Structure searching in CAS Online using STN Express:
An introductory workshop

Building structures: Specifying bonds

  • Put in Pencil tool mode, then:
  • Use Common Bond Pallette or go to Draw in menu bar and choose
    • Single
    • Double
    • Triple
    • Unspecified
    • Stereo (many compounds lack stereo coding)
  • Specifying bond characteristics
    • Ring
    • Chain
    • Ring/Chain
  • Bond values and characteristics determine the precision of the search
    • Unspecified, Single/Normalized, and Double/Normalized allow for variability
    • Single, Double, Triple, and Stereo restricts answers
    • Using default bond characteristics restricts the answers. Use Ring/Chain to allow for variability.
    • Changing the characteristics of a bond will change the characteristics of a node.

Normalized Bonds

There are 3 general situations when you have to allow for normalized bonds:

  1. In a ring or ring system that contains alternating single and double bonds
  2. When the structure contains atoms described by the “tautomer rule”
    • Tautomers as defined in structure searching do not always correspond with the chemists’ definition for tautomers. The notable difference occurs with the keto/enol tautomers of aldehydes and ketones.
    • Normalized bonds in tautomers are specified when:
      H 1 - 2 = 3 <--> 1 = 2 - 3 H
      1. A central atom (2) is connected to two hetero atoms (1 and 3)
        • 2 may be: C, N, P, As, Sb, S, Se, Te, Cl, Br, I
        • 1 and 3 may be: N, O, S, Se, Te (may not be C)
      2. A double bond can be drawn between one of the hetero atoms (1 and 3) and the central atom (2)
      3. A single bond can be drawn between the central atom (2) and the other hetero atom (3 or 1)
      4. One of the hetero atoms (1 or 3) has at least one hydrogen, hydrogen isotope, or charge
    • Exact bonds are specified if one or more of the above conditions is not met
  3. When your structure contains overlapping structural features that meet the above requirements