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Chemical Editor (CE): CTS's Chemical Editor (CE) appears at the beginning of all workflows and allows users to enter chemicals by their name, Chemical Abstracts Service Number (CAS#), simplified molecular-input line-entry system (SMILES) string, or by drawing the chemical's structure. ChemAxon's Marvin and JChem applications and EPA's CompTox Chemistry Dashboard are used to generate a standardized SMILES string, preferred common name, IUPAC name, chemical formula, relevant CAS numbers, average and monoisotopic mass, and the DTXSID (unique substance identifier assigned by EPA's National Center for Computational Toxicology (NCCT)) for the selected chemical.

• ChemAxon's MarvinExit
• ChemAxon's JChemExit
• ChemAxon's Plugin CalculatorsExit
• CompTox Chemistry Dashboard
• DTXSIDExit

Chemical Speciation (CS): CTS's Chemical Speciation (CS) workflow uses ChemAxon's Plugin Calculators to generate:

• The speciation of a chemical as a function of pH;
• The ionization constants;
• The dominant tautomer distribution; and
• Structures for all possible isomers.

Physicochemical Properties Module (PCP): CTS's Physicochemical Properties (PCP) module calculates physicochemical properties for the parent chemical and predicted transformation products based on the findings of multiple physicochemical property calculators. The PCP module is based on an approach that allows users to compare output from multiple calculators that use different approaches to calculate specific physicochemical properties.

1.  EPI Suite, which uses a fragment-based approach;
2.  Toxicity Estimation Software Tool (TEST), which uses QSAR-based approaches; and
3.  ChemAxonExit plug-in calculators, which use an atom-based fragment approach.
4.  OPERAExit, which uses QSAR-based modeling.

Users also have the option to request measured data that is available in the EPI Suite physicochemical property database.

Reaction Pathway Simulator (RPS): CTS's Reaction Pathway Simulator (RPS) generates potential transformation products based on user-specified reaction conditions. The output of the RPS is based on the selection and execution of reaction libraries that represent reaction schemes for the transformation of reactive functional groups, like reduction and hydrolysis. These reaction schemes denote viable transformation pathways based on the identification and transformation of the reactive functional groups. A rank is assigned to each one of the reaction schemes based on available experimental data. The rank is essentially a relative reaction rate, defined on a scale of one to six with six being assigned to the fastest reaction schemes. The rank of each scheme is used to calculate an approximate percentage production of each potential transformation product.

A reaction library for human metabolism for phase one transformations developed by ChemAxon is also available through the RPS. Developing reaction libraries allows scientists to "encode" the known process science published ‑ current and future ‑ in the peer-reviewed literature. Encoding process science is accomplished by using Chemical Terms Language and cheminformatics applications.

Executing these reaction libraries provides dominant transformation pathways and products for the chemical of interest as a function of environmental conditions. Users also have the option to execute the PCP for the calculation of physicochemical properties for the parent chemical and transformation products.