What is a Fluorophore?

A fluorophore is a chemical compound that is fluorescent, meaning it emits strong glowing colours. There are three key groups of chemical compounds that can fluoresce:

• Quantum dots
• Conjugated organic molecules
• Some proteins

Fluorophores are used in a range of applications across natural sciences, and engineering, including solar cells, LEDs, and medical imaging. Fluorescence in fluorophores happens when a photon is absorbed and is then re-emitted as another photon, usually of lower energy. This process happens through the transition of electrons between energy levels.

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How Does a Fluorophore Work?

Fluorophores fluoresce through the transition of electrons between different energy levels of a compound. Fluorophores such as quantum dots and conjugated organic molecules have electrons that can be easily promoted to an excited state. Their electrons can be promoted easily due to unique features of their chemical structures. The increased ability of their electrons to be excited then increases the number of photons released via fluorescence.

The fluorescence of these molecules can be explained in terms of transitions of electrons between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of a molecule.

The transfer of an electron from the HOMO to the LUMO happens after the absorption of energy by the molecule. During this transition the electron is promoted from the S₀ ground state energy level to the S₁ excited state energy level. Fluorescence happens when an electron transitions from the LUMO to the HOMO of a molecule, where the electron relaxes from S₁ to S₀ and emitting a photon in the process.

The HOMO-LUMO model is comparable to the conductance-valance band model sometimes used to explain fluorescence in quantum dots.

Three Types of Fluorophores

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The structure of fluorophores can vary significantly depending on the type of fluorescent chemical compound in question. Several key types of chemical compounds can fluoresce, including quantum dots, conjugated organic molecules, and proteins.

Type	Description	Properties	Common Examples
Quantum dots	Semiconducting crystals that are typically a few nanometres in size.	Have quantum mechanical properties not seen in the bulk chemical compound.	Graphene Quantum Dots Perovskite Quantum Dots
Conjugated organic molecules	Organic molecules with aromatic rings.	Contain systems of delocalized electrons that ease electronic transitions.	Ir(ppy)3 F8BT
Proteins	Naturally occurring polymeric organic molecules found in animals and plants.	Fluoresce naturally or fluorescent tags can be inserted into proteins.	Green fluorescent protein Red fluorescent protein

Quantum dots

Changing the size and structure of a quantum dot changes its electrical and optical properties: as the size of a quantum dot increases, the HOMO-LUMO gap decreases. This allows the properties of quantum dots to be tuned, and therefore its fluorescence wavelength to be changed.

Conjugated Organic Molecules

Conjugated molecules have alternating double bonds meaning their bonds are delocalized into shared electron clouds. The delocalisation of electrons results in a smaller HOMO-LUMO energy gap, meaning the promotion of an electron from the HOMO to the LUMO is easier. The structure of the conjugated system can change the size of the HOMO-LUMO gap, allowing the properties of the molecules to be tuned, similarly to quantum dots.

Proteins

Proteins that fluoresce naturally have conjugated organic groups in their structure that are able to absorb photons. Fluorescent tags can be added to proteins that are not naturally fluorescent to allow them to fluoresce. The fluorescent tags added to proteins are most often conjugated organic molecules, however quantum dots can also be used as fluorescent tags.

What are fluorophores used for?

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Fluorophores have applications in electronic devices, and in biological and medical research. Their optical, physical, and chemical properties can be exploited in scientific applications. The optical properties can be useful as a light source, or in medical imaging, for example where there are difficulties seeing what is happening in the body. The transfer of electrons that happens in fluorophores can be used in devices where semiconducting layers are necessary, or to measure distances between atoms using Förster Resonance Energy Transfer (FRET). FRET is an energy transfer between two compounds that absorb and reemit light.

Electrical Applications

In electronics, fluorophores are used as semiconducting layers and light sources in a range of electronic devices, such as:

• Light Emitting Diodes (LEDs)
• Solar Cells (Photovoltaics)
• Organic Field Transistors (OFETs)

Biological and medicinal applications

Fluorophores can be helpful in biological and medicinal research, and diagnostic applications, such as:

• Imaging
• Near Infrared
• Magnetic Resonance Imaging
• Fluorescent Imaging
• FRET Experiments
• Drug Delivery Systems

What Is Fluorescence?

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Fluorescence is a type of luminescence, a process where energy is released from a chemical compound via the emission of a photon. This process happens through the transition of electrons between energy levels.

Electron transitions

Which energy levels electrons move between governs the type of transition that occurs. Fluorescence is one of the processes of photon emission from a chemical compound. These transitions can be radiative or non radiative. Radiative transitions result in the emission of a photon, which is called luminescence. Non-radiative transitions release energy in other ways, for example molecular vibration.

Type of transition	Nature of transition	Energy levels involved
Internal Conversion	Non radiative	Sn to Sn-1
Intersystem Crossing	Non radiative	S1 to T1
Vibrational Relaxation	Non radiative	Vn to Vn-1
Fluorescence	Radiative	S1 to S0
Phosphorescence	Radiative	T1 to S0

In the ground state, S₀, the electrons are in the lowest energy electronic state. When the molecule absorbs energy, an electron is promoted from S₀ to the singlet electronic excited state, S₁. The electron then can relax from S₁ to S₀ via a variety of processes. Fluorescence is a radiative transition of an electron from the excited state S₁ to the ground state S₀.

The vibrational state of an electron, V_n, is the vibrational energy level that the electron sits in within the electronic energy level.

Process of Fluorescence

There are three steps in the process of fluorescence:

1. Absorption of energy in the form of light excites an electron in the chemical compound from S₀ to S₁.
2. Vibrational relaxation results in the excited state electron decreasing in vibrational energy but stays in S₁.
3. The electron relaxes from S₁ to S₀ via fluorescence. During fluorescence, a photon is emitted as the electron relaxes.

The strength of fluorescence emitted by a chemical compound can be measured using fluorescence spectroscopy. The strength of fluorescence is characterized by the compound's quantum yield and extinction coefficient. The quantum yield of a chemical compound is the amount of photons emitted divided by the number of photons absorbed. The extinction coefficient measures how strongly a chemical compound absorbs light. Fluorescence spectroscopy is commonly used in bioscience and chemistry to analyse samples and measure the amount of unwanted chemical compounds in the environment.

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