Stereochemistry of Organic Chemistry – Defination – Types – Applications

Stereochemistry is the Branches of Organic Chemistry. Meanwhile, stereochemistry is the composition of space that is formed by atoms and functional group in the main molecules. These molecules are the organic molecules in three dimensions object which are the result of hybridization and geometrical bond from atoms in molecule. Based on that definition, stereochemistry also can be described as the way atoms in a molecule are arranged in specific space according to other spaces. Stereochemistry is related with the arrangement of atoms in molecule within three dimensions space. Thus, on the opportunity will be explained about definition, fields, classifications, and everything you need to know about Stereochemistry.

There are three aspects that exist in stereochemistry. These aspects are:

  • Molecular Conformation: Molecular conformation is related with the shape of molecule and how the molecule changes due to free spin along the single C-C bond.
  • Molecular Configuration: Molecular configuration is related with molecular chirality. It’s about how the atoms around carbon atom are arranged which will cause the formation of isomer.
  • Geometrical Isomer: Geometrical isomer is formed due to the rigidity within the molecule which causes the formation of isomer.

Thus, these three aspects is the important aspect in Stereochemistry.

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1. Isomer

Isomer is carbon based compounds that have similar molecular formula but different structural formula. In hydrocarbon compounds, the chemical formula shows the amount of carbon atom and each element that exists within a molecular compound. There are several types of isomer, structural isomer and stereoisomer.

  • Structural Isomer

Structural isomer is the type of isomer in which the compounds are different in the arrangement of atoms that are bonded one to another. Variation in the structure of organic compound can be caused by the amount of atoms or the type of atoms within molecule. Thus, the variation in this structure also can be occurred because the order of the atom that is bonded one to another in a molecule.

For example, molecular formula of C2H6O can be written in two different structural formulas. Both of these structural formulas state two different compounds which are ethanol and dimethyl ether. Dimethyl ether and ethanol are the example of structural isomer. Alkane that consists of three carbons or less doesn’t have isomer. In each case, there is only one way to arrange the atoms. So, it can be concluded that the more carbon atoms in a molecule, the more isomers that molecule has.

  • Stereoisomer Compound

Stereoisomer is different compounds that have similar structure. These compounds are only different in the arrangement of the atoms within the structure. Stereoisomer is not structural isomer. The compounds that are stereoisomer only have similar order of the bonded atoms. Stereoisomer only has difference in the order of atoms within the structure. According to the structure, stereoisomer can be categorized into two types. These types are:

  • Enantiomer: The stereoisomer that one compound to another is like mirrored.
  • Diastereomer: The stereoisomer that one compound to another is not like mirrored.

According to the ability to change from one stereoisomer to another, stereoisomer can be categorized into two types. These types are:

  • Conformation Isomers

Conformation isomers are also known as conformer. This type of stereoisomer is the ones that can change from one stereoisomer to another only though single bond loading.

  • Configuration Isomers

Configuration isomers are the type of stereoisomer that can only change from one stereoisomer to another through dissolution and recontinuation of the covalent bonds.

Meanwhile, the types of Stereochemistry are atropisomerism, Cis-trans isomerism, confrontational isomerism, diastereomers, and enatiomers. That’s all the sub-Branches of Chemistry. Thus, on this opportunity will be explained about the Stereochemistry defination, braches, types, classification, and all the materials you need to learn here.

2. Cis-Trans Isomerism

In chemistry, cis-trans isomerism or geometrical isomerism or also known as configuration isomerism is the form of stereoisomerism which explains the orientation of functional groups within a molecule. Generally, this type of isomer has double bonds which can’t spin. Besides that, this type of isomer also appears due to molecular ring structure which causes the bond spins very limitedly.

The term “geometrical isomerism” is the old term that is no longer used and it’s also the synonym of “cis-trans isomerism”. Sometimes, this term also refers to the synonym for general stereoisomerism (for example, optical isomerism); the right term for non-optical stereoisomerism is diastereomerism.

There are two forms of cis-trans isomer, the Cis and the Trans. When substituent group oriented towards same direction, this diastereomer is called Cis and when the substituent group oriented towards different direction, this diastereomer is called Trans. The example of hydrocarbon molecule that shows cis-trans isomerism is 2-Butene. Alicyclic compound also can show cis-trans isomerism as well. The example of geometrical isomer that occurs due to the structure of the ring is 1 2-dichlorocyclohexane.

  • Conformation and Chiral Molecule

Conformation is the arrangement of atoms or groups that are bonded differently by sigma bonds in a structure due to atoms or groups rotation which circle the bonds. Meanwhile, Chiral is compound or ion that can’t be mirrored. The word chiral came from Greek word “cheir” which means “hand”. This term is generally used for describing an object that can’t be mirrored precisely with its shadow.

Chiral molecule is the type of molecule that came with mirrored shadow that is non-superimposable (can’t be stacked). An organic molecule can be considered as chiral molecule if the molecule has minimal one C atom that bonds four different groups. Chiral molecules have optical property which means that a chiral molecule has the ability to spin the plane of polarized light on a device called polarimeter. The difference between chiral molecule and achiral molecule is that only chiral compounds that can’t be mirrored.

Thus, Chirality is a condition that causes two molecules have similar structure but have different structure arrangement and configuration. The atom that becomes the center of chirality is known as chiral atom. The cause of chirality is because there is asymmetrical carbon compound.

  • Chiral Compounds

Chiral compounds will be formed when four different ligands are bonded to tetravalent carbon which result asymmetric molecule in which the carbon atom plays a role as the asymmetric center. Enantiomer is two stereoisomers that can’t be stacked to their mirrored shadow. Diastereomer usually have at least two asymmetric centers (one of them has similar configuration) and they are not the mirrored shadow. Generally, most chiral center is represented by tetrahedral carbon, even though other atoms such as nitrogen, sulfur, and phosphate can be found in stereoisomer. Compounds that have at least two enantiomers are chiral compounds.

The main characteristic of stereoisomers is represented by the spinning of polarized light towards different direction, counterclockwise (levo), and clockwise (dektro) or L(-)- isomer and D(-)- isomer. According to Fischer projection, generally the sugar compound and amino acids use the D and L symbols and this is based on the comparison to +(-)-glyceraldehydes and nowadays people also use Cahn-Ingold-Prelog notation that uses R and S.

Optical rotation for two enantiomers in racemic mixture are similar (will not spin the direction of polarized light). On the other hand, diastereomer is not similar to enantiomer. Diastereomer might have difference in boiling point, freezing point, and solubility.

The extraction of enantiomer from racemate, in other words, the racemate extraction, is a common thing in the studies about stereochemistry just like on preparation of biological active compound in drugs. The problem is that, unlike diastereomer and other types of isomer, enantiomer shows similar physical chemistry properties.

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3. Enantiomer Configuration

Some might know enantiomer as optical isomer. It refers to one of the stereoisomers which reflects one to another but non-superposable or not identical. The main characteristic of enantiomer represents by the polarized light rounding in a different way, one is in clockwise (dectro) and the other is the opposite (levo). The optical rotation between these two enantiomers in one rasemik compound is equal. Now let’s see the variations of enantiomer configuration.

  • Fischer Projection

By using Fischer projection, depiction systems of group configuration around different chiral centers (the order of atom’s structure or groups that attach to chiral carbon) are convention D and L. This method is usually used in biochemistry and organic chemistry, especially for carbohydrate and amino acids. Glyceraldehydes are stated as standard compound for determining the configuration of all carbohydrate compounds.

Fischer projection on glyceraldehydes with carbon chain is described vertically with the most oxidized carbon (aldehyde) is on the topmost. The OH group in chiral center is described on the right side for D isomer and on the left side for L isomer. This means that every sugar that has similar stereochemistry with D-glyceraldehydes belong to D group sugar (for example, D-glucose) while sugar that has stereochemistry that is similar with L-glyceraldehydes belong to L group sugar.

This condition will be analog for amino acids. If the Fischer projection is drawn (vertical carbon chain with the most oxidized carbon atom is on the topmost), then all “natural” amino acids that are found in human’s protein are known as amino acids that came with NH3+ group on the left side of the Fischer projection, which is similar to L-glyceraldehydes.

So, that these amino acids are known as L group amino acids. This type of amino acids is very useful and gives many benefits in healthcare field, especially in pharmacy field in designing drugs with selective toxicity test, where it is known that the amino acids on microorganism have contradict configuration which is D group, for example, Penicillin that blocks transpeptidase enzyme in synthesis of microbe’s cell wall. This is related with dipeptide D-alanine-D-alanine from microbe’s cell wall that looks like structure of penicillin. Therefore, penicillin is non-toxic for humans that have L-alanine in their body protein.

  • Cahn-Ingold-Prelog Notation

The most successful system that is used to show configuration of general compounds is the Cahn-Ingold-Prelog convention. This system is used the letter R or S for each chiral center in molecules and it’s also an option to determine the configuration of chiral center in drug’s molecules. The determination of each group that attaches to chiral center is according to the number of atom.

The number of atom with heavier weight has more important priority, thus the hydrogen atom (H) is listed on the end of the order. If all priorities around chiral center are determined, the next step is noticing the order of the group from the one that has low priority (usually H atom). If the order of priority on the group is arranged around chiral center clockwise, chiral carbon accepts the R (Rectus) configuration and if the order of priority on the group is arranged around chiral center counterclockwise, chiral carbon accepts the S (Sinister) configuration.

  • Chiral Compounds Analysis

The extraction of enantiomer is the type of research that is commonly done in chemistry analysis, especially in biology and pharmacy field, since chiral drugs are given as one of the enantiomers or as racemate mixture. In many cases, two enantiomers from the same racemate drug have different pharmacology effect. For example, S(+)-Propranolol is more active than its enantiomer.

Ketamine anesthetic is given as racemate mixture and the S(+)- ketamine is more potential than R(-)-ketamine. Moreover, the R(-)- form causes effects after surgery. Due to side effects that might be caused by components of racemate mixture in drugs, the pharmacy industry tends to make drugs with one enantiomer only. However the result, several drugs that go through stereoselective reaction or preparation process of enantiomer extraction can give impure materials.

So, the sensitive analysis method is needed since the high performance extraction is needed in order to control the synthesis process of chiral compounds for pharmacy preparations. One approach that is used in enantiomer extraction, sometimes it’s shown as indirectly enantiomer extraction, is involved the merger of enantiomer with additional chiral reagent to change the molecule into diastereomer. This diastereomer compound then can be extracted by using some achiral extraction techniques.

These days, the direct extraction method is usually done by placing the enantiomer in chiral environment. The use of selector chiral or irradiation chiral (for example, polarized light which consists of two circular chiral components that are polarized) can distinguish clearly between two enantiomers. Selector chiral can be a molecule or the match chiral surface. In relation with enantioselective from the interaction of both enantiomers, selector chiral changes one of the two enantiomers, with different speed, into a new chemical compound (kinetic enantioselective) or forms unstable molecule on different stability with that enantiomer (thermodynamics enantioselective), or the changing of L or D form with enzymatic selective system.

Other method that is usually used by chemists is biochemical route by using enzyme or microorganism to produce pure enantiomer. For example, (R)-Nicotine can be obtained by incubating the racemate (R)-Nicotine and (S)-Nicotine in container that is filled with Pseudomonas putida bacteria. The bacteria will only oxidize the (S)-Nicotine while the (R)-Nicotine will be left on the container.

  • Analytic Method

Analytic methods that are used for chiral compound component extraction process are including High Performance Liquid Chromatography, Thin Layer Chromatography, Gas Chromatography, and Capillary Electrophoresis which is mainly used for analysis from different groups of component, including organic and inorganic ion, peptide, protein, saccharide, drugs, and other optical isomers. In CE analysis, the extraction process will be achieved if analyte, under the influence of electrical field, moves towards the detector with different speed.

  • CE Method

CE method is not only analysis with high efficiency and extraction performance that can be compared to other methods but this method also has several other benefits as well. These benefits are:

  1. The sample and buffer volume that is needed is relatively small.
  2. The expensive chiral column can be prevented since the chiral selector can be added easily to BGE (Background Electrolyte).
  3. The extraction is very reproducible since buffer with chiral selector can be refilled during the process.

Drugs in Form of Racemic Mixture    

There are several types of drug that are marketed these days in the form of racemic mixture. These drugs are:

1. Thalidomide

This drug is marketed in Europe circa 1959 to 1962 as sedative. This drug has two enantiomers. The enantiomer that plays role as sedative is (R)-Thalidomide. However, pregnant women who consume the enantiomer of this drug which is the (S)-Thalidomide are having problems with the growth of the fetus’ body parts instead. At least there are 2000 cases of defective birth in 1960s. This is a major tragedy that will never be forgotten in the history of chiral drugs.

2. Nicotine

(-)Nicotine is reported more poisonous and harmful compared to (+)Nicotine. The “+” mark states the direction of polarimeter rotation is clockwise while the “-“ mark states that the direction of the polarimeter rotation is counterclockwise.

3. Thyroxine

Thyroxine is hormone that is produced by thyroid gland. (-)Thyroxine regulates body metabolism while (+)Thyroxine doesn’t produce any regulation effects.

4. Epinephrine

Epinephrine racemic is the 1:1 mixture of epinephrine D-isomer and L-isomer. The mechanism of epinephrine action occurs on adrenergic receptor. The epinephrine is proven causes vasoconstriction and reduces edema. The reduction of edema will increase the diameter of the airway so that inspiratory stridor and retraction will be reduced. L-Epinephrine is, at least, as effective as epinephrine racemic in laryngotracheitis treatment and will not cause risks or additional side effects. L-epinephrine is also more available and more affordable worldwide.

5. Tramadol

Tramadol HCl is strong analgesic that works on opioid receptors. Tramadol attaches stereospecifically on receptor in central nervous system so that it can stop painful sensation and responses to pain. Tramadol is the 1:1 racemic mixture of two enantiomers. Enantiomer (+)Tramadol and enantiomer (-)Tramadol have different potential to opioid receptor and monoamine uptake side. The enantiomer (+)Tramadol will show analgetic activity 10 times higher than enantiomer (-)Tramadol.

The enantiomer (-)Tramadol will block the norepinephrine reuptake by stimulating the alpha(2)-adrenergic receptor. The enantiomer (-)Tramadol approximately 5 times stronger in blocking the noradrenaline than serotonin. However, the enantiomer (+)Tramadol shows different effect to noradrenaline. Both enantiomers are given in tramadol analgesic treatment.

From the article, we can conclude that stereochemistry is one of the subdiscipline of chemistry that studies about atomic relative dimensional arrangement. Studying stereochemistry means also studying the chiral molecules. It will makes us understand how the arrangements of the atoms to form molecules. Thus, that’s about the definition, types, and applications of StereocheHopefully, this article will help you to understand stereochemistry better.

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