CTS: Chemical Transformation Simulator 1.2

About CTS

What is CTS?

The Chemical Transformation Simulator (CTS) is a web-based tool for predicting transformation pathways and physicochemical properties of organic chemicals. Specifically, for an organic chemical of interest, this software tool will:

  • Predict the identity of transformation products as a function of reaction conditions;
  • Assess which of the transformation products are likely to accumulate; and
  • Provide estimated physicochemical properties for both the parent chemical and transformation products.

CTS predictions can address data gaps associated with chemical registration and assessment, support alternative assessment activities for manufactured chemicals, and help identify transformation products detected during nontargeted analysis of environmental samples. Furthermore, CTS can be used as a parameterization tool for more complex exposure assessment models for environmental fate, transport, bioaccumulation and dose estimation.

What are the benefits of CTS?

Many exposure and risk assessments of synthetic organic chemicals focus only on the chemical in its manufactured form; however, it is well known that most if not all organic chemicals may be transformed in the environment through reaction with water, light, microbes, oxidants and reductants. Additionally, organic chemicals may be metabolized into new molecules when they are ingested by humans or ecological species. Products generated by environmental and metabolic transformations may differ from the parent chemical in their toxicity and tendency to bioaccumulate or partition into various environmental media (e.g., air, water, and soil).

Although our understanding of processes that control the fate of organic chemicals in natural systems has progressed significantly over the past 20 years, much of this science has not been incorporated into tools and mathematical models currently used to assess risks from chemical exposures. The CTS has been developed as a tool to systematically capture this scientific understanding and codify it in collections of transformation reaction schemes that can be used to predict likely transformation products in environmental and biological systems. Expanding chemical assessments to consider the formation of transformation products will provide a more holistic evaluation of the potential impacts to humans and ecological species from the manufacture and use of an organic chemical product.

Who should use CTS?

While no specific expertise is required to operate/run CTS, interpretation of the results requires some expertise regarding environmental processes controlling the transformation of organic chemicals and the use of physicochemical properties in environmental fate modeling.

  • Chemical exposure and risk assessors can use CTS to address data gaps associated with chemical registration and assessment and to support alternative assessment activities for manufactured chemicals.
  • Environmental exposure assessment modelers can use CTS as a parameterization tool for models that simulate/predict environmental fate, transport, bioaccumulation and dose estimation.
  • Laboratory scientists can use CTS predictions to help interpret the results of field and laboratory studies.

System Requirements

CTS is a web-based application that is accessed through standard web browsers. To provide CTS users with a rich user experience, we take advantage of features specified in the HTML 5 standards. We recommend using the latest version of Google Chrome, Microsoft Edge, or Mozilla Firefox. Internet Explorer does not fully implement support for HTML 5 standards. As a result, CTS functionality will be limited when using the Internet Explorer web browser.

How does CTS work?

CTS has been implemented as a collection of workflows. Each CTS workflow begins with the user specifying a chemical of interest by entering its name, CAS number or SMILES string, or by drawing the molecule using the Chemical Editor drawing tool.

  • The "Calculate Chemical Speciation" workflow can be used to predict the distribution of protonated/deprotonated forms of the molecule as a function of pH. This workflow can also be used to display the various stereoisomers and tautomer forms of the molecule.
  • The "Calculate Physicochemical Properties" workflow provides estimated physicochemical property values for the chemical of interest from four physicochemical property calculators that utilize different computational approaches (i.e., Quantitative Structure-Activity Relationships (QSARs), fragment-based methods and nearest neighbor algorithms). The physicochemical property workflow also provides the average of all the calculated property values as a consensus value and pulls available measured property values from a database.
  • The "Generate Transformation Products" workflow predicts likely transformation products of the chemical of interest for user-selected scenarios (e.g., within anaerobic aquatic environments or due to human metabolism). The prediction of transformation products is made possible through the development of CTS Reaction Libraries, which are collections of reaction schemes that specify how a molecular fragment will be modified by a particular transformation process. Briefly, CTS identifies the possible transformation pathways that may impact the chemical of interest by searching through Reaction Libraries for matches to specific structural fragments within the chemical of interest. For each fragment that matches a scheme, CTS generates the molecular structure of the transformation product by modifying the structural fragment in the chemical of interest according to the reaction scheme. Among the generated transformation products, CTS estimates which products are most likely to accumulate based on an integer rank that has been assigned to each reaction scheme within the CTS Reaction Libraries based on reported transformation rates in the scientific literature.

How can I get help?

Users are encouraged to consult the online documentation found in the left-hand menu of the CTS website. The CTS User's Guide provides first-time users with detailed instructions for each CTS workflow. Detailed information on how CTS predicts transformation products is available in the Reaction Libraries documentation. Links to additional information about the physicochemical property calculators implemented in CTS is available on the Property Calculators page. Questions can also be submitted in the text box on the CTS Contact page.