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Inorganic and organometallic chemistry: The Reaxys solution_may24_cf

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Our Reaxys webinar, presented by Chris Flemming on May 24th showed attendees how to: …

Our Reaxys webinar, presented by Chris Flemming on May 24th showed attendees how to:

- Draw and search for organometallic compounds
- Set up search strategies for finding inorganics and organometallics
- Use ligand codes

Published in: Technology, Education

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  • Welcome to this webinar about Reaxys, my name is Ani and I’m your host today. I’m here with our Reaxys expert Chris. Chris has a chemistry background and has been delivering Reaxys trainings for several years to a broad range of research chemists. She works closely with our product team and customers to understand how Reaxys provides a solution for differing chemistry research workflows. Today she’ll be introducing you to searching for inorganic and organometallic substances in Reaxys, showing how to set-up basic search strategies.   We’ll be placing this webinar online so you can listen to it again, at your own pace.  
  • Welcome to this webinar about Reaxys, my name is Ani and I’m your host today. I’m here with our Reaxys expert Chris. Chris has a chemistry background and has been delivering Reaxys trainings for several years to a broad range of research chemists. She works closely with our product team and customers to understand how Reaxys provides a solution for differing chemistry research workflows. Today she’ll be introducing you to searching for inorganic and organometallic substances in Reaxys, showing how to set-up basic search strategies.   We’ll be placing this webinar online so you can listen to it again, at your own pace.  
  • 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.
  • During the session you can send us your questions using the chat function on the webinar control panel, and towards the end of the sessionwe will try and answer all of your questions. If we run out of time, we will send you a Q&A by email.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.Chris, welcome, could you briefly introduce yourself and tell us all about reaxys?
  • Thank you, Ani. And thank you everyone, for joining us.
  • There’s an enormous amount of information in Reaxys, including data on catalysts, biomolecules, ceramics, glass, and alloys.You can access data relevant to electronics, magnetics, optics and nanoscience; zeolites and laser materials, as well as solid-state compounds, doped materials and minerals.
  • During this session I would like to show a variety of ways to find inorganic and organometallic substances.It’s important to know that you can find what you want in a variety of ways, and sometimes it is best to perform more than one search. However, generally speaking inorganics should be searched by name or molecular formula and organometallics should be searched by structure.
  • Here are a few of the questions that can be answered by using Reaxys.
  • Structure…name…..MF……CAS number. What’s the best way to formulate the query? As mentioned previously, the name and molecular formula fields are usually the best way to find inorganics.
  • But with certain common substances, using “Generate Structure from name” is a quick and easy way to find a substance. For example this search results in 224 substances, including salts, mixtures, and isotopes.
  • CAS number, Name, and Molecular formula fields are also easily used. Here we see the “Form-based” query tab.
  • If you know the CAS number, you can simply type it in, using hyphens.
  • With the MF field, it is best to use alphabetical order and capital letters when appropriate(Though “C”, “H”, and some elements may be written in either upper case or lower case, other elements must be written with the first letter in upper case and the second letter in lower case. For example lower case “ni” will be interpreted as nitrogen and iodine, but when it is written as “Ni” it will be interpreted as nickel). However, in general this field is very forgiving ……and in this case, these formats also work. You can also use Ranges or a Wildcard when needed.
  • With the Name field, it is not necessary to use capital letters, wildcards are allowed, and as with most fields, data operators are available.
  • You can also select entries from the index. For example, clicking here opens the index where you can begin typing. Then click on the appropriate name, begin typing again, etc. Click the Transfer button. That was the Form-based tab. Now we’ll look at the Advanced tab.
  • You can also do CAS number, Name, and MF querying from the Advanced tab.
  • The Advanced Search feature enables you to drill into the database and offers hundreds of searchable fields and data operators for creative querying. Advanced Search queries use the following syntax:<fieldcode> <operator> <field value>We already mentioned the CAS number…….the “Preferred Registry Number” lists the single CAS Registry Number that has been selected as the best choice for a compound from the one or more CAS RNs that may be present in the database. We’ve already looked at the “Chemical Name” field, so let’s move on to the “Chemical Name Segment” field and compare them. The name you enter will appear in a segmented manor. For example, a “chemical name” search for phosgene retrieves 51 substances.When you add wildcards to it, you will retrieve 224 substances with names like this.There is a subtle difference when you use phosgene in the CNS field. Notice that the name does not have letters immediately before or after the word. Instead it is “segmented” by a hyphen or bracket or something similar.
  • And now the MF fields……
  • The Linear Structure Formula contains a linearrepresentation of the structure of a compound. Use the Linear StructureFormula field when searching for compounds: with a particular charge……and for doped compounds. Divided into fragments if: discrete polyatomic ions, molecules, orligands with unknown coordination exist. For example, if you are searching for zirconium silicate, use IDE.LSF='Zr(4+)*O4Si(4-)‘.For doped compounds, the formulas of the dopants are separated from the basiscompound by the designation “dot”. For example, if you are searching for tin-doped chromium, use IDE.LSF=crdotsn.
  • Use the Fragment MolecularFormula field to retrieveall compounds containing a givenfragment, and the fragmentsthemselves. Let’s find substances containinghexacyanoferrate(III)fragments, using a wildcard.
  • The MF Range field allows the searching of ranges with molecular formula. It is calculated during the search "on the fly". Search for substances containing Barium, copper, and a variable amount of oxygen.
  • And there’s one more field to look at and that is the field for alloys.This field enables you to search for alloys, glasses and ceramic materials. The content of each constituent, an element or compound, is displayed in the results by a percentage value. The percentage may be shown as weight %, atom %, volume %, or unknown %.  
  • Using names and formulas is the best way to find inorganic substances, but with the organometallics and coordination substances, structures are your query of choice. For the most part, drawing these queries is no different than drawing any type of structure query…….the same query features are used.
  • Use templates to avoid possible mistakes from drawing the whole structure. To find coordination complexes of crown ethers, like these, use the templates in MarvinSketch, draw bonds, and use “M” for any metal. Search with substitution on heteroatoms.
  • Use Link Nodes to find copper diaza rings of varying size, like these. • Link Nodes are used to define repeating units. • The units can be rings or chains. • The Link Node is the atom that is selected. Anything within the brackets of the Link Node will be repeated. In MarvinSketch, rightclick the atom and select Edit Atom>Link Node and then select a number.
  • To find cyclopentadienyl-palladium complexes use either the “Single/Double Bond” or the “Any bond” on the Cp ring to ensure that no substances are missed. For this example: 1. Click the cyclopentane template. 2. Use the Structure Selection tool to select the ring. 3. From the Object menu, select Bond>Type>Single or Double. 4. Use the Single Bond tool to add 5 bonds to the structure. 5. Use the Lasso Select tool to click and drag each bond to a common point. 6. Click the More button, select Pd, click Close. Click the common point of the structure. • Click the Transfer Query button in MarvinSketch. • Set the Query Options to Substructure on all atoms in Reaxys
  • The ligand fields are divided into one-center ligands and multi-center ligands. A one-center ligand has at least one non-metal atom bound to one metal atom. A multi-center ligand has at least 1 non-metal atom bound to at least 2 metal atoms. • Multi-center ligands are indexed in Reaxys as both multi-center ligands and as individual one-center ligands. • These fields are powerful tools for finding ligand- metal complexes. • They are different from the other molecular formula fields in Reaxys because they use Ligand Codes, rather than element symbols.
  • Each type of ligand can be searched using the fields: Base Formula, Formula, Count. Base formula – This is the abstract formula of the coordination center(s) and all ligand codes of a compound. The ordering of the formula is as follows: 1. all metal centers (ordered alphabetically) 2. the ligand codes are ordered in the following manner: A, CN, CNO, CNR, CNS, CO, CS, D, L, Q, X 3. within the same ligand types, they are ordered on ascending denticity and the frequency is not taken into consideration Formula – the ligand formula field contains the ligand codes which describe the elements (in groups) and the number of the atoms that are connected to the central metal atom(s). A ligandformula is given for all structured compounds or fragments which contain at least one metal atom and at least one coordinating ligand atom of the classes "L, A, D, Q, X" or a special ligand (for special ligands, the substituent R has no further bond to metal atoms). The denticity of a ligand is put in parentheses in front of the ligand code. If a ligand is described by >1 code, they are ordered alphabetically and the denticity of the code is put in parentheses in front of the code. Count – the frequency of a certain ligand within the compound is indexed in this field. Note: The ligand formula field(LIGO.FORM) describes only the denticity of the ligand not the connectivity to the metal center(s).
  • Now that we’ve introduced you to this type of searching in Reaxys we would like to use the second half of the presentation to tell you more about the topic you prefer. Please let us know what you would like to learn.
  • We have come to the end of this Reaxys introduction webinar. Thank you for attending. Thank you Chris for your presentation.  The next online Reaxys session will be June 21. 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 the Q&A by e-mail 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.  
  • Transcript

    • 1. Your host: Ani Marrs Your presenter: Chris FlemmingWelcome to our Reaxys webinar!Searching for Inorganic and OrganometallicSubstances in Reaxys
    • 2. Your host: Ani Marrs Your presenter: Chris FlemmingWelcome to our Reaxys webinar!Searching for Inorganic and OrganometallicSubstances in Reaxys
    • 3. Need to know•Webinar control panel: ‘chat’ for questions or ‘ask a question’ minimize option for full screen view•Q&A after presentation
    • 4. Welcome to our Reaxys webinar!Searching for Inorganic and OrganometallicSubstances in Reaxys
    • 5. Alloys Dyes Glass Materials ElectronicsBiomolecules Polymers Batteries Ceramics
    • 6. Agenda •Search for inorganic substances using name, molecular formula, and structure queries •Search for organometallic and coordination compounds using structure queries •Search for organometallic and coordination compounds using ligand codes
    • 7. Inorganics
    • 8. I Need Information……. How can I find property data for copper sulfate? Are there any examples of reactions using Tin chloride as a catalyst?Is there any information on tin-doped chromium?
    • 9. How do I formulate the query? Structure Name Molecular CAS # Formula Stannous chloride Cl2Sn 7772-99-8 Tin (ii) chloride SnCl2 Tin dichloride
    • 10. Generate a Structure Copper sulfate
    • 11. Form-based Tab - Identification Data FieldsCASnumber, Name, andMolecularformulafields
    • 12. CAS NumberCASnumber, Name, andMolecularformulafields 7758-99-8 Include hyphens Retrieves 1 substance
    • 13. Molecular Formula These formats also work: Cu(SO4) Retrieves 9 CuSO4 substancesCASnumber, Na O4CuSme, andMolecular Best to use:formulafields Alphabetical order Capital letters CuO4S when appropriate Ranges and wildcards allowed
    • 14. Chemical NameCAS Retrieves 3number, Na substancesme, andMolecularformula Capital letters notfields necessary copper sulfate Wildcards allowed Use operators: is, starts with, ends with, and contains
    • 15. Chemical Name - Index Retrieves 6 substancesCASnumber, Name, and Use the Index toMolecular select namesformulafields copper sulfate
    • 16. Advanced TabThe Advanced Search tab offers hundreds of searchable fields and data operators for creative querying. CAS number Name Molecular Formula
    • 17. Advanced Tab - Name and CAS number fieldsAdvanced51 substances, i.e.Retrieves Search queries use IDE.CN = *phosgene* the following syntax: IDE.RN =7758-99-8 IDE.CN = = phosgene IDE.CNS phosgene “phosgene”“phosgene, (20percent)”<fieldcode> <operator> <field value>Retrieves 224 substances,i.e. “triphosgene”“phosgenedichloromethane”Retrieves 90 substances, i.e. “phosgene-pyridin” “Best” of several “[(11)C]phosgene” CAS numbers.
    • 18. Advanced Tab – Molecular Formula fields
    • 19. Advanced Tab – Molecular Formula fields(Linear Structure Field)Use alphabetical order IDE.LSF=Zr(4+)*O4Si(4-) tin-doped chromium IDE.LSF=CrdotSn Zirconium silicateUse the Linear Structure Use the LinearFormula field when Structuresearchingfieldcompounds Formula for whenwith a particular charge searching for doped compounds.For multi-fragment For doped compounds, thecompounds the dopants are formulas of theMol. formulas of the basis separated from individualfragments are separated compound by thefrom one another by designation “dot”.asterisks (*).
    • 20. Advanced Tab – Molecular Formula fields (Fragment MF Field)This field is searchable butnot displayable IDE.FMF = C6FeN6(3-)* Use the Fragment Molecular Formula field to retrieve all compounds containing a given fragment, and the fragments themselves. Find substances containing hexacyanoferrate(III) fragments
    • 21. Advanced Tab – Molecular Formula fields (MF Range Field)This field is searchable butnot displayable IDE.MOFO = Ba2Cu3O(6-8)The MF Range field allowsthe searching of rangeswith molecular formula. It iscalculated during thesearch "on the fly".
    • 22. AlloysThis field enables you tosearch for alloys, glasses andceramic materials. Thecontent of eachconstituent, an element orcompound, is displayed inthe results by a percentagevalue. The percentage may beshown as weight %, atom%, volume %, or unknown%.
    • 23. Organometallics and Coordination Compounds
    • 24. StrategiesUse templates
    • 25. StrategiesUse Link Nodes 5-membered ring 7-membered ring 8-membered ring 6-membered ring
    • 26. StrategiesUse bond Types Drag bonds to a common point
    • 27. Ligand Search Fields One-center ligand Multi-center ligand
    • 28. Ligand Codes Use these field codes when setting up your queries There are also “special” ligand fields
    • 29. Example Find substances where iron is bonded to at least one CO, at least one C, and also bonded to anything else. Query is: LIGO.BASE = fe* AND LIGO.FORM = l AND LIGO.FORM = co
    • 30. PollThe poll should appear on your screen shortly…
    • 31. Let’s take a look at Reaxys ……. …by going to Reaxys.com
    • 32. Questions and Answers
    • 33. Thank You For more information and questions please contact bdtraining@elsevier.com Our next Reaxys webinar will be June 21 and will it will be an introduction to Reaxys. Go to www.trainingdesk.elsevier.com/reaxys for all training related materials Please fill out the survey that appears on your screen after leaving the webinar.