For many molecular modelers, building a molecule from scratch using atoms might feel tedious—especially when dealing with basic structures like N-acetyl groups, sidechains, or small ligands. If you’re looking for intuitive tools to streamline this fundamental task, SAMSON offers a practical solution with real-time feedback and atom-aware insertion features. In this post, we’ll take a closer look at how to build molecules from individual atoms using SAMSON’s Add editor.
Common Problem: Precise But Friction-Prone Molecule Construction
Custom molecular design often requires constructing specific groups or chains atom by atom, especially in force-field validation, synthetic pathway planning, or educational contexts. Tools that don’t provide real-time structure validation or flexibility in editing can easily get frustrating. SAMSON aims to resolve this by combining interactive minimization and intelligent atom adjustments.
Start Simple: Adding Atoms with the Add Editor
SAMSON’s Add editor allows you to quickly place atoms in 3D space, and automatically adjusts hydrogen atoms based on molecular valency (as long as it’s enabled in the Preferences). For example, clicking the carbon symbol (C) inserts a methane (CH4) structure—hydrogens added automatically.
Two Modes of Adding Atoms
- Substitute an Atom: Hover over the atom (e.g., a hydrogen) you want to substitute and click. SAMSON uses covalent radii to place the new atom in realistic geometries.
- Bond Formation: Click and drag from an existing atom outward. SAMSON adds a new bond of appropriate length and valency.
Add Functional Groups
Switch elements via the Periodic table tool in the Asset Browser or quick-access buttons. In just a few clicks, add Nitrogen or Oxygen and build an N-acetyl group, as shown below:
Live Molecule Optimization
While building, you can press Z to activate interactive minimization. This provides immediate feedback on structure validity and energy minimization—very useful when determining stable geometries or avoiding implausible bonding.
Editing Bonds and Charges
Need to convert a bond into a double bond? Use the Edit Bonds tool (B). Just hover over and click to increment bond order:
Formal charges can also be adjusted interactively with the Edit Charges tool (C):
Combine with Asset Fragments
Although this guide focuses on building from atoms, SAMSON also allows you to switch seamlessly to fragment- or asset-based edits. This hybrid approach can make adding rings or chains much faster once atomic scaffolding is in place.
Conclusion
Constructing molecules atom by atom doesn’t have to be cumbersome. SAMSON’s Add editor offers a clean, predictable, and visually intuitive experience, especially when combined with live energy minimization and automatic hydrogen balancing. If you’re new to SAMSON—or just want faster iteration cycles—this workflow is worth exploring.
To learn more, visit the official documentation on building molecules in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.