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Administrator • In searching substructures, E-Notebook finds the substructure query regardless of its orientation or drawing presentation in the targeted molecules. E-Notebook does its best to follow your instructions even if those instructions are contradictory. For example, you can create a query such as the following: This indicates that the bond must NOT be in a ring Bonds All bonds explicitly drawn in the query must match in the target. E-Notebook recognizes the following standard bond types: Bond Type Single Dashed Description target must have single bond here same as Single Chn Hashed same as Single That bond is already in a ring, so no hits are returned for this query. General Properties E-Notebook allows the following general properties to be assigned to a query: • Atom • Bond • Substituents • Charges and radicals • Isotopes Atoms Atom types specified in the query must match atoms at corresponding positions in the target. Hydrogen is an exception see “Substituents”, below. Thick Wedged Hashed Wedged Wavy Hollow Wedged Dative Double same as Single specifies stereochemistry down from the point end to the wide end specifies stereochemistry up from the point end to the wide end specifies stereochemistry “either” at both ends same as Wedged same as Single target must have double bond; stereo dictated by geometry Double Either target must have double bond; any stereochemistry ok Double Bold same as Double 458• Searching <strong>CambridgeSoft</strong> Chemical Structure Search
Bond Type Description Finds: Does not find: OH Cl Triple target must have triple bond here HN O O NH 2 Substituents In E-Notebook, a substituent is defined as a nonhydrogen atom connected by a bond of any order. For example, a carbonyl oxygen is a substituent of the carbonyl carbon. All unfilled valences in the query may be filled by hydrogen atoms or by non-hydrogen substituents. The normal valence of an atom is determined from data in the periodic table. For example, carbon has a valence of 4, while sulfur has valences of 2, 4, and 6. Any explicit charges, radicals, or query properties modify the normal valence. For example, a carbocation has a valence of 3. Hydrogen atoms in the query may match nonhydrogen substituents in the target if the hydrogen in the query is implicit on an unlabeled carbon atom or heteroatom. Hydrogen atoms in the query must match hydrogens in the target when the query hydrogen is at the end of an explicit bond. The matched hydrogen in the target may be implicit in an unlabeled carbon. Query H H O N H H Charges and Radicals Charges or radicals specified on atoms in the query must match those in the target. The valence of a charged atom is taken to be the valence of the isoelectronic neutral atom With a Substructure Search: Query : Finds Br Br OH N NH 3 H 2 N NH 2 N O H H Does not find: OH NH 2 NH N OH E-Notebook N N OH <strong>ChemOffice</strong> 2005/E-Notebook Searching • 459 Chemical Structure Search
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CAMBRIDGESOFT ChemOffice Desktop to
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