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Chemical Literature (Chem 184/284) |
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The default option on the SciFinder Web Substance search screen is "Chemical Structure". Click the image of the substance drawing screen to search for substances (and, then, their associated references) by drawing structures or substructures.Note: Your workstation must be able to accept and run Java applets in order to use the structure search feature. The structure drawing applet will take a few moments to load. Be patient.
Structure and substructure searching is one of the most powerful features of SciFinder Web, reproducing the majority of the functionality of the command language electronic database, and providing far more powerful access than any print tool.
The structure input screen is rather complex, so here's a breakdown of the items on screen:
The icons from left to right are:
This area gives a description of the function of whichever tool (see the left hand toolbars) you currently have active.
| Pencil Tool -- Freehand drawing of atoms and bonds. Default atom is carbon, default bond is single. Click to place atoms, drag to draw bonds. | Eraser Tool -- Erase atoms or bonds with a click. |
| Atom Menu -- Click to get a periodic table of elements. Then click the desired element to select element as the current drawing atom. | Shortcut Menu -- Same function as Atom Tool, but provides frequently used groups of atoms (e.g. methyl, hydroxyl, carboxylic acid) | |
| Variable Groups Menu -- Same function as Atom Tool, but for variable groups, e.g. X = any halogen, M = any metal, Q = any atom other than C or H, A = any atom other than H. | User Defined R-Groups Tool -- Define an "R-group" containing atoms/shortcuts/variables. Example: R1 = N, X, MeO, CN | |
| Chain Tool -- Draws chains of 1-30 atoms. | Template Tool -- Use with Template Menu to place predefined structures. May not be attached to existing atoms/bonds, but atoms and bonds may be attached to structures once placed. | |
| Selection Tool -- Click on an atom/bond to select it; double-click for an entire structure. Can then move by dragging, delete, cut, copy, paste, etc. | Lasso Tool -- Click, hold and drag the lasso tool around structures or groups of atoms to select them. You may then click and drag that group, or delete it. | |
| Lock Out Rings Tool -- Click on a node, bond or structure to prevent rings from being fused to that site in a substructure search. | Lock Out Substitution Tool -- Click on a node to prevent substitution there in a substructure search. | |
| Rotation Tool -- Can be used to change orientation of a structure. Note that the orientation of the structure makes no difference when searching. | Flip Structure Tool -- Flips structures about a horizontal axis. As with rotation, the orientation of the structure does not affect searching, only display. | |
| Positive Charge Tool -- Use to place a positive charge on a node. Repeatedly clicking on the node increases charge. Note: Rarely useful for searching purposes. | Negative Charge Tool -- Use to place a negative charge on a node. | |
| Reaction Arrow Tool -- Used in reaction searching only. Will be discussed in the next set of lecture notes. | Reaction Role Tool -- Used in reaction searching only. Will be discussed in the next set of lecture notes. | |
| Reaction Atom Mapping Tool -- Used in reaction searching only. Will be discussed in the next set of lecture notes. | Reaction Bond Marking Tool -- Used in reaction searching only. Will be discussed in the next set of lecture notes. | |
| Functional Group Tool -- Used in reaction searching only. Can be used as a reference for how certain types of groups are drawn. |
Some general tips -- While you can do most functions in any order, I prefer to do the following:
First, use the ring drawing tools to draw in the ring portions of the structure -- the benzene ring tool for the benzene ring on the right, then the cyclohexane ring tool for the ring on the left. To attach the six-membered ring to the benzene ring on the right, place the cursor over the upper-right bond in the benzene ring. It should be highlighted in red. Then click, and a cyclohexane ring will be fused onto the benzene ring, as below:
Now, draw the chain connecting the two rings. Select the pencil tool, left-click on the starting atom in the cyclohexane ring on the left. Drag the tool a short distance and release the left mouse button, creating the first atom in the chain and its bond to the ring. Now click the left-mouse button again and drag (at a new angle, for easy viewing of where the atoms are). Repeat until you have six atoms in the chain, then click and drag from the last chain atom to the appropriate atom on the benzene ring to form that bond.
Continuing with the pencil tool, now draw in the other side chains on the rings and bridging chain. Don't worry about the fact that the atoms are carbon and the chains are all single bonds. We'll fix that part in a moment.
Now, we can use the Atom button, or the menu of atoms at the bottom of the screen with the pencil tool to change all the simple carbon atoms into oxygens where needed. Click on the "O" button at the bottom of the screen. Note how the window to the left of the buttons now shows an O. That is the current atom that will appear when you draw. Now, move the pencil too cursor over each atom in turn and click once to change it into an oxygen. Note that you don't have to draw in hydrogens; the system assumes that hydrogens will fill any unused bonds in your structure unless you specify otherwise.
Now let's assume that in my search, I don't want to allow substitution at any of the methyl groups or hydroxyl groups in the original drawing. I can use the Shortcut tool to select Me and OH groups for those spots. Click on "Short", then select the appropriate group from the table that appears. Note that when the cursor hovers over "Me", a structure diagram of a methyl group appears. Click on Me, then replace the appropriate carbon atoms, as you did with the oxygens above. Do the same to place the OH groups.
Finally, there are some single bonds that need to be changed to double bonds: the two ring C-O bonds and the cyclohexane C-C bond on the right of the right-most ring. To do that, change the atom back to C (click on the C button), then click on the double bond button in the row below it. Now move the pencil cursor to the appropriate bonds, make sure the bond is highlighted, then click to make the single bond a double bond.
Now, you're essentially done. You could add other restrictions, like locking one or both of the ring systems to forbid additional rings being fused to the system if you wanted. If not, then you're ready to select the type of search that you want: exact, substructure or similarity, and continue with your search.
"Filters" allows you to limit your search in advance to certain types of substances -- by class of substance, number of components, commercial availability, presence of references, or types of studies. Note that answer sets can be refined after the fact, but filtering in advance can sometimes allow very broad searches to run which would otherwise overload the system.
Note: if your structure would retrieve too many possible matches on a substructure search, the system will give you the option of modifying your search to limit it. See the error message below.
Once you have a structure search answer set, you can Analyze or Refine the set.
For example, here's a portion of the answer set from a search on "superconducting polymers" from 2004 to the present:
Clicking "Get Substances" gives the following set of substances whose Registry Numbers appear in the record set above.
I can now Refine by Structure Search to find, for example, just those compounds which contain a five-membered ring with sulfur in the ring and undefined bonds.
From the 239 substances I started with, I've found four sulfur-containing ring substances, of which two are polymers. I could then get references for the compounds of interest in this set, perhaps limiting to preparations or property studies.
Another use is to find structures where a particular substituent is desired, but the precise location of the substituent is unknown. Do a substructure search for the "parent" compound, then refine it by searching for the desires structure fragment (an atom, or a shortcut, or a drawn "piece" of structure.)
First, I search for Taxol using a "Substance Identifier" search on the name "Taxol".
Now, I'll copy that structure, ignoring stereochemistry, since simliarity searching will do so anyway:
If I wanted to, I could modify the structure with the structure drawing tools before proceeding. Now, I select "Similarity Search" and click "OK", then from the search screen, "Search". When the search is complete, rather than going directly to a substance answer set, I get a windown allowing me to select what degree of similarity (expressed as a percentage) I want in my answwer set. Note that there is an upper limit of 10,000 answer retrieved in a similarity search.
Here are some answers with a similarity score of 90-94% or higher. Note how the similarity score is listed to the right of the Registry Number for each answer.
The resulting answer set may then be refined, and used to retrieve references or reactions just like any other substance answer set. The Analysis options are not available for similarity search answer sets.