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- 2010- 3D Structures of Biological Macromolecules Chirality. Jürgen Sühnel email@example.com. Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany. Supplementary Material: www.fli-leibniz.de/www_bioc/3D/. Chirality.
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3D Structuresof Biological Macromolecules
Leibniz Institute for Age Research, Fritz Lipmann Institute,
Jena Centre for Bioinformatics
Jena / Germany
Supplementary Material: www.fli-leibniz.de/www_bioc/3D/
A chiral molecule is a type of molecule that lacks an internal plane of symmetry and has a non-superposable mirror image. The feature that is most often the cause of chirality in molecules is the presence of a so-called asymmetric carbon atom.
Two mirror images of a chiral molecule are called enantiomers or optical isomers. Pairs of enantiomers are often designated as "right-" and "left-handed."
Molecular chirality is of interest because of its application to stereochemistry in inorganic chemistry, organic chemistry, physical chemistry, biochemistry and supramolecular chemistry.
An aldopentose with 3 asymmetric carbon atoms has 23 = 8 stereoisomers:
Which of the following compounds would form enantiomers because the molecule is chiral?
Symmetry operation, Symmetry element
Reflection, Symmetry plane or Mirror plane
All amino acids are chiral except for glycine.
Chiral compounds rotate the plane of polarized light. Each enantiomer will rotate the light in a different sense, clockwise or counterclockwise. Molecules that do this are said to be optically active.
a - specific rotation
Because many optically active chemicals are stereoisomers, a polarimeter can be used to identify which isomer is present in a sample – if it rotates polarized light to the left, it is a levo-isomer, and to the right, a dextro-isomer.
Concentration and purity measurements are especially important to determine product or ingredient quality in the food & beverage and pharmaceutical industries. Samples that display specific rotations that can be calculated for purity with a polarimeter include:
Steroids, Diuretics, Antibiotics, Narcotics, Vitamins, Analgesics, Amino Acids,
Essential Oils, Polymers, Starches, Sugars.
Many biologically active molecules are chiral, including the naturally occurring amino acids (the building blocks of proteins) and sugars.
In biological systems, most of these compounds are of the same chirality: most amino acids are L and sugars are D. Typical naturally occurring proteins, made of L amino acids, are known as left-handed proteins, whereas D amino acids produce right-handed proteins.
By configuration: R and S.
Each chiral center is labeled as R or S according to a system by which its substituents are each assigned a priority, according to the Cahn-Ingold-Prelog priority rules (CIP), based on atomic number. If the center is oriented so that the lowest-priority of the four is pointed away from a viewer, the viewer will then see two possibilities: If the priority of the remaining three substituents decreases in clockwise direction, it is labeled R (for Rectus), if it decreases in counterclockwise direction, it is S (for Sinister).
This system labels each chiral center in a molecule (and also has an extension to chiral molecules not involving chiral centers). Thus, it has greater generality than the d/l system, and can label, for example, an (R,R) isomer versus an (R,S) — diastereomer.
The R / S system has no fixed relation to the (+)/(−) system. An R isomer can be either dextrorotatory or levorotatory, depending on its exact substituents.
The R / S system also has no fixed relation to the d/l system. For example, the side-chain one of serine contains a hydroxyl group, -OH. If a thiol group, -SH, were swapped in for it, the d/l labeling would, by its definition, not be affected by the substitution. But this substitution would invert the molecule's R / S labeling, because the CIP priority of CH2OH is lower than that for CO2H but the CIP priority of CH2SH is higher than that for CO2H.
For this reason, the d/l system remains in common use in certain areas of biochemistry, such as amino acid and carbohydrate chemistry, because it is convenient to have the same chiral label for all of the commonly occurring structures of a given type of structure in higher organisms. In the d/l system, they are nearly all consistent - naturally occurring amino acids are nearly all l, while naturally occurring carbohydrates are nearly all d. In the R / S system, they are mostly S, but there are some common exceptions.
After the substituents of a stereocenter have been assigned their priorities, the molecule is so oriented in space that the group with the lowest priority is pointed away from the observer. If the substituents are numbered from 1 (highest priority) to 4 (lowest priority), then the sense of rotation of a curve passing through 1, 2 and 3 distinguishes the stereoisomers. A center with a clockwise sense of rotation is an R or rectus center and a center with a counterclockwise sense of rotation is an S or sinister center. The names are derived from the Latin for right and left, respectively.
By optical activity: (+)- and (−).
An enantiomer can be named by the direction in which it rotates the plane of polarized light. If it rotates the light clockwise (as seen by a viewer towards whom the light is traveling), that enantiomer is labeled (+). Its mirror-image is labeled (−).
The (+) and (−) isomers have also been termed d- and l-, respectively (for dextrorotatoryand levorotatory). Naming with d- and l- is easy to confuse with d- and l- labeling and is therefore strongly discouraged by IUPAC.
When circularly polarized light passes through an absorbing optically active medium, the speeds between right and left polarizations differ (cL ≠ cR) as well as their wavelength (λL ≠ λR) and the extent to which they are absorbed (εL≠εR). Circular dichroismi s the difference Δε ≡ εL- εR.
Although the absorbance difference is usually measured, for historical reasons most measurements are reported in degrees of ellipticity. Molar circular dichroism and molar ellipticity, [θ], are readily interconverted by the equation:
Methods for estimating secondary structure in polymers, proteins and polypeptides in particular, often require that the measured molar ellipticity spectrum be converted to a normalized value, specifically a value independent of the polymer length. Mean residue ellipticity is used for this purpose; it is simply the measured molar ellipticity of the molecule divided by the number of monomer units (residues) in the molecule.
Two chiral objects that are mirror images of each other behave identically in achiral environments. Therefore, enantiomers can only be distinguished in chiral environments. Enantiomers have identical physical properties in almost every regard except one: their ability to rotate plane- polarized light, or optical activity. When plane-polarized light is passed through a solution containing chiral compounds, the plane is rotated by a number of degrees depending on the nature of the molecules in solution. Enantiomers have equal but opposite optical rotations.
Asymmetric synthesis, also called chiral synthesis, enantioselective synthesis or stereoselective synthesis, is organic synthesis that introduces one or more new and desired elements of chirality.This is important in the field of pharmaceuticals because the different enantiomers or diastereomers of a molecule often have different biological activity.
Chirality must be introduced to the substance first. Then, it must be maintained. Usually, chiral products are formed in racemic 50%/50% mixtures.
These mixtures can be separated by physico-chemical methods, for example by chiral chromatography.
One method is the usage of metal ligand complexes derived from chiral ligands. This method was pioneered by William S. Knowles and Ryōji Noyori (Nobel Prize in Chemistry 2001). Knowles in 1968 replaced the achiral triphenylphosphine ligands in Wilkinson's catalyst by the chiral phosphine ligands P(Ph)(Me)(Propyl), thus creating the first asymmetric catalyst.