Name _______________________________________________
Due: February 23, 2009
SciFinder Scholar – Reactions
1.
Find reactions in which the C-C bond between the two benzene rings in a 3,3’-biphenyl
substructure is formed during a reaction. (2 points)
 Draw the structure shown below, label it as a product, and perform a substructure search.
 “Ak” is short for alkyl groups -- from the “variable” menu icon.
 Mark the central C-C bond with the “bond breaking / bond forming” tool (the Reaction site
marking tool). This limits to only reactions in which this bond is formed.
 Lock out the rings for the two benzene rings. In this example SciFinder does not require that
you lock out the rings, but doing so will speed up the search significantly. If you were doing a
comprehensive search you would not lock out the rings. Your search in SciFinder Scholar
should look like this (note the rings are in bold when they are locked out):
O
O
Ak
Ak
Product
(a) In how many reactions is this product formed?
Number = _________ [2,100-2,500]
Find reactions where the reaction involves an organo-boron compound. You can do this by
refining the previous search by Chemical Structure with the following structure labeled as a
reactant/reagent.
B
O
Ak
Reactant/Reagent
Retrieve all reactions where the biphenyl substance is a “product” and the phenyl boron compound
is a “reactant/reagent”.
(b) How many preparative reactions are found?
Number = ________ [500-600]
(c) Get all references for these reactions.
Number = ________ [<70]
(d) Why are there fewer references than there are reactions?
2.
Find catalysts that have been used to make diphenyl ethers from phenols and halobenzenes. (2 points)
One way to do this is by analyzing the results of a reaction search. Search for the reaction drawn
below and include substructures in your search. Choose X from the “variables” icon (X stands for
any halogen atom: F, Cl, Br, I). Make sure that you indicate that one of the oxygen-benzene bonds
is formed during the reaction (use the “Reaction site marking” tool). As in the 1st problem, lock out
the rings (which will find fewer results, but will make the search go much faster). Your search in
SciFinder Scholar should look like this:
O
X
Reactant/Reagent
Reactant/Reagent
O
Product
(a) How many reactions are found?
Number = ___________ [30,000-32,000]
Analyze this search by “number of steps in reaction.”
(b) How many one-step reactions are there?
Number = ___________ [6,000-8,000]
Retrieve all the one-step reactions. Analyze these to identify possible catalysts for this coupling
reaction. Sort the results by frequency. What is the most common element that appears in chemical
substances that are used as a catalyst for this reaction?
(c) Most common element = _________ [Element … not compound!]
Check the box next to this element as the free element (ignore catalysts that contain this element and
other elements) and get reactions where the element is used as a catalyst.
(d) Number of reactions = __________
[200-300]
Get all references for reactions catalyzed by this element
(e) Number of references = ________ [< 50]
3. Let’s try three different approaches to finding “pinacol rearrangement” reactions using CASReact (The
name of the reaction database in SciFinder Scholar) and one approach in a keyword search. (6 points)
Approach #1 => Draw the reaction of pinacol to pinacoline (the “pinacol rearrangement”). Get
reactions where the structures are substructures of more complex structures. Make sure that you
draw the hydrogen atoms attached to the oxygen atoms in the reactant.
H
O
O
H
Reactant/Reagent
O
Product
(a) Number of reactions = __________ [1,000-1,500]
Get all references to these reactions.
(b) Number of references = __________ [< 300]
Refine these references by research topic “zeolite.”
(c) Number of references = _________ [< 40]
Approach #2 => Click on “New Task”. Search for the more general reaction shown below. Use the
“reaction atom mapping” tool to map two sets of atoms from the reactant into the product (as shown
below). When you chose “Get Reactions” limit by … reactions with substructures of more complex
structures and the number of reaction steps to 1. This will speed the reaction and will not cause you
to miss any reactions in which you are interested. Do not lock out rings – this search is designed to
find everything that is like the pinacol rearrangement.
1
O
1
O
H
O
2
H
2
Reactant/Reagent
Product
(d) Number of one-step reactions = ____________ [20,000-30,000]
Get all references to these one-step reactions.
(e) Number of references = ____________ [>7,000]
Refine these references by the research topic “zeolite”.
(f) Number of references = ____________ [< 40]
Save the references from part (f) as a Saved Answer Set. This will be used below.
Approach #3 => Click on “New Task” to perform an even more general approach. Use the icon
labeled “Reaction Functional Group List” to draw the reaction below. It is on the lower left of the
structure drawing window (alcohol, ketone, aldehyde). Select and highlight the desired functional
group, then use the cursor to place it in the structure drawing window. This is an extremely broad
search.
Glycol
KETONES
reactant/reagent
product
(g) Number of reactions = ____________ [65,000-80,000]
Because the “pinacol rearrangement” is a one-step reaction, use the “Refine” feature to limit to only
one-step reactions.
(h)
Number of one-step reactions = ____________ [5,000-7,000]
Get all the references for the reactions found in part (h).
(i) Number of references to these one-step reactions = __________ [2,000-5,000]
Refine these references by the keyword “zeolite”.
(j) Number of references with the keyword “zeolite” = _________ [> 20]
=> Combine the reference from part (j) with the Saved Answer Set from part (f). Chose the option
called “Combine Sets” which is the equivalent of the Boolean “OR”.
(k) Number of references in the combined search = _________ [30-35]
Save these references as a Saved Answer Set. This will be used below.
Since all of the references found in Approach #1 are also included in those in part (k), the references in
part (k) include everything found in the three reaction-based search approaches. Let’s see how effective
reaction-based searches were for finding articles about the pinacol rearrangement catalyzed by a zeolite.
The “categorize” tool also provides insight on this.
(l)
Categorize the references from part (k). Under “Synthetic Chemistry”, what is the most frequent
“reaction” and to how many references does it point?
1st reaction = _______________________________________ Number of references = ______
Keyword Approach => Click on “New Task.” In Research by Topic, search for “zeolite with pinacol
rearrangement.” Select the candidate which has 20 references in which the concepts “zeolite” and
“pinacol rearrangement” are present “anywhere in the reference”.
(m) Categorize these 20 references. Under “Synthetic Chemistry”, what are the two most frequent
“reactions” and to how many references does each point?
1st reaction = _______________________________________ Number of references = ______
2nd reaction = _______________________________________ Number of references = ______
Use the combine feature with the Saved Answer Set from part (k). Combine the searches and remove the
current set (m) “keyword approach” from the saved search (k). This removes only three references and
makes it clearer what kind of reactions were found by the reaction-based search approaches. Take a look
at the titles of these articles. Along with the Categorize analysis, this gives a clue as to how useful
reaction searches were at finding articles on the pinacol rearrangement.
(n)
Based on the results from parts (l) and (m), do most of the references in the combined
reaction-based search approaches deal with the pinacol rearrangement? Circle the best answer.
Yes
No