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.

Table 1: Inventory of Atoms Available in the Model Kits

Number of atoms / Element Symbol / Element Name / Color
30 / C / Carbon / Black
30 / H / Hydrogen / White
12 / O / Oxygen (4 bond) / Blue
4 / O / Oxygen (two bond) / Blue
18 / Cl / Chlorine / Green
5 / N / Nitrogen / Red
5 / S / Sulfur (4 bond) / Yellow
2 / S / Sulfur (two bond) / Yellow

Experimental Procedure:

Part I: Construction of Chemical Models

General Instructions: Construct a model of each of the following chemical substances. Place all of your models on your bench top for inspection by myself or by the TA. We must inspect your models and initial your lab sheet before you can continue to the next part of the exercise.

Use the following chart to determine the geometry of each of the chemical substances.

Number of atoms around the central atom
Number of / 4 / 3 / 2
sets of e- / 4 / tetrahedral / trigonal pyramidal / bent
around the / 3 / trigonal planar / bent
central atom / 2 / linear

Test for a Permanent Dipole in Simple Molecules:

1. A bentor 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 different element bonded to the central atom.

  1. Chlorine, a diatomic (two-atom) molecule. Use one white tube to represent the single bond.
  1. Water (H2O). Use white tubes for the bonds here.
  1. NCl3, nitrogen trichloride.
  1. SO3, sulfur trioxide – a component of acid rain.
  1. CH2O, formaldehyde – used in insulation.
  1. HCN, hydrogen cyanide – toxic gas.
  1. CHCl3, chloroform – the second useful general anesthetic for surgery

  1. CCl4, carbon tetrachloride – used to be used as a paint remover, but is liver toxic and environmentally harmful.
  1. CH2O2, formic acid – some ants use this to sting prey and for defense.

Part II: Build Your Own Molecule

You must prepare for this part before coming to lab. Do a little research—in the library or on the internet, for example—and find a biologically important molecule of your choosing. Learn enough about the molecule to build a model of it using the model kit provided in the lab (the kit’s inventory is listed below). In addition to the atoms listed, you will have 30 small wooden pegs for constructing single bonds between hydrogen (H) atoms and other elements; 10 long pegs for single bonds between other non-hydrogen atoms; and 10 springs, which may be used in combination to make double and triple covalent bonds between atoms.

You may use any source you wish to find your molecule. Good places would be the internet, textbooks, the Merck Index, the CRC Handbook, but there are numerous other resources you may use.

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 briefly describe the biological significance of the molecule.
  4. For BONUS POINTS:
  5. You will earn 3 bonus points if your chosen molecule is not selected by any other student in the class.
  6. Bring a copy of the information you found about your molecule to lab with you.
  7. The TA or I must inspect your molecule and initial your report sheet before proceeding to the next section.

Part III: 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 valid molecule in any way except:

and two hydrogens and one oxygen atom cannot be bonded together to make a valid molecule 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 unique 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:

1.Construct a model beginning with two carbon atoms and one oxygen atom in the carbon atoms:

Add six hydrogens to the molecule ensuring that you are still following the octet rule. Now construct another molecule beginning with two carbon atoms and one oxygen atom in the skeleton:

Add six hydrogens to the molecule.

The first molecule is dimethyl ether (C2H6O), and the second molecule is ethyl alcohol (C2H6O). Compare the two models. The formulas are identical, right? But ethyl alcohol is a compound that causes intoxication when ingested in sufficient quantities (beer, wine, etc.), and dimethyl ether is a close cousin of the ether that was the first general anesthetic used in surgery. Ethyl alcohol is boils at 78 ºC, while dimethyl ether boils at -24 ºC.

2.Construct a model of the following compound:

Now, try to construct two other different models of C2H2Cl2 in which the two carbon atoms are still linked by a double bond. Compare the three models. Which will have a net dipole? Why?

The Geometry of Chemical SpeciesDATA SHEET

Name ______Date______Section______

I.Construction of Chemical Models Instructor’s Initials ______

Molecule or Ion / Geometry / Net Dipole?
Chlorine / Yes No
Water / Yes No
Nitrogen Trichloride / Yes No
Sulfur Trioxide / Yes No
Formaldehyde / Yes No
Hydrogen cyanide / Yes No
Chloroform / Yes No
Carbon tetrachloride / Yes No
Formic acid / Yes No

II.Build Your Own MoleculeInstructor’s Initials ______

Name of your molecule:

Molecular Formula:

Molecular Weight:

Biological Significance:

Instructor’s Initials ______

III.Why Chemical Formulas are Not Enough to Identify a Compound

1.Comment on the differences between ethyl alcohol and dimethyl ether, in terms of their molecular geometry, shape, symmetry, and dipoles.

2.Draw the three models of C2H2Cl2 that you constructed. Indicate using a dipole arrow the net dipole of each molecule. If the molecule has no net dipole, write “NO DIPOLE”.