Designing nanostructures from atomic rings can be a time-consuming process if done purely manually, especially when building repeated patterns such as carbon nanotubes. Molecular modelers often need to carefully position and rotate molecules using fine controls, which can be tedious and prone to small misalignments that impact simulation quality.
Fortunately, the Pattern Editors in SAMSON offer an intuitive way to create and arrange molecular structures in linear and circular repetitions. In this post, we’ll walk through how to manually construct a carbon nanotube using the built-in tools in SAMSON, combining precision with visual feedback, and drastically simplifying the alignment process.
From Ring to Tube: Step-by-Step
We’ll break down how to use SAMSON’s pattern editors to create a carbon nanotube structure from a single molecular ring. This method shows how powerful the interface becomes when creating larger, more complex systems from a simple base unit.
1. Start with a Ring
Use SAMSON’s editor tools to build a carbon ring (e.g., a six-member ring for graphene-like structures). For accurate bonding later:
- Remove any hydrogen atoms.
- Rotate the ring as needed so edges can align seamlessly when duplicated in a circle.
2. Forming the Circular Chain
Activate the Circular Pattern Editor by pressing W or selecting it from the toolbar. Use the handlers or widgets near the ring to:
- Set the number of ring instances (e.g., 12 for a closed circle).
- Adjust the radius to bring carbon atoms close enough for bonding.
Once you’re satisfied, click the “Accept” button (✔) to generate the ring. Nearby atoms are automatically merged for proper connectivity.
3. Aligning and Stacking with Linear Patterns
To transform the circular base into a tube, align the ring with the XY plane using Edit > Align. Then, activate the Linear Pattern Editor (shortcut: L) to duplicate the circular ring along the Z-axis. You can:
- Set translation increments (e.g., 2 Å in Z-direction).
- Rotate each consecutive ring if a helical twist is needed.
Use the central widget to preview and fine-tune your stacking. Click “Accept” to confirm and build the full tube.
4. Final Adjustments
Once your nanotube geometry is complete, optionally run a geometry minimization via SAMSON extensions to relax bond lengths and angles. You may also add hydrogen atoms to saturate dangling bonds, if desired.
Why This Matters
Building carbon nanotubes or similar repeating nanostructures using standalone ring units often involves a lot of tedious copy-paste steps and manual alignment, especially in traditional molecular editors. SAMSON’s pattern tools reduce this workflow to a few interactive steps with real-time previews and precise rotational and translational controls.
This method is helpful not just for nanotech applications (like carbon nanotubes or molecular gears) but also for building customized biomolecular repeats and nanoscale materials with structurally repetitive motifs.
To dig deeper into pattern-based construction features in SAMSON, read the full documentation page: Creating patterns in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.