Molecular reaction simulator

Open reaction studio · build a solution batch →

Run atom-by-atom molecular dynamics in explicit solution, including steered bond-breaking and bond-forming trajectories. Explore the reaction bank below, or build and import molecules in the workbench.

Reaction data programme

Reaction bank

Explore quantum reference reactions and the simulation roadmap. Reference paths include molecular structures, quantum energies, atomic forces and independent validation evidence.

Explore quantum energies and forces →

Simulation roadmap

—roadmap reactions

—playable now

—mechanism families

—pilot / released samples

Loading the versioned reaction catalogue…

Optional particle sandbox (LJ teaching toy — not molecular chemistry)

LJ status: running

Molecular solution viewport

This is the molecular simulator: bonded atoms, explicit solvent, calculated forces, trajectory controls, and reaction-coordinate diagnostics.

engine untitled 0 atoms · 0 bonds ready

no trajectory solvent

Atom inspector

Click an atom in the 3D view to inspect element, index and coordinates. Use Select / move to drag it.

—

Import & library

Library / mini-proteins SMILES

Import MOL/SDF Import PDB

Waterise

Mode

Solution

pH 7.0 After pH change Salt 0.15 M Cation Anion

Reaction (generic event · xTB)

Reaction workflow

Live solution reaction

Starts a new steered GFN2-xTB dynamics job. Each calculated frame streams into the molecular viewport above while the job is running.

Play a saved trajectory without waiting: glycine proton transfer with a fixed 34-atom QM region, or the aqueous SN2 example.

Reactants Solution response

Ready. Responsive mode moves the complete solution with xTB + OpenMM forces. It remains steered dynamics, not an unbiased rate.

Mechanism Gas-path continuum (debug)

Build/import compound · waterise (explicit TIP3P)
Waterised react — embedded path in the box → reinsert → MD
Or gas-only: load demo → play mechanism → optional water MD
Scrub path · inspect acceptance · export pack

Waterise first to enable waterised react. Uses generic ReactionEvent (no mechanism-specific public fields).

SN2 vertical slice (validated prototype)

Neutral Cl⁻ + CH₃Br + Na⁺ + TIP3P → frozen MM embedding → restrained reactant → predicted product path → inverse reinsert + minimise → unrestrained ~2 ps MD. Electronic GFN2-xTB only — not ΔG‡ or rates. Path max = candidate, not a validated TS.

Idle — ~40 s typical on this host.

No background job

Mechanism / MD readout

image—

ΔE / PE—

dist A—

dist B—

T / RMSD—

Rg—

Path images = electronic coordinate. MD frames report PE/T/RMSD/Rg when available.

Solvated QM tools need explicit Waterise first (optional for gas/ALPB demos).

Advanced QM controls

QM seeds

Using all solute atoms as seeds.

Bond hops Charge Explicit water shell (Å) Expectation SMILES (validation only)

Product from reinsert is pending review.

Results

GFN2-xTB electronic estimates only — not ΔG‡ or experimental rates.

Trajectory

—

MD trajectory

Show solvent shell (water around molecule)

Play from the bar under the 3D view. Frames stream in live during Waterise.

Solute unwrapped (no teleport). Closed walls later.

2D builder (Ketcher bridge)