Chemistry Structure and Properties, Lecture notes of Chemistry

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Chemistry Structure and Properties

Organic Stereochemistry

Chirality

Hybrid Orbitals

sp3 Hybridization Comprised of one s orbital and three p orbitals.

Lone pairs can also feature in sp3 hydrid orbitals.

sp2 Hybridization Comprised of one s orbital and two p orbitals.

Isomerism and Chirality

Optical Activity Chiral molecules rotate the plane of polarised light that is passed through them by a specific angle.

Molecules that rotate to the right are called dextrorotatory, whilst those that rotate to the left are called laevorotatory. Note that the direction of rotation of a given substance can only be determined experimentally, and has nothing to do with whether the species is R- or S-.

The amount of rotation depends upon the concentration of optically active compounds in the sample, the length of the cell, and the wavelength of light used. The specific rotation can be expressed as:

Cahn-Ingold-Prelog Rules

1. The higher the atomic number of the immediate substituent atom, the higher the priority. Different isotopes are assigned a priority according to their atomic mass. For example, H < C < N < O < Cl
2. If two substituents have the same immediate substituent atom, evaluate atoms progressively further away from the chiral center until a difference is found For example, CH3 < C2H5 < ClCH2 < BrCH2 < CH3O
3. If double or triple bonded groups are encountered as substituents, they are treated as an equivalent set of single-bonded atoms (on each atom involved in the double or triple bond) For example, C2H5 < CH2 =CH < HC≡C

D/L Nomenclature and Fisher Projections This is an older method for representing 3D information in a 2D format that is still commonly used for sugars. The rules apply a configuration to the entire molecule, not to each chiral centre:

1. Draw the parent chain vertically up the page
2. Position the most oxygenated carbon (aldehyde, ketone, carboxylic acid) towards the top of the page

Diastereomers A compound with chiral centres has a maximum of stereoisomers.

Diastereomers are stereoisomers that are not mirror images of each other. Diastereomers have opposite configurations at some (one or more) chirality centres, but have the same configuration at others. By contrast, enantiomers have opposite configuration at all stereocentres.

Diastereomers have a different shape (3D) and have therefore different chemical and physical properties.

Meso Compounds Meso compounds are achiral, despite containing chirality centres. Such molecules can be identified as they contain a plane of symmetry.

Separation of Enantiomers Enantiomers have identical physical and chemical properties, except that they rotate the plane of polarized light into opposite directions. As such, they cannot be separated easily, which is often required because only one enantiomer has the desired properties.

A convenient way to separate enantiomers is via a 3-step procedure:  Converting them into diastereomers  Separate the diastereomers  Re-transform them into enantiomers

Note that the configuration of the product is unrelated to the site of attack at the prochiral sp centre - the priority of the incoming substituent relative to the existing substituents is what matters.

Designation of sp3 Prochiral Centres To distinguish between the two identical atoms (or groups) on a prochirality centre, we imagine a change that will rise the priority of one atom over the other without affecting its priority with respect to the other attached groups. An easy way to do this is simply to replace a hydrogen with a deuterium atom.

Chirality in Nature Enantiomers have the same physical properties (except the rotation of the plane of polarized light into opposite directions), but they often have different biological properties.

A large reason for this is that enzymes themselves are generally chiral, as the amino acids which they are comprised of are themselves chiral.

A consequence of this is that racemic mixtures may be produced by lab synthesis where pure chiral substances are produced biologically.

For example, aspartame is an artificial sweetener which only functions as such in one of its two chiral forms.

The reason for this is that a chiral molecule must fit into a chiral receptor at some target site. For aspartame: various hypotheses have been proposed, but the most widely accepted one is the three- point attachment theory.

Cyclic Rings

Chair Conformation Cyclohexane is not a planar molecule. Because of the sp3 hybridized carbons, it has a 3D structure. The so-called 'chair conformation' has the lowest energy, and flip-flops very rapidly between its two possible conformations.

Ring Flip Equatorial substituents are energetically favoured because they reduce they 1,3-diaxial strain existing between all axial substituents.

In the case of bulky substituents like t-butyl, the equatorial configuration is essentially the only one observed. With say the t-butyl 'freezes' this conformation.

Disubstituted Cyclohexanes 1,2 disubstitution – geometrical and conformational isomers

1,3 disubstitution – geometrical and conformational isomers

1,4 disubstitution – geometrical and conformational isomers

The formation of epoxides proceeds via the anti-periplanar arrangement, which means that if this form is not a major variant of the molecule, then the reaction will be very slow. This occurs, for example, in the formation of trans-2-chlorocyclohexanol.

Contrast this with the cis-2-chlorocyclohexanol isomer, which has no anti-periplanar conformation. As such, an oxiran cannot be formed by HCl elimination. Thus we see how “minor” chemical changes can lead to totally different reaction products.

Stereochemistry and Reactions

Substitution Reactions

SN1 Nucleophilic Substitution The SN1 reaction is a stepwise reaction. First the leaving group 'falls off', forming a carbocation.

The resulting carbocation is planar, and thus can be attacked by the nucleophile either from the top or the bottom face. Since neither reaction is preferred, the result is a 50:50 racemic mixture.

SN2 Nucleophilic Substitution In the SN2 reaction, cleavage of the leaving group and attack of the nucleophile occur in the same step, each happening on opposite sides of the reaction.

The result is an inversion of the stereocentre, a process called Walden inversion. If the initial mixture if enantiomerically pure, so will be the product.

Catalytic Hydrogenation of Alkenes These reactions involve hydrogen being adsorbed onto the metal surface, breaking the H-H bond. The alkene then approaches the H atoms and reacts with each of them, one either side of the double bond, thus eliciting a double addition reaction.

Addition to cis-2-Butene This reaction is of the form:

The bromonium ion can react with the Bromide ion either from the left or right side of the bottom face (it cannot attack from the top face, since this is blocked by Br+). Both possible attacks occur with the same probability, resulting in the formation of a (2S,3S)- and (2R,3R)-dibromobutane racemic mixture.

Addition to trans-2-Butene This reaction proceeds as follows:

Like before, the bromonium ion can react with the bromide ion either from the left or right side of the bottom face, and both attacks occur with the same probability. The result is that (2S,3R)- and (2R,3S)-dibromobutane are formed in equal amounts. However, closer inspection reveals that these are in fact the same molecule: it is a meso compound.

Addition to Cyclohexene In this reaction, the cyclic bromonium ion is attacked from either the bottom or the top of the plane of the epoxide. As such, the second bromide substituent is always trans to the original bromide.

Addition to Chiral Alkene If the reactant is chiral, the product has 2 stereocentres and four possible stereoisomers.