As a molecular modeler, building molecular structures can be one of the most rewarding yet challenging tasks. Whether you are constructing simple organic molecules or laying the foundation for larger, more complex systems, refining your workflow can make a significant difference. SAMSON, the integrative molecular design platform, offers intuitive tools that transform the molecule-building process into a streamlined and engaging experience.
Start Small: Building Molecules Atom by Atom
If you are new to molecular modeling, building molecules atom by atom is an excellent way to get acquainted with structural design principles. SAMSON’s “Add editor” makes it easy to gradually construct and shape molecules using individual atoms. Each step of the process has been designed to enhance usability and ensure that your molecule-building conforms to atomic valences and structural plausibility.
Let’s walk through the essential stages involved in constructing a molecule atom by atom:
Step 1: Activate the Add Editor
The “Add editor” is your tool of choice for building molecules in SAMSON. Once activated, you’ll notice quick access to common elements like carbon (C), nitrogen (N), hydrogen (H), and oxygen (O). For other elements, navigate to the Periodic Table within SAMSON’s interface. Clicking any element allows you to add it directly to the Viewport.
Step 2: Adjust Hydrogens Automatically
With the Adjust hydrogens… option enabled in the Preferences, SAMSON will automatically add the appropriate number of hydrogens to ensure a chemically valid structure (e.g., a single carbon becomes a CH4 methane molecule).
Step 3: Form Bonds Between Atoms
SAMSON allows two main approaches for creating bonds between atoms:
- Substitute an atom: Hover over an atom in the existing structure and click to substitute it with the selected element from the Add editor.
- Create a bond: Click on an atom and drag the cursor to another position to place a new atom that forms a bond with the first.
Step 4: Optimize Structure Using Interactive Minimization
With the interactive minimization feature (Z), SAMSON recalculates and optimizes geometries in real time as you build your structure, ensuring scientifically meaningful configurations. This is especially useful as you extend your molecule by adding nitrogen (N), oxygen (O), or complex fragments.
Step 5: Refine the Bond Orders
Once your basic structure is in place, you can easily change bond orders using the Edit bonds tool (B). Simply click on the bond you wish to change, then adjust the order by clicking the +/- options displayed.
Bonus: Work with Atom Charges
Need to modify formal charges on specific atoms? Activate the Edit charges editor (C) and hover over your target atom. Increment or decrement the charge with a single click on the + or – buttons that appear.
Why Benefit from Atom-Level Building?
Building molecules atom by atom not only offers you complete control over the structure but also allows you to explore different configurations, improve chemical accuracy, and understand molecular topologies. Whether you’re constructing a precise functional group or visualizing molecular interactions, SAMSON simplifies the minutiae of molecular design.
To explore a hands-on experience of the molecule-building tools in SAMSON, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today by downloading SAMSON from SAMSON Connect.