Chapter 1

Chapter 1

Structure and Bonding

Chapter 1 - Definitions• Organic Chemistry – is the study of carbon containing

compounds.• Orbitals – are the specific regions of an atom which

maintains electrons. This is defined by quantum mechanics.

• Covalent Bond – is formed when an electron pair is shared between atoms.

• Valance Bond Theory – maintains that bonding occurs by the overlapping of two atomic orbitals.

Chapter 1 - Definitions• Molecular Orbital (MO) Theory – maintains that bonds

results from the mathematical combination of atomic orbitals to give molecular orbitals, which belong to the entire molecule.

• Sigma () bonds – are bonds that are created by the overlap of two s orbitals (sphere).

What is Organic Chemistry?• Organic Chemistry is defined as the study of carbon

compounds.

• There are 10 atoms which are considered in organic chemistry. These atoms are carbon, nitrogen, oxygen, fluorine, silicon, phosphorous, sulfur, chlorine, bromine, iodine.

Defined Organic Molecules

1

H 2

He

3

Li4

Be5

B6

C7

N8

O9

F10

Ne

11

Na12

Mg13

Al14

Si15

P16

S17

Cl18

Ar

19

K20

Ca21

Sc22

Ti23

V24

Cr25

Mn26

Fe27

Co28

Ni29

Cu30

Zn31

Ga32

Ge33

As34

Se35

Br36

Kr

37

Rb38

Sr39

Y40

Zr41

Nb42

Mo43

Tc44

Ru45

Rh46

Pd47

Ag48

Cd49

In50

Sn51

Sb52

Te53

I54

Xe

55

Cs56

Ba57

La72

Hf73

Ta74

W75

Re76

Os77

Ir78

Pt79

Au80

Hg81

Tl82

Pb83

Bi84

Po85

At86

Rn

87

Fr88

Ra89

Ac104

Rf105

Db106

Sg107

Bh108

Hs109

Mt110

Ds

What is Carbon so special?• Carbon has the unique ability to bond together to form

long chains or ring structures.

• This allows carbon to make tens of billions of molecules.

• These molecules can range from DNA and plastics to pharmaceuticals.

Review (1) - Nucleus• An atom maintains 2 parts, the

nucleus and the shells.

• Protons, positively charge particles, and Neutrons, neutral charge particles are found in the nucleus of atoms.

• Although small the nucleus maintains all the mass of an atom with both protons and neutrons contributing to the atomic mass.

• Rule: All protons and neutrons are found in the nucleus.

Nucleus

NN

N = Neutrons+ = Protons

Review (2) – Electrons and Orbitals• Electrons, negatively charge particles,

circle around and through the nucleus in specific orbitals, which defines the electrons path, and shells, which defines the distance from the nucleus. Electron are extremely small when compared to the nucleus and contribute nothing to the molecular mass to the atom.

• Orbitals, are probability clouds which determine where the electron might be. This was determined by a mathematical equation called a wave equation, .

Nucleus

Shells

1s

2s

1s Orbital

= Nucleus= 1s Orbital

1s and 2s Orbitals


= 2s Orbital

Valance Shell

• The Valance Shell is the outermost shell which contains at least one electron.

• In this example the 2s is the valance shell.

Nucleus

Valence Shell = 2s

1s

2s

Energy Levels

Nucleus

Shells

1s

2s

1s

2s

2p

Additional Definitions

• Atomic Number (Z) – the number of protons in the atom’s nucleus.

• Mass Number (A) – the total number of protons and neutrons in its nucleus.

• Atomic Mass – are the weighted average mass unit (amu) of an element’s natural occurring isotopes is called the atomic mass (or atomic weight).

Review (3) – Types of Orbitals• There are many orbitals,

each with specific number of electrons, distance from the nucleus, and shape.

• Specifically there are 4 different types of orbitals, s, p, d, f with organic chemistry focusing on the s and p orbitals.

Nucleus

Shells

1s

2s

1s Orbital


p Orbitalsy

x

zy

x

z

= 2py Orbital

y

x

z

= 2pz Orbital

y

x

z

= 2px Orbital

p Orbitalsy

x

zy

x

z

= 2py Orbital

y

x

z

= 2pz Orbital

y

x

z

= 2px Orbital

Three Overlapping p Orbitals

y

x

z

= 2py Orbital= 2pz Orbital

= 2px Orbital

2s + 2p Orbitalsy

x

z

= 2pz Orbital

= 2px Orbital= 2py Orbital

= 2s Orbital

2s + 2p Orbitalsy

x

z

= 2pz Orbital


= 2s Orbital

= 1s Orbital= Nucleus

1s

2s

2p

Review (4) - Isotopes• Isotopes – atoms with

the same atomic number but different mass numbers.

• This is done by the addition of neutrons to the nucleus of an atom.

• Remember that the mass is from neutrons and protons not electrons.

NucleusHydrogen Deuterium

Nucleus

N

+ = protonN = Neutron

Review (5) – Shell/Orbital Differences

• Difference between a shell and a orbital.

• An orbital is the specific path that a pair of electron makes around the nucleus.

• The shell defines either one or several orbital that are a specific distance away with a node between them.

Nucleus

Shells

1s

2s

Defined Organic Molecules

1

H 2

He

3

Li4

Be5

B6

C7

N8

O9

F

11

Na12

Mg13

Al14

Si15

P16

S17

Cl18

Ar

19

K20

Ca21

Sc22

Ti23

V24

Cr25

Mn26

Fe27

Co28

Ni29

Cu30

Zn31

Ga32

Ge33

As34

Se35

Br36

Kr

37

Rb38

Sr39

Y40

Zr41

Nb42

Mo43

Tc44

Ru45

Rh46

Pd47

Ag48

Cd49

In50

Sn51

Sb52

Te53

I54

Xe

55

Cs56

Ba57

La72

Hf73

Ta74

W75

Re76

Os77

Ir78

Pt79

Au80

Hg81

Tl82

Pb83

Bi84

Po85

At86

Rn

87

Fr88

Ra89

Ac104

Rf105

Db106

Sg107

Bh108

Hs109

Mt110

Ds

10 Ne

= Orbital (2p) = Shells (1, 2, 3, 4, 5, 6)

Review (6) - Atomic Structure• These numbers denote a

series of orbitals that are a certain distance away from the nucleus, that are separated by a node.

• A node is a region where electron density is zero, or a space between different shells.

Nucleus

Shells

1s

2s

Electronic Shells

1s

2s

2p

3s

3p

3d

N = 1

N = 2

N = 3

Electronic ShellMax, Electrons

8

2

18

1 S Electronic Shells

1sN = 1

Electronic ShellMax, Electrons

2

2s + 2p Orbitalsy

x

z

= 2pz Orbital


= 2s Orbital

Take Home Message

• General Understanding:• 1) Atomic Structure • 2) Valance Shell• 3) Orbitals vs Shells

What are Bonds?

• Bond are the either the donation of an electron (ionic) or the sharing of electron(s) (covalent) between two different atoms.

Bonding

H HH = 1 proton, 1 electron

e- e-

H HH2 = 2 protons, 2 electrons

e-e-

1 covalent bond is formed

2 Single Hydrogen Atoms

1 Covalent Bond (H2)

Bonding


e-e-



e-e-



e-e-


Energy

Energy

0

-

H H

H H

HH

+

(too close)

(too far)

74 pm

Number of Single Bonds in Organic Chemistry

H CNO

= non-bonding electron(s)

1 Bond 2 Bonds 3 Bonds 4 Bonds

Bonds Formed

1

H 2

He

3

Li4

Be5

B6

C7

N8

O9

F

11

Na12

Mg13

Al14

Si15

P16

S17

Cl18

Ar

19

K20

Ca21

Sc22

Ti23

V24

Cr25

Mn26

Fe27

Co28

Ni29

Cu30

Zn31

Ga32

Ge33

As34

Se35

Br36

Kr

37

Rb38

Sr39

Y40

Zr41

Nb42

Mo43

Tc44

Ru45

Rh46

Pd47

Ag48

Cd49

In50

Sn51

Sb52

Te53

I54

Xe

55

Cs56

Ba57

La72

Hf73

Ta74

W75

Re76

Os77

Ir78

Pt79

Au80

Hg81

Tl82

Pb83

Bi84

Po85

At86

Rn

87

Fr88

Ra89

Ac104

Rf105

Db106

Sg107

Bh108

Hs109

Mt110

Ds

10 Ne

= Orbital (2p) = Shells (1, 2, 3, 4, 5, 6)

1

2 3 4 3 2 1

0

The Octet Rule

• The Octet rules states that most organic atoms needs 8 electrons to fill its outer shell. Only one example is found that wants only 2 electrons (HYDROGEN).

• Atoms that need 8 electrons: Carbon (C), Nitrogen (N), Oxygen (O), Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I).

Cheat Sheet

• (To fufill the octet) This number of bonds are formed:• 4 = Carbon (C)• 3 = Nitrogen (N), Phosphorus (P)• 2 = Oxygen (O), Sulfur (S)• 1 = Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I),

and Hydrogen (H)

Example

• If you have 1 carbon how many chlorines do you need?• 1 carbon makes 4 bonds. Chlorine makes one bond.

So you need 1 carbon and 4 chlorines.– CCl4– GeCl4– AlH3

– CH2Cl2– CH3NH2

– CH4

Hint – (chapter 1 only)

• 1) Look for the Central Atom• The central atoms in organic chemistry is

normally Carbon (C), Nitrogen (N), Sulfur (S), and Oxygen (O)

• 2) Once you have the central atoms in the molecule then they are filled in with Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I), and Hydrogen (H)

Electron-Dot Structure Examples

HH

HH C

H

HH

H

HOC C H

Methane Ethanol

1) Find the Central Atom.

2) Place the electrons around it. Make sure that you fill the electrons 1 for each orbital first (4 orbitals) until all electrons around the are used.

3) Then add the electrons from the remaining atoms.

Line Structures Examples

CH

HH

H CH

CH

HH

HO H

Methane Ethanol

1) Find the Central Atom.2) Place 1 straight line for each pair of electrons to the remaining atoms.

Line and Electron-Dot Structures

CH

HH

H CH

CH

HH

HO H

Methane Ethanol

HH

HH C

H

HH

H

HOC C H

sp3 Orbitals of Carbon (C)

HC

H HH

109.5oBond Length

109 pmC

• sp3 orbital is the combination the s and p orbitals.

• Geometry = 104.5 oC


1s

2s

2p

Normal

1s

2s

sp3 orbitals

2psp3

HC

H HH

• Normally you have 1s orbital and 3p orbitals. However in the case of Carbon (C) the S and P orbitals merge to form the sp3 orbitals.


• sp3 orbital is the combination the s and p orbitals.

• Example: 4 electrons from Carbon (C) and 4 electrons from the 4 Hydrogens (H)

sp3 orbitals

sp3

HC

H HH


~ 120 oC

134 pm

Pi() bond

CO

HH

XPi orbital

= Flat bonds ~120 oC


1s

2s

2p

Normal

sp2 orbitals

1s

2s

2psp2

CO

HH

• sp2 orbitals is the combination of 3 sp orbitals and 1 p orbital. 1 double bond is formed.

• Geometry = 120 oC flat.


electron

below

above

planar

orbital CO

HH

sp2 orbitals

2psp2

sp Orbitals of Carbon (C)x

yZ

= Flat bonds ~180 oCCCH H

180 oC

~113 pmC C HH

sp Orbitals of Carbon (C)

sp orbitals

1s

2s

2psp

1s

2s

2p

Normal

CCH H

• Sp orbitals is the combination of 2 sp orbitals and 2 p orbital. 1 triple bond is formed.

• Geometry = 180 oC

Structure of Nitrogen, Oxygen, Phosphorus, and Sulfur

NHH CH3

Lone Pair of Electrons

~108 oC

OH CH3

2 Lone Pair of Electrons

~108.5 oC

P

O

O

OO

CH3

~110 oC

SH CH3

2 Lone Pair of Electrons

~98 oC

Nitrogen Oxygen

PhosphorusSulfur

Molecular Orbital Theory

• Combination of atomic orbitals from different atoms to form molecular orbitals. – All of the electrons from each atom is place

on an energy diagram which includes both a bonding and anti-bonding level.

• Bonding is the lower level. • Anti-bonding is the higher level.

– When the Anti-bonding level is totally filled then the bonds are broken and the octet is filled.

Molecular Orbital Theory

1) Sigma bonding

1) Sigma anti-bonding

H H

1) Sigma bonding


He He

Bonding is found between two hydrogen atoms

There is no bonding between two helium atoms

More Complex Molecular Orbital Diagrams

1) Sigma bonding


2) Sigma bonding


2) Pi bonding

2) Pi anti-bonding

Carbon(6 electrons)

Carbon(6 electrons)

Bonding is found between two carbon atoms

Drawing Skelton Structures• For each carbon bond

draw a line that represents one carbon bound to another.

• Write out all other atoms except hydrogens bound to the carbon atom. hydrogens fill in the rest of the molecules.

• Double and triple bonds are represented by two and three lines respectively.

H

HH

H

HOC C H

C CH

HH

H

HO H

OH

Skelton or Condensed Structures

CC

C CC

H HH

H

H HH

H

CCC

CCC

CH

HH

H

HH

H H

H

H

HH

H H

CC

CCH

H

H H

H HH

HH

H

CC

CCC

CC

CH

HH

H

HH

H

H

O HCC

CCC

CO H

H

HH

H

H

Skeleton TotalName

Isoprene, C5H8

Phenol, C6H6O

Methylcyclohexane, C7H14

Butane, C4H10

Vinyl-benzene, C8H8

What is the Skeleton Structure?

NC

C

CCC

H

H O

OH

H

H

HH

HOOH

Glutamic Acid

NH

H O

OH

O OH

Glutamic Acid

CC

CCC

CH

HH

H

HH

BenzeneBenzene

CC C

CC

HH

H

HH H

HH

HH

Cyclopentane

Cyclopentane

CC

CCC

CCCC

C

HH

HH

HH

HH

NaphthaleneNaphthalene

Things to Know

• Orbitals• Number and Type of Bonding• Valance Shell• Octet Rule• sp3, sp2, sp orbital bonding• Electron-Dot, Line, Condensed (Skeleton)

Structures

Chapter 1

Documents

nucleus of atoms

atoms nucleus

atomic mass

specific orbitals

s orbitals sphere

mass number

molecular orbitals

s orbital1s