An electron and an electron hole that are attracted to each other by the Coulomb force can form a bound state called an exciton. It is an electrically neutral quasiparticle that exists mainly in condensed matter, including insulators, semiconductors, some metals, but also in certain atoms, molecules and liquids. The exciton is regarded as an elementary excitation that can transport energy without transporting net electric charge.
Photoluminescence is light emission from any form of matter after the absorption of photons. It is one of many forms of luminescence and is initiated by photoexcitation, hence the prefix photo-. Following excitation, various relaxation processes typically occur in which other photons are re-radiated. Time periods between absorption and emission may vary: ranging from short femtosecond-regime for emission involving free-carrier plasma in inorganic semiconductors up to milliseconds for phosphoresence processes in molecular systems; and under special circumstances delay of emission may even span to minutes or hours.
Quantum dots (QDs) or semiconductor nanocrystals are semiconductor particles a few nanometres in size with optical and electronic properties that differ from those of larger particles via quantum mechanical effects. They are a central topic in nanotechnology and materials science. When a quantum dot is illuminated by UV light, an electron in the quantum dot can be excited to a state of higher energy. In the case of a semiconducting quantum dot, this process corresponds to the transition of an electron from the valence band to the conductance band. The excited electron can drop back into the valence band releasing its energy as light. This light emission (photoluminescence) is illustrated in the figure on the right. The color of that light depends on the energy difference between the conductance band and the valence band, or the transition between discrete energy states when the band structure is no longer well-defined in QDs.
A fluorophore is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with several π bonds.
Supramolecular chemistry refers to the branch of chemistry concerning chemical systems composed of a discrete number of molecules. The strength of the forces responsible for spatial organization of the system range from weak intermolecular forces, electrostatic charge, or hydrogen bonding to strong covalent bonding, provided that the electronic coupling strength remains small relative to the energy parameters of the component. While traditional chemistry concentrates on the covalent bond, supramolecular chemistry examines the weaker and reversible non-covalent interactions between molecules. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi–pi interactions and electrostatic effects.
Förster resonance energy transfer (FRET), fluorescence resonance energy transfer, resonance energy transfer (RET) or electronic energy transfer (EET) is a mechanism describing energy transfer between two light-sensitive molecules (chromophores). A donor chromophore, initially in its electronic excited state, may transfer energy to an acceptor chromophore through nonradiative dipole–dipole coupling. The efficiency of this energy transfer is inversely proportional to the sixth power of the distance between donor and acceptor, making FRET extremely sensitive to small changes in distance.
Texas Red or sulforhodamine 101 acid chloride is a red fluorescent dye, used in histology for staining cell specimens, for sorting cells with fluorescent-activated cell sorting machines, in fluorescence microscopy applications, and in immunohistochemistry. Texas Red fluoresces at about 615 nm, and the peak of its absorption spectrum is at 589 nm. The powder is dark purple. Solutions can be excited by a dye laser tuned to 595-605 nm, or less efficiently a krypton laser at 567 nm. The absorption extinction coefficient at 596 nm is about 85,000 M−1cm−1.
In chemistry, quenching refers to any process which decreases the fluorescent intensity of a given substance. A variety of processes can result in quenching, such as excited state reactions, energy transfer, complex-formation and collisions. As a consequence, quenching is often heavily dependent on pressure and temperature. Molecular oxygen, iodine ions and acrylamide are common chemical quenchers. The chloride ion is a well known quencher for quinine fluorescence. Quenching poses a problem for non-instant spectroscopic methods, such as laser-induced fluorescence.
Cyanines, also referred to as tetramethylindo(di)-carbocyanines are a synthetic dye family belonging to the polymethine group. Although the name derives etymologically from terms for shades of blue, the cyanine family covers the electromagnetic spectrum from near IR to UV.
Squaraine dyes are a class of organic dyes showing intense fluorescence, typically in the red and near infrared region. They are characterized by their unique aromatic four membered ring system derived from squaric acid. Most squaraines are encumbered by nucleophilic attack of the central four membered ring, which is highly electron deficient. This encumbrance can be attenuated by the formation of a rotaxane around the dye to protect it from nucleophiles. They are currently used as sensors for ions and have recently, with the advent of protected squaraine derivatives, been exploited in biomedical imaging.
Quantum biology is the study of applications of quantum mechanics and theoretical chemistry to aspects of biology that cannot be accurately described by the classical laws of physics. An understanding of fundamental quantum interactions is important because they determine the properties of the next level of organization in biological systems.
The optical properties of carbon nanotubes are highly relevant for materials science. The way those materials interact with electromagnetic radiation is unique in many respects, as evidenced by their peculiar absorption, photoluminescence (fluorescence), and Raman spectra.
Fluorescence is used in the life sciences generally as a non-destructive way of tracking or analysing biological molecules. Some proteins or small molecules in cells are naturally fluorescent, which is called intrinsic fluorescence or autofluorescence. Alternatively, specific or general proteins, nucleic acids, lipids or small molecules can be "labelled" with an extrinsic fluorophore, a fluorescent dye which can be a small molecule, protein or quantum dot. Several techniques exist to exploit additional properties of fluorophores, such as fluorescence resonance energy transfer, where the energy is passed non-radiatively to a particular neighbouring dye, allowing proximity or protein activation to be detected; another is the change in properties, such as intensity, of certain dyes depending on their environment allowing their use in structural studies.
eFluor nanocrystals are a class of fluorophores made of semiconductor quantum dots. The nanocrystals can be provided as either primary amine, carboxylate, or non-functional groups on the surface, allowing conjugation to biomolecules of a researcher's choice. The nanocrystals can be conjugated to primary antibodies which are used for flow cytometry, immunohistochemistry, microarrays, in vivo imaging and microscopy.
Core–shell semiconducting nanocrystals (CSSNCs) are a class of materials which have properties intermediate between those of small, individual molecules and those of bulk, crystalline semiconductors. They are unique because of their easily modular properties, which are a result of their size. These nanocrystals are composed of a quantum dot semiconducting core material and a shell of a distinct semiconducting material. The core and the shell are typically composed of type II–VI, IV–VI, and III–V semiconductors, with configurations such as CdS/ZnS, CdSe/ZnS, CdSe/CdS, and InAs/CdSe Organically passivated quantum dots have low fluorescence quantum yield due to surface related trap states. CSSNCs address this problem because the shell increases quantum yield by passivating the surface trap states. In addition, the shell provides protection against environmental changes, photo-oxidative degradation, and provides another route for modularity. Precise control of the size, shape, and composition of both the core and the shell enable the emission wavelength to be tuned over a wider range of wavelengths than with either individual semiconductor. These materials have found applications in biological systems and optics.
YOYO-1 is a green fluorescent dye used in DNA staining. It belongs to the family of monomethine cyanine dyes and is a tetracationic homodimer of Oxazole Yellow, typically available as tetraiodide salt. In aqueous buffer, free YOYO-1 dye has very low fluorescence quantum yield. However, the intensity of fluorescence increases 3200 times upon binding through bis-intercalation to double-stranded DNA.
The Elliott formula describes analytically, or with few adjustable parameters such as the dephasing constant, the light absorption or emission spectra of solids. It was originally derived by Roger James Elliott to describe linear absorption based on properties of a single electron–hole pair. The analysis can be extended to a many-body investigation with full predictive powers when all parameters are computed microscopically using, e.g., the semiconductor Bloch equations or the semiconductor luminescence equations.
SYBR Safe is a cyanine dye used as a nucleic acid stain in molecular biology. SYBR Safe is one of a number of SYBR dyes made by the Life Technologies Corporation. SYBR Safe binds to DNA. The resulting DNA-dye-complex absorbs blue light and emits green light.
Light harvesting materials harvest solar energy that can then be converted into chemical energy through photochemical processes. Synthetic light harvesting materials are inspired by photosynthetic biological systems such as light harvesting complexes and pigments that are present in plants and some photosynthetic bacteria. The dynamic and efficient antenna complexes that are present in photosynthetic organisms has inspired the design of synthetic light harvesting materials that mimic light harvesting machinery in biological systems. Examples of synthetic light harvesting materials are dendrimers, porphyrin arrays and assemblies, organic gels, biosynthetic and synthetic peptides, organic-inorganic hybrid materials, and semiconductor materials. Synthetic and biosynthetic light harvesting materials have applications in photovoltaics, photocatalysis, and photopolymerization.
Black Hole Quencher 1 (BHQ1) is an example of dark quencher, which is used to quench green and yellow dyes, such as 6-carboxyfluorescein (6-FAM), tetrachlorofluorescein (TET), and hexachlorofluorescein (HEX). The role of quenchers is to absorb energy from a fluorophore and to re-emit the energy in the form of either heat or visible light. The absorption range of BHQ1 is from 480 to 580 nm with maximum absorption at 534 nm.
