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Reaxys (English): Tips & Tricks

Information about Reaxys, a web-based chemical database

Structure editors

This is the default editor in Reaxys. Below you find some tips. For more information on MarvinSketch, check this Guide.  
Prefer working with Chemdraw? Click on the grey tab ChemdrawJS!

Copy a structure from Chemdraw to MarvinSketch
Copy your structure as MOLtxt in Chemdraw (select structure, go to Edit select Copy as, select MOL text), then you can paste your structure into Reaxys Structure Editor.

Abbreviated groups (button at top right)
Choose e.g. Boc or tBu; no need to draw the whole group! Use right-click 'Expand' to see the structure. On this website you'll find a link to a document with all 807 abbreviated groups.

Generic groups (button with the orange R, top right)
Search for a class of compound (e.g. 'alkoxy' or 'cyclic group')

Generic atoms (button A, top right)
Search for any (hetero) atom/metal

Atom properties (select atom, right click)
E.g. add an R-group, choose absolute stereo, define the number of substituents.

Bond properties (select a bond, right click on bond)
E.g. indicate that this bond should be broken or formed in the reaction, or define what bond it can be ('any')

Manual mapping (bottom left 1>1 button)
Select 1 atom before the arrow and connect it to the corresponding atom after the arrow.

In Reaxys, you can switch editors by choosing ChemdrawJS on the top left. To use this editor, no ChemDraw software is necessary. You will have to download the extension once. To do that, first select ChemDraw as your editor: 

When you do this, the instructions appear on your screen:

Choose Allow

This notification will appear:

Click on the gray clipboard:

This screen will appear:

Click on the link in step 1 (in Firefox, you might have to grant permission), next click on the link in step 2, then go back to the Reaxys tab and refresh (step 3). The ChemdrawJS editor will work and the clipboard icon on the bottom left will be green.

Copy a structure from Reaxys to ChemDraw:
Select your structure, copy it (CTRL C), go to ChemDraw, right-click, choose 'paste special' and then 'MOL/CDXML text'

Copy a structure from ChemDraw to Reaxys:
Select your structure, go to 'Edit', then 'Copy as' and choose MOL text. Go to Reaxys and paste (CTRL V).

Endnote & other reference managers

If you searched in Documents, it says 'Literature Management Systems' under the Export button. That's what you choose for Endnote or other reference managers. However, if you've searched in Substances or Reactions, you won't find that option. It's because there are several references per hit. Depending on what you want, there are two ways to get these specific documents.

  1. You want ALL documents of that search. Click on 'Documents' on top. When in the Documents section, you can select all hits and choose Export as indicated above. Please take care how much you export at once!
  2. You want all documents of a selected group of hits: select those hits and choose 'Limit to' on top. Then export as indicated above. 

You won't use these options a lot, since when you're searching for a reaction, you will probablly be most interested in the reaction conditions and need literature on that specific part.


Pay attention when exporting your results: even though you only select a few, standard is to 'export all'. Make sure to change that.