Product: ChemDraw
When I choose Check Structure or Analyze Structure, it says there is an invalid valence in a nitro group.
Because of its many resonance forms, there are many plausible ways to draw a nitro group. Three of the most popular ways are shown below, along with a discussion of how ChemDraw will interpret them.
| Structure | Analyze Structure | Discussion |
 |
Succeeds | This diagram observes the octet rule for all three atoms, at the expense of producing a structure that appears to be asymmetric. Nonetheless, this is the industry-standard way of drawing a nitro group. It will be recognized by most online and desktop databases, as well as ChemDraw. |
 |
Succeeds (Requires ChemDraw 4.0 or later) |
This diagram leaves the nitro group as an atom label. ChemDraw recognizes this structure as identical to the first and this diagram will be analyzed without problems. When writing files (such as MDL Molfiles) that require chemical meaning, this atom label will automatically be expanded into the first form, so it will also be recognized by most online and desktop databases. |
 |
Fails | This diagram produces a symmetric structure, but violates the octet rule to do so. Second-row elements such as sulfur and phosphorus can form five bonds, but the d orbitals in nitrogen are not accessible. Any diagram with five bonds to a nitrogen is a poor representation of experimental reality, and ChemDraw will indicate an error if you Analyze Structure or Check Structure on this drawing. |
Conclusion: The Analyze Structure and Check Structure commands in ChemDraw are designed to assist in finding errors in chemical diagrams. ChemDraw will mark anything that looks questionable. There is nothing wrong with drawing something that ChemDraw does not understand, such as the third diagram above. Live human beings are a lot smarter than computers, and will probably stay that way for a long time. As long as your drawing is clear to you and to the other people who look at it, ChemDraw's opinion doesn't mean much. You should always feel free to override any recommendations it makes.
(Note: similar issues are relevent for other sorts of nitrogen N-oxides and N-sulfides): 