CHEM 184/284 (Chemical Literature) - Huber - Winter 2025: Lecture 5

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

 

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)., Results, Synthesis Planner (see below), and History (i.e. the search history for your current session.)
• Note at right the Register and Sign In options and Help icon. From the Register screen (below) you can create a personal account,   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, substance 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:

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

• 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.
• Note at the top of screen, you can select either the ChemDraw JS or Marvin JS structure dawing tools. In this lecture, we will focus on the Marvin JS tool.
•  

• Also at the top, notice the "Insert structure from name" option. With it, you can search on a chemical name, CAS RN, INChi key or SMILES string, find a desired substance, and load its structure into the drawing wndow as a starting point for your drawing.

• 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 - R groups are user-defined structure fragments that can be used to defined substructures for searching.
    • Attach R-group
    • Reaction Arrow/Atom Mapping - Lets you designate which atoms                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       in reactants correspond to atoms in the products.
    • 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
• For more information on using the structure buider, see: Tips for Using Marvin JS and Video Tutorial: How to create a structure drawing in Reaxys.

Query Builder

• This screen allows you to assemble complex queries by dragging and dropping options 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 Builder 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:

​

• Note in "Melting Point" 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.
• For more information on the Query Builder, see: How do I search with the Query Builder? and Video tutorial: Using the Query Builder in Reaxys

​Results Displays

Substances Display

• 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

• 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

 

• 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:

• 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 (starting from a substance record)

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

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

 

Retrosynthesis

Clicking on the Retrosynthesis link at the top of the opening screen take syou to the screen below.

 

• Note that in order to save tretrosynthesis plans beyond your current session, you must log into your personal Reaxys account.

• The main drawing screen is identical to the structure drawing tool discussed above.
• The black bar on the lefthas links to pull up the drawing screen, retrieve saved retrosyntheis searches (if you have any).
• On the right are the options for specifying the parameters of the retrosynthesis:
  • Published - Note that, at present, the UC subscription to Reaxys only allows finding published synthesis.  The tool for creating predicted syntheses cost extra.
  • Depth of search - Lets you specify how many steps back from the final product you wish to go.
  • Number of branches
  • Max. number of steps -
  • Stop if substance is commercially available (yes/no)

Here's a sample drawn structure:

 

Here is the initial results screen. To see the generated plans, click on the View link on the right.

 

Here's the linear display of the first two results.

 

Clicking on the link to the right of a given reaction play gives the branched view of that plan.

 

• Note that retrosynthesis plans may be saved to your account, or exported for incorporation in reports.

• Clicking on one of the substances displayed will take you t the subestnce record.
• Clicking on the numbered step lets you see the reaction conditions fthat step, remove the step, or copy it.

 

© 2024 Charles F. Huber

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.