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View Compound Workbench

To move atoms, rotate bonds, and flip topology

To move atoms in the 2D workspace

In the 2D workspace you can move an atom, a bond, or a selected group of atoms and/or bonds without changing the positions of atoms and bonds that are not directly connected to the selected components:

  1. In the 2D workspace, select the atoms and/or bonds to be moved.
  2. Place the cursor over any of the selected items and press down the left mouse button. (If you do not press down exactly on a selected atom or bond, you will end up either drawing a selection rectangle or moving the whole molecule.)
  3. Keeping the button pressed down, move the mouse. The selected item or selected group of objects moves with the cursor. Release the mouse button when the selected items are in the desired location.
For example, you can draw a stylized chair conformer of a cyclohexane derivative in the 2D workspace:

  1. Start with the model produced by 2D Beautify. Select three contiguous atoms and their substituents.
  2. Place the cursor over any of the atoms you want to move and press the left button. Move the cursor. The atom under the cursor moves, and the other selected atoms move with it, maintaining the bond angles and bond lengths between the selected atoms.
  3. Release the button when the molecule is in a stylized chair conformation.

To flip topology in the 2D workspace

When you select a bond and it is highlighted with knurls, in the 2D workspace you can flip the topology around the bond by clicking one of the knurls. If several bonds are selected, only the last rotatable bond selected has knurls.

Notice that the stereochemistry display changes when you click knurl B and the stereocenter is flipped:

Dynamic modeling in the 3D workspace

In the 3D workspace you can rotate single bonds and flip rings, either statically or dynamically. When you perturb the position of some topology by bond rotation or by flipping a ring, the rest of the molecule dynamically adjusts its shape in response to the change, to try to preserve preferred bond lengths and angles. This adjustment is called dynamic modeling in Catalyst.

In the 3D workspace, when you select bonds or atoms and they display knurls, you can perform dynamic modeling as follows:

When you rotate a single bond, you can choose whether the rotation should be dynamic or rigid. If it is rigid, only the group at the rotating end of the bond changes its position. When you dynamically model a ring, other atoms and bonds in the molecule adjust their positions in response to the perturbations you introduce. You also can specify van der Waals forces for Catalyst to compute and apply during dynamic modeling.

For more information:

To rotate a single bond in 3D

When you rotate a single bond (using a knurl), you can choose whether the rotation is to be rigid or dynamic using the Modeling/Dynamic Bond Rotations menu item. If you choose rigid rotation, only the group adjacent to the knurl you are rotating moves. If you choose dynamic rotation, the atomic structure adjacent to the inactive knurl also dynamically adjusts its shape to maintain correct bond lengths and angles in response to the bond rotation.

To rotate a molecule about a bond:

  1. Select a single bond in the 3D workspace. If the bond can be rotated, a knurl appears at each end of the bond.
  2. Place the cursor over the knurl next to the part of the structure that you want to rotate, and press the left mouse button.
  3. Holding the button down, drag the cursor away from the molecule, keeping it in line with the knurl.
    The structure adjacent to the active knurl moves with the rotating bond.
    If the Modeling/Dynamic Bond Rotations menu item is toggled off, the rotation affects only the structure adjacent to the active knurl.
    If the Modeling/Dynamic Bond Rotations menu item is on, all atoms in the molecule adjust their positions in response to the bond rotation except for the atoms at each end of the highlighted bond and one additional atom connected to the inactive knurl end of the bond. These remain fixed, because there must be three fixed atoms to keep the molecule from moving or rotating while the bond is being rotated.
  4. Release the mouse button when the molecule is in the desired conformation.

To flip rings in 3D

You can manipulate the configuration of a ring (flip a ring) in a 3D workspace by rotating a knurl on an atom. However, you cannot dynamically model atoms at bridgeheads. Ring flipping in the 3D workspace is always dynamic, as other atoms and bonds in the ring move to adjust to the perturbations introduced.

To manipulate the configuration of a ring:

  1. Select an atom in the ring. If this atom can be moved, a knurl appears.
  2. Place the mouse cursor over the knurl. Press and hold down the left button.
    Move the cursor very slightly. The cursor turns into a hand. Move the hand slowly away from the atom, keeping it in line with the knurl to rotate it.

    The selected atom moves. All other atoms and bonds in the molecule adjust their positions in response to the atom rotation except for the two atoms connected to the moved atom and one additional atom connected to one of the fixed atoms. This third fixed atom is the one that has the least bond distortion and restoring forces acting on it. These three remain fixed because there must be three fixed atoms to keep the molecule from moving or rotating while the bond rotates.
  3. When you have finished moving the atom, release the mouse button. Wait for the molecule to stop moving before you move the cursor again.

To select additional forces for dynamic modeling

During dynamic modeling, the molecule adjusts its shape to try to maintain preferred bond lengths and bond angles when parts of the molecule are perturbed. You can select additional forces to be applied during dynamic modeling by switching on items in the Modeling menu.

The menu items on the Modeling menu are toggles. If a menu item is toggled on, a button to its left is highlighted and the selected force is applied during dynamic modeling. If a menu item is toggled off, no highlighted button appears at the left of the name and the force is not applied during dynamic modeling.

For example, if you want Catalyst to apply van der Waals forces during dynamic modeling, assure that the Modeling/van der Waals Forces menu item is on. If you do not want to apply van der Waals forces during dynamic modeling, make sure that the menu item is off.

Forces chosen with the Modeling menu apply to all types of dynamic modeling except for the Dynamic Bond Rotation menu item, which allows you to choose whether rotation about a single bond is to be dynamic or rigid.

To clean up and align molecules

You can clean up the shape of molecules and align the 2D and 3D molecules:

Examples

The following five pictures illustrate the use of the 2D Beautify, Generate Standard 3D, and Orient 3D to 2D menu items.

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Last updated April 2000.
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