When working with molecular models and simulations, it’s often important to quickly locate molecular fragments with specific electronic characteristics. One common use case: identifying structural groups with a particular range of partial charges — whether for reactivity analysis, parameter tuning, or visualization purposes.
In SAMSON, the Node Specification Language (NSL) lets you do just that, precisely and efficiently. In this post, we explore how to work with the partial charge attribute of structural groups using the NSL — an integrated tool available directly in SAMSON.
Why care about partial charges?
Partial charges reflect the uneven distribution of electrons in a molecule’s atoms. Whether you’re building a force field, studying polar interactions, or generating electrostatic potential maps, knowing (and selecting) substructures with a particular partial charge helps refine your analysis and simplify workflows.
Using sg.pc to match structural groups
The attribute space sg corresponds to structural group nodes in SAMSON. Within it, the short name pc represents partial charge. Here’s the basic idea:
sg.pc 1— matches structural groups with a total partial charge equal to 1.sg.pc > 1.5— matches groups with a partial charge greater than 1.5.sg.pc 1.5:2.0— selects groups with partial charge values between 1.5 and 2.0.
This makes it easy to build complex filters and extract just the parts of your molecular system that you’re interested in.
Example use cases
Let’s say you’re studying functional groups with high electronic density. You could use sg.pc < -0.5 to find regions with strongly negative partial charges—highlighting potential nucleophilic sites. Or maybe you’re interested in identifying protonated amines: sg.pc > 0.9 may help locate them when combined with a filter on Nitrogen count, like sg.nN > 0.
A quick tip on syntax
The NSL allows range queries and standard comparisons. You can combine conditions using logical operators to create powerful queries across attributes. For example:
|
1 |
sg.pc 1.5:2.0 and sg.nO > 2 |
This matches structural groups with partial charges between 1.5 and 2.0 that also contain more than two oxygen atoms.
When is this helpful?
Whether you’re modeling a charged surface, preparing structures for molecular mechanics, or validating chemical states in a docking analysis, selecting substructures by partial charge supports informed decision-making and speeds up iteration cycles.
To explore all the available structural group attributes, consult the full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.