Reaxys - Getting the most from MarvinSketch - webinar 16th Oct 2012


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Our webinar (including time for questions), was presented by Chris Flemming, our Reaxys experts and she covered the following:

• Determined which atom and bond query tools work best with a given situation
• Created a template and save it to your toolbar
• Used abbreviations and reaction-specific query tools.

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  • Welcome to this webinar about getting the most out of using MarvinSketch with Reaxys. My name is Annn-Marie and I am your host today. I am here with our Reaxys expert Chris.Chris has a chemistry background and has delivered Reaxys training for several years. She works closely with the Reaxys product team and our customers to understand how Reaxys provides a solution for many different workflows. Today she will talk aboutMarvinSketch, showing you, for example how to create a template and use reaction query features.I would like to point out that we will place this webinar online, so that you can listen to it again, but then in your own time!
  • Before we get started with Reaxys I would briefly like to put Reaxys into context with the other activities that go on at Elsevier. Elsevier serves 3 main and interlinked areas which may be of interest to you, Biology, Chemistry and Medicine. [first click] Reaxys is one of the products serving your needs in chemistry and we also have Embase, our tool for biomedical searching, Pharmapendium, giving searchable access to all FDA and EMA approval documentation and our new target finding and validation tool, Target Insights within the biology and medicine spheres. Furthermore, Reaxys is linked with SciVerseScienceDirect and SciVerse Scopus. Scopus is a multi-disciplinary, all-science abstract and citation database. [second click] This should help put Reaxys into context, and with that we can move to today’s Reaxys session… which Chris will be walking us through.
  • This session is being recorded and we will send you a link to the recording in a follow-up email.We welcome your questions and will try to answer them during the webinar. Please use either the “Question” or the “chat” functionality on the control panel to send us your questions.Click on the red arrow for full screen. Your control panel will be hidden. Click again on the red arrow to see your control panel again.
  • Structural queries can consist of complete structures or fragments and can contain atom and bond query features. There are 3 structure editors that come with Reaxys and require no installation: MarvinSketch, Elemental, and GGA Ketcher,shown on the left.Reaxys can also be used with the 5 structure editors shown on the right. Connection software is required and can be downloaded from the Reaxys infosite.
  • When you enter Reaxys through IP recognition, you can switch between the 3 structure editors from this button. When you enter with UN/PW, click the “My Settings” button and then select” Modify Application Settings”.
  • Reaxys has a feature called “Generate structure from name”. Marvin has a similar feature. I am copying a name from an article and then pasting the name into Marvin….the structure appears.
  • I’d like to display the structure differently. You don’t have to select the structure before flipping. Just select Object>Flip or Object> Mirror.
  • To sprout: Select a template and then move your mouse arrow to an atom on the main structure, then click.To fuse: Select a template and then move your mouse arrow to a bond on the main structure, then click.
  • Use abbreviations: Type an abbreviation. More abbreviations can be found underTemplates>Groups.
  • It is not always necessary to click the Bond tool before changing bond order. Just select a bond and type “1”, “2”, or “3 for single, double, or triple bonds.
  • Notice that “E” is displayed in Marvin. Bring the structure into Reaxys and run a substructure search.
  • Reaxys will not recognize the configuration unless you label the bond.
  • Repeat the search. Now only the “E” configuration is retrieved.
  • Let’s save this structure as a template. The query feature “stereo bond” will be part of the template. First,save the structure to a folder on your computer.
  • Next step is shown.
  • Next step is shown.
  • Next step is shown.
  • Likewise, you can add any of the template to your toolbar by clicking Properties and then selecting Display on Toolbar.
  • Unlike (E) and (Z) stereochemistry, structures with up and down bonds do not need a stereochemistry label. Reaxys will recognize the up and down bonds and retrieve the appropriate substances. (14 substances).
  • If you draw the up and down bonds, but then decide that you want to retrieve all configurations….you don’t have to redraw, just click the box for “Ignore stereo”. (BTW, this is also the result you would get if you drew the query with regular bonds, not up and down bonds). (75 substances)
  • A note about up and down bonds: If you need to draw the (R) configuration, for example, but you don’t want to figure out which bonds should be up and which should be down…….Marvin will draw the bonds (as shown above).
  • Ritalin is a chiral compound. You are not only interested in preparations of Ritalin (with substitution allowed), you would like to compare reactions where the configuration of the starting material was inverted in the product to reactions where the configuration of the starting material was retained in the product. How can your searches be limited in this manner? First, let’s do a substructure search for preparations of Ritalin without specifying stereochemistry. 906 reactions are found.
  • Now, we will specify “Inversion of configuration”. It is not necessary to pick a particular configuration by drawing up and down bonds, we’re just looking for the relative configurations. In Marvin, right click the chiral center and select Edit Atom>Reactions>Inversion. Run the search. 4 reactions are retrieved.
  • How does this compare to “Retention of Configuration”?
  • Select the ring, right-click and then select Edit structure>Add >Position Variation Bond.
  • Right click,select Edit Atom>Link Nodes and select L1-2. Repeat with the other atom.
  • The next online Reaxys session will be on the 18nd of Oct. and will be an introduction to Reaxys. When you leave the session, a survey will pop up. Please fill out what your thoughts are regarding this webinar. Besides this you will receive a follow up email shortly and we will place the recording of this session on the Elsevier training desk website. Many thanks again, good luck with exploring Reaxys further and we hope to meet you again soon.  
  • Reaxys - Getting the most from MarvinSketch - webinar 16th Oct 2012

    1. 1. Your Presenter: Your Host: Christine Flemming Anne-Marie RocheWelcome to our Reaxys webinar!Getting the Most out of MarvinSketch
    2. 2. Need to know•Webinar control panel: ‘chat’ for questions or ‘ask a question’ minimize option for full screen view•Q&A after presentation
    3. 3. Structure EditorsMarvinSketch Elemental GGA Ketcher
    4. 4. IP access Log in
    5. 5. Copy and Paste “1-methyltryptamine” 1-methyltryptamine Copy Paste
    6. 6. Flip
    7. 7. Shortcuts Mouse wheel scrolls F6 resizes the structure canvas vertically
    8. 8. Attaching Templates Undo button Sprout Fuse Undo
    9. 9. Abbreviation GroupsAdd a single bond and type cooh Templates>Groups
    10. 10. Bond Shortcuts Type “1”, “2”, or “3” for single, double, or triple bonds
    11. 11. Select a portion How to Move or Rotate a portion of the structurePress thespace bar once Stretch the bondHit spacebar a Rotate thesecond time bond in 2DHit spacebar a Rotate thethird time bond in 3D
    12. 12. Search for (E) And (Z) Stereochemistry
    13. 13. Results The search retrieves both E and Z
    14. 14. Add (E) And (Z) Stereochemistry BondRight click
    15. 15. Search Again
    16. 16. Create a template
    17. 17. Up and Down BondsThe query shows beta-DThe search retrievesonly beta-D
    18. 18. Up and Down Bonds – Ignore Stereo
    19. 19. Draw the (R) configurationRight click (R) configuration
    20. 20. (R) and (S): Reactions Ritalin
    21. 21. Inversion of configuration Apply the “Inv” label, then search by substructure. 4 reactions are retrieved.
    22. 22. Retention of configuration
    23. 23. Make or Break a Bond
    24. 24. Audience Poll: Voted for “Position VariationBond” and “Link Nodes”
    25. 25. Link Nodes
    26. 26. Thank You For more information and questions please contact Our next Reaxys webinar is scheduled for Thursday, Oct. 18 and will be an Introduction to Reaxys Go to for all training related materials Please fill out the survey that appears on your screen after leaving the webinar.