Editing Molecular Structure
Applicability: Cranium, Synapse (core versions 0315+)

Many estimation techniques require knowledge of a chemical's molecular structure. Some techniques require only information about the chemical's family, e.g., is the chemical chlorinated. Other techniques, e.g., group contribution techniques, require a chemical's structure to be completely dissected into molecular fragments.

Cranium and Synapse use a simple connectivity model to represent molecular structure. Atoms and bonds are connected into a simple graph.

Example: Enter a molecular structure for a new chemical
  1. Open a knowledge base document. (Open a "working" document or create a copy of a document (see here) if you are just experimenting with this functionality.)
  2. Change to the Chemicals Chapter and press the Add toolbar button (the large plus sign). Alternatively you can choose the Add Page command from the Edit menu or use the crtl-a keyboard accelerator. The application will add a new, blank page to the Chemicals chapter.
  3. Scroll the data pane to the Chemical Structure section, located near the top of the pane, and click the left mouse button in the Structure field. Cranium displays the molecular structure edit dialog.

    The tool buttons on the dialog's left are used to change drawing modes. The controls at the dialog’s top are used to specify the current element and the current bond type. The large central window is the canvas on which you draw your structure.

    Selection Tool: Click on an atom to select it or click and drag the mouse to select several atoms.
    Eraser Tool: click on atoms or bonds to remove them from the current structure.
    Atom Tool: click anywhere in the edit plane to create a new atom using the current element. (You cannot place a new atom on top of an existing atom.)
    Bond Tool: click on pairs of atoms to connect them with the current bond type.
    Grid Option: press this tool button to have atoms aligned to the grid when created or moved.
    Auto-bond Option: press this tool button to have a new atom automatically bonded to the previously created atom.
    Subtractable Option: press this tool button to have new atoms be non-subtractable atoms.
  4. Press the Atom button (the large A). Cranium now adds an atom wherever you click the mouse in the canvas pane.
  5. Move the mouse onto the canvas pane and click the left mouse button several times in several different locations. Cranium creates and adds several new carbon atoms.
  6. Cranium uses the current element, specified at the dialog's top, to create new atoms at the location of your mouse click. Click the left mouse button on the elements control. Choose Oxygen from the list of available elements.
  7. Click the left mouse button on the canvas pane to add a new oxygen atom.
  8. As you add each atom, Cranium adds the appropriate number of assumed hydrogens. Cranium automatically updates the number of assumed hydrogens as you bond atoms together.
  9. Press the Bond button (the diagonal line). Cranium is now ready to create bonds between atoms.
  10. Click the left mouse button on the first atom to be bonded. Cranium redraws the atom in green and surrounds it with four small, solid rectangles.
  11. Click the left mouse button on the second atom to be bonded. Cranium creates a bond of the currently selected bond type and attaches it to this atom and the first bonding atom.
  12. The current bond type is changed using the bond type control located at the top of the dialog. Click the left mouse button on the bond type control. Cranium displays a list of available bond types.
  13. Choose the Double Bond type from the list.
  14. Continue the process, selecting pairs of atoms to bond, until all atoms are bonded.
  15. You have now completed editing your new structure. Press the Save button. Cranium will store the structure in the knowledge base and redisplay it in the structure field. (See documentation for the Structure Edit Dialog for details on editing molecular structure.)
Editing Group Structures

Group molecular structures are edited in a similar manner as chemical molecular structures. The key difference is that a group structure can include special elements, non-subtractable atoms and ring bonds. For example:

  • Free Atoms: During a structure match, a free atom will match any other atom. For example, the free atom in the methyl group displayed here will match the oxygen atom in methanol as well as the chlorine atom in methyl chloride.
  • Non-Subtractable Atoms: During a structure dissection, a non-subtractable atom will match a specific atom but it will not be removed before other matches are done. For example, when the methyl group below is subtracted from propane's molecular structure, the central carbon atom remains. This remainder can then be matched using the methylene group shown below.

See documentation on the Structure Edit Dialog for further details on editing molecular structures.

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