Absolute configuration

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Absolute configuration showing the determination of the R and S descriptors R S configuration.png
Absolute configuration showing the determination of the R and S descriptors

Absolute configuration refers to the spatial arrangement of atoms within a chiral molecular entity (or group) and its resultant stereochemical description. [1] Absolute configuration is typically relevant in organic molecules where carbon is bonded to four different substituents. This type of construction creates two possible enantiomers. Absolute configuration uses a set of rules to describe the relative positions of each bond around the chiral center atom. The most common labeling method uses the descriptors R or S and is based on the Cahn–Ingold–Prelog priority rules. R and S refer to rectus and sinister, Latin for right and left, respectively.

Contents

Chiral molecules can differ in their chemical properties, but are identical in their physical properties, which can make distinguishing enantiomers challenging. Absolute configurations for a chiral molecule (in pure form) are most often obtained by X-ray crystallography, although with some important limitations. All enantiomerically pure chiral molecules crystallise in one of the 65 Sohncke groups (chiral space groups). Alternative techniques include optical rotatory dispersion, vibrational circular dichroism, ultraviolet-visible spectroscopy, the use of chiral shift reagents in proton NMR and Coulomb explosion imaging. [2] [3]

History

Until 1951, it was not possible to obtain the absolute configuration of chiral compounds. [4] It was at some time decided that (+)-glyceraldehyde was the D-enantiomer.[ citation needed ] The configuration of other chiral compounds was then related to that of (+)-glyceraldehyde by sequences of chemical reactions. For example, oxidation of (+)-glyceraldehyde (1) with mercury oxide gives (−)-glyceric acid (2), a reaction that does not alter the stereocenter. Thus the absolute configuration of (−)-glyceric acid must be the same as that of (+)-glyceraldehyde. Nitric acid [ citation needed ] oxidation of (+)-isoserine (3) gives (–)-glyceric acid, establishing that (+)-isoserine also has the same absolute configuration. (+)-Isoserine can be converted by a two-stage process of bromination[ citation needed ] and zinc reduction to give (–)-lactic acid, therefore (–)-lactic acid also has the same absolute configuration. If a reaction gave the enantiomer of a known configuration, as indicated by the opposite sign of optical rotation, it would indicate that the absolute configuration is inverted.

Relative absolute configuration.svg

In 1951, Johannes Martin Bijvoet for the first time used in X-ray crystallography the effect of anomalous dispersion, which is now referred to as resonant scattering, to determine absolute configuration. [5] The compound investigated was (+)-sodium rubidium tartrate and from its configuration (R,R) it was deduced that the original guess for (+)-glyceraldehyde was correct.

Despite the tremendous and unique impact on access to molecular structures, X-ray crystallography poses some challenges. The process of crystallization of the target molecules is time- and resource-intensive, and can not be applied to relevant systems of interest such as many biomolecules (some proteins are an exception) and in situ catalysts. Another important limitation is that the molecule must contain "heavy" atoms (for example, bromine) to enhance the scattering. [6] Furthermore, crucial distorsions of the signal arise from the influence of the nearest neighbors in any crystal structure and of solvents used during the crystallization process.

Just recently, novel techniques have been introduced to directly investigate the absolute configuration of single molecules in gas-phase, usually in combination with ab initio quantum mechanical theoretical calculations, therefore overcoming some of the limitations of the X-ray crystallography. [7]

Conventions

By absolute configuration: R- and S-

Examples of absolute configuration of some carbohydrates and amino acids according to Fischer projection (D/L system) and Cahn-Ingold-Prelog priority rules (R/S system) Absolute configuration.svg
Examples of absolute configuration of some carbohydrates and amino acids according to Fischer projection (D/L system) and Cahn–Ingold–Prelog priority rules (R/S system)

The R/S system is an important nomenclature system for denoting enantiomers. This approach labels each chiral center 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. When the center is oriented so that the lowest-priority substituent of the four is pointed away from the 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 Latin : rectus  – right); if it decreases in counterclockwise direction, it is S (for Latin : sinister  – left). [8]

(R) or (S) is written in italics and parentheses. If there are multiple chiral carbons, e.g. (1R,4S), a number specifies the location of the carbon preceding each configuration. [9]

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 the commonly occurring structures of a given type of structure in higher organisms. In the D/L system, nearly all naturally occurring amino acids are all L, while naturally occurring carbohydrates are nearly all D. All proteinogenic amino acids are S, except for cysteine, which is R.

By optical rotation: (+)- and (−)- or d- and l-

An enantiomer can be named by the direction in which it rotates the plane of polarized light. Clockwise rotation of the light traveling toward the viewer is labeled (+) enantiomer. Its mirror-image is labeled (−). The (+) and (−) isomers have been also termed d- and l- (for dextrorotatory and levorotatory); but, naming with d- and l- is easy to confuse with D- and L- labeling and is therefore discouraged by IUPAC. [10]

By relative configuration: D- and L-

An optical isomer can be named by the spatial configuration of its atoms. The D/L system (named after Latin dexter and laevus, right and left), not to be confused with the d- and l-system, see above, 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 chiral 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 (it's achiral).

The D/L labeling is unrelated to (+)/(−) – it does not indicate which enantiomer is dextrorotatory and which is levorotatory. Rather, it indicates the compound's stereochemistry relative 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 the side-chain)

are arranged around the chiral center carbon atom. With the hydrogen atom away from the viewer, if the arrangement of the CO→R→N groups around the carbon atom as center is counter-clockwise, then it is the L form. [11] If the arrangement is clockwise, it is the D form. As usual, if the molecule itself is oriented differently, for example, with H towards the viewer, the pattern may be reversed. The L form is the usual one found in natural proteins. For most amino acids, the L form corresponds to an S absolute stereochemistry, but is R instead for certain side-chains.

See also

Related Research Articles

<span class="mw-page-title-main">Cahn–Ingold–Prelog priority rules</span> Naming convention for stereoisomers of molecules

In organic chemistry, the Cahn–Ingold–Prelog (CIP) sequence rules are a standard process to completely and unequivocally name a stereoisomer of a molecule. The purpose of the CIP system is to assign an R or S descriptor to each stereocenter and an E or Z descriptor to each double bond so that the configuration of the entire molecule can be specified uniquely by including the descriptors in its systematic name. A molecule may contain any number of stereocenters and any number of double bonds, and each usually gives rise to two possible isomers. A molecule with an integer n describing the number of stereocenters will usually have 2n stereoisomers, and 2n−1 diastereomers each having an associated pair of enantiomers. The CIP sequence rules contribute to the precise naming of every stereoisomer of every organic molecule with all atoms of ligancy of fewer than 4.

Monosaccharides, also called simple sugars, are the simplest forms of sugar and the most basic units (monomers) from which all carbohydrates are built. Simply, this is the structural unit of carbohydrates.

<span class="mw-page-title-main">Stereoisomerism</span> When molecules have the same atoms and bond structure but differ in 3D orientation

In stereochemistry, stereoisomerism, or spatial isomerism, is a form of isomerism in which molecules have the same molecular formula and sequence of bonded atoms (constitution), but differ in the three-dimensional orientations of their atoms in space. This contrasts with structural isomers, which share the same molecular formula, but the bond connections or their order differs. By definition, molecules that are stereoisomers of each other represent the same structural isomer.

<span class="mw-page-title-main">Stereochemistry</span> Subdiscipline of chemistry

Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation. The study of stereochemistry focuses on the relationships between stereoisomers, which by definition have the same molecular formula and sequence of bonded atoms (constitution), but differ in the geometric positioning of the atoms in space. For this reason, it is also known as 3D chemistry—the prefix "stereo-" means "three-dimensionality".

<span class="mw-page-title-main">Optical rotation</span> Rotation of the plane of linearly polarized light as it travels through a chiral material

Optical rotation, also known as polarization rotation or circular birefringence, is the rotation of the orientation of the plane of polarization about the optical axis of linearly polarized light as it travels through certain materials. Circular birefringence and circular dichroism are the manifestations of optical activity. Optical activity occurs only in chiral materials, those lacking microscopic mirror symmetry. Unlike other sources of birefringence which alter a beam's state of polarization, optical activity can be observed in fluids. This can include gases or solutions of chiral molecules such as sugars, molecules with helical secondary structure such as some proteins, and also chiral liquid crystals. It can also be observed in chiral solids such as certain crystals with a rotation between adjacent crystal planes or metamaterials.

In chemistry, a racemic mixture or racemate, is one that has equal amounts of left- and right-handed enantiomers of a chiral molecule or salt. Racemic mixtures are rare in nature, but many compounds are produced industrially as racemates.

<span class="mw-page-title-main">Enantiomer</span> Stereoisomers which are non-superposable mirror images of each other

In chemistry, an enantiomer – also called optical isomer, antipode, or optical antipode – is one of two stereoisomers that are non-superposable onto their own mirror image. Enantiomers are much like one's right and left hands; without mirroring one of them, hands cannot be superposed onto each other. No amount of reorientation in three spatial dimensions will allow the four unique groups on the chiral carbon to line up exactly. The number of stereoisomers a molecule has can be determined by the number of chiral carbons it has. Stereoisomers include both enantiomers and diastereomers.

In chemistry, racemization is a conversion, by heat or by chemical reaction, of an optically active compound into a racemic form. This creates a 1:1 molar ratio of enantiomers and is referred to as a racemic mixture. Plus and minus forms are called Dextrorotation and levorotation. The D and L enantiomers are present in equal quantities, the resulting sample is described as a racemic mixture or a racemate. Racemization can proceed through a number of different mechanisms, and it has particular significance in pharmacology as different enantiomers may have different pharmaceutical effects.

<span class="mw-page-title-main">Fischer projection</span> Method of representing 3D organic molecules as a 2D image

In chemistry, the Fischer projection, devised by Emil Fischer in 1891, is a two-dimensional representation of a three-dimensional organic molecule by projection. Fischer projections were originally proposed for the depiction of carbohydrates and used by chemists, particularly in organic chemistry and biochemistry. The use of Fischer projections in non-carbohydrates is discouraged, as such drawings are ambiguous and easily confused with other types of drawing. The main purpose of Fischer projections is to show the chirality of a molecule and to distinguish between a pair of enantiomers. Some notable uses include drawing sugars and depicting isomers.

<span class="mw-page-title-main">Stereocenter</span> Atom which is the focus of stereoisomerism in a molecule

In stereochemistry, a stereocenter of a molecule is an atom (center), axis or plane that is the focus of stereoisomerism; that is, when having at least three different groups bound to the stereocenter, interchanging any two different groups creates a new stereoisomer. Stereocenters are also referred to as stereogenic centers.

<span class="mw-page-title-main">Diastereomer</span> Molecules which are non-mirror image, non-identical stereoisomers

In stereochemistry, diastereomers are a type of stereoisomer. Diastereomers are defined as non-mirror image, non-identical stereoisomers. Hence, they occur when two or more stereoisomers of a compound have different configurations at one or more of the equivalent (related) stereocenters and are not mirror images of each other. When two diastereoisomers differ from each other at only one stereocenter, they are epimers. Each stereocenter gives rise to two different configurations and thus typically increases the number of stereoisomers by a factor of two.

<span class="mw-page-title-main">Meso compound</span> Optically inactive isomer in a set of stereoisomers

A meso compound or meso isomer is an optically inactive isomer in a set of stereoisomers, at least two of which are optically active. This means that despite containing two or more stereocenters, the molecule is not chiral. A meso compound is superposable on its mirror image. Two objects can be superposed if all aspects of the objects coincide and it does not produce a "(+)" or "(-)" reading when analyzed with a polarimeter. The name is derived from the Greek mésos meaning “middle”.

<span class="mw-page-title-main">Chirality (chemistry)</span> Geometric property of some molecules and ions

In chemistry, a molecule or ion is called chiral if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes. This geometric property is called chirality. The terms are derived from Ancient Greek χείρ (cheir) 'hand'; which is the canonical example of an object with this property.

<span class="mw-page-title-main">Axial chirality</span> Type of symmetry in molecules

In chemistry, axial chirality is a special case of chirality in which a molecule contains two pairs of chemical groups in a non-planar arrangement about an axis of chirality so that the molecule is not superposable on its mirror image. The axis of chirality is usually determined by a chemical bond that is constrained against free rotation either by steric hindrance of the groups, as in substituted biaryl compounds such as BINAP, or by torsional stiffness of the bonds, as in the C=C double bonds in allenes such as glutinic acid. Axial chirality is most commonly observed in substituted biaryl compounds wherein the rotation about the aryl–aryl bond is restricted so it results in chiral atropisomers, as in various ortho-substituted biphenyls, and in binaphthyls such as BINAP.

The molecular configuration of a molecule is the permanent geometry that results from the spatial arrangement of its bonds. The ability of the same set of atoms to form two or more molecules with different configurations is stereoisomerism. This is distinct from constitutional isomerism which arises from atoms being connected in a different order. Conformers which arise from single bond rotations, if not isolatable as atropisomers, do not count as distinct molecular configurations as the spatial connectivity of bonds is identical.

<span class="mw-page-title-main">Chiral derivatizing agent</span> Reagent for converting a chemical compound to a chiral derivative

In analytical chemistry, a chiral derivatizing agent (CDA), also known as a chiral resolving reagent, is a derivatization reagent that is a chiral auxiliary used to convert a mixture of enantiomers into diastereomers in order to analyze the quantities of each enantiomer present and determine the optical purity of a sample. Analysis can be conducted by spectroscopy or by chromatography. Some analytical techniques such as HPLC and NMR, in their most commons forms, cannot distinguish enantiomers within a sample, but can distinguish diastereomers. Therefore, converting a mixture of enantiomers to a corresponding mixture of diastereomers can allow analysis. The use of chiral derivatizing agents has declined with the popularization of chiral HPLC. Besides analysis, chiral derivatization is also used for chiral resolution, the actual physical separation of the enantiomers.

<span class="mw-page-title-main">Isomer</span> Chemical compounds with the same molecular formula but different atomic arrangements

In chemistry, isomers are molecules or polyatomic ions with identical molecular formula – that is, same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism refers to the existence or possibility of isomers.

<span class="mw-page-title-main">Chirality</span> Difference in shape from a mirror image

Chirality is a property of asymmetry important in several branches of science. The word chirality is derived from the Greek χείρ (kheir), "hand", a familiar chiral object.

In chemical nomenclature, a descriptor is a notational prefix placed before the systematic substance name, which describes the configuration or the stereochemistry of the molecule. Some listed descriptors are only of historical interest and should not be used in publications anymore as they do not correspond with the modern recommendations of the IUPAC. Stereodescriptors are often used in combination with locants to clearly identify a chemical structure unambiguously.

Chemical compounds that come as mirror-image pairs are referred to by chemists as chiral or handed molecules. Each twin is called an enantiomer. Drugs that exhibit handedness are referred to as chiral drugs. Chiral drugs that are equimolar (1:1) mixture of enantiomers are called racemic drugs and these are obviously devoid of optical rotation. The most commonly encountered stereogenic unit, that confers chirality to drug molecules are stereogenic center. Stereogenic center can be due to the presence of tetrahedral tetra coordinate atoms (C,N,P) and pyramidal tricoordinate atoms (N,S). The word chiral describes the three-dimensional architecture of the molecule and does not reveal the stereochemical composition. Hence "chiral drug" does not say whether the drug is racemic, single enantiomer or some other combination of stereoisomers. To resolve this issue Joseph Gal introduced a new term called unichiral. Unichiral indicates that the stereochemical composition of a chiral drug is homogenous consisting of a single enantiomer.

References

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  3. ↑ Pitzer, Martin; Kunitski, Maksim; Johnson, Allan S.; Jahnke, Till; Sann, Hendrik; Sturm, Felix; Schmidt, Lothar Ph. H.; Schmidt-Böcking, Horst; Dörner, Reinhard; Stohner, Jürgen; Kiedrowski, Julia; Reggelin, Michael; Marquardt, Sebastian; Schießer, Alexander; Berger, Robert; Schöffler, Markus S. (6 September 2013). "Direct Determination of Absolute Molecular Stereochemistry in Gas Phase by Coulomb Explosion Imaging". Science. 341 (6150): 1096–1100. Bibcode:2013Sci...341.1096P. doi:10.1126/science.1240362. ISSN   0036-8075. PMID   24009390. S2CID   206549826.
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  5. ↑ Bijvoet, J. M.; Peerdeman, A. F.; van BOMMEL, A. J. (August 1951). "Determination of the Absolute Configuration of Optically Active Compounds by Means of X-Rays". Nature. 168 (4268): 271–272. Bibcode:1951Natur.168..271B. doi:10.1038/168271a0. ISSN   0028-0836. S2CID   4264310.
  6. ↑ Haesler, J.; Schindelholz, I.; Riguet, E.; Bochet, C. G.; Hug, W. (March 2007). "Absolute configuration of chirally deuterated neopentane" (PDF). Nature. 446 (7135): 526–529. Bibcode:2007Natur.446..526H. doi:10.1038/nature05653. ISSN   0028-0836. PMID   17392783. S2CID   4423560.
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  8. ↑ Andrew Streitwieser & Clayton H. Heathcock (1985). Introduction to Organic Chemistry (3rd ed.). Macmillan Publishing Company.
  9. ↑ Klein, David R. (2013-12-31). Organic Chemistry (2nd ed.). Wiley. p. 208. ISBN   978-1118454312.
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  11. ↑ "Nomenclature and Symbolism for Amino Acids and Peptides". Pure Appl. Chem. 56 (5): 595–624. 1984. doi: 10.1351/pac198456050595 .
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