A Step-by-Step Guide to Building Custom Molecules Atom by Atom in SAMSON

Molecular modelers frequently need to construct specific chemical structures not readily available in molecular libraries. Whether you’re reproducing a model from a journal article or exploring new chemical scaffolds, building molecules atom by atom is often a key part of the workflow.

Fortunately, the SAMSON platform provides a hands-on environment to efficiently build molecules one atom at a time. This blog post walks you through constructing a custom N-acetyl group using SAMSON’s Add editor—with interactive minimization, intuitive bond formation, hydrogen adjustment, and even charge editing.

Why atom-by-atom modeling?

Pre-built fragments are great, but sometimes you need full control. Maybe you want to insert a reactive intermediate, a transition state, or a less common radical. SAMSON’s atom-level construction tools let you build exactly what you need—with immediate visual feedback thanks to real-time minimization and structural validation.

Step 1: Start with a Carbon Atom

Activate the Add editor and click on the Carbon icon (), then click in the viewport to place a carbon atom. With hydrogen adjustment enabled in Preferences, you’ll immediately get a methane (CH4) structure.

Add carbon atom

Step 2: Growing the Chain

To connect more atoms:

  • Substitute a hydrogen: hover over the hydrogen on CH₄ and click to replace it with another carbon atom.
  • Create a new bond: click, drag away from the carbon, and release to extend a C–C bond.

Add via substitution

You can repeat this process to build the carbon backbone you need.

Step 3: Switch Atoms and Add Nitrogen and Oxygen

Now switch to adding Nitrogen and Oxygen atoms. Simply click their respective icons and place them as needed in your structure:

Add nitrogen and oxygen atoms

Step 4: Adjust Bond Orders

Sometimes, you’ll need to specify double or triple bonds. Use the Edit bonds tool () to increment or decrement bond orders between atoms.

Change bond order

Step 5: Edit Formal Charges (If Needed)

To set charges, activate the Edit charges tool (), then mouse over the atom and click + or – to assign formal charges:

Edit atom charge

Extra Tips

  • Use the interactive minimization (Z key) to relax your structure as you build.
  • Press and hold Shift while adding fragments to control substitution sites.
  • Rotate fragments with Shift + Right Click for precise placement.
  • Use the Periodic Table to add less common elements.

By combining intuitive drawing tools with chemically-aware features like hydrogen adjustment and structural validation, SAMSON lets you go from a blank canvas to a tailored molecular model in just a few clicks.

To learn more, visit the full documentation page at https://documentation.samson-connect.net/users/latest/building-molecules/.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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