View Compound Workbench

To build a molecule

The easiest way to build a simple molecule is to place carbon atoms in the desired locations in the workspace. Then you can change the appropriate carbons to the correct element.

Here are some suggestions for building a molecule, starting with a View Compound workbench that has empty workspaces.

Selecting a currently active element or substituent

By default, carbon is highlighted in the Periodic Table as the currently active element, which means that when you click in the workspace, you place a carbon in that location. Or if you click an existing atom, you change it to a carbon (unless you have made some other component currently active).

To change the currently active element, first deselect everything in the workspace. Then select a different element by clicking its symbol in the Periodic Table. The button for the new currently active element is highlighted.

You can use keyboard shortcuts for placing the most common types of atoms and for changing the currently active element..

To select a substituent, first deselect everything in the workspace. Then click the appropriate menu title at the bottom of the Periodic Table and choose a substituent from the menu that appears. For example, to select the aldehydic form of the amino acid cysteine as the next group to be added to your molecule, select the Amino Acids/Cysteinyl menu item. The selected substituent becomes currently active, and its name appears at the right side of the Periodic Table.

Placing an atom or substituent in a workspace

Click in the 2D or 3D workspace. The currently active element or substituent appears in both workspaces. For elements, the currently selected element remains active; for substituents, the currently selected element becomes active again after you have placed the substituent. Catalyst automatically adds hydrogen atoms according to the chemical valence, while maintaining the correct coordination geometry. For example, if you click in the workspace while carbon is currently active, Catalyst draws a carbon atom bonded to four hydrogen atoms, with the four bonds arranged in a tetrahedral geometry.

By default, the 2D workspace does not show hydrogens, except for aldehydic and acetylenic hydrogens and hydrogens that are bonded to atoms other than carbon. (Such hydrogens are considered to be "important".)

By default, the 3D workspace shows all atoms. You can display the hydrogen atoms in the 2D workspace by selecting the View/Hydrogens/2D menu item from the workbench menu bar.

When the cursor is in the 2D workspace, a rubber band is connected from the cursor to the atom you just added (or to an atom you have selected).

Selecting the bond type and display style

Select a type of bond (left column of the toolbox) and a 2D display style (right column of the toolbox) for adding the next atom or group to the molecule. When you select a bond type or display style and nothing is selected in the workspace, that bond type or display style becomes active and its button is highlighted. Until you change the default, the single bond type and normal line display style are active.

buttons buttons

When you add another atom or group to the molecule, it is bonded with the currently active bond type. The bond appears in the 2D workspace in the currently active bond style.

Double-bond alignment in the 2D workspace

To change the alignment of the lines representing a double bond in the 2D workspace (illustrated below), select the double bond in the workspace and then select the Double Bond tool. Click the Double Bond tool several times, to cycle through the three different alignments. You also can cycle through the alignments by selecting the double bond and then pressing the equals key (=) several times to display each of the alternatives.

molecules

Placing the next atom or substituent

In the 2D or 3D workspace

Click the hydrogen that is to be replaced by the new atom or substituent. For example, suppose you want to add another carbon atom to methane to turn it into ethane. The 3D workspace in the figure below shows a carbon atom bonded to four hydrogen atoms. Click one of the hydrogen atoms to replace it with a new carbon.

molecules

In the 2D workspace

Click near the previously placed atom to add the next atom or substituent. The rubber band in the 2D workspace is always connected to the most recently added atom ro group.

Each time an additional atom or substituent is added, Catalyst makes sure that the appropriate number of hydrogen atoms are present.

Undoing mistakes

If you make a mistake, such as accidentally adding a substituent or accidentally changing a hydrogen to something else in the 3D workspace, you can delete the unwanted atoms by clicking the Erase tool in the toolbox or by pressing the <Backspace> or <Delete> key while the unwanted atoms are still highlighted. Catalyst deletes the selected items and, if necessary, restores the appropriate hydrogens.

Adding a different element or substituent

To add a different element or substituent, first deselect everything. Then select a different element or substituent from the Periodic Table. Finally, select the attachment point for the new atom or group.

To deselect all items, you can click the Deselect tool in the toolbox. Alternatively, you can drag out a small empty selection rectangle in an empty area of the workspace.

button

To add a different type of component in the 2D workspace, click the atom to which to bond the new atom or group, then click in the workspace where you want the new component to appear. Or, in the 2D or 3D workspace, click the hydrogen that you want to be replaced by the new atom or group.

Changing the element type after placing an atom

To change the element of an atom (other than a hydrogen) after it has been placed in a workspace, first select the atom in either workspace, then click the element you want to change it to in the Periodic Table. The selected atom is converted to the selected element. You can do the same with hydrogen if you select it first with the extend-select method (using the middle mouse button).

Changing the type or style of a bond after you have placed it

To change the bond type or display style of a bond after it has been placed in a workspace, first select the bond in either workspace. Then from the toolbox select the bond type or display style to which you want to change it. Catalyst converts the selected bond to the selected bond type or style.

Closing a ring

To close an open ring, make sure that one of the unconnected atoms is selected in the 2D workspace. Then click the atom to which you want to bond the selected atom to close the ring, as shown below. A bond of the currently active type appears between the two atoms.

molecules

To close a ring in the 3D workspace, use the technique described in To add bonds (close rings) in the 3D workspace.

Deselecting to stop building a molecule

Deselect the atom or group you just added by clicking it in either workspace. To deselect everything that is selected, click the Deselect button in the toolbox or draw an empty selection rectangle.

Cleaning up a molecule

To display molecules in a standard configuration in the 2D and 3D workspaces, select the Tools/2D Beautify/Generate Standard 3D menu item from the workbench menu bar.

Saving intermediate versions of a molecule

If you want to save an intermediate version of a molecule you are building -- for example, as a basic fragment from which you will create several related molecules -- you can use the Save as a Local Object menu item.

Saving the molecule to the Stockroom or a lab

When you have finished building the molecule, save it by selecting the Data/Save To Lab As menu item. See To save an object to a lab for details.

Clearing the workspaces

To clear the display, select the Edit/Clear Display menu item. This action deletes all objects from both 2D and 3D workspaces.

Warning: Any unsaved molecules that were displayed in the workspace are lost.

Summary of rules for selecting components

When you select an element button or a substituent menu item in the Periodic Table:

If no atoms are selected in the workspace, the selected Periodic Table element or menu item becomes the currently active element or substituent. No change occurs in the workspace.
If one or more atoms are selected in the workspace, each one changes to the type that is selected in the Periodic Table. If you selected an element from the Periodic Table, the currently active element does not change after the change is made in the workspace. If you selected a substituent from the Periodic Table, the currently selected element becomes active again after the change is made in the workspace.

When you select a bond type button or a bond display style button from the toolbox:

If no bonds are selected in the workspace, the selected bond type or display style becomes the currently active bond type or display style. No change occurs in the workspace.
If one or more bonds are selected in the workspace, each one changes to become the type that is selected in the toolbox. The currently active bond type or style does not change.

When you add or change an element, substituent, or bond, Catalyst uses the currently active type of element or substituent and bond. There is always a currently active type of bond and element or substituent.

The currently active bond type, bond display style, and element are indicated by having their buttons highlighted. For example, when carbon is the currently active element, the C button in the Periodic Table is highlighted. When a substituent is currently active, its name appears in the right side of the Periodic Table.

Clicking in the 2D or 3D workspace

Each time you click in an empty part of the 2D or 3D workspace, an atom or substituent of the currently active type is added to the workspace. If a new bond is created, it uses the currently active bond type and style.

If there is a selected component with a rubber band attached, clicking in the 2D workspace attaches the new component to the atom from which the rubber band extends. If there is no rubber band visible, the new component is added to the workspace as a separate molecule, not connected to any existing component. You can join separate molecules by creating bonds between them.

To add an element or substituent of the currently active type to an existing molecule, click the hydrogen atom to be replaced by the new atom or substituent.

Ionizing and deionizing atoms

When you add an atom to the workspace in the View Compound workbench, it is a neutral atom. You can adjust its ionization state by protonation or deprotonation. For example, an amine nitrogen can be protonated to form an ammonium ion, and a carboxyl group can be deprotonated to form a carboxylate ion. You can restore any charged atom to its uncharged state by selecting the atom and then selecting the element for that atom in the Periodic Table.

To protonate an atom

In Catalyst you can protonate nitrogen (to form an ammonium ion), phosphorous (to form a phosphonium ion), or any other atom that has a charge of zero or less and a coordination number less than 4.

For example, to protonate nitrogen:

Display the nitrogen compound in the 2D workspace of the View Compound workbench.
Select the atom to protonate. A rubber band extends from the selected atom.
Select the Tools/Chemistry/Protonate menu item. A new hydrogen appears, and the atom to which the hydrogen was added increases its charge by one.

To deprotonate an atom

You can reduce the charge on an uncharged or positively charged atom with an attached hydrogen by removing the hydrogen from it:

Display the compound in the workspace of the View Compound workbench.
Select the hydrogen to be removed by using the extend-select method. Or you can draw a region-selection rectangle around the hydrogen.
Select the Erase button in the toolbox or press the <Backspace> or <Delete> key.
The selected hydrogen disappears, and the charge on the atom to which it was connected is reduced by one.
You can delete additional hydrogens, if necessary, to increase the negative charge.

To restore an atom to its un-ionized state

Whenever you select an element or group in the Periodic Table when one or more atoms is selected in the workspace, the selected atoms are converted to the currently active element or substituent in the Periodic Table. You can use this feature to remove the charge from charged atoms:

Select the charged atom.
Click the element of the charged atom in the Periodic Table. For example, if you selected a charged oxygen atom, click O in the Periodic Table.
The selected atom is restored to its usual valence, with its correct complement of hydrogens.

[Top] [Index]