Chemistry 2100

Fall 2011

Bloom’s Taxonomy

Richard C. Overbaugh, Lynn SchultzOld Dominion University

Student Objectives for this course

• Analyze and explain chemical differences among the various classes of organic compounds

• Evaluate carbohydrate structure and reactivity• Compare and contrast the four main classes of key

biomolecules• Explain the processes of protein folding and

enzymatic catalysis• Use knowledge of replication, transcription, and

translation to predict the outcome of genetic diseases

• Relate biochemical concepts to digestion, metabolism, and nutrition

Organic & Biological Chemistry

VIIAVIAVA IVAIIIA

IIBIBVIIBVIBVBIVBIIIBMg

24.31

12

O16.00

8Ne20.18

10F19.00

9N14.01

7B10.81

5Be9.012

4Li6.941

3

He4.003

2

IA

1

2

3

4

5

6

7

IIA

VIIIA

VIIIB Na22.99

11

H1.008

1

Al26.98

13Si28.09

14P30.97

15S32.07

16Cl35.45

17Ar39.95

18

K39.10

19 20

40.08Ca

21

44.96Sc

22

47.88Ti V

50.94

23 24

52.00Cr

25

54.94Mn

26

55.85Fe

27

58.93Co

28

58.69Ni

29

63.55Cu

30

65.38Zn

31

69.72Ga

32

72.59Ge

33

74.92As

34

78.96Se

35

79.90Br

36

83.80Kr

37

85.47Rb

38

87.62Sr Y

88.91

39 40

91.22Zr

41

92.91Nb

42

95.94Mo

43

(98)Tc

44

101.1Ru

45

102.9Rh

46

106.4Pd

47

107.9Ag

48

112.4Cd

49

114.8In

50

118.7Sn

51

121.8Sb

52

127.6Te I

126.9

53 54

131.3Xe

55

132.9Cs

56

137.3Ba

57

138.9La

58

140.1Ce

59

140.9Pr

60

144.2Nd

61

(145)Pm

62

150.4Sm

63

152.0Eu

64

157.3Gd

65

158.9Tb

66

162.5Dy

67

164.9Ho

68

167.3Er

69

168.9Tm

70

173.0Yb

71

175.0Lu

72

178.5Hf

73

180.9Ta W

183.9

74 75

186.2Re

76

190.2Os

77

192.2Ir

78

195.1Pt

79

197.0Au

80

200.6Hg

81

204.4Tl

82

207.2Pb

83

209.0Bi

84

(209)Po

85

(210)At

86

(222)Rn

87

(223)Fr

88

(226)Ra

89

(227)Ac

104

(261)Rf

105

(262)Db

106

(263)Sg

107

(262)Bh

108

(265)Hs

109

(266)Mt

110

(269)Uun

111

(272)Uuu

112

(277)Uub

114

(289)Uuq

116

(289)Uuh

118

(293)Uuo

90

232.0Th

91

(231)Pa U

238.0

92 93

(238)Np

94

(244)Pu

95

(243)Am

96

(247)Cm

97

(247)Bk

98

(251)Cf

99

(252)Es

100

(257)Fm

101

(258)Md

102

(259)No

103

(260)Lw

C6

12.01

C

General Chemistry

H 1 0

C 4 0

N 3 1

O 2 2

X 1 3

element covalent bonds lone pairs

~109.5°

H

CH

H

H

x

x

x

C HxH

H

H

Valence Shell Electron Pair Repulsion Theory

4 tetrahedral 109.5°

3 trigonal planar 120°

2 linear 180°

regions of predicted predicted electron density geometry bond angles

~109.5°

• •

C N

H

HH

H

H

CC

H

HH

H

120° C CH H

180°

NC

HH

H••

120°

Meet the Elements

http://www.youtube.com/watch?v=Uy0m7jnyv6U

English LanguageCursive

Print

Shorthand

Type

The language of Chemistry

O HC

H

C

H

H

H

H OH

Molecular Formula

C2H6O

Structural Formula

Condensed Structural Formula

CH3CH2OH

3D Structural Formula

Molecular Representation

Skeletal, line-angle Formula

O H

H

H

H

H

H

or

Alkanes

• Simplest hydrocarbons• Composed of only single bonds• Often referred to as aliphatic

hydrocarbons– From Greek aleiphar (fat or oil)

• Also called Paraffins– From Latin parum affinis (barely reactive)

• General formula: CnH2n+2

Methane & Ethane

H-C-HH

HH-C-C-H

H

H

H

H

Methane Ethane

Propane & Butane

C

H

H

H

C

H

H

C

H

H

H

CH3CH2CH2CH3CH3CH2CH3 CH3CH2CH2CH2CH3CH3CH2CH2CH3CH3CH2CH3 CH3CH2CH2CH2CH3PentaneButanePropane PentaneButanePropane

Condensedstructural

formula

Line-angleformula

Ball-and-stick model

C

H

H

H

C

H

H

C

H

H

C

H

H

H

Butane & Constitutional Isomers

C

H

H

H

C

H

H

C

H

H

C

H

H

H

CH3CH2CH2CH3 CH3CHCH3

CH3

Butane(bp -0.5°C)

2-Methylpropane(bp -11.6°C)

C

H

H

HC

C

H H

H

H

C

H

H

H

n-butaneisobutane

C4H10

How many constitutional isomers?

C5H12 3

C6H14 5

C10H22 75

C20H42 366,319

C30H62 > 4 billion

C40H82 > 65 trillion

C20H42 366,319

C30H62 > 4 billion

C40H82 > 65 trillion

constitutional (structural) isomers

Naming Conventions: IUPAC Nomenclature

• International Union of Pure and Applied Chemistry

• Gives a set of unambiguous names• Despite this, common names are still

used

Naming Alkanes

#C Prefix + -ane

C3 "prop" Gr., protos pion (first fat)*

C4 "but" L., butyrum (butter)C5 "pent" Gr., pente (five)

C6 "hex" Gr., hex (six)

C7 "hept" Gr., hepta (seven)C8 "oct" L., octo (eight)C9 "non" L., nona (nine)C10 "dec" L., deca (ten)

C1 "meth" Gr., methy (wine)*

C2 "eth" Gr., aithein (blaze)

Alkyl groups

-CH2CH3

-CH3

-CH2CH2CH3

-CHCH3CH3

-CH2CH2CH2CH3

-CH2CHCH3CH3

-CHCH2CH3CH3

-CCH3

CH3

CH3

tert-butyl

sec-butyl

isobutyl

butyl

isopropyl

propyl

ethyl

methylName

CondensedStructural Formula

CondensedStructural FormulaName

Naming Algorithm

(a) parent C-chain

(b) substituents

(c) numbers

(d) alphabetical listing

Parent

—Suffix

IUPAC Rules

Substituents—

Dreadful Details!• 1. The name for an alkane with an

unbranched chain of carbon atoms consists of a prefix showing the number of carbon atoms and the ending -ane.

• 2. For branched-chain alkanes, the longest chain of carbon atoms is the parent chain and its name is the root name.

• 3. Name and number each substituent on the parent chain and use a hyphen to connect the number to the name.

• 4. If there is one substituent, number the parent chain from the end that gives the substituent the lower number.

Dreadful details (part 2)!• 5. If the same substituent occurs more than once:

– Number the parent chain from the end that gives the lower number to the substituent encountered first.

– Indicate the number of times the substituent occurs by a prefix di-, tri-, tetra-, penta-, hexa-, and so forth.

– Use a comma to separate position numbers.

• 6. If there are two or more different substituents– List them in alphabetical order.– Number the chain from the end that gives the lower

number to the substituent encountered first.– If there are different substituents at equivalent positions on

opposite ends of the parent chain, give the substituent of lower alphabetical order the lower number.

• 7. Do not include the prefixes di-, tri-, tetra-, and so forth or the hyphenated prefixes sec- and tert- in alphabetizing; – Alphabetize the names of substituents first, and then insert

these prefixes.

Alkane Origins

Physical Properties of Alkanes

CH4CH3CH3CH3CH2CH3CH3(CH2)2CH3

CH3(CH2)3CH3

CH3(CH2)4CH3

CH3(CH2)5CH3

CH3(CH2)6CH3CH3(CH2)7CH3

CH3(CH2)8CH3

methane

ethanepropane

butane

pentane

hexane

heptane

octanenonane

decane

Name

CondensedStructrualFormula

mp(°C)

bp(°C)

-182

-183

-190-138

-130

-95

-90

-57-51

-30

-164

-88

-420

36

69

98

126151

174

(a gas)

(a gas)

(a gas)(a gas)

0.626

0.659

0.684

0.7030.718

0.730

*For comparison, the density of H2O is 1 g/mL at 4°C.

Mol wt(amu)

16.0

30.144.1

58.1

72.2

86.2

100.2

114.2128.3142.3

Density of Liquid

(g/mL at 0° C)*

Isomers and Physical Properties

pentanebp 36°C; mp -130°C

d 0.626 neopentanebp 9°C; mp -16°C

d 0.606

CH3 CH2 CH2 CH2 CH3

CH3 C CH3

CH3

CH3 CH3 CH

CH3

CH2 CH3

isopentanebp 28°C; mp -160°C

d 0.620

Alkane Origins

Gasoline, Combustion, & Octane Ratings

OH

C6-C12 mixture

CH4 + 2O2 CO2 + 2H2O + 212 kcal/mol

CH3CH2CH3 + 5 O2 3 CO2 + 4H2O + 530 kcal/mol

but…

2 CH3CH2CH3 + 7 O2 2 CO2 + 2 CO + 2 C + 8H2O + < 530 kcal/mol

Octane Rating – Controlled Explosions

2,2,4-trimethylpentane(iso-octane)Octane rating 100

HeptaneOctane rating 0

EthanolOctane rating 105

OctaneOctane Rating -20

Halogenation

n

F F

F F

F F

F F

Perfluorodecalin

polytetrafluoroethylene (PTFE) Teflon

Cl Cl

F F

dichlorodifluoromethaneFreon

dichlorodiphenyltrichloroethaneDDT

CycloalkanesCnH2n

60° 90° 108° 120° 128° 135°

60° 88° 105° 109° 109° 109°

Interesting Cycloalkane Derivatives

Testosterone

Cholesterol

Estradiol

Muskone

Cyclohexane

Cyclohexane – the Chair C

C

CC

C

C

1

2

3

5

6

4

"chair"

Cyclohexane Substituents H

H

CH3

CH3

H

H

H

H

1

6 5

4

3 (3)

(3')(1)

2

3

2

1

65

4

(3)

(3')

(1)

95% 5%1,3-diaxial interactions

H

H

CH3

CH3

H

H

H

H

1

6 5

4

3 (3)

(3')(1)

2

3

2

1

65

4

(3)

(3')

(1)

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Constitutional

IsomersStereoisomers

ConformationalIsomers

GeometricIsomers

Enantiomers Diastereomers

single bond rotation

chiral achiral

sameconnections

differentconnections

notmirrorimages

mirrorimages

Isomers

Geometric Isomers, a.k.a.cis-trans isomers

perspectiveHaworth

Cl

Cl

ClClH

H HH

cis-1,2-dichlorocyclopentane

perspective

HaworthCl

H

ClHH

Cl HCl

trans-1,2-dichlorocyclopentane