Constructing carbon nanotubes manually is a common yet time-consuming task in nanoscale modeling. Molecular modelers often spend significant time aligning repeating subunits, ensuring correct bonding distances, and stacking rings into tubular shapes — and that’s before even getting to energy minimization.
With SAMSON’s Circular and Linear Pattern Editors, much of that work can now be done in a few guided steps, with interactive controls that offer both speed and precision. Here’s a breakdown of how you can simplify nanotube construction using these tools.
1. Build a Base Ring
Create a small carbon-based ring structure using atom editing tools or by modifying a fragment. Remove any hydrogen atoms that could interfere with bonding during ring closure, and rotate the structure if needed to align bonding edges along the plane you are designing in.
2. Switch to Circular Pattern Mode
Activate the Circular Pattern Editor (shortcut: W). A transformation widget appears around your selected structure.
The central handle allows you to set radius and rotation for the pattern. Your goal is to generate a closed ring:
- Increase the instance count (e.g., 12 copies) to encircle the original ring.
- Adjust the radius until the edges of the rings are touching and aligned for bonding.
Click Accept to finalize the ring structure. Overlapping atoms will be merged automatically based on preferences you’ve set.
3. Align the Ring
Use the Edit > Align tools to position your ring correctly (e.g., flat on the XY plane). This helps ensure accurate stacking in the next step.
4. Stack into a Tube
Now switch to the Linear Pattern Editor (shortcut: L) and apply it to the ring you just created.
- Use drag handles to move copies along the Z-axis.
- For precise control, click the widget’s center and set a translation (e.g., 2 Å) and optional rotation offset between layers.
- Add enough copies to form the desired nanotube length.
Again, click Accept to finalize.
5. Minimize and Refine
Once your structure is complete, use the Minimization tool to relax atomic positions. You may also choose to add hydrogens after minimization to stabilize the ends or interfaces.
Why It Matters
Designing nanotubes or other repetitive arc-based nanostructures doesn’t have to involve dozens of manual transformations. SAMSON’s pattern-based editors let you offload repetitive spatial arrangements while offering precise control. Drag-and-drop visual handles, snapping, and direct input of transformation parameters streamline what used to take minutes or even hours into seconds.
This approach isn’t limited to nanotubes either — you can design rings, ladders, helices or any repeating nanoscale architecture that follows linear, circular, or curved paths.
To explore SAMSON’s pattern editors in more detail, visit this guide on creating patterns.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.