Do you ever… 

…run an analysis in SYNTHIA™ for which you already have a starting material in mind for your synthesis?  

Because of how SYNTHIA™ searches the complex graph of possible synthetic routes for your target molecule, it is not possible to directly specify a starting material for your analysis—but there are ways to direct SYNTHIA™ toward the ones you want. One way is to use our Do-Not-Cut feature. 

If the starting material you want to use is a part of your final product, you can tell SYNTHIA™ to not cut this part of the molecule by marking those bonds as not a reacting center.

How do I mark the bonds that I want to keep intact?   

You can mark these bonds in the molecule editor while you are setting up your analysis. Start by highlighting the portion of the molecule you want to use as a starting material and double click on one of the selected bonds to open the bond menu.

Double click on one of the selected bonds to open the bond menu. Under ‘Reaction Center’, select ‘Not center’ and click ‘Apply’. 

You can see which bonds have been marked as Do-Not-Cut, as they show an ‘X’ crossing through them. 

When you are done marking the bonds you do not want to be disconnected as Not Reaction Center, select your analysis parameters and start the analysis.

Once the analysis is started, all the pathways SYNTHIA™ proposes should start from compounds with these bonds intact, and you will be more likely to find the starting material you wanted to use. 

Do-Not-Cut is great in other situations too! 

In addition to finding desired starting materials, you can use this feature to preserve a stereocenter or avoid a known route by marking the key disconnections as Do-Not-Cut. 

Something to remember… 

SYNTHIA will still need to meet the stop conditions for an automatic retrosynthesis analysis. If the starting material you want to use is not present in our databases of published compounds or commercial compounds, SYNTHIA™ may not be able to find any routes when you mark that part of the molecule as Do-Not-Cut. You can quickly check if the starting material you want to use is listed in our database, by looking for it as a target molecule by name, SMILES or CAS number. 

You may also want to lower the popularity threshold for Published compounds if the starting material is the database but has not been published many times. 

Incorporating your Custom Inventory into SYNTHIA™ can help make sure the compounds you want to use are available as starting materials. Contact our team to find out more about adding this feature to your license.

Try it for yourself! Explore Do Not Cut today!