Many pigments, such as retinal, make use of conjugated electron systems to absorb visible light.
A conjugated system is a system of connected p-orbitals with delocalized electrons in molecules with alternating single and multiple bonds, which in general may lower the overall energy of the molecule and increase stability. Aromaticity is a special type of conjugation describing a conjugated system in a planar ring where the number of π delocalized electrons that is even, but not a multiple of 4. That is, 4n + 2 number of π electrons, where n=0, 1, 2, 3, and so on. This is known as Hückel's Rule. Aromaticity allows for the electrons in the molecule's pi system to be completely delocalized around the ring. Aromaticitiy increases the molecule's stability to a greater degree than normal conjugation.
From the role of stable conjugated intermediates in enzyme reactions, to the in behavior of electron transporters such as NADH or ubiquinone, to the absorption qualities of pigments, concepts from conjugation and aromaticity come up again and again within biochemistry. For this reason, this is an area of particular focus within organic chemistry for the new MCAT.
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Conceptual Vocabulary for Conjugation and Aromaticity
Aromaticity is a chemical property in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone.
A chemically conjugated system is a system of atoms covalently bonded with alternating single and multiple bonds in a molecule of an organic compound.
Delocalized electrons are electrons in a molecule that are not associated with a single atom or to a covalent bond.
Pi bonds are covalent chemical bonds where two lobes of one involved electron orbital overlap two lobes of the other involved electron orbital. Only one of the orbital's nodal planes passes through both of the involved nuclei.
Dienes are hydrocarbons which contain two double bonds.
Benzene is an organic aromatic chemical compound whose molecules contain six carbons and six hydrogens.
Hückel's rule estimates whether a planar ring molecule will have aromatic properties. It was first expressed succinctly as the 4n+2 rule by von Doering in 1951.
An aromatic ring current is an effect observed in aromatic molecules if a magnetic field is directed perpendicular to the plane of the aromatic system.
Heterocyclic compounds are organic compounds that contain a ring structure containing atoms in addition to carbon, such as sulfur, oxygen or nitrogen, as part of the ring.
Often compounds with extended conjugated systems, a pigment is a material that changes the color of light it reflects as the result of selective color absorption.
Stacking in supramolecular chemistry refers to a stacked arrangement of aromatic molecules, which interact through aromatic interactions.
In the context of organic molecules, aryl refers to any functional group or substituent derived from a simple aromatic ring.
A set of points in space is coplanar if the points all lie in the same geometric plane.
Naphthalene is a crystalline, aromatic, white, solid hydrocarbon, best known as the primary ingredient of mothballs.
Polyenes are poly-unsaturated organic compounds that contain one or more sequences of alternating double and single carbon-carbon bonds.
Polycyclic aromatic hydrocarbons are chemical compounds that consist of fused aromatic rings and do not contain heteroatoms or carry substituents.
Cross-conjugation is a special type of conjugation in a molecule, when in a set of three pi bonds only two pi-bonds interact with each other by conjugation, the third one is excluded from interaction.
Toluene, also known as methylbenzene or phenylmethane, is a clear, water-insoluble liquid with the typical smell of paint thinners.
Xylene refers to a group of 3 benzene derivatives which encompasses ortho-, meta-, and para- isomers of dimethyl benzene.
The Hückel method is a very simple LCAO MO Method for the determination of energies of molecular orbitals of pi electrons in conjugated hydrocarbon systems, such as ethene, benzene and butadiene.
Homoaromaticity in organic chemistry is found in conjugated cyclic systems that are able to skip a part of the ring as opposed to regular aromaticity.
Cyclobutadiene is the smallest [n]-annulene, an extremely unstable hydrocarbon, failing Hückel's rule, because its ring has 4 pi-electrons, and 4 is not twice an odd number.
Antiaromatic or pseudoaromatic molecules are cyclic systems containing alternating single and double bonds, where the pi electron energy of antiaromatic compounds is higher than that of its open-chain counterpart.
The PAH world hypothesis is a biological hypothesis that proposes that polycyclic aromatic hydrocarbons provided a means for a pre-RNA World basis for the origin of life.