Molecule Cards

Molecule Cards provide additional information on any molecule in your pathways. You can directly access Molecule Cards from Path View by clicking on any molecule structure. In Graph View, click on any molecule node to see its structure information in a pop-up window. 

Open the three-dot menu to see the following options:

• More information: Open the molecule card to see detailed information about the compound
  
  
• Shop now: For commercially available compounds, click ‘Shop now’ to add the compound into your Shopping List (See “Shopping List” in the Analyses Dashboard User Guide to learn how to set up and use your Shopping List for selecting commercial compounds you would like to buy).  
  >> Shopping List
  
  
• Add to clipboard: Send the molecule to the clipboard in the left panel (see “Clipboard” for more details)
  
  
• Add to molecule set: Add the molecule directly to one of your molecule lists (see “Molecule Lists” for more information about creating and using Molecule Lists)
  
  
• Copy structure: Copy the structure of the molecule in mol file format to your computer’s clipboard, paste into any molecule editor
  
  
• Start new analysis: Begin a new manual or automatic retrosynthesis search for the selected molecule
  
  
• Add filter: Use the molecule as a filter to exclude or view only the pathways containing it (see “Filters” for more details)
  >> Filters

Select ‘More information’ to open the card.

Details

In the left panel, find basic information about the molecule, such as its name, molecular formula, molecular weight. If the molecule is included in our database of published molecules, you may also find its cost, popularity, CAS number, GHS hazard pictograms and Greener Alternative Product icon when applicable, and a link to its PubChem entry.
>> Greener Products & Solutions 
>> PubChem

The vendor information can be found in the third lower panel on the right of the card. This is particularly useful when the vendor is not Sigma-Aldrich®, as a link to the vendor website and a catalog ID number are listed.

You can use the left/right and up/down arrows in the control box at the lower right of the card to navigate to the next or previous reaction in the pathway. Click on the molecule to go back to the molecule card ‘Details’ tab.

Molecule Strain and 3D View

When this feature is selected, several calculations are run on the desired molecule to determine bond lengths, angles, and strain within the molecule. If molecular strain is detected, affected centers will be highlighted in red. 

The 3D model can be rotated by clicking on the structure and holding, while moving your mouse in the desired direction. You can save the 3D structure by right clicking on it, and selecting ‘Save image as’ or ‘Copy image’.

Protections

When enabled, this tab displays which functional groups may need to be protected, as well as suggested protecting groups that will be compatible with the reaction conditions.

It is important to note that the list of compatible protecting groups is not exhaustive. SYNTHIA™ will only list a few options, even if there are many different possible protecting groups that could be used in a specific reaction.