Reactions and mechanisms in Marvin JS
Reaction
In Marvin JS there is an option to draw a reaction by the Reaction tool buttons.
|
Reaction arrow symbol |
Reaction arrow type |
|
|
Straight arrow |
|
|
Two-headed arrow (Resonance arrow.) |
|
|
Equilibrium arrow |
Creating Reactions in Marvin JS: With Reaction tool you can draw "+" signs, arrows, and you also can map the reactions. You can read detailed description about the creation in the Reaction page in Drawing features section. (For more information about mapping see below.)
Multistep reactions and graphical charts also can be displayed by the Reaction tool.
Technical details - Export reactions
-
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 will be separate blocks for reactants, products and agents, making it possible to use the exported file in a reaction search.)
In this case, only those file formats are available in the Export dialog which support reactions (MRV, RXN, SMILES, CXSMILES, SMARTS, CXSMARTS, CML, RXN V3000, SDF, CSSDF, CDX, SKC).
Please note that the conversion of the structure to a reaction file happens on server side and requires the reaction converter web service to be available.
-
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.
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 should 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 way 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 atom map number automatically.
This feature is only available with Standardizer license.
Please, note that Auto-map function only works for structures which are in the same reaction. (In other words: there should 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 describes 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 |
Function |
|
Single ( |
Visualizing a single electron movement. |
|
Double ( |
Displaying the movement of electron pairs. |
) 
) These arrows also can represent bond formation see details here.
Creation of 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 should be switched on.
Manage the arrows in Marvin JS: You can change the position, the size, and the type (simple, incipient bond) of the arrows after creation. See details here.