The Power of 3D Molecule Visualisation in Chemistry Education

Navigate Molecules3D.com: A Beginner’s Guide

Written by Elena Skelton | Jun 19, 2025 2:17:34 PM

Welcome to Molecules3D.com, where molecules like H2O and CO2 spin in dazzling 3D glory! Whether you’re a chemistry newbie or just curious, this guide will have you navigating the site like a molecular maestro. Built with three.js, this interactive viewer is your ticket to exploring chemistry with a joy. Let’s dive into this microscopic adventure!

Step 1: Homepage—Your Molecular Starting Line

Landing on Molecules3D.com, you’ll find a launchpad for molecular exploration. Look for a top-right menu—your command center for navigating the site. It includes a default Formula, Number of bonds Molecular Analysis and Viewr3D to browse a collection of 3D models, from simple H2O to complex organic compounds. If you’re feeling artsy, check out galleries like “Organic” or “Amino Acids” for curated molecule collections that look almost too pretty to be science.

Step 2: The 3D Viewer—Spin, Zoom, and Admire!

Once you select a molecule, you’re in the 3D viewer, where the fun really starts. Your molecule (say, CO2) floats on-screen, slowly auto-rotating for a full view. To take control, drag your mouse to orbit around it like a satellite—left to swing sideways, up to tilt. Zoom in with the “+” button or out with “-” using the control bar at the bottom. This bar also shows the molecule’s name and lets you toggle auto-rotation or switch models with arrow buttons. Want a new look? Head to the center of the control bar to choose display modes: “Ball-and-Stick” for clear bonds or “Space-Filling” to see the molecule’s compact shape. Play with these—it’s like giving your molecule a wardrobe change

Step 3: Customise and Explore—Make It Yours

The top-right menu is your go-to for tweaking the experience. Collapse it to a single line if it’s hogging space, or expand it for options like “Field of View” to adjust your camera’s perspective. Toggle the grid (visible when dragging) for a sense of the molecule’s orbit path. Lighting settings can make your molecule glow dramatically—try viewing it with light sources behind or beside it for an artistic vibe. The menu also adds info about your chosen molecule, like its chemical properties, so you can geek out over details. If you’re curious, explore galleries like “Aldehydes” for specialized molecule sets.

Step 4: Need Help? You’re Covered!

If you’re stuck, look for a “Help” under the "?", or write your question here. The site’s creators love feedback, so check for a contact form to share your thoughts. 

Keep Spinning and Exploring!

Molecules3D.com is a chemistry playground that’s easy to navigate once you get the hang of it. Spin those molecules, try new modes, and let your curiosity run wild. Who knew atoms could be this fun? Happy exploring!