{ "scope": "Saved research records used for an editorial graph. No new simulations or experiments. Reported synthesis routes, source saddle-search bookkeeping and proposed machine integration remain distinct.", "snapshot": "2026-10-21", "notebookSources": [ { "path": "research/catalog/bootstrap/registry.json", "sha256": "0f95f4f4d1286fa917e5eb00e217077e90d73786e61bfd7d98fe8ae2beae0f82" }, { "path": "research/catalog/bootstrap/reaction-network/evidence.json", "sha256": "5928fb10351fcf970861543ac2d6e85e276020ca738509dbff983c289d394923" }, { "path": "research/catalog/bootstrap/reaction-network/official-supplement-audit.json", "sha256": "74ef81827e8d58a25799123761a0bf2e2a1390ee60919dd6dd7ed749783f1290" } ], "records": [ { "id": "dcpd", "kind": "molecule", "title": "endo-Dicyclopentadiene", "summary": "The ten-carbon precursor for the reference hydrogenation.", "status": "Structure available", "sourceIds": [ "orgsyn" ], "facts": [ { "label": "Formula", "value": "C10H12" }, { "label": "Identity", "value": "Pinned stereochemical representative: PubChem CID 11815882" }, { "label": "Geometry", "value": "Reused computed conformer; not a measured reactor configuration" } ], "missing": [ "Lot-specific endo/exo composition and inhibitor content." ], "structureKey": "dcpd", "composition": { "C": 10, "H": 12 }, "charge": 0 }, { "id": "hydrogen", "kind": "molecule", "title": "Molecular hydrogen", "summary": "Two H2 molecules supply four H atoms per DCPD molecule.", "status": "Identity specified", "sourceIds": [ "orgsyn" ], "facts": [ { "label": "Formula", "value": "H2" }, { "label": "Notation", "value": "H2 is the molecule; hydrogen-2 denotes deuterium." }, { "label": "Phase", "value": "Gas supply; dissolved concentration depends on reactor conditions." } ], "missing": [ "Dissolved H2 / mass-transfer model." ], "composition": { "H": 2 }, "charge": 0 }, { "id": "endo-thdcpd", "kind": "molecule", "title": "endo-Tetrahydrodicyclopentadiene", "summary": "Hydrogenated precursor; same formula as adamantane, different connectivity.", "status": "Structure available", "sourceIds": [ "orgsyn" ], "facts": [ { "label": "Formula", "value": "C10H16" }, { "label": "Identity", "value": "PubChem CID 9812790" }, { "label": "Geometry", "value": "Reused aligned computed conformer" } ], "missing": [ "Source-matched electronic energies and reactive intermediates." ], "structureKey": "endo-thdcpd", "composition": { "C": 10, "H": 16 }, "charge": 0 }, { "id": "exo-thdcpd", "kind": "molecule", "title": "exo-Tetrahydrodicyclopentadiene", "summary": "Distinct stereoisomer and reported rearrangement intermediate; not interchangeable with the endo input.", "status": "Structure available", "sourceIds": [ "orgsyn", "ionic", "zehe-thermo" ], "facts": [ { "label": "Formula", "value": "C10H16" }, { "label": "Geometry", "value": "Published CBS-QB3 equilibrium geometry reused; connectivity and stereochemistry checked." } ], "missing": [ "Material composition and catalyst-specific reactive intermediates." ], "structureKey": "exo-thdcpd", "composition": { "C": 10, "H": 16 }, "charge": 0 }, { "id": "adamantane", "kind": "molecule", "title": "Adamantane", "summary": "First target cage, with existing mechanical and electronic calculations.", "status": "Structure available", "sourceIds": [ "orgsyn", "adamantane-supply" ], "facts": [ { "label": "Formula", "value": "C10H16" }, { "label": "Existing evidence", "value": "Relaxation, normal modes, forces and stiffness are separate from reaction feasibility." } ], "missing": [ "Complete synthesis mechanism, source-matched rates and local experimental validation." ], "structureKey": "adamantane", "composition": { "C": 10, "H": 16 }, "charge": 0 }, { "id": "env-pt", "kind": "environment", "title": "Hydrogenation · Pt precursor / ether", "summary": "Source conditions for the checked preparation; not the Pd/C kinetic experiment.", "status": "Source reported", "sourceIds": [ "orgsyn" ], "facts": [ { "label": "Source scale", "value": "200 g purified DCPD in 100 mL dry ether; 1 g PtO2 precursor" }, { "label": "Source pressure/time", "value": "50 psi H2; reported uptake over 4–6 h" }, { "label": "Temperature", "value": "Mixture warms; no resolved temperature-time history in this record." } ], "missing": [ "Gauge/absolute pressure convention; active catalyst state; gas uptake and temperature traces; heat/mass transfer." ] }, { "id": "env-pd", "kind": "environment", "title": "Hydrogenation · Pd/C / ethanol", "summary": "A separate, promising physical-time benchmark.", "status": "Source reported", "sourceIds": [ "hao" ], "facts": [ { "label": "Temperature domain", "value": "323–353 K" }, { "label": "Hydrogen pressure domain", "value": "0.5–1.5 MPa" }, { "label": "Catalyst loading domain", "value": "0.25–1.00 wt% as reported; denominator and Pd fraction need full-text audit." }, { "label": "Transport", "value": "Authors report removing internal and external diffusion effects." } ], "missing": [ "Full recipe, rate laws, parameter units, observations and reactor geometry." ] }, { "id": "env-rearrangement", "kind": "environment", "title": "Cage rearrangement · heated AlCl3 mixture", "summary": "A distinct hot reaction stage after precursor isolation.", "status": "Source reported", "sourceIds": [ "orgsyn" ], "facts": [ { "label": "Source conditions", "value": "Molten endo precursor; 150–180 °C for 8–12 h." }, { "label": "Source charge", "value": "200 g precursor and 40 g anhydrous AlCl3." } ], "missing": [ "Active acid species, water/initiator sensitivity, mixing/temperature history and complete product distribution." ] }, { "id": "env-biological", "kind": "environment", "title": "Enzyme-compatible reaction medium", "summary": "Requirements record for a future biological reaction; not a selected adamantane synthesis environment.", "status": "Proposed", "sourceIds": [ "p450" ], "facts": [ { "label": "Variables", "value": "Buffer/pH, temperature, O2, substrate delivery, redox partners, cofactors and recycling." } ], "missing": [ "Source-specific assay recipe and solvent tolerance; activity under planned conditions." ] }, { "id": "cage-enzyme", "kind": "catalyst", "title": "Adamantane cage-forming enzyme · design gap", "summary": "No qualified protein sequence or complete enzymatic route to plain adamantane has been established in this audit.", "status": "Unresolved", "sourceIds": [ "cage-bio", "scine" ], "facts": [ { "label": "Closest biological lead", "value": "HsCPTa/b produce substituted bicyclononane PPAP intermediates." }, { "label": "Design contract", "value": "Mechanism → catalytic motif → protein scaffold → QM/MM and experimental validation." } ], "missing": [ "Substrate/mechanism selection, catalytic requirements, viable sequence, expression, selectivity, turnover and release." ] }, { "id": "hydrogenation-pt", "kind": "reaction", "title": "Hydrogenate · checked Pt/ether route", "summary": "Overall preparation: endo-DCPD + 2 H2 → endo-THDCPD.", "status": "Source reported", "sourceIds": [ "orgsyn" ], "facts": [ { "label": "Reported isolated yield", "value": "96.5–98.4% hydrogenated precursor" }, { "label": "Meaning", "value": "Two reductions, not one elementary event; no local reactive simulation." } ], "missing": [ "Elementary intermediates/barriers, active sites and calibrated rates." ], "reactants": [ { "id": "dcpd", "coefficient": 1 }, { "id": "hydrogen", "coefficient": 2 } ], "products": [ { "id": "endo-thdcpd", "coefficient": 1 } ] }, { "id": "hydrogenation-pd", "kind": "reaction", "title": "Hydrogenate · Pd/C kinetic variant", "summary": "A source-specific sequential hydrogenation network to recover before running in physical time.", "status": "Source reported", "sourceIds": [ "hao" ], "facts": [ { "label": "Reported apparent activation energies", "value": "3.19 and 31.69 kJ/mol for two fitted steps" }, { "label": "Important distinction", "value": "These are fitted kinetic-model quantities, not DFT transition-state energies." } ], "missing": [ "Intermediate identity, full equations, prefactors, adsorption constants, units and independent observations." ], "reactants": [ { "id": "dcpd", "coefficient": 1 }, { "id": "hydrogen", "coefficient": 2 } ], "products": [ { "id": "endo-thdcpd", "coefficient": 1 } ] }, { "id": "rearrangement-alcl3", "kind": "reaction", "title": "Rearrange · precursor to adamantane", "summary": "Same formula, new cage connectivity; side products and catalyst chemistry remain important.", "status": "Source reported", "sourceIds": [ "orgsyn" ], "facts": [ { "label": "Principal isolated collection", "value": "13.5–15.0% in checked preparation" }, { "label": "Do not infer", "value": "Yield is not conversion, a rate constant or an elementary-step probability." } ], "missing": [ "Reactive atom map; complete charged network and side-product mass balance; free-energy barriers and rates." ], "reactants": [ { "id": "endo-thdcpd", "coefficient": 1 } ], "products": [ { "id": "adamantane", "coefficient": 1 } ] }, { "id": "rearrangement-ionic", "kind": "reaction", "title": "Rearrange · ionic-liquid alternative", "summary": "Alternative catalyst family using exo-THDCPD; candidate for a lower-temperature comparison.", "status": "Source reported", "sourceIds": [ "ionic" ], "facts": [], "missing": [ "Verify complete procedure, isolated vs analytical yield, catalyst reuse, impurities and kinetic data." ], "reactants": [ { "id": "exo-thdcpd", "coefficient": 1 } ], "products": [ { "id": "adamantane", "coefficient": 1 } ] }, { "id": "isolation", "kind": "operation", "title": "Isolate and verify adamantane", "summary": "Separate target from catalyst and other hydrocarbons, then verify identity and purity.", "status": "Source reported", "sourceIds": [ "orgsyn" ], "facts": [ { "label": "Reference operations", "value": "Extraction, decolorization/filtration, concentration and crystallization." }, { "label": "Output contract", "value": "Identity and purity must be measured; targets and required amount are not yet fixed." } ], "missing": [ "Scale-specific recovery, solubility, waste quantities and acceptance thresholds." ] }, { "id": "p450-hydroxylation", "kind": "reaction", "title": "Modify the existing cage enzymatically", "summary": "Optional bootstrap capability: selective oxidation, not production of plain adamantane.", "status": "Source reported", "sourceIds": [ "p450" ], "facts": [], "missing": [ "Exact product mapping, O2/redox/cofactor stoichiometry and full assay reproduction." ] }, { "id": "analytical-verification", "kind": "study", "title": "Product verification contract", "summary": "Distinguish purity, conversion, selectivity and isolated yield.", "status": "Proposed", "sourceIds": [ "orgsyn" ], "facts": [ { "label": "Proposed assays", "value": "Calibrated GC with authentic reference; independent structural identity by NMR where appropriate; isolated mass and recovery." }, { "label": "Dataset", "value": "Record calibration, response factors, sample handling, replicates and uncertainty." } ], "missing": [ "Validated analytical method, detection limits, impurity specification and facility quote." ] }, { "id": "env-mit1", "kind": "environment", "title": "Rearrangement · MIT-1 source conditions", "summary": "Keep the solid-catalyst experiment separate from heated AlCl3.", "status": "Source method recovered; operating details incomplete", "sourceIds": [ "gallego-2017", "gallego-thesis-2019" ], "facts": [ { "label": "Reported reaction", "value": "Parr mechanically stirred high-pressure batch reactor; 300 C, 6 MPa N2, 1200 rpm. MIT-1 observation at 180 min. Pressure convention unspecified." }, { "label": "Source charge", "value": "30 mg catalyst; 8 g of 0.147 M endo-tricyclodecane solution in cyclohexane. Solution volume and density are absent: substrate moles remain unknown." }, { "label": "Source activation", "value": "Catalyst in reactor under N2 at 300 C for 3 h; nitrogen initially 1 MPa before charging, then final 6 MPa. Ramps and pressure reference temperature remain missing." }, { "label": "Analysis", "value": "Feed and final mixtures: Agilent 7890A GC-FID, HP-5 capillary 30 m, dodecane external standard. Calibration and uncertainty not supplied." } ], "missing": [ "Reactor model, volume, wetted materials and headspace", "Feed purity, solution density/volume and concentration reference temperature", "Pressure convention, ramp, charging temperature, time-zero and sampling/termination details", "GC calibration, response factors, peak assignments, chromatograms and selectivity denominator", "Phase, complete reactor specification and an independently qualified operating procedure." ] }, { "id": "rearrangement-mit1", "kind": "reaction", "title": "Rearrange · MIT-1 zeolite alternative", "summary": "Source reports precursor conversion and product selectivity, not a complete atomic mechanism.", "status": "Source reported", "sourceIds": [ "gallego-2017", "gallego-thesis-2019" ], "facts": [ { "label": "Observation", "value": "50.8% endo conversion and 33.4% adamantane selectivity at 180 min." }, { "label": "Yield distinction", "value": "Multiplication gives 16.9672% only under compatible fraction definitions; not measured isolated yield." } ], "missing": [ "Complete analytical basis, product spectrum, source model and isolation." ], "reactants": [ { "id": "endo-thdcpd", "coefficient": 1 } ], "products": [ { "id": "adamantane", "coefficient": 1 } ] }, { "id": "p2-environment", "kind": "environment", "title": "Promoted AlBr3 reaction mixture · P2", "summary": "Named feed and promoter in a source-described multiphase mixture; no added reaction solvent.", "status": "Source conditions; no validated simulation box", "sourceIds": [ "hoffmann-promoted-process" ], "facts": [ { "label": "Temperature", "value": "Room-temperature examples; Example 2 uses 55 C. Catalyst preparation is about −5 C in the PDF." }, { "label": "Pressure", "value": "Atmospheric pressure preferred in general description; no example-specific pressure trace" }, { "label": "Phase", "value": "Example 1 describes a dense catalyst phase and an upper hydrocarbon phase. Volumes, compositions, partition and stirring transfer are unmeasured." }, { "label": "No added solvent / acid", "value": "These are source input statements, not proof of absent acid species or general biomolecular compatibility." } ], "missing": [ "Phase composition, active species, heat release, water content and time courses" ] }, { "id": "p2-rearrangement", "kind": "reaction", "title": "Cage synthesis with AlBr3 and promoter · P2", "summary": "Overall source transformation; keep the microscopic hypothesis separate.", "status": "Patent-reported synthesis", "sourceIds": [ "hoffmann-promoted-process" ], "facts": [ { "label": "Source result", "value": "Example 4 reports 82% at room temperature after 24 h; not a local yield prediction." } ], "missing": [ "Exact active aluminum/halide species, promoter fate and hydride donor evidence", "Matched-phase configurations and competing activation/termination channels", "Reaction calorimetry, phase contact and time-course/replicate data", "Resolved Example 5 mass/mole discrepancy and assay/purity information", "Full work-up material balance, supplier costs and qualified apparatus" ], "reactants": [ { "id": "endo-thdcpd", "coefficient": 1 } ], "products": [ { "id": "adamantane", "coefficient": 1 } ] } ], "sources": [ { "id": "orgsyn", "title": "Checked adamantane synthesis · Organic Syntheses 42, 8", "url": "https://www.orgsyn.org/demo.aspx?prep=cv5p0016", "scope": "Procedures A/B and notes: preparative operations, yields, separation. No elementary mechanism or calibrated kinetic model.", "accessed": "2026-10-19", "access": "Primary source inspected" }, { "id": "hao", "title": "Hao et al. · Pd/C hydrogenation kinetics (2010)", "url": "https://pubmed.ncbi.nlm.nih.gov/19785473/", "scope": "DOI 10.1021/jp9060363. Separate catalyst/solvent/pressure domain; rate coefficients and raw validation observations not recovered.", "accessed": "2026-10-19", "access": "Primary abstract inspected; full equations not recovered" }, { "id": "zehe-thermo", "title": "Zehe & Jaffe · C10H16 quantum thermochemistry (2010)", "url": "https://ntrs.nasa.gov/citations/20110016006", "scope": "DOI 10.1021/jo100050w. Main Table 2 and ACS SI DOI 10.1021/jo100050w.s001 recovered. Gas-phase endpoint enthalpies and six configurations reused; source discrepancies preserved. Not a catalytic mechanism. SI repository lists CC BY-NC 4.0.", "accessed": "2026-10-19", "access": "Primary article and supporting information inspected; hash-pinned copies" }, { "id": "ionic", "title": "Huang et al. · acidic ionic-liquid rearrangement (2009)", "url": "https://www.sciencedirect.com/science/article/abs/pii/S1566736709002210", "scope": "Alternative exo precursor route. Exact full-text procedure and quantitative details need recovery.", "accessed": "2026-10-19", "access": "Primary abstract located; full record pending" }, { "id": "p450", "title": "Bell et al. · engineered CYP101D2 (2013)", "url": "https://pubmed.ncbi.nlm.nih.gov/22820521/", "scope": "Y96A increases adamantane binding/activity. Hydroxylation of an existing cage; no cage synthesis.", "accessed": "2026-10-19", "access": "Primary abstract inspected" }, { "id": "cage-bio", "title": "Ernst et al. · bridged bicyclononane biosynthesis (2024)", "url": "https://www.nature.com/articles/s41467-024-48879-w", "scope": "HsCPTa/b form substituted PPAP bicyclic intermediates; not a complete route to plain C10H16 adamantane.", "accessed": "2026-10-19", "access": "Primary source inspected" }, { "id": "scine", "title": "Steiner & Reiher · reaction-network exploration (2024)", "url": "https://www.nature.com/articles/s41467-024-47997-9", "scope": "Reusable exploration workflow; not an adamantane result.", "accessed": "2026-10-19", "access": "Primary source inspected" }, { "id": "adamantane-supply", "title": "TCI A0696 · adamantane", "url": "https://www.tcichemicals.com/US/en/p/A0696", "scope": "US listing >99% GC; 25 g $28, 500 g $210. Price snapshot excludes tax/shipping; stock and quote not guaranteed.", "accessed": "2026-10-19", "access": "Primary source inspected" }, { "id": "gallego-2017", "title": "Gallego et al. · designed zeolite catalysts (2017)", "url": "https://www.sciencemagazinedigital.org/sciencemagazine/10_march_2017_Main?pg=120", "scope": "DOI 10.1126/science.aal0121. Final Table 2: seven catalyst observations at 300 C and 6 MPa. Author manuscript inspected separately; complete supplementary recipe remains missing.", "accessed": "2026-10-19", "access": "Final publisher digital edition and public author manuscript inspected" }, { "id": "hoffmann-promoted-process", "title": "Hoffmann and Trottier, Preparation of adamantane, US3457317A (1969)", "url": "https://patents.google.com/patent/US3457317A/en", "accessed": "2026-10-19", "scope": "Applicant-reported preparation, seven examples and thirteen promoter rows. No independent replication, mechanistic proof or quantitative purity.", "access": "All three primary PDF pages rendered and inspected; hash and source discrepancies preserved" }, { "id": "gallego-thesis-2019", "title": "Gallego Sánchez thesis · source-matched zeolite methods (2019)", "url": "https://riunet.upv.es/handle/10251/134015", "accessed": "2026-10-20", "scope": "Section 3.4.4, PDF pages 107–108, and Table 6.2.3, PDF page 233, visually inspected. Same author and seven matching outcome rows; not independent replication. Pressure convention and analytical calibration remain missing.", "access": "Public institutional PDF, 290 pages; DOI 10.4995/Thesis/10251/134015. Repository date 2020-01-07; citation year 2019." } ], "structures": { "dcpd": { "formula": "C10H12", "smiles": "C1=C[C@H]2[C@@H](C1)[C@H]1C=C[C@@H]2C1", "inchiKey": "HECLRDQVFMWTQS-RGOKHQFPSA-N", "charge": 0, "multiplicity": 1, "units": "angstrom", "atoms": [ { "element": "C", "position": [ -0.4004, 0.80179, -0.7682 ], "formalCharge": 0 }, { "element": "C", "position": [ -0.386, -0.76331, -0.812 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.0076, 1.13229, -0.202 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.0314, -1.10661, -0.2823 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.8416, 0.04449, -0.8987 ], "formalCharge": 0 }, { "element": "C", "position": [ -1.619, 1.21119, 0.065 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.144, 0.63299, 1.2178 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.1618, -0.70691, 1.1703 ], "formalCharge": 0 }, { "element": "C", "position": [ -1.559, -1.15481, 0.0222 ], "formalCharge": 0 }, { "element": "C", "position": [ -2.222, -0.09111, 0.4879 ], "formalCharge": 0 }, { "element": "H", "position": [ -0.4838, 1.20379, -1.7867 ], "formalCharge": 0 }, { "element": "H", "position": [ -0.511, -1.11351, -1.8436 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.3563, 2.15289, -0.3647 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.3988, -2.10661, -0.5168 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.8984, 0.04509, -0.6016 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.7804, 0.08239, -1.9925 ], "formalCharge": 0 }, { "element": "H", "position": [ -2.3357, 1.76669, -0.5493 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.3571, 1.83259, 0.9262 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.1702, 1.24269, 2.1067 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.2041, -1.37731, 2.0136 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.8411, -2.17921, 0.2187 ], "formalCharge": 0 }, { "element": "H", "position": [ -3.1047, -0.15811, 1.1081 ], "formalCharge": 0 } ], "bonds": [ [ 0, 1, 1 ], [ 0, 2, 1 ], [ 0, 5, 1 ], [ 0, 10, 1 ], [ 1, 3, 1 ], [ 1, 8, 1 ], [ 1, 11, 1 ], [ 2, 4, 1 ], [ 2, 6, 1 ], [ 2, 12, 1 ], [ 3, 4, 1 ], [ 3, 7, 1 ], [ 3, 13, 1 ], [ 4, 14, 1 ], [ 4, 15, 1 ], [ 5, 9, 1 ], [ 5, 16, 1 ], [ 5, 17, 1 ], [ 6, 7, 2 ], [ 6, 18, 1 ], [ 7, 19, 1 ], [ 8, 9, 2 ], [ 8, 20, 1 ], [ 9, 21, 1 ] ], "provenance": "Subset of preserved PubChem conformer CID 11815882. Removed display-only H2 fragments; no optimization.", "sourceUrl": "https://pubchem.ncbi.nlm.nih.gov/compound/11815882", "sourceSha256": "df20fc6934403a73306a657025473948c072bf1d316168898053c046a4b68da1" }, "endo-thdcpd": { "formula": "C10H16", "smiles": "C1C[C@@H]2[C@@H]3CC[C@@H](C3)[C@@H]2C1", "inchiKey": "LPSXSORODABQKT-YNFQOJQRSA-N", "charge": 0, "multiplicity": 1, "units": "angstrom", "atoms": [ { "element": "C", "position": [ -0.39323, 0.796733, -0.810887 ], "formalCharge": 0 }, { "element": "C", "position": [ -0.37932, -0.745889, -0.864043 ], "formalCharge": 0 }, { "element": "C", "position": [ 0.994633, 1.131678, -0.215969 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.014522, -1.096119, -0.292502 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.856056, 0.046768, -0.87618 ], "formalCharge": 0 }, { "element": "C", "position": [ -1.642503, 1.196342, -0.034573 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.117506, 0.734753, 1.264167 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.130943, -0.799784, 1.211488 ], "formalCharge": 0 }, { "element": "C", "position": [ -1.62071, -1.220428, -0.117781 ], "formalCharge": 0 }, { "element": "C", "position": [ -2.077896, -0.044055, 0.736279 ], "formalCharge": 0 }, { "element": "H", "position": [ -0.446108, 1.208326, -1.827514 ], "formalCharge": 0 }, { "element": "H", "position": [ -0.425306, -1.087423, -1.906475 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.311683, 2.15779, -0.414884 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.34978, -2.100324, -0.561283 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.840505, 0.084335, -1.970843 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.894238, 0.044157, -0.526742 ], "formalCharge": 0 }, { "element": "H", "position": [ -2.43424, 1.461355, -0.746613 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.489919, 2.063539, 0.614384 ], "formalCharge": 0 }, { "element": "H", "position": [ 0.318781, 1.133153, 1.89358 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.086219, -1.172713, 1.600024 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.452127, -2.127407, 0.470086 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.609209, -0.073857, 1.723573 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.066454, 1.096865, 1.677889 ], "formalCharge": 0 }, { "element": "H", "position": [ 0.339711, -1.254341, 1.811375 ], "formalCharge": 0 }, { "element": "H", "position": [ -2.407987, -1.449997, -0.846967 ], "formalCharge": 0 }, { "element": "H", "position": [ -3.160434, -0.059403, 0.899305 ], "formalCharge": 0 } ], "bonds": [ [ 0, 1, 1 ], [ 0, 2, 1 ], [ 0, 5, 1 ], [ 0, 10, 1 ], [ 1, 3, 1 ], [ 1, 8, 1 ], [ 1, 11, 1 ], [ 2, 4, 1 ], [ 2, 6, 1 ], [ 2, 12, 1 ], [ 3, 4, 1 ], [ 3, 7, 1 ], [ 3, 13, 1 ], [ 4, 14, 1 ], [ 4, 15, 1 ], [ 6, 7, 1 ], [ 6, 18, 1 ], [ 6, 22, 1 ], [ 7, 19, 1 ], [ 7, 23, 1 ], [ 5, 9, 1 ], [ 5, 16, 1 ], [ 5, 17, 1 ], [ 8, 9, 1 ], [ 8, 20, 1 ], [ 8, 24, 1 ], [ 9, 21, 1 ], [ 9, 25, 1 ] ], "provenance": "PubChem calculated 3D conformer; no local optimization. Product rigidly aligned on carbon atoms. Reactant H2 molecules placed schematically at 0.74 Å bond length; their separation from the precursor is only display layout.", "sourceUrl": "https://pubchem.ncbi.nlm.nih.gov/compound/9812790", "sourceSha256": "b954972f454e6d163d9f9714a344632e261bf3ba36d1968606f1dd1463a69730" }, "exo-thdcpd": { "formula": "C10H16", "smiles": "C1C[C@@H]2[C@H]3CC[C@H](C3)[C@@H]2C1", "inchiKey": "LPSXSORODABQKT-FIRGSJFUSA-N", "charge": 0, "multiplicity": 1, "units": "angstrom", "atoms": [ { "element": "C", "position": [ 2.65036, 0, -0.167108 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.730325, -1.208583, 0.077825 ], "formalCharge": 0 }, { "element": "C", "position": [ 0.364424, -0.789723, -0.512927 ], "formalCharge": 0 }, { "element": "C", "position": [ 0.364424, 0.789723, -0.512927 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.730325, 1.208583, 0.077825 ], "formalCharge": 0 }, { "element": "C", "position": [ -0.898759, 0, 1.375227 ], "formalCharge": 0 }, { "element": "C", "position": [ -0.887544, -1.134927, 0.328178 ], "formalCharge": 0 }, { "element": "C", "position": [ -2.14046, -0.782574, -0.509255 ], "formalCharge": 0 }, { "element": "C", "position": [ -0.887544, 1.134927, 0.328177 ], "formalCharge": 0 }, { "element": "C", "position": [ -2.14046, 0.782574, -0.509255 ], "formalCharge": 0 }, { "element": "H", "position": [ 3.539737, 0, 0.469087 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.9956, 0, -1.207521 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.640425, -1.389157, 1.155017 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.640425, 1.389158, 1.155016 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.799317, 0, 1.996139 ], "formalCharge": 0 }, { "element": "H", "position": [ -0.028593, 0, 2.035469 ], "formalCharge": 0 }, { "element": "H", "position": [ -2.090193, -1.203861, -1.516669 ], "formalCharge": 0 }, { "element": "H", "position": [ -2.090193, 1.203861, -1.51667 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.110421, -2.13124, -0.368333 ], "formalCharge": 0 }, { "element": "H", "position": [ 0.26509, -1.188058, -1.526823 ], "formalCharge": 0 }, { "element": "H", "position": [ 0.26509, 1.188057, -1.526823 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.110421, 2.13124, -0.368334 ], "formalCharge": 0 }, { "element": "H", "position": [ -0.88944, -2.154243, 0.720251 ], "formalCharge": 0 }, { "element": "H", "position": [ -3.045283, -1.174862, -0.037309 ], "formalCharge": 0 }, { "element": "H", "position": [ -0.88944, 2.154243, 0.72025 ], "formalCharge": 0 }, { "element": "H", "position": [ -3.045283, 1.174862, -0.037309 ], "formalCharge": 0 } ], "bonds": [ [ 1, 0, 1 ], [ 2, 1, 1 ], [ 3, 2, 1 ], [ 4, 3, 1 ], [ 4, 0, 1 ], [ 6, 5, 1 ], [ 6, 2, 1 ], [ 7, 6, 1 ], [ 8, 5, 1 ], [ 8, 3, 1 ], [ 9, 8, 1 ], [ 9, 7, 1 ], [ 10, 0, 1 ], [ 11, 0, 1 ], [ 12, 1, 1 ], [ 13, 4, 1 ], [ 14, 5, 1 ], [ 15, 5, 1 ], [ 16, 7, 1 ], [ 17, 9, 1 ], [ 18, 1, 1 ], [ 19, 2, 1 ], [ 20, 3, 1 ], [ 21, 4, 1 ], [ 22, 6, 1 ], [ 23, 7, 1 ], [ 24, 8, 1 ], [ 25, 9, 1 ] ], "sourceUrl": "https://ndownloader.figshare.com/files/4448275", "sourceSha256": "6fea26383eaa9a918e0f601b93b8f79a95dc1bf583c92007b21f6b0b2950e998", "provenance": "Zehe and Jaffe 2010 SI section (I-A), CBS-QB3. Published computed coordinates, unchanged. Connectivity inferred by RDKit and valence checked; not a reaction atom map." }, "adamantane": { "formula": "C10H16", "smiles": "C1C2CC3CC1CC(C2)C3", "inchiKey": "ORILYTVJVMAKLC-UHFFFAOYSA-N", "charge": 0, "multiplicity": 1, "units": "angstrom", "atoms": [ { "element": "C", "position": [ -0.2509, -1.5735, 0.7789 ], "formalCharge": 0 }, { "element": "C", "position": [ 0.4447, -0.3667, 1.4331 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.6717, 0.0263, 0.5917 ], "formalCharge": 0 }, { "element": "C", "position": [ 1.2365, 0.3932, -0.8381 ], "formalCharge": 0 }, { "element": "C", "position": [ 0.5365, -0.8179, -1.4794 ], "formalCharge": 0 }, { "element": "C", "position": [ -0.697, -1.2157, -0.6498 ], "formalCharge": 0 }, { "element": "C", "position": [ -1.6717, -0.0263, -0.5917 ], "formalCharge": 0 }, { "element": "C", "position": [ -0.9842, 1.1893, 0.0547 ], "formalCharge": 0 }, { "element": "C", "position": [ -0.5365, 0.8179, 1.4794 ], "formalCharge": 0 }, { "element": "C", "position": [ 0.2509, 1.5735, -0.7789 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.1191, -1.8751, 1.3777 ], "formalCharge": 0 }, { "element": "H", "position": [ 0.4324, -2.4312, 0.754 ], "formalCharge": 0 }, { "element": "H", "position": [ 0.7601, -0.6268, 2.4496 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.1873, 0.8761, 1.0557 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.3879, -0.8041, 0.5635 ], "formalCharge": 0 }, { "element": "H", "position": [ 2.1136, 0.672, -1.4325 ], "formalCharge": 0 }, { "element": "H", "position": [ 0.235, -0.5757, -2.5059 ], "formalCharge": 0 }, { "element": "H", "position": [ 1.2332, -1.6627, -1.543 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.1914, -2.078, -1.1107 ], "formalCharge": 0 }, { "element": "H", "position": [ -2.011, 0.2294, -1.603 ], "formalCharge": 0 }, { "element": "H", "position": [ -2.5642, -0.3014, -0.0163 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.6823, 2.0328, 0.0936 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.4095, 0.5572, 2.0902 ], "formalCharge": 0 }, { "element": "H", "position": [ -0.0587, 1.6812, 1.9587 ], "formalCharge": 0 }, { "element": "H", "position": [ -0.0555, 1.8566, -1.7934 ], "formalCharge": 0 }, { "element": "H", "position": [ 0.7422, 2.4497, -0.3383 ], "formalCharge": 0 } ], "bonds": [ [ 0, 1, 1 ], [ 1, 2, 1 ], [ 2, 3, 1 ], [ 3, 4, 1 ], [ 4, 5, 1 ], [ 5, 6, 1 ], [ 6, 7, 1 ], [ 7, 8, 1 ], [ 7, 9, 1 ], [ 5, 0, 1 ], [ 8, 1, 1 ], [ 9, 3, 1 ], [ 0, 10, 1 ], [ 0, 11, 1 ], [ 1, 12, 1 ], [ 2, 13, 1 ], [ 2, 14, 1 ], [ 3, 15, 1 ], [ 4, 16, 1 ], [ 4, 17, 1 ], [ 5, 18, 1 ], [ 6, 19, 1 ], [ 6, 20, 1 ], [ 7, 21, 1 ], [ 8, 22, 1 ], [ 8, 23, 1 ], [ 9, 24, 1 ], [ 9, 25, 1 ] ], "provenance": "Reused E40 reference SDF: PubChem CID 9238 connectivity; RDKit ETKDGv3 seed 4001 and MMFF94s relaxation. Coordinates are calculated, rounded in the saved SDF, and are not an experimental crystal structure or a quantum-validated geometry. No new optimization was run.", "sourceUrl": "https://pubchem.ncbi.nlm.nih.gov/compound/9238", "sourceSha256": "eaf7f647c82d66dff786afafa60ff8c5e7b82bb98a35611c5543ee98cb487c65" }, "p4-adduct": { "formula": "C2H5AlBr4", "smiles": "CCBr.Br[Al](Br)Br", "inchiKey": "", "charge": 0, "multiplicity": 1, "units": "angstrom", "atoms": [ { "element": "C", "position": [ -2.807132758309962, -0.7038480470702995, 0.5607376647614284 ], "formalCharge": 0 }, { "element": "C", "position": [ -1.472960235582965, -0.7889948388527955, 1.24859617574546 ], "formalCharge": 0 }, { "element": "Br", "position": [ -0.06987860795364226, 0.09487050124440317, 0.15562938333018445 ], "formalCharge": 0 }, { "element": "H", "position": [ -3.1304003592213454, 0.33686462638196346, 0.4189761018758464 ], "formalCharge": 0 }, { "element": "H", "position": [ -2.8006959433637175, -1.2141581177994643, -0.41251690022408155 ], "formalCharge": 0 }, { "element": "H", "position": [ -3.5496524236847917, -1.2056990276541868, 1.2024270357563656 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.0930881113419342, -1.8114772941183839, 1.3689186208345716 ], "formalCharge": 0 }, { "element": "H", "position": [ -1.4243893748790706, -0.25224732034754704, 2.2045220803585184 ], "formalCharge": 0 }, { "element": "Al", "position": [ 1.9088158945005083, -0.34760766733579457, 1.7662312672927085 ], "formalCharge": 0 }, { "element": "Br", "position": [ 1.8526080847294695, -2.631113993403699, 1.854678326848264 ], "formalCharge": 0 }, { "element": "Br", "position": [ 3.55887031352069, 0.6490995702232627, 0.560395170550676 ], "formalCharge": 0 }, { "element": "Br", "position": [ 1.1429698365609335, 0.7078877339647008, 3.6436788123577957 ], "formalCharge": 0 } ], "bonds": [ [ 0, 1, 1 ], [ 1, 2, 1 ], [ 0, 3, 1 ], [ 0, 4, 1 ], [ 0, 5, 1 ], [ 1, 6, 1 ], [ 1, 7, 1 ], [ 8, 9, 1 ], [ 8, 10, 1 ], [ 8, 11, 1 ] ], "provenance": "Same neutral fragment connectivity. Refined-grid PBE0/D3 geometry search from a saved B2 geometry, with fresh optimizer history. No assigned interfragment bond or qualified minimum. P4 returned stationary candidate; evaluation 8. Vacuum model, not the bulk material or measured liquid species.", "sourceUrl": "https://pyscf.org/user/dft.html", "sourceSha256": "ad79365f4de395a448b9fa40f64e668ac0836905ce5c016e9e797b68aacf9e93" } }, "network": { "nodes": [ "A", "A'", "D", "F", "G", "G'", "J", "K", "L", "M", "N", "Q" ], "edges": [ { "id": "r4-step-1", "proposedFrom": "A", "proposedTo": "A'", "relaxedFrom": "A", "relaxedTo": "A'", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -641.45, "unchangedEndpoints": true, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 4, "category": "unchanged", "compositeTableCovered": true, "compositeTsLabel": "TS-AA'", "differences": { "CBS-QB3": { "tsMinusFromHartree": "0.01289", "tsMinusToHartree": "0.01289", "toMinusFromHartree": "0.00000", "tsMinusFromKjMol": 33.842690352895914, "tsMinusToKjMol": 33.842690352895914, "toMinusFromKjMol": 0, "negativeTsDifference": false }, "L-W1X": { "tsMinusFromHartree": "0.01247", "tsMinusToHartree": "0.01247", "toMinusFromHartree": "0.00000", "tsMinusFromKjMol": 32.73998050431435, "tsMinusToKjMol": 32.73998050431435, "toMinusFromKjMol": 0, "negativeTsDifference": false } }, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-2", "proposedFrom": "A", "proposedTo": "B", "relaxedFrom": "A", "relaxedTo": "A", "transitionStateLocated": false, "imaginaryFrequencyCmInverse": null, "unchangedEndpoints": false, "sourceNote": "Search converged to a minimum.", "sourcePage": 4, "category": "not-located", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-3", "proposedFrom": "B", "proposedTo": "C", "relaxedFrom": "A", "relaxedTo": "D", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -457.05, "unchangedEndpoints": false, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 4, "category": "redirected", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-4", "proposedFrom": "C", "proposedTo": "D", "relaxedFrom": "D", "relaxedTo": "D", "transitionStateLocated": false, "imaginaryFrequencyCmInverse": null, "unchangedEndpoints": false, "sourceNote": "Search converged to a minimum.", "sourcePage": 4, "category": "not-located", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-5", "proposedFrom": "B", "proposedTo": "E", "relaxedFrom": "A", "relaxedTo": "F", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -598.77, "unchangedEndpoints": false, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 4, "category": "redirected", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-6", "proposedFrom": "E", "proposedTo": "F", "relaxedFrom": "F", "relaxedTo": "F", "transitionStateLocated": false, "imaginaryFrequencyCmInverse": null, "unchangedEndpoints": false, "sourceNote": "Search converged to a minimum.", "sourcePage": 5, "category": "not-located", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-7", "proposedFrom": "F", "proposedTo": "G", "relaxedFrom": "F", "relaxedTo": "G", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -538.36, "unchangedEndpoints": true, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 5, "category": "unchanged", "compositeTableCovered": true, "compositeTsLabel": "TS-FG", "differences": { "CBS-QB3": { "tsMinusFromHartree": "0.01045", "tsMinusToHartree": "0.03311", "toMinusFromHartree": "-0.02266", "tsMinusFromKjMol": 27.436471232564955, "tsMinusToKjMol": 86.93029306317949, "toMinusFromKjMol": -59.493821830614536, "negativeTsDifference": false }, "L-W1X": { "tsMinusFromHartree": "0.01027", "tsMinusToHartree": "0.03314", "toMinusFromHartree": "-0.02287", "tsMinusFromKjMol": 26.963881297458574, "tsMinusToKjMol": 87.00905805236388, "toMinusFromKjMol": -60.04517675490531, "negativeTsDifference": false } }, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-8", "proposedFrom": "G", "proposedTo": "G'", "relaxedFrom": "G", "relaxedTo": "G'", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -171.2, "unchangedEndpoints": true, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 5, "category": "unchanged", "compositeTableCovered": true, "compositeTsLabel": "TS-GG'", "differences": { "CBS-QB3": { "tsMinusFromHartree": "-0.00106", "tsMinusToHartree": "-0.00106", "toMinusFromHartree": "0.00000", "tsMinusFromKjMol": -2.783029617848694, "tsMinusToKjMol": -2.783029617848694, "toMinusFromKjMol": 0, "negativeTsDifference": true }, "L-W1X": { "tsMinusFromHartree": "-0.00101", "tsMinusToHartree": "-0.00102", "toMinusFromHartree": "0.00001", "tsMinusFromKjMol": -2.651754635874699, "tsMinusToKjMol": -2.678009632269498, "toMinusFromKjMol": 0.026254996394799, "negativeTsDifference": true } }, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-9", "proposedFrom": "G", "proposedTo": "H", "relaxedFrom": "G", "relaxedTo": "J", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -460.8, "unchangedEndpoints": false, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 5, "category": "redirected", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-10", "proposedFrom": "H", "proposedTo": "J", "relaxedFrom": "J", "relaxedTo": "J", "transitionStateLocated": false, "imaginaryFrequencyCmInverse": null, "unchangedEndpoints": false, "sourceNote": "Search converged to a minimum.", "sourcePage": 5, "category": "not-located", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-11", "proposedFrom": "J", "proposedTo": "K", "relaxedFrom": "J", "relaxedTo": "K", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -750.29, "unchangedEndpoints": true, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 5, "category": "unchanged", "compositeTableCovered": true, "compositeTsLabel": "TS-JK", "differences": { "CBS-QB3": { "tsMinusFromHartree": "0.03887", "tsMinusToHartree": "0.02519", "toMinusFromHartree": "0.01368", "tsMinusFromKjMol": 102.05317098658371, "tsMinusToKjMol": 66.13633591849869, "toMinusFromKjMol": 35.916835068085035, "negativeTsDifference": false }, "L-W1X": { "tsMinusFromHartree": "0.03842", "tsMinusToHartree": "0.02492", "toMinusFromHartree": "0.01350", "tsMinusFromKjMol": 100.87169614881776, "tsMinusToKjMol": 65.42745101583911, "toMinusFromKjMol": 35.44424513297865, "negativeTsDifference": false } }, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-12", "proposedFrom": "K", "proposedTo": "L", "relaxedFrom": "K", "relaxedTo": "L", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -166.92, "unchangedEndpoints": true, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 6, "category": "unchanged", "compositeTableCovered": true, "compositeTsLabel": "TS-KL", "differences": { "CBS-QB3": { "tsMinusFromHartree": "0.00171", "tsMinusToHartree": "0.00485", "toMinusFromHartree": "-0.00314", "tsMinusFromKjMol": 4.489604383510629, "tsMinusToKjMol": 12.733673251477516, "toMinusFromKjMol": -8.244068867966886, "negativeTsDifference": false }, "L-W1X": { "tsMinusFromHartree": "0.00172", "tsMinusToHartree": "0.00496", "toMinusFromHartree": "-0.00324", "tsMinusFromKjMol": 4.515859379905428, "tsMinusToKjMol": 13.022478211820305, "toMinusFromKjMol": -8.506618831914876, "negativeTsDifference": false } }, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-13", "proposedFrom": "L", "proposedTo": "M", "relaxedFrom": "L", "relaxedTo": "M", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -1359.35, "unchangedEndpoints": true, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 6, "category": "unchanged", "compositeTableCovered": true, "compositeTsLabel": "TS-LM", "differences": { "CBS-QB3": { "tsMinusFromHartree": "0.07683", "tsMinusToHartree": "0.08609", "toMinusFromHartree": "-0.00926", "tsMinusFromKjMol": 201.7171373012407, "tsMinusToKjMol": 226.0292639628246, "toMinusFromKjMol": -24.312126661583875, "negativeTsDifference": false }, "L-W1X": { "tsMinusFromHartree": "0.07654", "tsMinusToHartree": "0.08575", "toMinusFromHartree": "-0.00921", "tsMinusFromKjMol": 200.95574240579154, "tsMinusToKjMol": 225.1365940854014, "toMinusFromKjMol": -24.18085167960988, "negativeTsDifference": false } }, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-14", "proposedFrom": "L", "proposedTo": "N", "relaxedFrom": "L", "relaxedTo": "N", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -394.35, "unchangedEndpoints": true, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 6, "category": "unchanged", "compositeTableCovered": true, "compositeTsLabel": "TS-LN", "differences": { "CBS-QB3": { "tsMinusFromHartree": "0.01458", "tsMinusToHartree": "0.00487", "toMinusFromHartree": "0.00971", "tsMinusFromKjMol": 38.27978474361694, "tsMinusToKjMol": 12.786183244267113, "toMinusFromKjMol": 25.49360149934983, "negativeTsDifference": false }, "L-W1X": { "tsMinusFromHartree": "0.01395", "tsMinusToHartree": "0.00402", "toMinusFromHartree": "0.00993", "tsMinusFromKjMol": 36.625719970744605, "tsMinusToKjMol": 10.554508550709198, "toMinusFromKjMol": 26.071211420035407, "negativeTsDifference": false } }, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-15", "proposedFrom": "M", "proposedTo": "N", "relaxedFrom": "M", "relaxedTo": "N", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -1062.67, "unchangedEndpoints": true, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 6, "category": "unchanged", "compositeTableCovered": true, "compositeTsLabel": "TS-MN", "differences": { "CBS-QB3": { "tsMinusFromHartree": "0.04990", "tsMinusToHartree": "0.03093", "toMinusFromHartree": "0.01897", "tsMinusFromKjMol": 131.012432010047, "tsMinusToKjMol": 81.20670384911331, "toMinusFromKjMol": 49.805728160933704, "negativeTsDifference": false }, "L-W1X": { "tsMinusFromHartree": "0.04994", "tsMinusToHartree": "0.03080", "toMinusFromHartree": "0.01914", "tsMinusFromKjMol": 131.1174519956262, "tsMinusToKjMol": 80.86538889598091, "toMinusFromKjMol": 50.252063099645284, "negativeTsDifference": false } }, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-16", "proposedFrom": "L", "proposedTo": "P", "relaxedFrom": "L", "relaxedTo": "Q", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -467.59, "unchangedEndpoints": false, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 6, "category": "redirected", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-17", "proposedFrom": "M", "proposedTo": "P", "relaxedFrom": "M", "relaxedTo": "Q", "transitionStateLocated": false, "imaginaryFrequencyCmInverse": null, "unchangedEndpoints": false, "sourceNote": "Search found a different mechanism.", "sourcePage": 6, "category": "not-located", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-18", "proposedFrom": "N", "proposedTo": "P", "relaxedFrom": "N", "relaxedTo": "Q", "transitionStateLocated": true, "imaginaryFrequencyCmInverse": -492.65, "unchangedEndpoints": false, "sourceNote": "One imaginary reaction-coordinate frequency reported.", "sourcePage": 7, "category": "redirected", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null }, { "id": "r4-step-19", "proposedFrom": "P", "proposedTo": "Q", "relaxedFrom": "Q", "relaxedTo": "Q", "transitionStateLocated": false, "imaginaryFrequencyCmInverse": null, "unchangedEndpoints": false, "sourceNote": "Search converged to a minimum.", "sourcePage": 7, "category": "not-located", "compositeTableCovered": false, "compositeTsLabel": null, "differences": {}, "ircVerified": false, "ratePerSecond": null } ], "coverage": { "attempts": 19, "locatedSaddles": 13, "unchangedEndpoints": 8, "redirectedEndpoints": 5, "notLocated": 6, "compositeEnergySteps": 8, "unchangedComponents": [ [ "A", "A'" ], [ "D" ], [ "F", "G", "G'" ], [ "J", "K", "L", "M", "N" ], [ "Q" ] ], "conditionalComponents": [ [ "A", "A'", "D", "F", "G", "G'", "J", "K", "L", "M", "N", "Q" ] ], "strictDirectedAtoQ": null, "conditionalDirectedAtoQ": [ "r4-step-5", "r4-step-7", "r4-step-9", "r4-step-11", "r4-step-12", "r4-step-16" ], "conditionalPathQualification": "Shortest by arrow count only. Changed endpoint pairs are hypotheses until IRC connectivity is checked; Q is not assigned as the product.", "redirectedPathSteps": [ "r4-step-5", "r4-step-9", "r4-step-16" ] }, "scope": "A graph of reported evidence, not a reactive trajectory or validated kinetic network." }, "officialSource": { "id": "prasad-official-si", "title": "Prasad et al. · official 110-page supporting information", "url": "https://pubs.rsc.org/cp/article-supplement/802186/pdf/d3cp03523a1_suppl/", "landingUrl": "https://pubs.rsc.org/en/content/articlelanding/2024/cp/d3cp03523a", "doi": "10.1039/D3CP03523A", "path": "data/bootstrap/reaction-network-official-si/d3cp03523a1_suppl.pdf", "sha256": "ee8a06938847d9aca1fa618e9bb9603f90263c2f38cf2d82131bf2be16badb94", "bytes": 742040, "pdfPages": 110, "accessed": "2026-10-20", "access": "Public supplement downloaded from the publisher landing-page link after automatic verification. Main article remains access-restricted; no purchase, login or CAPTCHA action.", "scope": "Original scheme, optimization remarks, coordinates and composite table. No IRC, energy-correction convention or P2 liquid validation recovered." }, "evidenceLoop": { "scope": "Proposed research architecture, not an implemented end-to-end system, trained neural network or demonstrated autonomous laboratory. Libraries constrain compatible expansions, not a full Cartesian-product enumeration. Simulation methods evaluate candidates, they are not reactant inputs. Evidence examples are blank record templates; outcomes and uncertainties are not fabricated.", "bench": { "scope": "Read-only notebook record intake for a conceptual evidence loop and bench-capability illustration. No new experiment, installed apparatus or trained model is claimed.", "source": "/Users/andrenuyens/Code/nanofactory-notebook/research/catalog/bootstrap/registry.json", "sourceSha256": "0f95f4f4d1286fa917e5eb00e217077e90d73786e61bfd7d98fe8ae2beae0f82", "registryUpdatedAt": "2026-10-20", "records": [ { "id": "p2-bench-inputs", "kind": "bench", "title": "Specify the inputs · promoted route", "summary": "Match molecular identity, lot composition and measured charge before interpreting a yield.", "status": "Requirements only · unqualified", "sourceIds": [ "hoffmann-promoted-process" ], "relatedIds": [ "promoted-bench-plan", "endo-thdcpd", "albr3", "ethyl-bromide", "promoted-input-costs", "supply-precision-balance", "p2-apparatus-comparison" ], "facts": [ { "label": "Published observation", "value": "Example 4 names endo-THDCPD, aluminum bromide and ethyl bromide." }, { "label": "Source location", "value": "Patent PDF page 2, Example 4" }, { "label": "Required function", "value": "Mass and volume measurement appropriate to the chosen scale; Lot identity, assay, water content and transfer records" }, { "label": "Handoff", "value": "An identified, measured material inventory; no conversion yet." } ], "missing": [ "Selected local scale and acceptable measurement uncertainty", "Source-compatible lots and complete storage/transfer specification" ] }, { "id": "p2-bench-prepare", "kind": "bench", "title": "Prepare the catalyst · promoted route", "summary": "Control the preparation temperature and characterize the catalyst mixture that enters the reaction.", "status": "Requirements only · unqualified", "sourceIds": [ "hoffmann-promoted-process" ], "relatedIds": [ "promoted-bench-plan", "p2-catalyst", "catalyst-speciation-p3", "p2-environment", "supply-ika-glass-probe-candidate", "supply-ika-hrc2-lite-candidate", "supply-julabo-cd200f-candidate", "p2-apparatus-comparison", "p2-cooling-loop" ], "facts": [ { "label": "Published observation", "value": "Inherited preparation is about −5 °C; this is distinct from the 20 °C reaction." }, { "label": "Source location", "value": "Patent PDF page 2, Examples 1 and 4; minus sign checked in PDF" }, { "label": "Required function", "value": "Cooling method, temperature measurement and mixing; Vessel, probe and transfer materials compatible with this mixture" }, { "label": "Handoff", "value": "A source-described catalyst mixture; active species are still unresolved." } ], "missing": [ "Heat-release and cooling-load data", "Mixing rate, addition control, water tolerance and active-species composition", "Bath choice, probe immersion and a complete connected assembly" ] }, { "id": "p2-bench-react", "kind": "bench", "title": "Form the cage · promoted route", "summary": "Maintain the reacting mixture and record temperature, mixing and composition over time.", "status": "Requirements only · unqualified", "sourceIds": [ "hoffmann-promoted-process" ], "relatedIds": [ "promoted-bench-plan", "p2-workflow", "p2-environment", "promoted-process-p2", "supply-hotplate", "p2-apparatus-comparison", "supply-p2-three-neck-flask", "supply-p2-compact-reactor", "p2-cooling-loop" ], "facts": [ { "label": "Published observation", "value": "Example 4 reports 20 °C for 24 h. Example 1 describes magnetic stirring and two phases." }, { "label": "Source location", "value": "Patent PDF page 2, Examples 1 and 4" }, { "label": "Required function", "value": "Temperature-controlled mixing and time-resolved sampling; A defined vessel, working volume, headspace and material-contact list" }, { "label": "Handoff", "value": "An unassayed reaction mixture, not purified adamantane." } ], "missing": [ "Example-4-specific vessel size; the 100 mL flask is stated for Example 1 at 50 g feed", "Phase volumes, viscosity, mixing speed and mass-transfer dependence", "Measured heat release, pressure behavior, conversion and selectivity" ] }, { "id": "p2-bench-recover", "kind": "bench", "title": "Separate the product · promoted route", "summary": "Account for product, residual feed, solvents, catalyst-derived material and losses in each stream.", "status": "Requirements only · unqualified", "sourceIds": [ "hoffmann-promoted-process" ], "relatedIds": [ "promoted-bench-plan", "p2-recovery", "p2-recovery-balance", "recovery-source-benchmarks", "sodium-hydroxide", "ether", "potassium-carbonate" ], "facts": [ { "label": "Published observation", "value": "The inherited work-up names aqueous NaOH, ether extraction, K₂CO₃ drying, filtration and concentration." }, { "label": "Source location", "value": "Patent PDF page 2, Example 1, inherited by Example 4" }, { "label": "Required function", "value": "Defined quench, phase-separation, drying and filtration duties; Solvent recovery/collection and waste-stream inventory" }, { "label": "Handoff", "value": "An isolated material plus separated waste streams, all awaiting a measured balance." } ], "missing": [ "Work-up volumes, controlled transfer conditions and heat release", "Partition coefficients, emulsion behavior, product losses and residual aluminum/bromide", "Filter choice and solvent-removal conditions; no vacuum duty specified" ] }, { "id": "p2-bench-verify", "kind": "bench", "title": "Verify what we made · promoted route", "summary": "Measure identity, purity, isolated mass and carbon/material recovery against reference material.", "status": "Requirements only · unqualified", "sourceIds": [ "hoffmann-promoted-process" ], "relatedIds": [ "promoted-bench-plan", "p2-fraction-assay", "analytical-verification", "supply-adamantane", "supply-pmrc", "supply-precision-balance" ], "facts": [ { "label": "Published observation", "value": "Example 4 gives an 82% yield, with no raw chromatogram or quantitative purity." }, { "label": "Source location", "value": "Patent PDF page 2, Example 4" }, { "label": "Required function", "value": "Identity and quantitative assay with calibration standards; Analysis of residual feed, product fractions and relevant impurities" }, { "label": "Handoff", "value": "Measured product quality and yield with uncertainty; only then a qualified material handoff." } ], "missing": [ "Validated assay, sampling schedule and uncertainty", "Sample-service acceptance, instrument/staff time and cost", "Local reproducibility; source yield is not a local prediction" ] }, { "id": "p2-fraction-assay", "kind": "operation", "title": "Measure the product & account for the batch", "summary": "Follow each sample from input lot to collected product and remaining fractions. Separate identity, purity, conversion, yield and recovery.", "status": "Proposed measurement contract; no laboratory data", "sourceIds": [ "bipm-isrd06", "eurachem-mv-2025", "hoffmann-promoted-process", "gallego-thesis-2019" ], "relatedIds": [ "promoted-bench-plan", "p2-bench-verify", "analytical-verification", "p2-recovery", "p2-recovery-balance", "recovery-source-benchmarks", "promoted-process-p2", "separation-s1", "supply-adamantane", "supply-precision-balance", "supply-pmrc", "bench-facility", "endo-thdcpd", "ethyl-bromide", "albr3", "adamantane", "exo-thdcpd", "competing-isomer-n7", "p2-apparatus-comparison", "supply-acmebay-chemistry", "supply-valley-research-park", "dodecane-standard" ], "facts": [ { "label": "Purpose", "value": "Reusable sample, calibration and measurement records for the source P2 route. All quantities and qualification outcomes remain unmeasured." }, { "label": "Measurement equipment", "value": "The B2 balance candidate has 1 mg readability. Its suitability for analytical aliquot preparation is unestablished; the lab must specify weighing uncertainty and sample sizes. No microbalance or spectrometer purchase is selected." }, { "label": "Laboratory brief", "value": "Prepared locally; no provider contacted, sample accepted or analysis price established." } ], "missing": [ "Sample handling and matrix-compatible methods", "Calibration, independent checks and acceptance criteria", "Measured fractions with uncertainty and raw data", "Quoted method development and routine sample costs" ] }, { "id": "p2-apparatus-comparison", "kind": "bench", "title": "Flask or jacketed reactor? · equipment & costs", "summary": "Compare two apparatus candidates, their included parts, missing connections and Bay Area laboratory costs.", "status": "Priced apparatus candidates; installed budget incomplete", "sourceIds": [ "apparatus-compact-catalog", "apparatus-compact-system", "apparatus-velp-motor", "apparatus-three-neck-flask", "hoffmann-promoted-process", "ika-rct", "ika-hrc2-lite-us", "bakar-bio-faq" ], "relatedIds": [ "promoted-bench-plan", "p2-bench-prepare", "p2-bench-react", "p2-bench-inputs", "promoted-input-costs", "bench-facility", "p2-fraction-assay", "promoted-process-p2", "equipment-plan-b2", "supply-p2-three-neck-flask", "supply-hotplate", "supply-ika-glass-probe-candidate", "supply-precision-balance", "supply-p2-compact-reactor", "supply-ika-hrc2-lite-candidate", "p2-cooling-loop" ], "facts": [ { "label": "Decision", "value": "Evaluate a process-approved shared laboratory first and keep the simpler flask as the initial apparatus candidate. The jacketed system becomes worthwhile if specified heat-transfer, mixing or measurement requirements justify it." }, { "label": "Scope", "value": "Two proposed equipment architectures for planning. No procurement selection, laboratory qualification or local operating protocol." }, { "label": "Cost comparison", "value": "The two subtotals contain different functions and different omissions. Their difference is not a complete-system saving. Shared equipment savings and a dedicated/shared break-even point cannot yet be calculated." } ], "missing": [ "Recovery glassware, solvent collection and waste handling", "Delivery, tax, calibration and commissioning", "Process-approved space, ventilation, storage and utilities", "Validated assay and outside analytical service", "Rent/deposit and installation for a dedicated site", "Shared-lab acceptance, actual hood access and equipment provision", "Staff time, sampling, solvents, assays, waste and maintenance" ] }, { "id": "p2-cooling-loop", "kind": "bench", "title": "Connect the cooling loop · coolant, hoses & measurement", "summary": "Keep the external heat-transfer circuit separate from the reaction mixture. Compare hose limits and identify the measurements still needed.", "status": "Specified external utility; assembly and cooling duty unqualified", "sourceIds": [ "ika-hrc2-lite-manual", "ika-hsi8-2026", "ika-lt530-2026", "ika-hrc2-lite-us", "apparatus-compact-catalog" ], "relatedIds": [ "p2-apparatus-comparison", "supply-ika-hrc2-lite-candidate", "supply-p2-compact-reactor", "p2-bench-prepare", "p2-bench-react", "supply-ika-hsi8-loop-screen", "supply-ika-lt530-loop-candidate", "supply-ika-eg28-fluid-spec" ], "facts": [ { "label": "Mass boundary", "value": "Heat crosses the vessel wall; the chemical charge is not intended to mix with the coolant." }, { "label": "Control boundary", "value": "Internal temperature stability; not absolute accuracy or reactor-temperature tolerance." }, { "label": "Cost boundary", "value": "The two hose packages are alternatives with different limits. Neither is added to the existing basket, and included olives are not bought twice. Fluid, seals, adapters and qualification remain unpriced." } ], "missing": [ "Mixture-compatible probe and reader, placement and immersion", "Calibration and synchronized logging", "Heat release and thermal capacity", "Vessel heat-transfer coefficient and measured coolant flow", "Controller response under the actual heat load", "Reactor jacket pressure rating, adapter pitch, seals and hose reach", "Confirmed coolant formulation, volume and supplier price" ] } ], "sources": [ { "id": "ika-rct", "title": "IKA RCT basic · 0020112668", "url": "https://www.ika.com/en/Products-LabEq/Magnetic-Stirrers-pg188/RCT-basic-25008259/", "scope": "Displayed $862.40 promotion / $1,078 list. 115 V variant; heating plate to 310 C. Stainless PT1000 probe and two stir bars included; chemical suitability unqualified.", "accessed": "2026-10-19", "access": "Manufacturer product and technical data inspected" }, { "id": "bakar-bio-faq", "title": "Bakar Bio Labs — published rental prices and admissions", "url": "https://bio.bakarlabs.org/faqs/", "accessed": "2026-10-19", "scope": "Published facility offering; does not establish process acceptance, availability or a custom quote.", "access": "Primary provider page inspected and HTML cached with hash" }, { "id": "hoffmann-promoted-process", "title": "Hoffmann and Trottier, Preparation of adamantane, US3457317A (1969)", "url": "https://patents.google.com/patent/US3457317A/en", "accessed": "2026-10-19", "scope": "Applicant-reported preparation, seven examples and thirteen promoter rows. No independent replication, mechanistic proof or quantitative purity.", "access": "All three primary PDF pages rendered and inspected; hash and source discrepancies preserved" }, { "id": "ika-hrc2-lite-us", "title": "IKA HRC 2 lite · 115 V technical data and US price", "url": "https://www.ika.com/en/Products-LabEq/Temperature-Control-pg272/HRC-2-lite-20104311/Technical-Data-cptd.html", "accessed": "2026-10-19", "access": "Primary page read through browser research retrieval; direct local HTML retrieval returned HTTP 403. Observations below are a manual structured transcription, not a cached full source.", "scope": "Manufacturer equipment specification and price observation; no process qualification." }, { "id": "bipm-isrd06", "title": "BIPM ISRD-06 · quantitative NMR reference guidance", "url": "https://www.bipm.org/documents/20126/27085544/bipm%2Bpublication-ID-3286.pdf/6fc31b65-bb6c-805d-9f3c-3d318e9d09fc?download=true&t=1607934555100&version=1.9", "accessed": "2026-10-20", "access": "Original publisher PDF retrieved; relevant text read and key equation/selectivity pages rendered and visually inspected.", "scope": "Purity calculation connects signal ratios to a characterized standard and weighed sample. Identity, signal interference and preparation uncertainty must be checked. This is not an adamantane assay." }, { "id": "eurachem-mv-2025", "title": "Eurachem · Fitness for Purpose of Analytical Methods, third edition", "url": "https://eurachem.org/images/stories/Guides/pdf/MV_guide_3rd_ed_V1_EN.pdf", "accessed": "2026-10-20", "access": "Original publisher PDF retrieved; relevant text read and key equation/selectivity pages rendered and visually inspected.", "scope": "Assess selectivity, matrix effects, calibration, bias, precision and uncertainty for the intended samples. A calibration fit alone does not establish method validity." }, { "id": "apparatus-compact-catalog", "title": "Chemglass · 100 mL compact reactor illustrated parts list", "url": "https://chemglass.com/Download/getfileupload/03451e4c-26c9-405c-9e9e-98eb8b238b9a", "accessed": "2026-10-20", "access": "Primary source cached and inspected; PDF pages also rendered and visually checked.", "scope": "Equipment specification or displayed price; no process qualification." }, { "id": "apparatus-compact-system", "title": "Chemglass · 100 mL compact reactor package prices", "url": "https://chemglass.com/chemrxnhub-compact-systems-100ml-jacketed-lab-reactors-mini-lab-reactors", "accessed": "2026-10-20", "access": "Primary manufacturer HTML cached and exact SKU row inspected.", "scope": "Equipment specification or displayed price; no process qualification." }, { "id": "apparatus-velp-motor", "title": "Chemglass · Velp compact motor specifications", "url": "https://chemglass.com/miniature-over-head-stirrers-with-remote-digital-speed-control-velp", "accessed": "2026-10-20", "access": "Primary manufacturer HTML cached and exact SKU row inspected.", "scope": "Equipment specification or displayed price; no process qualification." }, { "id": "apparatus-three-neck-flask", "title": "Chemglass · 100 mL three-neck flask", "url": "https://chemglass.com/flasks-heavy-wall-round-bottom-3-necks-1?sku=CG-1524-41", "accessed": "2026-10-20", "access": "Primary manufacturer HTML cached and exact SKU row inspected.", "scope": "Equipment specification or displayed price; no process qualification." }, { "id": "gallego-thesis-2019", "title": "Gallego Sánchez thesis · source-matched zeolite methods (2019)", "url": "https://riunet.upv.es/handle/10251/134015", "accessed": "2026-10-20", "scope": "Section 3.4.4, PDF pages 107–108, and Table 6.2.3, PDF page 233, visually inspected. Same author and seven matching outcome rows; not independent replication. Pressure convention and analytical calibration remain missing.", "access": "Public institutional PDF, 290 pages; DOI 10.4995/Thesis/10251/134015. Repository date 2020-01-07; citation year 2019." }, { "id": "ika-hrc2-lite-manual", "title": "IKA HRC 2 lite · June 2024 English manual", "url": "https://www.ika.com/owa/ika/catalog.get_file?iProduct=&iDoc=0000000000000020000035798&iType=ma&iLang=EN", "accessed": "2026-10-20", "access": "Official 19-page PDF downloaded in browser; printed pages 10-11, 26-27, 32-35 visually checked.", "scope": "Coolant limits, supplied DN8 olives, accessory specifications and internal control ratings; no reaction qualification." }, { "id": "ika-hsi8-2026", "title": "IKA H.SI.8 · silicone hose specifications and US price", "url": "https://www.ika.com/en/Products-LabEq/Temperature-Control-pg272/HSI8-Tube-4569000/", "accessed": "2026-10-20", "access": "Current manufacturer product page inspected in browser; DOM snapshot retained.", "scope": "One US listed package price and equipment limits. Availability, discounts and process compatibility unverified." }, { "id": "ika-lt530-2026", "title": "IKA LT 5.30 · threaded hose specifications and US price", "url": "https://www.ika.com/en/Products-LabEq/Temperature-Control-pg272/LT-530-Tempering-hose-800-mm,-2-pcs-20108012/", "accessed": "2026-10-20", "access": "Current manufacturer product page inspected in browser; DOM snapshot retained.", "scope": "One US listed package price and equipment limits. Availability, discounts and process compatibility unverified." } ] }, "illustration": "A jacketed vessel is one apparatus candidate, not the selected starting apparatus. External coolant and reaction mixture are separate; the immersed probe, mixer, reader and vials depict capabilities whose performance and complete connections require qualification. Schematized energy surface and network diagram are visual metaphors without numerical values or model results.", "referenceSources": [ { "url": "https://www.nature.com/articles/s41467-024-47997-9", "role": "Selective reaction-network exploration and model refinement" }, { "url": "https://www.nature.com/articles/s43588-023-00406-5", "role": "Active-learning cycles linking selected calculations to model updates" } ] }, "additionalSources": [ { "id": "p450-redox", "url": "https://pubmed.ncbi.nlm.nih.gov/19779713/", "scope": "Primary CYP101D2 electron-transfer-system reference. O2/redox partners are abbreviated co-inputs; the drawing is not a complete balanced enzymatic recipe." } ], "geometry": { "scope": "Static projections of saved conformers; independent magnifications. Hypothetical joining edges never imply atom mapping or a discovered recipe. Existing-cage hydroxylation is separate from cage biosynthesis.", "connector": { "id": "E109–E110", "sourceAttribution": "Source-derived fragment of Merkle et al. molecular linkage proposal; local graph repair and MMFF94s assessment.", "sourceUrl": "https://arxiv.org/html/1801.03534v2", "scope": "Conditional local fixed-topology MMFF reference; shared body free. Harmonic covariance is not a sampled thermal distribution or validated reliability. No finite load, held phase, clock, chemical attachment or fabrication claim.", "display": "Carbon positions and carbon-carbon bonds only, from the existing saved relaxedNm dataset. Hydrogen omitted at this magnification.", "sha256": "ce3cea0d8bbf9abe1199172b875976eced3c61de58817d615a76d944934043a4" }, "hydroxylated": "Illustrative bridgehead hydroxylated cage. Constructed geometry, no claimed enzyme regioselectivity or optimized coordinates." }, "renderingAudits": { "bench": { "depthSamples": 398, "depthMismatches": 0, "parts": 118, "faces": 915, "paintedPolygons": 2108, "routes": 3, "width": 440, "height": 240, "projection": { "origin": [ 166.69647931486855, 84.01105316491785 ], "scale": 1.5802240434684018, "azimuth": 48, "elevation": 29 } }, "dcpd": { "depthSamples": 120, "depthMismatches": 0, "parts": 48, "faces": 1054, "paintedPolygons": 2320, "routes": 0, "width": 320, "height": 240, "projection": { "origin": [ 169.72348626499826, 111.96408474147589 ], "scale": 33.91011539230317, "azimuth": 47, "elevation": 26 } }, "endo-thdcpd": { "depthSamples": 123, "depthMismatches": 0, "parts": 54, "faces": 1232, "paintedPolygons": 2715, "routes": 0, "width": 320, "height": 240, "projection": { "origin": [ 167.5375090664701, 113.78277479392152 ], "scale": 33.35081609270659, "azimuth": 47, "elevation": 26 } }, "exo-thdcpd": { "depthSamples": 122, "depthMismatches": 0, "parts": 54, "faces": 1232, "paintedPolygons": 2697, "routes": 0, "width": 320, "height": 240, "projection": { "origin": [ 160.67651136900278, 127.54959970995866 ], "scale": 33.993500083617974, "azimuth": 47, "elevation": 26 } }, "adamantane": { "depthSamples": 118, "depthMismatches": 0, "parts": 54, "faces": 1232, "paintedPolygons": 2686, "routes": 0, "width": 320, "height": 240, "projection": { "origin": [ 168.13687196324196, 120.60897875475523 ], "scale": 32.940969259066605, "azimuth": 35, "elevation": 26 } }, "hydroxylated": { "depthSamples": 81, "depthMismatches": 0, "parts": 56, "faces": 1279, "paintedPolygons": 2708, "routes": 0, "width": 320, "height": 240, "projection": { "origin": [ 165.61517263215995, 137.6824793831401 ], "scale": 27.57871824765871, "azimuth": 47, "elevation": 26 } }, "p4-adduct": { "depthSamples": 93, "depthMismatches": 0, "parts": 22, "faces": 554, "paintedPolygons": 1023, "routes": 0, "width": 320, "height": 240, "projection": { "origin": [ 141.23877130448636, 163.82150976719828 ], "scale": 35.755236381405474, "azimuth": 47, "elevation": 26 } } }, "legend": { "warm": "Route under study, not a complete qualified route", "solid": "Selected reported overall transformations, not elementary mechanisms", "dashed": "Open research handoff or changed endpoint hypothesis; see local scope", "mechanismInset": "N1 source saddle-search bookkeeping only. Retained endpoints do not verify IRC connectivity. Q is not assigned to neutral adamantane." } }