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.Construction of Chemical Models

General Instructions: Construct a model of each of the following chemical substances. Work individually, but feel free to consult with your classmates. 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.

  1. Chlorine, a diatomic (two-atom) molecule. Use one stick to represent the single bond.
  1. Water (H2O). Use sticks for the bonds here.
  1. NCl3, nitrogen trichloride. Do NOT use the nitrogen with 5 holes!
  1. CH2O, formaldehyde. This molecule contains a double bond: use twosprings to represent the double bond that links the C-atom to the O-atom.
  1. HCN, hydrogen cyanide. Use three springs to represent the triple bond in this molecule. Do NOT use the nitrogen with 5 holes!
  1. 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.
  1. C2H5OH, ethanol. Build this model in much the same manner as you constructed the butane molecule: begin with a "chain" of two carbons and one oxygen, then affix the hydrogen atoms.
  1. CO32-, carbonate ion. So far, all models have been of molecules. However, polyatomic (several-atom) 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. Tell how many bonds you used to make carbonate ion:

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.

Table 1: Inventory of Atoms Available in the Model Kits

Number of atoms / Element Symbol / Element Name / Color
10 / C / Carbon / Black
2 / N / Nitrogen / Blue
28 / H / Hydrogen / Yellow
6 / O / Oxygen / Red
4 / Cl / Chlorine / Green
2 / Br / Bromine / Orange
2 / I / Iodine / Purple

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:

a.You will earn 3 bonus points if your chosen molecule is not selected by any other student in the class.

b.You will earn 6 bonus points if your chosen molecule correctly uses more atoms than any other molecule in the class.

5.Bring a copy of the information you found about your molecule to lab with you.

6.I or the TA must inspect your molecule and initial your report sheet before proceeding to the next section.

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 skeleton:

Add six hydrogens to the skeleton. Now construct another molecule beginning with two carbon atoms and one oxygen atom in the skeleton:

Add six hydrogens to this skeleton.

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 water-soluble and boils at 78 ºC, while dimethyl ether is water-insoluble and boils at -24 ºC.

2.Construct a model of the following compound:

Use springs to represent the double bond between the two carbon atoms.

Now, try to construct two other different models of C2H2Cl2 in which the two carbon atoms are still linked by a double bond. Note: since you only have four Cl atoms, you will need to pretend that the two orange Br atoms are also Cl atoms for this exercise. Compare the three models.

3.Take apart these three models, and build a model of CHBrClI. Now try to build a second model of CHBrClI that is different from the first. Set the molecules side-by-side and convince yourself that they are different.

Date ______Name ______

I.Construction of Chemical Models Instructor’s Initials ______

Molecule or Ion / Geometry / Net Dipole?
chlorine
water
nitrogen trichloride
formaldehyde
hydrogen cyanide
butane
ethanol
carbonate anion

II.Build Your Own MoleculeInstructor’s Initials ______

Name of your molecule:

Molecular Formula:

Molecular Weight:

Biological Significance:

Structural Formula:

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

Instructor’s Initials ______

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”.

3.Draw the two structures of CHBrClI.Describe the differences between the two models of CHBrClI. Do they differ in geometry or in molecular dipole?