Free, interactive tools for introductory organic chemistry, built by the Stolley Group to help students see, rotate and test the ideas that are hardest to picture on a page.
Organic chemistry asks students to picture molecules in three dimensions, track electrons and weigh competing pathways. Many students find that hard to do in their heads. These tools put the molecule on the screen, where students can rotate it, change it and see what happens.
Each tool follows standard textbook conventions and shows the rules behind its answers, so students can check their reasoning rather than just the result.
Draw it, then see it in three dimensions.
Draw structures with bonds, rings, wedges and hashes, charges, text and arrows, and label atoms with any element or group abbreviation (OTBDMS, Boc, CO2Me). Clean up a rough drawing in one click, rotate it in 3D as a line drawing, see formulas and molar masses as you build, and save .mol files or images or send them to the 3D Builder.
Open tool →Build molecules in 3D with atoms that snap to VSEPR geometries. Show lone pairs, read steric number, shape and hybridization, and minimize the structure: it flips chairs and rotates bonds to relieve steric strain.
Open tool →Orbitals, three-dimensional arrangement, conformation and crystal packing.
See atomic orbitals for H, B, C, N, O and Cl in 3D, follow how overlap builds σ and π bonds, and watch hydrogens bond to sp³, sp² and sp centres beside a live MO diagram.
Open tool →Rotate stereocenters, assign R and S step by step, compare enantiomers, diastereomers and meso compounds side by side, and test whether two isomers superimpose.
Open tool →Rotate ethane and butane about a C–C bond and flip cyclohexane chairs, with Newman projections, energy diagrams, barriers and conformer populations.
Open tool →Open any .cif file to see the asymmetric unit, the complete molecule, the unit cell and how molecules pack, with hydrogen bonds, symmetry colouring and distance and angle measurement.
Open tool →Electrons, protons and how reactions choose a pathway.
Step through resonance contributors, push curved arrows yourself with a rules check, and see how the hybrid shares charge and bond order.
Open tool →Send any structure from the Sketch or the 3D Builder to see polar bonds, bond and molecular dipoles, partial charges and an electron-density map, with its functional groups and resonance contributors highlighted.
Open tool →Predict which way a proton transfer goes from pKa values, explain conjugate-base stability with ARIO, and follow how pH sets the charge on a molecule.
Open tool →Compare SN2, SN1, E2 and E1. Choose the nucleophile or base, leaving group, carbon, solvent and temperature, watch each mechanism and see which pathway wins.
Open tool →Know where your students are starting from.
A 15–20 minute, ungraded check of mental imagery (VVIQ), paper folding and mental rotation, with no chemistry required. Run it at the start, middle and end of a course; students export their results and you combine a class set from Canvas in one step.
Open tool →An 8–10 minute, ungraded check-in for the middle and end of a semester: attendance, study time and habits, use of visualization tools, getting help, and comfort in class. Includes a codebook and a printable copy for IRB applications.
Open tool →Link to any tool from a Canvas page, module or assignment. Each tool runs entirely in the student’s browser and works on laptops and tablets. The 3D tools are easiest with a mouse or trackpad.
The tools do not collect or send student data. Drawings and results stay on the student’s device until they choose to save or submit them.
Students can draw a structure in the Sketch and press Open in 3D to see it in the 3D Builder, with its stereochemistry kept as drawn.
Using these in a class, or have an idea for a new tool? Email Dr. Stolley.