Friday, 24 April, 2026
CSIA Isotopy
CSIA (Compound-Specific Isotope Analysis) measures the isotopic composition of an individual compound separated from a complex matrix, rather than a global bulk signal. This approach allows for tracking the transformation of a specific pollutant through its degradation, thanks to isotopic fractionation which enriches the residual compound as it disappears. In IsoFind, CSIA is exposed to the simulation engine and the reporting module via the molecule_csia_bridge, which queries 56 documented fractionations across 28 molecules in 9 families. This page presents the principles, tabulated data, and programmatic access modes.
Principle of Isotopic Fractionation
When a pollutant molecule degrades, the chemical bonds targeted by the reaction have slightly different kinetics depending on whether the involved atom is a light or heavy isotope. For a given compound, the C-¹²C bond breaks slightly more easily than the C-¹³C bond. The result is that the non-degraded fraction becomes progressively enriched in the heavy isotope, while the degradation product starts off "lighter." This enrichment is measured and quantified, transforming an isotopic signature into evidence of degradation.
δ(t) = δ₀ + ε · ln(f)
The Rayleigh equation describes this evolution: δ(t) is the isotopic signature of the residual at time t, δ₀ is the initial source signature, ε is the isotopic enrichment factor (in ‰), and f is the fraction of the compound still present relative to the initial mass (f = C/C₀ between 0 and 1). This equation is at the heart of CSIA diagnostics: when δ(t) is measured on a sample and δ₀ and ε are known, f can be calculated, thereby quantifying the degradation rate even without knowing the exact age of the plume.
All 56 fractionations tabulated in IsoFind are in rayleigh mode. The equilibrium and kinetic modes are supported by the bridge, but no entry is currently in equilibrium mode in the molecular catalog, which is consistent with field degradation realities: dominant biotic and abiotic processes are almost exclusively irreversible and follow a Rayleigh model.
The Epsilon Factor and AKIE
The enrichment factor ε is the slope linking δ to ln(f). It is expressed in ‰ (per mil) and typically ranges between 0 and approximately −70 ‰ depending on the case. A value close to zero indicates low fractionation (degradation hardly distinguishes between isotopes); a highly negative value indicates marked fractionation, providing a powerful diagnostic CSIA signal.
AKIE (Apparent Kinetic Isotope Effect) is another expression of the same phenomenon used in mechanistic literature. It is expressed as a ratio of the kinetic constants of light and heavy isotopes, normally greater than 1. For a typical intramolecular fractionation where only one atom is involved in the reaction, AKIE ≈ 1 − ε/1000. Extreme values in the catalog range from 1.005 (TCA, moderate fractionation) to 1.045 (DCM by Methylobacterium, the largest biotic fractionation reported in the literature).
The Four Supported Elements
The IsoFind CSIA bridge supports four primary isotopic elements. The current distribution of the 56 tabulated fractionations reflects the state of the art in the literature.
| Element | System | Number of Entries | Primary Use |
|---|---|---|---|
| Carbon | ¹³C / ¹²C (VPDB) | 36 | Universal element, present in all organic molecules |
| Nitrogen | ¹⁵N / ¹⁴N (AIR) | 9 | Triazine pesticides, pharmaceuticals, nitro explosives |
| Chlorine | ³⁷Cl / ³⁵Cl (SMOC) | 9 | Chlorinated solvents (dual C/Cl diagnostics) |
| Hydrogen | ²H / ¹H (VSMOW) | 1 | PAHs (δ²H highly diagnostic for naphthalene) |
| Oxygen (special case) | ¹⁸O / ¹⁶O | 1 | Perchlorate ClO₄⁻ |
The resolve_csia() bridge accepts a preferred_element parameter (default 'C') to select the preferred element for resolution. If the requested element is unavailable for the chosen pathway, the bridge automatically falls back to carbon.
Distribution by Chemical Family
The 28 molecules with CSIA data in the catalog are distributed across nine families, with a strong concentration on chlorinated solvents and pesticides.
| Family | CSIA Molecules | Fractionations |
|---|---|---|
| Chlorinated Solvents | 9 | 21 |
| Pesticides | 5 | 13 |
| Pharmaceuticals / EC | 3 | 6 |
| PFAS | 5 | 5 |
| PAHs | 2 | 4 |
| Explosives | 2 | 4 |
| Perchlorates | 1 | 2 |
| PCBs | 1 | 1 |
The Dual Isotope Plot and Lambda Parameter
For molecules measured on two different isotopic elements for the same degradation pathway, a dual isotope plot can be constructed: Δδ of the secondary element versus Δδ of the primary element. The slope of this plot, denoted as Λ (lambda), is a mechanistic discriminant far more powerful than single-element fractionation. The bridge exposes this calculation via resolve_dual_isotope().
Λ = ε_secondary / ε_primary
Λ Interpretation for C/Cl (Chlorinated Solvents)
The C/Cl case is the most well-codified, which is why the bridge includes explicit interpretative thresholds for this pair.
| Absolute Value of Λ | Interpretation |
|---|---|
| Λ < 0.4 | Biotic mechanism (Dehalococcoides, co-metabolism) |
| 0.4 ≤ Λ < 0.7 | Variable or mixed biotic pathway |
| Λ ≥ 0.7 | Abiotic mechanism (Fe-ZVI, chemical oxidation) |
Λ Interpretation for C/N (Pesticides and Pharmaceuticals)
For triazine pesticides, pharmaceuticals, and explosives, the relevant pair is C/N with different thresholds.
| Absolute Value of Λ | Interpretation |
|---|---|
| Λ ≤ 1.5 | Both atoms participate in bond cleavage |
| 1.5 < Λ ≤ 3 | Preferential nitrogen targeting |
| Λ > 3 | Peripheral nitrogen (secondary amine, minor impact) |
Available Dual Isotope Pairs
Eighteen pairs of measurements on two elements for the same pathway are tabulated, allowing for dual isotope diagnostics across a wide panel.
| Family | Molecule | Pair |
|---|---|---|
| Chlorinated Solvents | PCE, TCE, cDCE, DCM, Chloroform, 1,2-DCA | C / Cl |
| Pesticides | Atrazine (2 pathways), Diuron, Glyphosate | C / N |
| Pesticides | S-Metolachlor | C / Cl |
| Pharmaceuticals / EC | Carbamazepine, Diclofenac, Sulfamethoxazole | C / N |
| Explosives | RDX, TNT | C / N |
| PAHs | Naphthalene | C / H |
| Perchlorates | Perchlorate (ClO₄⁻) | O / Cl |
Automatic Degradation Pathway Selection
A molecule can have several tabulated degradation pathways for different conditions (aerobic vs. anaerobic, biotic vs. abiotic). The CSIA bridge uses an explicit three-level selection rule to choose the relevant pathway.
| Priority | Criterion | Behavior |
|---|---|---|
| 1 | Explicit pathway name (pathway_name) | The requested pathway is used directly, with partial matching as fallback |
| 2 | Redox conditions (Eh, O₂) | If Eh < 50 mV or O₂ < 0.5 mg/L: anaerobic pathway. Otherwise: strict aerobic |
| 3 | Sub-surface default | Fastest natural pathway (shortest half-life), excluding photolytic and PRB |
The default context is sub-surface aquifer, which excludes photolytic pathways (no UV at depth) and artificial reactive barrier pathways (Fe-ZVI). These pathways remain accessible by requesting them explicitly via pathway_name or by disabling the sub-surface flag.
The resolve_csia Response Structure
The resolve_csia(molecule_name, pathway_name, preferred_element, conditions) call returns a comprehensive dictionary that feeds both the simulation engine and report blocks.
| Field | Type | Content |
|---|---|---|
| molecule, molecule_id | str, int | Resolved molecule (tolerant of abbreviations) |
| famille, masse_molaire | str, float | Taxonomic context |
| pathway, pathway_category, environment | str | Chosen pathway and its conditions |
| element | str | Selected element (C, N, Cl, H, O) |
| epsilon, epsilon_min, epsilon_max, uncertainty | float | Fractionation and its uncertainty |
| mode | str | rayleigh | equilibrium | kinetic |
| akie, lambda | float | AKIE and multi-element coupling |
| k_deg, half_life_days | float | Kinetic constant (d⁻¹) and half-life (days) |
| metabolites | list | List [{name, formula, mass, molar_yield_max}] |
| reference, n_records | str, int | Bibliographic reference and number of entries found |
Usage Chain in IsoFind
CSIA is not an isolated module: it actively feeds several other software components. The same resolution serves multiple destinations.
| Destination | Use of CSIA Result |
|---|---|
| 3D Simulation Engine | Replaces default epsilon, provides k_deg for kinetics, triggers metabolite cascade |
| Sample Interface (Molecules tab) | Suggestions for isotopic measurements to perform for a given sample |
| Nexus Quick Match Module | Mechanistic diagnostics (biotic vs. abiotic) from field signatures |
| Report Blocks | Blocks such as csia_diagnosis, dual_isotope_plot, degradation_fingerprint |
API Access
Four endpoints directly expose the CSIA bridge to client applications.
| Endpoint | Usage |
|---|---|
| GET /api/molecules/csia/list | List of available molecules with CSIA (28 molecules, with counters) |
| GET /api/molecules/csia/{molecule_name}/pathways | Tabulated degradation pathways for a molecule |
| POST /api/molecules/csia/resolve | Full CSIA resolution with optional conditions (Eh, O₂, pH, T) |
| POST /api/molecules/csia/dual | Dual isotope with Λ calculation and coded C/Cl or C/N interpretation |
Limitations and Best Practices
- CSIA requires sufficient concentrations for analysis: below the CSIA LOQ (generally higher than standard LOQ), uncertainty on δ becomes prohibitive. It is common for a sample meeting regulatory limits to be below the CSIA LOQ.
- The tabulated epsilon is a representative value from controlled condition studies. Inter-strain variability can be significant; the IsoFind catalog preserves min-max ranges to bracket this uncertainty.
- An enriched δ value alone does not prove a specific degradation pathway. Only the dual isotope plot with the Λ value allows for robust mechanistic attribution.
- The source δ₀ signature is rarely measurable directly. It is often estimated from raw material data sheets, non-degraded field controls, or the least enriched value in the plume.
- Rayleigh models assume a closed system. On an open plume with continuous inputs, interpretation must integrate mixing, which the IsoFind simulation engine does automatically via its geochemical prior.
Going Further
- Chlorinated Solvents: The reference family for CSIA, 21 tabulated fractionations.
- Pesticides: CSIA on C/N for triazines and phosphonates.
- Degradation Pathways: The 50 tabulated pathways underlying the fractionations.
- Speciation and Propagation: How the simulation engine uses CSIA results.