Designing nanostructures like carbon nanotubes can be tedious when you’re confined to repetitive manual replication and alignment. For computational chemists, nanomodelers, and molecular designers, the lack of intuitive pattern generation tools has been a long-standing bottleneck—especially when aiming to preserve atomic-level precision across hundreds of repeated units.
In SAMSON, an integrative platform for molecular design, this challenge is significantly reduced thanks to the recently introduced Pattern Editors. These tools allow users to replicate and arrange molecular structures in linear, circular, or curved patterns using interactive widgets and precise input mechanisms.
In this post, we focus on a particularly illustrative and practical example: manually constructing a carbon nanotube by assembling rings into a tubular shape using the Circular and Linear Pattern Editors.
Why build it manually?
SAMSON does include a dedicated Carbon Nanotube Editor—but learning to build it by hand using Pattern Editors provides flexibility and understanding. You can tailor ring types, add chemical features, or create variations like open-ended or capped nanotubes with custom geometry.
Step-by-step: Nanotube construction
- Create a carbon ring:
Start by building a basic planar carbon ring. You can remove hydrogen atoms to leave only carbons. Align the ring so that edges meet cleanly when rotated. - Form the base ring using the Circular Pattern Editor:
Activate the circular pattern editor (W) and duplicate the original unit to form a closed ring. For example, create 12 copies evenly spaced in a full circle. Adjust the radius carefully so that carbon atoms bond seamlessly.- Use translation handles to tweak spacing.
- Click the center of the widget to input exact radius or angle values if needed.
Then, Accept the result to merge overlapping atoms, resulting in a fused ring structure.
- Align the ring to prepare for stacking:
UseEdit > Alignto position the ring flat in the XY plane; this ensures vertical stacking will be consistent. - Stack the rings into a tube:
Activate the linear pattern editor (L) and set the translation along the Z-axis to stack copies of the ring vertically. For instance, a 2 Å translation per copy creates a close-packed tube.- Apply incremental rotation if required for bond matching between layers.
- Use Ctrl (Cmd on macOS) + scroll to control the number of layers efficiently.
Click Accept to finalize the nanotube structure.
- Relax the geometry:
Finally, run a geometry minimization to relieve any atomic overlap or stress, and optionally reintegrate hydrogen atoms where necessary.
What makes this process valuable?
While predefined nanotube generators are great, what makes this manual approach useful is the level of control and adaptability it offers. Want a non-standard cross-section? Done. Need alternating chemical modifications between layers? You’re in charge. Plus, by learning how the Pattern Editors work together, you can use the same concepts to build helices, custom nanorings, or multi-walled structures.
To learn more about other Pattern Creation features in SAMSON—like curved arrangements, precise snapping, and atom merging settings—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 download SAMSON from https://www.samson-connect.net.