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Administrator The hit list will include the following: OH OH The dot indicates an atom shared between the two fragments. The hit list will not include this molecule if the overlap option is deselected. Full Structure Searching Selecting the Full Structure radio button in the Search Type Preferences finds structures that completely match the query. You may get more than one hit if there are duplicates in the database or if there are stereoisomers in the database and you did not specify a particular one to be matched. For more information, see “Stereochemistry” on page 322. Stereochemistry You can specify whether or not you want a structure search to consider stereochemistry. Given a structure with one or more stereocenters, you can store four different possibilities: • A given absolute configuration. To specify this, centers must be drawn with stereo bonds, and the entire structure marked Abs (CHIRAL). • A racemic mixture of the drawn configuration and its mirror image. This is drawn as above, but without the Abs (CHIRAL) mark. • An unmarked structure, representing unknown stereochemistry, or a mixture of all possible stereoisomers. • A given relationship between 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 stereo bonds. If these options are checked in the Search tab of the Preferences dialog, then any stereochemistry indicated on the query must be matched by the target. For more information on changing searching preferences, see “Setting Search Details Preferences” on page 327. 3D Properties 3D queries are particularly useful in pharmacophore searching where you are looking for a particular 3D relationship among atoms and bonds, for example in a series of potential receptor ligands. You can create a 3D query in ChemDraw Pro by adding geometries (lines, planes, etc.) and constraints (specified as ranges) to a query structure. For example, you might specify that two atoms must be between 4Å and 5Å apart, or that two planes must be separated by 80-100°. ChemFinder can then use these properties to refine a search. See the ChemDraw User’s Manual for information on how to add 3D properties to structures. Reaction Searches You can search and store reactions. In a reaction, one or several compounds (reactants) are transformed into other compounds (products). Individual reactants (or products) are separated from each other with plus signs. The reactants are separated from the products with an arrow. Reactions may have multiple steps, for example (A) (B) (C) (D). Here, (A) is the reactant and (D) is the product. (B) and (C) are intermediates for the complete reaction. A multi-step reaction is actually a shorthand notation for many related reactions. In the example above, (B) is an intermediate for the complete reaction, but it is also a reactant relative to (C) or (D). It is also a product relative to (A). The 322•Searching <strong>CambridgeSoft</strong> Reaction Searches
complete reaction implies many subreactions, such as: (B) (D) and (A) (B). Reaction Centers The most important part of a reaction is the part that actually changes from the reactants to the products. This part, which probably includes a number of atoms and bonds, is called the reaction center. For example, only the bold bond below (and the two atoms on either side) is part of the reaction center. The rest of the structure is unchanged from the reactant to the product: By default, ChemFinder considers reaction centers whenever you search for reactions. ChemFinder assumes that any atoms and bonds that change in the query must be part of the reaction center of the target. For example: does not hit O F Cl F Cl F Cl OH compound. If you deselect the Reaction query must hit reaction center preference, this query hits the target above. When creating reaction queries, it is important to consider what sort of information you are really looking for. Suppose you want to convert n-decanal to n-decanol: Are you really interested only in these two compounds? You might be interested in any reaction that converts a straight-chain aldehyde to the alcohol: H H H O Since the corresponding n-octanal n-octanol reaction would probably occur under very similar conditions, it is a reasonable thing to look at. Generally, you want to use substructure queries that include little beyond the reaction center in question when you are searching for reactions. O OH H H H OH ChemFinder O F Cl F Cl when the Reaction query must hit reaction center preference is selected. Even though there is a C-F bond in the target reactant and a C-Cl bond in the target product, these bonds do not participate in the reaction, which really affects another part of the OH NOTE: ChemFinder supports several query properties to allow you to specify exactly how a bond participates in a reaction center. For more information about these properties, see “Setting Search Details Preferences” on page 327. Atom-to-Atom Mapping The second most important part of reaction searching is the atom-to-atom map. You can specify maps in ChemDraw, where they are stored <strong>ChemOffice</strong> 2005/ChemFinder Searching • 323 Reaction Searches
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A Guide to CambridgeSoft Manuals An
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