Designing carbon nanotubes from scratch can be complicated and time-consuming, especially when precise atomic alignment and control over periodicity are essential. If you’re a molecular modeler in materials science or nanotech, you’ve likely spent time manually replicating rings, adjusting rotations, and fine-tuning geometries—often through tedious trial and error.
In SAMSON, the Pattern Editors simplify this process dramatically. By combining circular and linear patterning in a few guided steps, you can build a carbon nanotube manually with full control over atomic positioning—and without coding or complex scripting. This approach is ideal for rapid iteration and customization, especially when prebuilt solutions aren’t flexible enough.
Step-by-Step: Building a Carbon Nanotube
To get started, you’ll need to use two editors from the toolbar: the Circular Pattern Editor and the Linear Pattern Editor. Here’s how these tools can be used in combination to construct a nanotube:
- Create a ring of carbon atoms. You can do this using atomic building tools manually or by selecting a small fragment from a molecule. Remove any hydrogen atoms and rotate the ring to align its bonding edges.
- Activate the Circular Pattern Editor (W key or use the Editors Toolbar).
Set the number of copies (e.g., 12) to form a complete circular ring. Adjust the radius visually to ensure overlapping atoms align precisely for bonding. Accept the result to merge overlapping atoms and finalize the ring. - Align your ring to the XY plane using the Edit > Align feature. This ensures a consistent foundation for stacking multiple rings.
- Use the Linear Pattern Editor (L) to replicate the ring vertically along the Z-axis.
Set the translation spacing (e.g., 2 Å) between rings. You can optionally rotate each successive ring incrementally to better match the helical structure of some nanotubes. Accept to generate the 3D nanotube structure. - Minimize the resulting structure using SAMSON’s geometry optimization tools to relax the atomic positions, then optionally add hydrogens.
This method allows for detailed control over the nanotube’s diameter, length, alignment, and bonding. It’s particularly useful when exploring custom constructions that don’t fit predefined templates, or when visual and spatial precision is important—such as in simulations or educational animations.
Why Not Use the Carbon Nanotube Editor?
SAMSON also includes a built-in Carbon Nanotube Editor, which can instantly generate common nanotube structures. However, manually building with pattern editors can be more flexible, especially if you’re modeling modifications, defects, or unconventional segments. If you’re experimenting with functionalized rings or stacking variations, the manual approach gives you full freedom.
For visual learners, the video tutorial demonstrates how to follow this exact process interactively.
Helpful Tips
- Use snapping options to constrain translations and rotations to specific intervals.
- Ctrl/Cmd + scroll adjusts the number of copies faster when using Pattern Editors.
- Use visual widgets to preview structural alignment before finalizing.
- You can further organize patterns using Edit > Align / Distribute.
To explore more pattern-based modeling strategies in SAMSON, including curved and custom paths, check the full guide on pattern creation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.