Building Carbon Nanotubes by Hand: A Practical Workflow in SAMSON

Designing carbon nanotubes manually can sound like a daunting challenge—but for molecular modelers needing custom nanotube topologies, it often becomes necessary. Whether you’re tweaking radii, optimizing ring positioning, or exploring non-standard conformations, having hands-on control over nanotube construction is essential.

This post provides a step-by-step workflow using SAMSON’s Pattern Editors to manually build carbon nanotubes from scratch. It’s ideal for those who want to construct unique nanotube geometries beyond what’s generated automatically by predefined tools.

Why build nanotubes manually?

While automated nanotube builders are convenient, they can limit structural flexibility. Manual assembly is useful when you want precise control over:

  • Diameter and curvature of the ring
  • Inter-ring spacing and rotational alignment
  • Bond connectivity between repeating units
  • Customization of chirality or defects

Workflow: Step-by-step guide

Here’s how to build a CNT manually in SAMSON:

  1. Create a molecular ring
    Start by building a carbon ring using the atomic building tools. Remove hydrogens to leave reactive edges available for bonding.
  2. Rotate and align the ring
    Using the Move editor or transformation tools, rotate it to align horizontally in the XY plane. This ensures better stacking later.
  3. Replicate using the Circular Pattern Editor
    Activate the Circular Pattern Editor (shortcut W):

    • Set a number of instances (e.g., 12) to form a full loop.
    • Adjust the radius so atoms from neighboring copies are close enough to bond.
    • Use the visual widget to fine-tune until you get the ring closure effect you want.
    • Click Accept to finalize the new molecule.

    If overlapping atoms are close, SAMSON can optionally merge them automatically depending on your preferences.

  4. Align the duplicated ring
    Use Edit > Align to place the result on a preferred plane or axis (e.g., align with the XY plane).
  5. Stack rings into a tube
    Activate the Linear Pattern Editor (shortcut L):

    • Set the translation along Z-axis (e.g., 2 Å) to stack multiple rings vertically.
    • If needed, apply rotation between each copy for helical or twisted structures.
    • Use Ctrl (or Cmd on macOS) + click on the widget center for precise numerical input.
    • Click Accept to create the full tube.
  6. Relax the final geometry
    Optionally, open the Minimization tool to optimize the structure and add hydrogen atoms if necessary.

Visual feedback and control options

You’ll interact with intuitive 3D widgets throughout this process. Quick tips:

  • Mouse wheel: Adjust the number of copies easily.
  • Snapping: Useful for aligning transformations to fixed distances and angles.
  • Ctrl / Cmd + click: Precise edits for rotation or translation.

When manual beats automatic

This manual approach is especially helpful for modeling custom (n, m) nanotubes, simulating distortions, or preparing input structures for studies involving defects, functionalization, or mechanical stress.

With full control of each step, and visual feedback as you go, SAMSON’s pattern builders offer a fast and interactive way to build large, structurally rich nanotubes with tens or hundreds of thousands of atoms.

Interactive tutorial in SAMSON

Learn more on the SAMSON documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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