When working with large molecular models, quickly locating structures with specific electronic properties can significantly speed up your workflow. One such case—frequently encountered in charge-based simulations, electrostatic analyses, or simply in identifying reactive species—is the need to find molecules with particular partial charges.
In SAMSON, the integrative molecular design platform, this is made possible through the partialCharge attribute in the Node Specification Language (NSL). If you’re dealing with charged or polarized systems, this can be an efficient way to filter out only what you need.
What is a Partial Charge?
Partial charge represents an atom’s or molecule’s net electronic distribution due to differences in electronegativity. Unlike formal charges, partial charges are calculated and more representative of actual molecule behavior in simulations.
In SAMSON, the structuralModel.partialCharge attribute, accessed as sm.pc, allows you to match models based on these values.
Why This Matters
Let’s say you’re analyzing a library of molecules for candidates likely to participate in ionic interactions or hydrogen bonding. Rather than manually checking each one, you can use NSL expressions to rapidly filter them.
For example:
sm.pc > 1.5— Retrieves only those molecules with a total partial charge greater than 1.5sm.pc 1.5:2.0— Targets a specific charge window between 1.5 and 2.0
This can be incorporated into broader NSL queries to include additional properties like the number of atoms, chains, or material visibility:
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sm.pc 1.5:2.0 and sm.nC < 10 |
…which returns all structural models with partial charge between 1.5 and 2.0 and fewer than 10 carbon atoms.
Best Practices
Before querying, it’s useful to:
- Ensure that partial charges have been computed or imported into your structural models.
- Use ranges rather than fixed values to accommodate floating-point variations.
- Combine attributes to build compound selection logic tailored to your analysis.
Going One Step Further
The elegance of this system is that it’s not limited to charge. You can chain sm.pc with other properties like formal charge (sm.fc), atom counts (sm.nat), or even visibility (sm.v) to create dynamic, context-specific filters in complex models.
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sm.pc > 0.5 and sm.visible and sm.nat 50:100 |
This matches visible structural models with partial charge over 0.5 and between 50 and 100 atoms — useful for visual set selection or export routines.
You can learn more about the partialCharge and other attributes in SAMSON’s NSL by visiting the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from www.samson-connect.net.