CH-180
The Geometry of Chemical Species
Perhaps the most significant problem that we encounter when we try to understand chemistry is
our inability to see an individual ion or molecule. Single atoms, and the individual ions and
molecules composed of atoms, are much too small to see, even with the help of the most powerful
microscopes. Nevertheless, chemists have discovered much about the structure of single ions and
molecules by observing the behavior of large collections of identical ions and molecules: from their
observations, they were able to devise models (much as we did in the "Scientific Models" lab) of
the individual ions and molecules that were consistent with all observations made.
Those who devised the model systems knew that the human mind (theirs, and most everyone
else's) understands concepts more readily if those concepts are illustrated by a drawing, photograph,
virtual reality image, or a three-dimensional model that can be studied from any angle. Indeed,
psychologists tell us that about 80% of the information that the human mind processes is visual.
Therefore, some chemists build models of ions and molecules that convey much information about
the structure (geometry) of the chemical species.
Some model systems, such as the electron-dot formulas (also called Lewis-Dot formulas) are
two-dimensional, i.e., the models are drawn on a flat piece of paper.
Such models are easy to construct, but they tell us relatively little about
the arrangement of the atoms in space. The ball-and-stick models that
we will use tell us more information about the chemical species than
the electron-dot formula can: for example, the angles formed by the
bonds can be measured. However, the ball-and-stick models fail to
give us a true picture of the relative size of each atom in the chemical
species. So-called spacefilling models can show the relative size of
each atom, but such models are the most difficult and time-consuming
to build. In general, the tradeoff is this: the easier a model is to build,
the less faithful the model is to the true structure of the ion or
molecule.
Experimental Procedure
I. Model of a Biologically Important Molecule
Thanks to G. N. Lewis, electron-dot formulas give us a way to picture how valence electrons are
shared to satisfy octets in covalent compounds. Because covalent compounds can become very
complex, chemists have agreed to several conventions that make electron-dot formulas easier to
draw and to interpret.
1. a line (___) equals two electrons ( : ), a covalent bond.
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2. Since carbon (C) is very common in covalent compounds, we don't usually write out the C's.
Instead, we let the corners and line ends show us where the carbons are.
3. Like most elements, carbon seeks to satisfy the octet rule. In our experience, hydrogen (H)
often bonds with carbon. So, we do not write out hydrogens bonded to carbon. Instead, we
assume the number of hydrogens present to fill out carbon's octet.
4. To give a sense of the molecule's three-dimensionality, bond lines are sometimes modified to
show that the bonds are coming out of the page (a solid wedge,
) and into the page (a
dashed wedge,
).
The sugar molecule depicted below uses some of the conventions described above. In the lab,
you will find models of a sugar molecule that is often found in living organisms. Obtain (do not
build) one of these models, and note the following features:
1. The black spheres represent carbon; the red
spheres represent oxygen, and the yellow spheres
represent hydrogen.
2. The model represents the arrangement of atoms in
space much more accurately than does the drawing
shown on the next page:
Note that most of the C atoms in the sketch are
omitted for clarity. Since carbon (C) is the basis of
nearly all biologically important molecules, chemists
often abbreviate the drawings by considering corners in the drawings to represent carbon atoms,
unless a different element is drawn in at the corner. In particular, notice how the pentagon ring
formed by four of the C atoms and one of the O atoms is puckered (bent so as not to be flat) in the
model, but no indication of puckering is observed in the drawing.
3. Note how most of the oxygens are bonded to single hydrogen atoms: these -OH groups are also
seen in water molecules! Does this help to explain why most sugars readily dissolve in water?
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Lab exercise: The model represents one of the following sugars:
Threose
Ribose
Fructose
Lactose
Use the model and the table, "Physical Constants of Organic Compounds" found in the CRC
Handbook, to name the sugar represented by the model. Note: not all editions of the CRC
Handbook have information on all four sugars, but all editions do contain information on the
correct sugar.
II. Build Your Own Molecule
Now do a little research to find a biologically important molecule of your choice. Learn
enough about the molecule to build a three-dimensional model of your molecule using a model
kit. The model kit will contain the items listed in Table I.
Table I. Inventory of Atoms Available in Model Kits
Elemental Symbol Element Name Number of Atoms
C
H
O
O
Cl
N
S
S
Carbon
Hydrogen
Oxygen
Oxygen
Chlorine
Nitrogen
Sulfur
Sulfur
30
30
12
4
18
5
5
2
Color
Form
Black
White
Blue
Blue
Green
Red
Yellow
Yellow
Tetrahedral
Single electron atom
Tetrahedral
Double electron atom
Single electron atom
Tetrahedral
Tetrahedral
Double electron atom
There are also 85 covalent electron bonds - the white tubes that link the atoms together.
You may use any source you wish to find your biologically important molecule: the Internet, the
textbook, other books, the Merck Index, the CRC Handbook, other reference texts at the library,
personal interviews of pharmacists, paramedics, nurses, etc., who have knowledge of biologically
important molecules.
Your chosen molecule must meet the following criteria:
1. You must be able to build it from the inventory available in your model kit.
2. The selected molecule is not mentioned anywhere in this handout.
3. You must be able to briefly describe the biological significance of the molecule. For example, if
you were to pick ethanol (C2H5OH), you would be able to explain that the molecule, when
metabolized by the human body, causes intoxication.
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4. You must know the molecule’s name and the number of atoms of each element present.
You may earn 3 bonus points if your molecule was not selected by any other CH-180 student.
For full credit, bring to lab a photocopy, printout, or hand-drawn sketch of the
information that you found about your molecule. Build the molecule: Insert pegs on
the atoms into the white tubes to establish bonds. The number of bonds is determined by the
number of electrons an atom is willing to share. A "single electron atom" is one that will share
one electron with another atom; such atoms can establish a single bond. Likewise, a "double
electron atom" shares two electrons, and will establish up to two single bonds. "Tetrahedral"
atoms share up to four electrons. The tetrahedral atoms in the kit can establish single bonds using
single white tubes, but double and triple bonds are also possible: a double bond is made by
bending TWO white tubes to connect TWO pegs on one atom with TWO pegs on another atom.
As you would expect, a triple bond is made by bending THREE white tubes to connect THREE
pegs on one atom with THREE pegs on another atom.
III. Construction of Chemical Models
General Instructions: Work individually, but feel free to consult with your classmates. Place all of
your models on your benchtop for inspection. The instructor or lab assistant will inspect your
models before you proceed to the next section, and give you a score based on how many models are
constructed correctly. Now build models for each of the compounds listed:
1. Chlorine, a diatomic (two-atom) molecule. Use one white tube to represent the single bond.
2. Water. Use white tubes for the bonds here.
3. NCl3, nitrogen trichloride.
4. SO3, sulfur trioxide.
5. CH2O, formaldehyde. This molecule contains a double bond: use two white tubes to represent
the double bond that links the C-atom to the O-atom.
6. HCN, hydrogen cyanide. Use three white tubes to represent the triple bond in this molecule.
7. C4H10 , butane. This molecule can be constructed by linking four carbon atoms together in a
chain (put the C atoms together to form a shape as close as possible to a straight line), then attach
the hydrogens.
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8. C2H5OH, ethanol. Build this model in much the same manner as you constructed the butane
molecule: begin with a "chain" of two carbons, then add one oxygen, then affix the hydrogen atoms.
9. CO32-, carbonate ion. So far, all models have been of molecules. However, polyatomic (severalatom) ions also exist, and can be constructed with the model kit. An effective strategy to build this
model is to begin by drawing the electron-dot formula, so that you will know whether to use any
double or triple bonds. Because carbonate is an ion, you must adjust the number of valence
electrons by the value of the ion's charge: in this case, ADD two electrons to the count of valence
electrons coming with the atoms. You will always add electrons if the ion's charge is negative, and
subtract electrons if the ion's charge is positive. Draw the electron-dot formula.
IV. Why Chemical Formulas are Not Enough to Identify a Compound
Some chemical formulas, such as Cl2, and H2O represent only one possible compound. In other
words, two Cl atoms cannot be bonded together to make a molecule in any way except:
Cl
Cl
and two hydrogens and oxygen cannot be bonded together in any way except:
For many formulas, however, more than one compound is possible. For example, the CRC
Handbook lists two compounds having the formula, C2H6O, three compounds having the formula,
C2H2Cl2, and twenty-one compounds having the formula, C4H10O2! Each compound is a different
substance, with its own set of physical and chemical properties. Models are sometimes the only
convenient way that we have of distinguishing compounds that have the same formula.
Instructions: After inspection by the instructor, disassemble all of the models from Part III except
the one for ethanol.
1. Construct a model beginning with two carbons and one oxygen in the skeleton:
add six hydrogens to the skeleton using short pegs. Compare the model to that for ethanol. Are the
formulas identical? The new model is for a compound called dimethyl ether; this compound has
properties quite different from those exhibited by ethanol, and is similar to the ether that was the
first general anesthetic used in surgery.
2. Construct a model of the following compound:
Use two white tubes to represent the double bond between the two carbons.
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Now, try to construct two additional models of C2H2Cl2, different from the sketch above, in which
the two carbon atoms are linked by a double bond.
3. Take apart the models built in the previous step, and then build a model of CHBrClI. (Since
we have no Br and I atoms in the kit, pretend that the red and blue N and O atoms represent Br
and I, respectively.) Now try to build a second model of CHBrClI that is different from the first.
Describe how this second model is related to the first.
4. After you have finished making any observations that may help you complete the report,
dismantle all of your models and return the kit to the chemistry stockroom.
Here is a handy table that you can use to determine the shapes of simple molecules:
Geometry of Simple Covalent Compounds
Number of
sets of earound the
central atom
4
3
2
Number of atoms around the central atom
4
3
2
tetrahedral
trigonal pyramidal
V-shaped
trigonal planar
V-shaped
linear
A major reason why we might wish to determine the shape of a molecule is categorize the
molecule as polar or nonpolar. A molecule is polar if it possesses a permanent dipole. A
permanent dipole exists when the molecule has recognizable positive and negative regions. As we
will see, many properties exhibited by molecules are determined by the presence or absence of a
permanent dipole. The following is a simple test that you can employ to determine if a molecule has
a permanent dipole.
Test For A Permanent Dipole in Simple Molecules
1. A V-shaped or trigonal pyramidal molecule will possess a permanent dipole.
2. A tetrahedral, trigonal planar, or linear molecule will possess a permanent dipole IF there is
more than one element around the central atom.
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Name _______________________
Geometry of Chemical Species Report
I. Model of a Biologically Important Molecule
Identity of the sugar __________________
Explain, using no more than two sentences, how you determined the sugar's identity.
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
II. Your Own Biologically Important Molecule
Instructor's Initials: photocopy?
model?
The name of the molecule: _________________________________
Its biological importance:
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
III. Construction of Chemical Models
Nine models inspected
(instructor's initials)
Score __________
Complete the table (on the following page) for the seven species other than butane and ethanol.
Choose from the following five shapes: tetrahedral has four atoms around the center, and every
bond has ~109.5o angle; in trigonal pyramidal, the center atom stands up in a point, with the three
terminal atoms forming the "feet" of a tripod; in trigonal planar, the center atom and the three
terminal atoms lie in a plane; v-shaped (bent) is self-explanatory, with the central atom at the V's
corner; linear is also self explanatory. Circle “Yes” or “No” to state the polarity of all except CO32.
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Species
chlorine
Name of Geometry
Polar?
Yes No
water
Yes No
nitrogen trichloride
Yes No
sulfur trioxide
Yes No
formaldehyde
Yes No
hydrogen cyanide
Yes No
carbonate ion
IV. Why Chemical Formulas are Not Enough to Identify a Compound
model structures
CHBrClI models inspected
original
(instructor's initials)
Question: An acid is, according to one definition, a substance that has a tendency to give up a hydrogen
ion (H+). Because H+ consists only of a nucleus, it does not exist free when dissolved in water. Rather,
H+ combines with H2O to form a new ion of formula H3O+. This new ion is named the hydronium ion.
i. Draw the electron-dot formula for a hydronium ion.
ii. Name the geometry (shape) of H3O+.
____________________