ChemIDplus - Part 2

Welcome to Part 2 of the ChemIDplus tutorial. In this tutorial, you will learn how to:

  • Search for chemical structures in order to identify a substance
  • Locate substances that share a similar structure
  • Locate substances that contain a specific structure

View Part 1 of this tutorial to learn how to search for substances by name/synonym, physical properties, molecular weight, and other criteria.

How to use this tutorial:

  • Follow along in the live ChemIDplus site in the right side frame.
  • Use the arrows below to navigate through the tutorial.
  • Jump to a specific section by clicking the menu button with three lines in the upper right-hand corner.
  • Important note: Use the arrows below or the menu button to navigate backwards or to a previous section. Using your browser's back button may cause you to exit the tutorial.

Click the arrow below to continue.

Getting Started with Structure Searching

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A chemical structure shows the atoms and their arrangement, including the types of bonds and any positive or negative charges.

The structure is important because it relates to the physical and chemical properties of the substance.

You might search for a chemical structure to:

  • identify it
  • look for substances that contain it
  • find substances with a similar structure

The ChemIDplus Advanced search interface allows you to search for similar structures and substructures. You can also draw your own structure to search with.

Getting Started with Structure Searching

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The Structure search is on the right-side of the Advanced search interface. 

There are several structure search options. Click the information button (the small i icon) next to Structure Search Options to learn your choices, and then answer the question below. 

Which structure search option will allow you to find chemical structures that are at least 70% similar to another chemical structure. 

Searching by Similarity

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Similarity searching can be useful because sometimes a similar structure can imply similarity in function.

In other cases, similar structural features may give entirely different properties or biological activity.

Suppose you'd like to know if there are any substances that have a structure highly similar to the insecticide DDT. To find those, we need to retrieve the record for DDT.

Searching by Similarity

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Try It:

In the Substance Identification box, select Name/Synonym and equals from the drop-down menus.

Type DDT in the search box.

Click the Search button. 

This should retrieve the record for DDT, and you should see the structure on the right.

To the right of the structure are several light blue buttons. You can hover over each button with your mouse to see what that button does. Click the top button to transfer the structure into the Advanced search interface. This could take a moment to load.

Once your structure has loaded, you’ll see it in the Structure search box on the Advanced search interface.

Searching by Similarity

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Now you can use the Structure search to find substances with structures similar to DDT.

Select the radio (round) button next to Similarity Search. Change the percentage to 90%.

Click the Search button.

This should retrieve about 9 substances that are highly similar in structure to DDT, including DDT as the first result (100% similar).

You can scan the results and notice the high degree of similarity.

Searching by Substructure

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You can also use the structure search to locate substances that contain your structure. This is useful for finding a set of compounds that share a common substructure, which may cause a particular type of biological activity.

On your results page for structures similar to DDT, click the Modify Query button. This should return you to the Advanced search interface with the DDT molecule diagram still in the Structure search.

Important Note: If the structure disappeared, repeat the process you used to locate the DDT record and transfer its structure to the Advanced search interface again.

Searching by Substructure

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Try It: 

Under Structure Search Options, select the radio (round) button next to Substructure Search.

Click the Search button.

You should retrieve about 17 substances that contain the same structure as DDT. Look at the second page of results and notice that mixtures with DDT are also retrieved.

Searching by Substructure

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Return to the first page of results using the Previous Page button at the bottom of the screen.

Scroll up until you see the DDT record at the top of the screen.

Look again at the blue buttons to the right of the structure. Click the bottom button labeled 3D.

A 3D model of the structure will open in a new window or tab. You can:

  • rotate the substance
  • change the model type
  • zoom in
  • and many more options.

Take a minute to explore the 3D model features. Close the 3D viewer window or tab when you’re finished.

Click Start New Query to return to the Advanced search interface.

Drawing Structures

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You can also draw a substance and search for it. You might use this to identify an unknown substance.

Watch this 4-minute video to learn how to draw a structure, like the one below.

 chemical structure

Drawing Structures

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You have reached the end of the ChemIDplus - Part 2 tutorial! You should now be able to: 

  • Search for chemical structures in order to identify a substance
  • Locate substances that share a similar structure
  • Locate substances that contain a specific structure

To learn more about ChemIDplus, browse the Help page

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