Lecture 15b: SciFinder Scholar, Part 5
Searching by Chemical Substance: Chemical Reactions

CASREACT -- the CA database for organic chemical reaction searching

CASREACT, on the other hand, is more focused. It covers selected journal articles in organic chemistry (1840-present) and organic chemistry patents (1982-present). It indexes EVERY single-step and multi-step reaction described in the papers, including reactants, reagents and products, with yield information where available. At present, over 14.5 million reactions from over 600,000 documents are included in CASREACT.

Therefore, when searching for organic reaction information, if a truly comprehensive search is needed, both Reaction Searching and the other two approaches mentioned above should be employed. Reaction Searching alone is very detailed for organic reactions, but covers selected journals and patents only. Substance Searching is less powerful, but will extend your search to a wider range of source documents. Research Topic searching may pick up some additional reactions from the 1907-1966 literature.

Finally, remember that the CASREACT database does not index reactions by "name reactions", so you can't use "Diels-Alder" or "Heck reaction" in a reaction search as such. However...you can do a reaction search, Get References and then refine the references for the "name reaction" you're looking for or you can do a Research Topic search for the desired name reaction, then Get Related Reactions, and Refine the resulting set of reactionss by a further Substance or Reaction search.

Reaction Input

Vertical Tool Bar

	Reaction Site Marking Tool -- Used to identify bonds that must be modified in a reaction, e.g. C=O -> C-OH.	Reaction Role Tool -- Used to assign or change reaction roles of substances drawn on screen (e.g. reactant, reagent, product, "any role".) Also may be used with functional groups (see below), including "non-reacting" functional groups.
	Reaction Arrow Tool -- Used to automatically assign reaction roles. Click and drag the arrow tool. Structures at the tail of the arrow are assigned reactant/reagent roles; structures at the tip of the arrow are assigned product roles.	Reaction Mapping Tool -- Used to match atoms in reactants with the corresponding atoms in products.
	Functional Group Tool -- Used to search for classes of functional groups, without having to specify how they are attached to the underlying structure. Both broad and narrow classes are available. See sample at right.

Drawing Reactions

• Since the set of reactions being searched in CASREACT is far smaller than the set of substances in the REGISTRY file, more general structures will frequently work.
• If a functional group or other part of the structure is going to be affected in the reaction, you cannot use a shortcut to represent it.
• Draw your structures with long enough bonds so that you can easily highlight them for use of the Reaction Site Marking Tool.
• If you want to use a Registry Number copy-and-paste as a template for your reactant or product, remember that SciFinder will only let you copy one structure in this fashion. However, you can use the Selection Tool, with copy and paste within the Structure Drawing Screen to copy a structure and then modify it, which can save time when drawing complex structures.
• Use the Functional Group Tool to see how CA draws structures with ambiguous bonding (e.g. nitro, azido.)
• Note that Preview does not work with Reaction Searches.

Here's an example of a reaction drawn, making use of the Site Mapping Tool, Reaction Arrow Tool, Reaction Role Tool and the Functional Groups Tool.

• The phenyl rings were drawn with the Benzene Tool; the amine and nitro groups attached to them were drawn with the Pencil Tool. Note that since these groups are involved in the reaction, I can't use the NH₂ and NO₂ shortcuts to represent them.
• The Reaction Arrow Tool can be used to designate the structure on the left as a reactant, and that on the right as a product.
• The Functional Group Tool is used to indicate that there is another nitro group on the reactant as well, in an unspecified site on the molecule. If I had a specific site (or sites) for the nitro group, I could have drawn it in (using a shortcut) on both reactant and product (using the Multiple Attachment tool for multiple sites). Since it's going to be non-reacting, I don't have to draw it on the product side.
• The Reaction Role Tool was used to designate the "Nitro" group as non-reacting. I could have also used it to identify the reactant and product.
• The Reaction Mapping Tool is used to specify that the nitrogen in the nitro group in the reactant becomes the nitrogen in the amine group in the product.
• Since no bond changes between two atoms which remain unchanged, the Reaction Site Marking tool doesn't come into play.

Clicking on the Get Reactions button leads to the following screen (with Filters displyed.) Note that you can limit variations to only specified positions (i.e. variable groups or R-groups), or do a full substructure search (similarity searching is not available for reactions.) You can also pre-limit to specific reaction classes, or to reactions from patents or from a range of publication years.

Here's are two sample records retrieved by searching the above reaction query. Note that the substructure searched for are highlighted in red in the reaction diagrams.

To see the document record for any particular reaction, click on the highlighted citation. To retrieve the document records for multiple documents, select the reactions using the check boxes, then click the "Get References" button. To see all the reactions indexed for a given record or records, get the reference(s), then use the "Get Related" button and choose "Reactions" to retrieve all the reactions, not just the one(s) that matched your search strategy.

As mentioned in the previous lecture, in any reaction diagram, you may click on any structure or molecular formula or chemical name to reveal the menu below for that compound, and retrieve (where available) other reactions involving the compound, other references to the compound, the REGISTRY record for the substance (with possible chemical data), commercial sources or regulatory information, or use that compound as the basis to refine the reaction search or do a whole new structure search. This is a simple way to build multi-step reactions: find a desired reaction, than check each of the reactants for reactions in which they are the products, and so on.

Refining Reaction Answer Sets

• Refine by Reaction Structure -- This option lets you go back and modify your reaction search to make it more or less specific.
• Refine by Product Yield -- This option lets you specify a range of yields.

Note that not all reaction records have yield information, so you might want to use the "include reactions that do not have yield information option", so as not to exclude useful possibilities. Note also that if there are multiple products of a reaction with multiple yields reported, SciFinder does not associate the particular yield with a particular reaction so you may pull up records where your desired reaction is a side reaction.

• Limit by Number of Steps -- Lets you limit to either single or multiple step reactions.
• Limit by Reaction Classification -- Lets you pick a type of reaction from the list below, and either limit to that class or classes, or exclude that class or classes:
  

Note that if you select more than one type, you get all reactions that fit either classification, not just those reactions that fit both. If you want to find reactions that fit two or more categories, refine by the first set, then refine again by the second set.

Analyzing Reaction Answer Sets

Combining Reaction Answer Sets