Christine Flemming
Elsevier Product Training Manager
June 17, 2014
FINDING REACTION
INFORMATION IN REAXYS
The video for th...
TRANSFER HYDROGENATION
OF KETONES
• ATOM MAPPING
• REACTION DETAILS
SEARCH FORM
• REAXYS TREE
• ASK REAXYS
2
Transfer hydr...
MANY WAYS TO BEGIN A REACTION SEARCH
3
Five direct ways to get to reaction information
DRAW AND MAP THE REACTION
4
1. Click the Reactions theme. Click the white box
to open the structure editor (MarvinSketch)....
QUERY
5
Results: 1682 reactions are retrieved
6
REACTION DETAILS FORM
Structure-related
Information from experimental
procedure section of an
article/patent, or other
‘...
SELECTED EXAMPLES OF AVAILABLE SEARCHABLE FIELDS
REACTION DETAILS FORM
7
Record Type Reaction
Classification
Reaction Type...
QUERY
8
RESULTS
9
Results: 65 reactions are retrieved
HOW DO I VIEW ONLY THE FILTERED REACTION DETAILS?
FILTER BY REAGENT OR SOLVENT
10
11
EXPORT FILTERED RESULTS
12
Click the
Output button
Select hits
Make
selections.
Click OK.
Suggestion:
Use the document’s h...
ADD TO REPORT
13
Mouse over the corner,
then make a selection
from the
menu that
appears.
Click the Report button,
change ...
REAXYS TREE
14
Uncheck the
topics you are not
interested in.
This group will retrieve
many more citations
than the one below
because it r...
16
ASK REAXYS
REACTIONS
CITATIONS
ASK REAXYS
17
Over 1000 citations found
Two choices are given:
Citations and Reactions
The query components
are ...
SEARCH BY CATALYST
18
19
Start with a similar
structure and right click,
and select ‘copy Structure
to query’………
Or draw the whole
structure in ...
THANK YOU
ANY QUESTIONS?
Please complete the survey that
appears at the end of this webinar
Thank you!
c.flemming@elsevier...
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Reaxys reactions june2014

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Explains different ways to find reaction information in Reaxys. This was presented in a webinar on June 17, 2014.

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  • This presentation covers most of the basics that are shown here in this list.
    The topic I’ll use to illustrate these features is: Finding information on the transfer hydrogenation of ketones.
  • Chemical reaction information in Reaxys may be searched:
    In >46 Million bibliographic records
    In >36 Million single- and multi-step reaction records
    Through records in >57 million unique substances
    Searches may be performed:
    By structure
    By natural language text queries through Ask Reaxys
    By text queries through search forms
    Through reaction taxonomies in ReaxysTree
    Syntheses may be planned through the Synthesis Planner
  • Click the Reactions query theme, then open a structure editor. Draw the reaction that was shown in Slide #2. Map the reaction to ensure that an atom in the reactant is analogous to an atom in the product by clicking the Mapping button ……..and then clicking and dragging. Open substitution in 3 places. The easiest way to do this is to use the lasso tool, click and type 3 keys……. . s 6. This is a shortcut that means “maximum substitution allowed”.
    When you see the abbreviation on the mouse cursor, click the atoms that you want to designate for substitution. There is another way to do it…….right click an atom and select Edit atom>substitution count>s6, but you would have to do this for each atom individually. Transfer query.


  • Select Product, as drawn, and any other options you’d like. This results in over 1000 reactions. Notice that reactions can have hundreds of reactions details with them. The details for some might show a focus on transfer hydrogenation reagents and catalysts and may not for others.
     
    You can narrow the focus either by filtering or in the query itself.



  • Looking at the query form, you see that the top deals with options that pertain to a drawn structure.
     
    The bottom deals with reaction-related information taken from an article or patent and categorized into searchable fields
     
    Many more fields can be added to your form by clicking “Add/Remove Fields”.
  • These are a few fields to consider when you are looking for particular information in your reaction results.
     
    Record type, for example, for limiting to full or multi-step reactions…..Reactions classification when looking for chemical behavior as opposed to preparations …….Reaction type, like named reactions or something like “hydrogen transfer”,……..subject studied …….here we might want to select “catalytic behavior”……….the reaction full text field is a way of searching over just the experimental procedure section…and you may already be familiar with the Reaction Basic index field…….this is a way of searching over all of the reaction details fields (this does not include the titles and abstracts).
  • Return to the query and add a field…………subject studied……..and then select “catalytic behavior”.
  • 65 reactions are retrieved. Notice that catalytic behavior is highlighted….this is important because with some reactions there may be hundreds of reaction details and you wouldn’t want to look through all of them to find the few that specifically mention “catalytic behavior”. Another thing to note is that the “Subject Studied” category is not one of the filters and is used only when setting up the query.

  • As you scroll through your hits, notice that a lot of the catalysts are used with isopropyl alcohol. Let’s say that you wanted to see all the reactions in the list that use isopropyl alcohol.
     
    Use the filter and check the box for isopropyl alcohol.
    You can see that the list was filtered by looking at the breadcrumbs at the top…it shows that several reactions were eliminated that did not use isopropyl alcohol.
     
     
  • So, the filtering was done correctly, But, your results are still highlighting “catalytic behavior”, not “isopropyl alcohol”. If you use the “by value” tab on the filter and type in isopropyl you will then see the word highlighted in the results. (add a wildcard so you don’t have to type in 2 words). Now, the isopropyl alcohol is highlighted.
  • Export the filtered results. You can either select the reactions first or type in ranges on the export page. I’ll select #8. Click the Limit to button and then the Output button.
     
    Select “hit data only” to isolate the details that contain “isopropyl alcohol”. Click OK. Click Download.
     
    Here are the results as a PDF…..this shows the query, the filtering and even the hits selected…………Each of these details contains isopropyl….you can see it better by highlighting the word.



  • Use the Reports feature to select individual reaction details to add to a customizable report that can be emailed to colleagues.
  • [Another way to find information about transfer hydrogenation is to do a literature search. So you can open the Literature theme and type “transfer hydrogenation of ketones” into the Citation Basic Index field. This retrieves a list of over 1000 citations.]
     
    The Reaxys Tree is another way of doing a citation search of the chemical literature. The tree represents a hierarchy of indexed terms.
    This will result in a very focused search…..not necessarily the same comprehensive search that you would get from the Literature search form, but a quick way to get to specific information.
     
    Type in hydrogenation……a list will appear to let you know if the term is in the tree. Select it and then click search.
  • Now you can see where the terms fall in the tree and just uncheck the ones you do not want, like enthalpy of hydrogenation or the 2 on dehydrogenation.
     
    The 2 groups that are left may look identical, but they are not. The top one shows these 2 Named reactions as being part of a bigger branch called hydrogenation…..and you cannot uncheck one w/o unchecking the others.

    This other group shows the same 2 named reactions, but they are standing on their own and will result in far fewer results than the previous ones.
  • Ask Reaxys is designed to be somewhat like a google search and can interpret your query as either a reactions, substances, or citation query.
     
    When you type in “Noyori hydrogenation” you are presented with a few options and clicking the “Show Query” link will give more details about the proposed query. One option might be a citation search for authors name noyori….. Another one may also be a citation search, but a topic search (not an author search)…..and you will also see a reaction search that will result in examples of Noyori hydrogenations.
  • Entering “transfer hydrogenation of ketones” into ASK Reaxys is a convenient search that will result in pretty much the same list that we retrieved previously from the citation basic index field on the Literature search form.
  • The reaction searches revealed information about catalysts……and ruthenium catalysts came up frequently.
  • If you need to do a search for a class of catalysts. Start with a similar structure and right click, and select ‘copy Structure to query’………
    Or draw the whole structure in a Structure Editor.
    Use query features to generalize the query
    Search by ‘Reagent/Catalyst’
  • Reaxys reactions june2014

    1. 1. Christine Flemming Elsevier Product Training Manager June 17, 2014 FINDING REACTION INFORMATION IN REAXYS The video for this presentation can be seen here: http://youtu.be/-jLcb9f2Nlo
    2. 2. TRANSFER HYDROGENATION OF KETONES • ATOM MAPPING • REACTION DETAILS SEARCH FORM • REAXYS TREE • ASK REAXYS 2 Transfer hydrogenation occurs when hydrogen is added to a substance (from a source other than H₂). What are the hydrogen transfer reagents and catalysts? • FILTERING • EXPORTING • CATALYST SEARCH
    3. 3. MANY WAYS TO BEGIN A REACTION SEARCH 3 Five direct ways to get to reaction information
    4. 4. DRAW AND MAP THE REACTION 4 1. Click the Reactions theme. Click the white box to open the structure editor (MarvinSketch). 2. Draw the reaction 3. Click the Atom Mapping tool, click a carbon in the reactant, and drag to the analogous carbon in the product. 4. Use the Lasso tool, click in the white space and type the following keys (one after the other): Click each of the 6 atoms that will be allowed to have substituents.
    5. 5. QUERY 5 Results: 1682 reactions are retrieved
    6. 6. 6 REACTION DETAILS FORM Structure-related Information from experimental procedure section of an article/patent, or other ‘categorized’ reaction-related sections. In other words, categorized into Reaxys Reaction Details search fields. Many more fields can be added by clicking here
    7. 7. SELECTED EXAMPLES OF AVAILABLE SEARCHABLE FIELDS REACTION DETAILS FORM 7 Record Type Reaction Classification Reaction Type Subject Studied Fulltext of Reaction Reaction Basic Index
    8. 8. QUERY 8
    9. 9. RESULTS 9 Results: 65 reactions are retrieved
    10. 10. HOW DO I VIEW ONLY THE FILTERED REACTION DETAILS? FILTER BY REAGENT OR SOLVENT 10
    11. 11. 11
    12. 12. EXPORT FILTERED RESULTS 12 Click the Output button Select hits Make selections. Click OK. Suggestion: Use the document’s highlight features to make the filtered word stand out when viewing the exported document. Click the Limit to button
    13. 13. ADD TO REPORT 13 Mouse over the corner, then make a selection from the menu that appears. Click the Report button, change the order of the items, make annotations, and send the report to colleagues.
    14. 14. REAXYS TREE 14
    15. 15. Uncheck the topics you are not interested in. This group will retrieve many more citations than the one below because it refers to all hydrogenations as well as the 2 named reactions that are shown. This group refers to only the 2 named reactions shown.
    16. 16. 16 ASK REAXYS REACTIONS
    17. 17. CITATIONS ASK REAXYS 17 Over 1000 citations found Two choices are given: Citations and Reactions The query components are color-coded and also defined by clicking Show Query
    18. 18. SEARCH BY CATALYST 18
    19. 19. 19 Start with a similar structure and right click, and select ‘copy Structure to query’……… Or draw the whole structure in a Structure Editor. Use query features to generalize the query Search by ‘Reagent/Catalyst’
    20. 20. THANK YOU ANY QUESTIONS? Please complete the survey that appears at the end of this webinar Thank you! c.flemming@elsevier.com

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