|
Shapes of Molecules |
Chapter 1: Chemical Bonding |
In order to view some of the structures for this section, you will need the
web "plug-in", "CHIME". If you do not have it already installed, you should
be able to download it for free from the linked
Website. CHIME is a browser that allows you to visualise and manipulate
molecules as 3D structures. Check here
if you don't know how to use Chime.
When determining the shape of a molecule the premise is that groups of electrons surrounding an atom are repelled as far as possible from each other to minimize the overall energy of the molecule. Groups of electrons can refer to electrons that participate in bonding (single, double, or triple) or to those that are non-bonding (e.g. lone pair electrons). The number and types of groups are determined from a Lewis diagram.
Not only is it important for a chemist to be able to visualize a structure, they must also be able to effectively (clearly!) transfer this knowledge onto a piece of paper!!!!!!
A molecule is visualized as if it were centered in the plane of the paper and, generally, so that the most number of atoms possible are in that plane. Unbroken lines are used to represent bonds in the plane of the paper, hashed wedges represent bonds going back out of the plane of paper and solid wedges represent bonds coming out of the plane of the paper.
There may be several different ways that you can represent a molecule on a piece of paper. You should be able to discriminate which of those drawings most clearly represent the structure of a molecule.
You should be able to determine the shape of a molecule by looking at the electronic and molecular geometry about all non-terminal atoms. In doing so you must be able to present clear drawings of your conclusions. Try some questions. If you are having problems doing this you will need to review VSEPR.
Once the shape of a molecule is known, by referring to the sum of the bond polarities, the molecular polarity can be determined. This is important when examining the reactivity of a molecule.
You should be able to indicate a molecule's polarity.
VSEPR - Predicting the Shapes of Molecules
Looking first at simple molecules, where a central atom is surrounded by two or more other atoms, there are only six unique electronic geometries that an organic chemist needs to be readily familiar with. The electronic geometry is determined by how many bonding and non-bonding electron groups surround a central atom.
For each electronic geometry, there may be a number of different molecular geometries (the shape of a molecule when only bonded atoms are considered). Representations are given below, manipulate the molecular geometries and see how they relate to the parent electronic geometry.
Though not important
when determining the structure of most organic compounds, the trigonal bipyramidal
and octahedral geometries are important when considering transition
states during SN2 mechanisms or the geometry about transition metals in reagents
or proteins.
| Electronic Geometry | Molecular Geometries | ||||||||||||
|
Linear |
|
||||||||||||
|
Trigonal planar |
|
||||||||||||
|
Tetrahedral |
|
||||||||||||
|
Trigonal bipyramidal |
|
||||||||||||
|
Octahedral |
|
Representing Molecular Shapes on a Piece of Paper:
Consider the molecule CH4. Below left can be found its Chime image. Figure I shows how this Chime image would be represented on a piece of paper. Unbroken lines are used to represent bonds in the plane of the paper, hashed wedges represent bonds going back out of the plane of paper and solid wedges represent bonds coming out of the plane of the paper. See if you can manipulate the molecule in the Chime image below to match the drawing in figure II.
CH4
Can you manipulate the trigonal bipyramidal transition state, given in the Chime
image below, so that it matches the drawings in each of the figures immediately
to the right?
Notice that bonds that are in the process of being formed or broken are given as dashed lines. The representations that are clearest then are those that place those bonds in the plane of the paper so that they do not get confused with the dashed wedges that represent bonds coming out of the plane of the paper (Figure I III).
C2H7OBr
The most desirable drawings are usually the simplest, generally they place as many atoms as possible in the plane of the paper.
Consider the molecule n-butane,
whose Chime image is given below. Manipulate the molecule so that it matches
the drawing in Figure IX.
|
|
Figure IX |
So what happens when lone pairs of electrons are involved? The most desirable drawings still place the most bonding sites in the plane of the paper even though lone pairs of electrons are most easily represented as being in the plane of the paper (it is not easy to wedge and hash a lone pair).
Consider the Chime image
for NH3 given below. Figure X would be the best drawing since it considers
the lone pair on nitrogen as being in a bonding site in the plane of the paper.
As you can see in Figure XI it is much more confusing if you choose to represent
the lone pair as coming out of the paper.
|
|
|
Ethyl methyl ether is a
structure where the opposite is true. Drawing the lone pairs in the plane
of the paper would be far more confusing than if you consider them as being
out of the plane.
|
C3H8O |
Figure XII |
You
need to learn to discriminate which drawings most clearly represent the structure
of a molecule.
Help with chime
files
