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Chapter 1-1

What is Organic Chemistry?

Chem 61

Organic Chemistry

 

What is it? Why is it a two semester course? Why is it important to careers in health care?

Organic chemistry is essential to the understanding of the intricate details of life The interactions and reactions of organic molecules are what define living systems.

One needs to understand bonding, structure, properties, reactions, and synthesis to understand natural systems.

 

CHAPTER 1

INTRODUCTION

 

Organic Chemistry: the study of carbon compounds

 

organic compounds contain the elements C, H, N, O, S, Cl, Br, etc.

 

Organic compounds were originally thought to come only from living

organisms

thus

the term organic (until about 1830)

Inorganic compounds were all those which came from non-living sources

Scientists thought a vital force was necessary to produce organic compounds and that they could not be synthesized in the lab.

In 1828 Fredreich Woeller synthesized urea, an organic compound excreted

as waste, from

ammonium cyanate, and vitalism slowly died out.

 

Organic compounds range from methane , CH 4 (natural gas) to DNA, the genetic coding material, and taxol, a plant derived substance which is a potential anticancer agent.

Organic chemistry is fundamental to many scientific disciplines polymer chemistry, microbiology, botany, pharmacy, medicine

biochemistry,

since

living

systems are composed primarily of organic compounds and water.

Chapter 1-2

Electronic Structure of Carbon

Chem 61

STRUCTURAL THEORY AND BONDING

Carbon is intermediate in electronegativity, therefore it neither completely

donates or completely accepts electrons. As a result it forms covalent bonds to itself and other atoms. It can bond to itself to form chains and

This allows the formation of a staggering number of organic

compounds. 95% of all known compounds are organic.

rings

catenation.

ATOMIC STRUCTURE

It is important to understand molecular structure to understand reactivity of organic compounds. Molecular structure depends on atomic structure.

Atomic structure of carbon

C: 1s 2 2s 2 2p 2

that is, carbon has 2 electrons in the lowest energy level, the 1s orbital

2

electrons in the next energy level, the 2s orbital

2

electrons in the third energy level, the 2p orbital

1s, 2s, 2p orbitals

1s is spherical with the same phase throughout

2s is spherical with a node node is where ψ2 = 0

2s is spherical with a node node is where ψ 2 = 0 2s 2p three

2s

2p

three orbitals of equal energy (degenerate)

spherical with a node node is where ψ 2 = 0 2s 2p three orbitals of

2p x

spherical with a node node is where ψ 2 = 0 2s 2p three orbitals of

2p y

node

spherical with a node node is where ψ 2 = 0 2s 2p three orbitals of

2p z z

1s

spherical with a node node is where ψ 2 = 0 2s 2p three orbitals of

Chapter 1-3

Rules for Electronic Configuration

Chem 61

Pauli Exclusion Principle: Maximum of two electrons per orbital.

Electrons have a spin of +1/2 or -1/2 which gives rise to a small magnetic field since electrons are charged.

Repulsion between the electrons is reduced if they have opposite spins and thus opposite magnetic moments.

If two electrons occupy the same orbital they must have opposite spins or be paired.

Aufbau Principle: orbitals are filled from lower to higher energy

4s

3p

3s

2p

order of filling of atomic orbitals

2s

1s

THUS: Li

1s 2 2s 1

Hund's Rule: orbitals of equal energy (degenerate) receive one electron until there is one electron in each orbital: then pairing of electrons begins.

THUS: C 1s 2 2s 2 2px 1 2py 1

Chapter 1-4

Atomic Radius and Electronegativity

Chem 61

ATOMIC RADIUS

Atomic Radius: distance between the nucleus and the outermost electrons (valence electrons) or one half the bondlength of a diatomic molecule

H—H bond length is 0.74Å, atomic radius is 0.37Å

Atomic radius increases with increasing number of electron shells within an atom and decreases with the increase in the number of protons within an atom

Thus atomic radius decreases from left to right within the same row of the periodic table (increasing number of protons in the nucleus) and increases from top to bottom within a group of the periodic table (increasing number of electronic shells)

ELECTRONEGATIVITY

Electronegativity: a measure of an atom's attraction for outer bonding electrons

Electronegativity increases with increasing charge on the nucleus and with decreasing distance between the nucleus and the electrons

Thus electronegativity increases from left to right within a row of the periodic table and from bottom to top within a group in the periodic table

Chapter 1- 5

Chemical Bonding

Chem 61

CHEMICAL BONDING

G.N. Lewis put forth the first explanation of the nature of the chemical bond.

Ionic Bond

one

or more electrons is completely transferred from one atom to

another creating

ions: a cation (positively charged) and an anion (negatively

charged).

the ions are held together by electrostatic attractions

ionic bonds generally occur between atoms of highly different electronegativies. e.g.

Na o

e

Na + +

e

Cl o

+

e

Cl

Na o + Cl o

Na + Cl

one

merge into shared or molecular orbitals

Covalent Bond

or more electrons is shared by atoms

atomic

orbitals

covalent bonds are usually formed between atoms of similar electronegativities

since carbon is intermediate in electronegativity it usually forms covalent bonds

Generally

such that each atom may obtain the stable noble gas electronic configuration

[OCTET RULE]

atoms

not having the noble gas configuration tend to form bonds

4H

+ :C:

H

H H C::O H H H
H
H
C::O
H
H
H

single bond

double bond

H:C:::C:H

triple bond

Atoms of the elements of organic compounds can form a fixed number of bonds.

C
C

O

N
N

H

e b o n d H:C:::C:H triple bond Atoms of the elements of organic compounds can

Chapter 1- 6

Chemical Bonding

Chem 61

COVALENT BONDS

Bond lengths: the distance between two covalently bonded nuclei

Bond angle: the angle formed between two covalent bonds

Bond dissociation energy: the energy required for homolytic cleavage of a bond;

Cl Cl

H

H 3 C

Cl

H 3 C

.

+

.

Cl

+

.

H

.

two radicals

Heterolytic cleavage:

one atom which is part of the bond

cleavage of a bond to give a cation and an anion; the covalent bond retains both electrons from

Cl Cl

H

H 3 C

Cl + +

Cl

H 3 C +

+

H

cation

anion

H (change in enthalpy) for homolytic cleavage of many covalent bonds has been determined

H 3 C—H

H—H

Br—Br

H—OH

104

kcal/mole

104

kcal/mole

CH

3

—CH 3

88 kcal/mole

46 kcal/mole

CH

2

=CH 2

163 ckal/mole

110

kcal/mole

HCCH

230 kcal/mole

Chapter 1-7

Polar Covalent Bonds

Chem 61

POLAR COVALENT BONDS

covalent bonds between atoms of similar electronegativities are said to be nonpolar bonds since each atom shares the electrons of the bond approximately equally

H—H CH 3 —CH 3

if atoms of different electronegativities form a covalent bond, the more electronegative atom will have a stronger attraction for the electrons and polarize the bond giving a polar covalent bond in which one atom is partially negatively (δ )charged and one atom is partially positively charged (δ+)

δ+

δ−

H 3 C—Cl CH 3 —NH 2

δ+

δ

H—Cl

δ+

δ−

H 2 C=O

δ+

δ−

H 3 C—OH

δ+

δ−

If any entire molecule has an overall dipole, then the molecule is said to be polar.

CCl 4 nonpolar, polar covalent bonds cancel each other because of tetrahedral symmetry HCCl 3
CCl 4
nonpolar,
polar covalent bonds cancel each other because of tetrahedral
symmetry
HCCl 3
polar
H 2 O, NH 3
very
polar
δ _
Cl
Cl
δ _
Cl
δ _
δ +
C
δ _
C
Cl
H
O
Cl
Cl
δ _
H
H
+
Cl
δ +
δ
δ +
dipoles cancel
δ _
+
δ
dipoles add
dipoles add
+ C δ _ C Cl H O Cl Cl δ _ H H + Cl

Chapter 1-8

Polar Covalent Bonds

Chem 61

ATTRACTIONS BETWEEN MOLECULES

 

ion-ion forces: the attraction between oppositely charged ions and

repulsion between like charges very strong compounds

not

often encountered in organic

van der Waals forces: all dipole-dipole forces are both repulsive and

attractive

the distance at which the repulsive forces are minimized and the

attractive forces are maximized is called the van der Waals radius

Induced dipole-dipole interactions or London forces: small temporary dipoles occur and induce dipoles in another molecule due to small uneven distribution of electron density.

Dipole-dipole interactions: permanent dipoles in molecules attract or repel

Hydrogen bonding: a specific type of dipole-dipole interaction; very strong

occur only between a hydrogen atom bonded to an electronegative atom O,

N, S and a lone pair on

O, N, S

 

O

H

:N

7

kcal /mole

N H

:N

3

kcal/mole

N

H

:O

2

kcal/mole

O H

:O

5

kcal/mole

Intermolecular hydrogen bonds increase the boiling points of compounds and increase their solubility in water.

Hydrogen bonds also can influence the shapes of biomolecules by internal hydrogen bonding as well as hydrogen bonding between molecules.

Chapter 1-9

Formulas and Formal Charge

Chem 61

CHEMICAL FORMULAS

empirical formula: gives the types and ratios of atoms in a molecule

molecular formula: gives the type and actual number of atoms

structural formula: gives the type, number and attachment of atoms

actual structure

the

for example:

hexane: C 6 H 14 CH 3 CH 2 CH 2 CH 2 CH 2 CH 3

C 3 H 7

molecular formula

empirical formula

LEWIS STRUCTURES

structural formula

1. draw the molecular skeleton

2. count the number of available valence electrons (be sure to account for

any overall charge on the species)

3. draw covalent bonds between all the atoms giving as many as possible

an octet (duet for hydrogen)

4. assign charges in the molecule

FORMAL CHARGE

formal charge on an atom = # valence electrons - # shared pairs of

electrons

1

HNO 3 Lewis structure:

3

- # unshared electrons

:O:

N:O:H

N

5-4-0

= +1

O1

6-2-4

= 0

O2

6-1-6

= -1

O3

6-2-4

= 0

H

2 SO

4

H

1-1

Lewis = O Structure

:O:

2

SO 4 -2

:O:

:O:S:O:

:O:

O

6-1-6

= -1

S

6-4-0

= +2

overall charge (+2) + 4(-1) = -2

:O: 2 SO 4 - 2 :O: :O:S:O: :O: O 6-1-6 = -1 S 6-4-0 =

Chapter 1-10

Formulas and Formal Charge

Chem 61

Structural Formulas

Lewis Structures: as described above using dots for electrons

Line-bond formulas: a line is used to represent two electrons forming a bond (a shared pair)

Condensed formulas: bonds are not always shown and atoms of the same type bonded to another atom are grouped together

H

Othe same type bonded to another atom are grouped together H H line-bond HCCH line-bond H

H

line-bond

HCCH

line-bond

H .

.

. C::O . .

.

H

Lewis

H

2 C=O

condensed

H:C:::C:H HCCH

Lewis

condensed

H H H . . H . C C C::C . . . . H
H
H H .
. H
.
C
C
C::C .
. .
.
H H
H .
H
line-bond
Lewis

CH 2 =CH 2

condensed

Polygon formulas: polygon formulas are often used to represent cyclic compounds for simplicity;

each carbon is assumed to have enough additional hydrogens to give each carbon four bonds

enough additional hydrogens to give each carbon four bonds cyclohexane H H H H H H

cyclohexane

H

H

H H H

H C C C C C C H H H H
H
C
C
C
C
C
C
H
H
H
H

H

H

H H H H H H C C C C C C H H H H

benzene

H H H H H H C C C C C C H H H H

cyclopropane

cyclobutane

cyclopentane

decalin

H H H H H H C C C C C C H H H H

Chapter 1-11

Acids and Bases

Chem 61

ACIDS AND BASES

Bronsted-Lowry:

acid: a proton donor base: a proton acceptor

Strong acid: completely ionized or dissociated in water e.g., HCl, H 2 SO 4 , HNO 3 , HBr

Weak acid: only partially dissociated in water:

carboxylic acids are weak acid

CH 3 CO 2 H acid

+

H 2 O

base

CH 3 CO 2 - CH 3 CO 2 -

+

H 3 O +

conjugate base

conjugate acid

CH 3 NH 3 +

+

HO

conjugate acid

conjugate base

amines are weak bases

CH 3 NH 2

base

+

H 2 O

acid

amines are weak bases CH 3 NH 2 base + H 2 O acid Generally: strong

Generally: strong acids have weak conjugate bases and weak acids have strong conjugate bases

that is, as acid strength increases, the basicity of the conjugate base decreases

Thus the ability of the conjugate base to stabilize a negative charge determines the strength of an acid

Conjugate Acids

HCN CH 3 CO 2 H H 3 PO 4 HCl H 2 O 15.75
HCN
CH 3 CO 2 H
H 3 PO 4
HCl
H 2 O
15.75
6.37
4.75
2.12
-7
pK a
increasing acid strength
Conjugate Bases
HO –
NC –
CH 3 CO 2 –
H 2 PO 4 –
C l –

decreasing base strength

increasing acid strength Conjugate Bases HO – NC – CH 3 CO 2 – H 2

Chapter 1-12

Acids and Bases

Chem 61

Factors affecting Acidity:

the electronegativity and the size of the atom which carries the negative charge influence its ability to stabilize the negative charge

size of the atom

H—F

H—Cl

H—Br

H—I

pK a

3.45

-7

-9

-9.5

increasing size of halogen, increasing acid strength
increasing size of halogen, increasing acid strength

electronegativity

(CH 3 ) 3 C—H

pK a

50

(CH 3 ) 2 N—H

35

CH 3 O—H

15.5

F—H

3.45

increasing electronegativity of atom, increasing acid strength

ACIDITY CONSTANTS, Ka's

for acetic acid

CH 3 CO 2 H + H 2 O

CH 3 CO 2 H + H 2 O C H 3 C O 2 –

CH 3 CO 2 + H 3 O +

K a = [CH 3 CO 2 ] [H + ] [CH 3 CO 2 H]

since stronger acids are more ionized, the larger Ka, the stronger the acid

pKa = -logKa, the lower the pKa, the stronger the acid

also, the higher the pKa, the weaker the acid or the stronger the base

the stronger the acid, the more stable the anion produced by ionization of the acid.

Chapter 1-13

Lewis Acids and Bases

Chem 61

LEWIS ACIDS AND BASES

Lewis acid: electron pair acceptor: any species with an electron deficient atom

BBr 3 , AlCl 3 ,

H 3 C +

Lewis base: electron pair donor; any species with an unshared pair of electrons

H 3 N:, CH 3 CH 2 OH, H 2 C=O:

Chapter 1-14

Quantum Mechanics

Chem 61

QUANTUM MECHANICS

Molecular

Orbitals

In 1923 Louis De Broglie postulated that electrons have properties of three

dimensional waves

Later a wave equation was developed. Solutions (Ψ) to this wave equation give the various electronic states known as atomic orbitals.

= probability of finding an electron in a certain space = electron

Ψ

probability density

plots of Ψ

2

2

give the familiar s,p,d

orbitals

WAVE PROPERTIES

The amplitude of a wave may be above the resting state (positive) or below

(negative)

no

charge implied

+ – + –
+
+

A

node is a point at which the amplitude is zero

Waves reinforce creating a wave of higher amplitude if they they are in phase.

+ – + – + – + –
+
+
+
+

Waves interfere if they are out of phase and create a wave which is of lower amplitude. Complete interference results in the cancelling of one wave by another.

Chapter 1-15

Quantum Mechanics

Chem 61

1s, 2s, 2p orbitals

 

1s is spherical with the same phase throughout

 

+

2s is spherical with a node node is where ψ 2 = 0

2s is spherical with a node node is where ψ 2 = 0

 
 

+

-

node

2p

three orbitals of equal energy (degenerate)

2p x
2p x

node

2p y
2p y
2p z
2p z

4s

3p

3s

2p

order of filling of atomic orbitals

2s

1s

Chapter 1-16

Molecular Orbitals

Chem 61

MOLECULAR ORBITALS

Molecular orbitals = Linear combination of atomic orbitals

2 Atomic Orbitals must produce 2 Molecular Orbitals (the number of molecular orbitals equals the number of atomic orbitals which were combined to form them)

the hydrogen molecule σ* >∆E H 2 H 1s ∆E σ Ψ 1
the hydrogen molecule
σ*
>∆E
H 2
H 1s
∆E
σ
Ψ 1

H 1s

molecule σ* >∆E H 2 H 1s ∆E σ Ψ 1 H 1s Ψ 2 .

Ψ

2

. . antibonding Ψ 1 − Ψ 2 . . bonding Ψ 1 + Ψ
.
.
antibonding
Ψ 1 − Ψ 2
.
.
bonding
Ψ 1 +
Ψ 2

the energy of the hydrogen molecule with two electrons in the sigma orbital is 104 kcal/mole more stable than the separate hydrogen atoms; E = 52 kcal/mole

if one electron is in the sigma and one in the sigma*, the molecule is of higher energy than the two separate atoms because the s* is slightly >E higher than the s orbitals while the s is E lower

Bonding orbital

high

electron density between nuclei

Antibonding orbital

node

between nuclei (zero electron density)

σ bond is cylindrically symmetrical

Aufbau principle

fill

lowest energy orbitals first

Hund's Rule

place

one electron in each degenerate orbital first, then pair

up

Pauli Exclusion Principle opposite spins

two

electrons in the same orbital must have

Chapter 1-17

Molecular Orbitals of Carbon

Chem 61

MOLECULAR ORBITALS ON CARBON Overlap between atomic orbitals in complex molecules often results in electron
MOLECULAR ORBITALS ON CARBON
Overlap between atomic orbitals in complex molecules often results in
electron repulsions which destabilize the molecule. Hybrid orbitals allow for
better overlap and a more accurate prediction of molecular structure.
Methane CH 4 has a central carbon with four equivalent bonds to hydrogen
bond angles = 109.5°
bond lengths = 1.09Å
sp 3 Hybridization
carbon has electronic configuration 1s 2 2s 2 2p 2
2p
2p
96 kcal
hybridize
2s
2s
sp 3
1s
1s
1s
-
-
+
+
+
109.5° apart
3-3p's
4-sp 3 's
2s
sp 3 orbitals point toward the corners of a tetrahedron, 109.5° apart
any carbon bonded to four other atoms is sp 3 hybridized, e.g. CH 4 , H 3 CCH 3 ,
C—C bond length = 1.54Å
H
H
C-H σ bonds require 104 kcal/mol to be broken
C
methane
H
H
bond angles = 109.5°; tetrahedral

Chapter 1-18

sp 2 Molecular Orbitals of Carbon

Chem 61

sp 2 Hybridization sp 2 hybridized carbons are trigonal planar with atoms 120° apart 2p
sp 2 Hybridization
sp 2 hybridized carbons are trigonal planar with atoms 120° apart
2p
2p
2p
96 kcal
hybridize
sp 2
2s
2s
1s
1s
1s
ethylene: trigonal planar
H
H H
H
H
H
C
C
C
C
H
H
120°
H H
H
H
sigma orbital
2p
sp 2
H
H
H
H
H
H
C
C
C
C
C
C
H
H
H
H
H
H
pi orbital
sigma* orbital
pi* orbital
bond angles = 120°; C=C bond length = 1.34Å
pi (π) bonds are formed by the side by side overlap of two p-orbitals (approx. 68
kcal/mol)
pi bonds are above and below the plane where the sigma bond is located
pi bonds make the molecule rigid between the two atoms preventing rotation
sigma σ*
pi π*
E
ethylene C=C double bond: one sigma, one pi
pi π
sigma σ

Chapter 1-19

sp 2 Molecular Orbitals of Carbon

Chem 61

sp Hybridization sp hybridized carbons are linear with atoms 180° apart 2p 2p 2p hybridize
sp Hybridization
sp hybridized carbons are linear with atoms 180° apart
2p
2p
2p
hybridize
sp
96 kcal
2s
2s
1s
1s
1s
ethylene: trigonal planar
-
+
+
1-2p
2-sp's
180° apart; the remaining two 2p
orbitals are 90° to the sp and
each other
2s
Acetylene: linear; bond angles 180° C=C bond length = 1.20Å
acetylene has two perpendicular pi bonds and one sigma bond
H
H
H
C
CH
2-sp's
acetylene σ-orbital
H
H
H
CC
H
2-2p's on each carbon
combine to form pi-orbitals
acetylene π-orbitals
C—C σ*
C—C π*
E
C—C π
C—C σ

Chapter 1-20

Functional Groups

Chem 61

FUNCTIONAL GROUPs

CH 3 CH 3 CH 2 CH 2 alkanes alkenes CH 3 OH CH 3
CH 3 CH 3
CH 2
CH 2
alkanes
alkenes
CH 3
OH
CH 3
OCH 3
alcohols
ethers
O
O
CH 3
CH 3
C
C H
CH
3
aldehydes
ketones

HC CH

CH 3 CH 3 C C H CH 3 aldehydes ketones H C C H alkynes

alkynes

CH 3

NH 2

amines

CH 3

O

OHketones H C C H alkynes CH 3 NH 2 amines CH 3 O carboxylic acids

carboxylic acids

CH 3

Br

alkyl halides

O CH 3 C OCH 3 esters
O
CH 3
C
OCH 3
esters

Hybrid orbitals of oxygen and nitrogen

Nitrogen: sp3 2p hybridize 2s 1s
Nitrogen: sp3
2p
hybridize
2s
1s
N: 1s 2 2s 2 2p 3 N H CH 3 H H H H
N: 1s 2 2s 2 2p 3
N
H
CH 3
H H
H
H
ammonia
methyl amine
2 2s 2 2p 3 N H CH 3 H H H H ammonia methyl amine

1s2 2s 2 2p 3 N H CH 3 H H H H ammonia methyl amine

sp 3

one sp 3 orbital already filled with an unshared pair of electrons bonding can occur to three other atoms

pair of electrons bonding can occur to three other atoms Oxygen: sp 3 2p hybridize 2s
Oxygen: sp 3 2p hybridize 2s 1s 1s
Oxygen: sp 3
2p
hybridize
2s
1s
1s

sp 3

O: 1s 2 2s 2 2p 4

two sp 3 orbitals already filled with an unshared pair of electrons bonding can occur to two other atoms

O H O H H CH 2 CH 3 water ethanol
O
H O
H
H
CH 2 CH 3
water
ethanol
sp 3 sp 2 CH 3 O O C CH 2 CH 3 CH 2
sp 3
sp 2
CH 3
O
O C
CH 2 CH 3
CH 2 CH
CH 3
3
diethyl ether
acetone

Chapter 1-21

Resonance Structures

Chem 61

RESONANCE STRUCTURES

Chapter 6; Bruice, Pages 260 - 282:

Some molecules cannot be accurately represented by one simple line-bond formula:

they are "hybrids" of two or more structures

O O

O

C
C

O

O

C
C

O

O

OCO

1. Resonance structures exist only on paper

hybrids of all the resonance structures

O –2/3 2/3– O O –2/3 C the actual structures are
O –2/3
2/3– O
O –2/3
C
the
actual structures are

2. Resonance structures differ only in the position of electron pairs

atoms

not

3. All structures should be proper Lewis structures (exceptions)

4. All resonance structures should have the same number of unpaired

electrons

Nonequivalent Resonance Structures

1. Structures with a maximum number of octets is preferred.

2. Charges should be located on atoms with compatible electronegativity.

3. Minimize charge separation.

4. Charge separation may be enforced by the octet rule (atoms may be

charged if they have an octet.)

charge separation. 4. Charge separation may be enforced by the octet rule (atoms may be charged

Chapter 2-1

Hydrocarbons

Chem 61

CHAPTER 2

Hydrocarbons: compounds containing only hydrogen and carbon: alkanes, alkynes, alkenes

alkanes contain only C—H and C—C single bonds C n H 2n+2 ; alkenes C n H 2n contain C— C double bonds and alkynes C n H 2n-2 contain C—C triple bonds

Alkanes do not react with hydrogen, but alkenes and alkynes can react with hydrogen under certain conditions

CH 2 CH 2 alkene CH C C CH 3 3
CH 2
CH 2
alkene
CH
C
C
CH 3
3

alkyne

H 2 , catalyst

2 CH 2 alkene CH C C CH 3 3 alkyne H 2 , catalyst 2H

2H 2 , catalyst

C C CH 3 3 alkyne H 2 , catalyst 2H 2 , catalyst CH 3

CH 3

CH 3

alkane

H 3 C–H 2 C CH 2 –CH 3

ISOMERISM

Structural Isomers:

differ in the order in which the atoms are bonded to one another

compounds with the same molecular formula that

CH 3

CH 3 C CH 3
CH 3
C
CH 3

CH 3

C

5 H 12

2,2-dimethylpropane

CH 3

H CH 3 C C CH 3 H H
H CH 3
C
C
CH 3
H
H

C

5 H 12

2-methylbutane

CH 3

H H H CCC H H H
H
H
H
CCC
H
H H

C

5 H 12

n-pentane

CH 3

CH 3 H CH 3 C C CH 3 H H C 5 H 12 2-methylbutane

Chapter 2-2

Nomenclature

Chem 61

NOMENCLATURE

Alkanes are named by the following parent names

CH

CH

CH

CH

CH

CH

CH

CH

CH

CH

4

3

3

3

3

3

3

3

3

3

CH

CH

(CH

(CH

(CH

(CH

(CH

(CH

(CH

3

2 CH 3

2 ) 2 2 ) 3 2 ) 4 2 ) 5 2 ) 6 2 ) 7 2 ) 8

CH

CH

CH

CH

CH

CH

CH

3

3

3

3

3

3

3

methane

ethane

propane

butane

pentane

hexane

heptane

octane

nonane

decane

C1

C2

C3

C4

C5

C6

C7

C8

C9

C10

Cyclic alkanes are named the same but with cyclo as a prefix

Cyclic alkanes are named the same but with cyclo as a prefix cyclohexane cyclobutane Branched hydrocarbons

cyclohexane

cyclobutane

Branched hydrocarbons are named from the parent with a substituent as a prefix hydrocarbon

branches are named by dropping ane from the parent and adding

thus

methane:

methyl

ethane:

ethyl

propane:

propyl , etc.

-yl

special trivial names for branches

CH 3

propyl , etc. -yl special trivial names for branches CH 3 CH 3 CH 3 C

CH 3

CH 3

-yl special trivial names for branches CH 3 CH 3 CH 3 C H 3 H

CH 3

H CH 3

isopropyl

tert-butyl

H CH 3 C C CH 3 H H
H CH 3
C
C
CH 3
H
H

isobutyl

H CH 3 C C CH 3 H H sec-butyl
H
CH 3
C
C
CH 3
H
H
sec-butyl
3 C H 3 H CH 3 isopropyl tert-butyl H CH 3 C C CH 3

– 23 –

Chapter 2-3

Nomenclature

Chem 61

BASIC RULES OF NOMENCLATURE

1. Find the longest continuous chain (not necessarily drawn as a straight

line) and name the parent

2. Number the parent chain starting at the end nearest the branch

3. Identify the branch and its position

4. Attach the number and the name of the branch to the parent name.

H CH 3

and the name of the branch to the parent name. H CH 3 the branch is
and the name of the branch to the parent name. H CH 3 the branch is

the branch is CH 3 ; therefore methane

butane is the parent

CH 3 C C CH 3 4 3 2 1 H H
CH 3
C
C
CH 3
4 3
2
1
H
H
2-methylbutane H H CH 3 H CH 3 C C C C
2-methylbutane
H
H CH 3 H
CH 3
C
C
C C

CH 3

3,3,5-trimethylhexane

H 3 C H CH 3 H Other Functional Substitutents —CO 2 H C H
H 3 C
H CH 3 H
Other Functional Substitutents
—CO 2 H
C
H
O
C
increasing
O
priority
—OH
—NR 2
—C=C—
—C≡C—
R—,
C
6 H 5 —,
Cl—, Br—,
—NO 2

-oic acid

-al

-one

-ol

-amine

-ene

-yne

prefix

substituents

R—, C 6 H 5 —, Cl—, Br—, —NO 2 -oic acid -al -one -ol -amine

methyl

R—, C 6 H 5 —, Cl—, Br—, —NO 2 -oic acid -al -one -ol -amine

– 24 –

Chapter 2-4

Nomenclature

Chem 61

alkenes H H CH 3 C C C C CH 3 H H CH 3
alkenes
H H
CH 3
C
C
C
C
CH 3 H
H
CH 3

CH 3

2,5-dimethyl-2-hexene

alcohols H H CH 3 CH 3 CCC HO H H
alcohols
H H
CH 3
CH 3
CCC
HO
H
H

H 2-pentanol

carboxylic acids

H H H HCCC Br H H
H
H
H
HCCC
Br
H
H

COOH

4-bromobutanoic acid

aldehydes and ketones

CH 3

H H CH 2 CH 3 CCC CHO
H H
CH 2 CH 3
CCC
CHO

H CH 3 H

2-ethyl-3-methylpentanal

H O CH 2 CH 2 CH 3 CH 3 CCC CH 3 H H
H
O
CH 2 CH
2 CH 3
CH 3
CCC
CH
3
H
H
4-methyl-3-heptanone
CHO H CH 3 H 2-ethyl-3-methylpentanal H O CH 2 CH 2 CH 3 CH 3

– 25 –

Chapter 2-5

Alkanes

Chem 61

ALKANES

Physical Properties

nonpolar compounds

C1 to C4 are gases;

C5 to C17 are liquids;

>C17 are solids

Boiling points increase about 30°C for each additional CH 2 unit

branching lowers the boiling point due to disruption of van der Waals attractions

insoluble in water; soluble in organic solvents like diethyl ether, benzene

Chemical Properties

very unreactive compounds

Halogenation

CH 3 CH 3

+

Cl 2

light

compounds Halogenation CH 3 CH 3 + Cl 2 light Oxidation of Alkanes Combustion CH 3

Oxidation of Alkanes

Combustion

CH 3 CH 2 CH 2 CH 2 CH 3

+ 8O 2

CH 3 CH 2 Cl + HCl + other products

spark

3 + 8O 2 CH 3 CH 2 Cl + HCl + other products spark 5CO

5CO 2

+

6H 2 O

oxidation: a reaction that either removes a hydrogen atom from a carbon or adds an electronegative element to the molecule (O, N, S, halogen).

low oxidation level

to the molecule (O, N, S, halogen). low oxidation level high oxidation level CH 3 CH

high oxidation level

CH 3 CH 3

CH

CH

CH

CH

2

3

3

3

=CH 2

CH

CH

CH

2

2

2

OH

NH 2

Cl

HCCH

CH

CH

CH

3

3

3

CH=O

CH=NH

CHCl 2

CH

CH

CH

3

3

3

CO 2 H CN CCl 3

CO 2

CCl 4

2 OH NH 2 Cl HC ≡ CH CH CH CH 3 3 3 CH=O CH=NH

– 26 –

Chapter 2-6

Oxidation and Reduction

Chem 61

"Complete"/"incomplete" oxidation (combustion) of propane

CH 3 CH 2 CH 3

2 CH 3 CH 2 CH 3

CH 3 CH 2 CH 3

5O 2 7O 2 2O 2
5O 2
7O 2
2O 2

3

O=C=O + 4 H 2 O "complete" combustion

6

CO

+ 8 H 2 O

"incomplete" combustion

3

C + 4 H 2 O

"incomplete" combustion

Heat of Combustion: energy released when a compound is completely oxidized to CO 2 and water; depends mostly on number of CH 2 units:

approximately 157 kcal/ methylene unit

Reduction of Alkenes, Alkynes

reduction: a reaction that either adds H atoms or removes an electronegative atom from the molecule

CH CH 3 3 CH =CH 2 2 HC≡CH
CH
CH 3
3
CH
=CH 2
2
HC≡CH

Pd, Ni,or Pt; H 2

Pd, Ni,or Pt; H 2

Pd, Ni,or Pt; H 2

Pd, Ni,or Pt; H 2

Pt; H 2 Pd, Ni,or Pt; H 2 Pd, Ni,or Pt; H 2 heat no reaction

heat

no reaction (NR) CH CH 3 3 Pd, Ni, Pt CH =CH 2 2 H
no reaction (NR)
CH
CH 3
3
Pd, Ni, Pt
CH
=CH 2
2
H 2

CH 3 CH 3

Pd, Ni,or Pt; H 2 Pd, Ni,or Pt; H 2 heat no reaction (NR) CH CH

Chapter 2-7

Conformations of Acyclic Hydrocarbons

Chem 61

CONFORMATIONS OF OPEN CHAIN COMPOUNDS

Molecular Mechanics

Steric Energy: (isolated molecule in gas phase at 0° K): relative energy of a conformation or stereoisomer calculated using classical mechanics (atoms and bonds treated as balls and springs)

Stretch (bond length): energy associated with stretching or compressing bonds from their optimal length

Bend (bond angle): energy associated with deforming bond angles from their optimal angle

Stretch-Bend: energy required to stretch two bonds involved in a severely compressed bond angle

dipole-dipole: energy associated with interaction of bond dipoles

out of plane: energy required to distort a trigonal center out of planarity

torsional strain: destabilization from eclipsing of bonds on adjacent atoms

van der waals strain: destabilization from two atoms being too close together

Ethane

E

Ethane

dimensional

H

H

H H C C H
H
H
C
C
H

H

staggered

Newman projection

H H H H H H H H H H H H staggered eclipsed
H
H
H
H
H
H
H
H
H
H
H H
staggered
eclipsed
eclipsed ∆H = 3 kcal/mole 0 kcal staggered
eclipsed
∆H = 3 kcal/mole
0 kcal
staggered
eclipsed eclipsed ∆H = 3 kcal/mole 0 kcal staggered 0 60 120 180 240 300 360

0

60

120

180

240

300

360

Butane

E

eclipsed methyls eclipsed 4.5 kcal 3.8 kcal gauche 0.9 kcal anti 0 60 120 180
eclipsed methyls
eclipsed
4.5 kcal
3.8 kcal
gauche
0.9 kcal
anti
0 60
120
180
240
300
360
CH 3 H H H H H H H CH 3 H H H CH
CH 3
H
H
H
H
H
H
H CH 3
H
H
H CH 3
H H
H H
H H
H H
H
H
H
CH 3
CH 3
H
H CH 3
CH 3
CH 3
H 3 C CH 3
H CH 3
CH 3
eclipsed 1
anti
gauche
eclipsed 2
gauche
eclipsed 3

Chapter 2-8

Conformations of Cyclic Hydrocarbons

Chem 61

CYCLIC COMPOUNDS

Strain energy -∆H (kcal/mole) -∆H per CH 2 strain energy per CH 2 total strain
Strain energy
-∆H
(kcal/mole)
-∆H
per CH 2
strain energy
per CH 2
total strain energy
499.8
166.6
cyclopropane
9.2
27.6
655.9
164.0
cyclobutane
6.6
26.4
793.5
158.7
cyclopentane
6.5
1.3
944.5
157.4
cyclohexane
0
0
cyclopropane: bond angles 60°; tetrahedral 109.5°
sp 3 orbitals are 109.5° apart
cyclopropane bond angles 60°
maximum overlap cannot be achieved
cyclobutane and cyclopentane
H
H
H
H
H
H
H
H
H
H
H
H H
H H
H
H
H

puckered cyclobutane

envelope cyclopentane

puckering allows bond angles to be at or close to the tetrahedral angle and minimizes torsional strain (electron—electron repulsions in eclipsed bonds) between adjacent C—H bonds

angle and minimizes torsional strain (electron—electron repulsions in eclipsed bonds) between adjacent C—H bonds

Chapter 2-9

Conformations of Cyclohexane

Chem 61

E

cyclohexane H H H H H equatorial bonds H H H H H H H
cyclohexane
H
H
H
H H
equatorial bonds
H
H
H
H
H
H
H
chair cyclohexane
axial bonds
half chair
boat
twist boat
7.1
5.5
10.8 kcal
chair
0
60
120
180
240
300
360
H
H
H
H H
H
H
H H
H
H
H
H
H
H
H
H
H
H H
H H
H H H
H
H
H
H H
H
H H
H
H H
chair
half chair
boat
chair
twist boat

Chapter 2-10

Conformations of Cyclohexane

Chem 61

Substituted Cyclohexanes

substitutents on cyclohexanes preferntially occupy equatorial positions due to 1,3 diaxial interactions in axially substituted cyclohexanes

E

H H H H C H H CH 3 H H more stable by 1.8
H H
H H
C
H
H
CH 3
H
H
more stable by
1.8 kcal/mole
H
H
H
H
H
1,3-diaxial interactions
gauche
H CH 3
H H
H
C
H
H
C
H
anti
H
H
C
H
C
CH 3
H H
H
H

axial substitution similar to gauche butane equatorial substitution similar to anti butane

CH 3 H CH 3 CH 3 C H H H H
CH
3
H CH 3
CH 3
C
H
H
H
H

G = -RTlnK

H H H H H
H
H
H H
H

C(CH 3 ) 3

5.6 kcal/mole

more stable

G = -(1.98 kcal/mol°)(298)(2.94) = - (1.98 kcal/mol°)(298)(ln19)

= -1.74 kcal/mole for methylcyclohexane

more stable ∆ G = -(1.98 kcal/mol°)(298)(2.94) = - (1.98 kcal/mol°)(298)(ln19) = -1.74 kcal/mole for methylcyclohexane

Chapter 3-1

Stereochemistry: Geometric Isomers

Chem 61

Chapter 3 STEREOCHEMISTRY

Geometric isomerism in cyclic compounds

OH OH
OH
OH
OH H H
OH
H
H

OH

OH

OH

trans-1,2-cyclohexanediol CH 3 CH 3
trans-1,2-cyclohexanediol
CH 3
CH 3

trans-1,3-dimethylcyclobutane

cis

H H Br Br Br
H
H
Br
Br Br

cis

cis

Geometric Isomerism in alkenes

68 kcal/mole to cleave a carbon-carbon pi bond thus no "free" rotation

H CH 3 C C CH 3 H
H
CH 3
C
C
CH 3
H

trans-2-butene

H CH 3 C C CH 3 CH 2 H
H
CH 3
C
C
CH 3 CH 2
H

trans-2-pentene

CH

H H C C CH 3 3
H H
C
C
CH 3
3

cis-2-butene

H H C C Cl Cl
H
H
C
C
Cl Cl

cis-1,2-dichloroethene

CH 3
CH 3

Chapter 3-2

Absolute Configuration

Chem 61

Stereoisomers: compounds with the same structures differing only in their arrangement of atoms in space.

not cis or transdiffering only in their arrangement of atoms in space. CH 3 Cl C C CH 3

CH 3 Cl C C CH 3 CH 2 H
CH 3
Cl
C
C
CH 3 CH 2
H

E entgegen (across)

Cl F C C Br I
Cl
F
C
C
Br
I

Z zusammen (together)

Cahn-Ingold-Prelog Sequence rules

1. if the atoms are different, highest atomic number gets highest priority

2. if two isotopes of the same element, the one with the higher mass gets

higher priority

3. if the atoms are the same, the atomic numbers of the next atoms are used

to assign priority

4. atoms attached by double or triple bonds are given single bond

equivalencies

R

O

C
C

R'

R

bonds are given single bond equivalencies R O C R' R CR' = R = (O)

CR'

= R

=

(O)

C R' O (C)
C
R'
O (C)

R

O

OHR O C R' R CR' = R = (O) C R' O (C) R O

(O)

C OH O (C) (C)
C
OH
O
(C)
(C)
RCH H C R'
RCH
H
C
R'

(C)

= R

(C)

R C (C) R C C—R' R' C (C) H H
R
C
(C)
R
C
C—R'
R'
C
(C)
H
H

(C)

O (C) R O OH (O) C OH O (C) (C) RCH H C R' (C)

Chapter 3-3

Stereochemistry: Chirality

Chem 61

CHIRALITY

An object or molecule which cannot be superimposed on its mirror image is said to be chiral

Br C* CH 3
Br
C*
CH 3

If an object or molecule can be superimposed on its mirror image, it is achiral.

Enantiomers: isomers which are nonsuperimposable mirror images.

mirror plane

Cl Br I H
Cl
Br
I
H
Cl I Br H
Cl
I
Br
H
Cl Cl I Br H Br I H
Cl
Cl
I
Br
H
Br
I
H

Stereogenic carbon atom: a carbon with four different groups bonded to it (designated *).

H H OH Cl CH CH C* Cl 3 3 CH C* CH CH H
H
H
OH
Cl
CH
CH
C* Cl
3
3
CH
C*
CH
CH
H
3
2
3
CH 2 CH
enantiomers
CH 2 CH 3
3
CH 2 CH
CH
2
3
Fischer Projections
by convention: horizontal bonds come out of the paper
vertical bonds go back into the paper
CH 3
H H
CH 3
H
C
OH
H
OH
H
OH
H
OH
CH 2 CH 3
H
C
OH
H
OH
CH 2 CH 3
CH 3
CH 3

Chapter 3-4

Stereochemistry: Chirality

Chem 61

OPTICAL ROTATION

enantiomers have almost all the same physical and chemical properties

properties which differ are:

1. interaction with other chiral substances

2. interactions with polarized light

Polarimeter
Polarimeter

lamp

ordinary

polarized light

rotated light

light

ordinary polarized light rotated light light
ordinary polarized light rotated light light
ordinary polarized light rotated light light
ordinary polarized light rotated light light

polarizer

solution of

sample

if plane polarized light is passed through a solution of a single enantiomer, the light is rotated either to the right or the left; the opposite enantiomer will rotate the light in the opposite direction

optically active: a compound which rotates plane polarized light optical isomers: enantiomers

dextrorotatory: rotates plane polarized light to the right, also (+) or d levorotatory: rotates plane polarized light to the left, also (–) or l

racemic mixture: a 1:1 (50:50) mixture of two enantiomers

does not rotate plane polarized light; therefore optically inactive

Chapter 3-5

Stereochemistry: Absolute Configuration

Chem 61

Absolute configuration: the order of arrangement of the four groups around a stereogenic center

enantiomers have opposite configurations

(R) and (S) Cahn-Ingold-Prelog System

R: rectus or right S: sinister or left

To assign R and S to an asymmetric atom

1. Rank the four attached groups from 1 (highest) to 4 (lowest) priority

based on the Cahn-Ingold -Prelog Sequence rules

2. Project the molecule with the lowest priority group to the rear

3. Draw a semicircle from 1 to 2 to 3

4. If the direction of the semicircle is clockwise; configuration is R; if

counterclockwise; configuration is S

1

3 CH 3 Br C Cl
3
CH 3
Br
C
Cl

H

4

R

2

3 CH 3 2 CH 3 CH C OH 1 2 H 4 R
3
CH 3
2 CH 3 CH
C
OH
1
2
H
4 R

If lowest priority group is out; assign the configuration as usual and then reverse it

1

2

Cl Br C CH 3
Cl
Br
C
CH 3

4

H

3

lowest priority group out

as usual and then reverse it 1 2 Cl Br C CH 3 4 H 3
R
R

S

2 Cl
2
Cl

3

CH 3

C

H

4

Br

S

1

as usual and then reverse it 1 2 Cl Br C CH 3 4 H 3

Chapter 3-6

Stereochemistry: Diastereomers

Chem 61

Molecules with Two or more Asymmetric centers

If a molecule has n asymmetric carbon atoms, it contains a maximum of 2 n isomers; may not have that many

diastereomers

diastereomers

diastereomers

diastereomers
diastereomers
diastereomers
diastereomers
diastereomers
diastereomers
diastereomers
CH 2 OH H C OH H C OH
CH 2 OH
H
C
OH
H
C
OH

CH 3

HO

HO

enantiomers

CH 2 OH CH 2 OH C H H C OH C H HO C
CH 2 OH
CH 2 OH
C
H
H
C
OH
C
H
HO
C
H
CH 3
CH 3
CH 2 OH HO C H H C OH
CH 2 OH
HO
C
H
H
C
OH

CH 3

enantiomers

two asymmetric carbons; 4 isomers

diastereomers: stereoisomers which are not enantiomers; may have different physical and chemical properties

Meso compounds

meso compounds contain an internal plane of symmetry and are achiral: that is the mirror image is identical to the original

diastereomers

meso: identical

meso: identical
meso: identical
meso: identical
meso: identical

CH 2 OH

H C OH H C OH
H
C
OH
H
C
OH

CH 2 OH

CH 2 OH CH 2 OH HO C H H C OH HO C H
CH 2 OH
CH 2 OH
HO
C
H
H
C
OH
HO
C
H
HO
C
H
CH 2 OH
CH 2 OH
CH 2 OH HO C H H C OH
CH 2 OH
HO
C
H
H
C
OH

CH 2 OH

superimposable

enantiomers

H CH 3
H
CH 3

mirror plane

meso

H

CH 3

a n t i o m e r s H CH 3 mirror plane meso H

H

H CH 3 CH 3
H
CH 3
CH 3

chiral

H HO OH HO H H H OH meso chiral mirror plane
H
HO
OH HO
H
H H
OH
meso
chiral
mirror plane

Chapter 3-7

Stereochemistry: Asymmetric Synthesis, Resolution

Chem 61

Preparation of Enantiomerically Enriched Compounds

Generating chiral compounds from achiral compounds

Enzymes

O

O

chiral compounds from achiral compounds Enzymes O O OEt yeast HO O H >98% R OEt

OEt

yeast

HO

O

H >98% R
H
>98% R

OEt

Asymmetric Reagents

O H OH

H O t-BuOOH OH (+)-diethyl tartrate H Ti(i-OPr) 4
H
O
t-BuOOH
OH
(+)-diethyl tartrate
H
Ti(i-OPr) 4

>95%

one enantiomer

Resolution of a Racemic Mixture

(R) R*COOH

+

(S) R*COOH

racemic

separated salt converted back to acid

+ (S) R*NH 2

+

+

(R) R*COO (S) R*NH 3 +

(S) R*COO (S) R*NH 3

(R) R*COOH

+

diastereomeric salts (separable)

(S) R*COOH

(R) R*COO – (S) R*NH 3 + (S) R*COO – (S) R*NH 3 (R) R*COOH +
(R) R*COO – (S) R*NH 3 + (S) R*COO – (S) R*NH 3 (R) R*COOH +

Chapter 4-1

Acids and Bases

Chem 61

ACIDS AND BASES

Bronsted-Lowry:

acid: a proton donor base: a proton acceptor

Strong acid: completely ionized or dissociated in water e.g., HCl, H 2 SO 4 , HNO 3 , HBr

Weak acid: only partially dissociated in water:

carboxylic acids are weak acid

CH 3 CO 2 H acid

+

H 2 O

base

CH 3 CO 2 - CH 3 CO 2 -

+

H 3 O +

conjugate base

conjugate acid

CH 3 NH 3 +

+

HO

conjugate acid

conjugate base

amines are weak bases

CH 3 NH 2

base

+

H 2 O

acid

amines are weak bases CH 3 NH 2 base + H 2 O acid Generally: strong

Generally: strong acids have weak conjugate bases and weak acids have strong conjugate bases

that is, as acid strength increases, the basicity of the conjugate base decreases

Thus the ability of the conjugate base to stabilize a negative charge determines the strength of an acid

Conjugate Acids

HCN CH 3 CO 2 H H 3 PO 4 HCl H 2 O 15.75
HCN
CH 3 CO 2 H
H 3 PO 4
HCl
H 2 O
15.75
6.37
4.75
2.12
-7
pK a
increasing acid strength
Conjugate Bases
HO –
NC –
CH 3 CO 2 –
H 2 PO 4 –
C l –

decreasing base strength

increasing acid strength Conjugate Bases HO – NC – CH 3 CO 2 – H 2

Chapter 4-2

Acids and Bases

Chem 61

Factors affecting Acidity:

the electronegativity and the size of the atom which carries the negative charge influence its ability to stabilize the negative charge

size of the atom

H—F

H—Cl

H—Br

H—I

pK a

3.45

-7

-9

-9.5

increasing size of halogen, increasing acid strength
increasing size of halogen, increasing acid strength

electronegativity

(CH 3 ) 3 C—H

pK a

50

(CH 3 ) 2 N—H

35

CH 3 O—H

15.5

F—H

3.45

increasing electronegativity of atom, increasing acid strength

ACIDITY CONSTANTS, Ka's

for acetic acid

CH 3 CO 2 H + H 2 O

CH 3 CO 2 H + H 2 O C H 3 C O 2 –

CH 3 CO 2 + H 3 O +

K a = [CH 3 CO 2 ] [H + ] [CH 3 CO 2 H]

since stronger acids are more ionized, the larger Ka, the stronger the acid

pKa = -logKa, the lower the pKa, the stronger the acid

also, the higher the pKa, the weaker the acid or the stronger the base

the stronger the acid, the more stable the anion produced by ionization of the acid.

Chapter 4-3

Lewis Acids and Bases

Chem 61

LEWIS ACIDS AND BASES

Lewis acid: electron pair acceptor: any species with an electron deficient atom

BBr 3 , AlCl 3 ,

H 3 C +

Lewis base: electron pair donor; any species with an unshared pair of electrons

H 3 N:, CH 3 CH 2 OH, H 2 C=O:

Chapter 5-1

Alkenes: Structure and Isomerism

Chem 61

ALKENES Alkene Structure sp 2 hybridized carbons are trigonal planar with atoms 120° apart 2p
ALKENES
Alkene Structure