Building structures: Specifying non-carbon atoms
- Put in Pencil tool mode
- Use Common Atom Palette or go to Draw in menu bar. Choices include:
- Note ability to Exclude an atom at a certain position
|A||anything, except hydrogen|
|Q||anything, except carbon or hydrogen|
|M (*)||any metal|
|Ak||any carbon chain|
(*) Metals are defined as all elements except Ar, As, At, B, Br, C, Cl, F, H, He, I, Kr, N, Ne, O, P, Rn, S, Se, Si, Te, Xe.
Variable points of attachment
- Draw non-carbon atom that you want to be attached in more than one location on blank screen next to structure.
- Select Rectangle tool from tool bar. Highlight non-carbon atom by clicking once with Rectangle tool. Now highlight locations for variable points of attachment on main structure.
- Go to Draw menu bar and select Variable Points of Attachment.
- Lines should appear to indicate where the bonds occur for the VPA. If the lines do not appear, go to the Display menu bar and choose Show VPA.
- Select Draw from menu bar. Choose G-Groups.
- New G-group: Choose New.
- Modify existing G-group. Choose Modify.
- Choose atoms, shortcuts, or variables to define G-group.
- Specify single or multiple use and then place G-group in structure.
Precision vs. recall
|Most Specific <-----------------------------------> Most Generic|
- A = any node that is not hydrogen
- Ak = any chain carbon
- Cb = any carbocycle
- Cy = any cyclic group
- Hy = any heterocycle
- M = any metal
- Q = any node that is not carbon or hydrogen
- R = non-structural group
- X = any halogen
Tip: Do not use R in structure queries.
- What you draw is what you get
- Potential values: Ring, Chain, Ring/Chain
- Changing a node characteristic does not change the value of a bond characteristic.