Working with aromatic systems is an essential part of structure-based molecular modeling, from visualizing planar ring systems to performing conformational analysis on drug-like molecules. But selecting these atoms precisely can be time-consuming—especially when your molecules are large or complex.
This is where the Node Specification Language (NSL) in SAMSON comes in handy. It allows you to quickly and flexibly select atoms based on their properties, including aromaticity. Let’s explore how to do this effectively using the a.ar attribute, which identifies aromatic atoms in any structure.
Why Select Aromatic Atoms?
Whether you’re modeling π-stacking interactions, designing aromatic-linker compounds, or building force field inputs with custom parameters, extracting aromatic atom subsets is critical. Yet, many platforms require you to rely on atom names or guesswork.
a.ar: Your Shortcut to Aromaticity 🌿
In NSL, the a.ar attribute stands for atom.aromatic and evaluates whether an atom is aromatic. You can use it alone or in combination with other criteria.
Examples
a.ar: selects all aromatic atoms in the system.a.s C and a.ar: selects only aromatic carbon atoms.a.ar and a.inRing: selects aromatic atoms that also lie in a ring.
Combining Criteria?
You can use NSL’s logical operators (and, or, not) to build more specific selections:
a.ar and not a.het: aromatic atoms that are not heteroatoms.a.ar and a.sy "C.2": aromatic atoms with SYBYL type C.2.
What Counts as Aromatic?
Aromaticity in SAMSON is determined by structure analysis algorithms and, where needed, resonance information from connected atoms (see a.reso for resonance involvement). If your aromatic atoms are not showing as such, double-check your molecular structure and bonding assignments.
Bonus: Planar Aromatic Atoms
Want to find atoms that are both aromatic and lie in a plane (e.g., for better π-stacking analysis)? Combine a.ar with a.pl:
a.ar and a.pl: matches aromatic atoms that are also planar.
This type of query is especially useful when analyzing force field parameters or computing interaction energies that rely on geometry.
Minimal Typing, Maximum Focus
Once you become comfortable with NSL syntax, you’ll find yourself building detailed selections with just a few keystrokes—saving time and reducing errors.
Want more? You may refer to the full documentation of the a.ar attribute and others here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.