ChemIDplus - Part 2

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ChemIDplus - Part 2

Welcome to Part 2 of the ChemIDplus tutorial. In this tutorial, we'll focus on searching chemical structures. This tour allows you to follow along in the live ChemIDplus site in the right frame.

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Searching by Chemical Structure

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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, or find substances with a similar structure.

The ChemIDplus Advanced Search allows users to search for similar structures and substructures, or draw their own structure. 

Searching by Chemical Structure

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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 info button next to Structure Search Options to learn about the choices. 

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

Similarity Searching

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Suppose you'd like to know if there are any substances that have structure highly similar to the insecticide DDT.

In the Substance Identification box select Name/Synonym and Equals. Type DDT in the query box and click search.

The record for DDT is retrieved and you should see the structure on the right.

To the right of the structure are several light blue boxes. You can hover over each icon with your mouse to see the functions. Click the top button to transfer the structure into the advanced search page. (It may take a moment to load).

Similarity Searching

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

Click search.

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. 

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.

Substructure Searching

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You can also use the structure search to search for 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 Modify Query. This should return you to the advanced search page with the DDT molecule still in the structure search.

Under Structure Search Options, select the radio button next to Substructure Search and click search.

You should retrieve about 18 substances that contain the same structure as DDT. Look at the second page of results and notice that mixtures with DDT are also retrieved.

Substructure Searching

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

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

This 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 play with the features here, and close the 3D viewer window or tab when finished. 

Drawing Structures

Click Start New Query to return to the Advanced Search page. 

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

Watch the video to learn how to draw a structure, like the one below. 

 2 six-sided rings

Drawing a structure in ChemIDplus

What structure did you draw?

 You have reached the end of the ChemIDplus - Part 2 Tutorial. 

Return to Moodle.

 

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