Geochemistry Module

In IsoFind, the Geochemistry module consolidates everything related to the chemistry of analyzed samples, from major elements to trace organic micropollutants. It is built around a reference catalog of 156 molecules organized into 11 families, complemented by inorganic geochemical data (major, trace, redox speciation), and coupled with isotopic measurements when available. Its consistency with the IsoFind Nexus module via the CSIA bridge makes it a central component for process identification.

Module Organization

The module is structured into two main components reflecting the distinction between organic chemistry (molecules, micropollutants) and inorganic chemistry (major and trace elements, speciation).

Molecular

156 reference molecules: pesticides, PFAS, PAHs, chlorinated solvents, pharmaceuticals, explosives, and associated CSIA.

Inorganic

Major elements (Ca, Mg, Na, K, Fe, Mn), traces (As, Sb, Cr, U), diagnostic ratios, and redox speciation.

The 11 Molecule Families

The IsoFind molecular catalog is organized into eleven families reflecting standard nomenclature in environmental chemistry and chemical forensics. The distribution of the catalog by family provides an immediate overview of the scope covered.

Family	Count	Representative Sub-families
Pesticides	38	Triazines, organophosphorus, neonicotinoids, chloroacetamides, phenylureas
PFAS	26	PFCA (C2 to C12), PFSA (C4 to C10), FTS, FOSA, Cl-PFAS, PFCA-alt
Pharmaceuticals & EDCs	21	Estrogens, bisphenols, NSAIDs, sulfonamides, parabens, UV filters
PAHs	19	2 to 6-ring PAHs, methylated PAHs
Chlorinated Solvents	16	Chlorinated ethylenes, chlorobenzenes, chlorinated methanes and ethanes
Explosives	12	Nitroaromatics, nitroesters, nitramines, organic peroxides, precursors
PCBs	9	Indicator PCBs, dioxin-like PCBs
Perchlorates	4	Inorganic ions
Dioxins and Furans	4	PCDDs, PCDFs with TEF
Cyanides	4	Simple cyanides, cyano complexes, cyanated derivatives
Inorganics (oxyanions)	3	Nitrogen and phosphorus oxyanions

The catalog distribution by pollutant type is 144 organic molecules to 12 inorganics. This predominance reflects IsoFind's forensic focus on micropollutants while maintaining coverage of classic inorganic cases (perchlorates, cyanides, nitrates, phosphates).

Three Access Levels

Each molecule in the catalog is assigned an access level that determines its availability across IsoFind editions. The current distribution is balanced.

Access Level	Count	Typical Content
free	67	Common molecules: Priority EPA PAHs, WFD pesticides, EU 2020/2184 PFAS
pro	77	Specialized molecules: Extended PFAS, pharmaceuticals, explosives, isomers
defense	12	Molecules of defense interest: specific explosives, precursors, agents

Data per Molecule

Each molecule in the database carries a set of metadata that transforms it into a functional datasheet beyond a mere name. This metadata is utilized in the entry interface, report blocks, and integration with the simulation engine.

Field	Role
nom, nom_iupac, cas	Common name, IUPAC name, CAS number identifiers
formule, masse_molaire	Basic chemical properties
mz_principal, mz_secondaires	MS transitions for quantification
famille, sous_famille	Taxonomic classification
type_polluant	Organic or inorganic classification
seuil_eau, seuil_sol, seuil_unit	Regulatory thresholds for water and soil matrices
reglementation	Reference normative text (WFD, Dir. 98/83, EPA, WHO, Stockholm)
lod, loq, methode_ref	Analytical limits and reference method
actif, version_db	Catalog management flags

Three Supplementary Tables

Beyond the main catalog, three tables associate each molecule with the advanced properties required for isotopic analysis and simulation.

Table	Content	Current Entries
molecule_degradation_pathways	Degradation pathways with kinetics, environment, and metabolites	50 pathways
molecule_isotope_fractionation	Isotope fractionation data with epsilon, mode, lambda, AKIE	56 entries
molecule_metabolites	Parent-metabolite links with stability and molar yield	49 relations
ref_molecules_isotopes	Isotopic interpretation by molecule and element	18 entries

Access and Available Actions

The Geochemistry module is accessible from the main menu of an open project. Key actions are grouped into dedicated tabbed views.

Open Project > Sample View > Molecules or Geochemistry Tab > Data Entry or Consultation

Available actions include: consulting the reference catalog, importing a molecule into the project, entering sample measurements, automatically recalculating compliance, generating isotopic suggestions, and solving a CSIA pathway for a given molecule.

Coupling with the Nexus Engine

The CSIA bridge (molecule_csia_bridge) links the molecular catalog to the Nexus engine. For a given molecule and set of geochemical conditions (pH, Eh, temperature, oxygen), it returns the most probable degradation pathway, corresponding epsilon, half-life, kinetic constant, and list of expected metabolites. This output feeds both the 3D simulation engine and report blocks.

The coupling of the molecular catalog and Nexus is what distinguishes IsoFind from a simple database. A molecule is not just defined by its datasheet; it carries a function usable by other modules. This integration is described in detail on the dedicated CSIA Isotopy page.

Learn More

Molecular: details on organic pollutant families.
Inorganic: major elements, traces, and speciation.
Reference Database: catalog structure and enrichment.
CSIA Isotopy: coupling with the Nexus engine.