1. EFN-313 Lífræn efnafræði
11. kafli

2. “The most important hypothesis in all of
biology…is that everything that animals do,
atoms do. In other words, there is nothing
that living things do that cannot be
understood from the point of view that
they are made of atoms acting according
to the laws of physics.”
Richard Feynman ( )

3. Lífræn efni byggjast öll á kolefni
C, CO, CO2 og CO3 teljast ólífræn
Önnur C sambönd kallast lífræn
Annaðhvort sameindir eða sameindajónir
Óendanlega mörg lífræn efni til, á öllum formum með mismunandi eiginleika.

4. C-atóm eru einstök Mynda óskautað samgild tengi við Vetni
Mynda samgild tengi sín á milli og mynda langar keðjur
Mynda samgild tengi við aðra málmleysingja t.d. P,O,N,S og halogena
C-C og C-H tengi eru óskautuð (nonpolar)

5. Raun lögun etan sameindar
Fjögur sp3 hybridised orbitals mynda ferflötung
sp3 hybridised orbitals frá 2 C atómum geta skarast og myndað C-C σ-tengi
Each sp3 orbital contributes one electron to form C-C [C..C]
C-C s bond

6. sp3 svigrúmablanda (rafeindir) flýr eins langt frá kjarnanum og hægt er og tengist í þær áttir.

7. s bonds: symmetrical about the bond axis
Carbon sp3 orbitals can overlap with Hydrogen 1s orbitals to form Carbon-Hydrogen s bonds
Each sp3 orbital contributes one electron; each s orbital contributes one electron to form C-H [C..H]
s bonds: symmetrical about the bond axis

8. Bond Dissociation Energy
C-C N-N O-O
Bond Dissociation Energy
(kJ mol-1)
Carbon-Carbon bonds: especially Sterk samgild tengi
Kolefni: Einstakt, myndar catenate [Keðjur]
Forms molecules composed of C-C bonds
Línulaga/Linear Greinótt/Branched Hring/Cyclic

9. Organic molecules = Carbon-based molecules
Organic chemistry = Chemistry of carbon-based molecules
Some properties of organic molecules
Stability: composed of stable C-C covalent bonds
Defined molecular structures
Defined three-dimensional shapes

10. Organic chemicals are universal
Biological matter
Plants
Animals
Microbes
Geological matter
Fossil Fuels
Other
Organic
Chemicals
Atmospheric
and
cosmic matter
Manufactured
products

11. Biological organic chemicals
Natural fibres
Antibiotics
Fermentation products
Natural flavours
Natural fragrances
Plant & microbial products
Bio-matter
Sugars
Proteins
Fats & oils
Vitamins
DNA & RNA
Wood
Natural rubber
Essential oils

12. Organic chemicals in manufactured products
Imaging agents
Medicines
Veterinary medicines
Disinfectants
Bio-active
products
Herbicides
Antiseptics
Pesticides
Fertilizers
Fungicides
Plant growth hormones

13. Organic chemicals in manufactured products
Plastics
Coatings & lacquers
Fibres & clothings
Paper
Materials
Films
Packaging
Wound dressings
Medical implants

14. Organic chemicals in manufactured products
Fibre
Fats & Oils
Vitamins
Sugars
Foods
Flavourings
Dietary supplements
Anti-oxidants
Colourants
Methanol/Ethanol
“Petrol”
“Diesel”
Fuels
Peat/Turf
Coal
LPG
Natural gas

15. Organic chemicals in manufactured products Miscellaneous
Lubricants
Cosmetics
Fragrances
Pigments
Dyes
Inks
Adhesives
Explosives
Detergents
Surfactants
Emulsifiers
Coolants
Photographic agents
Anti-scalants
Forensic chemicals
Liquid crystal displays

16. Hydrocarbons - Kolvetni
Kolvetni eru einföldustu lífrænu efnin
Kolvetni eru gerð úr Kolefni og Vetni
Kolvetni þar sem öll tengi milli atóma eru einföld kallast ALKANar
Öll eintengi eru sigmatengi (σ-bonds) og um þau frjás snúningur.
Einföldustu: CH4, C2H6, C3H8

17. Um kolvetni
Mettað kolvetni (Saturated hydrocarbon): Kolvetni eingöngu með eintengi
Alkane: Mettuð kolvetni þar sem kolefnin raða sér í opna keðju.
Aliphatic hydrocarbon: Annað nafn á alkan

18. Hydrocarbons

19. Bygging
Lögun
Ferflötungslaga
Öll horn tengja um 109.5°

20. Drawing Alkanes Nokkrar aðferðir við að teikna byggingu
Endi og horn eru kolefnisatóm (line-angle)

21. IUPAC International Union of Pure and Applied Chemistry
Látum nægja að læra utanað upp í 10 en allt ofar þarf að kannast við.
Sjá annars töflu 11.1 í bók.

22. Línulaga - Beinkeðjualkanar
Nafn # Kolefni Byggingaformúla
Methane 1 CH4
Ethane 2 CH3CH3
Propane 3 CH3CH2CH3
Butane 4 CH3CH2CH2CH3
Pentane 5 CH3CH2CH2CH2CH3
The names of organic compounds are determined by the IUPAC rules (International Union of Pure and Applied Chemistry). The stem of the name states the number of carbon atoms in the carbon chain of the compounds. The suffix, in this case –ane, indicates the alkane family.

23. IUPAC NAMES Hexane 6 CH3CH2CH2CH2CH2CH3
Nafn # C-atóma Byggingaformúla
Hexane CH3CH2CH2CH2CH2CH3
Heptane CH3CH2CH2CH2CH2CH2CH3
Octane CH3CH2CH2CH2CH2CH2CH2CH3
Nonane CH3 CH2 CH2CH2CH2CH2CH2CH2CH3
Decane 10 CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3

24. Dæmi A. Hver er byggingaformúla… H H H H H C C C C H
B. Hver er mólikúlformúlan?
C. Hvert er nafnið?

25. Lausn
A. CH3CH2CH2CH3
B. C4H10
C. butane

26. Nafnakerfi - IUPAC
Forskeyti/Prefix segir fjölda C-atóma

27. Nöfn: Greinóttra alkana
Finndu lengstu kolefniskeðjuna.
Númera keðjuna, byrja þaðan sem styst er í fyrstu hliðargrein.
Nefnið hliðarhópa og notið númer á C sem staðsetningu.
Raðið hliðarhópum (substituents) í stafrófsröð.
Notið di-, tri-, ef sami hópur kemur oft fyrir =>

28. Lengsta keðjan
Fjöldi kolefnisatóma í lengstu keðju ræður orðstofni/Nafni
Ef það eru tvær keðjur jafnlangar velst sú keðja sem hefur fleiri hliðarhópa.
=>

29. Númera C -atóm Byrjið við endann næst fyrsta hliðarhóp.
Ef tveir hl.hópar eru jafn langt frá skoðið þá aðra hópa. 1 2 3 4 5 6 7
=>

30. Nöfn hliðarhópa – ALKYL hópar
CH3-, methyl
CH3CH2-, ethyl
CH3CH2CH2-, n-propyl
CH3CH2CH2CH2-, n-butyl
=>

31. Alphabetize Raðið í stafrófsröð. Ignore di-, tri-, í stafrófsröðinni.
3-ethyl-2,6-dimethylheptane
=>

32. Flóknari hliðarhópar
Ef greinin er greinótt, númerið C in frá tengi við aðalkeðju.
Nefnið og númerið hliðarkeðju í hliðarkeðju.
Setjið sviga utanum flókna hliðarhópinn. 1 2 3
1-methyl-3-(1,2-dimethylpropyl)cyclohexane =>

33. Nomenclature - IUPAC Parent name: the longest carbon chain
Substituent: a group bonded to the parent chain
alkyl group: a substituent derived by removal of a hydrogen from an alkane; given the symbol R-

34. Nomenclature - IUPAC
1.The name of a saturated hydrocarbon with an unbranched chain consists of a prefix and suffix
2. The parent chain is the longest chain of carbon atoms
3. Each substituent is given a name and a number
4. If there is one substituent, number the chain from the end that gives it the lower number

35. Nomenclature - IUPAC
5. If there are two or more identical substituents, number the chain from the end that gives the lower number to the substituent encountered first
indicate the number of times the substituent appears by a prefix di-, tri-, tetra-, etc.
use commas to separate position numbers

36. Nomenclature - IUPAC
6. If there are two or more different substituents,
list them in alphabetical order
number from the end of the chain that gives the substituent encountered first the lower number

37. Nomenclature - IUPAC
7. The prefixes di-, tri-, tetra-, etc. are not included in alphabetization
alphabetize the names of substituents first and then insert these prefixes

38. Nomenclature - IUPAC
Alkyl groups

39. Nomenclature - Common
The number of carbons in the alkane determines the name
all alkanes with four carbons are butanes, those with five carbons are pentanes, etc.
iso- indicates the chain terminates in -CH(CH3)2; neo- that it terminates in -C(CH3)3

40. Propyl Groups H H n-propyl isopropyl A primary carbon
A secondary carbon
=>

41. Butyl Groups H H n-butyl sec-butyl A primary carbon A secondary carbon
=>

42. Isobutyl Groups H H isobutyl tert-butyl A tertiary carbon =>
A primary carbon

43. Alkyl Groups Branches on carbon chains H H C CH3 methyl H H
H C C CH3CH2 ethyl
An alkyl group is composed of one or more carbon atoms attached to a carbon chain. An alkyl group is derived from an alkane by removing one hydrogen. The ending –ane of the alkane is changed to –yl. The carbon branch from methane is the methyl group. The carbon branch from ethane is the ethyl group.

44. Branched Alkanes CH3 CH3CHCH3 methyl groups CH3 CH3 CH3CHCH2CHCH3
In the structural formula of an alkane, the alkyl group is typically attached vertically above or below the carbon chain.

45. Naming Branched Alkanes
CH methyl branch
CH3CH2CH2CHCH2CH3
Count
A branched-chain alkane is named by indicating the attached groups on the longest carbon chain. In this example, the longest carbon chain has 6 carbon atoms.

46. Naming Branched Alkanes
CH methyl branch
CH3CH2CH2CHCH2CH3
Count
3-Methylhexane
on third C CH six carbon chain
group
The chain is numbered to give the side group or methyl group a location on carbon 3 in the chain.

47. Naming Summary 1. Count the C’s in the longest chain
2. Name each attached group
3 Count the longest carbon chain to give the first attached group the smallest number
4. Name and locate each group

48. Dæmi
A CH CH3
CH3CHCH2CHCH3
B CH CH3
CH3CH2CHCH2CCH2CH3
CH3

49. Svör A. CH3 CH3 CH3CHCH2CHCH3 2,4-dimethylpentane B. CH3 CH3
CH3CH2CHCH2CCH2CH3
CH ,3,5-trimethylheptane

50. Dæmi Write a condensed structure for A. 3,4-dimethylheptane
B. 2,2-dimethyloctane

51. Solution Alk5 A. 3,4-dimethylheptane CH3 CH3CH2CHCHCH2CH2CH3 CH3
2,2-dimethyloctane CH3
CH3CCH2CH2CH2CH2CH2CH3

52. Constitutional/structural Isomerism
Byggingaisomerur: Efni með sömu mólikúlformúlu en ólíka byggingaformúlu t.d.: C4H10

53. Byggingaisomerur 11.6 Eru þetta byggingaisomerur?
Finndu lengstu keðjuna
Númerið að fyrsta hliðarhóp
Berið saman lengd og greinar

54. Constitutional Isomerism
World population
is about
6,000,000,000

55. Learning Check Alk6
Write 3 isomers of C5H12 and name each.

56. Solution Alk6 CH3 CH3CH2CH2CH2CH3 pentane CH3CHCH2CH3 2-methylbutane
CH3CCH3 2,2-dimethylpropane

57. Dæmi Write a condensed structure for A. 3,4-dimethylheptane
B. 2,2-dimethyloctane

58. Svör A. 3,4-dimethylheptane CH3 CH3CH2CHCHCH2CH2CH3 CH3
2,2-dimethyloctane CH3
CH3CCH2CH2CH2CH2CH2CH3

59. Dæmi
Write 3 isomers of C5H12 and name each.

60. Svör CH3 CH3CH2CH2CH2CH3 pentane CH3CHCH2CH3 2-methylbutane
CH3CCH3 2,2-dimethylpropane

61. Cycloalkanes Hringmyndanir (CH2 groups) Formula: CnH2n
Óskautaðir og óleysanlegir í vatni eins og alkanar
Bræðslu, suðumörk og flestir eiginleikar svipaðir og hjá samsvarandi alkönum =>

62. Nafnakerfi Sykloalkanar eru venjulega orðstofninn
Hringur á hvorki upphaf né endi – en sé hliðarhópur þarf að númera….
Raða í stafrófsröð.
Stöku sinnum finnast cyklo sem hliðarhópar eins og syklopentyl.
=>

63. Cycloalkanes Hringir með 5 og 6 C algengastir
Structure and nomenclature
if two substituents, number from the substituent of lower alphabetical order
if three or more substituents, number to give them the lowest set of numbers and then list substituents in alphabetical order

64. Cycloalkanes
Teiknaðir
Lína er C-C bond
Horn og lína þýðir C

65. Cycloalkanes
Example: name these cycloalkanes

66. Bicycloalkanes
Bicycloalkane: an alkane that contains two rings that share two carbons
Bicyclo[4.4.0]decane
(Decalin)
Bicyclo[4.3.0]nonane
(Hydrindane)
Bicyclo[2.2.1]heptane
(Norbornane)

67. Bicycloalkanes Nomenclature
parent is the alkane of the same number of carbons as are in the rings
number from a bridgehead, along longest bridge back to the bridgehead, then along the next longest bridge, etc.
show the lengths of bridges in brackets, from longest to shortest

68. Chair Conformer
=>

69. Boat Conformer
=>

70. Conformational Energy
=>

71. Axial and Equatorial Positions
=>

72. Monosubstituted Cyclohexanes
=>

73. 1,3-Diaxial Interactions
=>

74. Disubstituted Cyclohexanes
=>

75. Cycloalkanes Cyclopropane CH2 CH2 CH2 Cyclobutane CH2 CH2
The is a group of alkanes that have a cyclic structure. These cycloalkanes contain a carbon chain that is in a ring. Each cycloalkane has a formula that is 2C less than the corresponding alkane. For example, propane is C3H8 whereas cyclopropane ic C3H6. Butane is C4H10 and cyclobutane is C4H10. The names of the cyclic structures use the prefix cyclo in from of the alkane name for the carbon chain.

76. More Cycloalkanes
Cyclopentane CH2
CH CH2
CH CH2
Cyclohexane
CH2

77. Naming Cycloalkanes with Side Groups
Number of Naming
side groups
One Side group name goes in front of the cycloalkane name.
Two Number the ring in the direction that gives the lowest numbers to the side groups.

78. Cycloalkanes with Side Groups

79. Dæmi

80. Lausn

81. Chapter 11.8 Alkenes and Alkynes
Geometric Isomers / rúmísomerur Alkena
Alken hefur C=C tvítengi
Alkýn hefur CC

82. Mettuð/Saturated og ómettuð/Unsaturated
Mettuð kolvetni hafa mesta mögulega fjölda vetnisatóma. CnH2n+2 fyrir alkan
Ómettuð kolvetni hafa færri vetnisatóm en mettuð
Ómettuð kolvetni hafa tví eða þrítengi milli C atóma
Milli tví og þrítengja er enginn snúningur

83. ALKEN C=C tvítengi Endar á EN H2C=CH2 ethen (ethylen)
H2C=CH-CH3 propen (propylen)
cyclohexen

84. Alkyn Carbon-carbon triple bonds Endar á -yn HCCH ethyn (acetylen)
HCC-CH3 propyn
Alken mun algengari en alkyn

85. Nafnakerfi alken/alkyn
Þegar keðja hefur 4 eða fleiri C, þá númera keðju þaðan sem styst er í tvítengi án tillits til alkýl hliðarhópa.
CH2=CHCH2CH3 1-buten eða But-1-en
CH3CH=CHCH3 2-buten eða But-2-en
CH3CHCHCH3 2-butyn eða But-2-yn

86. Dæmi
Ritið nöfn þessara efna:
A. CH3CH2CCCH3
CH3
B. CH3C=CHCH3 C.

87. Lausn IUPAC nöfnin eru: A. CH3CH2CH=CHCH3 2-pentyne CH3
B. CH3C=CHCH3 C.
3-methyl-2-butene methylcyclopentene

88. Þar sem engin snúningur er um tvítengi geta myndast rúmísomerur (geometric isomers)
Rúmisomerur geta myndast ef keðja er 4C eða lengri. Rúmisomerur myndast á C no. 2 eða ofar
Sömu megin úr tvítengi er CIS
Sitthvoru megin úr tvítengi er Trans

89. Cis and Trans Isomers Efnið er 2-buten Cis/trans eru mögulegar
CH3 CH CH3
CH = CH CH = CH
cis trans CH3

90. Cis/trans Cis/trans isomerur hafa mikil áhrif á lögun sameinda
Náttúran notar oftast Cis í lífverum og allar fitusýrur í náttúrunni eru Cis
Cis og trans hafa líka ólík bræðslu og suðumörk

91. Trans fitusýrur - ómettaðar

92. Sömu ómettuðu – CIS

94. 12.8 Alkenar och Alkynar π orkumeira, Léttara brjóta - hvargjarnara
 Stöðugra, orkulægra
óhvarfgjarnt

95. Nafnareglur Liknar det för alkaner –en -yn
1. Namnge den kolkedja som innehåller längsta kedja med dubbel trippel bindning
2. Numrera kedjan från den ände som ger dubbel trippel bindning lägst siffra.
3. Placera siffra och namnet på substituenter framför alken-alkyn namn
2-etyl-1-buten

96. Hefur efnið tvo tvíbindinga kallast það DÍEN
Cykloalkanar, þar er talið yfir tvíbinding til hliðarhóps
Hefur efnið tvo tvíbindinga kallast það DÍEN
Hexatrien
Butadien

97. Cis-trans isomer
stereoisomeri,cis-trans
Almennt er trans stöðugra

98. Cis-trans isomer
Cis och trans isomeri kräver att de grupper som binder till kolet är OLIKA

100. 11.9 Aromatic Compounds Aromatic compounds innihalda benzene.
Benzene C6H6 has 6 C atoms and 6 H Atoms
Two possible ring structures show benzene.

101. Benzene Structure
The structures for benzene are also written as one formula with a circle within the ring to represented the alternating double bonds.
Benzene
structure

102. Aromatic Compounds in Nature and Health
Many aromatic compounds are common in nature and in medicine.

103. Naming Aromatic Compounds
Aromatar hafa Bensen sem orðstofn og hliðarhópar settir fyrir fram. (stundum!!!!).
methylbenzene chlorobenzene

104. Þegar bensen er tvískipt
(tveir hliðarhópar) er hringur númeraður þannig að hóparnir fái sem lægst númer.
Forskeytin ortho (1,2), meta (1,3-) and para (1,4-) eru einnig notuð.

105. Aromatar hafa verslunarnöfn
(common name). Ef tvískipt, þá oft með
ortho-, meta-, para-.

106. Dæmi Select the names for each structure: 1. Chlorocyclohexane
2. Chlorobenzene
3. 1-chlorobenzene
1. Meta-methyltoluene
2. Meta-dimethylbenzene
3. 1,3-dimethylbenzene

107. Svör Select the names for each structure: 2. Chlorobenzene
1. Meta-methyltoluene
2. Meta-dimethylbenzene
3. 1,3-dimethylbenzene

108. Dæmi Ritið byggingaformúlur: A. 1,3-dichlorobenzene
B. Ortho-chlorotoluene

109. Svör Byggingaformúlurnar: A. 1,3-dichlorobenzene
B. Ortho-chlorotoluene

110. Learning Check Alk11
Identify the organic family for each:

111. Solution Alk11 Identify the organic family for each: alkane
cycloalkane
aromatic

112. Fused Benzene Rings

113. Carcinogens Fused ring of benzene cause cancer
Contain four or more fused rings
Present in tobacco smoke, auto exhaust, and burned food
The more a person smokes, the greater the risk of developing cancer

114. Unsaturated Fatty Acids
Fatty acids in vegetable oils are omega-6 acids (the first double bond occurs at carbon 6 counting from the methyl group)
A common omega-6 acid is linoleic acid
CH3CH2CH2CH2CH2CH=CHCH2CH=CH(CH2)7COOH 6
linoleic acid, a fatty acid

115. Trans Fats
In vegetable oils, the unsaturated fats usually contain cis double bonds.
During hydrogenation, some cis double bonds are converted to trans double bonds (more stable) causing a change in the fatty acid structure
If a label states “partially” or “fully hydrogenated”, the fats contain trans fatty acids.

116. Trans Fats
In the US, it is estimated that 2-4% of our total Calories is in the form of trans fatty acid.
trans fatty acids behave like saturated fatty acids in the body.
Several studies reported that trans fatty acids raise LDL-cholesterol. Some studies also report that trans fatty acid lower HDL-cholesterol
The trans fatty acids controversy will continue to be debated.

117. Fats and Atheroschlerosis
Inuit people of Alaska have a high fat diet and high blood cholesterol levels, but a very low occurrence of atherosclerosis and heart attacks.
Fat in the Intuit diet was primarily from fish such as salmon, tuna and herring rather than from land animals (as in the American diet).

118. Omega-3 Fatty Acids
Fatty acids in the fish oils are mostly the omega-3 type (first double bond occurs at the third carbon counting from the methyl group).
linolenic acid 18 carbon atoms
CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH 
eicosapentaenoic acid (EPA) 20 carbon atoms CH3CH2(CH=CHCH2)5(CH2)2COOH

119. Atherosclerosis
Plaques of cholesterol adhere to the walls of the blood vessels
Blood pressure rises as blood squeezes through smaller blood vessels
Blood clots may form
Omega-3 fatty acids decrease the “sticking” of blood platelets (fewer blood clots)
Omega-3 fatty acids can increase bleeding time

120. Learning Check HA6 (1) Ture or (2) False
A. ____ There are more unsaturated fats in vegetable oils.
B. ____ Vegetable oils have more omega-3 oils than found in fish.
C. ____ Hydrogenation of oils converts some cis-double bonds to trans- double bonds.
D. ____ Animal fats have more saturated fats.

121. Solution HA6 (1) True or (2) False
A. _T__ There are more unsaturated fats in vegetable oils.
B. _F__ Vegetable oils have more omega-3 oils than found in fish.
C. _T__ Hydrogenation of oils converts some cis-double bonds to trans- double bonds.
D. _T__ Animal fats have more saturated fats.