Reactions and Mechanisms in Marvin JS

Reaction

In Marvin JS there is an option to draw a reaction with the Reaction Tools.

Reaction arrow symbol

Reaction arrow type

images/download/attachments/1803154/image2015-2-4_14_53_2.png

Straight arrow

images/download/attachments/1803154/image2015-2-4_14_53_20.png

Two-headed arrow (Resonance arrow.)

images/download/attachments/1803154/equilibrium_arrow.png

Equilibrium arrow

Creating Reactions in Marvin JS: With the Reaction tools, you can draw + signs, arrows, and you also can map the reactions. For a detailed description of how to create reactions in Marvin JS, see Reaction.

Multi-step reactions and graphical charts also can be created with Reaction tools.

Reaction Export - Technical Details

If the structure on the canvas contains only a single step reaction, then it will be automatically exported as a reaction file by Marvin JS.

This means that, in the exported file, there are separate blocks for reactants, products, and agents, making it possible to use the exported file in a reaction search.

In this case, only file formats that support reactions are available in the Export Dialog (MRV, RXN, SMILES, CXSMILES, SMARTS, CXSMARTS, CML, RXN V3000, SDF, CSSDF, CDX, SKC).

When the structure contains more than one reaction or a multistep reaction (or when the reaction converter web service is not available), the structure will not be converted into a reaction file.

In this case, there will not be reactant/product/agent blocks in the exported files, and the + signs and arrows of the reaction(s) will be exported as text characters.

Before Marvin JS 16.9.12, the conversion of the structure to a reaction file happened on the server-side and required the reaction converter Web Service. You can try out this with the EXTERNAL property.

Atom Mapping

Marvin JS provides the option to set map numbers to individual atoms. Unlike atom indices, map numbers remain constant during editing the molecule. Mapping can be useful if you want to identify corresponding atoms in the reactant and product side of a reaction.

Atom map visibility must be turned on to display the atom map numbers.

Creating and maintaining map numbers in Marvin JS: There are two ways for adding map numbers to the atoms. You can add map number to every single atom manually from the Atom properties dialog or if you would like to map the same atom with the same number, you can map these atoms by dragging from atom to atom when the Reaction tool is active. Both ways are suitable for changing or deleting the corresponding numbers.

Auto-mapping

Click the Auto Map button. In this case, every atom in the reaction would get an atom map number automatically.

The auto-map function only works for structures that are in the same reaction, that is, there must be only one reaction (one arrow) on the canvas where every molecule would be a reactant or a product of it.

Reaction Mechanisms

Marvin JS supports the detailed display of reaction mechanisms by using electron flow arrows (or mechanism arrows) to describe the formation and breaking of chemical bonds.

Electron flow arrows describe the movement of electrons in the elementary reaction steps of a complex mechanism.

In Marvin JS, you can choose between two types of electron flow arrows:

Type

Icon

Function

Single

images/download/thumbnails/1805400/Electron_Flow_Single_Arrow_Icon.png

Visualizing a single electron movement.

Double

images/download/thumbnails/1805400/Electron_Flow_Arrow.png

Displaying the movement of electron pairs.

Creating curved arrows: If you want an atom to be the source of an electron flow arrow, the atom has to have a radical electron or a lone pair. Lone pair visibility must be switched on.

Managing the arrows in Marvin JS: You can change the position, the size, and the type (simple, incipient bond) of the arrows after creation.