Changing Bond Orders, Formal Charges, and Elements

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Once you have built a structure, you may want to make changes in connectivity, formal charges, or the elements that make up the structure. When changes are made, by default Maestro automatically adds or removes hydrogen atoms to ensure that the valence is satisfied. This behavior is controlled by a preference (see Behavior settings in the Preferences Panel). It is possible to make changes that violate valence, particularly when drawing, so you should check the structure after making changes.

Changing bond orders

Bond order changes are done by increasing or decreasing the order, rather than setting the order to a particular value. You can decrease the bond order to zero, which maintains the connection between the atoms, but there is considered to be no covalent bond. Zero-order bonds are used to represent ionic bonding and noncovalent interactions; most interactions with metals are formally considered as ionic or dative bonds, with a zero formal order. Breaking and forming bonds also changes the bond order, of course. See Drawing Structures for more information.

When the bond order is changed, hydrogen atoms on either end of the bond are added or deleted, to maintain valency; however they are not added if the valence is filled (or over-filled). The addition of hydrogen atoms is controlled by a preference, under Builder - Behavior in the Preferences Panel; the preference is on by default.

To change the bond order for one bond, right-click on the bond and choose Increase Bond Order or Decrease Bond Order.

If the 3D Builder is open, to change the bond order, do the following:

  1. Select the bond that you want to change.

  2. Click the Increase bond order or Decrease bond order button.

You can change the bond order for several bonds at the same time, by selecting the bonds and then using one of the above methods.

If the atom selection for changing the bond order includes adjacent bonds, the bond order change applies to every other bond (alternating bonds), not to all bonds. For example, if you selected all the carbon atoms in butane, three bonds are selected, but only the first and third are affected when you change the bond order. Bonds in a ring can also be changed, but if the entire ring is selected, the alternating bond pattern is ambiguous, and so the bond orders are not changed. If the number of bonded atoms in the chain is odd, the ambiguity is resolved by starting from the atom with the lowest atom number.

If you are drawing a structure in 3D (from the 3D Builder) you can do the following to change the bond order:

  • In Draw mode, click a bond to increase its order by 1.
  • In Erase mode, click a bond to decrease its order by 1 if its order is already greater than 1. If it is already a single bond, the bond is deleted.

See Drawing Structures for more information.

After changing bond orders, the structure will not be optimal, so you should consider minimizing it before using it for modeling.

To assign bond orders to structures that do not have the correct bond orders, choose Edit → Assign → Bond Orders . Bond orders are assigned as follows:

  • If you have a Workspace selection that is 300 atoms or less, bond orders are assigned for all the selected atoms.
  • If the selection has more than 300 atoms, bond orders are assigned for all residues in the selection that do not have any multiple bonds.
  • If there is no selection, bond orders are assigned for all residues in the Workspace that do not have multiple bonds.

The assignment is based on a range of factors, including connectivity, bond length, bond angles and dihedral angles. Occasionally the bond order cannot be assigned, or is assigned incorrectly. You should always check your structure after using this command, especially for bonds that are unusual in any way. If you find any errors, you can correct them using the 3D Builder.

In the Materials Science profile, this item is Unsaturated Bond Orders, and it sets the bond order for multiple bonds regardless of the number of atoms. The main difference occurs if the selection has more than 300 atoms: if a residue already has one multiple bond but others have not been assigned, they are not assigned in the default Maestro profile, but they are assigned in the Materials Science profile.

Bond order assignment is done automatically when you prepare proteins with the Protein Preparation Workflow Panel.

Changing formal charges

Formal charges are changed with the tools in the 3d Builder. To change formal charges:

  1. Select the atoms that you want to change.

  2. Click the Increase formal charge or Decrease formal charge button.

Formal charges on atoms are used when force fields are assigned in molecular mechanics or dynamics calculations, and other kinds of classical simulations. They are not used in quantum mechanical calculations.

Changing to a different element

It is often useful to quickly build a structure from carbon-based pieces, and then change the carbon atoms into other elements. There are a few ways to change the element. The first step is to select the atoms you want to change.

If you have the 3D Builder panel open, you can do one of the following:

  • If the element symbol is a single letter, type the upper-case letter (e.g. use Shift+H for hydrogen). For Cl you can use Shift+L).

  • If the element is displayed on the Set element button, click the button.

  • Click the arrow on the Set element button, and click the element symbol in the palette, if it is present. If not, click the More (dots) button in the palette to open a periodic table and then select the element.

You can also change the element by using the Workspace shortcut menu:

  1. Select the atoms you want to change.

  2. Right-click on the selection and choose Set Element.

  3. Click the element symbol in the palette, if it is present. If not, click the More (dots) button in the palette to open a periodic table and then select the element.

The atoms are changed to the new element. The element you just used is displayed on the Set element button in the 3D Builder, and if it isn't already shown in the elements palette, it is placed in the first of the two cells at the bottom, which are for the most recently used elements.

By default, the number of hydrogen atoms is changed to satisfy the valence. If it is not possible to change the number of hydrogen atoms (or if the preference to do so is turned off), the charge on the new element is changed instead. So for example, if you change a carbon in benzene to a nitrogen, the hydrogen atom is removed if the preference is on, but if it is off, the hydrogen remains and the nitrogen is given a +1 formal charge. Any unpaired electrons are preserved when hydrogens are added or removed.