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

In a graphical chemical design, you specify the elements and bonds used to construct new chemical candidates and the constraints those new candidates must satisify. Synapse then provides a set of graphical tools enabling you to graphically design new molecular structures. As you draw the structure, Synapse estimates the relevant physical properties and evaluates each design constraint. Chemical candidates whose properties satisfy all design constraints are retained for further examination.

The Graphical Chemical Design Chapter is found in chemical design documents. The chapter stores the elements, bonds and constraints used to perform a graphical chemical design.

Chapter Sections

The chapter's datapane is divided into seven 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 Structures Section contains two fields managing the elements and bonds used to graphically construct chemical candidates.
Constraints Section contains one large field managing the storage and editing of the physical and structural constraints used to contrain the designed chemical candidates.
Intermediate Candidates Section contains one large field managing the designed intermediate chemical candidates. (An intermediate candidate is a chemical whose physical and structural properties may not satisfy all design constraints.)
Design Candidates Section displays the final designed chemical candidates in tabular and graphical formats. (A final candidate is a chemical whose physical and structural properties satisfy all design constraints.)
General Notes Section used to store any general notes about the current 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 Graphical 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 Graphical Chemical Design Dialog which enables you to design chemical candidates by drawing chemical structures while Synapse evaluates each of the 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.