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- 2010- 3D Structures of Biological Macromolecules Chirality. Jürgen Sühnel [email protected] Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany. Supplementary Material: Chirality.

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3D Structuresof Biological Macromolecules


Jürgen Sühnel

[email protected]

Leibniz Institute for Age Research, Fritz Lipmann Institute,

Jena Centre for Bioinformatics

Jena / Germany

Supplementary Material:


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.

Chirality – Asymmetric Carbon Atoms

  • An asymmetric carbon atom is a carbon atom that is attached to four different atoms or four different groups of atoms.

  • Knowing the number of asymmetric carbon atoms, one can calculate the maximum possible number of stereoisomers for any given molecule as follows:

    • If n is the number of asymmetric carbon atoms then the maximum number of isomers = 2n.

    • As an example, malic acid has 4 carbon atoms but just one of them is asymmetric:

An aldopentose with 3 asymmetric carbon atoms has 23 = 8 stereoisomers:


Which of the following compounds would form enantiomers because the molecule is chiral?

Chirality - Alanine


Symmetry operation, Symmetry element

Reflection, Symmetry plane or Mirror plane

All amino acids are chiral except for glycine.


Chirality – Optical Active Compounds

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.

Chirality – Optical Active Compounds

a - specific rotation

Chirality – Optical Active Compounds

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.

Chirality – Molecules of Life

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.

Chirality: R/S Naming System

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.

Chirality: Cahn-Ingold-Prelog Priority Rules

  • 1. Compare the atomic number (Z) of the atoms directly attached to the stereocenter; the group having the atom of higher atomic number receives higher priority.

  • 2. If there is a tie, we must consider the atoms at distance 2 from the stereocenter—as a list is made for each group of the atoms bonded to the one directly attached to the stereocenter. Each list is arranged in order of decreasing atomic number. Then the lists are compared atom by atom; at the earliest difference, the group containing the atom of higher atomic number receives higher priority.

  • 3. If there is still a tie, each atom in each of the two lists is replaced with a sub-list of the other atoms bonded to it (at distance 3 from the stereocenter), the sub-lists are arranged in decreasing order of atomic number, and the entire structure is again compared atom by atom. This process is repeated, each time with atoms one bond farther from the stereocenter, until the tie is broken.

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.

Chirality: Cahn-Ingold-Prelog Priority Rules

Chirality: Cahn-Ingold-Prelog Priority Rules




















Chirality: Cahn-Ingold-Prelog Priority Rules

Chirality: d/l Naming System Naming System

  • By configuration: d- and l.

  • An optical isomer can be named by the spatial configuration of its atoms. The d/l system does this by relating the molecule to glyceraldehyde. Glyceraldehyde is chiral itself, and its two isomers are labeled d and l (typically typeset in small caps in published work). Certain chemical manipulations can be performed on glyceraldehyde without affecting its configuration, and its historical use for this purpose (possibly combined with its convenience as one of the smallest commonly used chiral molecules) has resulted in its use for nomenclature.

  • In this system, compounds are named by analogy to glyceraldehyde, which, in general, produces unambiguous designations, but is easiest to see in the small biomolecules similar to glyceraldehyde.

  • One example is the amino acid alanine, which has two optical isomers, and they are labeled according to which isomer of glyceraldehyde they come from. On the other hand, glycine, the amino acid derived from glyceraldehyde, has no optical activity, as it is not chiral (achiral). Alanine, however, is chiral.

  • The d/l labeling is unrelated to (+)/(−); it does not indicate which enantiomer is dextrorotatory and which is levorotatory.

  • Rather, it says that the compound's stereochemistry is related to that of the dextrorotatory or levorotatory enantiomer of glyceraldehyde—the dextrorotatory isomer of glyceraldehyde is, in fact, the d-isomer. Nine of the nineteen l-amino acids commonly found in proteins are dextrorotatory (at a wavelength of 589 nm), and d-fructose is also referred to as levulose because it is levorotatory.

  • A rule of thumb for determining the d/l isomeric form of an amino acid is the "CORN" rule. The groups:

    • COOH, R, NH2 and H (where R is a variant carbon chain)

  • are arranged around the chiral center carbon atom. Sighting with the hydrogen atom away from the viewer, if these groups are arranged clockwise around the carbon atom, then it is the d-form. If counter-clockwise, it is the l-form.

Chirality: (+)/(-) Naming System Naming System

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.

Chirality – Circular Dichroism

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.

  • Usually, the so-called absorbance difference

  • is measured. It can also be expressed, by applying Beer's law, as:

  • Where εL and εR are the molar extinction coefficients for LCP and RCP light, C is the molar concentration and l is the path length in centimeters (cm).

  • Then

  • is the molar circular dichroism. This intrinsic property is what is usually meant by the circular dichroism of the substance. Since Δε is a function of wavelength, a molar circular dichroism value (Δε) must specify the wavelength at which it is valid.

Chirality – Circular Dichroism

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.

  • Secondary structure can be determined by CD spectroscopy in the "far-UV" spectral region (190-250 nm). At these wavelengths the chromophore is the peptide bond, and the signal arises when it is located in a regular, folded environment. Alpha-helix, beta-sheet, and random coil structures each give rise to a characteristic shape and magnitude of CD spectrum. 

  • Like all spectroscopic techniques, the CD signal reflects an average of the entire molecular population.  Thus, while CD can determine that a protein contains about 50% alpha-helix, it cannot determine which specific residues are involved in the alpha-helical portion.

Chirality : Poly-Lysine CD Spectrum

Chirality : Property Differences of Stereoisomers

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.

Chirality : Property Differences of Stereoisomers - Thalidomide

Chirality : Property Differences of Stereoisomers - Aspartame

Chiral (Asymmetric) Synthesis

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.

Chiral (Asymmetric) Synthesis

  • The oldest asymmetric synthesis is the enantioselective decarboxylation of the malonic acid2-ethyl-2-methylmalonic acid mediated by brucine (forming the salt) as reported by Willy Marckwald in 1904.

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.