Modeling nanostructures like carbon nanotubes (CNTs) can be a time-consuming task in molecular design platforms—especially if you’re constructing them atom-by-atom. If you’ve ever wished for a faster and more intuitive way to build precise nanotube structures without writing code or managing complex geometrical operations, this tutorial might ease your workflow.
In this post, we’ll walk through a practical, step-by-step approach to manually building a carbon nanotube using SAMSON’s Pattern Editors, which are integrated tools that let you clone and position molecular fragments in linear, circular, or curved configurations with interactive control. The method we describe will provide you both flexibility and precision—making sure your nanotube isn’t just fast to build, but chemically meaningful.
Why manual nanotube construction?
SAMSON includes a Carbon Nanotube Editor, but for users who want more control over tube dimensions or you are using custom ring structures, building CNTs manually using Pattern Editors is highly effective. This also allows for experimentation with non-standard configurations.
Step-by-step: From ring to tube
- Create the building block: Begin by building a small ring of carbon atoms. You can use SAMSON’s structure-building tools to create a molecular ring. Remove hydrogen atoms if they were added by default and rotate it properly to expose connectable edges.
- Activate Circular Pattern Editor: Press
Wor use the Editor Toolbar to access the Circular Pattern Editor. Use this to duplicate your base ring along a circular path.- Set the number of instances (e.g., 12) to complete a closed ring.
- Adjust the radius manually or set precise values via Ctrl/Cmd+click to ensure overlapping atoms merge correctly.
Accept the pattern to build the complete ring structure.
- Align the ring to a reference plane (like the XY plane) using Edit > Align. Good alignment aids in stacking and minimizes distortion in the final structure.
- Build the tube: With the full ring selected, switch to the Linear Pattern Editor by pressing
L. This tool will stack rings along a linear axis.- Translate along the Z-axis (e.g., 2 Å between rings)—you can either drag the widget handles or input the value precisely.
- To match bond orientations between stacked rings, consider rotating each subsequent ring slightly using the interactive widget or numerical input.
Accept the pattern to finalize the tube.
- Minimize the structure: Use SAMSON’s minimization tools to relax geometry and optionally re-add hydrogen atoms at open valencies.
Visual example
Below is an image from the documentation showing the interactive tutorial focused on atomic-level building:
Tips for better control
- Use the Ctrl (Windows/Linux) or Cmd (macOS) key while clicking the widget center to input exact rotation and translation values.
- Enable the snapping option to manage increments in movement and rotation during widget manipulation.
- Use Edit > Align / Distribute to automate spacing and orientation of structures.
This workflow is useful not only for building carbon nanotubes but also for designing other custom periodic nanostructures that rely on repeated motifs. It reduces tedious duplication tasks and ensures that alignment and distances are geometrically consistent.
To explore more about pattern creation and other advanced molecular modeling tools, visit the full documentation: 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.