ChemInform RxnFinder


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  • In the followin sections the basic functionality of RXNFinder will be demonstrated based on use cases. After a brief introduction of the user interface a transformational search will we performed followed by a discussion of reaction schemes and reaction details. A following substructure search demonstrates the application of filters and cluster analaysis. In the last section the seamless connection to Wiley‘s Smart Article will be shown as part of a use case.
  • This is the the web client of RXNFinder. The functionality is organised in Tabs. The reaction query tab is activated by default. Result, details, retrosynthesis and selected hits tabs are populated when a search has been taken place.On the left the detailed query fields are displayed with the sub-sections Reaction, Molecule, Citation, All. These fields are used to restrict the search results appropriately. In the middle three buttons are placed to open the structure drawing tool, acces a library of structure templates and upload a structure in standard formats such as SDFile or Molfile.On the right the various search functions are available:Exact search retrieves reactions which include the identical query structureReaction Similarity search takes into account the reaction centers and a molecular similarity. The latter is based on a set of structure features such as existence of rings, arrangment of heteroatoms etc.Reaction substructure search can be performed with or without autmapping of the query. Automapping usually reduces the result set by supressing reactions which are not consistent with the query.Transformational search is based on the comparison of reaction centers in reactants and productsOn the bottom left features for query handling are available.
  • Transformational broad: only the reaction center is compared. The result set is large.Transformational medium: the reaction center and the atoms in the first sphere are taken into account. The result sets are significantly smallerTransformation narrow: first and second sphere are taken into account. The result sets a small, often zero.
  • Upload transformation.rxn from the local disk. The trifluoromethyl group is transformed into a carboxyl group.The rest of the molecule is not taken into account in the search. Transformation broad search (see explaination on slide 3) has been chosen. Submit query sends the reaction query to the cartridge.
  • 13 hits result from the transformational broad search. The 3rd hit has been chosen for further explaination of featureson the result list.If a chemist wants to get more information about the chemistry in the article he needs to go to that article andread it. A time saving alternative is to look at the reaction scheme.
  • The reaction scheme is a unique feature of ChemInform. It includes a summary of the featured reactions described in an article. The chemist sees immediately what chemistry is discussed in the article. Not only his query is shown in the scheme but also relatedInformation. The schemes have been generated by chemists at Wiley Information Service who compiled the most important information and rejectedsecondary or trivial chemistry. Other database vendors usually collect everything with the disadvantage that valuable information isoften hidden in large result sets.
  • Open articles will be discussed in another use case. The link show details opens a page where reactant, conditions and products are displayed in more details
  • Products, Reactants, Catalysts and solvents are listed in separate sections. If the reaction is part of a multistep synthesis the individual steps would show upon the left. In the given case we have a single step reaction.Structure descriptors such as molecular formula, molecular weight and INCHI‘sare assigned to the compounds. Other data typical for reactions such as yield and reaction temperature are also displayed in the details record.
  • In the next section the focus will be on substructure search, filtering and hitlist refinement. We again start from a use case: see text(A pharmacophore is a part of a molecule which is responsible for biological effects)
  • Geiparvarin.mol is uploaded from the disk. A click on the edit button opens the structure in the structure editor. The lasso functionality (top left) is used to mark the structure part in the molecule which has to be removed. A click with the eraser removes the selected part. Now an arrow is drawn on the left side of the structure fragment and the query is ready for search. Transfer to query moves the structure into the query field.
  • ChemInform RxnFinder

    1. 1. The Best Database Workflow Tool for Organic Synthesis
    2. 2. Who is it for ? Research chemists in chemical companies and at universities. Research areas:  Chemistry (Dyes, Intermediates, Agriculture Polymers)  Petro Chemistry  Pharmaceutical and Medical Chemistry  Biotechnology  Cosmetics  Food Industry
    3. 3. RxnFinder - What does it do ? RxnFinder answers questions around chemical reactions: A+B Reagents C Product  How to synthesize a potential drug?  What reaction conditions lead to the best yield?  What catalyst has been used for this functional group transformation?  What chemistry can I find beyond my query?  How to synthesize this reagent?  Is there information if this reaction fails?
    4. 4. Facts: Scope of chemistry covered: synthetic organic and organometallic chemistry Chemical reactions: about 2 million Number of substances: over 1,7 million Updating: inhouse quarterly/online monthly Journals covered: about 100 (the most important ones) Dates covered: 1990 - present (100,000 reactions added per year)
    5. 5. The abstracts in the ChemInform provide you with the latest developments in preparative chemistry, including:  novel catalysts and reagents  protecting groups  functional group transformations  approaches to heterocyclic scaffolds  new strategies in natural product synthesis
    6. 6. Search in the pool of ChemInform reactions for:  structures and substructures  reaction types  experimental conditions (e.g. reagent, solvent, yield, e.e.)  bibliographic data (e.g. author, journal, year, title)  combinations thereof
    7. 7. Unique Features:  Focus on NOVEL or improved methods, new reagents and catalysts.  Full reaction schemes show the scope and limitations of the reaction, electronic, structural and stereochemical effects.  Elimination of spurious or duplicated results through rigorous selection criteria.  ‘Failed reactions’ are also included (Yield = 0).
    8. 8. Chemical Reactions One of the main tasks of researchers in chemical and pharmaceutical Industry is to synthesize new chemical compounds applied in the areas agriculture, pharma, intermediates, dyes and more. Most efficient tool to make this work succesful is reaction databases with carefully selected and curated experimental data. Besides the reaction centers conditions and yield is the Information the researcher is interested in Reactant Product Catalyst Temperature Solvent Yield
    9. 9. Table-of-contents Section 1: The RxnFinder User Interface Section 2: Transformational Search, Schemes, Reaction Details Section 3: Substructure Search, Filters, Cluster Analysis Section 4: From RxnFinder to Wiley‘s Smart Article
    10. 10. Section 1: RxnFinder User Interface Tabs: Query, Results, Details, Retrosy nthesis, Hitlist handling Query Fields: Reaction, Molecule, Cit ation, All Reaction Search: Exact, Similarity, Substructure, T ransformational Upload or Draw structure queries Query Handling: Save, History
    11. 11. Section 2: Transformational Search, Schemes, Reaction Details Use case: One of the most powerful reaction searches is the reaction center search or transformational search. Reactions with similar reaction centers can be identified using this technique. An example is the functional group transformation, e.g., from a trifluoromethyl to a carboxyl group.
    12. 12. Section 2 Select the Search Type Transformation broad (default) Submit Query Upload or Draw the reaction query
    13. 13. 13 Hits match the Query Open the Reaction Scheme Section 2
    14. 14. Section 2 ….the Transformation he was looking for ….other Transformations which might also be of Interest The scheme is a comprehensive summary of the most important reactions in an article. At a glance the chemist gets the crucial details of reactions…..
    15. 15. Section 2 To display the Reaction Details the link Show Details is clicked
    16. 16. Section 2 This reaction details page displays: • Products Reactants • Catalysts • Solvents and • Keywords • Structure Properties • Yield • Temperature
    17. 17. Section 3: Substructure Search, Filters, Cluster Analysis Use case: Geipavarin is a natural compound known as a potential anti-cancer drug A pharma researcher identifies the 5-membered ring as being a potential pharmacophore (important part of the molecule) and wants to find products including this ring.
    18. 18. Section 3 The structure is sent to the Editor The geipavarin structure is uploaded The left part of the molecule is removed using the lasso/ delete function of the editor
    19. 19. Section 3 The arrow on the left of the structure indicates that a search for products will take place Reaction Substructure Search has been chosen Submit query To restrict the results, only recent articles are selected
    20. 20. Section 3 The Cluster Analysis provides another tool to refine hit lists. 56 hits result The researcher may be interested in a certain reagent and selects it
    21. 21. Section 3 One article remains. The reaction scheme again contains information about the context No OH protection required if the R substituents are aliphatic Protection required if the R substituents are aromatic
    22. 22. Section 4: From RxnFinder to Wiley‘s Smart Article Use Case : A research chemist who works on heterocycles wants to start from nicotinaldehyde as the reagent. The products shall have molecular weights in the range 300 to 500 Dalton (see Lipinsky‘s „Rule of 5“ defining drug likeness with 5 criteria) What has recently been published in the Journal of Heterocyclic Chemistry on this research field?
    23. 23. Draw/ Upload Nicotinaldehyde as reagent Section 4 Select the Journal JHET Exact search Recent literature Molecular weight range
    24. 24. Section 4 20 Hits result Open Article
    25. 25. Section 4 All compounds identified by the author as primary are displayed on the Abstract page
    26. 26. The Featured Compounds are the Chemistry Gateway to Wiley Online Library Section 4 Exact structure search in Wiley Online Library Views all instances of the compound in the article Links to the compound record with properties, molfile export, external links to Google, PubChem, Che mSpider
    27. 27. For more information, please visit the website at