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CHEM6612: Scientific Communication in Chemistry II

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Search Chemical Structures

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Start a Structure Search

Structure drawing of octahydro-1H-benzimidazole

SciFindern

Select  Substances tag selected on SciFinder-n opening search screen then click Draw button, adjacent to search button .

Reaxys

In Quick search, click Draw button . In Query builder click  Create Structure / Reaction Drawing button .

Surprising "As Drawn" Results

SciFindern (2:18)

Although this video refers to the older version of SciFinder, it explains why "As Drawn" structure search results may include multiple substances. Use Filters after the search to focus the results.

Reaxys

"As drawn" structure searches return similar variations. You can remove many of them before running a structure search.

ChemDraw Access at Boston College

ChemDraw at Boston College BC Community Only

Expand Structure Search Results

Expand a Structure Search in SciFindern or Reaxys
Strategies SciFindern Reaxys
Remove filters ✓ ✓
Simplify the structure Eraser button Eraser button (tooltip is 'Delete')
Remove H Try attaching pre-set variable A Add/Remove explicit H button
Use pre-set variables and/or define R-groups Buttons for pre-defined variable and user-defined R-group 4 buttons. Clockwise from top left: Smart R-group, (select atoms from) Periodic table, Reaxys Group Generics, Any (pull-down menu of pre-defined variable), R-Group attachement
Make > 1 bond less specific Unspecified Bond button Single [1] button has a pull-down menu. Any [0] is one of the options.

Narrow Structure Search Results

Narrow a Structure Search in SciFindern or Reaxys
Strategies SciFindern Reaxys
Add filters ✓ ✓
Build a more complex structure ✓ ✓
Add H Pencil (draw) button adjacent to Hydrogen button Add/Remove explicit H button
Lock atoms, chains, and/or rings Lock ring fusion or formation button adjacent to Lock atoms button Lock Atoms button

Or right-click atoms to change their properties
Set stereochemistry for > 1 bond 5 buttons for specifiying stereochemistry Full pull-down menu from Single [1] button reveals 15 bond options

Or right-click bonds to change their properties