organic chemistry 2

Chapter 2Basics of Organic Chemistry

2.1Types of Chemical Formulae

Base

Les di!érents types de formules chimiques

47

trivial name IUPAC name molecularformula

condensedformula

structure formulae

isobutane 2-methylpropane C!H"# CH$ -CH(CH$ )-CH$

isopropyl alcohol propan-2-ol C$H%O CH$ -CH(OH)-CH$

acetone propan-2-one C$H&O CH$-C(O)- CH$ C CO

C

C CC

C

H3C

O

CH3

H3C

OH

CH3

CH3

CH3H3CH

H H HH

HH

HHH

C COH

CH

H

HH

HHH

H

HH

H

H H

O

H

H H HH

HH

HHH

OH

H

H

HH

HHH

H

HH

H

H H

O

OH

Base

Di!erent Types of Chemical Formulae

48

trivial name IUPAC name molecularformula

condensedformula

structure formulae

acetic acid ethanoic acid C'H!O' CH$-C(O)-OH CH$COOH

benzene benzene C&H& C&H&

styrene 1-phenylethene C%H% C&H(-CH=CH'

C CO

OH

CCC C

CC

CC C C

CC C C

H3C

O

OH

CH2

H

HH

H

H

HH

H

H

H

H

HH

HH

H

H

O

OHH

HH

H

H

HH

H

H

H

H

HH

HH

H

H

O

OH

2.2Names of Functional Groups

Basics

Overview of Hydrocarbon Derivatives

50

hydrocarbons compounds that only contain C and H

alkanes hydrocarbons that only contain single bondsalkenesalkynesarenes

linearalkanes

branchedalkanes

cyclicalkanes

alkanes with a single carbon backbonewithout branching points

RR RR R R R

R RR

R R

CmHn

Basics

Overview of Functional Groups – Monovalent Functional Groups

51

haloalkanes alcohols amines miscellaneous

R F

R Br

R Cl

R I

RNR

R N R

R

R

R OH

R

R

OH

R

R OH

H

HNR

H

OH

R O R

!uoroalkane

bromoalkane

iodooalkane

chloroalkane

primary alcohol

secondary alcohol

tertiary alcohol

primary amine

secondary amine

tertiary amine

phenol

ether

Basics

Overview of Functional Groups – Divalent and Trivalent Functional Groups

52

divalent derivativescarbonyl & related derivatives

trivalent derivativescarboxyl derivatives

tetravalent derivativescarbonic acid derivatives

miscellaneousderivatives

R H

O

R OH

O

HO OH

O

R O

O O

R

aldehyde (carboxylic) acid carbonic acid

carbonateketone ester

anhydride

R R

O

R OR

O

RO OR

O

acetal

RO NR2

O

R NR2

O

R H

RO ORR C N

nitrileurethaneamide

R2N NR2

O

R Hal

O

R R

RO OR

ketal acid halogenide urea

2.3Basic Rules of Nomenclature

Nomenclature

Nomenclature of Linear Alkanes and the corresponding Alkyl Residues (“Radical Groups”)

54

methane

hexane

pentane

butane

propane

ethane

méthane

hexane

pentane

butane

propane

éthane

HH H H

H H HH

H H H

H H H

H

H H H

H HH

H H H

H H

HH H

H HH

H H

H H

H

H H

HH

H H

H

HH

HH

H

H

H

H

H

HH C

HH

H

H CH

CH

HH

H

H CH

CH

CH

HH

H

H

H CH

CH

CH

HCH

HH

H

H

H CH

CH

CH

HCH

HCH

HH

H

H

H CH

CH

CH

HCH

HCH

HCH

HH

H

H

CH4

CH3(CH2)4CH3

CH3(CH2)3CH3

CH3(CH2)2CH3

CH3CH2CH3

CH3CH3

analogous for the higher alkanes: heptane, octane,nonane, decane, undecane, dodecane, tridecane, tetradecane, pentadecane, hexadecane, heptadecane, octadecane, nondecane, eicosane (C20H42), heneicosane (C21H44), docosane (C22H46), tricosane (C23H48) ... tricontane (C30H62), ... tetracontane (C40H82) ...

X CH3

X CH3

CH3

X CH3

X CH3

XCH3

X

methyl

hexyl

pentyl

butyl

propyl

ethyl

CH3H3C

CH3H3C

CH3H3C

CH3H3C

CH3H3C

Nomenclature

Basic Rules of Nomenclature of Branched Alkanes (Rules)

55

1. Find and name the longest carbon chain in the molecule• if two chains are equally long, choose the one that has more substitutents

2. Name all residues attached to this chains as alkyl chains• if the side chains are further bracnhed, the same rules apply: )nd the longest carbon chain, then name the subsittuents to it (iterative)

3. Number the atoms of the main chain starting with the end that is closest to first substituent• if two substituents are at the same distance from the two ends, one decides on the basis of the alphabetic order of these substituents

• if there is more than one substitutent, the one chooses the one (of two) possibilities that results in the lowest number for the )rst case of di*erence

4. Number the atoms in the substituents starting with the first atom attached to the main chain

5. Put the substituents into alphabetic order• the substituents are preceded with a numbering indicating the atom of the main chain they are attached to

• if a molecule contains the same type of substituents multiple times, its name is preceded with a numbering pre)x (di-, tri-, tetra-, etc.)

Nomenclature

Nomenclature of Branched Alkanes (Examples)

56

Nomenclature


57

1 32

1 32 4 3

4 65

23

4 65

54

3 12

1 76

21

2-methylpropane 2-methylbutanenot 3-methylbutane

3-methylhexanenot 2-propylbutane

3-ethyl-4-methylhexane 3-methyl-4-propylheptanenot 4-propyl-5-methylheptanenot 4-(1-methylpropyl)heptane

Nomenclature


58

Nomenclature


59

1 32

12

13

2

41 3

2 45

6

4 23

34

56

78

1011

1213

1415

9134 2

3 12 5

67

89

16

1

2,2-dimethylbutane 2,2,4-trimethylhexane 5-(2,2-dimethylpropyl)nonane

3-methyl-7-(3,3-dimethylbutyl)-12-(1-ethyl-2-methylpropyl)hexadecane

Nomenclature

Important Trivial Names of Alkyl Groups

60

isopropyl (1-methylethyl)

isobutyl (2-methylproyl)

isopentyl (3-methylbutyl)

cyclohexyl

sec.-butyl (1-methylproyl)

CH3

CH3

CH3

CH3

CH3

CH3CH3CH3

CH3

CH3

CH3CH3

CH3

CH3

H3C CH3

H3C CH3

CH3

tert.-butyl (1-methylproyl)

neopentyl (2,2-dimethylpropyl)

tert.-hexyl (1,1,2,2-tetramethylpropyl)

Nomenclature

Nomenclature of Alkanes Using Trivial Names of Alkyl Groups

61

1

1 32 4

56 1 3

2 45

6

12

1 32

78 7

89

10

1 32 4

56

12

78

2-cyclohexylhexaneor 1-(2-hexyl)-cyclohexane

4-(1-methylethyl)octaneor 4-isopropyloctane

4-(1,1-dimethylethyl)octaneor 4-(tert.-butyl)octane

5-(2,2-dimethylpropyl)decaneor 5-neopentyldecane

La nomenclature des alcènes et alcynes

Nomenclature

Nomenclature of Alkenes and Alkynes (Rules)

62

1. Name the longest chain that contains the double/triple bond• the molecule may well contain longer carbon chains, but the one that contains the double/triple bond has priority

2. Indicate the position of the double/triple bond • give the number of the carbon atom of the double/triple bond that is closer to the end of the chain

3. Replace the su"x “ane” by “ene” or “yne”• if a molecule contains more than one double/triple bond, the su+x is preceded with a numbering pre)x (di-, tri-, tetra-, etc.)

Nomenclature

Nomenclature of Alkenes and Alkynes (Examples)

63

Nomenclature


64

1 32 4

12

1 32 4

34

5

1 2 3 1 2 3

4

1 2 3 4

5 6

67

1-buteneor but-1-ene

4-propyl-3-heptene2-buteneor but-2-ene

1-butyneor but-1-yne

2-butyneor but-2-yne

5-méthyl-2-hexyne

Nomenclature


65

Nomenclature


66

54

3 12

54

3 12

6

6 5 4 3

21

23

4

65

1

4-ethyl-3-methyl-2-hexene 3-ethyl-4-propyl-1,5-hexadienenot 3,4-di(ethenyl)heptane

2-ethylhex-1-ene-4-yne 4-ethyl-3-propylhex-1-ene-5-ynenot 3-ethyl-4-propylhex-5-ene-1-yne

Nomenclature

Nomenclature of Aromatic Compounds

67

1. The aromatic residue is (typically) considered to be the core of the molecule• typically, trivial names are used

• all other residues attached to it are treated as substituents

benzene naphthalene anthracene

tetracene pentacene

Nomenclature

Nomenclature of Aromatic Compounds

68

1-hexylbenzene 1-butyl-2-ethylbenzene 1-(4-ethylhexyl)benzene

12

34

56

12

3

45

6

12

34

56 1 3 52 64

Nomenclature

Important Trivial Names of Alkenyl, Alkynyl, and Aromatic Substituents

69

vinyl (1-ethenyl) ethynyl (1-ethynyl) phenyl

allyl (2-propenyl) propargyl (2-propynyl) benzyl (1-phenylmethyl)

Nomenclature

Naming of Unsaturated Compounds with Trivial Names

70

1 32 4

56

78

1 32 4

56

78

1 32 4

56

78

21

4-vinyl-1,7-octadieneor 4-(eth-1-enyl)-1,7-octadiene

4-phenyl-1,7-octadiene 4-benzyl-1,7-octadiene 1-phenyl-1-etheneor vinylbenzene

or styrene

Nomenclature

Nomenclature of Haloalkanes

71

• indicate the position of the halogen and its nature with a prefix (fluoro, chloro, bromo, iodo)

2-!uoropropane 2-chlorobutane 1-bromo-2-methylpentanenon 2-(1-bromomethyl)pentane

1-bromo-5-chloro-3-(1-iodoethyl)pentane

F Cl

1 32

1 32 4 Br2

3 54

23

12

I

1 Cl45

1Br

Nomenclature

Nomenclature of Alcohols

72

• find the longest chain that contains the alcohol, name it, and append the su"x “ol”

• alternatively, indicate its position on the alkane (or alkyl residue) and use prefix “hydroxy”

2-propanolor propan-2-ol

or 2-hydroxypropaneou isopropanol

1,3-butandiolor butan-1,3-diol

or 1,3-dihydroxybutane

2-ethyl-1-pentanolor 2-ethylpentan-1-ol

or 3-(1-hydroxymethyl)hexane

3-propyl-1,4-hexandiolnot 4-(2-hydroxyethyl)-3-heptanol

OH OH

1 32 4 2

3 1 OH2

3 54

3

4 65

HO

OH21

1

OH

Nomenclature

Nomenclature of Amines

73

2-propanamineor propan-2-amineor 2-aminopropaneor isopropylamine

2,4-pentandiamineor pentan-2,4-diamineor 2,4-diaminopentane

2-propan-(N,N-diéthyl)amineor 2-(N,N-diethyl)aminopropane

or diéthylisopropylamine

2-(1-aminométhyl)-1,4-butandiolnot 2-(1-hydroxyméthyl)-4-hydroxy-1-butanamine

NH2 NH2

1 32 5 3

4 2 N 2H2N OH34

NH2

1

21 3

1HO

1

• find the longest chain that contains the amine, name it, and append the su"x “amine”

• alternatively, indicate its position on the alkane (or alkyl residue) and use prefix “amino”

Nomenclature

Nomenclature of Aldehydes

74

• find the longest chain that contains the aldehyde, name it, and append the su"x “al”

propanal propandial 3,4-dimethylhexanalnot 3,4-dimethyl-5-hexanal

not 2-ethyl-3-methyl-5-pentanal

3-ethyl-5-hydroxypentanalor 3-ethyl-pentanal-5-ol

not 3-ethyl-pentan-5-al-1-ol

H

OH

O

4

3 12

3

OH4

5

O2 15

O

H

O

HH

6

Nomenclature of Ketones

75

• find the longest chain that contains the ketone, name it, and append the su"x “one”

propanone 2,4-pentandione 3-propylhexan-2-onenot 4-(2-acetyl)heptane

3-ethylhexanal-4-one

O O O2

3 54 3

4 65

O

O2 1

O1

1 32 4

5 6

Nomenclature of Carboxylic Acids

76

OH

O

HO

O

HO O

2 43

3

45

HO

O2 1

O

OH 1 O

OH OH

propanoic acid propandioic acidold: methanedicarboxylic acid

2-propyl-butandioic acid

old: pentane-1,2-dicarboxylic acid

3-ethyl-4-hydroxypentanoic acid

• find the longest chain that contains the acid function, and append the su"x “oic acid”

Nomenclature

Important Trivial Names for Aldehydes, Acids, Esters, and Acyl Residues

77

aldehydes carboxylic acids esters acyl residues examples

H H

O

H OH

O

H O

O

H

O

O

O

H

O

OH

O

O

O O

H

O

OH

O

O

O O

H

O

OH

O

O

O O

H

O

OH

O

O

O O

O

O

H

NH

O

formaldehydemethanal

acetateethanoate

propionatepropanoate

valerylpentanoyl

butyrylbutanoyl

propionylpropanoyl

acetylethanoyl

formatemethanoate

formylmethanoyl

éthyl propanoateou acide éthyl ester

propionique

phényl formateou acide phényl ester

méthanoïque

N-acétyl-2-pentanamine

valeric acidacide pentanoic acid

butyric acidbutanoic acid

propionic acidpropanoic acid

valeratepentanoate

butyratebutanoate

acetic acidethanoic acid

valeraldehydepentanal

butyraldehydebutanal

propionaldehydepropanal

acetaldehydeethanal

formic acidmethanoic acid

2.4Isomerism

Isomers

Isomers

79

• Isomers have the same molecular formula (e.g., C5H10O2) but di!erent structural formula

H3CO

OH

O

H

H3C

O

OH

CH3

H3C

O

OHCH3

HOO

H

HO

CH3

H3CO

H

OH

HO OH

HOOH

OHHO

OHHOH3C

O

H

OH

Isomers

Types of Isomers (1)

80

chemical compoundssame molecular formula?

no yesisomers

same connectivity of atoms?di!erent compounds

stereoisomersconversion without breaking bonds?

constitution isomerssame functional groups?

enantiomers

functionalisomers

same carbon skeleton?

no yesconfiguration isomers

di*erence in spatial orientation at double bond?chainisomers

positionisomers

conformersrotation around one single bond?

yes

rotamers

no yes

no yesyes no

no yes geometric isomers

no yesdiastereomers

isomers like object and mirror image?

Isomers


81

chemical compoundssame molecular formula?

no yesisomersdi!erent compounds

H3CO

OH H3CO

OH

CH3

H3C

O

OH H3CO

H

CH3H3C CH3

H3C

C5H10O2 C6H12O2

C4H8O2 C5H10O

C5H10 C5H8

• All types of isomers have the same molecular formula but di!erent structural formula

H3CO

OH

H3C

O

OH

CH3

H3CO

O CH3

H3CO

H

OH

OH

OH

C5H10O2 C5H10O2

HO

HO

C5H10O2 C5H10O2

C5H10O2 C5H10O2

Isomers


82

isomerssame connectivity of atoms?

stereoisomersconstitution isomers no yes

functional isomers

chain isomers

position isomers

H3CO

OH

O

HHO

acid alcohol aldehyde

O

HHO H3CO

H

OH

pentanoic acid methylbutanoic acid

5-hydroxypentanal 3-hydroxypentanal

conformers

geometric isomers

diastereomers or enantiomers

H3C

O

H

OH

H

CH3 O

HHOH

interconversion without breaking bonds

interconversion would require rotation around double bond

H3CCH3 H3C

CH3

no interconversion by real or hypothetical bond rotation

CH3 O

HHOHH3C O

HHO

H

H3C

O

OH

CH3H3C

O

OH

Isomers


83

stereoisomersconversion without breaking bonds?

configuration isomers conformersno yes

Natta projection

Sawhorse projection

Newman projection

geometric isomers

diastereomers

enantiomers

H3C

EtHOH

COOHBr

H3C

COOHHOH

EtBr

H3C

H OH

BrHOOC

Et H3C

H OH

Et

COOHBr

BrCOOH

EtCH3

H OH

BrHOOC

Et

CH3

H OH

CH3 O

HHOHH3C O

HHO

H

OHHO OHHO

H3CCH3 H3C

CH3

no mirror images

mirror images

Isomers


84

configuration isomersdi*erence in spatial orientation at double bond?

no yesgeometric isomersdiastereomers or enantiomers

but not

but not

N CH3 NCH3

H3CCH3 H3C

CH3

H3C

OH CH3

H3C

CH3

O

HH3C

HO

CH3

O

HH3C

O

CH3

OHH

(E) (Z)

(E) (Z)

(E) (Z)

diastereomers

enantiomers

CH3 O

HHOHH3C O

HHO

H

OHHO OHHO

no mirror images

mirror images

Isomers

Enantiomers and Diasteromers

85

• Tetrahedral carbon atoms with four di!erent residues are called “chiral centers” or “stereocenters”

• Stereocenters, Chirality, Diastereomers, and Enantiomers• Chiral centers give rise to two non-superimposable stereoisomers with di"erent “handedness”, or “chirality• Molecules with one stereocenter are chiral; they exist as two enantiomers (non-superimposable mirror images)• Molecules with multiple stereocenters are not chiral in the presence of an intramolecular mirror plane• Molecules with multiple stereocenters are enantiomers if con#guration of all stereocenters is inverse

diastereomers

enantiomerschiral

identicalachiral

HO OH

* *

HO OH

* *

HO OHHO OH

* * * *

BD

A

C

BD

A

C

* *

Isomers

Nomenclature of Stereocenters (1)

86

H2N H

COOHH3C

H2NH

H3C

COOH

L-alanineL-2-aminopropanoic acid

D-alanineD-2-aminopropanoic acid

• Fischer projection (for amino acids, carbohydrates, and related biomolecules)

• Most natural amino acids have L-configuration, natural carbohydrates have D-configuration

• arrange molecule such that the backbone is bent downwards and project• arrange molecule such that carbon in highest oxidation state points “up” (in view)• if closest amino/hydroxy function points left, con#guration is L, if right, it is D

HH2NCOOH

CH3

HH2NCOOH

CH3

H NH2

COOH

CH3

* *

HH2NCOOH

CH3H

O

OHNH2

HH2NCOOH

CH2OH*

O

OHNH2

OH

OOH

HOHOH OH

OHOHHHHOOHHOHH

CH2OH

OH

*

glycine2-aminoethanoic acid

L-serineL-2-amino-3-hydroxypropanoic acid

D-glucoseD-2,3,4,5,6-pentahydroxyhexanal

Isomers

Nomenclature of Stereocenters (2)

87

(S)-2-bromopropanoic acid

• IUPAC nomenclature, following the “Cahn-Ingold-Prelog” rules• assign priorities to substituents at stereocenter according to increasing atomic weight of the connecting atom• if the #rst connecting atom is the same, proceed to the substituents on this atom• turn the moleule such that the substituent with the lowest priority (i.e., 4) is pointing to the back• if the substituents 1→ 2→ 3 are arranged clockwise, the con#uration is (R), and if counterclockwise, it is (S)

CH3O

BrH

OH

4

3 2

1

H3CO

BrH

HO

4

H3CO

HBr

OH

4

3 2

1

H3CO

BrH

OH

4

3 2

1**

32

1

H3CO

OHBr

H3CO

OHBr

2S,4S-dihydroxypentane 2S,3R-dihydroxypentandioic acidD,L-tartric acid

2R,3S,4R,5R,6-pentahydroxyhexanalD-glucose

(S)(S) (S)(S)

OH OH1 1

22 33 (R)(R)(S)(S)

OOH

OH

1

1

22

OH

HO

O(S)(S)

O

OHNH2O

HO

1

23

2S-aminobutandioic acidL-glutamic acid

(R)-2-bromopropanoic acid

(S)(S)(R)(R) (R)(R)

OOH

HOH

(R)(R)

OH OH

OH

1

2

Isomers

Conformations of Alkanes

88

E

!0 60 120 180

staggeredtrans

staggeredgauche(–)

eclipsedeclipsed

eclipsedeclipsed

staggeredgauche(+)

240 300 360

3.8 kJ/mol

14.2 kJ/mol

14.2 kJ/mol

CH3

H H

HH

CH3

CH3

H H

CH3H

H

CH3

H H

HH3C

H

HH

H3CCH3

H HHH

H3CCH3

H H

H3CH

HCH3

H H HCH3

HCH3

H H

organic chemistry 2

Documents

alkyl chains

longest carbon chain

methylpropane c4h10

ol c3h8o ch3 choh

higher alkanes

single carbon backbonewithout

main chain

branched alkanes rules551