💡 Photochemistry — Fluorescence, Phosphorescence & the Jablonski Diagram

Photons excite molecules up a Jablonski diagram, then relax back down via fluorescence or the much slower afterglow of phosphorescence. Watch the Stokes shift and decay lifetimes play out live.

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Left: Jablonski diagram with live photon events · Right: molecule population, flashes and photon-count graph · Adjust flux, quantum yield, ISC and phosphorescence lifetime

How it Works

This simulation renders two synchronized views of photoexcitation. On the left, a Jablonski diagram stacks the ground state S0, the excited singlets S1 and S2, and the triplet state T1. Absorbed photons pump molecules straight up (occasionally via S2, which relaxes to S1 almost instantly through internal conversion, a wavy nonradiative arrow). On the right, a population of individual molecule dots lights up as photons strike them, then dims again as each one decays back to the ground state after a randomly sampled lifetime.

From S1, an excited molecule has three possible fates: emit a fluorescence photon straight back to S0 (fast, nanosecond timescale, spin-allowed), cross over nonradiatively to the triplet state T1 via intersystem crossing (spin-forbidden but enabled by spin-orbit coupling), or relax nonradiatively to S0 releasing only heat. Once trapped in T1, a molecule lingers far longer before finally phosphorescing back to S0 — this is why the population panel keeps flashing with slow, long-lived glows even after you turn the excitation flux down, and why the emitted phosphorescence photon is shifted to an even longer wavelength than the fluorescence photon.

Stokes shift: Δλ = λ_emit − λ_absorb (nm, always positive)
Fluorescence lifetime: τ_fl ~ 1–20 ns (S₁ → S₀, spin-allowed)
Phosphorescence lifetime: τ_phos ~ 10⁻³–10² s (T₁ → S₀, spin-forbidden)
Quantum yield: Φ_fl = (photons emitted) / (photons absorbed)

Frequently Asked Questions

What does a Jablonski diagram show and how do I read it?

A Jablonski diagram is a stack of horizontal energy levels for a molecule: the ground state S0 at the bottom, excited singlet states S1 and S2 above it, and a triplet state T1 slightly below S1. Straight vertical arrows represent radiative transitions where a photon is absorbed or emitted; wavy arrows represent nonradiative transitions such as internal conversion and intersystem crossing, where energy is lost as heat instead of light.

What is the Stokes shift and why is emitted light always lower energy?

The Stokes shift is the difference in wavelength between the photon a molecule absorbs and the photon it later emits. Before emission, an excited molecule quickly loses some energy nonradiatively through internal conversion and vibrational relaxation down to the lowest excited state. The emitted photon therefore carries less energy, meaning a longer wavelength, than the absorbed photon.

What is the difference between fluorescence and phosphorescence?

Fluorescence is a spin-allowed S1 to S0 transition that happens almost immediately, on a timescale of nanoseconds. Phosphorescence is a spin-forbidden T1 to S0 transition that can take milliseconds to many seconds, because flipping the electron's spin is normally disallowed. This is exactly why glow-in-the-dark materials keep glowing long after the light source is switched off.

What is intersystem crossing and why is it "forbidden but possible"?

Intersystem crossing is the nonradiative transition from the excited singlet state S1 to the triplet state T1. It requires the excited electron's spin to flip, which is forbidden by standard selection rules. Spin-orbit coupling, a relativistic interaction between an electron's spin and its orbital motion, weakly allows the transition anyway, especially in molecules containing heavy atoms.

What does fluorescence quantum yield mean?

Fluorescence quantum yield is the fraction of excited molecules that relax by emitting a fluorescence photon, rather than losing their energy nonradiatively as heat or crossing over to the triplet state. A quantum yield near 1 means almost every absorbed photon is re-emitted as fluorescence; a low quantum yield means most excitation energy is dissipated without light.

What is the heavy-atom effect?

The heavy-atom effect describes how atoms with large atomic number, such as bromine, iodine, or heavy metals, strengthen spin-orbit coupling within a molecule. This makes intersystem crossing far more efficient, which is why molecules containing heavy atoms often phosphoresce strongly instead of fluorescing.

How is fluorescence used in biological imaging and dyes?

Fluorescent dyes and proteins, such as fluorescein and GFP, are attached to specific biological structures and imaged under a microscope tuned to their excitation and emission wavelengths. Because fluorescence lifetimes are so short, images can be captured essentially in real time, making fluorescence microscopy central to modern cell biology.

Why do glow-in-the-dark materials keep glowing after the light is turned off?

Glow-in-the-dark pigments contain phosphorescent compounds whose molecules become trapped in the long-lived triplet state T1 after absorbing light. Because the T1 to S0 transition is spin-forbidden, molecules leak out of the triplet state slowly, over seconds to hours, producing a steady afterglow long after excitation has stopped.

What other real-world applications use photochemistry like this?

Beyond dyes and glow-in-the-dark pigments, these same photophysical pathways power photodynamic therapy, where light-activated triplet states generate reactive oxygen to destroy diseased tissue; OLED displays, which rely on carefully tuned fluorescent and phosphorescent emitters for each pixel color; and sunscreen chemistry, where UV-absorbing molecules dissipate absorbed photon energy safely as heat instead of damaging skin.

About this simulation

Written by MySimulator Team · Reviewed by MySimulator Editorial Review

Last updated: 11 July 2026

This simulator pairs a Jablonski diagram with a live population of molecules so you can watch photoexcitation happen twice at once — once as an energy-level cartoon, once as hundreds of individual decay events. Absorbed photons kick molecules up to S1 or S2; from S1 they either fluoresce quickly back to S0, cross over into the long-lived triplet state T1 via intersystem crossing, or quietly lose their energy as heat. Molecules trapped in T1 linger far longer before finally phosphorescing, which is exactly why the right-hand panel keeps flashing with a slow amber-green afterglow even once you turn the excitation flux down — the same physics behind glow-in-the-dark toys and safety signage.

🔬 What it shows

Two synchronized views of the same molecules: a Jablonski diagram on the left with animated absorption, internal-conversion, fluorescence, intersystem-crossing, and phosphorescence arrows, and a population panel on the right where each dot glows and flashes as it is excited and decays, plus a running graph of cumulative fluorescence versus phosphorescence photon counts.

🎮 How to use

Drag the excitation flux slider to pump more or fewer molecules per second, then adjust the fluorescence quantum yield and intersystem crossing sliders to change how excited molecules choose their decay path. The phosphorescence lifetime slider controls how long molecules stay trapped in T1, and the fluorophore dropdown loads presets for quinine-like blue fluorescence, fluorescein-like green fluorescence, and a long-glowing phosphorescent material.

💡 Did you know?

Intersystem crossing is technically spin-forbidden, yet it happens all the time because spin-orbit coupling quietly breaks the selection rule — and it happens far more efficiently in molecules containing heavy atoms like bromine or iodine, a phenomenon chemists call the heavy-atom effect.

Frequently asked questions

What does the excitation photon flux slider control?

It sets how often ground-state S0 molecules absorb a photon and jump up to an excited singlet state. Turning it up floods the population panel with more simultaneous excitations and absorption arrows on the Jablonski diagram; turning it down slows new excitations, which is the easiest way to watch the phosphorescence afterglow persist after the "light" is effectively switched off.

What does the fluorescence quantum yield slider do?

It sets the probability that an excited S1 molecule relaxes by emitting a fluorescence photon rather than losing energy nonradiatively or crossing over to the triplet state. High values, like the fluorescein-like preset near 92%, produce bright, frequent fluorescence flashes; low values leave more molecules available to undergo intersystem crossing instead.

What does the intersystem crossing rate slider change?

Among the S1 molecules that do not fluoresce, this slider sets what fraction instead cross over nonradiatively into the triplet state T1 rather than simply relaxing to S0 as heat. Raising it feeds more molecules into the slow phosphorescence pathway, which is why the glow-in-the-dark preset uses a much higher intersystem crossing rate than the fluorescent dye presets.

What does the phosphorescence lifetime slider control, and why does the glow linger?

It sets the average time a molecule spends trapped in the triplet state T1 before finally emitting a phosphorescence photon and returning to S0. Because the T1 to S0 transition is spin-forbidden, this lifetime is set in seconds rather than nanoseconds, which is why the population panel keeps flashing with a slow afterglow long after fresh excitation events have stopped.

What do the molecule and fluorophore presets represent?

Each preset loads absorption and emission wavelengths, a fluorescence quantum yield, an intersystem crossing rate, and a phosphorescence lifetime typical of a class of real material: quinine-like compounds fluoresce blue with a high quantum yield and little intersystem crossing, fluorescein-like dyes fluoresce green even more efficiently, and the glow-in-the-dark preset favors intersystem crossing and a long phosphorescence lifetime over fast fluorescence.

Why do the flashes in the population panel have different colors?

Flash color encodes which photon was just involved: the absorption color when a molecule is excited, a fluorescence color for a fast S1 to S0 emission, and a separate, longer-wavelength phosphorescence color for a slow T1 to S0 emission. Watching the mix of colors and their timing directly shows the Stokes shift and the very different lifetimes of the two emission pathways.