Creating Reactions

Only reactions that contain a single reaction arrow can be interpreted chemically and saved in chemical formats.

The following arrows are interpreted chemically:

  • Single Arrowimages/download/attachments/1802567/g-arrow24.png

  • Retrosynthetic Arrowimages/download/attachments/1802567/g-retrosynthetic-arrow24.png

  • Equilibrium Arrowimages/download/attachments/1802567/g-equilibrium-arrow24.png

  • Resonance Arrowimages/download/attachments/1802567/g-doublearrow24.png

The following arrows have no chemical meaning:

  • Curved Arrowimages/download/attachments/1802567/g-curved-arrow24.png

  • Dashed Arrowimages/download/attachments/1802567/g-dashed-arrow24.png

  • Crossed Arrowimages/download/attachments/1802567/g-crossed-arrow24.png

These arrows and + signs (beside molecules) can be formatted by using Edit > Format or the context menu.

Place a Reaction Arrow

  1. Select the Arrow > Reaction > Atom Map tool. The reaction arrow is placed on the tip of the cursor when the mouse is moved into the canvas area.

  2. Click to place the tail of the arrow.

  3. Drag the mouse and release the mouse button to place the arrowhead.

Reaction arrows snap every 7.5 degrees. Pressing Shift enables the free rotation of reaction arrows.

It is possible to place a reaction arrow at any time, even on a blank canvas.

The length and direction of the arrow can be changed.

Automatic Plus Signs in Single Step Reactions

Since version 16.5.2, it is possible to draw reactions with automatically placed plus signs (this is the default behavior). To switch the automatic mode off, uncheck the Automatic Plus Signs in Single Step Reactions checkbox on the Structure Tab.

With this option enabled, once a reaction arrow has been drawn, non-movable plus signs between reactants and product molecules are placed automatically.

To avoid plus signs between specific reactants and/or products, select the relevant fragments and use Structure > Reaction > Merge Reactants (Products).

To remove one or more molecules from such a merged item, select the relevant molecules, and use Structure > Reaction > Unmerge Reactants (Products).

When a second reaction arrow is drawn the + signs become movable and erasable. Moreover, and the content of the canvas is handled as a graphical model.

Manual Plus Signs

When the Automatic Plus Signs in Single Step Reactions function is switched, the Arrow/Reaction/Atom Map button has dual functions. Clicking with it places a + sign while dragging with places a reaction arrow on the canvas.

It is possible to place a reaction arrow or a + sign at any time, even on a blank canvas.

The manually placed + sign can be moved and deleted at any time.

Align and Distribute

It is possible to align and/or distribute the objects of the reaction scheme by selecting the relevant option in Edit > Object.

Selected agent fragments and texts are moved together with the arrow while keeping the distance between them.

Save and Export

Single-step reactions are automatically saved as reaction files.

In that case, only those File Formats are available in the Save dialog which supports reactions, these are as follows:

  • MRV

  • CXSMILES

  • CXSMARTS

  • CSRXN

  • RXN

  • RDF

  • SMILES

  • SMARTS

  • CML

  • CDX

  • SKC

In the exported file separate blocks are created for reactants, products, and agents so that it can be used in reaction search.

The No Structure label can be used to annotate unknown structures.

These labels can be saved in .mrv, .skc, and .cdx formats.

The graphical components of reactions can be aligned and distributed by using the corresponding menu item of the Edit menu.

Analysis boxes containing chemical information can be added from the Structure menu or by pressing the Ctrl+I shortcut.