1. Go to the “Reaction Drills” section of the Reaction Explorer main setup page.
2. Select the parameters for the Reaction Drills to be prepared:
   1. Pre-constructed Examples: Select one of the pre-constructed sets from the “Reaction List” drop list, or...
   2. Random Examples:
      1. Leave “Reaction List” as “(Generate Random Reactions)”
      2. Select one or more “Reaction Subject Categories”
      3. Enter the number of reactions that will be generated under “Components to Predict”
3. Select which “Component to Predict” in the drills.
   (Select “Any” to randomize the choice, or select “Products” as a more appropriate choice for the pre-constructed examples.)
4. Click on [Generate Problems] to proceed to the Reaction Drills page.
5. Scroll to the very bottom of the page, and look for a “Link” in the bottom-left
6. Right-click on the “Link” and select “Copy Shortcut” or “Copy Link Location.”
7. Paste the results into your external application as a link to the Reaction Drills.

1. Go to the “Synthesis Explorer” section of the Reaction Explorer main setup page.
2. Select the parameters for the synthesis problem to be prepared (the User ID and User Class fields can be left blank):
   1. Pre-constructed Examples: Select one of the pre-constructed problems from the “Synthesis Problem” drop list, or...
   2. Random Examples:
      1. Leave “Synthesis Problem” as “(Generate Random Synthesis)”
      2. Select one or more “Reaction Subject Categories”
      3. Enter the “Maximum Steps” that the randomly generated problem should be.
3. Click on [Generate Problem] to proceed to the Synthesis Explorer page
4. Scroll to the bottom of the “Target Product” frame in the top-right, and look for a “Link” in the bottom-left
5. Right-click on the “Link” and select “Copy Shortcut” or “Copy Link Location.”
6. Paste the results into your external application as a link to the Synthesis Explorer problem.

1. Go to the “Mechanism Explorer” section of the Reaction Explorer main setup page.
2. Select one of the pre-constructed mechanism problems from the “Mechanism Problem” drop list. (All other fields may be left blank)
3. Click on [Prepare Mechanism] to proceed to the Mechanism Explorer page.
4. Scroll to the very bottom of the page and look for a “Link” in the bottom-left.
5. Right-click on the “Link” and select “Copy Shortcut” or “Copy Link Location.”
6. Paste the results into your external application as a link to the Mechanism Explorer problem.

1. Go to the Data Query / Admin page.
2. Use the query interface to search for the Reaction Drills, Synthesis, Mechanism, or Subject Category of interest
3. Click on the Preview link to be taken to the problem view for the respective Reaction Drills, Synthesis, or Mechanism. If a Subject Category was chosen, instead a view for a randomly generated synthesis problem based on the category content will be presented.
4. Scroll to the bottom of the page or Product frame and look for a “Link” as above.
5. Right-click on the “Link” and select “Copy Shortcut” or “Copy Link Location.”
6. Paste the results into your external application as a link to the respective problem.

• Synthesis Explorer and Mechanism Explorer problems support graded and non-graded problems.
• By default, the links generated above assume the problems are to be graded.
• These links include a parameter at the end similar to “completionSeed=62543,” except that the number is randomized.
• This completionSeed number is completely arbitrary. Reaction Explorer uses this number to provide students with a completion code upon solving the problem.
• To discourage student copying, the code that Reaction Explorer generates will not actually equal the completionSeed number. Instead, if the external link includes a completionSeed of X, then Reaction Explorer will generate a completion code for the student equal to a multiple of X, up to 9X.
• For example, if the external link has a completionSeed=1111, then Reaction Explorer will generate a completion code for the student randomly selected from (1111, 2222, 3333, 4444, 5555, 6666, 7777, 8888, 9999).
• The external application should be coded to accept any of the above 9 responses as “correct” answers to match the problem links.

The Reaction Explorer system is setup to generate random reaction drills and synthesis problems, based only on the selection of subject categories the generation is to be based upon. External applications thus need only to link to these as described in the previous section. The steps below outline how to construct specific (non-random) reaction drills, synthesis and mechanism problems for students to work on.

The general method for constructing any new problems is to use the standard Synthesis Explorer interface to specify the appropriate reactions and save these reactions for later use. These saved reactions / problems can then be labeled with descriptive names and relevant book chapter section numbers.

1. Go to the Data Query / Admin page.
2. Select the “Reaction Category / Subjects” that the problem applies to (this will determine what reagents are available)
3. Click on [Create Problem] to proceed to the Synthesis Explorer interface.
4. Use the standard Synthesis Explorer interface to enter in a series of reaction steps representing the “correct” steps to be used in a synthesis problem.
   (If desired starting materials are not available in the top-left Reactants frame, custom reactants may be added via the pencil icon and [Add] button at the top of the Reactants frame.)
5. Once all steps have been entered, find the text field under the big [Apply Reaction…] button containing “(Enter Label)” and enter a brief descriptive label for the problem.
6. Click on the [Save Problem] button to save the reaction steps to the database and be redirected to the Data Query page for further customization.
   (This Data Query page allows you to find and customize properties for all pre-constructed problems, but at this point it should be pre-loaded with the new problem you just created. This is represented by a row of fields in the Query Results table in the bottom half of the page.)
7. Click on the checkbox under the Edit column of the results table to allow modification of the problem information. Fields appropriate for editing:
   1. Code: If you wish to relabel the problem (only instructors will see this label, students will not)
   2. Class: Defaults to “Synthesis,” assuming this is a Synthesis problem, but can be changed to represent a Mechanism or Reaction Drill.
   3. Solomons Position, Brown Poon Position, etc.: Enter the numerical chapter section in the respective book that this problem is appropriate for.
      (Number entered should actually be an integer that will be divided by 100 to give the section label. For example, if the problem is meant for chapter 18, section 7, then enter “1807” which the system will later display as “18.07”)
   4. In general, the other fields should not be modified.
8. Click on the [Save Changes] button and make note of the new problem’s ID number (next to the Edit checkbox).
9. The problem should be saved to the system and available for assignment or linking. Because the system caches the list of problems in memory, it may take several minutes before your new problem appears in the available list.

• The procedure for constructing Mechanism problems is essentially identical to constructing Synthesis problems.
• Go through the same steps as above until you get to the Synthesis Explorer interface.
• Instead of entering a series of reaction steps representing a synthesis, you only need enter a single reaction, whose auto-calculated mechanism will represent the mechanism problem.
• It is also possible to enter multiple reactions here. In this case, users who request the problem will get a mechanism randomly selected from the list of reactions you entered. Given this, the multiple reactions entered should have similar mechanisms.
• After saving the problem and being redirected to the Data Query page, be sure to edit the problem information and change the Class to “Mechanism,” otherwise the system will assume this is a Synthesis problem by default.

• The procedure for constructing Reaction Drills is essentially identical to constructing Synthesis problems.
• Go through the same steps as above until you get to the Synthesis Explorer interface.
• Instead of entering a series of reaction steps representing a synthesis, enter a series of reaction steps to be used as Reaction Drills.
• After saving the problem and being redirected to the Data Query page, be sure to edit the problem information and change the Class to “Reaction Drills,” otherwise the system will assume this is a Synthesis problem by default.

• The Data Query / Admin page can be used to find and customize the basic information of any pre-constructed problems.
• Once problems are created, they cannot be permanently deleted. However, you can use the Data Query page to modify their Class to “(Disabled),” which effectively discards the problem to a Recycle Bin.
• Disabled problems can later be recovered by finding the problems through the Data Query page with a Query Type of “Any Non-Random Problems.”

• To modify which reactions are under a given problem / reaction list, click on the "Details" link for the problem in the Data Query results table.
  • Select reactions from the list you want to move, by clicking on their [Select] buttons on the right.
  • In the big list of pre-constructed reaction lists and synthesis problems at the bottom, choose which reaction list / synthesis problem you want the selected reaction steps to be reassigned under.
  • Click on [Reassign Reaction Steps] to complete the process.
  The above should allow you to make every significant problem edit of interest:
  • Removing Reactions: Reassigning a reaction step to another reaction list effectively removes the reaction from the current reaction list. To really "discard" a reaction, just reassign it to an unused reaction list, whose status can later be changed to "(Disabled)."
  • Adding Reactions: Reassigning a reaction step to another reaction list effectively adds the reaction to the other reaction list. To really add a fresh reaction, create a temporary new reaction list through the above interface with the desired reaction, then reassign the reaction steps from the temporary list into this one. You can change the temporary reaction list's status to "(Disabled)" if it is no longer needed.

• In addition to supporting the maintenance of problem lists, the Data Query page can find and customize the information and contents of the Reaction Subject Categories that the system is organized by.
• Clicking on the “Details” link for a category in the Data Query page will bring up a page to customize the default selection of starting material reactants and reagents that belong to each subject category.
• Creation of new subject categories can be done by "[Save and Clone]" an existing category from the Data Query page.

Subject Categories allow for the specification of underlying Reactants and Reagents to "intended" steps in a synthesis to provide for very robust control over Synthesis problems randomly generated based on the category content.

To start, map out a synthesis with a series of expected steps and reagents. For example, this example will be based on a planned synthesis problem framework:

1. Terminal Alkyne -(NaNH2 deprotonation)-> Acetylide Anion
2. Add Primary Halide to Acetylide Anion from prior step -(Mix in Aprotic Solvent)-> Sn2 Substitution Product
3. Internal Alkyne (Substitution Product) -(H2 + Lindlar's Catalyst)-> cis-Internal Alkene Final Product

For purposes of problem generation, the "R-groups" on the starting materials are irrelevant, so we'd like to take advantage of the random problem generation framework to satisfy the Synthesis template above but with any randomly selected reactants that satisfy the relevant functional group requirements.

1. Go to the Data Query page.
2. Query for or create (Save and Clone) a (new) Subject Category of interest and click on the Details link.
3. Use the Pencil icon under the Starting Materials section to sketch and submit multiple possible starting material reactants that can be used in the first step of the synthesis template. For this example, draw several Terminal Alkynes with random, non-reactive R-groups
4. Under the [Add as Intended for] button below, select Step 1 and then click on [Add as Intended For] to save this list of Terminal Alkynes as appropriate reactants for use in the first synthesis step.
5. Under the Available Reagents section below, look for the NaNH2 reagent, and click on it to select it.
6. To the right of the Available Reagents label, and right of the [Add Selected as Intended for] button, select Step 1 and then click on [Add Selected as Intended for] to save the NaNH2 reagent as the only appropriate reagent intended for the first step of any randomly generated syntheses for this category.
7. Go back to the Pencil icon under the Starting Materials section to sketch and submit multiple Primary Halides.
8. Click on [Add as Intended for] for the Primary Halides sketched above after designating them appropriate for Step 2 of the syntheses.
9. Under the Available Reagents section, find and select the "Mix Reactants in DMSO..." reagent
10. Click on the [Add Selected as Intended for] button under Available Reagents after designating it as appropriate only for Step 2 of the synthesis.
11. Under the Available Reagents section, find and select the "H2 Lindlar's Catalyst" reagent
12. Click on the [Add Selected as Intended for] button under Available Reagents after designating it as appropriate only for Step 3 of the synthesis.
13. To make for more interesting problems, add other distractor Starting Materials and Reagents, but assign them to No Specific Step. These will not be used in any generated synthesis problem, but will be presented to the user as other possible materials to use in the synthesis plan.