Would you like to… 

… learn more about how to use the molecule editor in SYNTHIA™?

Our Molecule Editor, Ketcher, allows you to quickly draw structures using bond and atom tools.

Key Features

• Bond and Atom Tools: Select bond types and atoms from the corresponding icons in the editor.
• Template Bar: Access simple ring templates at the bottom of the editor.

• Structure Library: Use the Structure Library icon on the right side of the bottom bar to access:
  • Common functional groups
  • Libraries of complex rings
  • Natural product templates

Note: Always draw exact structures for analysis. SYNTHIA™ does not recognize query bonds or query atoms for target molecules.

Keyboard Shortcuts

Accelerate structure drawing with these shortcuts:

Import Structures

You can paste structures drawn in other Molecule Editors directly into SYNTHIA™. The editor recognizes common structure formats, such as:

• SMILES
  
• MOL text
• InChi

How to import:

• Copy the molecule from another editor and paste it directly into SYNTHIA™’s drawing space.
• If you experience issues, copy the molecule as SMILES and paste it into the editor using Ctrl+v.

Atom Properties Menu

When the Selection Tool is active, double-click on any atom to open the Atom Properties Menu.

Functions:

• Change Element: Type the element abbreviation in the Label textbox to change the atom.
• Modify Isotopes: Enter the isotope number in the Isotope textbox.
  • Example: Type 13 for a ¹³C isotope or 2 for deuterium with H as Label.
• Modify Charge: Type the charge number in the Charge textbox.
  • Example: Type 1 for a positive charge or -1 for a negative charge.
• Alternatively, use the Charge Tools in the left bar and click the atom to modify its charge.

Bond Properties Menu

When the Selection Tool is active, double-click on any bond to open the Bond Properties Menu.

Functions:

• Avoid Pathways: Select Not Center in the Reacting Center dropdown to prevent SYNTHIA™ from proposing pathways forming the selected bond. The bond will be marked with an X.
• Favor Pathways: Select Center in the Reacting Center dropdown to prioritize pathways forming the selected bond. The bond will be marked with a #.