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Chemical Literature (Chem 184/284) |
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The top right option on the SciFinder Scholar Explore screen is "Chemical Structure". Selecting this option allows your to search for substances (and, then, their associated references) by drawing structures or substructures.
Structure and substructure searching is one of the most powerful features of SciFinder Scholar, reproducing the vast 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:
This area gives a description of the function of whichever tool (see the left hand toolbars) you currently have active. The Help icon at the right will take to to the Help pages for structure drawing.
| Pencil Tool -- Freehand drawing of atoms and bonds. Default atom is carbon, default bond is single. Click to place atoms, drag to draw bonds. | Chain Tool -- Draws chains of 1-30 atoms. |
| Atom Menu -- Click and hold mouse button to get a periodic table of elements. Drag cursor to desired element and release to select element. | 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 | |
| Repeating Group Tool -- Lets you use a "click and drag" tool to put a box around any group of atoms you wish to have repeat. Then enter the range of repetitions (from 0 to 20) in the box in the Info Bar. | Variable Attachment Position Tool -- Used to allow a given subtituent to be attached at any selected position on a ring structure. Draw the ring, then draw the substituent off to one side. Then use the Variable Attachment tool to click on the substituent and drag it to each ring atom you want as a potential site. Note that this cannot be used on chains, only on rings. | |
| Cyclopentadiene Tool -- Lets you place a cyclopentadiene ring with one click. Can attach to existing atoms or bonds. | Cyclopentane Tool -- Lets you place a cyclopentane ring with one click. | |
| Benzene Tool -- Lets you place a phenyl ring with one click. | Cyclohexane Tool -- Lets you place a cyclohexane ring with one click. | |
| 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. | Variable Ring Tool - Place 3-15 member rings using current atoms and bonds. | |
| Eraser Tool -- Erase atoms or bonds with a click. | 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. | |
| 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. | Rotation Tool -- Can be used to change orientation of a structure. Note that the orientation of the structure makes no difference when searching. | |
| 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. | |
| Lock Out Substitution Tool -- Click on a node to prevent substitution there in a substructure search. | Lock Out Rings Tool -- Click on a node, bond or structure to prevent rings from being fused to that site in a substructure search. | |
| Reaction Site Marking Tool -- Used in reaction searching only. Will be discussed in the next set of lecture notes. | Reaction Role Tool -- Used in reaction searching only. | |
| Reaction Arrow Tool -- Used in reaction searching only. | Reaction Mapping Tool -- Used in reaction searching only. | |
| 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, then replace the appropriate carbon atoms, as you did with the oxygens above.
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 click "Preview" or "Get Substances" and continue with your search.
Options which do not apply to the structure you have drawn will be greyed out. Select the desired option and continue.
In "Real Atom Attachments", click on the atom whose possible substituents you want to check. You can choose to modify your structure by selecting one of the possibilities which appear in the right hand box.
Similarly, "Preview Variable" shows what the matches are for variables you may select.
"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.
"AutoFix" will generally lock out ring fusion. You can also specify a range of molecular weights to limit the search.
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":
Doing "Get Related: 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.
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".
Then, I can select the Registry Number and Copy it (using the Copy item on the Edit menu). Now, I open a Explore by Chemical Structure search, and Paste the structure for Taxol into the search window. Alternatively, I could click on the structure in the taxol substance record, and select "Explore by Chemical Structure" from the menu that appears. Either way, I now have the structure for taxol available for searching (with modification if I choose) without drawing in the structure by hand.
If I wanted to, I could edit the structure with the structure drawing tools before proceeding. Now, I click on Get Substances, and select "Similarity Search". In this case, since Taxol has a specified stereochemistry, I receive a warning that similarity searching ignores stereo bonds. 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 98% or higher. Note how the similarity score is listed below 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.
On the other hand, Refining a substance answer set lets you search for very common structural elements within an existing answer set. Attempting to do the same thing by combining sets would fail, because the "common" answer set would exceed system limits.