- Science Honors Program -

Computer Modeling and Visualization in Chemistry

Atoms, Electrons,
Chemical Bonding,
and Orbitals

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This presentation is for educational, non-profit purposes only.
Please do not post or distribute this presentation to anyone outside
of this course.

Many of the graphics in this presentation are from:

Bruice, Paula Yurkanis. Organic Chemistry, 4th Ed.; Prentice Hall,

2003.
http://wps.prenhall.com/wps/media/objects/724/741576/

McMurry, John; Fay, Robert. Chemistry, 4th Ed.; Pearson Education,

2003.
http://wps.prenhall.com/wps/media/objects/602/616516/

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Ionization Energy of Atoms

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Electronegativity
Ionization Energy (IE):
amount of energy
necessary to remove an
electron from a neutral
atom.

Electron Affinity (EA):

amount of energy
released when an atom
absorbs an extra
electron.

Electronegativity:
Average of above two
properties for an isolated
atom.

What type of bond will form between two atoms?

1. Ionic 2. Covalent 3. Polar covalent
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Ionic Bond

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 Covalent Bonding
An electron density plot for the H2
molecule shows that the shared
electrons occupy a volume equally
distributed over BOTH H atoms.

Electron Density for the H2 Potential energy (kJ/mol)

molecule

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Polar Covalent Percent Ionic Character of Diatomic Molecules

Molecule % Ionic Molecule % Ionic

H2 0 CsF 70
CO 2 LiCl 73
NO 3 LiH 76
HI 6 KBr 78
ClF 11 NaCl 79
HBr 12 KCl 82
HF has a polar covalent bond. It has a
HCl 18 KF 82
dipole moment.
HF 41 LiF 84
NaF 88

The difference in electronegativity between the two bonded atoms determines the
ionic character (or covalent character) of the bond.

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What is an Atom?

Protons and neutrons make up the heavy, positive core, the

NUCLEUS, which occupies a small volume of the atom.

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Photoelectric Effect
Photoelectric Effect: the ejection of electrons from the
surface of a substance by light; the energy of the electrons
depends upon the wavelength of light, not the intensity.

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Atomic Orbitals Wave-particle duality.
Traveling waves vs. Standing Waves.

Atomic and Molecular Orbitals are 3-D STANDING WAVES

that have stationary states.

Example of 1-D guitar string standing wave.

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Atomic Orbitals: How do electrons move around the nucleus?

Density of shading represents the

probability of finding an electron
at any point.
The graph shows how probability
varies with distance.

Wavefunctions:
Since electrons are particles that have wavelike properties, we cannot
expect them to behave like point-like objects moving along precise
trajectories.

Erwin Schrdinger: Replace the precise trajectory of particles by a

wavefunction (), a mathematical function that varies with position

Max Born: physical interpretation of wavefunctions. Probability of finding a

particle in a region is proportional to 2. 12
s Orbitals

Wavefunctions of s orbitals of
Boundary surface encloses surface with
higher energy have more
a > 90% probability of finding electron
complicated radial variation
with nodes.
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electron density

wave function

radial probability
distribution

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p orbitals:

3 p orbitals l = 1,
ml = +1, 0 -1

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d orbitals: Five d orbitals l = 2, ml = +2, +1, 0 - 1,
-2

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Atomic Orbital Hybridization: sp

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Atomic Orbital Hybridization: sp2

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Atomic Orbital Hybridization: sp3

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Covalent Bonding
- bond: e- density in the bond is distributed symmetrically about
the bond axis.
- bond: e- density in the molecular orbital has a nodal plane that
contains the bond axis.

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 bond
H2

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 bond H2

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 bond
p-orbital
end-to-end
F2

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 bond
mixed
HCl CH4

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Lone Electron Pairs

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 - bond

-orbital bonding
side-to-side

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 Double Bonds: Examples
Double bonds
consist of 1 and
1 bonds in these Allene
molecules.

Double Bond ==
Bond Order 2

Ethene

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 Triple Bonds
Triple bonds
consist of 1 and
2 bonds.

Triple Bond ==
Bond Order 3
Ethyne (acetylene)

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Valence Bond Theory vs. Molecular Orbital Theory
For Polyatomic Molecules:

Valence Bond Theory: Similar to drawing Lewis structures. Orbitals for

bonds are localized between the two bonded atoms, or as a lone pair of
electrons on one atom. The electrons in the lone pair or bond do NOT
spread out over the entire molecule.

Molecular Orbital Theory: orbitals are delocalized over the entire

molecule.

Which is more correct?

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Delocalization Resonance Structures
Benzene

OR

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Benzene
The six MOs of benzene
showing lobe phases
and relative energies.

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Visualization Surfaces
Electron Density Surface

Electrostatic Potential Map

Electrostatic Potential Maps of Hydrogen Halides

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Exercise
Atoms.
Do a 1 electron atom such as H, or He+, then do multi-electron atom
Do quantum calculation.
Visualize orbitals.
What is the 1st IE of the molecule?
Pick a binary compound.
Verify with me if molecule makes sense.
Do quantum calculation.
Draw electron density surface
Draw electrostatic potential map.
Is molecule polar?
What is electronegativity difference between atoms?
Find bond length.
Bond order?
Visualize the orbitals. Which ones are bonding, anti-bonding?
Which are sigma, which are pi?
What is the 1st IE of the molecule?
Do same as above for a polyatomic molecule, such as benzene
Not too big, or well wait for ever for the calculation.
Verify with me if molecule makes sense.

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