Designing carbon nanotubes manually in molecular modeling platforms can be a slow and repetitive process. If you’ve ever painstakingly duplicated and aligned atomic rings to form tubes, you know how tedious it can get—especially when you’re aiming for atomic precision and working at the nanometer scale.
SAMSON, the integrative molecular design platform, now includes a set of Pattern Editors that offer an easier way. They let you replicate molecular structures in linear, circular, and curved arrangements, and they allow you to build CNT-like architectures in just a few clicks.
Why Pattern Editors Solve a Common Pain
Creating stacked ring structures—for example, a nanotube with aligned aromatic rings—typically involves several manual steps. You need to carefully duplicate a ring, position it, rotate it, and merge atoms. Precision matters, and small alignment errors add up.
With SAMSON’s Pattern Editors, this process is streamlined using intuitive drag-and-drop widgets, as well as keyboard and mouse shortcuts for granular control. Here’s how you can construct a nanotube manually using SAMSON’s built-in tools.
Step-by-Step: Constructing a Carbon Nanotube
- Create a single ring structure using standard molecule building tools. Remove hydrogen atoms and align edges so that they can form proper bonds with replicated units.
- Activate the Circular Pattern Editor (shortcut: W) to replicate the ring in a loop. Set the instance count (e.g., 12) and adjust the radius and orientation so that the copies form a closed molecular circle:
- Use drag handles to position or rotate the pattern interactively.
- Hold Ctrl / Cmd and click the widget to set translation and rotation values precisely.
- Merge the pattern. Click the center widget Accept button to finalize the ring and merge overlapping atoms.
- Align the circular ring to the XY plane using the Edit > Align function. This ensures your next pattern transformation works along a consistent direction.
- Stack the rings linearly to form a tube. Activate the Linear Pattern Editor (shortcut: L) and set the copy spacing along the Z-axis (e.g., 2 Å). Optionally, apply incremental rotation between layers to match bond arrangements.
- Finalize and minimize. Once satisfied with your tube structure, click Accept to apply changes, and use the geometry minimization tool to relax any high-strain areas. Add hydrogens if needed.
This method dramatically reduces the number of steps involved and ensures much higher consistency between repeated ring structures. It’s suitable not just for CNTs but for any kind of nested or stacked pattern—common in material simulations or nanostructure design.
Visual Example from SAMSON
Final Thoughts
Whether you’re working on molecular electronics, nanomechanics, or just experimenting with new molecular architectures, using SAMSON’s Circular and Linear Pattern Editors can save you hours of manual work. The interactive controls and precision widgets make it easy to design and iterate before committing to a structure.
To learn more and dive deeper, visit the full documentation page here:
https://documentation.samson-connect.net/users/latest/creating-patterns/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.