The Chemical Structure section is one of the most important sections in the Chemicals Chapter. With knowledge of only a chemical's molecular structure, Cranium and Synapse can estimate many physical properties.

The section contains a single large field:

The Chemical Structure Section displays the molecular structure of both known molecules and newly design candidate chemicals.

• After the addition of a new, blank chemical page the minimum data to add are typically the chemical's name and the chemical's molecular structure.
• After new chemicals have been designed, either graphically or combinatorially, they are often transferred to a knowledge base for futher analysis. One of the key values transferred is the candidate chemical's molecular structure.

Clicking the right mouse button in the structure field's edit control displays the commands menu.

In addition to commands for copying and pasting molecular structure, the field's command menu contains several commands for generating chemical formulae, mol files and smiles strings.

• Copy Structure to Text: this menu contains two submenus
  • SMILES Notation: this command converts the entered molecular structure into a SMILES string and then copies this string to the clipboard
  • Mol File Format: this command converts the entered molecular structure into the textual contents of a mol file and then copies this text to the clipboard.
• Form Formula: the command will generate the chemical's formula and display it in the Formula from Structure Dialog.

1. Open the MKS Core Knowledge Base, change to the Chemicals Chapter and navigate to 1,2-propylene glycol. (See Navigation Menu for details on navigation.)
2. Click the right mouse button on the structure field's large molecular structure control. The application will display the field's command menu.
3. Select the Mol File Format command from the submenu of the Write Text to File menu item. The application will prompt for the name of file into which the Mol File text will be written.
4. Enter a name for the output file and press the dialog's Save button. The application generates the text for the chemical's mol file and writes the text to the selected file.

1. Open the MKS Core Knowledge Base, change to the Chemicals Chapter and navigate to 1,2-propylene glycol. (See Navigation Menu for details on navigation.)
2. Click the right mouse button on the structure field's large molecular structure control. As above, the application displays the field's command menu.
3. Select the menu's Form Formula command. The application will display the Formula from Structure dialog. (Generating a chemical formula is often a good way to quickly check if the molecular structure has been entered correctly.)

Clicking the left mouse button in the large edit control activates the Structure Editing dialog.

The Structure Editing dialog enables you to quickly and easily draw, insert or import molecular structures. Use of the dialog is detailed in the Structure Dialog documentation.

Topic	Description
Chemical Structure Dialog	enables you to create and edit the molecular structure of chemicals and groups.
Estimating Chemical Properties	a short video demonstrating how to estimate the physical properties of chemicals using either Synapse or Cranium.
Getting Started using Cranium	provides a quick tour of Cranium's capabilities including a discussion of structure editing.
Getting Started using Synapse	provides a quick tour of Synapse's capabilities including examples of chemical product design.
Chemicals Chapter	the chemicals chapter contains numerous sections for entering and displaying data and estimates including the chemical structure section.