Second left-hand vertical tool bar:
Bertical tool bars on the righthand side of the drawing window:
This tool allows you to specify that a given atom/group may be attached at multiple possible points on a ring structe. To do so, draw the ring structure, then draw the desired atom/group as an unattached fragment, and clig on the Multiple Points of Attachment tool, then click on the fragment, and draw lines to the desired ring atoms. Below is an example using a Cl atom and a naphthalene ring.
Note how the resulting structure shows a solid line from the Cl tothe center of one of the naphthalene rings, with dotted lines going to the selected ring atoms.
To create an R-group including structure frangments, first draw each individual frgment you wish to create. In the example below, I created an amide group, a triphenylsilyl group and a alkyl, sulfonyl group. Then, click the Fn tool, and click on the point of attachment you desire on each fragment. Note that if you want to use a fragment as a bridging group, you can create multiple points of attachment on the same fragment.
Note how each attachment point is labeled, and the fragment as a whole hs an F-number assigned.
Then, click on the R tool, choose an unused R number, and select the atoms, variables shortcuts or fragments you wish to include in the R group. Fragments will appear in a table at the bottom of the R-group window. In this case, R1 includes fluorine, trifluoromethyl, and the three structure fragments I drew. I could now close the window and attach R1s wherever I want in my desired molecular structure for searching.
With the tools above, drawing structures in SciFinder-n is relatively straightforward. SciFinder automatically checks for "normalized" bonds in aromatic structures or tautomers.
Some general tips -- While you can do most functions in any order, I prefer to do the following:
As an example, let's take a look step-by-step at the drawing of the structure of feropolone (Note: the screenshots below were made with the CASDraw editor, but the procedure is essentially the same ith the ChemDoodle editor.
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 t or chain tool, draw a six-membered chain, then use the pencil to bond to the ring.
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, use the Shortcut tool to add methyl (Me) and hydroxyl (OH) groups where needed. Notice that whenever your cursor hovers over a shortcut group, either in the table of shortcuts or in the drawing window, CAS Draw shows you what the fully drawn out shortcut would look like.
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.
Always check over your structure before clicking OK. If you made a mistake and forgot to check it, you can always come back and fix it, but it saves time to check it over first.
The structure search box appears at the right. Note that you can return to the editing tool or remove the structure. You can also add other substance search terms to search with the structure.
We will discuss the Patent Markush search option below.
When you click OK after creating a structure, you get back a substance answer set. The initial answer set display for feropolone is shown below:
Note that the display above is basically the same as for the aspirin etc. answer set EXCEPT for the indication of "as drawn", substructure and similarity answer sets.
Here's another example. The structure drawn is that of dibenzothiophene. After clicking OK we come to this screen:
In SciFinder-n, Markush structure searching is separate from the "as drawn"/substructure/similarity searching. In part, this is because the markush search does not retrieve specific substances. Rather it retrieves Markush structures (see Lecture 7) and the patents with which they are associated. Note taht SciFinder-n Markush searches use structure searching only, not other types of substance search.
Below is a portion of the answer set for a Markush search of dibenzothiophene.
Chemscape Analysis is a new feature in SciFinder-n; a visualization tool that can be applied to any Substance answer set created by a structure search. To use it, click the Create Chemscape Analysis button as seen in any of the answer set examples above. A new tab will open with the Chemscape results.
Chemscape visualizes the similarity and patent landscape for a set of substance results. The location of the substance bar in the visualization corresponds to the similarity of the substance to the query and the height of the substance in the visualization corresponds to the number of patents in which the sequence has been published.
Below is an example of the opening Chemscape display for the substructure search sown above, filtered to commerically available substances only.
Above is the initial display of the Chemscape analysis of the answer set., which opens in a new tab.
Icons on the upperleft:
My Chemscape - Displays a list of saved Chemscapes
Substance - Displays the box shon in the image, with the following options
Structural Similarity - Lets you select the range of strucutre similarity displayed.
Molecular Weight - Lets you select the range of molecular weights displayed.
Current Assignee - Lets you display substances by the assigne of patents in which they appear Click on the Add button next to a group sto see a list of assignees. Select from them to create the Group yoou've chosen.
CPC - Lets you create Groups using the CPC classifications codes. Click on Add to see a list of CPC codes from the patents in which the compounds appear.
IPC - Same as above, but using the IPC (International Patent Classification Code) codes.
Publication Year - Create Groups by publication year of the patents
Jurisdiction - Create Groups by theissuing patent office/country (e.g. US, China, WIPO)
Filters - Lets you filter the results by a patent count, range of patent counts, or limit to substances with no patent filed.
Add structure - Lets you add new structures to your current Chemscape and map their positions.You can search for structures to add by name or by structure drawing.
Search - Lets you search for specific patents by keyword (title, abstract, description and/or claims) legal status, publication date and/or current assignee. You may also do a structure search within the answer set.
Toggle control panel - Opens and closes the current control panel
Bottom right controls - Let you adjust your screen view: move left or right, expand/contract the image, or take a screen shot.
Click and drag on an empty portion of the display to rotate the 3-D viewing angle.
Click on a substance "tower" to see the CAS Registry Number, structure diagram, patent count, names/synonyms, molecular weight of the substance. You can mark the substance for later reference. If you click on the CAS Registry Number, a new tab will open with the Substance Detail record for the substance, from which you can then view properties, retrieves References or Reactions, and do all the other functions you can do from a Substance record in SciFinder-n.
Select Structure - Click on this button, then you can click and drag to create a rectangular selection box for viewing that region of the Chemscape, or saving as a new Chemscape.
Save - Lets you cave the current Chemscape, assign a name and (optionally) a description for future reference. This creates a saved Substance search in your Search History. . Click Rerun Search to be able to see the saved Chemscape.
You can save substance (or Markush) searches and create search alerts. Whenever a new substance appears matching your query, you will be notified. Alternatively, you can take the results of a substance search, retrieve the References associated with them and creaate a Reference search alert. In that case, whenever a new Reference containing one of the substances in your original answer set appears, you will be notified. There is currently no way in SciFinder-n to create an alert that finds new substances and automatically retrieves the references that they appear in (though there is such a function in STN). You have to create the Substance search alert, then, when you receive a notification, get the References manually, then look at the resulting References.
. © 2023 Charles F. Huber
This work by Charles F. Huber is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Based on a work at guides.library.ucsb.edu
SciFinder-n screenshots are copyright © 2023 by American Chemical Society and are used under fair use for educational purposes only.