Reaction Cards

Reaction Cards provide a lot of additional information and details on any reaction suggested based on expert-coded rules, or any published reaction. You can directly access Reaction Cards from Path View by clicking on any reaction name. In Graph View,  click on any reaction node to see the reaction name and scheme in a pop-up window. Open the three-dot menu to see the following options:

• More information: Open the reaction card to see detailed information about the reaction.
  
• Add to clipboard: Send the molecule to the clipboard in the left panel (see “Clipboard” for more details).
  
• Copy reaction: Copy the reaction in rxn format to your computer’s clipboard, paste into any molecule editor.
• Add filter: Use the reaction as a filter to exclude or view only pathways containing it (see “Filters” for more details).

Select ‘More information’ to open the reaction card.

Details

The ‘Details’ tab displays additional information about the selected reaction, including typical reaction conditions, retrosynthesis ID, and illustrative references. Click on a reference DOI to open a link to the original article. When listed, click on a reference link to open the corresponding article or Google patent page in a new tab.

When a reaction has protection requirements, is not selective, or is only diastereoselective, a warning sign is shown in the upper right of the reaction, along with a corresponding indication.

For Automatic analyses, you can navigate through the different reactions in a pathway by using the left/right and up/down arrows at the lower right of the card. Click on any molecule to switch to the molecule card Details tab. To go back to your reaction, either click the right arrow if the molecule is a substrate of the reaction, or the left arrow if the molecule is a product of the reaction. 

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.

Similar Reactions

Select this option to search the published reaction database for similar reactions that may have appeared in scientific literature. If the proposed transformation is found on similar substrates, these reactions will be listed, along with the name of the article, the percent similarity to the proposed transformation, the published yield and reaction conditions, and the reference.

The similarity score is expressed by the Tanimoto coefficient calculated from comparing the degree of similarity between structure fingerprints from the proposed reaction and published reactions. It ranges from 0 for no similarity to 1 for an exact match. 

Side Reactions

Selecting this option will query the reaction rules to predict possible side reactions for the proposed transformation. The potential reactions listed are not necessarily predicted to occur, but they may explain possible side products you may encounter when running this reaction. Not every transformation will have predicted side reactions.

Simultaneous Reactions

Simultaneous Reactions are a combination of reactions that share similar reaction conditions, and can be applied on a precursor to carry out multiple transformations at once (e.g. hydrogenolysis of benzyl ethers and benzyl amines, or deprotections of Boc-protected amines and TBDMS ethers).

The reaction card for a simultaneous reaction shows the complete transformation from precursor to product. The names of the discrete transformations are listed in the box under the reaction. You may check if there are similar reactions, or side reactions related to the overall transformation by clicking on their respective tabs.

To see detailed information for each discrete transformation, open the menu on the top right of the card, and select the transformation you would like to check. Alternatively, you can click on the name of the transformation listed under the reaction.

The card will display the reaction scheme, as well as the reaction name, typical conditions, and illustrative references related to the selected transformation.

You may also view similar reactions for the selected transformation by clicking on the corresponding tab. Side reactions are not available for individual transformations.

To go back to the overall reaction, select ‘Simultaneous Reactions’ in the drop-down menu.

Feedback on Reactions

If a reaction looks unrealistic, you can send direct feedback to the SYNTHIA™ team by using the ‘Thumbs down’ icon found in the central section of the ‘Details’ window.

In the pop-up window, select the issue from a preset menu, and add detailed comments.

To help the SYNTHIA™ team determine if a correction needs to be made to the corresponding rule, the reaction scheme will be sent along with the information you entered. If you do not wish to share confidential information, you may modify the reaction scheme in the molecule editor before it is sent to the team.

Note: Significant modifications of the reaction scheme may result in loss of meaningful information, and prevent the team from understanding and resolving your issue.

On the other hand, if a reaction looks particularly interesting, you may share this feedback with the SYNTHIA™ team by using the ‘Thumbs up’ icon found in the central section of the ‘Details’ window.

In the pop-up window, select an explanation from a preset menu, and add your comments.

The reaction scheme will be sent along with the information you entered. If you do not want to share confidential information, you may modify the reaction scheme in the molecule editor before it is sent to the team.