Combinatorial Chemical Design Chapter
Applicability: Synapse (core versions 0315+)

In a combinatorial chemical design, you specify the groups used to construct new chemical candidates and the constraints those new candidates must satisify. Synapse then automatically assembles the design groups into all possible molecular structures, estimates the properties of each structure and finally uses these properties to evaluate each design constraint. Chemical candidates whose properties satisfy all design constraints are retained for further examination.

The Combinatorial Chemical Design Chapter is found in chemical design documents. The chapter stores the design limits, design groups, substructure limits and constraints used to perform a combinatorial chemical design.

Chapter Sections

The chapter's datapane is divided into eight sections:

Section Description
Source Knowledge Base Section used to specify the knowledge base that will be used as the source of all structural information, e.g., element valences, and physical property estimation techniques.
Design Parameters Section contains fields specifying the limits on the groups and rings candidates may contain.
Design Groups Section contains one large field specifying the design groups and limits used by Synapse to construct candidate chemical structures.
Substructure Limits Section contains one large field specifying the substructure limits. Candidates that contain occurrences of these substructures that are not within the specified limits are eliminated from the design results.
Constraints Section contains one large field managing the storage and editing of the physical and structural constraints used to constrain the designed chemical candidates.
Design Candidates Section displays the final designed chemical candidates in tabular and graphical formats. (A final candidate is a candidate chemical whose physical and structural properties satisfy all design constraints.)
General Notes Section used to store any general notes about the current design. Often a brief summary of the design's objective is entered in this field.
Associated Documents Section used to store links to any documents associated with the current design.
Chapter Commands

The Combinatorial Chemical Designs chapter has commands for reporting, testing constraints, transferring candiates and designing chemicals. These commands are available from the chapter's Commands menu.

  • Open Source Knowledge Base: opens the knowledge base stored in the source knowledge base section.
  • Test Design Constraints: runs each of the current design's constraints on a chemical selected from an open knowledge base. The results are presented in the Chemical Candidate Dialog. This command is extremely useful for testing the applicability of design constraints.
  • Report Design Properties: activates the Report Properties Dialog that enables you to select properties, design attributes and results to add to an open Report Document.
  • Transfer Chemical Candidates: activates the Transfer Chemical Candidates Dialog which enables you to copy final design candidates from the current design into an open knowledge base. A new chemical entity is created for each design candidate. The candidate's name and molecular structure are copied to the new chemical.
  • Design Candidates: activates the Combinatorial Chemical Design Dialog that automatically generates chemical structures, estimates physical properties and evaluates each candidate against the entered design constraints.
Common Commands

The menubar provides numerous other commands for navigation, bookmarking, file operations, units conversion, etc. See the documentation on Common Commands for details.

Related Documentation
Topic Description
Getting Started using Synapse provides a quick tour of Synapse's capabilities including examples of chemical product design.
Getting Started using Cranium provides a quick tour of Cranium's capabilities including a discussion of structure editing.
Estimating Chemical Properties a short video demonstrating how to estimate the physical properties of chemicals using either Synapse or Cranium.
Estimating Mixture Properties a short video demonstrating how to estimate the physical properties of mixtures using either Synapse or Cranium.