Building molecular structures with precision is a common challenge for molecular modelers. Whether you’re creating simple chemical groups or assembling more complex systems, SAMSON offers a structured and user-friendly approach. One key pain point for scientists is efficiently building molecules from individual atoms with proper hydrogens, bonds, and orientations. In this blog post, we’ll guide you through a practical example: constructing an N-acetyl group using SAMSON’s powerful tools.
Why Build Molecules from Atoms?
Constructing molecules from atoms ensures total control over the creation process. This method is invaluable when assembling custom functional groups, modifying local structures, or tweaking specific chemical properties. SAMSON provides dynamic tools to simplify this process, making it accessible for both beginners and professionals in the field of molecular modeling.
Step-by-Step Guide to Building an N-Acetyl Group
Before we begin, ensure your preferences are properly set up. Go to the Preferences menu (Interface > Preferences > Editors: Add) and enable the following options:
- Adjust hydrogens when adding fragments… – Automatically adjusts hydrogens when atoms/fragments are added or linked.
- Prevent unexpected substitutions – Guides substitutions with green overlays for acceptable actions and red overlays for forbidden ones.
- Merge neighboring atoms – Allows collision-free fragment merging.
1. Adding Carbon
Start by activating the Add editor (A). Then, click on the C icon in the Asset Browser, which provides quick access to common atoms like hydrogen, carbon, nitrogen, and oxygen. Place a carbon atom in the viewport by clicking anywhere. With hydrogen adjustment enabled, it automatically forms CH4 (methane).
2. Building Connections
Connecting Atoms via Substitution: To attach additional atoms, hover above an existing atom (e.g., hydrogen) you wish to replace and click it. SAMSON intuitively predicts plausible placements based on covalent radii.
Connecting Atoms With Bonds: Click and hold on an atom, drag outward, and release the mouse at a distance corresponding to a bond length. Build the backbone of your molecule incrementally using these techniques.
3. Adding Nitrogen and Oxygen
Continue the process by adding nitrogen and oxygen atoms to grow your structure. Use a similar substitution or bonding technique. Below is a visualization:
Tip: You can activate interactive minimization (Z) to automatically optimize geometry as you build.
4. Modifying Bond Orders
Lastly, let’s adjust bond orders, such as introducing a double bond between the oxygen and carbon atoms. Activate the Edit Bonds editor (B), hover over the bond, and use the – and + controls to modify the bond order directly.
The result? A chemically accurate N-acetyl group, ready for integration into your molecular system.
Why SAMSON?
The flexibility of SAMSON’s tools simplifies molecular construction, whether you’re working atom-by-atom or assembling fragments. By incorporating features like structural preferences, interactive minimization, and smart bond handling, SAMSON reduces repetitive tasks and ensures a smooth modeling process.
Learn more about SAMSON’s molecular building tools, including preferences and advanced features, at the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can access SAMSON at SAMSON Connect.