1. CHE2060 Topic 1: Atoms, orbitals & bonding
Atoms, Orbitals & Bonding Topics:
Very quick history of chemistry…
What is organic chemistry?
Atomic models: nuclear to quantum
All about orbitals
How orbitals fill: electron configuration
Basic bonding: valence electrons & molecular orbitals
Lewis dot structures of molecules
Electronegativity & bond polarity
Resonance: a critical concept
Orbital hybridization: key to carbon’s “flexibility”
sp3
sp2 sp
Free electron pairs & radicals
VSEPR: classifying molecular geometry & orbital hybridization
Daley & Daley, Chapter 1
Atoms, Orbitals & Bonds

2. Basic bonding: valence electrons &
CHE2060 Topic 1: Atoms, orbitals & bonding
Basic bonding: valence electrons &
molecular orbitals

3. Lewis dots “visualize” valence e-
Lewis dot diagrams simply represent each valence electron as a dot placed around an elements “letter” symbol.
H Mg B C N O Cl / +1 +2 +3
In order to obtain a full valence shell atoms will often gain or lose valence electrons.
If their shell is less then half full, they lose electrons to empty that shell, revealing the next intact shell.
Octet Rule • • •• •• •• -3 -1 -2
If greater than half full they gain electrons to reach an octet.
Gain or loss of electrons causes neutral atoms to become charged ions. The Law of Conservation of Mass requires that lost electrons are gained by other atoms, so the formation of cations & anions is a complementary process. • • • • • • • • • • • •• • • • •• •• ? ..
Once formed, oppositely charged ions are attracted to one another via the Law of Electrostatic Attraction, & form molecules via ionic bonding. Molecular net charge = 0.
.Mg :Cl > :Cl: Mg :Cl: (MgCl2 = magnesium chloride)

4. Carbon forms covalent bonds…
…because it’s valence shell is half-full.
So it’s not likely to achieve a full valence shell by gaining or losing. Instead, it pools its resources to achieve an octet.
A covalent bond is defined as two e- that are shared when orbitals overlap. . . . ..
For which are all octets satisfied? . . .
H : H
C : C
C : H
: O : H . . . .
H. + H. --> H : H + heat
H : H + heat --> H. + H.
Why the heat?
Heat is released by the formation of bonds, and is required to break bonds. This is called bond enthalpy; here 104 kcal/mol for the H-H bond.
Bond length? x meters = 0.74 Å
Bond length & bond enthalpy are characteristic of covalent bonds linking specific pairs of atoms.
D&D p.28-29

5. Covalent bonds are really “molecular orbitals”
Molecules are formed when atoms collide & their valence orbitals overlap, leading to sharing of e-s in pairs - one from each atom.
Shared atomic orbitals become molecular orbitals.
In-phase overlap of 1s  H2
The interaction of orbitals is like the interaction of waves:
Waves traveling in the same direction add; the summed wave is larger.
Waves traveling in opposite directions cancel one another out.
Orbitals interact via in-phase or out-of-phase overlap
The bonding molecular orbital
The antibonding molecular orbital
Out-of-phase overlap of 1s forms a node.
Antibonding molecular orbitals are usuallynot occupied; ie empty.
D&D p.30-31

6. Bonding & antibonding? Huh?
When two atomic orbitals overlap, two molecular orbitals are formed.
The bonding molecular orbital has lower energy then the antibonding. The lower energy orbital (bonding) is occupied.
H atom
H atom H2
Notice that when the two H atoms bond, the overall energy state drops. The molecule, H2, forms because it allows the atoms to be in a lower energy state.
Lower energy states rule!
D&D p.32

7. Another view
Notice that a node separates the nuclei of the two atoms in the antibonding orbital, while the bonding orbital allows the two nuclei to share electrons.
Bruice (2007)

8. So, why don’t two He atoms bond?
Let’s see if another example can clarify the issue of bonding orbitals, antibonding orbitals and energy levels.
H atoms bond to form H2, but He atoms don’t form He2 molecules. Why?
He2 antibonding orbital
He atom 1s 1s
He atom
He2 bonding orbital
The e- configuration of He is 1s2, so it’s s orbital is full.
Therefore, if 2 He atoms overlapped and tried to bond, both bonding and antibonding obitals would be filled.
Overlapped molecular energy levels aren’t lower than nonoverlapped atomic energies.
Therefore, formation of the He2 molecule is not favored.
D&D p.32

9. Bonds form at energy minima
Each pair of atoms form a bond only at a specific distance from each other. Why? Because at that distance their combined energy levels are minimized.
In chemistry, molecules always seek to remain in the lowest energy state.
Atoms are too close. + nuclei repel each other, increasing energy
Atoms are too distant. Long distance decreases attractive force.
Bond length is the distance between atomic nuclei at the minimal energy level. Distance at which a bond forms!
H2 bond length = 0.74 Å
The sweet spot! At this distance, the nucleus of atom A is maximally attracted to the e- of atom B & vv.
D&D p.33

10. Example: H2 gas
The molecule H2 is formed by the overlap of the 1s orbitals of two H atoms.
Each atom brings its single e- to the party.
When the orbitals overlap a single sigma (σ) bond is formed.
The bond distance (nucleus to nucleus) is 0.74 Å.
Electron density is highest in the space between the two nuclei.
The size of the H2 molecule is smaller than that of a single H atom!!!
Why? The two nuclei attract the electrons inward more powerfully, shrinking the diameter of the molecule so that it’s smaller than predicted.
sweet spot, 0.74Å
M&B p.10

11. Shorter bonds are stronger bonds
Generally, bond strength increases as bond length decreases.
Bond
Bond length
(nm)
Bond energy
(kJ/mol)
C - F
0.138
452
C - Cl
0.177
339
C - Br
0.194
280
C – I
0.214
230
Chlorofluorocarbons (CFCs) used to be used as refrigerants and aerosol propellants.
The bonds between carbon and chlorine or fluorine are short and strong, so CFCs are not easily broken down; they are stable and don’t break down.
When released into the atmosphere CFCs accumulate in the upper layers of the atmosphere. Exposure to UV light breaks CFC bonds and forms halogen radicals. The radicals react with ozone and break it down to oxygen gas. Loss of ozone then allows harmful levels of UV radiation to penetrate to the earth’s surface.
What does this mean for chlorofluorocarbon chemistry?
H&P p.11