Partial charges in molecules play an essential role in understanding molecular interactions, reactivity, and recognition processes. If you’re working in drug discovery, molecular dynamics, or modeling biomolecular systems, being able to filter and select molecular groups based on their total partial charge is often crucial.
In SAMSON, the integrative molecular design platform, the Node Specification Language (NSL) provides a structured way to search for and manipulate elements in molecular models. One useful feature is the ability to work with partial charges of structural groups through the sg.pc attribute.
Why Care About Partial Charges?
Partial charges affect how different atoms and groups interact electrostatically. For example, understanding which regions in your structure carry higher partial charges might help you predict potential binding sites, explain molecular geometries, or filter fragments for further modeling or simulation.
Rather than calculate and check partial charges manually across large biomolecular systems, SAMSON allows you to search and filter these instantly.
Using NSL: Select Structural Groups Based on Partial Charges
The structuralGroup.partialCharge attribute (shortened as sg.pc) helps you match structural groups that have a certain total partial charge.
Examples:
sg.pc 1– matches structural groups with a total partial charge of exactly 1sg.pc 1.5:2.0– matches structural groups whose partial charge lies between 1.5 and 2.0sg.pc > 1.5– selects all structural groups with partial charge greater than 1.5
When Might This Be Useful?
You might use this attribute in cases such as:
- Filtering out groups with high local polarity for solvation studies
- Selecting charged groups near a binding interface for docking or scoring
- Preparing subsets of your model for quantum calculations, where avoiding neutral or highly polar groups can improve accuracy
How Partial Charge Searches Differ from Formal Charges
Unlike formal charges, which are integer values used in Lewis structures, partial charges are real-valued and derive from electronic distributions. They provide a more nuanced way to examine your system.
This distinction means sg.fc (formal charge) may not detect subtle polarity or localized charges, while sg.pc can help identify groups contributing to electrostatic interactions even in overall neutral molecules.
Flexible Input
You can combine this attribute with other filters, like number of atoms (sg.nat), visibility (sg.v), or atomic composition to build rich and intuitive queries. For example:
|
1 |
sg.pc > 2.0 and sg.nC > 5 |
This query selects structural groups with partial charge greater than 2.0 and more than five carbon atoms.
You can explore more about structural group attributes in the official documentation: https://documentation.samson-connect.net/users/latest/nsl/structuralGroup/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.