If you want to conduct a search for a certain drawing as a substructure instead of an exact match, you may wish to set points with hydrogen-only substitution. There are two ways to do this:
Manually adding the Hydrogen to the diagram (see image below, right example).
Using the Lock Atoms tool (see image below, left example).
Searching Structures in SciFinder-n will automatically return structures both with charge and without charge in your results.
You can apply a charge to a given atom by using the Positive and Negative Charge tools.
If you want to search for atoms that specifically do not have a charge, the Lock Atoms tool (discussed above) also locks the charge for a selected atom.
If you wish to search for an isotope at a specific location of a structure, you can do this by right clicking on a specific atom and specifying its atomic mass.
By default, CAS searches for any isotope of an atom drawn.
Selecting "Abnormal" causes CAS to search for any isotope but the common isotope.
Selecting "Specific" causes CAS to search for a specific isotope according to what atomic mass you input (which can be the common isotope).
Setting Bond Order and Topology
By default, ring-only or chain-only topology is not considered when searching by structures in SciFinder-n. Consider the following diagram:
If searched as a substructure, the topology of this structure can vary. Consider the following examples of diagrams with the previous diagram as a substructure:
However, for more specificity on the topology of the structure, you can use the "Lock Ring Fusion or Transformation" tool to ensure ring isolation topology or chain topology.
In the following example, the left is a locked ring, whereas the right is a locked chain.
Creating R-Groups
Using the button labeled "R" in the CAS Draw menus, you can apply R groups to search for substances that might have a number of different elements at a certain point.
When doing so, you must define the R groups before initiating a search. Applying an R1 will open a menu with the period table.
Using this periodic table, you can assign what atoms would be able to appear for a given R point.
If using both an R1 and an R2, you must define both of these points. If necessary, you can have multiple R1 points, as well.
Fragmenting with R-Groups
You may want to have a specific root structure which connects at a given point to a number of different other structures. This can be done with fragmenting, and is done in conjunction with R Groups.
First, draw the root structure which the fragments will connect to.
Second, draw the fragment structures that will connect to the root structure.
Next, define the points where the fragment structures can connect to the root structure. You can do this using the tool labeled Fn.
For any fragment structures where the root structure may be able to connect at multiple points, you will have to draw separate diagrams for each of these points.
Next, set an R point on the root structure using the "R" tool. This will be the point where the fragments can connect.
After setting this R point, a menu to edit the R-Group Definitions will appear. Navigate to the "Fragments" dropdown, open it, and select whatever fragments should attach to the structure in your search.
You may still attach atoms to the R point is desired.
Setting Variable Points of Attachment
To set topology for a structure, first draw the root structure, then draw a fragment structure that will detached from the root structure.
After drawing these two structures, select the tool "Variable Attachment Points." For each point of connection on the root structure, click and drag from that point and connect it to the fragment structure in the appropriate place.
Repeating Units
You can use the Repeating Units tool to search for rings or chains of a variety of sizes. This tool has some limitations on it:
The unit to be repeated must be located between two other atoms; you cannot repeat a terminal atom.
You can repeat a unit anywhere from 0 to 20 times. If you repeat the unit zero times, it will not appear in the substance, and the atoms on either side of it will be connected directly to one another.
You cannot cheat and try to find more than 20 repetitions of the unit by drawing two identical repeating units side by side; the system is too clever for that and will give you an error message.
After drawing the structure, use the Repeating Units tool to select the point at which a structure should be able to repeat.
Once you select a point in the structure, CAS Draw will prompt you to input a range of lengths for the repeated units.
