CHEM 116BL (Laverman, Spring 2024): Reaxys

Reaxys

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 Apr. 2022, the number of records searchable  in Reaxys is: over 95 million documents, about 253 million substances and over 58 million reactions.
• Reaxys is text searchable, structure searchable, and data searchable, and in any combination of the above.

Searching Reaxys

Reaxys is restricted to on-campus access, or through the VPN or proxy server. If you go to the link in the Databases list, you will be prompted to log into the proxy server with your UCSBnetID and passord if you have not already done so.

 

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 option s 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 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:

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 reigh to fthe desired answer set.

Structure Searching

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

• 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
    • 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 varianle length
    • Increase Charge
    • Decrease Charge
    • Repeating Group - Select a group of atoms, then designate how many times that group may repent in the molecule.
    • Smart R Group
    • Use scroll button to see the following options
    • Attach R-group
    • Reaction Arrow/Atom Mapping
    • Increase Radical
  • ​Bottom Horizontal Row
    • ​Abbreviated Groups - click on button, then search for shortcut groups
    • Reaxys Group Generics  - select from table of generic groups
    • Cyclopropane ring
    • Cyclobutane ring
    • Cyclopentane ring
    • Cyclopentadiene ring
    • Cyclohexane ring
    • Benzene ring
    • Cycloheptane ring
    • Cyclooctane ring
    • Glucopyranose
    • Glucofuranose
  • Vertical right-hand bar
    • Periodic Table - for selecting non-carbon atoms
    • Hydroge, Carbon, Nitrogen Oxygen, Sulfur, , Fluorine, Phosphorus, Bromine and Iodine get indivdual entries scroll down to see all"
    • Asterisk 
    • A - click in right-hand corner to select variable groups like Q, M, X.
  • 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, Kep 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

• This screen allows you to assemble complex queries by dragging and dropping optoins to the center scree
• Along the right hand side are drop=down menus of properties to choose from:
  • Basic Indexes - 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
  • 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
• ​Here's an example of such a query:

​

• Note the options along the top, including the choice to search substances, reactions or documents.

​Results Displays

Substances

• At the top of list, the total number of substances found is given.
• 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 avaiabilty and Reaxys Registry Numbers, in ascending or descending order.
• On the left-hand side are options for analyzing and filtering youyr results.
• The brief records given a structure diagram, chemical name, molecular formula, molecular weight, Reaxys Registry Number, and CAS Registry Number (where available).
• 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 subtance name opens up all the property fields.  Clicking a specific property type opens uup just that section.
• Clicking on the structure diagram oeins up Options and Snthesize.  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.)
• Synthesize 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 the analysis/filter options are now suited to reactions.
• Sort default is " Reaxys  Ranking"; you may also sort by number of references, reactant availability, product avaiability, molecular weight of product, yield, and publication year in ascending or descending order.
• You can display reaction conditions info, get data on individual reactants and products, and add reactions to a synthesis plan.

Documents Display

 

• Note tht the analyze/filter options are now appropriate to documents.
• 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 subjstances 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.