Making and Breaking Bonds

Making and breaking bonds—changing the connectivity—is central to building structures. There are several ways you can make and break bonds in Maestro. Closely related to this is increasing or decreasing the bond order: for this task, see Changing Bond Orders, Formal Charges, and Elements.

When you make or break bonds, hydrogens can be added or removed to satisfy the valence of the bonded atoms. This behavior is controlled by the Adjust number of hydrogens following build operations preference, under Builder - Behavior settings in the Preferences Panel.

Using the 3D Builder

The 3D Builder offers two tools for making and breaking bonds:

To make a bond between two atoms:

  1. Select the two atoms you want bonded.
  2. Click the Add bond button.

A single bond is added between the atoms. If they are already bonded, the bond order is increased, so you can click multiple times to create a multiple bond.

To break a bond between two atoms:

  1. Select the bond you want to break.
  2. Click the Delete bond button.

The bond is broken, regardless of the bond order. This is different from decreasing the bond order to zero, which creates a zero-order bond so that the connectivity is still registered in applications that need it.

This tool allows you to break more than one bond. If you select multiple atoms, any bonds between the selected atoms are broken when you click the Delete bond button.

Using the Draw Tool in the 3D Builder

The Draw tool also allows making and breaking of bonds. To display this tool, click the Draw button in the 3D Builder panel.

To draw a bond between two atoms:

  1. Select the Draw tool in the Draw Structure banner.

    The pointer changes to a pencil.

  2. Drag with the left mouse from one atom to the other atom.

You can draw bonds between atoms that are already bonded, to create multiple bonds.

To erase a bond between two atoms:

  1. Select the Erase tool in the Draw Structure banner.

    The pointer changes to an eraser.

  2. Click the bond you want to erase, or drag over the bond.

    One bond is erased on each click, so you need to click multiple times if it is a multiple bond.

Using the Workspace Tools

The selection shortcut menus in the Workspace offer tools for adding and deleting bonds. These have the same behavior as the tools in the 3D Builder.

To make a bond between two atoms:

  1. Select the two atoms you want bonded.
  2. Right-click on one of the atoms and choose Add Bond.

A single bond is added between the atoms. If they are already bonded, the bond order is increased, so you can repeat this operation to create a multiple bond.

To break a bond between two atoms:

  • Right-click on the bond you want to break and choose Delete Bond.

To break several bonds at once:

  1. Select the bonds you want to break.
  2. Right-click on one of the bonds and choose Delete Bond.

Note that if you select multiple atoms, any bonds between the selected atoms are broken when you choose Delete Bond. So if you select two bonds that have one bond between them, the bond in between is also broken. To preserve the bond in between, you must break the bonds separately.

Creating Zero-Order Bonds

Zero-order bonds are used to represent ionic bonds or dative bonds to metals, and are drawn with a segmented line or tube. You can create a zero-order bond from any bond by decreasing its bond order to zero. For metals, there is a tool in the 3D Builder panel for creating zero-order bonds to neighboring ligand atoms that are within the appropriate range for a metal-ligand bond.

To create zero-order bonds to metals:

  1. Select the metal atoms.
  2. In the 3D Builder panel, click Other Edits

    and choose Create Zero-Order Bonds to Metals.