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Administrator HO HO HO N H H N N H H O OH OH O O OH Relative Tetrahedral Stereochemistry Relative Tetrahedral Stereochemistry, or RTS, specifies a given relationship between the centers. That is, a known orientation of the substituents with respect to each other, rather than a known absolute configuration. To specify this, centers are drawn, not with the standard hashed and wedged bonds, but with thick (bold) stereo bonds. Relative and absolute configurations may be registered separately in ChemFinder, and can be distinguished by various search options. The basic ChemFinder search philosophy can be summarized as follows: a more specific query is a more precise request, and should get fewer hits than a more general query. If the query represents a particular absolute configuration, it should hit only that; if it represents a mixture, it should hit any of the components. If you choose Same in the stereo search choices, you are requesting that whatever stereochemistry is specified in the query must match that of the target. If the query has relative bonds and RTS is activated, a hit must have the same relationship between centers. HO HO HO N H H N N H O OH OH O O OH MDL File Formats All bond styles available in ChemDraw are retained in CDX files. The same is not true of major MDL structure files: MolFiles, SDFiles, and RDFiles. In these formats, only three stereo bond types are available: hash, wedge, or either (squiggly bond); thick bonds are not recognized. This presents a problem for the ChemFinder user wishing to import or export structures having relative stereocenters. ChemFinder addresses this problem by using a proprietary tag in the file, recognized only by ChemFinder. The tag is BOND_RELS, and is applied to every stereo bond of thick type. For example, here is an excerpt from the bond table of a molfile with relative bonds. ... 4 5 1 0 0 0 0 2 6 1 1 0 0 0
• Mol- or SDFiles obtained from ISIS or other programs do not know about this tag, and thus cannot convey thick bonds. However, such files may be edited by hand to include the ChemFinder tag. • An MDL file written by ChemFinder, containing tags, should in principle be readable by any program which can import such a file. The unrecognized tags should simply be ignored. Normalization Closed rings of alternating single and double bonds match their alternative resonance forms if aromatic by the Hückel 4n+2 rule. With a full structure search and the Match Double Bond stereo option selected, the query: finds any of: OH does NOT find any of: Atom Properties ChemFinder allows special atom properties to be assigned to an atom in a query. These properties are usually only meaningful during a search. They generally serve to broaden or narrow the scope of the search. Special Atom Types ChemFinder recognizes six special atom types that can match any one of a predefined set of elements: • Amatches any non-hydrogen atom. • Qmatches any heteroatom (non-hydrogen, non-carbon). • Rmatches any atom, including hydrogen. • Xmatches any halogen (F, Cl, Br, I, At). • LNmatches a link node (placeholder for unspecified atoms). See “Searching Link Nodes and Multivalent Rs (MVRs)” on page 339 for details. • Mmatches any metal atom, shaded in the periodic table below: OH OH OH OH H O H O Atom Lists As with the predefined special atom types, an atom list is a list of atoms, one of which must match the target atom. For example: [Cl,Ag,N] atom must be Cl or Ag or N Appendices <strong>ChemOffice</strong> 2005/Appendix Structural Query Features • 681 Atom Properties
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