Designing carbon nanotubes (CNTs) atom by atom used to be a complex and time-consuming task. For researchers and students working in nanotechnology and materials science, this process often involved manually aligning atomic rings, estimating spatial parameters, and tweaking bonding arrangements. Small misalignments could easily lead to incorrect structures or force extended geometry relaxations.
If you’ve ever tried to model a nanotube from scratch, you already know how delicate the balance of duplication and alignment can be. The recent update to the SAMSON molecular design platform introduces a solution that significantly reduces this overhead: pattern editors. Specifically, the Circular Pattern Editor and the Linear Pattern Editor make constructing nanotubes a repeatable and precise operation—done visually, in just a few steps. Here’s how.
Creating the First Ring
The basic idea behind modeling a nanotube in SAMSON is to start with a molecular ring and use repeated patterns to assemble the full tube. You can begin by building a small atomic ring, such as a carbon-based ring, and removing any hydrogen atoms. Use the viewport manipulation tools (such as Move and Rotate) to align the ring edge along a known axis, like the XY plane. This sets up a good foundation for circular duplication.
Forming the Nanotube Cross Section
Activate the Circular Pattern Editor (shortcut: W) and duplicate the ring around a common center. By adjusting the number of copies and controlling the radius of the circular arrangement, you can create a closed loop where the atoms are close enough to potentially bond. To fine-tune the position, click on the central widget and set numeric values for radius or angles to match your target dimensions.
After accepting the operation, SAMSON offers the option to merge nearby atoms automatically, resulting in a chemically consistent ring. This becomes the cross-section of the nanotube.
Stacking the Rings into a Tube
Once the ring layout is done, align it to a principal axis like the XY plane using the Align feature (under Edit > Align). Then, switch to the Linear Pattern Editor (shortcut: L) to duplicate the ring along the Z-axis. With precise translation settings—say, 2 Å between each ring—you can create an extended nanotube of consistent geometry. Each replica can be rotated if needed to match bonding continuity.
After accepting, you’ll get a tube composed of neatly aligned rings. You can use the Minimization tool to relax the geometry and optionally re-add hydrogen atoms to saturate dangling bonds, depending on your modeling goal.
When to Use This Technique
This manual method offers flexibility for constructing CNTs of specific diameters, chiralities, or with custom modifications (e.g., vacancies, dopants). Compared to pre-built nanotube assets, pattern-based construction integrates tightly with design workflows and lets you extend or reshape structures piece by piece. That also makes it easier to combine CNT segments with other molecular systems, like binding proteins or functionalized end caps.
To explore the full workflow with video demonstrations and interactive guides, visit the SAMSON Pattern Creation guide.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.