Finding Substances and their Properties in Reaxys
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Presentation about finding chemical properties and tautomers, radicals, isotopes, and Markush structures in Reaxys. An Rgroup query and organometallic query are also included.
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Finding Substances and their Properties in Reaxys
- 1. TIPS AND TRICKS FOR FINDING SUBSTANCES AND THEIR PROPERTIES Webinar presented October 21, 2014 Christine Flemming Elsevier Product Training Manager Oct. 21, 2014 c.flemming@elsevier.com
- 2. AGENDA How to find: • Tautomers • Radicals • Isotopes • Markush How to find property data for these and other types of structures
- 3. 3 Boiling Point of cyclopropanols (and ethers) Create an Excel sheet of cyclopropanols (and ethers) along with their boiling points. Limit to substances that also contain a 6-membered ring. The query interpretation is shown on the Results page Limit to substances with 6- membered rings Analysis View tool
- 4. 4 Export to Excel
- 5. 5 Optical Rotatory Power of trimethylsilanes Filter for boiling point Eliminate nitriles Begin a report on selected property data
- 6. 6 Mouse over data and click red triangle to select and add to your report. Click “Send” to send a zipped html file to colleagues Create the Report Click the “Report” button to view your selections. Click the “Annotation” link in the upper right side to add text to your report
- 7. 7 Flash point of octanol
- 8. 8 Critical Micelle Concentration of sodium lauryl sulfate
- 9. 9 Solubility of alpha tocopherol
- 10. TAUTOMERS 10 Dihydrofolic Acid
- 11. Two substances are retrieved when Include Tautomers is not checked 11 Specified stereochemistry is the only difference
- 12. 12 Reaxys tautomers: • Substances that can be isolated and characterized • The structures are abstracted and displayed in Reaxys just as they are displayed in the literature • Tautomers are placed in separate records (they are not merged into one record) • Only covers the movement of real atoms, thus excluding charges and valences • Uses classic conjugated double bonds These are not tautomers Tautomers Tautomers
- 13. Repeat the search with the Include Tautomers box checked 26 substances are retrieved. 13 Examples:
- 14. RADICALS N-acetyl-glutamic acid Designate radicalization here Right-click Radical label in place
- 15. 15 Result of the Radical search
- 16. Radical Radikal Use the Chemical Name field to find radicals Example on next slide
- 17. 17 Riboflavin radicals Add Retrieves 4 substances
- 18. 18 Riboflavin radicals Delete Retrieves 24 substances (most show stereochemical variation)
- 19. 19 Riboflavin radicals Retrieves 23 substances Subtract one list from the other from the History page Results in 1 substance It may be necessary to search for radicals 2 different ways in some cases (see slide 17)
- 20. Niacin ISOTOPES = 22 substances 20 = 1 substance
- 22. MARKUSH STRUCTURES 22 Patent Description of claim
- 23. MARKUSH STRUCTURES 23 Text from the patent is put into a tabular format This is the Markush structure
- 24. 24 From the Citations tab, you can view the Markush structure(s) from a patent by clicking the Substances hyperlink. The Markush structures will appear at the end of the list.* *Not all patents will contain Markush strctures.
- 25. 25 Click the More Options link. Then check the box for Include Related Markush Please Note: Most options are selected
- 26. 26 27 structures retrieved when Include Related Markush is checked (26 of them are Markush structures) One substance is retrieved when Include Related Markush is not checked
- 27. 27 Repeat the previous search using the options shown below (this will result in a larger list) Please Note: Most options are NOT selected
- 28. 28 Markush structures will be at the end of the sorted list
- 29. ORGANOMETALLIC 29 Find niacin-metal complexes Create the atom list in MarvinSketch: 1. Click the More button 2. Click the Atom List button 3. Select atoms 4. Click Close. Click in the white space.
- 31. R-GROUP SEARCH 31 Find analogs of niacin This can be bonded to H or to a heterocyclic group An alkyl or halo can be attached at any of these sites
- 32. 32 1. Add a bond to the OH. Then click the “r” button and select CHH for “heterocyclic or hydrogen” 2. Use the Lasso tool and select these 3 atoms. 3. With the 3 atoms selected, right-click and select Edit Structure>Add>Posi-tion Variation bond 5. Draw the components of the Rgroup (ALK and X). 4. Click the atom on the end, type “R1”. 6. Select the ALK and X. While they are selected, type r1. While still selected, click the ALK and the X to add the attachment points.
- 33. THANK YOU ANY QUESTIONS? c.flemming@elsevier.com Please complete the survey that appears at the end of this webinar Thank you!
Notas do Editor
- Hello and welcome to this Reaxys webinar on finding substances and their properties. As the title implies, we will only be concerned with substances and there will be no mention of reactions. Please send me your questions through the questions box on your control panel.
- In this session we will take a look at some very easy ways to find property data and we’ll look at how to find different types of substances, like Tautomers, Radicals, Isotopes, and Markush structures …..
- I’ll start with a property search. I want to quickly create an Excel sheet of cyclopropanols along with their boiling points……and I want to limit to substances that contain 6-membered rings. So, I will open Reaxys……and use Ask Reaxys. Notice how quickly I found what I wanted. If you are not familiar with Ask Reaxys…….it is a relatively new feature…it just came out in April of this year and is designed to be like a Google search. It is still in beta, but it gets better all the time so stay tuned to even more improvements. With Ask Reaxys you can enter phrases like: “Preparation of ritalin” for a list of reactions “mechanism of the Mitsunobu reaction” for a list of citations
- Please note: The Excel sheet shown here was edited a bit to remove a few columns.
- Another example is the optical Rotatory power of trimethylsilanes. I’d like to filter for boiling boint, eliminate nitriles, and then begin a report.
- Tautomers I’ll use dihydrofolic acid as our first example. If you look up dihydrofolic acid in Wikipedia, this is the structure you will find. But this substance actually exists in a variety of tautomeric and stereochemical forms………….so, when I look for the structure from the name in Reaxys, I am presented with 7 different choices.
- I’ll choose the same one that is shown in Wikipedia. And when I run the search “As is” I retrieve these 2 substances. The only difference between these 2 is that the stereochemistry is specified in one and not the other. Notice that “Include Tautomers” is not checked by default. I will repeat the search with the box checked….but first let’s see what Reaxys considers to be a tautomer.
- Read the slide. And here are some examples of tautomers along with an example of what is not a tautomer.
- So when I repeat the search, I retrieve 26 substances (therefore, 24 of them are tautomers)…..and here are some examples with the relevant bonds highlighted.
- Radicals are next. Here is the structure for N-acetyl-glutamic acid….and you would like to find an example where radicalization took place at this location on the molecule. You can easily do this in MarvinSketch by right-clicking the atom and selecting Edit Atom>Radical>Monovalent.
- And here is the result.
- There is an important tip that I’d like to show you….. Notice that the word radical can be spelled 2 different ways. If you are looking for the radicals of a certain substance or class of substances, a quick way to do it is to use the Chemical Name field to help isolate the radicals in the results. But you have to remember to capture both possible spellings of the word. See the next slide for an example of this.
- We’ll use Riboflavin as an example. Here’s the query (make sure that the “No Radicals” box is not checked). Then add the chemical name portion, using Contains as the data operator. This results in 4 radicals. Notice the spelling of the chemical names.
- Now, let’s compare this to what is probably the most common way to find these substances: using the Query Options on the Substance Query form. First…….delete the text portion of the query, and then run the search. This results in 24 substances….most show stereochemical variation.
- Repeat the search with the “No Radicals” box checked. This results in 23 substances. If you had large lists of substances to deal with, you could easily find the radical(s) by subtracting one list from the other. (Go back to slide 17 to show the difference and explain that it may be necessary to perform the search both ways in some cases)
- I’ll use niacin for the next example. You can find isotopes in a similar manner that was shown with radicals: by using the query features box and subtracting one list from the other……
- …or you can use the Structure Editor to put an isotope label on an atom.
- The term “Markush structure” has a fairly narrow definition in Reaxys. Here you see the claims section of a patent that describes possible structures…….
- That text is put into a tabular format in Reaxys. And this structure is referred to as the Markush structure.
- When you view patent data from the Citations results tab in Reaxys, you can view a list of substances from the patent. If there are any Markush structures associated with the patent, they will typically appear at the end of the list.
- When you search for substances from the substances page using a structure search, you will retrieve all Markush structures related to the results if you check the box for Include Related Markush.
- 27 structures are retrieved when Include Related Markush is checked. One substance is retrieved when it is unchecked.
- Try the previous search using the options shown so that you retrieve a larger list.
- If you want to view the Markush structures from a large list of structures: first, sort by mol.wt. and then jump to the last page. Most of the Markush structures in the list will be in the last few pages.