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CHEM 184/284 (Chemical Literature) - Huber - Winter 2022: Lecture 5

A two-credit course in the techniques and tools for effective searching the literature of chemistry, biochemistry, chemical engineering and related fields.

Lecture 5: Data Collections, Part II: Beilstein + Gmelin = Reaxys

A Capsule History of the Biggest Chemical Data Collection of Them All

  • In 1817, Leopold Gmelin begins publishing his Handbuch der anorganischen Chemie, attempting to summarize everything that was known at the time about inorganic chemistry. It went through seven editions before the final print edition on began in 1924.
  • In the 1880's, Friedrich Konrad Beilstein begins his Handbuch der organischen Chemie, inspired by Gmelin. It will go through three complete editions before the final print series begins in 1918.
    • Hauptwerk (H) "Basic Series" Up to 1909
    • Ergangzungswerk (E)"Supplement"
      • E(I) - 1910-1919
      • E(II) - 1920-1929
      • E(III) - 1930-1949
      • E(IV)- 1950-1959
      • E(V) - 1960-1979
    • E(III) and E(IV) overlapped in production, so their heterocycle volumes were merged.
  • In the 1980's both the Beilstein and Gmelin handbooks switch their language of publication from German to English, reflecting the rise of English as the dominant language of science.
  • The first electronic versions of the Beilstein and Gmelin data began to appear in the late 1980's. In 1987, STN (a dataase provider jointly operated by Chemical Abstracts Service and FIZ-Karlsruhe) debuted an electronic formula index to the Gmelin printed volumes - the data itself wasn't indexed, but you could more quickly locate specific compounds in the print volumes. In 1989, the Beilstein Institute launched an electronic version of Beilstein on STN, with full bibliographic, structure and numeric data searching. A similar version of the Gmelin file launched in 1991.
  • About this time, the print versions of both Beilstein and Gmelin were dying, caught between rising production costs and static or declining library budgets. More and more academic libraries were canceling their subscriptions, which in turn forced more price increases, which caused more cancellations, etc. Moreover, as the volume of chemical literature grows, it's taking longer and longer to complete the printed editions.
  • The CrossFire client-server interface for the Beilstein database was released in 1995 by Beilstein Information Systems. It quickly gained popularity as a relatively economical alternative to the printed edition of Beilstein. A consortium of Midwestern universities struck a deal to mount the database on their server. This deal was later expanded to cover all interested North American universities under the name Minerva.
  • In 1997, the print version of Gmelin ceases publication.
  • In 1998, Beilstein Information Systems was purchased by the publishing giant, Reed-Elsevier, and merged into their recently acquired MDL, Inc. division, long-time providers of chemical data manipulation software.
  • Late in 1999, an agreement was reached between the creators of the Gmelin database, and Reed-Elsevier, the owners of the Beilstein database, to restart Gmelin, including coverage of the "missing years". Gmelin is now once again being produced, and the "missing years" are being filled in, in the CrossFire Gmelin database. Print Beilstein, like its Gmelin counterpart, is dead.
  • Several UC campuses purchased subscriptions to one or more of the CrossFire databases, but negotiations for a systemwide licence were finally concluded at the end of 2003. The UC's access was not through the Minerva consortium server (at the University of Wisconsin) but through a new server located at MDL itself.
  • Not long thereafter, MDL developed a Web interface for Beilstein, Gmelin and other chemical databases called DiscoveryGate. Elsevier began promoting DiscoveryGate heavily as a replacement for CrossFire, but continued to maintain both platforms.
  • In 2007, Elsevier sold MDL to Symyx Technologies (later merged with Accelrys; now known as Biovia.) In the sale, Elsevier retained the Beilstein and Gmelin databases and the CrossFire platform Symyx/MDL retained the DiscoveryGate platform.
  • Soon after, Elsevier decided that they wanted to have their own Web platform for the databases, and began development of the Reaxys system, which was released in late 2008.Elsevier also integrates its Patent Chemistry database, which indexes organic chemistry patents, into the Beilstein data for the Reaxys platform.
  • In January 2009, the Reaxys platform is launched.
  • In late 2009, Elsevier announced that the CrossFire platform would be dropped at the end of 2010, and the Beilstein and Gmelin databases would be withdrawn from DiscoveryGate at the same time. The University of California, after lengthy negotiations, switched from CrossFire to the Reaxys system as of January 1, 2011.

Note: In this course, we will be concentrating on the Reaxys database.  If you are interested in the organization of the print versions of Beilstein and Gmelin (which you may encounter in some libraries!) see the accompanying page.

Reaxys Content

  • The Reaxys database contains records from the mid 1800's to the present, for over 26 million substances, over 40 million reactions from 1771 to the present, in organic chemistry. Current data is indexed from major organic chemistry journals, plus organic chemical patents from the United States (USPTO), Europe (EPO)and Patent Cooperation Treaty (WIPO) patent offices. The database is updated weekly.
  • The inorganic and organometallic information derived from Gmelin contains over 2.2 million compounds and 1.6 million reactions from 1772 to the present, and 1.1 million citations, including titles and abstracts from 1995. Current data comes from major journals in inorganic and organometallic chemistry.
  • About 400 journals in total have been indexed for full chemical content.  Recently, Elsevier has begun adding data from some 16,000 journals indexed by other Elsevier databases (Scopus, Embase, Compendex, et al.)  Biblioraphic data from these journals is also being retroactively added.  For more detail on Reaxys coverage, see this Content FAQ page (https://service.elsevier.com/app/answers/detail/a_id/11579/supporthub/reaxys/kw/periodicals+indexed/)
  • Reaxys also searches chemical substance information from PubChem, and eMolecules.  The former is the National Library of Medicine's free chemical substance index; the latter is an interface for structure searching chemical substance information from vendors.
  • As of Nov. 2020, the number of records in Reaxys itself is: over 63 million documents, about 125 million substances (33.4 million of which are in Reaxys proper, the rest in PubChem) and over 53 million reactions.
  • Reaxys is text searchable, structure searchable, and data searchable, and in any combination of the above.

Reaxys System Requirements

  • Reaxys is a Web-based system. It is compatible with Windows 2000 through Windows 10, and Mac OS X 10.4 or higher.
  • Browser requirements: Internet Explorer 11 or higher, Microsoft Edge 27 or higher, Firefox484 or higher,, Google Chrome 53 or higher and Safari 9 or higher. In all cases JavaScript and cookies must be enabled.
  • Reaxys no longer requires Java for any of its functionality.
  • For more details, see the Reaxys Tech Specs page (https://www.elsevier.com/en-gb/solutions/reaxys/learn-and-support/tech-product-info
  • Reaxys has integrated the Java-free editor Marvin JS from ChemAxon and ChemDraw JS from Perkin Elmer into its interface. Both tools can accept structures copied from external structure editors. See the Reaxys Support Center's FAQ on using external structure editors for more details.

© 2020 Charles F. Huber

Creative Commons License
This work by Charles F. Huber is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Based on a work at guides.library.ucsb.edu

Screenshots of Reaxys are copyright © 2018 by Reed Elsevier Properties SA and are used for fair use educational purposes only

Reaxys (https://www.reaxys.com)

 

Reaxys - New Basic Search Screen

Reaxys Basic Search

  • The Reaxys Basic Search screen allows you to enter search terms, including keywords, molecular formulas, Registry Numbers, etc., and/or to draw substance structures or reaction diagrams (see below for details.).
  • Note the options at the top of the screen for Query Builder (the Reaxys advanced search mode, discussed below)., ResultsSynthesis Planner (see below), and History (i.e. the search history for your current session.)
  • Note at right the Sign In option and Help icon. From the Sign In screen (below) you can log into your personal account, or register to create one.  Personal accounts allow you to save searches and answer sets, and create search alerts.

  • The Help option in Reaxys is structured as an FAQ (Frequently Asked Questions) page, and is not particularly detailed.

Basic Searching

  • You may enter keywords, subjstance names, molecular formulas or Registry Numbers in the search window, and click the "Find" arrow on the upper right of the screen..  Reaxys will search across its collections of documents, , substances and reactions, and return a listing of answer sets.   Fpr example, a search on he reducing agent "sodium borohydride" returns the following:

Reaxys basic search for sodium borohydride

while a search on "retro-Diels Alder", a reaction type, yields:

Reaxys search results for retro-Diels-Alder

  • Note the "New" and "Edit" buttons on the upper left.  If you wish to do a new search, be sure to click the New button, rather than clicking on "basic Search" or using the browser back button.  Otherwise, your current search will be left in the system and your new search will be combined with the previous one.
  • To view an answer set, click the "View Results" tab to the right of fthe desired answer set.

Structure Searching

  • Clicking on "Create Structure or Reaction Drawing", opens the the "Marvin JS" structure drawing app.

Reaxys Marvin JS structure drawing tool

  • Component Tools
    • Top horizontal row:
      • Clear
      • Import
      • Export
      • Undo
      • Redo
      • Cut 
      • Copy
      • Paste
      • Zoom All
      • Clean - normalizes bonds and angles
      • Clean 3D - does the same for 3D structures
      • 3D Rotate
      • Add/Remove Explicit Hydrogens
      • Show Settings
      • About Marvin JS
    • ​Left vertical column
      • ​Rectangle Select Tool - click and drag a box around areas to delete, move, etc.
      • Delete
      • Draw Bonds - click on lower right corner of box to see available bond types
      • Draw Chain - click and drag to draw chains of variable length
      • Max Substitution Count
      • Lock Atom
      • Repeating Group - Select a group of atoms, then designate how many times that group may repent in the molecule.
      • Smart R Group
      • Attach R-group
      • Reaction Arrow/Atom Mapping
      • Manual Mapping
    • ​Bottom Horizontal Row
      • Cyclopropane ring
      • Cyclobutane ring
      • Cyclopentane ring
      • Pyrrrole ring
      • Cyclohexane ring
      • Benzene ring
      • Cycloheptane ring
      • Cyclooctane ring
      • Glucopyranose
      • Glucofuranose
    • Vertical right-hand bar
      • Abbreviated Groups (e.g. Me, Et). Can also access by pressing the Spacebar.
      • Reaxys Group Generics - generic acyclic and cyclic organic groups
      • Periodic Table - for selecting non-carbon atoms
      • A - Any atom. click in right-hand corner to select variable groups like Q, M, X.
      • Hydrogen 
      • Carbon 
      • Nitrogen
      • Oxygen 
      • Sulfur
      • Fluorine 
      • Phosphorus
      • Chlorine
      • Bromine
      • Iodine 
    • Structure search options (right hand side)
      • As drawn
      • As substructure
      • Similar
      • Check to include, leave blank to exclude: Tautomers, Stereo variants, Additional ring closures, Related Markush, Salts, Mixtures, Isotopes, Charges, Radicals.  
      • More options:
        • Ignore atom mappings
        • Keep Fragments, 
      • Specify:
        • Number of atoms,
        • Number of ring closures
        • Number of fragments
    • At top, middle-right, "Create structure template from hame" - allows you to enter a chemical name, CAS Registry Number, SMILES string or InChi string, and use that molecule as a starting structure for modification.

Query Builder

Reaxys query builder screen

  • This screen allows you to assemble complex queries by dragging and dropping optoins to the center scree
  • At the top right are buttons to select searching in Reactions, Substances or Documents
  • Below that are four "quick links" for searching:
    • Structures
    • Molecular Formula
    • Chemical Abstracts Service Registry Numbers (CAS RN). Note that not all substances in Reaxys have associated CAS RNs, even though an RN may exist for the substance.
    • Titles, Abstracts and Keywords
  • To the right of those links are three tabs:
    • Fields (see below for details)
    • Forms - These are saved Query Builde searches
    • History - List of your previous searches in that session.
  • Along the right hand side are drop-down menus of properties to choose from:
    • Topics and Keywords - keyword searching for substances, reactions, documents.
    • Identification - chemical name, Element symbols, Molecular formula, Molecular weight, Registry Number, InChi key and many more
    • Physical properties - such as: melting point, boiling point, and many more
      • Note that in numerical properties, you can search for a specific number, or a range.
      • Note also that for properties where conditions can affect the property, you can specify the conditions. Example: Specify pressure for a boiling point measurement.
    • Spectra
    • Pharmacological data
    • Ecotoxicology
    • Other (substance properties)
    • Reactions - yield, solvents, etc.
    • Bibliography - authors, journals, etc.
    • Other databases = You can search PubChem, eMolecules, LabNetwork and the Sigm-Aldrich catalog from within Reaxys
    • Structure
  • ​To add a given field to your query, hover your cursor over the desired field. When you see the four-pointed cursor appear, hold down the mouse button (left button for Windows) and drag the field to the query box.
  • When you do, four new options will appear on the upper left (see image beelow):
    • Import - lets you import saved queries
    • Save - lets you save a query form for future resuse
    • Reset form - Clears the vlalues you've entered in the from, but leaves the fields in place
    • Delete All - Removes all fields and values from the Query Builder screen.
  • Here's an example of such a query:

Reaxys query builder example

  • Note in "Melting Poilt" you can search for the presence of melting point data, as well as for numeric ranges, and you may specify the solvent from which the solid was recrystallized.

Results Displays

Substances Display

Reaxys display list of substances

  • At the top of list, the total number of substances found is given, in this case, 44.
  • Below that is a record of how many substances you have selected (in this case, 0) Two the right of that are two buttons
    • Export - Lets you export data in a variety of formats. Note: You must have a Reaxys account, and be logged in to use this feature.
    • Preparations - Takes you to a list of rections in which one of the substances in your list is a product.
  • To the right is a drop-down menu for sorting your results. The default sort order is by number of references.  A drop-down menu also offers: Number of fragments, Molecular weight, Molecular formula, Publication year, Commercial availabilty and Reaxys Registry Numbers, in ascending or descending order.
  • Also on the right, you can choose between tabular display (shown) or grid display of structure diagrams for the answer set.
  • On the left-hand side are options for filtering your results. Note that you can filter by either limiting to substances with the selected property or excluding substances with the selected property.
  • The brief records given a structure diagram, chemical name, molecular formula, molecular weight, Reaxys Registry Number, and CAS Registry Number (where available). Clicking on a property displays a drop-down list of the values of that property which appear in the substances in your anser set. Classes of properties available are:
    • Structure - Use to search for a particular structural feature within the substances in your answer set.
    • Substance Classes - includes Functional Group classification, and Ring classification
    • Molecular Weight 
    • Number of fragments
    • Availability - Is the substance commercially available for purchase, has a known preparation, or neither?
    • Availability in other databases - Is the substance listed in other databases, such as  PubChem, eMolecules or the Sigma-Aldrich catalog (among others)
    • Available Data - Gives a list of the data types which are available for one or more substances in your list.
    • Document Type - Source document(s) in which one or more of the substances appear, such as articles, patents, etc.
    • Publication Year - Year in which one or more of the source documents were published.
    • When you filter by a property, the records display will expand to show the values for that property for each substance.
  • The brief record also tells you how many examples of different types of data are avaialb, and links out to the associated reactions and documents for the substance, as well as preparations.
  • Clinking on the substance name opens up all the property fields.  Clicking a specific property type opens up just that section.
  • Clicking on the structure diagram opens up link buttons: Show Commercial Avaiability, Zoom, (enlarges the structure diagram), View Options and Create Synthesis Plan. Optons lets you:
    • Find Similar Structures
    • Find Related Markush structures
    • Copy to query (copies the structure in the structure window, where you may modify it and research.)
    • Use as filter (filers answer set to those substances where this is a substructure)
    • Open in database (the other accessible databases, such as PubChem.)
  • Create Synthesis plan lets you build a synthesis plan with the substance as a product, either manually or with "autoplan".
  • Check boxes let you select substances for export.

Reactions Display

Reaxys display list of reactions

  • Note that, next to the number of reactions is an Export button, and a Toggle Conditions button (hides/displays reaction conditions) In between is a Plan button for creating a synthesis play. It is inactive unless you have selected a reaction by checking the box next to the reaction.
  • At the right is the drop-down menu of sort options for reactions. The default option is Reaxys Ranking. Other options are: Number of References, Reactant Availability, Product Availability, Molecular Weight of product, Yield,  and Publication Year (of source reference) in ascending or descending order.
  • Note that the filter options are now suited to reactions.
    • Structure
    • Yield
    • Reagent/Catalyst
    • Solvent
    • Catalyst Classes
    • Solvent Classes
    • Product Availability
    • Reactant Availability
    • Reaction Classes
    • Document Type (of source document)
    • Publication Year (of source document)
    • Single step reactions only
    • Experiemntal procedure available only
  • Below each reaction is a toggle button to hide ordisplay reaction conditions,and the individual documents in which they appear. There is a link to the full Reaxys document record.
  • Find Similar finds reactions according to a similarity algorithm. Simialr reactions are lsited by degree of similarity and may contain or lack fstructural features which appear in the original source reaction.
  • The next button, which shows the Reaxys number for that reaction lets you create a synthesis plan based on that reaction.

Documents Display

Reaxys display of documents answer set

 

  • Note that the filter options are now appropriate to documents.
    • Index Terms (List) - keywords that appear in records in the answer set
    • Index Terms Reaxys Tree - controlled vocabulary terms used by Reaxys that appear in answer set records.
    • Publication Year
    • Document Type
    • Authors
    • Patent Assignee
    • Journal Title
    • Substance Classes - includes Functional Group Classes and Ring Classes
    • Reaction Classes
  • The index term (Reaxys Tree) option lets you work through a hierarchical arrangement of subject terms  See the example below for named reactions:

Reaxys Tree index term hierarchy

  • Default sort for documents is by relevance, but you can also sort by publication year, document type or "cited by".
  • Note the links to sujstances and reactions in each document as well as to full text.  For journal articles, Reaxys connects through UC-e-Links when you search from a UC IP address.

Synthesis Planning

  • From a substance record, when you click on Synthesize, and select Autoplan, you first see this options screen:

Reaxys synthesis autoplan options

  • After selecting the desired options, click "Create Plans", and Reaxys does its work.  Here's an example for Taxol.

Reaxys synthesis plan for taxol

  • Note that you can click on any molecule in the reaction diagram and add an autoplan for its synthesis to your reaction tree.
  • If you have created multiple synthesis plans for a given substance, you can select them from the list on the left.
  • Note that you can assign a name to a synthesis plan, using the tool on the upper left.
  • If you create a personal account in Reaxys, you can save synthesis plans (as well as searches and search alerts.)

© 2020 Charles F. Huber

Creative Commons License
This work by Charles F. Huber is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Based on a work at guides.library.ucsb.edu

Screenshots of Reaxys are copyright © 2020 by Reed Elsevier Properties SA and are used for fair use educational purposes only.

 

 


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