Designing carbon nanotubes manually often means repetitive placement, alignment, and checking of molecular fragments with painstaking attention to symmetry. If you’ve tried to stack molecules one by one to create a tubular structure, you know the struggle: time-consuming edits, tedious alignments, and visual guesswork to make sure atoms bond correctly. But what if you could build entire nanotubes in minutes, without scripting or third-party files?
In SAMSON, an integrative molecular design platform, you can create nanotubes in seconds using its pattern-based editors. This blog post focuses on a practical use case: building a carbon nanotube using the Circular and Linear Pattern Editors. The result? Repetitive molecular construction simplified and visualized in real-time.
Start from a Ring Structure
To begin, create a small carbon ring — for example, a hexagonal graphene-like fragment. Remove hydrogens to prepare the atoms for bonding and orient the ring so that its edges line up with symmetry axes.
Use the Circular Pattern Editor
Activate the Circular Pattern Editor (shortcut: W) to duplicate the ring structure around a central axis:
- Set the number of instances (e.g., 12) to form a complete 360° ring.
- Adjust the radius to bring adjacent carbon atoms within bonding distances.
- Click Accept (✔️) to confirm and merge overlapping atoms into a unified macro-ring.
If needed, align the entire structure using Edit > Align to ensure it’s centered and flat along the XY plane, preparing it for stacking.
Apply the Linear Pattern Editor to Stack Rings
With the ring selected, launch the Linear Pattern Editor (shortcut: L). This lets you build the nanotube along an axis:
- Set translation along Z-axis (e.g., 2 Å) to stack the ring structures.
- Apply incremental rotation to tweak bond alignment between layers if needed (e.g., 10° per ring).
- Accept to finalize and generate your multi-layered carbon nanotube.
The visual widget allows you to control spacing and rotation interactively. You can also hold Ctrl (or Cmd on macOS) and click on axis arrows to enter exact translation and angle values, making fine adjustments easy to achieve.
Relax and Finalize
Once the nanotube is complete, you can run a geometry minimization to remove residual strain. Optionally, add hydrogens to passivate surfaces.
Why This Workflow Helps
Compared to scripting or placing fragments by hand, SAMSON’s pattern editors offer a live, visual, and non-destructive tool that simplifies building complex, repetitive structures. Whether you’re working in nanotechnology or material science, it’s a faster route to structurally accurate models that you can visualize and simulate right away.
This method doesn’t require any programming skills and makes creating periodic structures feel more like interacting with 3D design software than coding complex input files. The pattern behaviors are editable in preferences, so advanced users can also control merging rules, group handling, and hydrogen adjustments.
Explore more about pattern creation in SAMSON: https://documentation.samson-connect.net/users/latest/creating-patterns/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.