Lect 12 3D Molecular Structure - Santiago Canyon College



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)

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 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

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 NH4+ H +

ion |

H - N - H

|

H

Sulfate ion, SO42- :Ö: 2-

|

:Ö - S - Ö:

|

:O:

Nitrate ion, NO3- |Ö| -

N = O|

| 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

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 3+3=6e, 3 bonds are formed, no lone pairs,

trigonal planar H

|

B

H H

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

All bond angles 109.5o

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

Electron configuration is still tetrahedral,

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

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

5 electron pairs around central atom

Trigonal bipyramid

Bond angles: 90 & 120º.

PF5 (but not NF5), SnCl5-

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)

6 electron pairs around central atom

Octahedron

Review of the step-by-step procedure:

POLARITY OF MULTIATOMIC MOLECULES

Covalent bond between atoms of different electronegativity is polar:

δ+ δ− δ+ δ− δ+ δ−

H – O C – O H – N

However the net polarity of a multiatomic molecule depends on the bond angle between polar bonds.

δ− δ+ δ−

O = C = O or

-----------------------

(( ((

[pic]

Be

B

H †††††††††††††††††††††††ഠ഍഍഍††⁈††††††††††††††††††††䠠‍††഍഍‍††ㄠ〸൯഍഍⁈††敂††ൈ䄍汬

H H

180o

H Be H

All bond angles are 120º

H

H

H

H

C

SF4 6+7(4= 34e-

|F – S – F |

|F| |F|

1 lone pair

“see-saw” molecule

Lone pair

2 lone pairs

2 lone pairs

XeF4 8+7(4 = 36e-

IF5 7+7x5= 42e-

|F – I – F|

|F| |F|

|F|

1 lone pair. El. configuration: octahedral

Molecule geometry: square pyramid

(109.5o

O C O

O

H H

Total polarity:

Two dipoles add to each other to a total molecular dipole

H

NH3

N

H

H

Three dipoles add to each other to a total zero molecular dipole

H2O

..

..

H : N : H

H

attract electron pair ((

repel

N N N

S S

S N

N S

N S

S

S

N

3 equatorial positions

structural formula shows that there are

4 C – H bonds, but none

of H to H

Group V: PCl3 & PCl5 both exist, but only NF3

1) In the molecular formula, PCl3

identify the central atom.

2) Count total valence e- P + 3Cl = 5+3(7 = 26 e-

3) Assign 8e- (or 4 el pairs) 3Cl take 3(8 = 24e-

to each ligand.

4) Assign one pair as bonding for each ligand [pic]

5) Assign remaining e-, if any, to the central 1 lone pair

atom as lone pair(s).

6) Count total (bonding & lone) pairs

around central atom – identify el. configuration 4 total pairs -

tetrahedron

[pic]

7) Out of the ligand positions only,

identify the geometry of the molecule trigonal pyramid

2 axial positions

Here 2 lone pairs are present.

They repel stronger, ( go to opposite positions.

The molecule geometry is square planar.

All bond angles 90º. SF6, SiF62-

S

P

IF3 28e-

I

|F F|

|F| “T-shape”

in CCl4 (tetrahedron)

4 C-Cl dipoles cancel each other to net zero.

F

B

F F

In BF3, 3 bond dipoles cancel each other to add up to zero total polarity

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