Chapter 1

The Basics Bonding and Molecular Structure

Ch. 1 - 1

1. Introduction

Organic Chemistry is the study of carbon compounds. Most also contain hydrogen Many contain nitrogen, oxygen, phosphorus, sulfur, chlorine, called heteroatoms

Ch. 1 - 2

2. Atomic Structure
Compounds made up of elements combined in different proportions Elements made up of atoms Atoms positively charged nucleus containing protons and neutrons with a surrounding cloud of negatively charged electrons Ch. 1 - 3

Each element is distinguished by its atomic number (Z) Atomic number = number of protons in nucleus

Ch. 1 - 4

Ch. 1 - 5

2A. Isotopes

Some atoms of the same element have different numbers of neutrons. Such atoms are called isotopes

Ch. 1 - 6

Examples
12C 13C 14C

(1)

(6 protons 6 neutrons)

(6 protons 7 neutrons)

(6 protons 8 neutrons)

(2)

1H

2H

=D

3H

=T

Hydrogen (1 proton 0 neutrons)

Deuterium (1 proton 1 neutron)

Tritium (1 proton 2 neutrons)

Ch. 1 - 7

Are deuterium and tritium radioactive?

A. B. C.

Yes, both No, neither Only tritium

0%
,b ot h

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tri tiu On ly m

Ye s

No ,n

Ch. 1 - 8

2B. Valence Electrons

The valence shell, is the outermost shell that an atom uses in making chemical bonds The number of electrons in the valence shell (called valence electrons) is equal to the group number

e.g. Nitrogen is in group VA Nitrogen has 5 valence electrons

Ch. 1 - 9

3. The Structural Theory of Organic Chemistry

Number of covalent bonds usually formed by some elements typically encountered in organic compounds
H C N 1 4 3 (or 4) F Cl Br 1 1 1

Element # of covalent bonds Element # of covalent bonds

1
Ch. 1 - 10

Thus C is tetravalent O is divalent H and halogens are monovalent

C O (divalent) H Br (monovalent)

(tetravalent)

Ch. 1 - 11

Important: Do not draw any structure with more than 4 bonds on a carbon
C C C

4 bonds

Ch. 1 - 12

3 bonds on carbon need a charge on carbon

Br C B C C C

H C

Never draw 5 (or more) bonds on carbon

Ch. 1 - 13

A Glance at Bond-Line Formulas

Ch. 1 - 14

Oxygen Usually divalent

O O H3C O H H3C CH3 (acetone)

(diethyl ether)

(methanol)

Ch. 1 - 15

e.g.

Lone pair electrons on oxygen can donate electrons to a Lewis acid 3 bonds on oxygen (with a positive charge on oxygen)
+

H3C H

H3C H

H3C H

dative covalent bond

Whats a Lewis acid?

Ch. 1 - 16

O H3C CH3 F

F B F
H3C

BF3 CH3

empty p-orbitals

Ch. 1 - 17

One bond on oxygen Usually need a negative charge on oxygen

e.g. O R O H OH
R O O

Ch. 1 - 18

3A. Isomers: The Importance of Structural Formulas

Different compounds that have the same molecular formula. Such compounds are called isomers
e.g. 1-Butanol OH O Diethyl ether

Ch. 1 - 19

 Both have the molecular formula C4H10O They are constitutional isomers Constitutional isomers usually have different physical properties (e.g., melting point, boiling point, and density) and different chemical properties (reactivity)
Ch. 1 - 20

3B. The Tetrahedral Shape of Methane

Ch. 1 - 21

4. Chemical Bonds: The Octet Rule

Ionic (or electrovalent) bonds are formed by the transfer of one or more electrons from one atom to another to create ions Covalent bonds result when atoms share electrons
Ch. 1 - 22

Octet Rule In forming compounds, they gain, lose, or share electrons to give a stable electron configuration characterized by 8 valence electrons When the octet rule is satisfied for C, N, O and F, they have an electron configuration analogous to the noble gas Ne

Ch. 1 - 23

Important Exceptions to the Octet Rule: BX3 (X is hydrogen or a halogen) O2

Ch. 1 - 24

Recall: electron configuration of noble (inert) gas # of e-s in outer shell He [1s2] Ne 1s2[2s22p6] Ar 1s22s22p6[3s23p6] 2 8 8

Ch. 1 - 25

4A. Ionic Bonds

Atoms may gain or lose electrons and form charged particles called ions An ionic bond is an attractive force between oppositely charged ions

Ch. 1 - 26

Electronegativity (EN) The intrinsic ability of an atom to attract the shared electrons in a covalent bond

Electronegativities are based on an arbitrary scale, with F the most electronegative (EN = 4.0) and Cs the least (EN = 0.7)
Ch. 1 - 27

element (EN) Li (1.0) Na (0.9) K (0.8) Rb (0.8) Cs (0.7) Be (1.6) Mg (1.2)

H (2.1) .. B (2.0) C (2.5) Si (1.8) N (3.0) P (2.1) O (3.5) S (2.5) F (4.0) Cl (3.0) Br (2.8) I (2.5)

...

.. ..

Ch. 1 - 28

4B. Covalent Bonds & Lewis Structures

Covalent bonds form by sharing of electrons between atoms of similar electronegativities to achieve the configuration of a noble gas

Preferred if electronegativity difference is small

Ch. 1 - 29

Example

:Cl.
[Ne] 3s2 3p5

. Cl:
[Ne] 3s2 3p5
covalent bonding

: :

: :

:ClCl:
Ch. 1 - 30

: : : :

Ions, themselves, may contain covalent bonds. Consider, as an example, the ammonium ion
H H N H H

N H

H+

(ammonia) (3 bonds on N)

(ammonium cation) (4 bonds on N with a positive charge on N)

Ch. 1 - 31

5. How to Write Lewis Structures

Show lone (same as non-bonding electrons) as dots, bonding electron pairs as lines Some variability acceptable Indicate all charges

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 (1)

Examples Lewis structure of CH3Br Total number of all valence electrons: C H Br

4 + 1 x 3 + 7 = 14
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H C Br

H
H H

: :

Br:
remaining 6 valence electrons
Ch. 1 - 34

8 H valence electrons

(2)

Lewis structure of methylamine (CH5N) Total number of all valence electrons: C H N

4 + 1 x 5 + 5 = 14
Ch. 1 - 35

H C N H

H
H
12 valence electrons

H
2 valence electrons left

:
N H

C
H

Ch. 1 - 36

6. Exceptions to the Octet Rule

Elements in the 2nd row in the periodic table usually obey the Octet Rule Elements in the 3rd row in the periodic table have d orbitals that can be used for bonding

Ch. 1 - 37

Examples
Cl P Cl Cl Cl Cl Cl P Cl Cl Cl Cl Cl P Cl Cl Cl

Cl

(PCl5)

Phosphorus pentachloride m.p. = 179oC

F Si F F

2F F

(SiF62-)

Ch. 1 - 38

Some highly reactive molecules or ions have atoms with fewer than eight electrons in their outer shell

F F B F

Ch. 1 - 39

7. Formal Charges and How to Calculate Them

F = Z - S /2 - U
where F is the formal charge, Z is the group number of the element, S equals the number of shared electrons, and U is the number of unshared electrons

Ch. 1 - 40

Examples (1) The Ammonium ion (NH4+)

H H NH H

Recall: F = Z - S /2 - U

Formal charge of H:
= 1 2/2 0 = 0
group number of H number of shared electrons number of unshared electrons
Ch. 1 - 41

Formal charge of N: = 5 8/2 0 = +1

group number of N number of shared electrons number of unshared electrons

Charge on ion = 4 x 0 +1 = +1
The arithmetic sum of all the formal charges in a molecule or ion will equal the overall charge on the molecule or ion

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(2) The Nitrate ion

O N

(NO3 )

Recall: F = Z - S /2 - U

Formal charge of O: = 6 2/2 6 = -1

group number of O number of shared electrons number of unshared electrons
Ch. 1 - 43

7A. A Summary of Formal Charges

Ch. 1 - 44

What is the formal charge of Oxygen in the following structure

A.
B. C. D. E.

+2 +1 0 -1 -2
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-1

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-2

What is the formal charge of Nitrogen in the following structure

A.

B.
C. D. E.

+2 +1 0 -1 -2
2

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1

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0

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-1

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-2

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8. Resonance Theory

In a Lewis structure, we draw a welldefined location for the electrons in a molecule. In many molecules and ions (especially those containing p bonds), more than one equivalent Lewis structure can be drawn which represent the same molecule

Ch. 1 - 47

We can write three different but equivalent structures, 13

O O C 1 O O O C 2 O O O C 3 O

Ch. 1 - 48

O O C 1 O

becomes O

O C 2 O

becomes O

O C 3 O

Structures 13, although not identical on paper, are equivalent; all of its carbonoxygen bonds are of equal length
Ch. 1 - 49

Resonance theory states that whenever a molecule or ion can be represented by two or more Lewis structures that differ only in the positions of the electrons, two things will be true:
None of resonance will be a realistic representation for the molecule or ion. The actual molecule or ion will be better represented by a hybrid (average) of these structures

Ch. 1 - 50

 Resonance structures, then, are not real structures for the actual molecule or ion; they exist only on paper
O O C O
O O C O O O C O

Ch. 1 - 51

 It is also important to distinguish between resonance and an equilibrium In an equilibrium between two or more species, it is quite correct to think of different structures and moving (or fluctuating) atoms, but not in the case of resonance (as in the carbonate ion). Here the atoms do not move, and the structures exist only on paper. An equilibrium is indicated by and resonance by
Ch. 1 - 52

We are only allowed to move electrons in writing resonance structures

CH2 H3C CH CH 2 CH2 1

H3C CH CH

These are resonance structures

H2C CH2 CH CH2

This is not a proper resonance structure of 1 and 2 because a hydrogen atom has been moved

Ch. 1 - 53

Are the molecules below resonance forms?

OH CH2 C CH3 CH3 O C CH3

A. B.

Yes No

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Ch. 1 - 54

All of the structures must be proper Lewis structures

H H C H O H

This is not a proper resonance structure of methanol

Ch. 1 - 55

The energy of the resonance hybrid is lower than the energy of any contributing structure. Resonance stabilizes a molecule or ion.

Ch. 1 - 56

The more stable a resonance structure is (when taken by itself), the greater is its contribution The more covalent bonds a structure has, the more stable it is Charge separation decreases stability

Resonance structures for formaldehyde Four covalent bonds O H C H

O H C H

Three covalent bonds

Ch. 1 - 57

more stable

less stable

Structures in which all the atoms have a complete valence shell of electrons (i.e., the noble gas structure) are more stable

Ch. 1 - 58

Examples

(1) Benzene

(2) Carboxylate ion (RCOO-) O R O

O R O R

O O

(3) Ozone (O3) O O O

Ch. 1 - 59

9. Quantum Mechanics & Atomic Structure

Wave mechanics & quantum mechanics

Electrons behave more like standing waves than like particles Locations called orbitals best described by wave functions
Ch. 1 - 60

9. Quantum Mechanics & Atomic Structure

Each wave function (y) corresponds to a different energy state for an electron

Each energy state is a sublevel where one or two electrons can reside
Ch. 1 - 61

The phase sign of a wave equation has nothing to do with the charge! Wave functions have the possibility of constructive interference and destructive interference

Ch. 1 - 62

Ch. 1 - 63

10. Atomic Orbitals and Electron Configuration

Ch. 1 - 64

On the previous slide, there were red and blue lobes shown. What do these colors indicate?
1. Different charges 2. Different orbitals 3. Wave functions have different signs 4. The blue ones are empty, the red ones are filled

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65

10A. Electron Configurations

Electrons of the three 2p orbitals have equal but higher energy than the 2s orbital Orbitals of equal energy (such as the three 2p orbitals) are called degenerate orbitals

Ch. 1 - 66

Aufbau principle Orbitals are filled so that those of lowest energy are filled first Pauli exclusion principle A maximum of two electrons may be placed in each orbital but only

when the spins of the electrons are paired

Ch. 1 - 67

Hunds rule
When we come to degenerate orbitals, we add one electron to each with their spins unpaired until each of the degenerate orbitals contains one electron. Then we begin pairing them up with opposite spins

Ch. 1 - 68

Ch. 1 - 69

11. Molecular Orbitals

Ch. 1 - 70

Heisenberg:

We cannot simultaneously know the position and momentum of an electron Orbitals rather than orbits

Ch. 1 - 71

When atomic orbitals combine to form molecular orbitals, the number of molecular orbitals that result always equals the number of atomic orbitals that combine

Ch. 1 - 72

A bonding molecular orbital (ymolec) results when two orbitals of the same phase overlap

Ch. 1 - 73

An antibonding molecular orbital (y*molec) results when two orbitals of opposite phase overlap

Ch. 1 - 74

Ch. 1 - 75

12. The Structure of Methane and Ethane: sp3 Hybridization

Ground state of a carbon atom C 1s 2s 2px 2py 2pz

Ch. 1 - 76

Hybridization sp3 covalent bond

H H C H (line bond structure) H

sp3 hybridized carbon

Ch. 1 - 77

Hybridization sp3
H

H C H H

(Lewis structure)

109o H

H C H H

Tetrahedral structure Carbon with 4 bonds

Ch. 1 - 78

(3-D stucture)

12A. The Structure of Methane

Ch. 1 - 79

Ch. 1 - 80

Ch. 1 - 81

Symmetrical around bonding axis: sigma bond!

Ch. 1 - 82

12B. The Structure of Ethane

Ch. 1 - 83

13. The Structure of Ethene (Ethylene): sp2 Hybridization

sp2
~120 H H ~120o C C H H ~120o
o

1 bond + 1 p bond sp2 hybridized carbon

Ch. 1 - 84

sp2
3-Dimensional View p-bond (p-orbitals overlap) H C H C H H

Planar structure Carbon with (3 + 1p) bonds

Ch. 1 - 85

Ch. 1 - 86

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13A. Restricted Rotation and the Double Bond

There is a large energy barrier to rotation associated with groups joined by a double bond ~264 kJmol-1 (strength of the p bond) To compare: rotation of groups joined by C-C single bonds ~13-26 kJmol-1
Ch. 1 - 90

13B. CisTrans Isomerism

Stereochemistry of double bonds

H H H R identical to H H R H

Ch. 1 - 91

H3C

CH3

different from CH3

CH3

(trans)

(cis)

Restricted rotation of C=C

Ch. 1 - 92

e.g.

Cis-Trans System Useful for 1,2 disubstituted alkenes

(1) Cl H Br vs. Cl Br H

H trans -1-Bromo2-chloroethane

H cis-1-Bromo2-chloroethane

Ch. 1 - 93

(2)

H vs. H trans -3-Hexene H H cis -3-Hexene

Br Br Br vs. Br Dibromopropene
Ch. 1 - 94

(3)

Dibromopropene

trans -1,3-

cis -1,3-

14. The Structure of Ethyne (Acetylene): sp Hybridization

sp
1 bond + 2 p bond H C 180o Linear structure Carbon with (2 + 2 p) bonds
Ch. 1 - 95

H sp2 hybridized carbon

Ch. 1 - 96

Ch. 1 - 97

Ch. 1 - 98

Ch. 1 - 99

Remember: A sigma () bond (a type of single bond) is one in which the electron density has circular symmetry when viewed along the bond axis

A pi (p) bond, part of double and triple carboncarbon bonds, is one in which the electron densities of two adjacent parallel p orbitals overlap sideways to form a bonding pi molecular orbital
Ch. 1 - 100

What is the correct molecular orbital diagram for the following structure

A. B. C. D. E.

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16. Molecular Geometry: The Valence Shell Electron Pair Repulsion Model

Valence shell electron pair repulsion (VSEPR) model: 1) Electrons (bonding or not) want to attain maximum distance

Ch. 1 - 102

2) nonbonding pairs (also called unshared pairs or lone pairs) repel more than bonding ones

This shapes the molecules!

Ch. 1 - 103

16A. Methane

Ch. 1 - 104

16B. Ammonia

A tetrahedral arrangement of the electron pairs explains the trigonal pyramidal arrangement of the four atoms. The bond angles are 107 (not 109.5) because the nonbonding pair repels more
Ch. 1 - 105

16C. Water

Ch. 1 - 106

16D. Boron Trifluoride

Ch. 1 - 107

16E. Beryllium Hydride

Ch. 1 - 108

16F. Carbon Dioxide

180
o

or

O :: C :: O

Ch. 1 - 109

Ch. 1 - 110

17. How to Interpret and Write Structural Formulas

Dash Structural Formulas
H C H H C H HH C O H H H H C H C HO C H H H C H HH H C C H H H O

H H Equivalent dash formulas for propyl alcohol

Ch. 1 - 111

17B. Condensed Structural Formulas

Ch. 1 - 112

17C. Bond-Line Formulas

Ch. 1 - 113

Ch. 1 - 114

17D. Three-Dimensional (Wedge)Formulas

H H H
H Br C H H OR H

H C C H OR H H

H C H C

H H etc. H
Br

Ethane H
C H Bromomethane Br OR H H

etc.

Ch. 1 - 115

Br H H OH Cl

H Examples of bond-line formulas that include three-dimensional representations

H NH2 HO Br H

An example involving trigonal planar geometry

An example involving linear geometry

Ch. 1 - 116

Which is the correct bond-line formula for the following structure?

A. B. C. D.
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