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Medicinal chemistry I
PHC 211
Credit Hour =3
[2 Theoretical +1 Practical
(2 Contact hours)]
‫الدوائية‬ ‫الكيمياء‬
-
1
Medicinal chemistry I
Lecture 1
(Hydrocarbons)
HYDROCARBONS
They are compounds whose
molecules contain only carbon
and hydrogen atoms.
Types of Hydrocarbons
1- Alkanes with a general formula (CnH2n+2)
2- Alkenes with a general formula (CnH2n)
3- Alkynes with a general formula (CnHn)
Timberlake LecturePLUS 5
Alkanes (Paraffin)
 Contain C and H only
 Contain single bonds C-C
 Have 4 bonds to every carbon (C) atom
 Are nonpolar
Physical properties
Non-polar or only weakly polar, cannot form hydrogen bond 
relatively weak intermolecular forces
Lower mp/bp; increase with size; decrease with branching
@ room temperature:
C1 – C4 are gases
C5 – C17 are liquids
> C17 are solids
alkanes are water insoluble
Nomenclature of alkanes and cycloalkanes
Trivial names or common names
IUPAC system (international Union of Pure and Applied Chemistry)
In this system we use a suffix and a prefix
Suffix for all alkanes (ane)
Prefix according to number of carbon atoms as following
Timberlake LecturePLUS 8
IUPAC Names
# carbons Structural Formula
Methane 1 CH4
Ethane 2 CH3CH3
Propane 3 CH3CH2CH3
Butane 4 CH3CH2CH2CH3
Pentane 5 CH3CH2CH2CH2CH3
Timberlake LecturePLUS 9
IUPAC NAMES
Name # carbons Structural Formula
Hexane 6 CH3CH2CH2CH2CH2CH3
Heptane 7 CH3CH2CH2CH2CH2CH2CH3
Octane 8 CH3CH2CH2CH2CH2CH2CH2CH3
Nonane 9 CH3 CH2 CH2CH2CH2CH2CH2CH2CH3
Decane 10 CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3
Timberlake LecturePLUS 10
Learning Check Alk1
A. What is the condensed formula for
H H H H
H C C C C H
H H H H
B. What is its molecular formula?
C. What is its name?
Timberlake LecturePLUS 11
Solution Alk1
A. CH3CH2CH2CH3
B. C4H10
C. butane
Cycloalkanes
Cyclopropane cyclopentane cyclohexane
CH2CH2CH2CH2CH3
1-Cyclobutylpentane
CH2CH3
CH3
CH3
CH
CH3
CH3
Br
CH2CH3
Ethylcyclohehane 1-Isopropyl-3-methylcyclohexane
(not 1-isopropyl-5-methylcyclohexane)
1
2
3 1
2
3
4
4-Bromo-2-ethyl-1-methylcyclohexane
(not 1-bromo-3-ethyl-4-methylcyclohexane)
Nomenclature of branched-chain alkanes
Alkyl group
Alkane
CH3- Methyl
CH3CH2- Ethyl
CH3CH2CH2- Propyl
CH3CH2CH2CH2- Butyl
CH3-H Methane
CH3CH2-H Ethane
CH3CH2CH2-H Propane
CH3CH2CH2CH2-H Butane
CH3CH2CH2 CH
CH3
H3C
Propyl Isopropyl
CH3CH2CH
CH3
CH3CH2CH2CH2
C
CH3
H3C
CH3
n-Butyl
sec-Butyl tert-butyl
- Locate the longest continuous chain of carbon atoms; this chain determines the
parent name for the alkane, this chain may or may not be shown in a straight line
CH3CH2CH2CH2CHCH3
CH3
CH3CH2CH2CH2CH
CH2
CH3
CH3
Longest chain (parent) is hexane Longest chain (parent) is heptane
- Number the longest chain (parent), beginning with the end of the chain nearer the
substituent
CH3CH2CH2CH2CH
CH2
CH3
CH3
CH3CH2CH2CH2CHCH3
CH3
1
2
3
4
5
6
Substituent 1
2
3
4
5
6
7 Substituent
CH3CH2CH2CH2CHCH3
CH3
CH3CH2CH2CH2CH
CH2
CH3
CH3
1
2
3
4
5
6
1
2
3
4
5
6
7
2-Methylhexane 3-Methylheptane
- When two or more substituents are identical, indicate this by the use of the
prefixes di-, tri-, tetra-, and so on
CH3CH CHCH3
CH3 CH3
CH3CHCHCHCH3
CH3
CH3
CH3
CH3CCH2CCH3
CH3 CH3
CH3 CH3
2,3-Dimethylbutane 2,3,4-Trimethylpentane 2,2,4,4-Tetramethylpentane
2,4-dimethylheptane
6-isopropyl-2,2-dimethylnonane
- When two chains of equal length compete for selection as the parent chain,
choose the chain with the greater number of substituents.
CH3CH2 CH
CH3
CH
CH2
CH2
CH3
CH CH
CH3 CH3
CH3
1
2
3
4
5
6
7
2,3,5-Trimethyl-4-propylheptane (four substituents)
- When branching first occurs at an equal distance from either end of the
longest chain, choose the name that gives the lower number at the first point of
difference
1
2
3
4
5
6
CH3 CH CH2 CH
CH3 CH3
CH
CH3
CH3
2,3,5-Trimethylhexane
(not 2,4,5-trimethylhexane)
“Classes of Carbons”
primary carbon (1o) – a carbon bonded to one carbon
secondary carbon (2o) – a carbon bonded to two carbons
tertiary carbon (3o) – a carbon bonded to three carbons
quaternary carbon (4o) – a carbon bonded to four carbons
CH3 CH3
CH3CHCH2CH2C-CH3
CH3
Classification of Hydrogen atoms
H2C CH
CH3
CH3
H3C
2o
hydrogen atom 1o
hydrogen atom
3o
hydrogen atom
1o
hydrogen atom
2-Methylbutane
Synthesis of alkanes and cycloalkanes
1- Hydrogenation of alkenes:
propene propane
cyclohexene cyclohexane
Ni / ethanol
25o / 50 atm
Ni / ethanol
25o
/ 50 atm
Alkenes react with hydrogen in the presence of metal catalyst such
as nickel and platinum to produce alkanes
2- Reduction of alkyl halide
Br
isopentyl bromide
isopentane
(1-bromo-3-methylbutane)
(2-methylbutane)
H
Zn
A- Most alkyl halides react with zinc and aqueous acid to produce
an alkane. In theses reactions zinc atoms transfer electrons to the
carbon atom of the alkyl halide. Therefore, the reaction is a
reduction of the alkyl halide.
A- with an active metal and an acid
R—X + metal/acid  RH
active metals = Sn, Zn, Fe, etc.
acid = HCl, etc. (H+)
CH3CH2CHCH3 + Sn/HCl  CH3CH2CH2CH3 + SnCl2
Cl
sec-butyl chloride n-butane
CH3 CH3
CH3CCH3 + Zn/H+  CH3CHCH3 + ZnBr2
Br
tert-butyl bromide isobutane
B. Reduction of an alkyl halide
b) hydrolysis of a Grignard reagent (two steps)
i) R—X + Mg  RMgX (Grignard reagent)
ii) RMgX + H2O  RH + Mg(OH)X
CH3CH2CH2-Br + Mg  CH3CH2CH2-MgBr
n-propyl bromide n-propyl magnesium bromide
CH3CH2CH2-MgBr + H2O  CH3CH2CH3 + Mg(OH)Br
propane
Reactions of alkanes:
alkane + H2SO4  no reaction (NR)
alkane + NaOH  NR
alkane + Na  NR
alkane + KMnO4  NR
alkane + H2,Ni  NR
alkane + Br2  NR
alkane + H2O  NR
(Alkanes are typically non-reactive. They don’t react with
acids, bases, active metals, oxidizing agents, reducing agents,
halogens, etc.)
The main reason for unreactivity of alkanes are:
1- The C-C and the C-H bonds are strong bonds.
2- Neither H nor C atoms in the paraffins have any unshared
electrons or any orbitals in their valency shells not
completely filled
3- No dipole moment between any C-C or C-H
Reactions of alkanes
Alkanes and cycloalkanes are relatively unreactive compared with
organic compounds containing functional groups
1) Halogenation
CH4 CH3Cl
UV
+
light other product
-The reaction of an alkane with a halogen is a substitution
reaction
-The halogenation of alkanes take place by a radical mechanism
- High temperature is needed
Photochemical or thermal halogenation
R H + X2 R X + HX
Cl Cl
UV
CH4 Cl
CH3
Cl Cl
Cl
CH3
CH3Cl Cl
HCl
:
light . chlorine radical
+ . +
.
.
: + +
.
step 1
step 2
step 3
step 1 (chain initiation)
Step 2 and 3 are called (chain propagation)
Further substitution reactions
H:Cl + 
CH2Cl
CH2Cl + Cl:Cl + Cl:CH2Cl
Cl
H:CH2Cl
Cl +
Chain propagation remain until either
1- All the Cl2 or CH4 is consumed, or
2- the process is terminated by the following reactions:
A- the recombination of Cl. Atoms to form Cl2 molecules
B- the recombination of the CH3
. to form CH3-CH3
Bromine is less reactive toward alkanes than chlorine, but
bromine is more selective in the site of attack
Br2
Br
Br
light / 127o +
(>99%)
(trace)
Cl2
Cl
Cl
light / 25o +
(37%)
(63%)
- Direct iodination is rarely carried out
- Flourine is much more reactive than chlorine, is even less selective than
chlorine

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organic cemstry

  • 1. Medicinal chemistry I PHC 211 Credit Hour =3 [2 Theoretical +1 Practical (2 Contact hours)] ‫الدوائية‬ ‫الكيمياء‬ - 1
  • 2. Medicinal chemistry I Lecture 1 (Hydrocarbons)
  • 3. HYDROCARBONS They are compounds whose molecules contain only carbon and hydrogen atoms.
  • 4. Types of Hydrocarbons 1- Alkanes with a general formula (CnH2n+2) 2- Alkenes with a general formula (CnH2n) 3- Alkynes with a general formula (CnHn)
  • 5. Timberlake LecturePLUS 5 Alkanes (Paraffin)  Contain C and H only  Contain single bonds C-C  Have 4 bonds to every carbon (C) atom  Are nonpolar
  • 6. Physical properties Non-polar or only weakly polar, cannot form hydrogen bond  relatively weak intermolecular forces Lower mp/bp; increase with size; decrease with branching @ room temperature: C1 – C4 are gases C5 – C17 are liquids > C17 are solids alkanes are water insoluble
  • 7. Nomenclature of alkanes and cycloalkanes Trivial names or common names IUPAC system (international Union of Pure and Applied Chemistry) In this system we use a suffix and a prefix Suffix for all alkanes (ane) Prefix according to number of carbon atoms as following
  • 8. Timberlake LecturePLUS 8 IUPAC Names # carbons Structural Formula Methane 1 CH4 Ethane 2 CH3CH3 Propane 3 CH3CH2CH3 Butane 4 CH3CH2CH2CH3 Pentane 5 CH3CH2CH2CH2CH3
  • 9. Timberlake LecturePLUS 9 IUPAC NAMES Name # carbons Structural Formula Hexane 6 CH3CH2CH2CH2CH2CH3 Heptane 7 CH3CH2CH2CH2CH2CH2CH3 Octane 8 CH3CH2CH2CH2CH2CH2CH2CH3 Nonane 9 CH3 CH2 CH2CH2CH2CH2CH2CH2CH3 Decane 10 CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3
  • 10. Timberlake LecturePLUS 10 Learning Check Alk1 A. What is the condensed formula for H H H H H C C C C H H H H H B. What is its molecular formula? C. What is its name?
  • 11. Timberlake LecturePLUS 11 Solution Alk1 A. CH3CH2CH2CH3 B. C4H10 C. butane
  • 12. Cycloalkanes Cyclopropane cyclopentane cyclohexane CH2CH2CH2CH2CH3 1-Cyclobutylpentane CH2CH3 CH3 CH3 CH CH3 CH3 Br CH2CH3 Ethylcyclohehane 1-Isopropyl-3-methylcyclohexane (not 1-isopropyl-5-methylcyclohexane) 1 2 3 1 2 3 4 4-Bromo-2-ethyl-1-methylcyclohexane (not 1-bromo-3-ethyl-4-methylcyclohexane)
  • 13. Nomenclature of branched-chain alkanes Alkyl group Alkane CH3- Methyl CH3CH2- Ethyl CH3CH2CH2- Propyl CH3CH2CH2CH2- Butyl CH3-H Methane CH3CH2-H Ethane CH3CH2CH2-H Propane CH3CH2CH2CH2-H Butane CH3CH2CH2 CH CH3 H3C Propyl Isopropyl CH3CH2CH CH3 CH3CH2CH2CH2 C CH3 H3C CH3 n-Butyl sec-Butyl tert-butyl
  • 14. - Locate the longest continuous chain of carbon atoms; this chain determines the parent name for the alkane, this chain may or may not be shown in a straight line CH3CH2CH2CH2CHCH3 CH3 CH3CH2CH2CH2CH CH2 CH3 CH3 Longest chain (parent) is hexane Longest chain (parent) is heptane - Number the longest chain (parent), beginning with the end of the chain nearer the substituent CH3CH2CH2CH2CH CH2 CH3 CH3 CH3CH2CH2CH2CHCH3 CH3 1 2 3 4 5 6 Substituent 1 2 3 4 5 6 7 Substituent
  • 15. CH3CH2CH2CH2CHCH3 CH3 CH3CH2CH2CH2CH CH2 CH3 CH3 1 2 3 4 5 6 1 2 3 4 5 6 7 2-Methylhexane 3-Methylheptane - When two or more substituents are identical, indicate this by the use of the prefixes di-, tri-, tetra-, and so on CH3CH CHCH3 CH3 CH3 CH3CHCHCHCH3 CH3 CH3 CH3 CH3CCH2CCH3 CH3 CH3 CH3 CH3 2,3-Dimethylbutane 2,3,4-Trimethylpentane 2,2,4,4-Tetramethylpentane
  • 17. - When two chains of equal length compete for selection as the parent chain, choose the chain with the greater number of substituents. CH3CH2 CH CH3 CH CH2 CH2 CH3 CH CH CH3 CH3 CH3 1 2 3 4 5 6 7 2,3,5-Trimethyl-4-propylheptane (four substituents) - When branching first occurs at an equal distance from either end of the longest chain, choose the name that gives the lower number at the first point of difference 1 2 3 4 5 6 CH3 CH CH2 CH CH3 CH3 CH CH3 CH3 2,3,5-Trimethylhexane (not 2,4,5-trimethylhexane)
  • 18. “Classes of Carbons” primary carbon (1o) – a carbon bonded to one carbon secondary carbon (2o) – a carbon bonded to two carbons tertiary carbon (3o) – a carbon bonded to three carbons quaternary carbon (4o) – a carbon bonded to four carbons CH3 CH3 CH3CHCH2CH2C-CH3 CH3
  • 19. Classification of Hydrogen atoms H2C CH CH3 CH3 H3C 2o hydrogen atom 1o hydrogen atom 3o hydrogen atom 1o hydrogen atom 2-Methylbutane
  • 20. Synthesis of alkanes and cycloalkanes 1- Hydrogenation of alkenes: propene propane cyclohexene cyclohexane Ni / ethanol 25o / 50 atm Ni / ethanol 25o / 50 atm Alkenes react with hydrogen in the presence of metal catalyst such as nickel and platinum to produce alkanes
  • 21. 2- Reduction of alkyl halide Br isopentyl bromide isopentane (1-bromo-3-methylbutane) (2-methylbutane) H Zn A- Most alkyl halides react with zinc and aqueous acid to produce an alkane. In theses reactions zinc atoms transfer electrons to the carbon atom of the alkyl halide. Therefore, the reaction is a reduction of the alkyl halide.
  • 22. A- with an active metal and an acid R—X + metal/acid  RH active metals = Sn, Zn, Fe, etc. acid = HCl, etc. (H+) CH3CH2CHCH3 + Sn/HCl  CH3CH2CH2CH3 + SnCl2 Cl sec-butyl chloride n-butane CH3 CH3 CH3CCH3 + Zn/H+  CH3CHCH3 + ZnBr2 Br tert-butyl bromide isobutane
  • 23. B. Reduction of an alkyl halide b) hydrolysis of a Grignard reagent (two steps) i) R—X + Mg  RMgX (Grignard reagent) ii) RMgX + H2O  RH + Mg(OH)X CH3CH2CH2-Br + Mg  CH3CH2CH2-MgBr n-propyl bromide n-propyl magnesium bromide CH3CH2CH2-MgBr + H2O  CH3CH2CH3 + Mg(OH)Br propane
  • 24. Reactions of alkanes: alkane + H2SO4  no reaction (NR) alkane + NaOH  NR alkane + Na  NR alkane + KMnO4  NR alkane + H2,Ni  NR alkane + Br2  NR alkane + H2O  NR (Alkanes are typically non-reactive. They don’t react with acids, bases, active metals, oxidizing agents, reducing agents, halogens, etc.)
  • 25. The main reason for unreactivity of alkanes are: 1- The C-C and the C-H bonds are strong bonds. 2- Neither H nor C atoms in the paraffins have any unshared electrons or any orbitals in their valency shells not completely filled 3- No dipole moment between any C-C or C-H
  • 26. Reactions of alkanes Alkanes and cycloalkanes are relatively unreactive compared with organic compounds containing functional groups 1) Halogenation CH4 CH3Cl UV + light other product -The reaction of an alkane with a halogen is a substitution reaction -The halogenation of alkanes take place by a radical mechanism - High temperature is needed Photochemical or thermal halogenation R H + X2 R X + HX
  • 27. Cl Cl UV CH4 Cl CH3 Cl Cl Cl CH3 CH3Cl Cl HCl : light . chlorine radical + . + . . : + + . step 1 step 2 step 3 step 1 (chain initiation) Step 2 and 3 are called (chain propagation) Further substitution reactions H:Cl +  CH2Cl CH2Cl + Cl:Cl + Cl:CH2Cl Cl H:CH2Cl Cl +
  • 28. Chain propagation remain until either 1- All the Cl2 or CH4 is consumed, or 2- the process is terminated by the following reactions: A- the recombination of Cl. Atoms to form Cl2 molecules B- the recombination of the CH3 . to form CH3-CH3
  • 29. Bromine is less reactive toward alkanes than chlorine, but bromine is more selective in the site of attack Br2 Br Br light / 127o + (>99%) (trace) Cl2 Cl Cl light / 25o + (37%) (63%) - Direct iodination is rarely carried out - Flourine is much more reactive than chlorine, is even less selective than chlorine

Editor's Notes

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