Mechanism questions
(using the Marvin JS chemical editor)

From the Atoms toolbar (on the right):

1. Select an atom, such as O Oxygen, or choose  Periodic table and then select an atom.

   The symbol appears on the tip of your pointer when over the canvas.

2. Place your pointer on the canvas to position the atom.

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.

• Select  Periodic table from the Atoms toolbar and then choose an atom.
• Enter the symbols for deuterium (D) and tritium (T) from your keyboard. These aren't listed in the periodic table.

1. From the Atoms toolbar (on the right), select a new atom or select the  Periodic table and then select an atom.

   The symbol appears on the tip of your pointer when over the canvas.

2. On the canvas, point to the atom you want to replace so that it's circled.

   

3. Point on the existing atom to replace with the new atom.

   Depending on the display set for the item, implied H atoms or explicit C atoms may also appear.

You "map" (identify) atoms in your answer by labeling them with a number.

Map an atom:

1. Select  Atom map (left toolbar).
   
2. On the canvas, point to an atom and select it.

   The map number appears to the right of the atom and enclosed in brackets.

   Example of two mapped atoms, [1] and [2]

   

To increase a map number — Point to the atom and click again.

Edit or unmap an atom:

1. Select  Atom map (left toolbar).
2. Double-click on a mapped atom.
3. Enter a number in the Map box that opens on the canvas. Enter 0 to unmap the atom.

   

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.

1. Choose the  Add/Remove explicit H (top toolbar) to add or remove the display of H atoms.

1. From the Atoms toolbar (on the right), select a new atom or select the  Periodic table and then select an atom.
2. Point to the location on the canvas where you want to add the new atom. A circle appears.
3. Press Shift and select the atom where you want to attach the new atom and bond.
   

• Add a bond to a single atom: Select a bond type (see below), point to the atom on the canvas, and then click and drag outwards from the atom.
• Add a bond between two atoms:Select a bond type (see below), click on an atom on the canvas, and then drag the pointer to another atom. Note that choosing a bond type and dragging your pointer on the canvas creates a bond with carbon atoms at both ends.

• Choose a bond type: Expand the bond menu by selecting the lower right of the bond button (left toolbar). Then, choose a bond type.
  Expanded bond menu (mechanism and 2D drawing)

  

  Bond buttons with names (Single, Double, and other)

  All bond buttons below are available for 2D drawing and mechanism questions. For 3D drawing, buttons marked with an asterisk (*) are available directly from the left menu.
  
  = Drawing
  = Single [1]*
  = Double [2]
  = Triple [3]
  = Aromatic [4]
  = Single up [5] (wedge)*
  = Single down [6] (dashed)*
  = Single up or down
  = Double cis or trans
  = R-Group attachment
  

• Change bond type: First, select a new bond type (instructions provided above). Then, choose the bond to be changed on the canvas.

  You can also right-click on the bond to choose another bond type from the list of available types. Mac users: Use an equivalent for right-clicking.

• Change bond direction (dashed or wedge): With either the Single up (wedge ) bond button or the  Single down (dashed) bond button, and then select the bond whose direction you want to change on the canvas.

1. Select an atom or compound at one end of the bond.
2. Drag it to change the length or the angle of the bond.

Choose  Chain (left toolbar) and then drag your pointer. As you drag, the tool displays the number of atoms in your chain.

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)

Select  Increase charge or   Decrease charge (left toolbar), and then click the atom on the canvas.

1. Select  Increase radical (left toolbar) and accept   Increase radical or  Increase lone pair.
2. Position the radical or lone pair on an atom or molecule on the canvas.
3. Continue to click on the canvas to add as many as you need.

1. Select  Rectangle (left toolbar).
2. Drag on the canvas to position the box.

Once you select a box, you can move or rotate it like any other object in the canvas.

1. Select the box on the canvas.
2. Drag a box edge or corner to resize.

   

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.

1. Select either  Electron flow double arrow (also known as double harpoon or curved arrow) or  Electron flow single arrow (also known as single harpoon) from the left toolbar.

   Be sure to choose the flow arrow for the correct number of electrons!

2. Drag the arrow on the canvas, as described below.
   From the electrons of an atom to an atom...

   Drag the arrow from one of the electrons (dot symbols) on the source atom to the target atom. For better visibility, select the source atom to enlarge it and then drag the arrow from the enlarged dot.

   From the electrons of an atom to bond...

   Drag the arrow to the midpoint of the target bond. (The bond must be adjacent to the source atom.)

   From bond to atom...

   Draw a single electron arrow from the original bond to an atom which will belong to the newly formed bond. The incipient bond will appear from one atom of the bond to the arrow again.

   From bond to bond...

   You can only draw an electron flow arrow from one bond to another if the two bonds have an atom in common.

Drag the arrow while either the electron flow arrow or a selection button ( Rectangle selection or Freehand selection) is active on the toolbar.

1. Select either  Straight arrow / Reaction or the  Two-headed arrow / Reaction from the toolbar.
2. Drag from one square hot spot of a box to another. (Hover over a box to see its hot spot squares.)

   

   If there isn't much space between boxes: The arrow may shrink and be difficult to see. Consider moving the boxes to provide enough space.

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.

1. Choose  Abbreviated groups from the left toolbar.
2. Search for a group name. As you type, select the group you want.

   

3. The next step depends how you want to work on the canvas.
   • To work with a contracted group (manipulate the group as an atom), select OK.
   • To work with the expanded abbreviated group, select Expand and then select OK.
     Expanded groups show special feedback...

     on the canvas and can be manipulated as molecules or fragments (rotated, dragged, cleaned in 2D, and more).

     If you edit an expanded abbreviated group...

     by changing/deleting an atom or a bond or by changing the charge or mass of atoms, the substructure loses its group status and the feedback around it disappears.

4. As you work on the canvas, you can still switch between the expanded and contracted forms of group abbreviations by making selections from the top toolbar.

   Expand group abbreviation
   

    Contract to group abbreviation

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.

Right-click on the canvas and choose Absolute stereo chiral to remove its check mark. Mac users: Use the equivalent for right-clicking.

Point to a template button for its name to display online.

Cyclopropane

Cyclobutane

Cyclopentane

Cyclohexane

Benzene

Cycloheptane

Cyclooctane

Bicyclo[2.2.2]octane

• Toolbar: Select  Undo.
• Keyboard: Press Ctrl+Z (Windows) or Command-Z (Mac OS).

• Toolbar: Select  Redo.
• Keyboard: Press Ctrl+Y (Windows) or Shift-Command-Y (Mac OS).

Point to the item on the canvas (a green highlight appears), and then select it.

1. Select either  Rectangle selection or  Freehand selection (left toolbar).
2. On the canvas, drag to include the objects you want to select.

Point on the canvas outside of the selected object(s).

• To delete objects individually: Choose  Delete (left toolbar) and then point on each object you want to delete.
• To delete a group of objects: Select the objects (see instructions provided in the row above), and then choose  Delete (left toolbar).

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).

With one of the selection tools active (  Rectangle selection or  Freehand selection), drag the atom or bond on the canvas.

1. Choose a selection tool ( Rectangle selection or  Freehand selection) and then select the elements or structure on the canvas that you want to move.

   The elements appear inside a green outline box.

2. Drag the selection to move it.

1. Choose a selection tool ( Rectangle selection or  Freehand selection).

   The selected element appears with a blue highlight inside a box with a broken blue line. The pink circle with a dot is the center (pivot point).

   

2. Rotate the molecule by choosing the green dot outside of the box and dragging your cursor on the canvas.

   As you drag, the angle of rotation (default is 6 degree increments) shows near the green dot. Press the Shift key to continue the rotation.

• Zoom in:
  Select  Zoom In from the top toolbar.
• Zoom out:
  Choose  Zoom Out from the top toolbar.
• Zoom all:
  Select  Zoom all from the top toolbar.