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Administrator To create the hitlist for the first part of this search: 1. Open the CS_Demo database. 2. Create the first query by drawing benzene in the Structure data box and entering 50-200 in the Molecular Weight Data Box. 3. Search the query. You get 75 hits. 4. From the Search menu, choose Save List. 5. Save the hitlist as benz.txt. To create another hitlist for the second part of the search: 1. Draw the query shown below in the Structure Data Box. If you had chosen the Replace current list option in the last step, then only the C-N records would be displayed. Choosing Intersect with current list would display those records in either list. Finally, choosing Union with current list would display all records from both lists. Using Atom Lists Using the text tool in ChemDraw, you can enter in a structural query a list of possible atom types, one of which must match in the target compound. If you want to search for molecules containing a benzene ring with an ether, amine or phosphane group, a query might look like the following: [O,N,P] C 2. Search the query. You get 103 hits. 3. From the Search menu, choose Save List. 4. Save the hit list as c-n.txt. Integrate the two hitlists: 1. From the Search menu, choose Restore List. 2. In the Open dialog box, open the benz.txt file. 3. In the Restore List dialog box, click Replace current list, and then click OK. You return to your first list of 75 hits 4. From the Search menu, choose Restore List. 5. In the Open dialog box, open the c-n.txt file. 6. In the Restore List dialog, click Subtract from current list, and then click OK. The hit list is reduced to the 60 records with compounds containing a benzene substructure, not containing a C-N substructure, and having molecular weights between 50 and 200. N Atom Types and Bond Types To broaden or narrow a search query, you can define the properties of the atoms and bonds in a structural query. These properties are definable in ChemDraw Pro using the Atom Properties and Bond Properties dialogs accessible from the Structure menu. Suppose you want to find all molecules that contain a non-oxygen chalcogenide bonded to another atom, not necessarily carbon. You also want the bond type between the chalcogen and the other atom to be a single or double bond. The query, drawn in ChemDraw Pro, may look like this: A S/D [S,Se,Te] This atom may be any non-hydrogen atom This bond may be single or double This atom must be S, Se, or Te 338•Searching <strong>CambridgeSoft</strong> Search Examples
The “A” label denotes that the atom may match any atom except hydrogen. The indicator near the bond indicates that the bond has been defined; in this case, in the Bond Properties dialog of ChemDraw, you specified that the bond type may be single or double, S/D. Finally, by entering “S,Se,Te” enclosed in brackets, you specified that one of these elements must match in the target molecules. Searching Link Nodes and Multivalent Rs (MVRs) ChemFinder versions 8 and later contain a new atom type, the link node. A link node is a placeholder for zero or more unspecified atoms. It is especially useful when searching for targets with any of several ring sizes, or chains substituted in particular ways at either end. While link nodes are traditionally divalent, ChemFinder places no constraints on the upper limit of the range. Multivalent R (and A) atoms are functionally similar to link nodes. They may be thought of as “higher valent” link nodes. O (CH 2 ) 1-2 Br (CH 2 ) 0-200 Br Searching Fullerenes A search of fullerenes can illustrate the restrictions you can place on a formula search. Suppose you want to find all fullerenes containing 20 to 80 carbon atoms, but you also do not want to include large organic molecules. The formula query could be: C20-80 H0 By designating zero hydrogen atoms, you exclude hydrocarbons from the hit list. By clearly capitalizing the elements and spacing the query, you avoid searching ambiguities, although there were no ambiguities in this example. Hits cyclopropanones, cyclobutanones, and ß-lactams Cl Ph A A multivalent “A” query Hits alpha, omegadibromides and bromine Cl Ph (LN) 1-999 The traditional representation of a link node is CH2, but this is misleading because any atom type can substitute for the link node. For this reason, ChemFinder represents link nodes as LN. NOTE: ChemDraw recognizes link nodes, but does not support an “LN” atom type. Use (R) instead of (LN) when drawing the query in ChemDraw or with the ChemDraw ActiveX control. Although any atom type of a target atom matches a link node, you can impose two restrictions the on the link node: • Unsaturation • Ring topology. ChemFinder <strong>ChemOffice</strong> 2005/ChemFinder Searching • 339 Search Examples
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