Chem3D won't let me draw a phosphate group!
(I get an error message: 'No atom types defined for P(2)')
There are two common ways to represent a phosphate group in three dimensions: a) with a P=O double bond and two P-O single bonds and b) with three P-O single bonds, and a formal positive charge on the phosphorus. If you're getting an error message, you're probably trying to draw a phosphate group the first way, with a double bond.
While it is often common to see a phosphate groups drawn in two-dimensional structures with a P=O double bond, different standards apply when you work in three dimensions. In three dimensions, symmetry is very important, and a double bond would break the symmetry of the phosphate group (particularly in its ionic state). By default, Chem3D attempts to guide your drawings to the most reasonable three-dimensional structure. For this reason, you can draw ethane and Chem3D will automatically position all of the hydrogens to have 109 degrees between them, in a tetrahedral orientation around each carbon. This default behavior is also designed to prevent P=O double bonds.
Phosphate groups drawn with double bonds cannot be minimized using MM2. The default behavior also helps you to create structures that MM2 can analyze. The fastest way to draw a phosphate group - including the correct bonding for MM2 to recognize - is to select a hydrogen that you want to change, type PO3H2, and press enter. This will replace the hydrogen with a correctly-drawn phosphate group.
To create a phosphate group with a P=O double bond, you must turn OFF the Automatically Correct Atom Types preference in the Building section of the Preferences window. After doing this, you may draw a phosphate group from scratch, or you may change the P-O bond order in an existing phosphate group. After you have done this, you WILL NOT BE ABLE TO USE MM2 on the resulting structure. Depending on your version of Chem3D, attempting to minimize energy using MM2 will either produce an error message or an incorrect structure. In no cases will it produce a correct structure with a P=O double bond. (It is possible to modify the MM2 parameters to enable this, but doing so is far from easy. Please consult your manual.)
Again, if you want to accurately minimize the energy of a phosphate group using MM2, you CANNOT include a P-O double bond. The following table summarizes this discussion:
|3D Model||(2D Structure)||Analyses||Discussion|
|This model shows the correct way to draw a phosphate group so that it can be analyzed using MM2. One way to easily draw this model is to draw a bond (creating ethane), select the rightmost carbon, type PO3H2, and press enter. You may need to rotate the resulting structure to reproduce this orientation.|
|This model shows a representation of a phosphate group containing a P=O double bond. It cannot be analyzed using MM2, and can only be created by turning OFF the Automatically Correct Atom Types preference in the Building section of the Preferences window.|
Conclusion: Chem3D is designed to help you create accurate 3D models. It is possible to use it to create inaccurate models as well, but you must disable some of the default settings before you do so.