1. Unit 3: Aromatic and Heterocyclic Chemistry
Cytotoxin- Inhibits DNA-topoisomerase enzymes
Happy Tree
(China)
Unit 3: Aromatic and Heterocyclic Chemistry

2. Aromatic Compounds
Many aromatic substances have rather simple structures and contain a six-carbon unit (C6H5)
Arenes = aromatic hydrocarbon
Aromatic: refers to the level of stability for an arene
Benzene: is the parent hydrocarbon of the class or aromatic compounds

3. When Is A Molecule Aromatic?
For a molecule to be aromatic it must:
Be cyclic
Have a p-orbital on every atom in ring
Be planar
Posses 4n+2 p electrons (n = any integer)
Erich Hückel

4. Benzene C6H6. 4

5. Discovery of Benzene
Isolated in 1825 by Michael Faraday who determined C:H ratio to be 1:1.
Synthesized in 1834 by Eilhard Mitscherlich who determined molecular formula to be C6H6.
Other related compounds with low C:H ratios had a pleasant smell, so they were classified as aromatic =>

6. Benzene properties
The carbon to hydrogen ration in benzene suggest a highly unsaturated structure, however it behaves as if it were saturated.
Does not decolorize bromine solution the way alkenes and alkynes do
It is not easily oxidized by potassium permanganate
Does not undergo addition reactions the same as alkenes or alkynes

7. Benzene
Benzene is one of the most important commercial organic chemicals with approximately 17 billion pounds produced annually the United States alone.

8. Two Lewis structures for the benzene ring.
Friedrich Kekule (1865) proposed the tetracovalence of carbon in the structure of benzene (alternating double single bonds) 8

9. Shorthand notation for benzene rings.9

10. Kekulé Structure
Proposed in 1866 by Friedrich Kekulé, shortly after multiple bonds were suggested.
Thus benzene is often written as a circle to remind us of the delocalize nature of the electrons
Failed to explain existence of only one isomer of 1,2-dichlorobenzene.
=>

11. Substitution Reaction Benzene
Benzene reacts mainly by substitution reaction

12. Some common mono-substituted benzene molecules
Toluene, sometimes you see this on marker pens ”contains no toluene”
Has the condensed structural formula C6H5CH3 12

13. Common Names of Benzene Derivatives
=>

15. Disubstituted Benzenes
The prefixes ortho-, meta-, and para- are
commonly used for the 1,2-, 1,3-, and 1,4-
positions, respectively.
m nitrotoulene
=>

16. 3 or More Substituents Use the smallest possible numbers, but
the carbon with a functional group is #1.
=>

17. Phenyl and Benzyl Aromatic hydrocarbons are classified as arenes.
The symbol Ar is used for an aryl group ( just as R symbolizes alkyl group)
Two groups with special names occur frequently in aromatic compounds: phenyl group and benzyl group

18. Phenyl and Benzyl Phenyl indicates the benzene ring
attachment. The benzyl group has
an additional carbon.
=>

19. 2, 4 dimethyl 3 phenyl pentane phenylcyclopropane
Benzyl chloride biphenyl

20. Common Names for Disubstituted Benzenes
=>

21. Fused Ring Hydrocarbons
Naphthalene
Anthracene
=>
Phenanthrene

22. Reactivity of Polynuclear Hydrocarbons
As the number of aromatic rings increases, the resonance energy per ring decreases, so larger PAH’s will add Br2.
(mixture of cis and trans isomers)
=>

23. Fused Heterocyclic Compounds
Common in nature, synthesized for drugs.
=>

24. Physical Properties
Melting points: More symmetrical than corresponding alkane, pack better into crystals, so higher melting points.
Boiling points: Dependent on dipole moment, so ortho > meta > para, for disubstituted benzenes.
Density: More dense than nonaromatics, less dense than water.
Solubility: Generally insoluble in water. =>

25. Electrophilic Aromatic substitution
The most common reaction of aromatic compounds involves substitution of other atoms or groups for a ring hydrogen
Chlorination
C6H6 + Cl C6H5Cl + HCl FeCl3 is catalyst

26. Electrophilic Aromatic substitution
bromination
nitration
sulfonation

27. Friedel-Crafts reaction
Refers to Alkylation of aromatics
The Friedel-Craft alkylation reaction has some limitations…it cannot be applied to an aromatic ring that already has one it a nitro or sulfonic acid group

28. Ortho, Para-directing and Meta-directing groups
Substituents already present on an aromatic ring determine the position taken by a new substituent.
Certain groups are ortho, para directing, and others are meta directing

29. all ortho, para directing
Directing and activation effects of common functional groups (groups are listed in decreasing order of activation)
Substituent group
-NH2, -NHR, -NR2
-OH, -OHCH3, -OOR O
-NHC—R
-CH3, -CH2,CH3, -R
________________________
-F, -Cl, -Br, -I
Name of group
Amino
Hydroxyl, alkoxy
acylamino
Alkyl
________________________
Halo
all ortho, para directing

30. Directing and activation effects of common functional groups (groups are listed in decreasing order of activation)
Substituent group
O O
-C-R, -C-OH acyl, carboxy
O O
-C-NH2, -C-OR carboxamindo, carboalkoxy O
-S-OH sulfonic acid
-C=N cyano
-N nitro
Name of group
meta dircting

32. Heterocyclic Chemistry
Cytotoxin- Inhibits DNA-topoisomerase enzymes
Happy Tree
(China)
Heterocyclic Chemistry
The largest class of organic compounds.
Most drugs contain herocyclic rings

33. Definition: Heterocyclic compounds are organic compounds that contain a ring structure containing atoms in addition to carbon, such as sulfur, oxygen or nitrogen, as the heteroatom. The ring may be aromatic or non-aromatic
Significance – Two thirds of all organic compounds are aromatic heterocycles. Most pharmaceuticals are heterocycles.
Examples
Pfizer: Viagra
Quinine
Erectile dysfunction
Treatment of malaria for 400 years (Peru)

34. Camptothecin Analogues
Treating stomach & intestinal ulcers
Camptothecin Analogues
Pfizer - Irinotecan
GSK - Topotecan
Ovarian & lung cancer
More soluble & less side-effects

35. Heteroatoms
Are atoms other than carbon or hydrogen that may be present in an organic compound.
The most common heteroatoms are oxygen, nitrogen and sulfur

36. Six Membered Heterocycles: Pyridine
Pyridine replaces the CH of benzene by a N atom (and a pair of electrons)
Hybridization = sp2 with similar resonance stabilization energy
Lone pair of electrons not involved in aromaticity
Pyridinium ion: pKa = 5.5
Piperidine: pKa = 11.29
diethylamine : pKa = 10.28
1H NMR: d
Pyridine is a weak base
Pyridine is -electron deficient
Electrophilic aromatic substitution is difficult
Nucleophilic aromatic substitution is easy

37. Chemistry of pyridine Electrophilic substitution in pyridine
Pyridine is less active, than benzene toward electrophilic agents, because nitrogen is
more electronegative, than carbon and acts like an electron withdrawing substituent,
including the meta-directing effect.
It undergoes this reaction only under drastic conditions, ex nitration or bromination and requires high temperatures and strong acid catalyst
Example: 37

38. DMAP (DimethylAminoPyridine)
Whereas acylations “catalyzed” by pyridine are normally carried out in pyridine as the reaction solvent. Only small amounts of DMAP are required to do acylations
Attempted Electrophilic Aromatic Substitution
Unreactive, Stable

39. Nucleophilic aromatic substitution
The reaction of pyridines
A nucleophile displaces a hydride or halide ion from the aromatic ring

40. Pyridine as a nucleophile
Use Pyridine as a solvent to make esters
E.g.
Acyl pyridinium ion
Reactive intermediate

41. E.g. Nucleophilic Substitution at 2- and 4-positions of
pyridine is most favoured
E.g.

42. Heterocycles
The pyridine ring can be fused with benze rings t produce polycyclic aromatic heterocycles.
Examples of 6-membered heterocycles include quinoline and isoquinoline

44. Five Membered Heterocycles: Pyrrole
Aromatic: Thus, 6 electrons
Sp2 hybridised and planar
Lone pair tied up in aromatic ring
Pyrrole is -electron excessive
Thus, Electrophilic Aromatic Substitution is Easy
Nucleophilic Substitution is Difficult
1H NMR: d

45. Electrophilic Aromatic Substitution preferred at the 2-position
Normal acidic nitration causes polymerization
Vilsmeier Reaction
Electron-withdrawing group allows substitution at the 3-position

46. Organic Synthesis with Pyrrole should avoid strong acids
i; 1 X SO2Cl2, Et2O
ii; 4 X SO2Cl2, Et2O ii

47. Indole Indole Alkaloids Aromatic due to 10 -electrons
Benzene part is non-reactive
Electrophilic aromatic substitution occurs at the 3-position
Indole Alkaloids
Lysergic acid (LSD)
Strychnine
Mitomycin C

48. Other Five Membered Heterocycles
The least aromatic:
The O atom is too electronegative
Least reactive
More aromatic than Furan
Less reactive than pyrrole, but substitution always at 2-position
Electrophilic Substitution, not addition
Can give addition, as well as substitution products when reacted with E+
Thiophene has similar reactivity to benzene

49. Electrophilic Aromatic Substitution of Thiophene
Avoid concentrated mineral acids or strong Lewis acids, e.g. AlCl3

50. Some Reactions of Furan
Furan is more reactive than thiophene
Addition product
Wittig reaction
Hydrolysis of acetal
Furan is easily cleaved to dicarbonyls

51. Furan is a source of 1,4-dicarbonyls in Organic Synthesis

52. Diels–Alder reaction
is an organic chemical reaction (specifically, a cycloaddition) between a conjugated diene( chemical with 2 double bonds) and a substituted alkene, commonly termed the dienophile, to form a substituted cyclohexene system

53. The Diels-Alder Reaction
Diene
4 system
dienophile
2 system
4+2 cycloaddition
Otto Diels
Electron rich
Electron poor
Kurt Alder
Noble Prize in 1950

54. The configuration of the dienophile is retained
Always reacts via the cis-diene
Under kinetic control

55. exo-product forms as the temperature is raised
Furan readily undergoes the Diels-Alder reaction with maleic anhydride
Thermodynamic
exo-product forms as the temperature is raised
endo-product
More stable due to less steric reasons
Aromaticity prevents thiophene from taking part in the Diels-Alder reaction
- SO2
This sulfone is not aromatic & very reactive

56. Five-membered Rings with Two or More Nitrogens
pKa = 14.5
(imidazole)
pKa = 16.5 (pyrrole)
Diazoles
Pyrazole
Imidazole
Imidazole is more basic than pyridine, but more acidic than pyrrole
Imidazole + H+
NaOH
Imidazole - H+
- H2O
Properties: Very stable cation and anion of imidazole is formed

57. Some Natural Imidazole Compounds
Histidine
Important ligand to many metalloproteins
Is one of the essential amino acids.
A relatively small change in cellular pH can result in a change in its charge
Body neurotransmitter & local immune response
histamine
histidine carboxylase
Dipeptide in high concentrations in the brain & muscles
- Improves social interactions & treatment of autism
Carnosine

58. Tetrazoles are used in drugs as replacements for CO2H
Indomethacin
Indomethacin
Tetrazole derivative
Anti-arthritis drug
- Non steroidal anti-inflammatory drug – reduces fever, pain, stiffness, delays premature labour & other uses

59. Bioreductive Anti-Tumour Agents10 1
Mitomycin C
Pyrrolo[1,2-a]benzimidazole (PBI)
IC50 ≈ 1.0 µM
E. B. Skibo et al., J. Med. Chem., 2002, 45, 1211
K. Fahey, F. Aldabbagh, Tetrahedron Lett., 2008, 49, 5235
More selective to hypoxia
Hypersensitive to Fanconi Anemia
IC50 ≈ µM
L. O’Donovan, F. Aldabbagh, Chem. Commun., 2008, 5592.
M. Lynch, S. Hehir, M. P. Carty, F. Aldabbagh, Chem. Eur. J. 2007, 13, 3218
S. Hehir, L. O’Donovan, M. P. Carty, F. Aldabbagh, Tetrahedron 2008, 64, 4196

60. Targeting Hypoxic Cells

61. Mitomycin C (MMC) SET - activation Two electron activation + 1 e-10
+ 1 e-
steps
- 1 e- 1
- 1 e- .
DNA alkylation
CY P450 reductase
Two electron activation
+ 2 e-
+ 2 H+
DNA alkylation
DT-diaphorase
S. E. Wolkenberg and D. L. Boger, Chem Rev., 2002, 102, 2477

62. Measuring the Effect of FANCD2 Expression on Cell Viability
●, ● PD20i cells (lack FANCD2)
▲, ▲ PD20:RV (express FANCD2)
K. Fahey, L O’Donovan, M. Carr, M. P. Carty, F. Aldabbagh, Eur. J. Med Chem. 2010, 45,

63. 3. Chemistry of pyrrole, furan, and thiophene63

64. Electrophilic substitution in pyrrole, furan and thiophene
X = O, NH, or S 64

65. Examples: 65

66. Furan is able to act as a diene in the reactions of cycloaddition
The Fisher synthesis of indoles 66

67. Nucleophilic substitution in pyridine
The presence of nitrogen enables pyridine to react with nucleophilic agents, like an
electron withdrawing substituents enables benzene to participate in such reactions,
including the ortho-directing effect. 67

68. Another example:
These reactions require very strong nucleophiles and heat, because H- is a very weak
leaving group. In ortho- or para-substituted pyridines nucleophilic substitution
proceeds much easier. 68

69. Organic Halogens:
Have practical uses for example: solvents, insecticides, herbicides, fire retardants, cleaning fluids, refrigerants, polymers ex teflon

70. Aryl Halides Ar-X
Organic compounds with a halogen atom attached to an aromatic carbon are very different from those compounds where the halogen is attached to an aliphatic compound(alkanes, alkenes, alkynes).
While the aliphatic compounds readily undergo nucleophilic substitution and elimination reactions, the aromatic compounds resist nucleophilic substitution, only reacting under severe conditions or when strongly electron withdrawing groups are present ortho/para to the halogen.

71. Nucleophilic substition
Nucleophile: electron rich reactants sharing electrons with electrophiles ex SN1 and SN2 and nuclephilic acyl substitution rxn
Electrophile: electron poor reactant . They seek electrons and form bonds with nucleophiles.
Nucleophilic substitution reaction: a reaction in which a nucleophile displaces a leaving group from a substrate.

72. Nucleophilic substition
OH + CH3CH2—Br H2O CH2CH3—OH + Br
Hydroxide ion is the nucleophile
It reacts with the substrate ethyl bromide
It displaces bromide ion which is the leaving group

73. Examples of Nucleophilic
The most common nucleophiles are :
Oxygen
Nitrogen
Sulfur
Halogens
carbon nucleopiles

74. Reactions of common nucleotides with alkyl halides

75. Substitution reactions in Table 6:1 have some limitations with respect to the structure of the R group in the alkyl halide
In aryl halides, the carbon to which the halogen is attached is sp2 hybrizided. The bond is stronger and shorter than the carbon-halogen bond in aliphatic compounds where the carbon is sp3 hybridized. Hence it is more difficult to break this bond and aryl halides resist the typical nucleophilic substitution reactions of alkyl halides.
The same is true of vinyl halides where the carbon is also sp2 hybridized and not prone to nucleophilic substitution.

76. Another limitation that often occurs is when the nucleophile is either an anion or a base or both

77. Nucleophilic substitution mechanisms
There are two main nucleophilic substitution mechanisms:
SN1
SN2
The SN part of each symbol stands for substitution nucleophilic
The numbers will be explained later

78. SN2 mechanism
Is a one-step process in which the bond to the leaving group begins t break as the bond to the nucleophile begins to form.
The nucleophile attacks from the back side of the C—L bond.
At some stage the nucleophile and the leaving group are both partly bonded to the carbon at which the substitution occurs.
As the leaving group departs with its electron pair, the nucleophile supplies another electron pair to the carbon atom.

79. SN2 mechanism
The number 2 to show that two molecules – the nucleophile and the substrate are involved

80. SN2 mechanism
SN2 mechanism is a one-step process favored for methyl and primary halides.
It occurs more slowly with secondary halides and usually not at all with tertiary halides.
It occurs with inversion of configuration and its rate depends on the concentration of both the nucleophile and the substrate

81. SN1 mechanism
A two step process where the bond between the carbon and the leaving group breaks first and then the resulting carbocation combines with the nucleophile
The number 1 designates the mechanism because the slow or rate determing step involves only one of the two reactants

83. SN1 mechanism
SN1 mechanism is a two step process and is favored when the alkyl halide is tertiary. The SN1 process occurs with racemization and its rate is independent of the nucleophile’s concentration.
Racemization: a 50:50 mixture of enantiomers

84. Enantiomers
A pair of molecules that are nonsuperimposable mirror images of one another

85. Comparison of Sn2 and Sn1 substitutions

86. Dehydrohalogenation, an elimination reaction: the E2 and E1 mechanisms
When an alky halide with a hydrogen attached to the carbon adjacent to the halogen-bearing carbon reacts with a nucleophile, 2 competing reaction paths are possible: substitution or elimination
Substitution
elimination

87. elimination reactions of alkyl halides
In an elimination ( dehydrohalogenation) reactions of alkyl halides, a hydrogen atom and a halogen atom from adjacent carbons are eliminated and a carbon-carbon double bond is formed.

88. Elimination reactions
E2 mechanism: reactions of alkyl halides : a one step process in which HX is eliminated and a C=C bond is formed .
B is the nucleophile, acting as a base, removes the proton (hydrogen on a carbon adjacent to the one that bears the leaving group designated X
At the same time the leaving group departs a double bond forms

89. Elimination reactions
E1 mechanism: is a two step process with the same first step as an SN1 reaction (slow and rate-determining ionization of the substrate to give a carbocation)

90. Polyhalogenated aliphatic compounds
Polyhalogenated compounds are industrially created compounds substituted with multiple halogens.
Many of them are very toxic and bioaccumulate in humans, and have a very wide application range.
They include the much maligned PCBs, PBDEs, and PFCs as well as numerous other compounds.

91. PCB and PBDE
Polychlorinated biphenyl: (PCB) is any of the 209 configurations of organochlorides with 1 to 10 chlorine atoms attached to biphenyl, which is a molecule composed of two benzene rings and is used as dielectric and coolant fluids, for example in transformers, capacitors, and electric motors
Polybrominated diphenyl ethers or PBDEs, are organobromine compounds that are used as flame retardant

92. PFC and CFC
perfluorinated compound (PFC) 1s an organofluorine compound with all hydrogens replaced by fluorine on a carbon chain
used to make fluoropolymers such as Teflon, among other applications
Chlorofluorocarbons (CFC) also known as freon are polyhalogenated compounds containing chlorine and fluorine