1. Carbon Backbone, Nomenclature, Physical & Chemical Properties
Chapter 2
Introduction to
Hydrocabons
Carbon Backbone, Nomenclature, Physical & Chemical Properties

2. HYDROCARBONS
Compounds composed of only carbon and hydrogen atoms (C, H). Each carbon has 4 bonds.
They represent a “backbone” when other “heteroatoms” (O, N, S, .....) are substituted for H. (The heteroatoms give function to the molecule.)
Acyclic (without rings); Cyclic (with rings); Saturated: only carbon-carbon single bonds; Unsaturated: contains one or more carbon-carbon double and/or triple bond

3. HYDROCARBONS
Alkanes contain only single ( ) bonds and have the generic molecular formula: [CnH2n+2]
Alkenes also contain double ( + ) bonds and have the generic molecular formula: [CnH2n]
Alkynes contain triple ( + 2) bonds and have the generic molecular formula: [CnH2n-2]
Aromatics are planar, ring structures with alternating single and double bonds: eg. C6H6

4. Types of Hydrocarbons
Each C atom is tetrahedral with sp3 hybridized orbitals. They only have single bonds.
Organic molecules can be divided into four categories. Alkanes have only single bonds. Alkenes contain a C-C double bond, and alkynes contain a C-C triple bond. Benzene is an example of an aromatic hydrocarbon.
Each C atom is trigonal planar with sp2 hybridized orbitals.
There is no rotation about the C=C bond in alkenes.

5. Types of Hydrocarbons
Each C atom is linear with sp hybridized orbitals.
Organic molecules can be divided into four categories. Alkanes have only single bonds. Alkenes contain a C-C double bond, and alkynes contain a C-C triple bond. Benzene is an example of an aromatic hydrocarbon.
Each C--C bond is the same length; shorter than a C-C bond: longer than a C=C bond.
The concept of resonance is used to explain this phenomena.

6. It is easy to rotate about the C-C bond in alkanes.
Propane
It is easy to rotate about the C-C bond in alkanes.
The structures of propane show that adjacent carbon atoms are able to rotate freely around C-C single bonds.

7. Naming Alkanes C1 - C10 : the number of C atoms present in the chain.
Each member C3 - C10 differs by one CH2 unit. This is called a homologous series.
Methane to butane are gases at normal pressures.
Pentane to decane are liquids at normal pressures.

9. Nomenclature of Alkyl Substituents

10. Examples of Alkyl Substituents

11. Constitutional or structural isomers have the same molecular formula, but their atoms are linked differently. Naming has to account for them.

13. C7H16 can be any one of the following:
A compound can have more than one name, but a
name must unambiguously specify only one compound
C7H16 can be any one of the following:

14. Alkanes (Different types of sp3 carbon atoms)
Primary, 1o, a carbon atom with 3 hydrogen atoms: [R- CH3]
Secondary, 2o, a carbon atom with 2 hydrogen atoms: [R- CH2-R]
Tertiary, 3o, a carbon atom with 1 hydrogen atom: [R-CH- R] R
Quaternary, 4o, a carbon atom with 0 hydrogen atoms: CR4

15. Different Kinds of sp3 Carbons and Hydrogens

16. Nomenclature of Alkanes
1. Determine the number of carbons in the parent hydrocarbon
2. Number the chain so that the substituent gets the lowest
possible number

17. 3. Number the substituents to yield the lowest possible number
in the number of the compound
(substituents are listed in alphabetical order)
4. Assign the lowest possible numbers to all of the substituents

18. 5. When both directions lead to the same lowest number for one
of the substituents, the direction is chosen that gives the lowest
possible number to one of the remaining substituents
6. If the same number is obtained in both directions, the first
group receives the lowest number

19. 7. In the case of two hydrocarbon chains with the same number of
carbons, choose the one with the most substituents
8. Certain common nomenclatures are used in the IUPAC system

21. Cycloalkane Nomenclature
CnH2n
Cycloalkane Nomenclature 26

22. Cycloalkanes
Cycloalkanes are alkanes that contain a ring of three or more carbons.
Count the number of carbons in the ring, and add the prefix cyclo to the IUPAC name of the unbranched alkane that has that number of carbons.
Cyclopentane
Cyclohexane 6

23. Cycloalkanes
Name any alkyl groups on the ring in the usual way. A number is not needed for a single substituent.
CH2CH3
Ethylcyclopentane 6

24. Cycloalkanes
Name any alkyl groups on the ring in the usual way. A number is not needed for a single substituent.
List substituents in alphabetical order and count in the direction that gives the lowest numerical locant at the first point of difference.
CH2CH3
H3C
CH3
3-Ethyl-1,1-dimethylcyclohexane 6

25. For more than two substituents,

26. 2.17 Physical Properties of Alkanes and Cycloalkanes4

27. Crude oil Naphtha Kerosene (bp 95-150 °C) (bp: 150-230 °C) C5-C12
Light gasoline
(bp: °C)
C15-C25
Gas oil
(bp: °C)
Refinery gas
C1-C4
Residue 2

28. Fig. 2.15

29. Example of Intramolecular Forces:
Protein Folding
15-16
Title:
Tertiary Interactions
Caption:
The four distinct interactions that stabilize tertiary protein structures.
Notes:
Note that the disulfide bridge is a covalent bond.
Ion-dipole
(Dissolving)
40-600kJ/mol
10-40kJ/mol
kJ/mol
kJ/mol
700-4,000kJ/mol

30. Intermolecular Forces
Ion-Dipole Forces ( kJ/mol)
Interaction between an ion and a dipole (e.g. NaOH and water = 44 kJ/mol)
Strongest of all intermolecular forces.

31. Ion-Dipole & Dipole-Dipole Interactions:
like dissolves like
Polar compounds dissolve in polar solvents
& non-polar in non-polar

32. Intermolecular Forces
Dipole-Dipole Forces
(permanent dipoles)
Dipole-Dipole Forces
Dipole-dipole forces exist between neutral polar molecules.
Polar molecules need to be close together.
Weaker than ion-dipole forces.
There is a mix of attractive and repulsive dipole-dipole forces as the molecules tumble.
If two molecules have about the same mass and size, then dipole-dipole forces increase with increasing polarity.
5-25 kJ/mol

33. Intermolecular Forces
Dipole-Dipole Forces

34. Boiling Points & Hydrogen Bonding Hydrogen Bonding
Special case of dipole-dipole forces.
By experiments: boiling points of compounds with H-F, H-O, and H-N bonds are abnormally high.
H bonded to an electronegative element : F, O, and N.
H-bonds are strong.
Eg. Ice Floating
Solids are usually more closely packed than liquids;
Therefore, solids are usually more dense than liquids.
However, Ice is an exception due to H-bonding.
Ice (solid) is less dense than water (liquid).
The H-O bond length is 1.0 Å.
The O…H hydrogen bond length is 1.8 Å.
Ice has waters arranged in open, regular hexagons.

35. Hydrogen Bonding
Hydrogen bonds, a unique dipole-dipole (10-40 kJ/mol).

37. Intermolecular Forces
Hydrogen Bonding

38. DNA: Size, Shape & Self Assembly
Views & Algorithms
10.85 Å
10.85 Å
15-23
Title:
Base Pairs
Caption:
Representation of the base pairings of thymine and adenine, and cytosine and guanine, in line as well as ball-and-stick models.
Notes:
Base pairs occur through hydrogen bonding.

39. Intermolecular Forces
London or Dispersion Forces
An instantaneous dipole can induce another dipole in an adjacent molecule (or atom).
The forces between instantaneous dipoles are called London or Dispersion forces ( kJ/mol).
London Dispersion Forces
Weakest of all intermolecular forces.
It is possible for two adjacent neutral molecules to affect each other.
The nucleus of one molecule (or atom) attracts the electrons of the adjacent molecule (or atom); a dipole forms.
London dispersion forces increase as molecular weight increases.
London dispersion forces exist between all molecules.
London dispersion forces depend on the shape of the molecule.

40. van der Waals Forces
The boiling point of a compound increases with the
increase in van der Waals force..and the Gecko!

41. Gecko: toe, setae, spatulae 6000x Magnification
Full et. al., Nature (2000)
5,000 setae / mm2
600x frictional force; 10-7 Newtons per seta
Geim, Nature Materials (2003)
Glue-free Adhesive
100 x 10 6 hairs/cm2
GECKOS tiny tropical lizards are able to run up walls and along ceilings extremely fast, yet they can stick to a sheet of polished glass with only one foot. The secret of their success lies in the rows of tiny hairs on the bottom of their feet. Thousands of these hairs, called setae, are arrayed like the bristles of a toothbrush across a gecko’s toes.
Microscopy reveals that the tip of each seta is divided into hundreds of tiny“spatulae”, each pointing in a different direction and tipped with a cone-shaped structure. This shape suggests a suction mechanism, but suction relies on air pressure—and gecko feet are known to stick to walls even in a vacuum. Robert Full of the University of California, Berkeley, Nature 2000.
Using a tiny micro-electro-mechanical force sensor, they conducted various experiments to measure the stickiness of a single seta. The maximum adhesive force that could be exerted by a single seta had already been estimated, by measuring the total force exerted by a foot and dividing by the number of setae (around 5,000 per square millimetre). But to their surprise, researchers found that a single seta can actually exert ten times as much force as this. Setae are, in other words, even stickier than expected—giving thegecko a surprisingly large safety margin.adhesive force is about 600 times greater than the simple frictional force between lizard skin and the surface. And a seta will stick to a surface most firmly if it is first pushed into the surface and then pulled along it by a few millionths of a metre. These findings suggest that setae operate at a molecular level, and exploit intra-molecular forces, called van der Waals forces, for their stickiness.
They detach by curling up the tips of their toes before moving, forming a sort of reverse fist. This allows them to peel their feet off the surface gently at a critical angle without damage, much like peeling a sticky label off a jar withot tearing it. The researchers found that setae reliably detach from the surface at an angle of about 30°.

42. Boiling Points of Alkanes
governed by strength of intermolecular attractive forces
alkanes are nonpolar, so dipole-dipole and dipole-induced dipole forces are absent
only forces of intermolecular attraction are induced dipole-induced dipole forces 6

43. Induced dipole-Induced dipole Attractive Forces+ – + –
two nonpolar molecules
center of positive charge and center of negative charge coincide in each 5

44. Induced dipole-Induced dipole Attractive Forces+ – + –
movement of electrons creates an instantaneous dipole in one molecule (left) 5

45. Induced dipole-Induced dipole Attractive Forces– + + –
temporary dipole in one molecule (left) induces a complementary dipole in other molecule (right) 5

46. Induced dipole-Induced dipole Attractive Forces– – + +
temporary dipole in one molecule (left) induces a complementary dipole in other molecule (right) 5

47. Induced dipole-Induced dipole Attractive Forces– – + +
the result is a small attractive force between the two molecules 5

48. Induced dipole-Induced dipole Attractive Forces– – + +
the result is a small attractive force between the two molecules 5

49. Boiling Points Increase with increasing number of carbons
more atoms, more electrons, more opportunities for induced dipole-induced dipole forces
Decrease with chain branching
branched molecules are more compact with smaller surface area—fewer points of contact with other molecules 8

50. Intermolecular Forces
London Dispersion Forces
Which has the higher
attractive force?

51. Boiling Points Increase with increasing number of carbons
more atoms, more electrons, more opportunities for induced dipole-induced dipole forces
Heptane bp 98°C
Octane bp 125°C
Nonane bp 150°C 8

52. 2,2,3,3-Tetramethylbutane: bp 107°C
Boiling Points
Decrease with chain branching
branched molecules are more compact with smaller surface area—fewer points of contact with other molecules
Octane: bp 125°C
2-Methylheptane: bp 118°C
2,2,3,3-Tetramethylbutane: bp 107°C 8

53. 2.18 Chemical Properties: Combustion of Alkanes
All alkanes burn in air to give carbon dioxide and water. 10

54. Heats of Combustion Heptane 4817 kJ/mol 654 kJ/mol Octane 5471 kJ/mol
Nonane
6125 kJ/mol
What pattern is noticed in this case? 11

55. Heats of Combustion Increase with increasing number of carbons
more moles of O2 consumed, more moles of CO2 and H2O formed 8

56. Heats of Combustion 5471 kJ/mol 5 kJ/mol 5466 kJ/mol 8 kJ/mol
What pattern is noticed in this case? 13

57. Figure 2.17 5471 kJ/mol 5466 kJ/mol 25 + O2 5458 kJ/mol 2 5452 kJ/mol
8CO2 + 9H2O 14

58. Heat of Combustion Patterns
Increase with increasing number of carbons
more moles of O2 consumed, more moles of CO2 and H2O formed
Decrease with chain branching
branched molecules are more stable (have less potential energy) than their unbranched isomers 8

59. Important Point
Isomers can differ in respect to their stability.
Equivalent statement:
Isomers differ in respect to their potential energy.
Differences in potential energy can be measured by comparing heats of combustion. (Worksheet problems) 12

60. 2.19 Oxidation-Reduction in Organic Chemistry
Oxidation of a carbon atom corresponds to an increase in the number of bonds to the carbon atom and/or a decrease in the number of hydrogens bonded to the carbon atom. See examples on the board. 15

61. increasing oxidation state of carbonOH HO O C OH H
increasing oxidation state of carbon O C H H C OH H C -4 -2 +2 +4 16

62. increasing oxidation state of carbonHC CH
increasing oxidation state of carbon C H C H -3 -2 -1 16

63. But most compounds contain several (or many) carbons, and these can be in different oxidation states.
CH3CH2OH
C2H6O 18

64. Working from the molecular formula gives the average oxidation state.
But most compounds contain several (or many) carbons, and these can be in different oxidation states.
Working from the molecular formula gives the average oxidation state.
CH3CH2OH
C2H6O
Average oxidation state of C = -2 18

65. How can we calculate the oxidation state of each carbon in a molecule that contains carbons in different oxidation states?
CH3CH2OH
C2H6O
Average oxidation state of C = -2 18

66. Table 2.5 How to Calculate Oxidation Numbers
1. Write the Lewis structure and include unshared electron pairs. •• 21

67. Table 2.5 How to Calculate Oxidation Numbers
• • ••
2. Assign the electrons in a covalent bond between two atoms to the more electronegative partner. 21

68. Table 2.5 How to Calculate Oxidation Numbers
• • ••
3. For a bond between two atoms of the same element, assign the electrons in the bond equally. 21

69. Table 2.5 How to Calculate Oxidation Numbers
• • •• •
3. For a bond between two atoms of the same element, assign the electrons in the bond equally. 21

70. Table 2.5 How to Calculate Oxidation Numbers
• • •• •
4. Count the number of electrons assigned to each atom and subtract that number from the number of valence electrons in the neutral atom; the result is the oxidation number.
Each H = +1
C of CH3 = -3
C of CH2O = -1 O = -2 21

71. Generalization
Oxidation of carbon occurs when a bond between carbon and an atom which is less electronegative than carbon is replaced by a bond to an atom that is more electronegative than carbon. The reverse process is reduction. C
oxidation C X Y
reduction
X less electronegative than carbon
Y more electronegative than carbon 20

72. Examples CH3Cl HCl CH4 Cl2 + Oxidation + 2Li LiCl CH3Cl CH3Li
Reduction 21

73. Functions, Nomenclature,
Chapter 4
Alcohols & Halides
Functions, Nomenclature,

74. Common Functional Groups
Class General Formula
Halohydrocarbons RX
Alcohols R
Ethers RR
Amines

75. Nomenclature of Alkyl Halides
In the IUPAC system, alkyl halides are named as substituted
alkanes

76. Structures of Alkyl Halides

77. Different Kinds of Alkyl Halides

78. Nomenclature of Ethers
???
As substituents:

80. Structures of Alcohol and Ether

81. Nomenclature of Alcohols
In an alcohol, the OH is a functional group
A functional group is the center of reactivity in a
molecule
1. Determine the parent hydrocarbon containing the functional
group

82. 2. The functional group suffix should get the lowest number
3. When there is both a functional group suffix and a substituent,
the functional group suffix gets the lowest number

83. 4. If there is more than one substituent, the substituents are cited
in alphabetical order

86. Nomenclature of Amines
The substituents are listed in alphabetical order and a number or
an “N” is assigned to each one

87. Structures of Amines

88. Naming Quaternary Ammonium Salts

89. Other Common Functional Groups
Class General Formula
Aldehydes
Ketones
Carboxylic Acids
Esters
Amides

90. Dipole–dipole interaction
Attractive Forces
Ionic bonds
Covalent bonds
Hydrogen bonds
Dipole–dipole interaction
Ion-dipole
Dispersion
Forces
van der Waals force
The greater the attractive intermoleclar forces between molecules, the higher is the boiling point of the compound, eg. water.

91. Protein Shape: Forces, Bonds, Self Assembly,
Folding (Intramolecular forces)
15-16
Title:
Tertiary Interactions
Caption:
The four distinct interactions that stabilize tertiary protein structures.
Notes:
Note that the disulfide bridge is a covalent bond.
Ion-dipole
(Dissolving)
40-600kJ/mol
10-40kJ/mol
kJ/mol
kJ/mol
700-4,000kJ/mol

92. A hydrogen bond is a special kind of dipole–dipole
interaction

93. Dipole–Dipole Interaction
Dipole–dipole interactions are stronger than van der
Waals force but weaker than ionic or covalent bonds

94. van der Waals Forces
The boiling point of a compound increases with the
increase in van der Waals force

96. Ion-Dipole & Dipole-Dipole Interactions:
like dissolves like
Polar compounds dissolve in polar solvents
& non-polar in non-polar

97. Chapter 3
Alkanes & Cycloalkane
Conformations

98. Conformations of Alkanes: Rotation about Carbon–Carbon Bonds

99. Conformational Analysis Drawing Acyclic Molecules
Newman Projections

100. Conformational Analysis Drawing Acyclic Molecules
Sawhorse Drawings

101. Different Conformations of Ethane
A staggered conformer is more stable than an eclipsed
conformer
Torsional strain: repulsion between pairs of bonding
electrons

102. Conformations of n-Butane
Steric strain: repulsion between the electron clouds of
atoms or groups

103. Cycloalkanes: Ring Strain
Angle strain results when bond angles deviate from the
ideal 109.5° bond angle

104. The Shapes of Cycloalkanes: Planar or Nonplanar?1

105. Adolf von Baeyer (19th century)
Assumed cycloalkanes were planar polygons.
Believed distortion of bond angles from 109.5° gives angle strain to some cycloalkanes.
One for two is great in baseball. 2

106. Types of Strain
• Torsional strain strain that results from eclipsed bonds (measure of the dihedral angle)
• Van der Waals strain or (Steric strain) strain that results from atoms being too close together.
• Angle strain results from distortion of bond angles from normal values, for a tetrahedron 109.5o 3

107. Measuring Strain in Cycloalkanes
Heats of combustion can be used to compare stabilities of isomers.
But cyclopropane, cyclobutane, etc. are not isomers.
All heats of combustion increase as the number of carbon atoms increase. 4

108. Measuring Strain in Cycloalkanes
Therefore, divide heats of combustion by number of carbons and compare heats of combustion on a "per CH2 group" basis. 4

109. Heats of Combustion in Cycloalkanes
Cycloalkane kJ/mol Per CH2
Cyclopropane 2,
Cyclobutane 2,
Cyclopentane 3,
Cyclohexane 3,
Cycloheptane 4,
Cyclooctane 5,
Cyclononane 5,
Cyclodecane 6, 4

110. Heats of Combustion in Cycloalkanes
Cycloalkane kJ/mol Per CH2
According to Baeyer, cyclopentane should
have less angle strain than cyclohexane.
Cyclopentane 3,
Cyclohexane 3,
The heat of combustion per CH2 group is
less for cyclohexane than for cyclopentane.
Therefore, cyclohexane has less strain than
cyclopentane. 4

111. Conformations of Cyclohexane
Heat of combustion suggests that angle strain is unimportant in cyclohexane.
Tetrahedral bond angles require nonplanar geometries.
The chair and boat conformations. 5

112. 6

113. The chair conformation of cyclohexane is free of strain

114. Chair is the most stable conformation of cyclohexane
All of the bonds are staggered and the bond angles at carbon are close to tetrahedral. 6

115. Boat conformation is less stable than the chair
180 pm
All of the bond angles are close to tetrahedral but close contact between flagpole hydrogens causes strain in boat. 6

116. Boat conformation is less stable than the chair
Eclipsed bonds bonds gives torsional strain to boat. 6

117. Skew boat is slightly more stable than boat
Skew or Twist Boat
Less van der Waals strain and less torsional strain in skew boat. 6

118. Generalization
The chair conformation of cyclohexane is the most stable conformation and derivatives of cyclohexane almost always exist in the chair conformation 2

119. Axial and Equatorial Bonds in Cyclohexane11

120. Drawing Cyclohexane

121. The 12 bonds to the ring can be divided into two sets of 6.

122. 6 Bonds are axial
Axial bonds point "north and south" 12

123. The 12 bonds to the ring can be divided into two sets of 6.

124. 6 Bonds are equatorial
Equatorial bonds lie along the equator 12

125. Conformational Inversion (Ring-Flipping) in Cyclohexane16

126. Conformational Inversion
chair-chair interconversion (ring-flipping)
rapid process (activation energy = 45 kJ/mol)
all axial bonds become equatorial and vice versa 17

127. 18

128. Half- chair 18

129. Half- chair
Skew boat 18

130. Half- chair
Skew boat 18

131. Half- chair
Skew boat 18

132. 45 kJ/mol
45 kJ/mol
23 kJ/mol 18

133. The Conformations of Cyclohexane
and Their Energies

134. Conformational Analysis of Monosubstituted Cyclohexanes
most stable conformation is chair
substituent is more stable when equatorial 19

135. Steric Strain of 1,3-Diaxial Interaction in Methylcyclohexane

136. Methylcyclohexane axial CH3 CH3 equatorial 5% 95%
Chair chair interconversion occurs, but at any instant 95% of the molecules have their methyl group equatorial.
An axial methyl group is more crowded than an equatorial one. 20

137. Methylcyclohexane 5%
95%
Hydrogen atoms closer than 2.4 Angstroms will cause steric strain.
This is called a "1,3-diaxial repulsion" a type of van der Waals strain or Steric strain. 20

138. Fluorocyclohexane F F 40% 60%
Crowding is less pronounced with a "small" substituent such as fluorine.
Size of substituent is related to its branching. 20

139. tert-Butylcyclohexane
C(CH3)3
C(CH3)3
Less than 0.01%
Greater than 99.99%
Crowding is more pronounced with a "bulky" substituent such as tert-butyl.
tert-Butyl is highly branched. 20

140. tert-Butylcyclohexane
van der Waals strain due to 1,3-diaxial repulsions 24

141. The larger the substituent on a cyclohexane ring, the
more the equatorial substituted conformer will be
favored
Keq = [equatorial conformer]/[axial conformer]

142. Disubstituted Cyclohexanes Cis-trans Isomerism16

143. Cyclic Alkanes Stereochemistry Cis -Trans Isomers

144. The Chair Conformers of cis-1,4-Dimethylcyclohexane

145. 1,2-disubstituted-cis-cyclohexane Stereochemistry
axial
equatorial

146. Cyclohexane Stereochemistry Drawings: Cis isomers & the need for perspective
Are the methyl groups axial or equatorial?
What is the actual conformational shape of the cyclohexane ring?

147. The Chair Conformers of trans-1,4-Dimethylcyclohexane

148. Cyclohexane Stereochemistry Trans isomers

149. 1-tert-Butyl-3-Methylcyclohexane

150. Cyclohexane Stereochemistry Cis -Trans Isomers
e,e or a,a a,e or e,a
e,a or a,e e,e or a,a
Complete the Table: a = axial; e = equatorial

151. Conformations of Fused Rings
Trans-fused cyclohexane ring is more stable than
cis-fused cyclohexane ring