Name
Lab Day
Molecular Models
Introduction:
The atom and molecule are truly small; 6 ×1023 carbon atoms
occupy about 4 cm3, or each atom has a volume of about 6 ×10–24 cm3.
Molecules, though larger than their constituent atoms, are still
staggeringly small. Some of the molecules in nature composed of tens of
thousands of atoms are visible only with sophisticated tools such as the
electron microscope. It is a wonder that so much is known about the
sizes, shapes, and arrangements of atoms in molecules.
The behavior of a large number of the same molecules is
dependent upon the structure of the individual molecule so that much
can be learned from studying the macroscopic properties of a compound.
A technique called x-ray crystallography has allowed the chemist to
determine which atoms are joined to which others and to determine the
distance between them. Spectrophotometric techniques (such as nuclear
magnetic resonance and infrared and ultraviolet absorption
spectroscopy) and more classical techniques (such as elemental analysis
and density determination) have given insights into the structure of
molecules. Still, many of these molecular structures are so complicated
and delicate that even the most sophisticated chemist has difficulty
envisioning them. It is only natural that what sometimes the mind
cannot see, the hands and eyes can.
The ideal situation would be to have models of the atoms that we
could assemble into structures having features reflecting the bonding
and electronic characteristics of the elements. Some of these
characteristics might be: size of the atom when bonded; angles at which
bonds are formed; nature of electrons not directly involved in bonding
(i.e., unshared pairs of electrons); positions of the nuclei in relationship
to the electrons and their relative flexibility in position, and so on. What
would be required would be a model that has these characteristics. In
practice, the materials from which models are constructed vary in their
ability to represent these qualities and we are constricted by the very
nature of the model.
One of the simplest models is the stick-and-ball scheme. A solid
sphere, not truly representing the nucleus but a compromise in
approximating the size of atoms as a whole, has holes drilled at angles
depicting the usual bonding angles. Plastic sticks of various lengths are
used to represent the pairs of electrons forming the bond and they fit
into the drilled holes connecting the spheres together. Sometimes,
flexible sticks are used as bonds to connect spheres when the bonding
angles are substantially different than the drilled holes.
2
Experimental:
Obtain a box containing a collection of sticks and balls. The black
colored balls with four holes drilled at angles of approximately 109.5º
represent carbon. The blue balls represent nitrogen; there are 3 drilled
holes on one side of the ball drilled at 120º representing the bonding
angles (the other hole can be used to represent the lone pair of electrons
on nitrogen). The white spheres with a single hole represent hydrogen.
The red balls with two holes drilled at about 120º are oxygen atoms. The
green, orange, and purple spheres with single drilled holes represent
chlorine, bromine, and iodine respectively.
The plastic sticks represent the bonds between atoms (spheres).
The shorter white sticks connect hydrogen to other elements. The short
grey plastic sticks serve as bonds between the other elements excluding
hydrogen. The flexible long grey plastic sticks are used to connect atoms
together in multiple bonding situations.
Activities:
A.
Before starting the lab, draw the Lewis dot structures for the
elements listed below:
carbon
nitrogen
oxygen
fluorine
chlorine
iodine
hydrogen
Next, fill in the table below:
element
C
N
O
F
Cl
I
H
# unpaired electrons
# pairs of electrons (2 e– = 1 pair)
3
Draw the Lewis dot structures for the molecules below:
H2
F2
O2
N2
# unshared
electron pairs
single, double,
or triple bond
type?
Fill in the table below:
molecule
# covalent bonds
H2
F2
O2
N2
B.
In lab, complete this section by (1) drawing the Lewis dot structure
for the indicated compound, (2) construct a stick-and-ball model, and (3)
using colored pencils, draw a replica for your model next to the dot
structure.
compound
C2H6
C2H4
C2H2
dot structure
stick-and-ball replica
4
Compare the three compounds. Note that C2H6 has four single
bonds to carbon. Applying the Valence Shell Electron Pair Repulsion
Model (VSEPR), what is the molecular geometry around each of the
carbon atoms? (choose from: tetrahedral, trigonal pyramidal, trigonal planar, bent,
or linear)
. What is the bond angle between the H–C–H
atoms? (choose from 109.5º, 107º, 120º, 105º, or 180º)
. Is the
molecule as a whole polar or is it non-polar?
.
The second compound, C2H4 has a double bond between the
carbon atoms. What is the molecular geometry around each of the
carbon atoms?
. What is the bond angle between the
H–C–H atoms?
. Is the molecule polar or is it non-polar?
.
The third compound, C2H2 has a triple bond between the carbon
atoms. What is the molecular geometry around each of the carbon
atoms?
. What is the bond angle between the H–C–H
atoms?
. Is the molecule polar or is it non-polar?
compound
dot structure
stick-and-ball replica
NH3
CO2
both O’s are
attached to the C,
not each other
H2CO
the H’s are attached
to C as is the O
NH3 is similar in shape to CH4 but in place of a hydrogen, nitrogen
has what?
. If nitrogen had the same geometry as carbon
in CH4, what bond angle would you find for H–N–H?
. The
actual bond angle is about 107º. What causes this deformation?
. Is NH3 polar or non-polar?
.
5
How many atoms are attached to carbon in CO2?
.
How many atoms are attached to carbon in H2CO?
.
Considering the shapes and number of atoms attached to carbon, what
is molecular geometry of CO2?
. Of H2CO?
. What is the O–C–O bond angle in CO2?
. What is the
H–C–O bond angle in H2CO?
.
In the Lewis dot formulation of a compound, it is sometimes
necessary for one atom to bond to another’s unused pair of electrons.
This bond is called a coordinate covalent or dative bond. Use this concept
in constructing models below:
compound
dot structure
stick-and-ball replica
H2SO4
use a black sphere.
the H’s are attached
to individual O’s, the
O’s are attached to S
HNO3
the H is attached to
an O, the O’s are
attached to N
H2CO3
use the flexible long
grey plastic sticks to
attach each O to C,
the H’s are attached
to O’s
What is the shape about the sulfur atom in H2SO4?
. What is the shape about the nitrogen atom in HNO3?
.
How many atoms are directly attached to the sulfur in H2SO4?
. How many atoms are directly attached to the nitrogen in HNO3?
. What is the O–S–O bond angle in H2SO4?
. What is the
O–N–O bond angle in HNO3?
.
6
Now let’s have some fun with H2CO3!
Remove the hydrogens, but not the connecting flexible grey plastic
sticks. Draw a Lewis dot structure below and a pencil sketch of the anion
CO3–2 (carbonate) that you just made.
Lewis dot structure
stick-and-ball replica
See how you could re-attach the flexible grey plastic sticks to the
carbon (remember carbon can make only four bonds). Draw the three
possibilities (try numbering each oxygen atom to tell them apart).
In detaching and re-attaching the flexible grey plastic sticks, the
atoms do not change their relative positions. The flexible grey plastic
sticks symbolize pairs of electrons as they move about the molecule.
What is this called?
.