Designing molecular nanotubes is a common task in areas like nanotechnology, materials engineering, and molecular simulation. But constructing nanotubes atom-by-atom is tedious and prone to alignment issues. The good news? If you’re using SAMSON, there’s now an intuitive way to build carbon nanotubes manually using pattern-based editors—delivering control and flexibility without complexity.
Why manual nanotube construction matters 🔧
While SAMSON includes a dedicated Carbon Nanotube Editor, manually constructing nanotubes using pattern tools gives users greater control over chirality, tube length, atom types, and bonding. Whether exploring unusual ring structures or experimenting with functionalized edges, manual construction lets you build exactly what you need.
Step-by-step: From ring to nanotube
Here’s how to construct a carbon nanotube manually using the Pattern Editors in SAMSON:
- Create a ring structure: Use SAMSON’s molecular building tools to construct a ring. Remove hydrogens and rotate the structure to align bondable edges.
- Form a closed loop using the Circular Pattern Editor (W):
- Set the number of copies (e.g., 12) to complete the ring.
- Adjust the radius so that atoms overlap cleanly at the ring edges.
- Click Accept to finalize and merge overlapping atoms.
- Align the ring: Use the Edit > Align feature to orient the ring (e.g., align to XY plane). This aligns future copies seamlessly.
- Stack the rings using the Linear Pattern Editor (L):
- Set a translation in the Z-axis (e.g., 2 Ă…) to space the rings.
- Optional: Apply a small rotational increment between copies to follow a helical twist.
- Click Accept to create the nanotube.
- Refine the structure: Relax the tube using the Minimization tool. Optionally add hydrogens for stability.
Key advantages of this method
- Precision control on translations, rotations, and angles at each stage.
- Reusable parametrized operations for building families of nanotubes or adjusting curvature.
- Visual feedback: Get immediate real-time updates as changes are made.
Visual tutorial
To see the method in action, check out this screenshot from the video tutorial showing building with atoms:
Who is this for?
This construction approach is particularly valuable for:
- Researchers exploring non-standard nanotube geometries
- Educators teaching atomic-scale fabrication concepts
- Anyone needing atomic-level control over structure generation
Head over to the full documentation for pattern creation in SAMSON to learn more.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.