If you’ve ever tried to build a carbon nanotube (CNT) manually in a molecular modeling software, you understand how tedious and error-prone it can be. Aligning rings, ensuring bond continuity, and managing overlapping atoms across copies is often a time-consuming task that distracts from what you actually want to focus on: designing nanoscale systems.
Fortunately, the Pattern Editors in SAMSON offer a practical and reproducible workflow to construct nanotubes manually with high control over geometry. This can be particularly useful when you’re designing non-standard CNTs, creating custom structures, or teaching nanoscale construction.
Why Use the Manual Method?
Sure, SAMSON has a Carbon Nanotube Editor. But working with the Linear and Circular Pattern Editors lets you visualize and control the fabrication process layer by layer. It’s also a way to explore more general tubular structures that are not necessarily based on carbon atoms or standard geometries.
Step-by-Step: Manual Carbon Nanotube Construction
- Create the building block:
Start by building a ring of carbon atoms, such as a planar hexagonal ring. Remove any hydrogen atoms to allow bonding between replicas. - Activate the Circular Pattern Editor (W):
With your ring selected, use the Circular Pattern Editor to form a closed ring by duplicating the structure around a circle.- Set the number of copies (e.g., 12) to complete the circle.
- Adjust the radius interactively or with precise values using Ctrl / Cmd-click.
- Merge overlapping atoms:
Once the circular pattern looks structurally connected, click Accept to finalize. Overlapping atoms will be automatically merged if the option is enabled in preferences. - Align the ring to a plane:
Use Edit > Align to position the ring on a desired plane (e.g., the XY plane). This sets the foundation axis for your tube. - Stack into a tube:
Activate the Linear Pattern Editor (L) with the ring selected. Stack multiple copies along the Z-axis:- Set translations (e.g., 2 Å along Z) between each ring.
- Apply a small rotation increment if needed to align edge bonds.
Finalize the pattern with Accept to generate the full nanotube.
- Relax the structure:
Once the tube is built, run a minimization to relax the geometry and optionally add hydrogen atoms at the ends.
When Will This Help You?
Using the manual method of building nanotubes might support your workflow when:
- You are exploring exotic or non-carbon-based tube architectures.
- You need control over the number of layers, axial twist, or bonding.
- You want a more visual and didactic way of constructing nanostructures for teaching or presentations.
Try It Yourself
This approach gives you fine control over atomic positioning and can help you develop a deeper intuition for nanoscale geometry. The interactive widgets in SAMSON’s Pattern Editors offer precise manipulations for translation and rotation, while real-time feedback lets you adjust as you go.
To explore more examples and watch a video tutorial on this workflow, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.