Dr. Mohammad Nahid Siddiqui

Dr. Mohammad Nahid Siddiqui
STEREOCHEMISTRY 8/6/2018 Dr. Mohammad Nahid Siddiqui

Stereochemistry is the study of molecules in space 1. Geometric isomers: how rigidity in a molecule can lead to isomerism 2. Conformations of molecules: the shapes of molecules and how they can change 3. Chirality of molecules: how the right- or left-handed arrangement of atoms around a carbon atom can lead to isomerism we strongly urge you to use a set of molecular models 8/6/2018 Dr. Mohammad Nahid Siddiqui

Section 4.1 Geometric Isomerism in Alkenes
Structural/Constitutional isomerism is only one type of isomerism Geometric Isomerism, which results from rigidity in molecules and occurs in only two classes of compounds: alkenes and cyclic compounds. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Two groups on the same side of the  bond are said to be cis (Latin, "on the side"). Groups on the opposite sides are said to be trans (Latin, "across"). Note: how the cis or trans designation is incorporated into the name. 8/6/2018 Dr. Mohammad Nahid Siddiqui

A. (E) and (Z) System of Nomenclature
When there are three or four different groups or atoms attached to the C=C bond, a pair of geometric isomers exists, But it is difficult to assign cis or trans rather (E) and (Z) system is used for such isomers: 8/6/2018 Dr. Mohammad Nahid Siddiqui

If the higher-priority atoms or groups are on opposite sides of the  bond, the isomer is (E). If the higher priority groups are on the same side, the isomer is (Z). 8/6/2018 Dr. Mohammad Nahid Siddiqui

Sequence Rules for Order of Priority:
A set of sequence rules to determine order of priority has been developed. These priority rules form the basis of the Cahn–Ingold–Prelog nomenclature system, named in honor of the chemists who developed the system. 8/6/2018 Dr. Mohammad Nahid Siddiqui

B. Sequence Rules 1. If the two atoms at the same C are different, the sequence order is by atomic number, with the atom of highest atomic number receiving the highest priority. 2. If two isotopes of the same element are present, the isotope of higher mass receives the higher priority. 8/6/2018 Dr. Mohammad Nahid Siddiqui

3. If two atoms are identical, the atomic numbers of the next atoms are used for priority assignment. If these atoms also have identical atoms attached, priority is determined at the first point of difference along the chain. The atom of higher priority has the higher priority. Do not use the sums of the atomic numbers, but look for the single atom of highest priority. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Look at the Next Atom of Difference
Naming is very important 8/6/2018 Dr. Mohammad Nahid Siddiqui

Equivalencies 4. Atoms attached by double or triple bonds are given single-bond equivalencies. Each doubly bonded atom is duplicated and triple bond is triplicated. Multi Bond Priorities 8/6/2018 Dr. Mohammad Nahid Siddiqui

Multi Bond Priorities 5 4 7 6 3 1 2 You should Never Confuse with the priorities of naming e.g. Acid alone… 8/6/2018 Dr. Mohammad Nahid Siddiqui

Section 4.2 Geometric Isomerism in Cyclic Compounds
8/6/2018 Dr. Mohammad Nahid Siddiqui

Carbon atoms of a cyclic structure such as cyclohexane form a plane. View the plane of the ring as being almost horizontal. The edge of the ring projected toward us is shaded more heavily. Both are same 8/6/2018 Dr. Mohammad Nahid Siddiqui

Plane of The Ring 8/6/2018 Dr. Mohammad Nahid Siddiqui

The methyl group and the hydroxyl group are on opposite sides of the plane of the ring, they are trans; when they are on the same side, they are cis. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Section 4.3 Conformations of Open-Chain Compounds
Groups attached by sigma (σ) bonds can rotate around these bonds, called conformations. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Look and concentrate on TWO carbons bonded by a σ bond only

Staggered & Eclipsed In staggered conformers, the hydrogen atoms or the attached groups are as far apart from one another as possible. Since the C—C bond can undergo rotation, the hydrogen atoms might also be eclipsed, or as close as possible, one behind the other in the Newman projection.. 8/6/2018 Dr. Mohammad Nahid Siddiqui

The eclipsed conformation of ethane is about 3 kcal/mol less stable (of higher energy) than the staggered conformer because of minor repulsions between the hydrogen atoms. To undergo rotation from a staggered conformation to an eclipsed conformation 3 kcal/mol is required 8/6/2018 Dr. Mohammad Nahid Siddiqui

Rotational Conformers Butane
Staggered has two forms, most stable is anti and less stable is gauche 8/6/2018 Dr. Mohammad Nahid Siddiqui

Energy of Conformers Butane

Bulky Groups The larger the groups attached to two carbon atoms, the greater is the energy difference between the molecule's conformations. It takes more energy to push together two bulky groups than two small groups. While it takes only 3 kcal/mol for ethane to rotate from staggered to eclipsed, it takes 4.5 kcal/mol for butane to rotate from anti to the conformation in which the methyls are eclipsed. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Section 4.4 Shapes of Cyclic Compounds
Baeyer ( ; Nobel Prize, 1905) theorized that cyclic compounds form planar rings. Baeyer further theorized that all cyclic compounds except for cyclopentane would be "strained" because their bond angles are not close to the tetrahedral angle of 109.5°. 8/6/2018 Dr. Mohammad Nahid Siddiqui

A. Ring Strain Baeyer's theory was not entirely correct. Cyclohexane and larger-sized rings are not more reactive than cyclopentane. Cyclohexane is not a flat ring with bond angles of 120°, but rather a puckered (wrinkled) ring with bond angles close to 109°, the normal sp3 bond angles. 8/6/2018 Dr. Mohammad Nahid Siddiqui

There is indeed what we call ring strain in the smaller ring systems. Cyclopropane is the most reactive of the cycloalkanes. Its heat of combustion is higher per CH2 group than that of other alkanes. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Reaction With Hydrogen Gas
When treated with hydrogen gas at moderate temperatures, unstrained cycloalkanes such as cyclopentane do not react, but cyclopropane undergoes ring opening. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Heat of Combustion Data
sp3 orbitals of the carbon atoms in cyclopropane cannot undergo complete overlap with each other. The σ bonds of cyclopropane ring are of higher energy than normal tetrahedral sp3 σ bonds. The cyclopropane bonds are more easily broken than most other C—C σ bonds. 8/6/2018 Dr. Mohammad Nahid Siddiqui

B. Ring Puckering and H–H Repulsions
If the cyclohexane ring were flat, all the hydrogen atoms on the ring carbons would be eclipsed. In the puckered (wrinkled) conformer that however, all the hydrogens are staggered. The energy of the puckered conformer of cyclohexane is lower than the energy of flat cyclohexane, both because of more favorable sp3 bond angles and also because of fewer H–H repulsions. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Cyclobutane and Cyclopropane
Cyclobutane (flat bond angles of 90°) also is puckered, even though the puckering causes more-strained bond angles. Cyclopropane must be planar; geometrically, three points (or three carbon atoms) define a plane. The hydrogen atoms in cyclopropane necessarily are eclipsed. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Section 4.5 The Conformers of Cyclohexane Chair form

Some other shapes the cyclohexane molecule can assume are as follows:

Equatorial and Axial Hydrogens
Each ring carbon of cyclohexane is bonded to two hydrogen atoms. The bond to one of these hydrogens is in the rough plane of the ring; called an equatorial hydrogen. The bond to the other hydrogen atom is parallel to the axis; this is an axial hydrogen. Each of the six carbon atoms of cyclohexane has one equatorial and one axial hydrogen atom. equatorial axial 8/6/2018 Dr. Mohammad Nahid Siddiqui

Chair Inversion Diaxial Repulsion Methyl is equatorial 8/6/2018 Dr. Mohammad Nahid Siddiqui

When the methyl group is in the axial position, the methyl group and axial hydrogens on the same side of the ring repel each other. Interactions between axial groups are called 1,3-diaxial interactions. When the methyl group is in the equatorial position, the repulsions are minimized. Thus, the energy of the conformer with an equatorial methyl is lower. At room temperature, about 95% of methylcyclohexane molecules are in the conformation in which the methyl group is equatorial. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Gauche Relationship in Axial Methylcyclohexane:
Methyl group is in the axial position, the conformation of the ring is similar to gauche form. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Anti Relationship in Equatorial Methylcyclohexane:
Methyl group is in the equatorial position, the conformation of the ring is similar to anti form. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Bulkier Group The bulkier (bigger than H) the group is, the greater is the energy difference between axial and equatorial conformers. A bulky substituent in cyclohexane ring is more stable in equatorial position. If the substituent group is tert-butyl, the difference in energies between the conformers becomes quite large and it always occupies the equatorial. 8/6/2018 Dr. Mohammad Nahid Siddiqui

For Mono Substituted Cyclohexane

B. Disubstituted Cyclohexanes
Two groups substituted on a cyclohexane ring may be either cis or trans. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Cis-1,2-dimethylcyclohexane

Trans-1,2-dimethylcyclohexane

A single and two methyl groups on a cyclohexane ring assume the equatorial positions preferentially, if possible. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Cis or Trans More Stable?
In the case of a 1,2-disubstituted cyclohexane, the trans isomer is more stable than the cis isomer because both substituents can be equatorial. It will dominate *If two Substituents are Different in cis conformer (i.e. methyl and Ethyl): the bigger substituent (Ethyl) will be Equatorial and it will be Major Product 8/6/2018 Dr. Mohammad Nahid Siddiqui

Two Substituents are 1,3 When the two substituents are at 1,3- position on a cyclohexane ring, the cis isomer is more stable than the trans isomer. The reason is that both substituents in the cis-1,3- isomer can be equatorial. In the trans-1,3- isomer, one group must be axial. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Summary of Substitutions
In monosubstitution, Big group will be equatorial For 1,2-dimethylcyclohexane cis: a,e = e,a both have same energies trans: e,e is more stable than a,a For 1,3-dimethylcyclohexane trans : a,e = e,a both have same energies cis : e,e is more stable than a,a For 1,4-dimethylcyclohexane = 1,2… ** If you have to choose between a,e or e,a then Bulky group will always be at “e” equatorial position. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Section 4.6 Chirality Chirality of Objects and Molecules Any object that cannot be superposed on its mirror image is said to be chiral. 8/6/2018 Dr. Mohammad Nahid Siddiqui

ACHIRAL Conversely, a plain cup or a cube is achiral (not chiral); these can be superposed on their mirror images 8/6/2018 Dr. Mohammad Nahid Siddiqui

Chiral Carbon Atoms An achiral molecule and its superposable mirror-image molecule are the same compound; they are NOT isomers. But a chiral molecule is NOT superposable on its mirror image; this molecule and its mirror-image molecule are different compounds, and represent a pair of stereoisomers called enantiomers. A pair of enantiomers is simply a pair of isomers that are non-superposable mirror images. It is also called an asymmetric carbon, asymmetric center, stereocenter, or stereogenic center. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Enantiomers A molecule that has four different groups attached to one single carbon atom is chiral and is not superposable on its mirror image. (Try it with models.) Carbon atom with four different groups attached to it is chiral and exists as a pair of enantiomers. A carbon atom with four different groups attached is often called a chiral carbon or chiral center, although, technically, it is the molecule and not the carbon atom that is chiral. 8/6/2018 Dr. Mohammad Nahid Siddiqui

In a chiral carbon, all four groups attached to the sp3-hybridized carbon are different. If the carbon is attached to two or more H atoms (—CH2— or —CH3), then the carbon cannot be a chiral. In a few cases, must inspect each entire group attached to the carbon in question, not just the atoms bonded directly to that carbon. Find out the point of difference. 8/6/2018 Dr. Mohammad Nahid Siddiqui

The interchange of any two groups around the chiral carbon results in the enantiomer. The following examples show two ways to convert the formula for one compound (A) to its enantiomer (B). 8/6/2018 Dr. Mohammad Nahid Siddiqui

C-Fischer Projection 2,3-dihydroxypropanal glyceraldehyde 2,3,4- trihydroxybutanal (erythrose) 8/6/2018 Dr. Mohammad Nahid Siddiqui

Fischer Projections Conventions
The molecule is completely stretched out. By convention, the carbonyl group (or group of highest nomenclature priority) is placed at or near the top. Thus, the top carbon is carbon 1. Each intersection of the horizontal and vertical lines represents a *chiral carbon. Each horizontal line represents a bond coming toward the viewer, while the vertical line represents bonds going back, away from the viewer. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Fischer Projections Conventions

Fischer Projection Rotated
A Fischer projection may be rotated 180° in the plane of the paper, but it may not be flipped over or rotated by any other angle. Either of these last two operations would take the formula out of the Fischer projection and lead to an incorrect structure. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Section 4.7 Rotation of Plane-Polarized Light
With the exception of chirality, the structures of a pair of enantiomers are the same. Therefore, almost all of their physical and chemical properties are the same. For example, each pure enantiomer of a pair has the same melting point and the same boiling point. Only two sets of properties are different for a single pair of enantiomers: interactions with other chiral substances interactions with polarized light. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Ordinary light travels in waves, and the waves are at right angles to the direction of travel. In Plane-polarized light all wave vibrations have been filtered out except for those in one plane. The plane-polarized light is rotated on passing through a solution containing enantiomer, called optical rotation. Compound is optically active and called optical isomers 8/6/2018 Dr. Mohammad Nahid Siddiqui

Polarimeter The amount of rotation depends on:(1) the structure of the molecules; (2) the temperature; (3) the wavelength; (4) the number of molecules in the path of the light; and, in some cases, and (5) the solvent. Specific rotation is the amount of rotation by 1.00 g of sample in 1.00 mL of solution in a tube with a path length of 1.00 decimeter (dm), at a specified temperature, wavelength, and solvent. The commonly used wavelength is nm (the D line of sodium), where 1.0 nm = 10-9 m. The specific rotation for a compound may be calculated from the observed rotation by the following formula: 8/6/2018 Dr. Mohammad Nahid Siddiqui

Relationship Between Compounds
A mixture of equal parts of enantiomer pairs is called a racemic mixture. It does not rotate the plane of light because of cancelling out. So it is optically inactive. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Section 4.8 Assignment of Configuration: the (R) and (S) System
The order of arrangement of four groups around a chiral carbon atom is called the absolute configuration around that atom. A pair of enantiomers have opposite configurations. If one is R then second must be S to make enantiomer pair. 8/6/2018 Dr. Mohammad Nahid Siddiqui

(R) and (S) System The letter (R) comes from the Latin rectus, "straight," or "right," while (S) comes from the Latin sinister, "left." Any chiral carbon atom has either an (R) or an (S) configuration; therefore, one enantiomer is (R) and the other is (S). A racemic mixture can be designated as (RS), meaning a mixture of the two. In the (R) and (S) system, groups are assigned a priority ranking using the same set of rules as are used in the (E) and (Z) system but in a slightly different manner. 8/6/2018 Dr. Mohammad Nahid Siddiqui

1. Rank the four groups (or atoms) attached to the chiral carbon in order of priority by the Cahn–Ingold–Prelog sequence rules . 2. Project the molecule with the group of lowest priority to the rear (backside). 3. Select the group of highest priority (1) and draw a curved arrow to the group of next highest priority (2). 4. If this arrow is clockwise, the configuration is (R). If the arrow is counterclockwise, the configuration is (S). 8/6/2018 Dr. Mohammad Nahid Siddiqui

Order of Priorities Highest atomic number atom gets highest priority Isotope of higher mass will get higher priority If two atoms are identical then atomic number of next atom will decide priority Atoms attached by double or triple bond are given single bond equivalencies. -OH Highest Carboxylic acid 1 7 5 6 4 3 2 You should never confuse with the priorities of naming e.g. Acid alone… 8/6/2018 Dr. Mohammad Nahid Siddiqui

R and S 8/6/2018 Dr. Mohammad Nahid Siddiqui

Let us illustrate the use of this procedure by assigning (R) and (S) to the enantiomers of 1-bromo-1-chloroethane. 8/6/2018 Dr. Mohammad Nahid Siddiqui

1) Rank the four groups, in the order of priority of the four atoms by atomic number is Br (1highest), Cl (2higher), C (3high), H (4lowest). 2) Draw projections with the lowest-priority atom (H) in the rear (back). (This atom is hidden behind the carbon atom in the following projections.) 3) Draw an arrow from highest priority Br (1) to second highest priority Cl (2). 4) Assign (R) and (S). Note how the (R) and (S) designation is incorporated into the name. 8/6/2018 Dr. Mohammad Nahid Siddiqui

An easy way to remember which enantiomer is (R) and which is (S) is to compare the curved arrow to the steering wheel on an automobile. Turning the steering wheel to the right is equivalent to (R); turning it to the left is equivalent to (S). 8/6/2018 Dr. Mohammad Nahid Siddiqui

Configurational Assignments Fischer Projections
In Fischer projections, vertical bonds go away from the viewer, while horizontal bonds come toward the viewer. Interchanging any two groups attached to a chiral carbon produces its mirror image (opposite configuration). Two consecutive two-group interchanges maintains the original configuration. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Since we change by Two rotation so original will be (S)
Lactic Acid 1.Assign priorities. The order of priority is OH (highest), CO2H, CH3, H (lowest). O highest atomic number followed by C of COOH. 2.Interchange the lowest priority H with third priority CH3 groups. Now interchange the OH and CH3 groups to restore the original configuration. 3.Going from OH to CO2H to CH3 is counterclockwise; the configuration is (S). (R) Since we change by Two rotation so original will be (S) 8/6/2018 Dr. Mohammad Nahid Siddiqui

Section 4.9 More Than One Chiral Carbon
No need of rotation if H is at the back or vertical position, just connect the priority atoms and find out R/S configuration. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Maximum Number of Optical Isomers
The maximum number of optical isomers for a compound is 2n, where n is the number of chiral carbons. If there are 2 chiral carbons, then there can be up to 4 stereoisomers (22 = 4); when there are 3 such carbon atoms, there can be up to 8 stereoisomers (23 = 8). 8/6/2018 Dr. Mohammad Nahid Siddiqui

A. (R) and (S) System for a Compound with Two Chiral Carbon Atoms
To assign (R) or (S) configurations to two chiral carbons in one molecule, Consider each chiral carbon at a time. Look at the sugar erthyrose to illustrate the technique. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Erthyrose Carbon 2 When lowest priority atom at front then you look at the chiral carbon from the back and it will not require any rotation 8/6/2018 Dr. Mohammad Nahid Siddiqui

Erthyrose Carbon 3 Lowest priority atom H is at the front then look at the chiral carbon from the back that H remains away from you and find the rotation. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Enantiomers are a pair of 2S, 3R and 2R, 3S
The IUPAC name for this stereoisomer is therefore (2R,3R)-2,3,4-trihydroxybutanal. Contrast this notation with (2RS,3RS)-2,3,4-trihydroxybutanal, which is a racemic mixture. Enantiomers are a pair of 2S, 3R and 2R, 3S or 2S, 3S and 2R, 3S 8/6/2018 Dr. Mohammad Nahid Siddiqui

B. Diastereomers When a molecule has more than one chiral carbon, not all of the optical isomers are enantiomers. By definition, enantiomers (mirror images) come in pairs. Any pair of stereoisomers that are not enantiomers are called diastereomers, or diastereoisomers. Diastereoisomers contains a minimum of two chiral carbons. Geometric isomers are also diastereomers by this definition. 8/6/2018 Dr. Mohammad Nahid Siddiqui

Diastereomers are a pair of 2S, 3R and 2R, 3R or 2S, 3S
A pair of enantiomers have identical physical and chemical properties except for interactions with other chiral molecules and with polarized light. Enantiomers are pair of 2S,3S & 2R,3R or 2S,3R & 2R,3S Diastereomers, however, are chemically and physically different. They have different melting points and different solubilities and often undergo chemical reactions in a different fashion. They are NOT mirror images Diastereomers are a pair of 2S, 3R and 2R, 3R or 2S, 3S 8/6/2018 Dr. Mohammad Nahid Siddiqui

C. Meso Compounds A compound with n chiral carbon atoms can have a maximum of 2n stereoisomers. Consider a pair of structures (A and B) with two chiral carbon atoms. At first glance, we might assume that A and B are enantiomers but they are NOT. 8/6/2018 Dr. Mohammad Nahid Siddiqui

The “Top” half of the molecule is the mirror image of the “Bottom” half A stereoisomer that contains chiral carbons but can be superimposed on its mirror images is called a meso form. on paper 8/6/2018 Dr. Mohammad Nahid Siddiqui

Internal Plane Of Symmetry

Isomers of Tartaric Acid
The “Top” half of the molecule is the mirror image of the “Bottom” half 8/6/2018 Dr. Mohammad Nahid Siddiqui

Meso Compounds If structures does NOT contain chiral carbons but have
It must contain both chiral carbon and plane of symmetry to be a meso. If structures does NOT contain chiral carbons but have plane of symmetry i.e. Top half is the mirror image of Bottom half. These are NOT Meso compounds. 8/6/2018 Dr. Mohammad Nahid Siddiqui

D. Conformational Enantiomers
Butane is an achiral because it has no chiral carbon but its gauche form is a chiral. 8/6/2018 Dr. Mohammad Nahid Siddiqui

E. Chiral Cyclic Compounds cis- and trans-dimethylcyclopropane
If H is up then towards you and if down then away from you. 8/6/2018 Dr. Mohammad Nahid Siddiqui

1,4-dimethylcyclohexanes include cis and trans
Neither the cis- nor trans-1,4-dimethylcyclohexane is chiral because there is NO chiral carbon in the structure. 8/6/2018 Dr. Mohammad Nahid Siddiqui

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