MOLECULAR STRUCTURE
Objective
To be able to figure out the shape, 3D structure of a molecule,
starting from the chemical formula.
For instance: to predict that, & explain why, H2O molecule is bent &
polar, though CO2 molecule is linear & non-polar.
Why important?
From the shape of molecule, one can predict physical properties of
material (say, that water is a strong dielectric).
Chemical properties are also determined by the shape of molecule:
how accessible are its electrons to attack by another
agent?
Say, why CH4 molecule is rather non-reactive, though NH3 violently
reacts with HCl, & C2H4 forms polymers?
What molecules can exist, & what can’t?
What do we already know?
Electrical charges of the same sign repel each other.
Especially important is that electrons repel each other.
There are valence (outermost) & core (inner-shell) electrons in
atoms.
Only valence electrons are shared by bonded atoms.
Covalent bond is a shared electron pair, occupying a MOLECULAR
ORBITAL.
The physical reason of pairing electrons is that each electron is a
small magnet. 2 electrons may cancel each other’s magnetic field 
(we say they have antiparallel SPINS, thi is a more stable situation:
an electron pair at the same molecular orbital) or sum up their
magnetic field  (unstable situation: both electrons cannot belong
to the same orbital)
repel
S
S
N
N
N
S
N
S
N
N
S
S
attract
N
electron pair 
S
Electron octet configuration is especially stable.
Lewis dot formulas of molecules are compiled to satisfy
the OCTET RULE: Chemical compounds form so that each
atom, by gaining, losing or sharing electrons has an octet
(8) of its valence electrons (2e- for H)
H:H
.. ..
:Cl:Cl:
.. ..
..
H:F:
..
H2
H–H
Cl2
Cl – Cl
HF
H–F
When more than 2 atoms bonded, there is a quest: which atoms are bound to each
other & which are not?
Methane, CH4
structural formula shows that there are
H
4 C – H bonds, but none
|
of H to H
H–C–H
|
H
In SF2 F – S – F there are two S – F bonds, but none of F to F
Structural formula shows the order of connectivity of atoms.
Ammonium
ion
NH4+
H
|
H-N-H
|
H
Sulfate ion, SO42-
:Ö:
|
:Ö - S - Ö:
|
:O:
Nitrate ion, NO3-
|
N = O|
Ö
2-
-
Ö|
|
+
VALENCE-SHELL ELECTRON-PAIR REPULSION
THEORY
VSEPR
predicts the shape of molecules.
1. Only outermost, or valence electrons, count.
Core electrons do not contribute to bonding,  do not affect the shape of a molecule.
2.
Valence electrons in molecules are arranged in pairs, when possible.
3.
Lewis electron-dot formula is valid, with bonding & lone electron pairs.
(H-Ö-H Oxygen in water has 2 bonding & 2 non-bonding electron pairs)
4.
All electron pairs (both bonding & non-bonding) repel each other &
occupy molecular orbitals (MO) located as far apart as possible.
5. Formation of double bonds do not affect the geometry.
Major Cases
Two electron pairs around central atom.
BeH2 total 2+ 2= 4 val. e-, 2 el. pairs & 2 bonds H-Be-H, no lone el. pairs, linear
molecule
Bond angle 180o

Be
180o

H
Be
H
2 double bonds & no lone el. pairs around central atom give the
same linear geometry, as in CO2
O=C=O
Bond multiplicity does not affect the basic geometry!
3 electron pairs around central atom
BH3
H
3+3=6e, 3 bonds are formed, no lone
pairs,
trigonal planar
H
|
B
B
H
H
H
All bond
H
angles are 120º
4 electron pairs around central atom*
The most important case
8 valence electrons (4 pairs) & 4 bonds around central atom.
The most remote location of electron pairs – tetrahedral.
CH4
tetrahedron
H
H
C
H
All bond angles 109.5
H
109.5o
o
4 electron pairs – 1 lone pair around central atom
:NH3
5+3=8e-, 4 MO, 3 bonds N-H, one lone e- pair on N
Lewis electron dot formula is
..
H: N:H
..
H
Electron configuration is still tetrahedral,
Lone pair
but the molecule geometry is
different:
4 electron pairs – 2 lone pairs around central atom
H2O 8e-, 4 MO, 2 bonds, 2 lone pairs on O,
: :
O
bent molecule:
H
H
while electron configuration is still tetrahedral
2 lone pairs
Electronic structures
with more than 8 e- around central atom
Octet rule is strictly valid for the elements of 2nd Period.
Starting with 3th period octet rule may be violated & more than
8 electrons,  more than 4 el. pairs surround the central atom.
For the surrounding atoms – ligands –
octet rule is still valid
2 axial
positions
5 electron pairs around central atom
Trigonal bipyramid
Bond angles: 90 & 120º.
PF5 (but not NF ), SnCl55
3 equatorial
positions
Group V:
PCl3 & PCl5 both exist, but only NF3
Lone pair, if present, repels other pairs stronger than bonding pairs. Therefore, lone
pair occupies an equatorial position (bond angle 120o), not an axial position (90o)
SF4 6+74= 34e|F
– S – F|
|F| |F|
1 lone pair
“see-saw” molecule
S
IF3 28e-
I
|
F|
F
|
F|
“T-shape”
6 electron pairs around central atom
Octahedron
All bond angles 90º.
XeF4 8+74 = 36e
-
SF6, SiF62-
Here 2 lone pairs are
present.
They repel stronger, 
go to opposite
positions.
The molecule geometry
is square planar.
IF5 7+7x5= 42e|
|
F – I – F|
F|
|
|
F|
F|
1 lone pair. El. configuration: octahedral
Molecule geometry: square pyramid
Review of the step-by-step procedure:
1) In the molecular formula,
identify the central atom.
2) Count total valence e-
PCl3
P + 3Cl = 5+37 = 26 e-
3) Assign 8e- (or 4 el pairs)
3Cl take 38 = 24e-
to each ligand.
Cl
Cl
P
4) Assign one pair as bonding for each ligand
5) Assign remaining e-, if any, to the central
atom as lone pair(s).
6) Count total (bonding & lone) pairs
around central atom – identify el. configuration
7) Out of the ligand positions only,
identify the geometry of the molecule
Cl
1 lone pair
4 total pairs tetrahedron
trigonal pyramid
POLARITY OF MULTIATOMIC MOLECULES
Covalent bond between atoms of different electronegativity is polar:

H–O
C–O
H–N
However the net polarity of a multiatomic molecule depends on the
bond angle between polar bonds.

O=C=O
or
O
C
NH3
H2O
N
O
H
O
H
Total polarity:
Two dipoles add to each other to a
total molecular dipole
H
H
H
Three dipoles add to each other to
a total zero molecular dipole
F
in CCl4 (tetrahedron)
4 C-Cl dipoles cancel
each other to net
zero.
B
F
F
In BF3, 3 bond dipoles
cancel each other to add
up to zero total polarity