2D and 3D molecular drawing 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. Point on the canvas to place 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 (on the right) 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. (See "Add/Remove explicit H atoms" below.)

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. Select 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 click on the atom where you want to attach the new atom and bond.
   

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

• Choose a bond type: For 2D drawing (and mechanism), expand the bond menu by choosing the lower right of the bond button (left toolbar). Then, select a bond type. For 3D drawing, choose from the single, wedge, or dashed bonds on the toolbar.
  Expanded bond menu (2D drawing and mechanism)

  

  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 click on 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 (2D drawing only) , 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 choosing the lower right corner of the active bond). Then, chose 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.

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. Select 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

Cyclohexane chair left

Cyclohexane chair right

Staggered perspective

Eclipsed perspective

Newman staggered 1

Newman eclipsed 1

Newman staggered 2

Newman eclipsed 2

Oxane chair

Piperidine chair

1. Select a template from the Advanced Templates toolbar at the bottom (available for 3D drawing).
2. Place the template on the canvas.
3. Replace the appropriate hydrogens with the appropriate CH₃ or other groups.

   Never delete the hydrogen atoms or bonds in the template or directly attached to the template. Also, don't try to move them by dragging. This will break the chair conformation or Newman projection structures. Just replace them!