Summary Essential Organic Chemistry
Chapter 6
¶ 2
Chiral: An object’s mirror image is not the same image as the image of the object itself (Nonsuperimposable). (Figure 1)
Achiral: Not chiral
¶ 3
The chirality of a molecule is often caused by an asymmetric centre.
Asymmetric centre: An atom which is bonded to four different groups. (Such as molecule A in figure 1)
¶ 4
Stereoisomer: Molecules with the same amount and sequence of atoms, yet having a different spatial structure.
Enantiomers: Molecules that are nonsuperimposable images of each other, and thus chiral. (Example in figure 1)
¶ 5
Enantiomers are analysed /drawn as perspective formulas (as seen in figure 1).
¶ 9
When there is more than one asymmetric centre, the maximum amount of stereoisomers the molecule can have is equal to 2n, where n equals the amount of asymmetric centres.
Diastereomers: Stereoisomers that are not identical and also not mirror images. In other words, they are stereoisomers that are not enantiomers.
Physical properties(e.g. melting/boiling points; solubilities) / Chemical properties
(e.g. reaction rates)
Enantiomers / Identical / Identical
Diastereomers / Different / Different
¶ 10
Meso compounds: A molecule which has more than one asymmetric centre, and a plane of symmetry. Its mirror image is the same as the molecule’s actual image.
Plane of symmetry: The image of one side of the plane is identical to the image of the other side.
Molecules which have a plane of symmetry are achiral and therefore do not have enantiomers. Meso compounds are diastereomers to the enantiomers
¶ 12
Enantiomers have an S and an R form. This allows for either one to bind better to a specific receptor than the other one.
Chapter 15
Carbohydrates are abundant in the biological world. They are often represented in the Fischer projection (figure 2). The Fischer represents the asymmetric carbon centres as a cross. The horizontal lines come out of the plane (towards you) and the vertical lines stick into the plane (figure 2).
¶ 1
Simple carbohydrates
-Monosaccharides (single sugars)
Complex carbohydrates
-Disaccharides (2 monosaccharides linked together)
-Oligosaccharides (3 to 10 monosaccharides linked together)
-Polysaccharides (more than 10 monosaccharides linked together)
Aldose: Polyhydroxy aldehydes
Ketose: Polyhydroxy ketones
Triose: Sugar with 3 carbons in it.
Tetrose: Sugar with 4 carbons in it.
Pentose: Sugar with 5 carbons in it.
Hexose: Sugar with 6 carbons in it.
Heptose: Sugar with 7 carbons in it.
By this naming convention, D-glucose is an aldohexose.
¶ 2
In Fischer projections, the carbonyl group is placed as high as possible. Once this is done, it can be determined whether a saccharide is in the D- or L- form. If the lowermost asymmetric centre in the Fischer projection has the OH group on the right, it is in D-form. If the OH group is on the left, it is in L-form. Almost all natural sugars are in D-form.
¶ 3
The maximum amount of enantiomers an aldose sugar has can be calculated by 2n, in which n equals the amount of asymmetric centres the sugar has. If a sugar only differs in configuration of one asymmetric centre to another sugar, these two sugars are called epimers.
¶ 4
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¶ 5
In a basic solution monosaccharides cannot undergo reactions due to epimerisation. Epimerisation changes the configuration of the C-2 carbon by deprotonating and subsequently protonating it. Due to this, an equilibrium is reached between two C-2 enantiomers. If instead of the C-2 carbon the C-1 carbon is protonated, this will lead to a rearrangement of an aldose to a ketose.
¶ 6
The reactions that aldehyde and ketone groups can undergo are similar to any other alcohol. The reduction reaction is the formation of an alditol from an aldose or a ketose. An alditol has no double bonds.
¶ 9
An open structure saccharide can react to form a cyclic structure saccharide. This happens by an attack of the aldehyde group onto the hydroxyl group on the second to last carbon. This reaction yields two cyclic forms: the α and the β form. This occurs because the aldehyde carbon becomes an asymmetric centre, and the side-groups –OH and –H occur in two configurations (figure 3). When the hydroxyl group is axial it is an α-saccharide, and when it is equatorial it is a β-saccharide. The α- and β- structures are called anomers. The asymmetric carbon is called the anomeric carbon. When converting a Fischer projection to a Haworth projection (planar projection), the hydroxyl groups to the right in the Fischer projection, are down in the Haworth projection. Those which are left in Fischer, are up in Haworth (figure 4).
Two anomers have different properties, such as specific rotation. However, because of the same open structure, the two anomers in aqueous solution will eventually have the same equilibrium of rotation. This phenomenon is called mutarotation.
Pyranoses: Six-membered-ring sugars
Furanoses: Five-membered-ring sugars
¶ 10
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¶ 11
A cyclic saccharide can react with an alcohol to form an acetal or ketal. The acetal or ketal of a saccharide is called a glycoside. The bond between an anomeric carbon and the alkoxy oxygen is called a glycosidic bond. Because of the mechanism that does this, one anomer (say α) can form both α- and β-glycosides.
¶ 14
Several polysaccharides are:
-Amylose: unbranched chains of D-glucose (α-1,4’-glycosidic linkage)
-Amylopectin: branched chains of D-glucose (“” + α-1,6’-glycosidic linkage)
-Glycogen: similar to amylopectin, but with more side branches
-Cellulose: unbranched chains of D-glucose (β-1,4’-glycosidic linkage)
-Chitin: similar to cellulose, but NHCOCH3 instead of OH on the C-2 position.
Amylose forms into an α-helix and is soluble in water.
Cellulose are linear and promote intermolecular hydrogen bonds. It is insoluble in water.
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Chapter 5
¶1
An electrophilic addition reaction(figure 5) is an addition reaction in which π-electrons add an electrophile, after which a carbocation is formed. Then the electrons of a nucleophile attack on this carbocation.
In general, the most stable intermediary will determine the major product.
¶2
The stability of a carbocation increases as the number of alkyl substituents bonded to the positively charged carbon increases. In stability, tertiarysecondaryprimarymethyl carbocation.
¶3
When an addition reaction yields two different products, these products are called constitutional isomers. If one of these constitutional isomers is created more predominantly than the other, the reaction is regioselective.
¶5
Alcohols can be used in an addition reaction to alkenes under influence of an acid.
¶16
Polymers are large molecules that are chains of repeated monomer building blocks.
-Biopolymers: synthesised by organisms (e.g. DNA, polysaccharides)
-Synthetic polymers: synthesised by scientists
- Step-by-step polymerisation
- Chain-growth polymerisation
Chain-growth polymers are synthesised by adding monomers to the end of a growing chain. The created polymer is a chain of the repeated monomer units.
The mechanisms for achieving this are:
-Cationic polymerisation
- Initiation: Under influence of BF3, an H+ atom is taken from water. The π-electrons of a monomer will attack on this proton, creating a carbocation.
- Propagation: The π-electrons of other monomers will attack on the carbocation on the latest monomer unit (i.e. the propagating site), creating a longer carbocation of more monomer subunits.
- Termination: A nucleophile is added, which will attack on the last carbocation, finishing the polymer.
-Radical polymerisation
- Initiation: an RO-OR radical initiator is cleaved to form two RO∙ radicals. One of these radicals will form a σ-bond with one of the π-electrons of a monomer, creating a new radical.
- Propagation: Similarly, each new monomer shares one π-electron with the polymer radical and becomes a radical itself.
- Termination: The polymer radical meets another radical, creating one σ-bond and thus stopping propagation.
Branching can occur in radical polymerisation. When branching occurs, an H atom of one polymer is used to stop the propagation of another polymer. This creates a radical group in the first polymer at a location other than the ends of the chain. This can result in branching. Branched polymers are more flexible than linear polymers.
Chapter 11
A carbonyl group is a carbon that is double bonded to oxygen (figure 6). Acyl groups, in which group R of figure 6 is an alkyl or an aromatic ring, are a form of carbonyl group.There are many derivatives of the carbonyl group, in which the B group is different. The most common structure is a carboxylic acid, in which –COOH is the defining group (B= OH). Carboxylic acid derivatives are similar to carboxylic acids in that the nature of the difference in the two molecules is the nature of the different B group.
¶1
The nomenclature of carbonyl groups is as follows:
Carboxylic Acids:
-The -e of the associated alkane is replaced with -oic acid. (Ethane Ethanoic acid)
-The carbon of the –COOH group is indicated the number 1. The rest of the main chain is numbered in ascending order: the C adjacent to the –COOH carbon is C-2, adjacent to that is C-3, etc.
-If Greek letters are used, the C adjacent to the –COOH carbon (C-2) is called α, C-3 is β, etc.
NB: The last two rules are the same for all carboxylic acid derivatives.
Acyl Chlorides:
-B=Cl
--ic acid-yl chloride
Esters:
-B=OR
-First - Name of R
-Second – Name of acid with -ic acid-ate
Salts of carboxylic acids:
-B=O-
-First – Name of cation
-Second – Name of acid with –ic acid-ate
Amides:
-B=NH2, NHR, NR2
-First – N-(name of substituent) in alphabetical order
-Second – Name of acid with–(o)ic acid-amide
¶2
In a carbonyl group, both the C and the O atoms are sp2 hybridised. Resonance structures can be formed in the case of esters, carboxylic acids and amides.
¶5
A nucleophilic acyl substitution reaction (figure 7) is a reaction in which a nucleophile (:Nu) attacks on the slightly positively charged C atom, after which a tetrahedral intermediate forms. Because this intermediate is instable, it will expel one of the bases (X or Nu), preferentially the weaker one.
The weaker a base, the better it is a leaving group.
¶6
Weak bases in a carbonyl group make it more reactive. This is because the weaker the base, the more electronegative it is. This gives the C in the carbonyl group a slightly higher δ+ charge, therefore making it more reactive. Weaker bases are also easier to eliminate in tetrahedral form.
¶7
Acyl chlorides are most commonly used to react because they are the least stable. They can react:
-With an alcohol to form an ester
-With water to form a carboxylic acid
-With an amine to form an amide (twice as much amines as acyl chlorides are used because HCl could react with yet unreacted amines, making them non-nucleophilic)
¶8
Hydrolysis reaction: Reaction with water, converting one compound into two compounds.
Alcoholysis reaction: Reaction with an alcohol, converting one compound into two compounds.
Aminolysis reaction: Reaction with an amine, converting one compound into two compounds.
Hydrolysis on an ester forms a carboxylic acid and an alcohol.
Alcoholysis on an ester forms a new ester and a new alcohol. One ester is converted into another, making it a transesterification reaction. Hydro-/alcoholysis is relatively slow, but can be catalised by an acid.
Aminolysis on an ester forms an amide and an alcohol. Not as slow as hydro-/alcoholysis. It cannot be catalysed by an acid.
¶9
The rate of ester hydrolysis can be increased by adding acid: (figure 8)
-Acid protonates carbonyl (lone) oxygen
-H2O (nucleophile) attacks the carbonyl carbon atom, creating a tetrahedral intermediate, and a proton of the H2O dissociates
-This proton can attack an OH group or the OR group
-If H2O is expelled, the original ester reforms. If ROH is expelled, a carboxylic acid + alcohol is formed.
The reaction forms an equilibrium, as H2O and ROH have approximately the same basicity.
Acid is a catalyst in this reaction, as it increases the rate of the reaction. In this case, it actually increases both the rate of forming a tetrahedral intermediate as well as the rate of the collapse of this intermediate. It does so by protonating the carbonyl group and the leaving group respectively.
This reaction can also be executed with an alcohol ROH (alcoholysis), which will give a product of a new alcohol and a new ester (transesterification)
¶11
Carboxilic acids can only react in an acidic environment. This is because the protonated version has a leaving group OH, which is a good leaving group, while the deprotonated form has an O-, which will not react. An O- group is even less reactive than an NH2 group.
The formation of an ester by reacting a carboxylic acid with an alcohol in an acid environment is called a Fischer esterification.
A carboxylic acid will not react with an amine, instead it will yield a salt.
¶12+13
Amides will generally not react, because they are bad leaving groups. However, they will react with water and alcohols if the reaction mixture is heated in the presence of an acid.
-Acid protonates carbonyl (lone) oxygen
-H2O (nucleophile) attacks the carbonyl carbon atom, creating a tetrahedral intermediate, and a proton of the H2O dissociates
-This proton can attack an OH group or the NH2 group, though the latter is favoured (stronger base)
-NH3 is expelled, forming a carboxylic acid
-NH3 is protonated to NH4+, which is not a nucleophile. The reverse reaction cannot take place
The base mechanism for this reaction is similar to the reaction found in figure 8. Without the use of a catalyst, the intermediate would be much harder to form. If it was formed it would expel –OH as a base, for it is stronger than –NH2.
¶14
In order to create a carboxylic acid derivative, a carboxylic acid is often converted to an acyl chloride. The latter is more reactive than the first and can be used to synthesise the other derivatives. It is synthesised under heat by the following reaction.
Chapter 16
Peptides and proteins are polymers of amino acids, linked by amide bonds. An amino acid is a carboxylic acid which has an amino group on the C-2 (α) carbon. The repeating parts are called amino acid residues.
-Dipeptide = 2 residues
-Tripeptide = 3 residues
-Oligopeptide = 3-10 residues
-Polypeptide = 10< residues
¶1
Amino acids differ only in the substituents (side chains) on the α-carbon. These side chains are what make each amino acid different in structure and function. Each amino acid has its own three- and one-letter abbreviation. There are 20 common amino acids in nature.
¶2
Except for glycine, all amino acids have an asymmetric α-carbon. This means each of these 19 amino acids has two enantiomers. In Fischer projection, this results in a D- and L-amino acid. In contrast to saccharides, it is the L-amino acid that is the natural configuration.
¶3
Compounds of an amino acid occur primarily in their protonated forms (acidic) in a solution that is more acidic than their pKa, and in their deprotonated (basic) forms in a solution that is more basic than their pKa value. The pKa values of the carboxyl groups and protonated amino groups in an amino acid are around 2 and 9 respectively. This means that in a neutral pH (≈7) the carboxyl groups will be deprotonated while the amino group is protonated. An amino acid in neutral pH therefore has a positive charge on one atom and a negative charge on another, and is therefore a zwitterion.
¶4
The isoelectric point(pI) of an amino acid is the pH value at which it has no net charge.
-Amino acids with a non-ionisable side chain have a pI of the average of the carboxyl group and amino group pKa values.
-Amino acids with an ionisable side chain have a pI of the average of the pKa values of similarly ionising groups.
¶5
Ways of separating amino acids.
Electrophoresis:
This is a separation technique based on pI values. A solution is added to a paper or gel and is than attracted to a cathode (negative electrode) or anode (positive electrode). The further an amino acid moves towards a certain electrode says something about its charge. The locations of amino acids are made visible by ninhydrin, which gives a purple-coloured product.
Ion-exchange Chromatography:
A mixture of amino acids is loaded onto a resin-packed column. Then a series of buffers is poured through the column. The rate at which a specific amino acid moves through the column depends on its charge and polarity. This separating technique also gives information about the relative amounts of amino acids present in the mixture.
¶6
Peptide bonds are formed between the amino group of one peptide and the carboxyl group of another. This particular bond has about 40% double bond character, as the C=O and the N groups share their electrons as seen in figure 10. This means that free rotation around an amide bond is prevented, resulting in amino acids lying in a plane.
When identities of the amino acids in a peptide are known, but not the order, they are generally written with commas:
Gly, Arg, Ala, Pro, Thr
If the order is known, then hyphens are used:
Ala-Pro-Arg-Thr-Gly
Where Ala is the N-terminal amino acid (having a free amino group) and Gly is the C-terminal amino acid (having a free carboxyl group). Since Pro is on position 4, it can be denoted as Pro 4.
Amino acids can also form disulphide bonds (of the natural amino acids, only Cys can). This means that two thiol groups (R-SH) form a disulphide (R-S-S-R). When two cysteines form a disulphide, it is called a cystine. The cystine can form a disulphide bridge between two parts of a peptide (or two different peptides).
¶7
When synthesising a peptide, one cannot just put all the amino acids together, as the will react at random. If a specific peptide needs to be created, one will need to do several extra steps.
-Protect the N-terminal amino acid with a protecting group (usually di-tert-butyl dicarbonate). In this way the amino group of this amino acid cannot react.
-Activate the carboxyl group of the protected amino acid (usually activated by DCC). This way the carboxyl group of this amino acid is more likely to react than that of another amino acid.
-Add the next amino acid.
-Repeat the previous two steps until the desired peptide is created.
-Remove the protecting group.
This technique will not produce high yields of the desires peptide however.
Chapter 7
Delocalised electrons are not confined to one or two atoms, but are instead shared by three or more atoms.
¶1
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¶2
Benzene is a planar molecule with formula C6H6. The molecule is circular, and because all carbons are sp2 hybridised it lies in a plane. The p-orbitals of each of the carbons are all perpendicular to the plane and all parallel to the other p-orbitals. This forms a continuous circular cloud of delocalised electrons above and below the C-ring. (Figure 11)