Mechanism questions
(using the Marvin JS chemical editor)
Updated 19 Feb 2024
Some Mastering questions include tools for drawing organic mechanism boxes, reaction arrows, and curved arrows to indicate electron flow using the Marvin JS chemical drawing tool.
Marvin JS is an advanced chemical editor from ChemAxon, Ltd that's used in pharmaceutical and other industries. Complete Marvin JS mechanism questions on a computer, not on a smartphone.
Watch a video: Answer chemical drawing questions
When available, open the Introduction to Mastering assignment and select the Introduction to Organic Mechanisms item. The tutorial contains instructions, videos, hints, and practice questions for you to answer using Marvin JS. This assignment provides practice items for different kinds of questions.
You can usually return to this assignment anytime during the course, even after its due date. If you completed this assignment, you can usually rework its items for practice.
Ease-of-use features
- Play videos about how to draw in Marvin —
Select Drawing Help from the top toolbar and then choose How-to Video Tours. - View the name or purpose of a button —
Point to a button. - Zoom in on structures on the canvas —
Choose the Zoom in or Zoom all (for maximum size) from the top toolbar. You can also access Zoom all from the right-click menu. Scroll bars become active if the structure is larger than the canvas. - If you accidentally delete drawn elements that are provided to you on the canvas, be sure to choose Undo right away.
Drawing features
- Identify atoms by "mapping" them to a number —
Select Atom map from the left toolbar. See next section for how to map/unmap atoms. - Set or edit charges and radicals —
Select options from the left toolbar. See next section for details about charges and radicals.To show more bonds or the drawing tool for mechanism drawing — Point in the lower right corner of the active bond button (left menu). For 3D drawing, bonds appear on the left toolbar.
- Any valence errors are highlighted in red for you to correct. This option may not be available for all questions.
- Add or remove explicit H atoms —
Choose Add/Remove explicit H button from the top toolbar.
- To draw more quickly, choose any of the following options.
- Drawing tool from the bonds menu (left toolbar).
Ctrl+D for Windows and Command-D for Mac also activates the drawing tool. - Chain tool or Abbreviated groups from the left toolbar
- Select a template from the bottom toolbar, like for Benzyne.
- Drawing tool from the bonds menu (left toolbar).
To draw in a larger window —
Choose Expand from the top toolbar. When you finish drawing, choose Return this drawing to the main window.
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Add atoms
From the Atoms toolbar (on the right):
From your keyboard: Place your pointer on the canvas and type the symbol for the atom from your keyboard, such as N for nitrogen. To get out of atom mode: Select another mode. For example, select a bond or charge. Periodic table of elements (to choose other atoms)
Change an atom on the canvas
Map/unmap atoms (identify atoms)
You "map" (identify) atoms in your answer by labeling them with a number. Map an atom:
To increase a map number — Point to the atom and click again. Edit or unmap an atom:
Add/remove explicit H atoms
When you place a non-metallic atom on the canvas, it may be automatically completed with implicit hydrogens according to the free valences of the atom. For example, instead of C, you might see CH4. This behavior can vary from question to question.
Sprouting (attach an atom and bond)
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Add bonds
Bond types
Change the length or angle of a bond
Draw a chain of bonds
Choose Chain (left toolbar) and then drag your pointer. As you drag, the tool displays the number of atoms in your chain. Drawing tool (multiple bonds)
When available, the drawing tool lets you create a framework of bonds without releasing your pointer. Add each bond by dragging your cursor towards a provided a gray dot. Toolbar:Expand the bonds menu from the left toolbar (by pointing in the lower right corner of the active bond). Then, choose the Drawing tool. Keyboard shortcut for the Drawing tool: Ctrl+D (Windows) or Command-D (Mac OS) |
Charges and Radicals |
Increase/decrease charge
Select Increase charge or Decrease charge (left toolbar), and then click the atom on the canvas. Change radical state
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Draw a box
Move or rotate a box
Once you select a box, you can move or rotate it like any other object in the canvas.
Resize a box
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Electron flow arrows should start on the electrons of an atom or a bond and should end on an atom, bond, or location where a new bond should be created. Draw electron flow arrows (one electron or two)
You can draw an electron flow arrow from the electrons of an atom so that its arrowhead lands either in the space between atoms or on an established bond. Marvin also lets you place electron flow arrows on an atom when a new bond is forming. However, Mastering may not always be able to interpret the atoms intended to form the new bond. To ensure the proper atoms are forming the new bond: Look for a dotted line connecting the atoms. When the electron flow arrow is active, select a curved arrow to rotate through possible interactions.
Resize electron flow arrow (change arc angle)
Drag the arrow while either the electron flow arrow or a selection button ( Rectangle selection or Freehand selection) is active on the toolbar. |
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Add arrows between reaction boxes
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Abbreviated groups (Superatom or S-groups) |
Show group in contracted or expanded form
Marvin provides a selection of abbreviated groups. You can make an abbreviated group part of a larger molecule by connecting the group to other fragments through an attachment point.
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Absolute stereo (chiral) |
Set absolute stereo
Right-click on an empty spot on the canvas and choose Absolute stereo (chiral). (Mac users: Use an equivalent for right-clicking.) A check mark appears next to the Absolute stereo (chiral) option to indicate that this has been set. This setting indicates that the molecule represents a single, well-defined stereoisomer. Remove absolute stereo
Right-click on the canvas and choose Absolute stereo chiral to remove its check mark. Mac users: Use the equivalent for right-clicking. |
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Templates can save you drawing time. Select a template button and then place the template on the canvas. (The templates provided for mechanism questions are the same as those for 2D drawing.) Available templates
Point to a template button for its name to display online. Cyclopropane Cyclobutane Cyclopentane Cyclohexane Benzene Cycloheptane Cyclooctane Bicyclo[2.2.2]octane |
Undo/Redo |
Undo a previous action
Redo the previous action
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Select an atom, bond or group
Point to the item on the canvas (a green highlight appears), and then select it. Select a molecule, chain, fragment, structure or box
Deselect
Point on the canvas outside of the selected object(s). Important: When asked to identify atoms for an answer, you must use atom mapping. Just selecting atoms is not enough for the system to interpret or grade as an answer. |
Delete |
Important: If you accidentally delete provided elements, select Undo immediately. Otherwise, contact your instructor. Delete objects you have drawn
Clear ALL elements
Important: Do not use these commands if elements have been provided for the question! Toolbar: Select Clear (upper left corner). Keyboard: Press Ctrl+Delete (Windows) or Command-Delete (Mac OS). |
Move an atom or bond
With one of the selection tools active ( Rectangle selection or Freehand selection), drag the atom or bond on the canvas. Move a selection
Rotate in 2D
Relocate the center of the rotation (pivot point)
Moving the center point allows you to rotate a molecule around any point on the canvas.
Zoom in/Zoom out
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See also: Marvin JS User's Guide
This searchable guide on the ChemAxon website includes the latest info about Marvin, including some features that are NOT applicable to Mastering
assignments.