Building Carbon Nanotubes by Hand: A Step-by-Step Guide in SAMSON

For many molecular modelers working on nanotechnology, designing carbon nanotubes (CNTs) is a frequent need—but doing it manually can be tedious and error-prone. Whether you’re trying to create a specific chirality or simulate functionalized tube ends, having fine control over your construction pipeline is crucial. This blog post walks through a streamlined manual approach to construct carbon nanotubes using pattern editors in SAMSON.

Why manual construction?

While SAMSON provides a Carbon Nanotube Editor for automated creation, manually building carbon nanotubes allows for custom ring configurations, edge modifications, and hybrid structures. This can be especially important when exploring functionalized nanomaterials or validating modeling hypotheses.

Step-by-step: Manual construction of a carbon nanotube

  1. Create a base ring:
    • Build a small carbon ring using SAMSON’s molecule builder tools.
    • Remove hydrogen atoms around the rim for better bonding alignment.
    • Use the rotation tool to align the ring in the XY plane for consistency.
  2. Use the Circular Pattern Editor:
    • Activate it with the shortcut W or via the Editors Toolbar.
    • Set the number of copies (e.g. 12) to form a complete hexagonal tube perimeter.
    • Adjust the radius until carbon atoms are closely aligned and ready for bonding.
    • Click Accept to finalize the ring structure.
  3. Align the ring precisely:
    • Go to Edit > Align and align the ring to the XY plane for clean stacking.
  4. Build the tube structure:
    • Use the Linear Pattern Editor (L) to duplicate the ring along the Z-axis.
    • Set a suitable translation value (around 2 Å) for proper atom overlap.
    • If needed, incrementally rotate each copy to improve connectivity between layers.
    • Click Accept to build the full-length nanotube.
  5. Refine the geometry:
    • Use the minimize tool in SAMSON to relax and optimize the full structure.
    • Optionally, add hydrogen atoms to cap open bonds if the tube ends should be passivated.

This approach gives you full control over the dimensions, bonding, and orientation of your CNT. It also makes it possible to interrupt the tube-building process at any point, insert heteroatoms, or graft functional groups for more tailored systems.

Visualizing the process

Interactive tutorial in SAMSON

You can watch a detailed demonstration in the SAMSON 2025 webinar to see each of these steps in action.

Beyond carbon nanotubes

The same manual pattern-building workflow lets you create other periodic nanostructures as well, such as nanoribbons or curved biological filaments. Circular, linear, or even curved duplication patterns can be combined to explore structural motifs in synthetic or biomolecular contexts.

To learn more, check out the full documentation on pattern creation at https://documentation.samson-connect.net/users/latest/creating-patterns/.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.

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