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CHEM6612: Scientific Communication in Chemistry II


Search Chemical Reactions


  • Identify acceptable variants of a reaction: substituents, functional groups, etc.
  • Try a variety of approaches: search by functional groups, structure, substance records, and text, or search for [retro]syntheses
  • Use filters to focus search results

By Functional Groups

Convert a glycol to an aldehyde


Draw a reaction using broadly defined R-groups, then search.

Reaction drawing: glycol reactant converting to aldehyde product. A user-defined R-group is highlighted. Tooltip contains definition: A (any atom except H), H.


Use Query builder.

  1. Scroll through Fields on the sidebar and click Reactions
  2. Click Reactant to create a querylet
  3. Change is to contains, enter "glycol"
  4. On the Fields sidebar click Product
  5. Change is to contains in the querylet, enter "aldehyde"
  6. Click Reactions button

From Structures

In addition to locking atoms, chains, or rings, you can specify:

  • which bond(s) should be formed or broken
  • which atoms are reaction centers ("mapped")


Specify bonds to form or break with  Button to mark bonds

Map atoms with  Map atoms button


Right-click a bond and select Bond properties. Under Reacting center, click an appropriate option.

To map atoms, click  Manual Mapping button , click an atom in the reactant, and then drag your cursor over to the appropriate atom in the product.


  1. Right-click an atom in the reactant
  2. Click Atom properties
  3. Click the lock item near Map
  4. Assign a number
  5. Repeat for the corresponding atom in the product

From Substance Records


  1. Search for the substance
  2. Click Reactions button
  3. (Filter by Substance Role of Product)


  1. Search for the substance
  2. Click Reactions
  3. (Click Preparations)
  4. Try the Find Similar options

Text Searches for Reactions

"Text" refers to titles, abstracts, and descriptive terms in database records.


  • Get started with an overview of text searching
  • Truncate or stem the right side of a character string using *:
  • "Wildcard" inside a character string using *:
  • More tips


  • Truncate or stem the right or left side of a character string using *:
  • "Wildcard" inside a character string using *
  • Contains is similar to searching for *character string*

Retrosyntheses or Syntheses


Click Create Retrosynthesis Plan within a substance record.


UseCreate synthesis plans buttonin a substance record to generate potential synthetic pathways