Designing nanoscale structures like carbon nanotubes (CNTs) is a common task in nanotechnology and materials science, yet can be time-consuming using traditional modeling tools. One of the most frequent pains reported by molecular modelers is the difficulty in manually assembling repeating units into curved or tubular architectures with precise control over positions and alignments.
SAMSON provides a flexible and visual solution to this challenge through its set of Pattern Editors. In particular, this blog post highlights how you can manually assemble a nanotube using standard molecular fragments and the Circular and Linear Pattern Editors in SAMSON.
Why manual nanotube construction?
Although SAMSON includes a pre-made Carbon Nanotube Editor, manual construction offers important benefits in exploratory modeling, educational settings, and when modeling non-standard substrate shapes. With intuitive design steps, users can assemble arbitrary curved nanostructures while maintaining atomic-level control over the geometry.
5 steps to assembling a basic nanotube
- Create a ring fragment: Start by building or importing a small carbon ring structure, such as a hexagonal carbon ring. Remove hydrogen atoms if present, and manually rotate it to align the edge atoms in a planar configuration.
- Form a closed ring using the Circular Pattern Editor (W): Activate the editor and set a number of instances (e.g., 12) to form a full circular structure. Adjust radius and rotation so that outer atoms bond smoothly. When satisfied, click Accept to apply the transformation and merge overlapping atoms.
- Align the structure: Use Edit > Align to orient the ring on a plane (e.g., XY). This ensures your next transformations proceed along the tube growth axis (Z-axis).
- Extend into a nanotube with the Linear Pattern Editor (L): Select the ring and activate the linear pattern tool. Use Z-axis translation (e.g., 2 Å between layers) to duplicate the ring structure vertically. Incremental rotation can be fine-tuned to align lattice edges between layers.
- Finalize and optimize: After accepting the pattern, use Minimize to relax the geometry and optionally add hydrogen atoms for stability.
This construction method provides a hands-on way to understand structural assembly, making it especially useful for students or researchers exploring the geometry of tubular materials beyond the default models.
Quick visual: tutorial image from SAMSON
To dive deeper into the pattern creation tools—including curved and linear replications—you can explore the official documentation and cross-linked tutorials.
Learn more and follow the full nanopatterning guide in the official documentation: https://documentation.samson-connect.net/users/latest/creating-patterns/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.