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Administrator Atom lists may contain only elements. Special atom types, nicknames (Ph), and structural fragments (NH 2 , OCH 2 CH 3 ) may not be included in an atom list. ChemFinder recognizes a maximum of five atoms in an atom list. Atom Not-Lists The opposite of an atom list is a list of atoms, none of which must match the target atom. For example: [NOT O,S,Se] atom must not be O or S or Se (but may be any of the 100 other elements) Atom not-lists have the same restrictions as atom lists. Substituents: Exactly This property specifies a precise value for the number of substituents on an atom, including those explicitly drawn. This property is only meaningful in a substructure search. HO O Cl Substituents: Up To This property specifies a maximum value for the number of substituents on an atom, including those explicitly drawn. This property is only meaningful in a substructure search. O O With a substructure search, the query: With a substructure search, the query: X3 This atom is marked with the atom property Substituents Exactly:3 U2 This atom is marked with the atom property Substituents Up to:2 finds any of: does NOT find any of: finds any of: does NOT find any of: H HO O O CH 3 682• Structural Query Features <strong>CambridgeSoft</strong> Atom Properties
Substituents: Free Sites The Substituents: Free Sites property specifies the maximum number of additional substituents that may be present on an atom. This property is only meaningful in a substructure search. NOTE: Specifying Free Sites: 0 is a quick way to indicate that you want no further substitution at a site. Target structures will match the query structure as drawn, with no additional ligands. With a substructure search, the query: finds any of: Cl ∗2 This atom is marked with the atom property Substituents Free Sites:2 does NOT find any of: This property is only meaningful in a substructure search. NOTE: This atom property does not affect the display of implicit hydrogens, only their presence in a search. For more information about displaying implicit hydrogens, see “Setting Preferences” on page 341. Unsaturation Sometimes it is useful to specify that an atom must or must not be attached to unsaturated (aromatic, double, or triple) bonds. ChemFinder allows searches for atoms whose unsaturation Must Be Absent (all bonds to the atom are single). It also allows searches for atoms with at least one multiple (double, triple, or aromatic) bond. The default value, Undefined, finds targets without regard to the hybridization of the atom. This property is only meaningful in a substructure search. With a substructure search, the query: HO O This atom is marked with the atom property Unsaturation: must be present S O OH O O finds any of: does NOT find any of: Implicit Hydrogens This atom property may have either of two values: Allowed (default) or Not Allowed. If implicit hydrogens are Not Allowed, the atom must be fully substituted in the target. Appendices <strong>ChemOffice</strong> 2005/Appendix Structural Query Features • 683 Atom Properties
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