Download FUNCTIONAL GROUPS ORGANIC COMPOUNDS CONTAINING

BIO-ORGANIC CHEMISTRY
(Organic Chemistry for Biology Students)
(SQBS 1603)
Organic Compounds Containing
Oxygen
Dr Nik Ahmad Nizam Bin Nik Malek,
BSc (Ind. Chem.)(UTM), MSc (Chem)(UTM), PhD (Chem)(UTM), A.M.I.C
Senior Lecturer,
Department of Biotechnology and Medical Engineering
Faculty of Biosciences and Medical Engineering
Physical properties of the alkanes
Alkanes are insoluble in
water
The alkanes have few direct
roles in biological systems
Biological systems are
aqueous (water based)
Adding functional groups
2
What is functional group?
Molecules possessing the
same functional group
belong to the same family of
organic compounds.
The chemical components that
are added to the simple
skeleton of an organic
compound.
To generate chemical diversity
and functionality.
Hydrocarbon
Groups containing oxygen
Groups containing nitrogen
Groups containing phosphorus
and sulfur
3
Amines
Amides
Thiols
phosphate
functional groups
Alcohol
Ethers
Ketone
Aldehyde
Esters
Carboxylic
acids
Functional groups
Biological importance of functional group
Functional group
Alcohol
Ethers
Ketone
Aldehyde
Carboxylic acids
Ester
Amines
Amides
Thiol
Phosphate
Biological importance
Lipids, carbohydrates
Archael plasma membranes
Metabolic intermediates
Reducing sugars such as glucose
Lipids, proteins
Bacterial and eukaryotic plasma membranes
Proteins, nucleic acids DNA and RNA
Proteins, nucleic acids DNA and RNA
Protein structure, Energy metabolism
ATP, DNA
5
Functional groups
Groups containing oxygen
Chemical
class
Group
Formula
Alcohol
Hydroxyl
ROH
Ketone
Aldehyde
Carbonyl
RCOR'
Aldehyde RCHO
Structural
Formula
Prefix
Suffix
hydroxy-
-ol
keto-, oxo-
aldo-
-one
-al
Example
Methanol
Methyl ethyl
ketone
(Butanone)
Acetaldehyde
(Ethanal)
Functional groups
Groups containing oxygen
Chemical
class
Carboxylate
(Carboxylic
acid)
Group
Formula
Structural
Formula
Prefix
Suffix
Example
Acetic acid
Carboxyl RCOOH
Esters
Ester
RCOOR'
Ethers
ether
ROR
Carboxy-
-oic acid
Ethyl butyrate
alkyl
(Ethyl butanoate)
alkanoate
Di-
-ether
Diethyl ether
7
Functional groups
Groups containing nitrogen
Chemical
class
Group
Formula
Structural
Formula
Prefix
Suffix
Example
Dimethylamine
Amines
Amino
RNH2
R2NH
R3N
amino-
-amine
Acetamide
Amide
Amide
RCONH2
RCONHR’
RCONR2
Carboxamide- -amide
Functional groups
Groups containing sulphur and phosporus
Chemical
class
Thiol
Group
Sulfhydryl
Formula
RSH
Structural
Formula
Prefix
MercaptoSulfanyl-
Suffix
-thiol
Example
Ethanathiol
(Ethyl
mercaptan)
Glyceraldehyde
3-phosphate
Phosphate
phoshate
ROP(=O)(OH)2
phospho-
9
Alcohol
• Alcohol
– Hydroxyl group : -OH functional group
– Generic formula: R-OH
– General structure
R
O
H
Alcohol
• Classification
C
C
Hydroxyl
group
H
R'
H
R
O
O
H
Primary (1)
H
R
C
R'
O
H
Secndary (2)
H
R
C
O
H
R''
Tertiary (3)
11
Naming Alcohols
CH3
OH
OH
H3C
H2
C
C
H
H2
C
C
H
CH3
C : 6  hexane  hexanol
Methyl at C5
CH3
H3C
C
H
6
5
OH
H2
C
C
H
H2
C
CH3
5-methyl-3-hexanol
4
3
2
1
12
Naming Alcohols
• Give the IUPAC name of the following alcohol
2
Methyl at C3
H3C
OH
3
1
4
6
5
C : 6  cyclohexane  cyclohexanol
3-methyl-cyclohexanol
13
Naming Alcohols
OH
OH
HO
Ethanol
-diol
IUPAC name: 1,2-ethanediol or Ethane-1,2-diol
Common name: ethylene glycol
14
Reactions of alcohol
• Dehydration
• Oxidation
15
Dehydration
• Loss of water (H2O)
• Elimination reaction
– Elements of the starting material are lost and a new
multiple bond is formed
H2SO4
C
C
H
OH
C
C
alkene
H2O is lost
H2O
Dehydration
• Examples
H
H
H
C
C
H
OH
H
H2SO4
H
H
C
C
H
H2O
H
Ethene
Ethanol
OH
H2SO4
H2O
H
Cyclohexanol
Cyclohexene
17
Dehydration
• Zaitsev rule
– The major product in elimination is the alkene that has
more alkyl groups bonded to it.
H
H
H
C
C
H
OH
CH2CH3
H2SO4
H
CH2CH3
C
H
H
But-1-ene
Butan-2-ol
H
H3C
C
H
C
C
CH3
OH H
Butan-2-ol
H2SO4
H3C
CH3
C
C
H
H
But-2-ene
Major
product
18
Oxidation
• Primary (1) alcohols
– Oxidized to aldehydes (RCHO)
– And further oxidized to carboxylic acids (RCOOH)
O
OH
[O]
[O]
R
C
C
H
R
H
H
alcohol
O
aldehyde
C
R
OH
Carboxylic
acid
19
Oxidation
• Secondary (2) alcohols
– Oxidized to ketones (R2CO)
O
OH
[O]
R
C
C
H
R
R'
R'
alcohol
ketones
20
Oxidation
• Tertiary(3) alcohols
– They are not oxidized
OH
R
C
R''
R'
21
Physical properties of alcohols
H
H
H
H
H
C
C
H
C
C
H
H
H
H
H
C
H
H
C
C
H
H
H
C
C
H
H
H
H
OH
C
H
H
H
hydroxyl group  oxygen + hydrogen  highly
electronegative atom  polar molecules
22
Physical properties of alcohols
hydroxyl group  oxygen + hydrogen
highly
electronegative
atom
polar
molecules
hydrogen
bonding
Strong non-covalent forces
Exhibit higher melting and boiling
points than alkanes
dipolar
interaction
dispersion
forces
soluble in
water in
small
quantity
23
Physical properties of alcohols
Ethanol
3HC
Low electron density
H2
C
-
O
Electron pulls towards
highly electronegative
oxygen atom
+
H
3HC
H2
C
high electron density
-
+
O
H
The distribution of electrons within
the molecules is unequal
The molecule is polar
24
Physical properties of alcohols
hydrogen bonding
O
H
H
H2
C
H3C
H
O
O
H
H
Ethanol is
attracted to the
water molecules
through
hydrogen bonds
O
H
H
25
Ether
– Alkoxy group : combination of an alkyl group
and oxygen atom (alkyl + oxygen = alkoxy)
– Generic formula: R-O-R’
– Similar to alcohol (hydroxyl group), except
that the H atom is replaced with an alkyl
group
O
R
O
H
Hydroxyl group
R
R'
Alkoxyl group
26
Ether
R
O
R groups are the
same
H3CH2C
O
R
H3C
CH2CH3
O
CH2CH3
R groups are
different
27
Naming Ether
Simple ethers: Usually assigned common names
O
Methyl-
O
Ethyl-
Ethyl methyl ether
(methoxy-ethane)
Ethyl-
Ethyl-
diethyl ether
(ethoxy-ethane)
28
Naming Ether
More complex ethers: IUPAC name
H3C
O
Methoxy-
H3CH2C
O
Ethoxy-
29
Naming Ether
6
8
9
7
9 C  nonane
5
2
4
3
1
O
H3CH2C
O
Ethoxy- at
position 3
3-ethoxy-nonane
30
Physical properties of ethers
Presence of oxygen  polar molecules
O
H3C
CH3
Two polar bonds
31
Aldehydes and Ketones
O
Carbonyl
group
Carbonyl carbon
C
O
O
Aldehyde
Ketone
C
R
32
C
H
R
R
Aldehydes and Ketones
O
O
Aldehyde
Ketone
C
C
R
O
O
C
H3C
H
H
Acetaldehyde
C
R
R
O
O
C
C
H
O
C
H3C
CH3
Propan-2-one
33
Naming aldehydes
IUPAC name
O
4 C  butane  butanal
H
CH3
4
H3 C
CH
3
O
2
CH
C
1
CH3
2,3-dimethylbutanal
34
Methyl  at 2 and 3 
dimethyl
H
Naming aldehydes
• Simple aldehydes have common names
that are widely used
• Examples:
O
O
O
C
H
C
C
H
H
Formaldehyde
35
H3C
H
Acetaldehyde
Benzaldehyde
Naming Ketones
IUPAC name
O
5 C  pentane  pentanone
C
O
1
H3C
C
2
3
CH
H3C
3-methyl-2-pentanone
36
H2
C
4
CH3
5
Carbonyl  position 2
Methyl  position 3
Naming Ketones
• Common names for ketones:
– Naming both alkyl group on the carbonyl
carbon.
– Arranging them alphabetically.
– Finally, adding the word ketone.
O
O
methyl
ethyl
C
H3C
CH2CH3
IUPAC name: 2-butanone
37
C
H3C
CH2CH3
common name:
Ethyl methyl ketone
Physical properties of aldehydes and
ketones
Presence of oxygen  polar molecules
Ether
Aldehyde
ketone
-
-
O
O
H3C
CH3
C
R
Two polar bonds
Electrons
O
pulled
towards
highly
C
electrone
H
R
gative
oxygen
atom
…….generating an uneven
distribution of electron: polar
38
molecule
R
Reactions of aldehydes and ketones
1. Oxidation of aldehydes
O
O
[O]
C
R
C
H
R
Aldehyde
OH
Carboxylic acid
2. Reduction of aldehydes and ketones
(addition reaction)
C
39
O
X
Y
C
O
X
Y
Oxidation of aldehydes
• Examples
O
H3CH2CH2C
O
K2CrO7
C
H3CH2CH2C
C
H
OH
Butyraldehyde
Butyric acid
• How about ketones?
O
H3CH2C
K2CrO7
C
No Reaction
CH3
40
Butan-2-one
Reduction of aldehydes and ketones
(addition reaction)
• Reduction
– Decrease in the number of C-O
– Increase in the number of C-H bonds
• The conversion of a carbonyl group (C=O) to an alcohol is
a reduction.
– The starting material has more C-O bonds than the
product
C
41
O
X
Y
C
O
X
Y
Reduction of aldehydes and ketones
(addition reaction)
• Aldehydes
– Reduce to primary (1) alcohol
H
O
[H]
R
C
R
H
Aldehyde
H
H
H
[H]
H3C
C
H
Acetaldehyde
42
O
primary alcohol
O
H3C
C
C
O
H
H
Ethanol
(CH3CH2OH)
Reduction of aldehydes and ketones
(addition reaction)
• Ketones
– Reduce to secondary (2) alcohol
H
O
[H]
R
C
R
R'
ketone
R'
H
Secondary
[H]
H3C
C
CH3
Propan-2-one
43
O
H
O
H3C
C
C
O
CH3 H
Propan-2-ol
((CH3)2CHOH)
Acetal formation
• Aldehydes and ketones undergo
addition reaction with alcohols to
form hemiacetals and acetals.
R'-OH
O
R
C
R
H (or R)
Aldehyde or ketone
H2SO4
O
H
C
OR'
H (or R)
hemiacetal
1 C is bonded to:
-One OH group
-One OR group
44
OR''
R''-OH
R
H2SO4
C
OR'
H (or R)
acetal
1 C is bonded to:
-two OR group
Acetal formation
• Example
CH3CH2OH
O
H2SO4
Propionaldehyde
CH3CH2OH
H3C
H2SO4
CH3
H2SO4
H
1-Ethoxy-propan-1-ol
1,1-Diethoxy-propane
hemiacetal
acetal
O H
CH3CH2OH
O CH2CH3
Ethanol
H3C C OCH2CH3
H3C C OCH2CH3
Propan-2-one
45
H
Ethanol
C
O CH2CH3
H3CH2C C OCH2CH3
H3CH2C C OCH2CH3
H
O
CH3CH2OH
Ethanol
Ethanol
C
H3CH2C
O H
CH3
2-Ethoxy-propan-2-ol
hemiacetal
H2SO4
CH3
2,2-Diethoxy-propane
acetal
Cyclic hemiacetals
1 C is bonded to:
-One OH group
-One OR group
OH
OH
OH
R C OR
O
H (or R)
O
1 C is bonded to:
-One OH group
-An OR group that is part of a ring
46
Cyclic hemiacetals
• Formation of cyclic hemiacetals
– Intramolecular reaction of a compound
that contain both a hydroxyl group (-OH)
and aldehyde or ketone.
O
O
5 4 3 2
HOH2CH2CH2CH2C
C
1
5-Hydroxy-pentanal
47
2
H
OH
1
H
2
OH
3
4
5
1
3
4
O
5
Carboxylic Acids
• Carboxyl group: Combining the
hydroxyl and carbonyl.
• Generic formula: RCOOH or RCO2H
O
carbonyl
C
R
48
OH
hydroxyl
Naming Carboxylic acids
• IUPAC system  suffix –oic acid
O
6 C  hexane 
hexanoic acid
OH
CH3
6
H3
C
CH
5
O
4
CH
CH3
4,5-dimethylhexanoic acid
49
H2
C
2
3
C
H2
C
1
OH
2 methyl at
position 4 and 5
 4,5-dimethyl-
Naming Carboxylic acids
• Many simple carboxylic acids are often
referred to by their common names.
O
O
O
C
C
C
H
50
OH
H3C
OH
OH
Formic acid
Acetic acid
IUPAC name:
methanoic acid
IUPAC name:
ethanoic acid
Benzoic acid
IUPAC name:
benzenecarboxylic
acid
Physical properties of carboxylic acids
2 oxygen
atoms
O
C
R
O
H
2 very electronegative atoms
attach with each other
51
Physical properties of carboxylic acids
O
• Polarity?
C
H
R
O
• Dipolar interaction?
• Hydrogen bonding between molecules
of same compound?
• Hydrogen bonding with water?
• Solubility in water?
• Boiling point?
52
Physical properties of carboxylic acids
Presence of oxygen + hydrogen
(carbonyl and hydroxyl group)  polar molecules
O
O
C
R
O
H
O
C
O
O
C
53
O
H
H
O
C
R
R
R
O
H
Hydrogen bonding
between molecules of
same compound
C
R
O
H
Physical properties of carboxylic acids
• Hydrogen bonding with water?
• Solubility in water?
H
H
H
H
O
O
O
C
R
O
H
H
H
O
54
The acidity of carboxylic acids
O
O
C
R
H3O
H2O
O
C
H
R
carboxylic acid
carboxylate anion
O
O
H3O
H2O
C
H3C
O
O
Acetic acid
H
C
H3C
O
Acetic acid anion
acetate
55
Reaction with bases
O
C
H3C
O H
Acetic acid
O
H-OH
NaOH
C
H3C
+
O Na
Sodium acetate
Carboxylate
anions
56
Carboxylate anions
O
O
NaOH
or
C
O
C
O
KOH
H
Na+ or
K+
Hexanoic acid
Carboxylate anions:
sodium or potasium hexanoate
Name of the
metal cation
(e.g: sodium)
+
Parent
(e.g. hexane)
+
-ate (suffix)
57
Conversion of carboxylic acids to
esters and amides
H2SO4
O
Formation
of ester
O
H-OR'
C
R
O H
Carboxylic acid
R
alcohol

C
O H
Carboxylic acid
R
O
H-NH2
R
O
ester
O
Formation
of amide
H-OH
C
ammonia
H-OH
C
R
NH2
amide
58
Esters
• A modified carboxyl group
• Generic formula: RCOOR’
OH and H
combined to form
H2O
O
Carboxylic
acid
C
R
H
O
H
O
R'
alcohol
O
O
C
R
O
R'
C
O
R
59
O
R'
Naming esters
• IUPAC system  suffix –ate
• Two parts
1. Name the acyl group (RCO-) by changing the –ic ending of
the parent carboxylic acid to the suffix –ate.
2. Name the R’ group bonded to the oxygen atom as an alkyl
group.
O
Acyl group
C
R
60
O
R'
Alkyl group
Naming esters
O
4 C  butanoic acid
 butanoate
O
O
H2
C
H3C
C
C
H2
Methyl butanoate
61
CH3
O
R’ = methyl
Physical properties of esters
O
O
OH
Carboxylic
acid
62
O
ester
Physical properties of esters
• Polarity?
• Dipolar interaction?
• Hydrogen bonding between molecules
of same compound?
• Hydrogen bonding with water?
O
• Solubility in water?
• Boiling point?
O
63
Ester formation from carboxylic
acids
• Substitution
– All acyl (RCO) compounds.
O
O
H-Y
C
R
Z = OH, OR', NR'2
64
R
Z
Y replaces Z
H-Z
C
Y
Y=OH, OR', NR2'
Ester formation
• Fischer esterification
– Treatment of carboxylic acid (RCOOH) with an
alcohol (R’OH) in the presence of an acid catalyst
forms an ester (RCOOR’).
– example
O
O
H-OCH2CH3
C
H3C
OH
Acetic acid
65
H-OH
C
H3C
OCH2CH3
ethyl acetate
REFERENCES
• Crowe, J., Bradshaw, T. and Monk, P. (2006), Chemistry for the
Biosciences: The Essential Concepts, Oxford University Press,
Oxford.
• Horton, H.R., Moran, L.A., Scrimgeour, K.G., Perry, M.D. and
Rawn J.D. (2006). Principles of Biochemistry, 4th Edition.
Pearson International Edition.
• Smith, J.G. (2010). General, Organic and Biological Chemistry.
McGraw-Hill Higher Education.
• Denniston, K.J., Toping, J.J. and Caret, R.L. (2008). General,
Organic and Biochemistry, 6th edition. McGraw-Hill Higher
Education.
MY PROFILE
Dr Nik Ahmad Nizam Bin Nik Malek,
BSc (Ind. Chem.)(UTM), MSc (Chem)(UTM), PhD (Chem)(UTM), A.M.I.C
Senior Lecturer,
Department of Biotechnology and Medical Engineering,
Faculty of Biosciences and Medical Engineering,
Universiti Teknologi Malaysia.
Email: [email protected], [email protected]
Website: http://www.staff.blog.utm.my/niknizam/