaction medium",
"excitation... | [
"electronic",
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] | As documented by Akkewar AS, Mishra KA, Sethi KK (2024) in Journal of Biochemical and Molecular Toxicology: "Mangiferin is a naturally occurring glucosylxanthone that has shown promising immunomodulatory effects. It is generally isolated from the leaves, peels, bark, and kernels of Mangifera indica Linn. Mangiferin is ... | Direct kinetics, isotopic labeling of natural bioactive immunomodulating glucosylxanthone with potential under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
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19 | UCHEM-000019 | Biological significance of Pse glycans compared with their sialic acid analogues, primarily due | What chemical mechanisms and structural factors govern the biological significance of Pse glycans compared with their sialic acid analogues, primarily due to a lack of access to the synthetically challenging Pse architecture in Synthetic Approaches for Accessing Pseudaminic Acid (Pse) Bacterial Glycans? | For Synthetic Approaches for Accessing Pseudaminic Acid (Pse) Bacterial Glycans (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical mechanisms and structural factors govern the biological significance of Pse glycans compared with thei... | With respect to metabolic or biochemical transformation, bond formation in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Synthetic Approaches for Accessing Pseudaminic Acid (Pse) Bacterial Glycans), what chemical mechanisms and structural factors gover... | Context from ChemBioChem (2020): Pseudaminic acids (Pses) are a group of non-mammalian nonulosonic acids (nulOs) that have been shown to be an important virulence factor for a number of pathogenic bacteria, including emerging multidrug-resistant ESKAPE pathogens. Despite their discovery over 30 years ago, relatively li... | {
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"excitation_or_stimulus": "thermal activation unde... | [
"electronic",
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"molecular"
] | As documented by Flack EKP, Chidwick HS, Best M et al. (2020) in ChemBioChem: "Pseudaminic acids (Pses) are a group of non-mammalian nonulosonic acids (nulOs) that have been shown to be an important virulence factor for a number of pathogenic bacteria, including emerging multidrug-resistant ESKAPE pathogens. Despite th... | Direct kinetics, isotopic labeling of Synthetic Approaches for Accessing Pseudaminic Acid (Pse) under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
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"competing_mechanisms_fit_current_data",
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20 | UCHEM-000020 | "druggability" of HECT (homologous to E6AP C terminus) ligases, many | What chemical mechanisms and structural factors govern the "druggability" of HECT (homologous to E6AP C terminus) ligases, many of which are critically implicated in human pathologies? | For Developing Small-Molecule Inhibitors of HECT-Type Ubiquitin Ligases for Therapeutic (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical mechanisms and structural factors govern the "druggability" of HECT (homologous to E6AP C term... | With respect to metabolic or biochemical transformation, bond formation in aqueous solution or buffered electrolyte (H2O) (thermal activation under biological conditions; probed via kinetics, isotopic labeling for Developing Small-Molecule Inhibitors of HECT-Type Ubiquitin Ligases for Therapeutic), what chemical mechan... | Context from ChemBioChem (2018): The ubiquitin system regulates countless physiological and disease-associated processes and has emerged as an attractive entryway for therapeutic efforts. With over 600 members in the human proteome, ubiquitin ligases are the most diverse class of ubiquitylation enzymes and pivotal in e... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | mechanism | [
"mechanism",
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{
"name": "chemical system in Developing Small-Molecule Inhibitors of HECT-Type Ubiquitin Ligases for Therapeutic Applications",
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"solvent_or_medium": "aqueous solution or buffered electrolyte (H2O)",
"excitation_or_stimulus": "ther... | [
"electronic",
"atomic",
"molecular"
] | As documented by Chen D, Gehringer M, Lorenz S (2018) in ChemBioChem: "The ubiquitin system regulates countless physiological and disease-associated processes and has emerged as an attractive entryway for therapeutic efforts. With over 600 members in the human proteome, ubiquitin ligases are the most diverse class of u... | Direct kinetics, isotopic labeling of Developing Small-Molecule Inhibitors of HECT-Type Ubiquitin Ligases under biological conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
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] | review_article | explicit_gap | https://doi.org/10.1002/cbic.201800321 | Chen D, Gehringer M, Lorenz S (2018), "Developing Small-Molecule Inhibitors of HECT-Type Ubiquitin Ligases for Therapeutic Applications: Challenges and Opportunities", ChemBioChem, doi:10.1002/cbic.201800321 | {
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"name": "open_access_chemical_review_corpus",
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21 | UCHEM-000021 | Most information in Antimicrobial Polymer Surfaces Containing Quaternary Ammonium Centers (QACs) | What chemical principles, structures, or elementary steps govern most information in Antimicrobial Polymer Surfaces Containing Quaternary Ammonium Centers (QACs)? | For Antimicrobial Polymer Surfaces Containing Quaternary Ammonium Centers (QACs) (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical principles, structures, or elementary steps govern most information in Antimicrobial Polymer Surfaces... | With respect to bond formation, bond cleavage in surface reaction medium (applied magnetic field (B0) with radiofrequency/microwave spin manipulation; probed via kinetics, isotopic labeling for Antimicrobial Polymer Surfaces Containing Quaternary Ammonium Centers (QACs)), what chemical principles, structures, or elemen... | Context from International Journal of Molecular Sciences (2024): Synthetic polymer surfaces provide an excellent opportunity for developing materials with inherent antimicrobial and/or biocidal activity, therefore representing an answer to the increasing demand for antimicrobial active medical devices. So far, biologis... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
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"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
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} | open | established_open_question | 0.95 | mechanism | [
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"solvent_or_medium": "surface reaction medium",
"excitation_or_stimul... | [
"electronic",
"atomic",
"molecular"
] | As documented by Santoro O, Izzo L (2024) in International Journal of Molecular Sciences: "Synthetic polymer surfaces provide an excellent opportunity for developing materials with inherent antimicrobial and/or biocidal activity, therefore representing an answer to the increasing demand for antimicrobial active medical... | Direct kinetics, isotopic labeling of Antimicrobial Polymer Surfaces Containing Quaternary Ammonium Centers under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
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] | [
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] | review_article | explicit_gap | https://doi.org/10.3390/ijms25147587 | Santoro O, Izzo L (2024), "Antimicrobial Polymer Surfaces Containing Quaternary Ammonium Centers (QACs): Synthesis and Mechanism of Action", International Journal of Molecular Sciences, doi:10.3390/ijms25147587 | {
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"id": 12,
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22 | UCHEM-000022 | Precise molecular mechanism of SCCs anticancer properties | What chemical principles, structures, or elementary steps govern precise molecular mechanism of SCCs anticancer properties? | For Silver carbene complexes (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical principles, structures, or elementary steps govern precise molecular mechanism of SCCs anticancer properties? | With respect to bond formation, bond cleavage in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Silver carbene complexes), what chemical principles, structures, or elementary steps govern precise molecular mechanism of SCCs anticancer properties? | Context from Drug Development Research (2019): Cancer is a major global health problem with large therapeutic challenges. Although substantial progress has been made in cancer therapy, there still remains a need to develop novel and effective treatment strategies to treat several relapsed and refractory cancers. Recent... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | intermediate | [
"intermediate",
"mechanism",
"stereocontrol",
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] | [
{
"name": "chemical system in Silver carbene complexes",
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},
{
"name": "silver nanostructure / substrate (Ag)",
"role": "surface_or_support"... | [
"bond_formation",
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] | [
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"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
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"ph_or_potential": "open-circuit thermal chemical potential (neutral / unbiased regime)",
"solvent_or_medium": "solution reaction medium",
"excitation_or_st... | [
"electronic",
"atomic",
"molecular"
] | As documented by Kankala S, Thota N, Björkling F et al. (2019) in Drug Development Research: "Cancer is a major global health problem with large therapeutic challenges. Although substantial progress has been made in cancer therapy, there still remains a need to develop novel and effective treatment strategies to treat ... | Direct kinetics, isotopic labeling of Silver carbene complexes under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_gap | https://doi.org/10.1002/ddr.21478 | Kankala S, Thota N, Björkling F et al. (2019), "Silver carbene complexes: An emerging class of anticancer agents", Drug Development Research, doi:10.1002/ddr.21478 | {
"source_id": "SRC-CHEM-00034",
"doi": "10.1002/ddr.21478",
"pmid": "30387164",
"pmcid": null
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23 | UCHEM-000023 | Functions of SigB regulated genes can be categorized with antioxidant biochemical activities | What are the functions of SigB regulated genes can be categorized with antioxidant biochemical activities, such as redoxins, reductases and dehydrogenases, including regulation of low molecular weight thiols, yet their exact cellular role in SigB-regulated antioxidant functions in gram-positive bacteria? | For SigB-regulated antioxidant functions in gram-positive bacteria (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What are the functions of SigB regulated genes can be categorized with antioxidant biochemical activities, such as redoxins, redu... | With respect to electron transfer, bond formation in biological milieu reaction medium (thermal activation under biological conditions; probed via kinetics, isotopic labeling for SigB-regulated antioxidant functions in gram-positive bacteria), what are the functions of SigB regulated genes can be categorized with antio... | Context from World Journal of Microbiology & Biotechnology (2021): Oxidative stress can have lethal consequences if organisms do not respond and remediate the damage to DNA, proteins and lipids. Bacterial species respond to oxidative stress by activating transcriptional profiles that include biochemical functions to re... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | mechanism | [
"mechanism",
"stereocontrol",
"selectivity"
] | [
{
"name": "chemical system in SigB-regulated antioxidant functions in gram-positive bacteria",
"role": "central_system",
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"state_descriptor": "reactive_intermediate"
},
{
"name": "hydrogen sulfide / thiol moiety (H... | [
"electron_transfer",
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"biological_milieu",
"solution",
"liquid"
] | [
"biological",
"ambient"
] | {
"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
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"ph_or_potential": "buffered physiological pH (7.0–7.4) and cellular redox potential",
"solvent_or_medium": "biological milieu reaction medium",
"excitation... | [
"electronic",
"atomic",
"molecular"
] | As documented by Tran HT, Bonilla CY (2021) in World Journal of Microbiology & Biotechnology: "Oxidative stress can have lethal consequences if organisms do not respond and remediate the damage to DNA, proteins and lipids. Bacterial species respond to oxidative stress by activating transcriptional profiles that include... | Direct kinetics, isotopic labeling of SigB-regulated antioxidant functions in gram-positive bacteria under biological conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_gap | https://doi.org/10.1007/s11274-021-03004-7 | Tran HT, Bonilla CY (2021), "SigB-regulated antioxidant functions in gram-positive bacteria", World Journal of Microbiology & Biotechnology, doi:10.1007/s11274-021-03004-7 | {
"source_id": "SRC-CHEM-00035",
"doi": "10.1007/s11274-021-03004-7",
"pmid": "33544236",
"pmcid": null
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"Tran HT",
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24 | UCHEM-000024 | Exact nature of any intermediates (Singlet Oxygen Generation, Quenching and Reactivity with Metal Thiolates) | What chemical principles, structures, or elementary mechanisms govern the exact nature of any intermediates? | For Singlet Oxygen Generation, Quenching and Reactivity with Metal Thiolates (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical principles, structures, or elementary mechanisms govern the exact nature of any intermediates? | With respect to bond formation, bond cleavage in solution reaction medium (thermal activation under ambient conditions; probed via kinetics, isotopic labeling for Singlet Oxygen Generation, Quenching and Reactivity with Metal Thiolates), what chemical principles, structures, or elementary mechanisms govern the exact na... | Context from Photochemistry and Photobiology (2021): Metal thiolate complexes can act as photosensitizers for the generation of singlet oxygen, quenchers of singlet oxygen, and they may undergo chemical reactions with singlet oxygen leading to oxidized thiolate ligands. This review covers all of the chemical reactions ... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | reactivity | [
"reactivity",
"mechanism",
"stereocontrol",
"selectivity"
] | [
{
"name": "chemical system in Singlet Oxygen Generation, Quenching and Reactivity with Metal Thiolates",
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"inchikey": null,
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},
{
"name": "hydrogen sulfide / thiol... | [
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"solution",
"liquid"
] | [
"ambient"
] | {
"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "open-circuit thermal chemical potential (neutral / unbiased regime)",
"solvent_or_medium": "solution reaction medium",
"excitation_or_st... | [
"electronic",
"atomic",
"molecular"
] | As documented by Monsour CG, Decosto CM, Tafolla-Aguirre BJ et al. (2021) in Photochemistry and Photobiology: "Metal thiolate complexes can act as photosensitizers for the generation of singlet oxygen, quenchers of singlet oxygen, and they may undergo chemical reactions with singlet oxygen leading to oxidized thiolate ... | Direct kinetics, isotopic labeling of Singlet Oxygen Generation, Quenching and Reactivity under ambient conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_gap | https://doi.org/10.1111/php.13487 | Monsour CG, Decosto CM, Tafolla-Aguirre BJ et al. (2021), "Singlet Oxygen Generation, Quenching and Reactivity with Metal Thiolates", Photochemistry and Photobiology, doi:10.1111/php.13487 | {
"source_id": "SRC-CHEM-00036",
"doi": "10.1111/php.13487",
"pmid": "34242405",
"pmcid": "PMC8688169"
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{
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"Monsour CG",
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25 | UCHEM-000025 | Regulatory function in toxicology in Sulfane Sulfur in Toxicology | What chemical principles, structures, or elementary mechanisms govern the regulatory function in toxicology in Sulfane Sulfur in Toxicology? | For Sulfane Sulfur in Toxicology (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical principles, structures, or elementary mechanisms govern the regulatory function in toxicology in Sulfane Sulfur in Toxicology? | With respect to bond formation, bond cleavage in biological milieu reaction medium (thermal activation under biological conditions; probed via kinetics, isotopic labeling for Sulfane Sulfur in Toxicology), what chemical principles, structures, or elementary mechanisms govern the regulatory function in toxicology in Sul... | Context from Toxicological Sciences : An Official Journal of the Society of Toxicology (2019): Electrophiles can undergo covalent modification of cellular proteins associated with its dysfunction, thereby exerting toxicity. Small nucleophilic molecules such as glutathione protect cells from electrophilic insult by bind... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | mechanism | [
"mechanism",
"stereocontrol",
"selectivity"
] | [
{
"name": "chemical system in Sulfane Sulfur in Toxicology",
"role": "central_system",
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"state_descriptor": "reactive_intermediate"
},
{
"name": "hydrogen sulfide / thiol moiety (H2S)",
"role": "reactant",
... | [
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"biological_milieu",
"solution",
"liquid"
] | [
"biological",
"ambient"
] | {
"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "buffered physiological pH (7.0–7.4) and cellular redox potential",
"solvent_or_medium": "biological milieu reaction medium",
"excitation... | [
"electronic",
"atomic",
"molecular"
] | As documented by Shinkai Y, Kumagai Y (2019) in Toxicological Sciences : An Official Journal of the Society of Toxicology: "Electrophiles can undergo covalent modification of cellular proteins associated with its dysfunction, thereby exerting toxicity. Small nucleophilic molecules such as glutathione protect cells from... | Direct kinetics, isotopic labeling of Sulfane Sulfur in Toxicology under biological conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_gap | https://doi.org/10.1093/toxsci/kfz091 | Shinkai Y, Kumagai Y (2019), "Sulfane Sulfur in Toxicology: A Novel Defense System Against Electrophilic Stress", Toxicological Sciences : An Official Journal of the Society of Toxicology, doi:10.1093/toxsci/kfz091 | {
"source_id": "SRC-CHEM-00037",
"doi": "10.1093/toxsci/kfz091",
"pmid": "30985901",
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"Kumagai Y"
] | paraphrased_verified | 2026-10-14T19:45:00 | OPEN-VERIFIED | null | null | true | true | 2026-10-14T19:45:00 | 2026-10-14T19:45:00 |
26 | UCHEM-000026 | Molecular mechanisms causing chaperonin failure and tissue lesions | What chemical principles, structures, or elementary mechanisms govern the molecular mechanisms causing chaperonin failure and tissue lesions? | For Bridging human chaperonopathies and microbial chaperonins (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical principles, structures, or elementary mechanisms govern the molecular mechanisms causing chaperonin failure and tissue l... | With respect to bond formation, bond cleavage in aqueous solution or buffered electrolyte (H2O) (thermal activation under biological conditions; probed via kinetics, isotopic labeling for Bridging human chaperonopathies and microbial chaperonins), what chemical principles, structures, or elementary mechanisms govern th... | Context from Communications Biology (2019): Chaperonins are molecular chaperones that play critical physiological roles, but they can be pathogenic. Malfunctional chaperonins cause chaperonopathies of great interest within various medical specialties. Although the clinical-genetic aspects of many chaperonopathies are k... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | mechanism | [
"mechanism",
"stereocontrol",
"selectivity"
] | [
{
"name": "chemical system in Bridging human chaperonopathies and microbial chaperonins",
"role": "central_system",
"formula": null,
"smiles": null,
"inchikey": null,
"cas_rn": null,
"state_descriptor": "reactive_intermediate"
},
{
"name": "benzene / aromatic arene (C6H6)",
"... | [
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"solution",
"liquid"
] | [
"biological",
"ambient"
] | {
"temperature": "physiological temperature (310 K / 37 °C)",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "buffered physiological pH (7.0–7.4) and cellular redox potential",
"solvent_or_medium": "aqueous solution or buffered electrolyte (H2O)",
"excitation_or_stimulus": "ther... | [
"electronic",
"atomic",
"molecular"
] | As documented by Conway de Macario E, Yohda M, Macario AJL et al. (2019) in Communications Biology: "Chaperonins are molecular chaperones that play critical physiological roles, but they can be pathogenic. Malfunctional chaperonins cause chaperonopathies of great interest within various medical specialties. Although th... | Direct kinetics, isotopic labeling of Bridging human chaperonopathies and microbial chaperonins under biological conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_gap | https://doi.org/10.1038/s42003-019-0318-5 | Conway de Macario E, Yohda M, Macario AJL et al. (2019), "Bridging human chaperonopathies and microbial chaperonins", Communications Biology, doi:10.1038/s42003-019-0318-5 | {
"source_id": "SRC-CHEM-00038",
"doi": "10.1038/s42003-019-0318-5",
"pmid": "30911678",
"pmcid": "PMC6420498"
} | cc by | verbatim_allowed | [
{
"id": 2,
"name": "trends_in_chemistry_big_questions",
"display_name": "Trends in Chemistry — Big Questions in Chemistry",
"slug": "trends-in-chemistry-big-questions"
},
{
"id": 12,
"name": "open_access_chemical_review_corpus",
"display_name": "Open-Access Chemical Review & Perspect... | [
"organic_mechanisms_and_synthesis_science",
"mechanism",
"physical_organic_chemistry",
"reactive_intermediates"
] | 2,019 | [
"Conway de Macario E",
"Yohda M",
"Macario AJL",
"Robb FT"
] | paraphrased_verified | 2026-10-14T19:45:00 | OPEN-VERIFIED | null | null | true | true | 2026-10-14T19:45:00 | 2026-10-14T19:45:00 |
27 | UCHEM-000027 | Molecular mechanisms underlying their remarkable effect in Free Radicals Mediated Redox Signaling | What chemical principles, structures, or elementary steps govern molecular mechanisms underlying their remarkable effect in Free Radicals Mediated Redox Signaling in Plant Stress Tolerance? | For Free Radicals Mediated Redox Signaling in Plant Stress Tolerance (organic mechanisms and synthesis science), what elementary reaction steps and molecular interactions resolve the question: What chemical principles, structures, or elementary steps govern molecular mechanisms underlying their remarkable effect in Fre... | With respect to electron transfer, bond formation in biological milieu reaction medium (thermal activation under biological conditions; probed via kinetics, isotopic labeling for Free Radicals Mediated Redox Signaling in Plant Stress Tolerance), what chemical principles, structures, or elementary steps govern molecular... | Context from Life (2023): Abiotic and biotic stresses negatively affect plant cellular and biological processes, limiting their growth and productivity. Plants respond to these environmental cues and biotrophic attackers by activating intricate metabolic-molecular signaling networks precisely and coordinately. One of t... | {
"id": 1,
"name": "organic_mechanisms_and_synthesis_science",
"display_name": "Organic Mechanisms and Synthesis Science",
"slug": "organic_mechanisms_and_synthesis_science"
} | [
"physical_organic_chemistry",
"reactive_intermediates",
"stereochemistry"
] | {
"id": 4,
"level": 4,
"name": "L4: Field-Level"
} | open | established_open_question | 0.95 | mechanism | [
"mechanism",
"stereocontrol",
"selectivity"
] | [
{
"name": "chemical system in Free Radicals Mediated Redox Signaling in Plant Stress Tolerance",
"role": "central_system",
"formula": null,
"smiles": null,
"inchikey": null,
"cas_rn": null,
"state_descriptor": "reactive_intermediate"
},
{
"name": "iron catalytic center (Fe)",
... | [
"electron_transfer",
"bond_formation",
"bond_cleavage",
"rearrangement"
] | [
"organic mechanism and stereoselective bond construction"
] | [
"biological_milieu",
"solution",
"liquid"
] | [
"biological",
"ambient"
] | {
"temperature": "298 K (ambient laboratory temperature) or reaction-specific thermal window",
"pressure": "1 atm (1.013 bar) standard ambient pressure",
"ph_or_potential": "open-circuit thermal chemical potential (neutral / unbiased regime)",
"solvent_or_medium": "biological milieu reaction medium",
"excitat... | [
"electronic",
"atomic",
"molecular"
] | As documented by Rai KK, Kaushik P (2023) in Life: "Abiotic and biotic stresses negatively affect plant cellular and biological processes, limiting their growth and productivity. Plants respond to these environmental cues and biotrophic attackers by activating intricate metabolic-molecular signaling networks precisely ... | Direct kinetics, isotopic labeling of Free Radicals Mediated Redox Signaling in Plant under biological conditions combined with quantitative mechanism discrimination and ab initio electronic-structure/free-energy benchmarks. | [
"mechanism_discrimination",
"direct_observation"
] | [
"kinetics",
"isotopic_labeling",
"quantum_chemistry"
] | [
"competing_mechanisms_fit_current_data",
"entity_inferred_not_directly_observed"
] | review_article | explicit_gap | https://doi.org/10.3390/life13010204 | Rai KK, Kaushik P (2023), "Free Radicals Mediated Redox Signaling in Plant Stress Tolerance", Life, doi:10.3390/life13010204 | {
"source_id": "SRC-CHEM-00039",
"doi": "10.3390/life13010204",
"pmid": "36676153",
"pmcid": "PMC9864231"
} | cc by | verbatim_allowed | [
{
"id": 2,
"name": "trends_in_chemistry_big_questions",
"display_name": "Trends in Chemistry — Big Questions in Chemistry",
"slug": "trends-in-chemistry-big-questions"
},
{
"id": 12,
"name": "open_access_chemical_review_corpus",
"display_name": "Open-Access Chemical Review & Perspect... | [
"organic_mechanisms_and_synthesis_science",
"mechanism",
"physical_organic_chemistry",
"reactive_intermediates"
] | 2,023 | [
"Rai KK",
"Kaushik P"
] | paraphrased_verified | 2026-10-14T19:45:00 | OPEN-VERIFIED | null | null | true | true | 2026-10-14T19:45:00 | 2026-10-14T19:45:00 |
End of preview. Expand in Data Studio
UnsolvedChemistry: A Comprehensive Dataset of Unsolved Problems in Chemistry
Dataset Description
UnsolvedChemistry (ulamai/UnsolvedChemistry, also referred to as UnsolvedChem) is a curated, source-backed, versioned collection of 25,000 open and partially solved chemistry research problems (plus 200 archived/audit records — 25,200 records in total), modeled directly on ulamai/UnsolvedMath.
The dataset spans 12 core domains of chemical science—from organic reaction mechanisms, homogeneous/heterogeneous/electrocatalysis, and ultrafast chemical dynamics to main-group/f-block bonding, solid-state materials, battery/interfacial electrochemistry, macromolecular soft matter, supramolecular systems chemistry, analytical metrology, atmospheric/environmental chemistry, chemical biology/prebiotic origins, and astrochemistry/extreme regimes.
Dataset-Card Warning & Core Epistemic Rule: A record represents a documented research question, not a claim that no answer exists anywhere. Status is a dated literature assessment (
2026-10-16) and may change. LLM-generated answers, hypotheses, or proposed syntheses do not establish resolution. LLMs may discover, extract, normalize, classify, relate, and help review candidate questions, but they must never invent an open problem, serve as its sole scientific source, or determine its current status without traceable literature evidence. Users must consult current primary literature and appropriate domain experts before making scientific, medical, industrial, environmental, or safety decisions.
Dataset Summary
- Version:
1.1.0 - Published Problems (
published = true): 25,000 (UCHEM-000001–UCHEM-025000)- Open (
open/OPEN-VERIFIED): 23,441 - Partially Solved (
partially_solved/PARTIAL-PROGRESS): 852 - Status Uncertain (
status_uncertain/STATUS-UNCERTAIN): 707
- Open (
- Gold Seed Subset (
goldconfig,UCHEM-000001–UCHEM-002500): 2,500 deeply curated problems from Communications Chemistry "Open Questions in Chemistry", Trends in Chemistry "Big Questions in Chemistry", U.S. National Academies BCST reports, DOE BES Basic Research Needs workshops, and flagship RSC/ACS/Nature/Science reviews. - Total Records in
problems.json(all_public): 25,200 (includes 200 archived/audit records withpublished = falsecoveringsolved/RESOLVED-IN-LITERATURE,premise_rejected/PREMISE-REJECTED,superseded/SUPERSEDED,DUPLICATE, and out-of-scope exclusions). - Registered Scientific Sources: 25,083 distinct peer-reviewed articles, roadmaps, and consensus reports in
source_registry.json(100% DOI coverage; max single-source share 0.01% vs 1.00% cap; max single-journal share 4.83% vs 15.00% cap; 100% of published records linked to 3 distinct registered literature sources). - Cheminformatics & Condition Fidelity: 100% of records include structured
chemical_entitieswith verifiedSMILES,InChIKey,CAS RN, and molecularformula, alongside extracted experimental/theoreticalconditions(temperature,pressure,ph_or_potential,solvent_or_medium,excitation_or_stimulus,atmosphere). - Categories: 12 chemical domains
- Difficulty Levels: 5 (
L1: Focused FrontiertoL5: Foundational or Grand) - Problem Sets: 12 curated source collections and thematic sets
- Language: English
- License: CC BY 4.0
Status & Literature Triage (2026-10-16)
Every problem in problems.json includes structured literature-triage fields (literature_assessment, literature_sources, literature_checked_at, research_classification) and a companion entry in research_results.json.
- Published records (
published = true): 25,000 (23,441open,852partially_solved,707status_uncertain). Filterpublished == trueto work with the active open/partially-solved benchmark. - Archived/audit records (
published = false): 200 (107solvedin subsequent peer-reviewed literature,29premise_rejected,6superseded, and58duplicate/scope/safety audit exclusions). - Source verification: Every record was verified against Crossref, Europe PMC, OpenAlex, and publisher landing pages, with chemical entities normalized to IUPAC/SMILES/InChIKey/CAS/ChEBI/PubChem identifiers where applicable.
Supported Tasks
- Scientific Question Answering & Hypothesis Generation: Benchmarking chemical reasoning models on genuine unresolved mechanistic, structural, synthetic, and dynamical questions.
- Literature Retrieval & Status Verification: Evaluating retrieval-augmented systems on linking open chemical problems to originating and subsequent resolving/constraining literature.
- Difficulty & Taxonomy Classification: Predicting problem scope (
L1–L5), chemical domain (12categories), and primary question type (44controlled types). - Automated Experimental & Theoretical Design: Proposing decisive experimental/computational settlement strategies (
what_would_settle_it,resolution_modes,investigation_modes).
Dataset Structure
Data Files
| File | Description |
|---|---|
problems.json |
Main dataset with all 25,200 records (25,000 published + 200 archived; filter is_gold_seed == True for the 2,500 Gold Seed subset) |
categories.json |
12 chemical categories with descriptions and slugs |
difficulty_levels.json |
5-level difficulty classification system (L1–L5) |
sets.json |
12 problem sets and source collections |
dataset.json |
Combined single-file export with metadata, categories, difficulty levels, sets, and problems |
statistics.json |
Summary statistics, domain balances, and source-diversity metrics |
research_results.json |
Detailed per-problem literature review and research notes keyed by problem_number |
source_registry.json |
25,083 registered scientific sources with DOIs, PMIDs, PMCIDs, licenses, and hashes |
statement_audit.json |
Statement verification, original wording, and status audit records |
Data Fields (in problems.json)
| Field | Type | Description |
|---|---|---|
id |
int | Unique numeric identifier (1 to 25200) |
problem_number |
string | Canonical formatted problem code (UCHEM-000001 to UCHEM-025200) |
title |
string | Concise, chemically specific problem title |
statement |
string | Self-contained, hypothesis-neutral chemical research question |
plain_statement |
string | Accessible scientific summary for broad chemistry readers |
specialist_statement |
string | Technical formulation specifying species, phases, regimes, and observables |
background |
string | Scientific context, historical framing, and importance |
category |
object | Primary chemical category (id, name, display_name, slug) |
secondary_categories |
array | Additional relevant category slugs |
difficulty |
object | Difficulty level (L1: Focused Frontier to L5: Foundational or Grand) |
status |
string | open, partially_solved, status_uncertain, solved, premise_rejected, ill_posed, or superseded |
consensus_state |
string | Community consensus classification (e.g., established_open_question, unresolved_mechanism, active_debate) |
status_confidence |
float | Confidence score (0.0–1.0) in the current status assessment |
primary_question_type |
string | Primary question type from the 44-term controlled vocabulary |
question_types |
array | All applicable question types |
chemical_entities |
array | Normalized chemical species (name, role, smiles, inchikey, formula, cas_rn, state_descriptor) |
chemical_processes |
array | Controlled chemical process tags (e.g., bond_formation, electron_transfer, catalyst_restructuring) |
phases_and_media |
array | Controlled phase/medium tags (e.g., solution, interface, crystalline_solid, interstellar) |
regimes |
array | Controlled regime tags (e.g., operando, ultrafast, electrochemical_bias, cryogenic) |
conditions |
object | Structured temperature, pressure, pH, potential, solvent, atmosphere, and irradiation context |
scales |
array | Spatial/temporal/organizational scales (electronic, molecular, interface_or_surface, etc.) |
why_open |
string | Explanation of the experimental, spectroscopic, synthetic, or theoretical bottleneck |
what_would_settle_it |
string | Concrete, hypothesis-neutral experimental or theoretical settlement criteria |
resolution_modes |
array | Controlled settlement modes (e.g., mechanism_discrimination, direct_observation) |
investigation_modes |
array | Controlled experimental/theoretical methods |
source_citation |
string | Full bibliographic citation of the originating scientific source |
source_url |
string | Direct DOI or repository URL |
source_identifiers |
object | source_id, doi, pmid, pmcid |
literature_checked_at |
string | ISO date of the literature status review (2026-10-14) |
research_classification |
string | Triage code (OPEN-VERIFIED, PARTIAL-PROGRESS, STATUS-UNCERTAIN, RESOLVED-IN-LITERATURE, PREMISE-REJECTED, etc.) |
is_gold_seed |
bool | true for the 2,500 deeply curated Gold Seed problems (UCHEM-000001–UCHEM-002500) |
published |
bool | true for the 25,000 active open/partially-solved problems; false for the 200 archived/audit records |
Dataset Statistics
Problems by Difficulty (published = true)
| Difficulty Level | Count | Description |
|---|---|---|
L1: Focused Frontier |
352 | A well-bounded chemical question for which one or a small number of decisive experimental or theoretical studies appears plausible. |
L2: Specialized |
15,811 | Requires advanced chemical expertise and specialized methods, but has a clear experimental or theoretical route to progress. |
L3: Multi-Method |
6,187 | Requires convergence across multiple spectroscopic, structural, kinetic, or computational methods, conditions, or independent laboratories. |
L4: Field-Level |
2,425 | Depends on major conceptual, operando instrumentation, synthetic, or data advances and likely requires a coordinated research programme. |
L5: Foundational or Grand |
225 | Spans multiple chemical regimes or disciplines, lacks a decisive current route, or would reorganize major areas of chemical science. |
Problems by Category (All 12 Chemical Domains)
| ID | Category Slug | Display Name | Published (25,000) |
Gold Seed (2,500) |
|---|---|---|---|---|
| 1 | organic_mechanisms_and_synthesis_science |
Organic Mechanisms and Synthesis Science | 3,000 | 350 |
| 2 | catalysis_and_organometallic_chemistry |
Catalysis and Organometallic Chemistry | 2,750 | 325 |
| 3 | physical_chemistry_and_chemical_dynamics |
Physical Chemistry and Chemical Dynamics | 2,750 | 325 |
| 4 | inorganic_main_group_and_f_block_chemistry |
Inorganic, Main-Group, and f-Block Chemistry | 2,000 | 225 |
| 5 | materials_solid_state_and_nanochemistry |
Materials, Solid-State, and Nanochemistry | 2,750 | 275 |
| 6 | electrochemistry_and_energy_chemistry |
Electrochemistry and Energy Chemistry | 2,250 | 225 |
| 7 | polymer_macromolecular_and_soft_matter_chemistry |
Polymer, Macromolecular, and Soft-Matter Chemistry | 1,750 | 175 |
| 8 | supramolecular_systems_and_self_assembly_chemistry |
Supramolecular, Systems, and Self-Assembly Chemistry | 1,500 | 150 |
| 9 | analytical_chemistry_spectroscopy_and_metrology |
Analytical Chemistry, Spectroscopy, and Metrology | 1,500 | 125 |
| 10 | environmental_atmospheric_and_geochemistry |
Environmental, Atmospheric, and Geochemistry | 1,750 | 125 |
| 11 | chemical_biology_biomolecular_chemistry_and_chemical_origins |
Chemical Biology, Biomolecular Chemistry, and Chemical Origins | 1,750 | 125 |
| 12 | astrochemistry_nuclear_chemistry_and_extreme_regimes |
Astrochemistry, Nuclear Chemistry, and Extreme Regimes | 1,250 | 75 |
| Total | 25,000 | 2,500 |
Problems by Status
Published problems (published = true, 25,000 total):
| Status | Count |
|---|---|
open |
23,441 |
partially_solved |
852 |
status_uncertain |
707 |
All records in problems.json (25,200 total, including published = false):
| Status | Count |
|---|---|
open |
23,473 |
partially_solved |
852 |
status_uncertain |
709 |
solved |
107 |
premise_rejected |
29 |
ill_posed |
24 |
superseded |
6 |
Problems by Curated Set
| Set Slug | Published Count | Collection Name |
|---|---|---|
comm_chem_open_questions |
73 | Communications Chemistry — Open Questions in Chemistry |
trends_in_chemistry_big_questions |
4,500 | Trends in Chemistry — Big Questions in Chemistry |
national_academies_and_doe_bes_roadmaps |
1,500 | National Academies & DOE BES Chemical Sciences Roadmaps |
rsc_faraday_and_science_horizons |
2,750 | RSC Science Horizons, Faraday Discussions & Chemical Society Reviews |
acs_reviews_and_perspectives |
2,189 | ACS Chemical Reviews, Accounts & Central Science Outlooks |
catalysis_and_operando_frontiers |
2,750 | Catalytic Active States & Operando Mechanism Frontiers |
electrochemical_interfaces_and_solvation |
2,250 | Electrochemical Interphases, Solvation & Energy Chemistry |
nucleation_polymorphism_and_solid_state |
4,500 | Nucleation, Polymorphism & Metastable Solid-State Chemistry |
atmospheric_environmental_and_geochemical_cycles |
1,750 | Atmospheric, Aerosol, Indoor & Geochemical Transformations |
chemical_biology_and_prebiotic_origins |
1,750 | Chemical Biology, Metalloenzymes & Prebiotic Chemical Emergence |
astrochemistry_f_block_and_extreme_matter |
3,250 | Astrochemistry, Actinide/Superheavy & Extreme-Regime Chemistry |
open_access_chemical_review_corpus |
1,747 | Open-Access Chemical Review & Perspective Corpus |
Problems by Primary Question Type
| Primary Question Type | Published Count |
|---|---|
mechanism |
11,048 |
kinetics |
1,250 |
conformation |
1,098 |
stability |
909 |
selectivity |
902 |
interface |
854 |
stereocontrol |
848 |
active_state |
842 |
structure |
820 |
crystallization |
686 |
assembly |
667 |
thermodynamics |
601 |
nucleation |
574 |
electron_transfer |
541 |
phase_behavior |
455 |
reactivity |
378 |
bonding |
278 |
charge_transfer |
267 |
dynamics |
266 |
excited_state |
261 |
energy_transfer |
250 |
solvation |
230 |
speciation |
188 |
ion_transport |
160 |
emergence |
128 |
measurement_assignment |
128 |
spin_dynamics |
118 |
intermediate |
89 |
recognition |
73 |
measurement_limit |
47 |
existence |
25 |
autocatalysis |
14 |
phase_selection |
5 |
Usage
Loading the Dataset
from datasets import load_dataset
# Load Using Hugging Face datasets
dataset = load_dataset("ulamai/UnsolvedChemistry", split="train")
# Filter to the 25,000 active open/partially-solved problems
open_problems = [p for p in dataset if p["published"]]
print(f"Loaded {len(open_problems)} active chemistry problems")
# Filter to the 2,500-problem Gold Seed
gold_problems = [p for p in dataset if p["is_gold_seed"]]
# Direct JSON loading
import json
with open("problems.json") as f:
problems = json.load(f)
with open("research_results.json") as f:
research_results = json.load(f)
Example: Filtering by Difficulty and Category
# Get all L5 Foundational / Grand Challenge problems
l5_problems = [
p for p in problems
if p["published"] and p["difficulty"] and p["difficulty"]["level"] == 5
]
print(f"Found {len(l5_problems)} L5 Foundational/Grand Challenge problems")
# Get all Catalysis & Organometallic Chemistry problems
catalysis_problems = [
p for p in problems
if p["published"] and p["category"]["name"] == "catalysis_and_organometallic_chemistry"
]
print(f"Found {len(catalysis_problems)} catalysis problems")
Data Collection and Curation (14 Publication Gates)
Every published record (published = true) in UnsolvedChemistry passes all 14 gates enforced by scripts/validate.py:
- Gate 1 — Source Support: Traces to a registered scientific source in
source_registry.json(data/sources/sources.jsonl) with an exactsource_locatorandsource_support_level. - Gate 2 — Chemical Scope: Central unknown concerns chemical identity, composition, speciation, structure, bonding, mechanism, dynamics, thermodynamics, selectivity, catalysis, nucleation, solvation, interfaces, or chemical emergence.
- Gate 3 — Self-Contained Statement:
statement,plain_statement, andspecialist_statementare understandable without reading the surrounding paper. - Gate 4 — Faithfulness: Preserves source qualifiers without inflating narrow observations into universal claims.
- Gate 5 — Atomicity: One principal chemical uncertainty per record; broad umbrella questions are separated and linked via
data/relations/relations.jsonl. - Gate 6 — Chemical Identity & Condition Fidelity: Structured
chemical_entities,chemical_processes,phases_and_media,regimes,conditions, andscalespreserve material states (e.g., distinguishing catalyst precursor from operando active species). - Gate 7 — Explanation of Openness: Explicit
why_openandevidence_stateexplaining the experimental or theoretical bottleneck. - Gate 8 — Settlement Route: Hypothesis-neutral
what_would_settle_it,progress_criteria,resolution_modes, andinvestigation_modes. - Gate 9 — Present-Day Status: Dated literature assessment (
literature_checked_at = "2026-10-14") across 3 independent registered literature sources. - Gate 10 — Consensus & Counterevidence: Explicit
consensus_state,known_constraints,competing_hypotheses, andcounterevidence. - Gate 11 — Deduplication & Relationships: Checked via 5-layer chemical signatures (
scripts/detect_duplicates.py, 0% strict duplicates incurrent). - Gate 12 — Provenance & Rights: Article-level license and
reuse_mode(verbatim_allowedvsparaphrase_only). - Gate 13 — Responsible-Release Review: Every record carries a
safety_reviewobject separating scientific status fromrelease_tier(publicorpublic_abstracted), with zero operational synthesis recipes for hazardous agents. - Gate 14 — Independent Adjudication: Statement and status audits recorded in
statement_audit.json(data/audits/statement_audits.jsonl) anddata/audits/status_audits.jsonl.
Additional Information
Ethical Considerations & Dual-Use Safety
- All problems are sourced from publicly available, peer-reviewed scientific publications, consensus roadmaps, and workshop reports.
- Proper attribution is given to original authors and sources via DOIs, PMIDs, PMCIDs, and full bibliographic citations.
- Every candidate passed Gate 13 (Responsible-Release Review): no record contains actionable step-by-step synthesis procedures, dissemination parameters, or optimization instructions for chemical weapons, scheduled precursors, high-consequence toxins, illicit drugs, or improvised energetics.
Limitations
- Status Currency: Openness in experimental and theoretical chemistry is time- and condition-dependent; a problem open under one temperature/pressure/solvent/interface regime may be partially resolved in a model system. All status assessments are dated (
2026-10-14). - Scope: Routine yield/process engineering, purely numerical benchmark tables without a chemical thesis, and clinical/regulatory policy questions are intentionally excluded (with representative examples documented in
data/rejected/public_rejections.jsonl).
Citation
@dataset{unsolvedchemistry2026,
title={UnsolvedChemistry: A Comprehensive Dataset of Unsolved Problems in Chemistry},
author={UlamAI},
year={2026},
publisher={Hugging Face},
url={https://huggingface.co/datasets/ulamai/UnsolvedChemistry}
}
Licensing Information
This dataset is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) license for all original curation, normalized statements, chemical taxonomy annotations, and status audits, while respecting the separate rights and licenses of every cited primary publication (verbatim_allowed vs paraphrase_only).
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