How to Select Aromatic Atoms (and Why It Matters)

When working with molecular structures, identifying aromatic atoms is a common—and crucial—task. Whether you’re building a QSAR model, analyzing ligand-receptor interactions, or just trying to debug a force field assignment, being able to filter aromatic atoms quickly is a real timesaver.

In SAMSON, the NSL provides a precise and flexible way to select atoms based on various attributes, including aromaticity. Here’s how you can use it to your advantage.

Why Select Aromatic Atoms?

• Understanding π-systems: Aromatic atoms are involved in delocalized π-electrons that affect molecular stability and reactivity.
• Drug design: Many drug-like molecules include aromatic rings for receptor binding and pharmacological activity.
• Visualization: Highlighting aromatic atoms helps in creating meaningful molecular visualizations.
• Filtering: You may want to isolate non-aromatic atoms from your selection to apply specific modifications or calculations.

How to Do It in NSL

The syntax is pleasantly minimal. In the NSL, you can use the aromatic attribute to filter aromatic atoms. Here’s how:

… returns all aromatic atoms.

Want aromatic atoms of a specific element? Combine it with the symbol attribute like this:

This filters all C atoms that are aromatic—perfect for locating aromatic carbons in complex structures!

Going a Step Further

Want to exclude aromatic atoms and focus on the rest?

This can be useful when defining force field rules or for coarse-graining steps where aromatic hydrogens might be excluded.

Combining with Other Filters

Let’s say you want to find only the aromatic atoms in chain A:

Need only the resonant aromatic atoms?

The NSL makes it easy to build these compound filters by combining attributes with simple and, or, and not operators.

Good to Know

• Aromaticity is a computed attribute. This means that, depending on your file format or data source, it might not be available until assigned or detected using a chemical property extension.
• Symbol and element are two distinct filters: a.e Oxygen matches by name, whereas a.s O matches by symbol. Aromaticity works well with both.

Want to dive deeper into all available atom attributes in NSL? Explore coordinates, charges, covalent radii, hybridization, and more with NSL’s extensive filtering options for atoms.

To learn more about all available atom attributes in SAMSON’s NSL, visit the official documentation: https://documentation.samson-connect.net/users/latest/nsl/atom/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.