Friday, 24 April, 2026
Degradation Pathways
The IsoFind catalog tabulates fifty documented degradation pathways in the molecule_degradation_pathways table. They cover twenty-eight molecules across eight families and form the kinetic foundation for the simulation engine and the CSIA bridge. This page presents the table structure, pathway categories, distribution by family and environment, kinetic statistics, and the logic IsoFind follows to select a pathway adapted to sample conditions.
Structure of a Tabulated Pathway
Each pathway is a row in the molecule_degradation_pathways table, containing twenty-one fields that together describe the "what, where, when," and the bibliographic sources of the pathway.
| Field | Type | Role |
|---|---|---|
| id, molecule_id | INTEGER | Primary key and link to ref_molecules |
| pathway_name | TEXT | Name of the pathway (e.g., "Anaerobic reductive dechlorination") |
| pathway_category | TEXT | biological, abiotic, or photolytic |
| environment | TEXT | aerobic, anaerobic, water-surface, water-PRB, etc. |
| conditions_eh_min / _max | REAL | Redox potential range in mV |
| conditions_o2 | TEXT | present, absent, or numerical value |
| conditions_ph_min / _max | REAL | Favorable pH range |
| half_life_days_min, _max, _typical | REAL | Min, max, and typical half-life in days |
| primary_metabolite | TEXT | Main metabolite produced |
| secondary_metabolites | TEXT | Other products, comma-separated list (47/50 pathways) |
| mineralization_possible | INTEGER | 0 or 1, indicates if the pathway can lead to CO₂ |
| reference, doi, year | TEXT, TEXT, INTEGER | Bibliographic source and year |
| notes | TEXT | Microbial strain, mechanistic specificity, warnings |
Three Pathway Categories
Tabulated pathways are divided into three categories reflecting the physicochemical nature of the process. This distinction is used by the CSIA bridge to filter pathways applicable to a given context.
| Category | Count | Mechanism |
|---|---|---|
| biological | 36 | Microbial mediation: bacteria, fungi, archaea |
| abiotic | 9 | Pure chemical reaction: hydrolysis, mineral redox |
| photolytic | 5 | UV photolysis, limited to surface waters |
The dominance of biological pathways (72% of the catalog) reflects environmental reality: most organic pollutant transformations in aquifers and soils are mediated by microbial communities. Abiotic pathways remain a minority but are essential for specific molecules or contexts (Fenton remediation, reactive barriers, long-term hydrolysis).
Eight Distinct Environments
The environment field specifies the niche in which the pathway occurs. The distribution reflects operational contexts encountered at contaminated sites.
| Environment | Count | Typical Eh range (mV) | Typical pH range |
|---|---|---|---|
| aerobic | 20 | +100 to +400 | 5.5 to 8.5 |
| anaerobic | 15 | −210 to +47 (average) | 5.5 to 8.5 |
| water | 5 | 0 to +600 | 4 to 11 |
| water-surface | 5 | +200 to +600 | 5 to 9 |
| water-PRB | 2 | −400 to −100 (highly reducing) | 6.5 to 9.5 |
| water-treated | 1 | +400 to +800 (advanced oxidation) | - |
| water-soil | 1 | +200 to +600 | 4 to 9 |
| anaerobic-sediment | 1 | −250 to 0 | 6 to 8 |
The water-PRB and water-treated environments are artificial: they correspond to remediation conditions (Fe-ZVI reactive barriers, advanced oxidation processes). The CSIA bridge excludes them by default for natural subsurface context queries, mobilizing them only if the user explicitly requests them via pathway_name.
Distribution by Molecular Family
The number of tabulated pathways varies significantly by family. Chlorinated solvents alone account for 36% of the catalog, reflecting the historical maturity of research on these compounds.
| Family | Pathways | Molecules Covered | Comment |
|---|---|---|---|
| Chlorinated Solvents | 18 | 9 | Full cascade PCE → TCE → cDCE → VC → ethene plus aerobic pathways |
| Pesticides | 10 | 5 | Atrazine 3 pathways (dealkylation, hydrolysis, mineralization) |
| PFAS | 7 | 5 | Rare degradation, only 1 mineralization pathway (Fenton on PFOA) |
| Pharmaceuticals / EC | 6 | 3 | Typical UV-A photolysis (carbamazepine, diclofenac, sulfamethoxazole) |
| Explosives | 4 | 2 | TNT and RDX, photolysis and biotransformation |
| PAHs | 3 | 2 | Limited to naphthalene and phenanthrene, no 4+ ring PAHs |
| Perchlorates | 1 | 1 | Perchlorate ClO₄⁻ |
| PCBs | 1 | 1 | PCB-28 in anaerobic sediment dechlorination |
Major Mechanistic Patterns
Pathway names in the catalog are grouped into several major mechanistic patterns that recur across families. Recognizing these patterns helps in navigating the table and understanding the intuition behind the tabulated values.
| Pattern | Occurrences | Where to find it |
|---|---|---|
| Reductive dechlorination | 8 | Chlorinated solvents (PCE, TCE, cDCE, VC, chloroform, 1,1,1-TCA, 1,2-DCA), PCBs |
| Biotic degradation (generic) | 8 | Pesticides, PFAS, pharmaceuticals, 1,2-DCA |
| Hydrolysis | 6 | Chlorinated solvents (TCA, 1,2-DCA), pesticides (atrazine, diuron), HFPO-DA |
| Photolysis | 5 | Pharmaceuticals, explosives, PFOS on surface |
| Aerobic oxidation | 5 | PAHs, chlorobenzene, chlorinated solvents (cDCE, TCE) |
| Fe-ZVI (reactive barrier) | 3 | PCE, TCE in PRB remediation |
| Defluorination | 2 | PFOA, PFHxS (very slow, 4,000 to 7,500 days) |
| Biotic dealkylation | 2 | Atrazine, simazine |
| Aerobic co-metabolism | 2 | Chloroform, TCE |
| Beta-oxidation | 1 | 6:2 FTS |
| N-demethylation | 1 | Diuron |
| Complete mineralization | 1 | Atrazine (Pseudomonas ADP) |
| Fenton advanced oxidation | 1 | PFOA in treated water |
Kinetics: Half-lives across five orders of magnitude
Tabulated half-lives range from 3 days (direct photolysis of diclofenac in surface water) to 23,000 days (chemical hydrolysis of 1,2-DCA in natural conditions, approx. 63 years). This range of five orders of magnitude reflects the diversity of processes covered and requires careful selection of the relevant pathway based on the context.
Fastest Pathways (natural conditions)
| Molecule | Pathway | Environment | Typical t½ (d) |
|---|---|---|---|
| Diclofenac | Direct UV-A photolysis | water-surface | 3 |
| Sulfamethoxazole | UV photolysis | water-surface | 5 |
| TNT | Direct photolysis | water-surface | 5 |
| Atrazine | Complete mineralization (Pseudomonas ADP) | aerobic | 15 |
| Glyphosate | Biotic degradation via AMPA | aerobic | 20 |
| DCM | Biodegradation (Methylobacterium) | aerobic | 20 |
Slowest Pathways
| Molecule | Pathway | Environment | Typical t½ (d) |
|---|---|---|---|
| 1,2-DCA | Chemical hydrolysis (substitution) | water | 23,000 (~63 years) |
| PFOA | Biotic defluorination (Acidimicrobium) | anaerobic | 7,500 |
| PFOS | Biotic defluorination | anaerobic | 5,000 |
| PFHxS | Biotic defluorination | anaerobic | 4,000 |
| PCB-28 | Anaerobic reductive dechlorination | anaerobic-sediment | 3,000 |
| HFPO-DA (GenX) | Abiotic hydrolysis | water | 2,500 |
The slowest pathways concern exclusively molecules known to be persistent: PFAS (all), PCBs, 1,2-DCA. These half-lives of several thousand days have operational consequences: on a human timescale, natural degradation is not a credible remediation lever for these molecules. Only active remediation pathways (PFOA Fenton, Fe-ZVI, targeted bioaugmentation) offer kinetics compatible with a site schedule.
Mineralization: Half the Catalog
The mineralization_possible flag distinguishes pathways that lead to complete mineralization (parent → CO₂ + inorganic elements) from those that stop at an intermediate organic metabolite. The distribution is strictly equal: 25 pathways allow mineralization, 25 block it at an intermediate stage.
| Mineralization | Count | Typical Cases |
|---|---|---|
| Possible (Final CO₂) | 25 | Aerobic oxidation of PAHs / BTEX / cDCE, Fe-ZVI, PFOA Fenton, atrazine mineralization |
| No (Intermediate stop) | 25 | PCE → TCE → cDCE cascade, PFAS defluorination, 1,2-DCA hydrolysis, chloroform → DCM dechlorination |
This distinction is essential for plume interpretation: the measured disappearance of a parent can correspond either to real mineralization (good sign) or to transformation into a metabolite that is still present and potentially more problematic. Only the analysis of by-products and potential CO₂ or Cl⁻ release can decide. The IsoFind simulation engine propagates cascades automatically based on this flag.
Secondary Metabolites
Forty-seven of the fifty pathways document secondary metabolites in addition to the primary_metabolite. These additional metabolites are typically minor products, short-lived intermediates, or accumulation products (chloride, CO₂, water). The secondary_metabolites field is a free-form comma-separated string.
| Example | Primary Metabolite | Typical Secondaries |
|---|---|---|
| PCE dechlorination | TCE | cDCE, VC, ethene |
| TCE Fe-ZVI | ethene / ethane | Cl⁻, acetylene |
| 1,2-DCA aerobic | 2-chloroethanol → glycolaldehyde | CO₂, Cl⁻ |
| DCM biodegradation | formaldehyde → CO₂ | Cl⁻, H₂O |
| TCA hydrolysis | 1,1-DCE | acetic acid, HCl |
Pathway Selection in the CSIA Bridge
The CSIA bridge applies a three-level priority selection rule to choose the relevant pathway when several are tabulated for the same molecule. This rule is coded in the _select_pathway() function.
| Priority | Criterion | Behavior |
|---|---|---|
| 1 | Explicit pathway name | Uses the requested pathway (exact match then partial match as fallback) |
| 2 | Eh / O₂ conditions provided | If Eh < 50 mV or O₂ < 0.5 mg/L → anaerobic pathways; otherwise strict aerobic pathways |
| 3 | Subsurface default | Pathway with the shortest typical half-life, excluding photolytic and PRB |
The default context is subsurface aquifer. In this context, photolytic pathways (UV exposure impossible at depth) and artificial reactive barrier pathways are automatically excluded. They remain accessible if the user explicitly requests them by pathway_name.
Pathways and Isotope Fractionation
Most tabulated pathways are associated with one or more isotope fractionations in the molecule_isotope_fractionation table. A single pathway can carry fractionations for several elements (C, N, Cl, H, O), fueling dual isotope diagnosis. Fractionations are linked to pathways by the pathway_id foreign key.
When resolve_csia() is called for a pathway, it automatically retrieves the corresponding fractionation for the requested element. If the requested element is not documented for that pathway, it falls back to carbon by default.
Ingestion into the Simulation Engine
The IsoFind simulation engine uses tabulated pathways in three ways during a simulation.
| Usage | Fields Consumed |
|---|---|
| Kinetic constant k_deg | k = ln(2) / half_life_days_typical |
| Residual isotope fractionation | Epsilon associated with the pathway via pathway_id |
| Metabolite cascade | primary_metabolite + molecule_metabolites table |
The metabolite cascade is propagated automatically: if the simulated molecule has a declared primary metabolite, and if that metabolite is itself in ref_molecules with tabulated pathways, the engine launches a coupled simulation of the metabolite in parallel with the parent. This logic allows for the reproduction of the four-stage PCE → TCE → cDCE → VC → ethene cascades without explicit configuration.
Quality of Bibliographic References
Each pathway carries a bibliographic reference in free-form format in the reference field, an optional DOI, and a year. References generally cover two to three independent sources per pathway, with the most recent works cited as a priority. The median year is recent, reflecting the scientific maturity of the field in this decade.
Bibliographic traceability of pathways is a design principle of the IsoFind catalog. Any tabulated numerical value (epsilon, half-life, Eh range) must be traceable to a verifiable scientific publication. This rigor distinguishes the IsoFind catalog from an aggregate database without source attribution. Report blocks systematically cite references in the generated content.
Current Catalog Limitations
The degradation pathways catalog is still under construction. Several areas are explicitly identified as incomplete, which transparency requires us to signal.
- Four-ring and larger PAHs (fluoranthene, pyrene, benzo[a]pyrene): no tabulated pathways. Data exists in the literature but is less reproducible than for naphthalene and phenanthrene.
- BTEX and aliphatic hydrocarbons: missing from the catalog; the entire family is yet to be integrated.
- Neonicotinoid pesticides (imidacloprid, clothianidin, thiamethoxam): molecules are in the molecular catalog but without tabulated pathways.
- Non-UV pharmaceuticals: biotic pathways in soil or aquifers for most drugs are poorly documented in the literature.
- Pathways specific to extreme conditions (high salinity, high or low temperatures): current ranges cover temperate fresh waters.