Molecular structure: how are the different atoms bonded together
(topology) and what is the 3-dimensional configuration (geometry)?
Lewis Theory: Each atom contributes its valence electrons. A covalent
bond is formed of 2 e-’s and every atom tries to satisfy the octet rule
while attaining a formal charge of zero. The 3-dimensional structure is
determined by maximizing symmetry and minimizing contacts.
H
C
1 e-
N
4 e-
X
P
S
7 e-
5 e-
6 e-
3-5 bonds
2-4 bonds
O
6 e-
5 e-
1 bond 4 bonds 3 bonds 2 bonds 1 bond
Formal Charge = #valence e- - (#bonds + lone-pair e-)
O
N
C
O
N
water
H2O, 8 e-
H
O
H
tetrahedral, – ~ 109˚
O
H
O
CH2O, 12 e-
H
O
C
H
H
nitrate ion
C
C
H
H
H
H
H
planar, – ~ 120˚
C
H
H
-
O
N
O
H
C
-
O
trigonal planar, – ~ 120˚
C
H
C2H4, 12 e-
NO3-, 24 e-
C
C
H
formaldehyde
ethylene
O
N
O
O
N
O
O
O
-
O
???
N
O
-
O
O
1
H
n-butane
H
C4H10, 26 e-
H
H
H
H
C
C
C
C
H
H
H
H
H
H
H H
C
C
H
C
H
H
H
iso-butane, C4H10
H3C
CH
H
H
H
H
H
CH3
C
H
CH3
H
C
H
C H
C
C
H
H
H
H3C
CH3
CH3
H
H
1-butene, C4H8
H2C
C
H
CH2
CH3
H
H
H3C
C
H
C
H
CH3
CH3
H3C
H
H
H
H3C
H
H
H
C
H
H
2-butene, C4H8
H
C
CH3
cis
trans
Review of Molecular Orbital Theory
Hydrogen atom
proton (+) charge
Electron (-) charge. NOT a “cloud” of negative charge but
a particle w/ wave-like properties. Its location at any point in
time is unknown but there is a 99% probability that at any
time it can be found within some volume, which is defined as
the “orbital”.
For any given atom or molecule,
there are discrete orbitals
defined by energy and shape
.
.
.
y3
E
y2
The orbital for a molecule is simply
the linear combination of the atomic
orbitals for all the atoms involved. For
example, to make the H2 molecule:
y1
-ground state orbital energy diagram
for a neutral hydrogen atom.
The lowest
energy orbital
for hydrogen is
an s orbital
±
y1
= ??
y1
2
Making of Molecular Orbitals: Hydrogen Molecule
±
y1
s* orbital is anti-bonding, which means
that it has no e- density between the
two atoms- i.e., they’re not bonded
y1
Anti-bonding
s*
E
y1
y1
s
Bonding
2 e-/orbital!
s orbital is defined by the maximum
e- density between the atoms along
the internuclear axis
Making of Molecular Orbitals: p Bonds
p* orbital is anti-bonding, which means
that it has no e- density between the
two atoms- i.e., they’re not bonded
±
y1
y1
Anti-bonding
p*
E
y1
y1
p
Bonding
p orbital is defined by the maximum
e- density between the atoms ABOVE
the internuclear axis- none along axis!
3
Orbital Hybridization: Methane
Methane = CH4
•Carbon = 6 protons, 6 electrons
•Configuration = 1s22s22p2 (px, py, pz)
•4 Hydrogen atoms = 4 electrons (s)
4 valence e- in an s and 3 p orbitals
Have 8 bonding electrons and with
2e- per bond, need 4 bond orbitals
x
y
H
z
Hybridize
(s + 3 p)
x
C
H
H
y
H
+ 4 H atoms
z
tetradedral
geometry
An sp3 hybridized
carbon atom
x
y
z
4 sp3 orbitals
Making More Complex Molecules
Rotational barrier is
about 85 kcal/mol
Lewis Formula
H
H
C
H
H
C
H
C
C
H
C
C
One less bond than
normal: (-) charge
Formamide, HCONH2
Rotational barrier is
about 15 kcal/mol
...
N
H
H
H
Resonance Forms
N+
H
H
N
C
H
..
..
..
H
C
-O
..
.
..
O -
O
H
H
sp2 carbons
H
H
C
H
H
p bond
H
Ethylene, C2H4
H
One more bond than
normal: (+) charge
4
A Momentary Digression ….
Thermodynamic Considerations …..
Kinetic Considerations……
Consider A + B = A-B, Keq=[A-B]/[A][B]
And Free energy, DG = -RTlnKeq
R = ideal gas constant
= 2 cal/mol Kelvin
Let’s say that the concentration of
product, [AB], is 10-fold higher than
reactants at equilibrium (favorable).
Rate a e-Ea/RT where Ea is the
activation energy (barrier)
Solve for DG and get DG = -1.4 kcal/mol
At room temperature (T = 300 K), RT
= 600 cal/mol = 0.6 kcal/mol
That is, each factor of 10 (10-fold) is
worth 1.4 kcal/mol.
The average energy is RT- many have
more, ie 5-10RT or 3-5 kcal/mol
At room temp. ~1% of the molecules
have ~3 kcal/mol thermal energy
H
H
H
H
H
C
H
H
C
H
H
Rotational barrier is about
1.5 kcal/mol- spins like a top
H
H
H
H
C
C
H
H
H
C
C
H
H
H
H
H
H
H
H
CH3
H
H
H
H
C
H
H
H
C
H
H
CH3
C
H
C
C
H
H
H
C
Barrier here is about 5 kcal/molspins like a sputtering top
Rotational barrier is 85 kcal/mol
Does not happen….
H
H
C
C
H
H
H
H
H
This conformation or rotamer
is about 1 kcal/mol higher in
energy- ratio ~ 1-to-7
H
CH3
H
CH3
5