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Modeling the Molecular Level

When chemists view the world they perceive more than they sense.

Sight, touch, smell and taste all bring the human organism into contact with physical matter. All physical matter is made up of tiny particles called atoms.

When a chemist sees his computer screen he sometimes thinks about how atoms absorb and emit light, making sight possible. When a chemist touches ice she may think about how the heat of her hand flows into it, making the molecules of the ice shiver faster and faster until they flow away from their rigid crystalline arrangement as liquid water. When a chemist smells the familiar and yet always attractive smell of vanilla he may reflect on the complex and chaotic pathway the molecules of vanilla took on their way from the bottle to the olfactory nerve. Or she may consider the still mysterious way in which the cells of that nerve can recognize (by touch!) the thousands of molecules she can recognize by smell. When a chemist tastes salt he often considers the positive and negative ions that make up salts and how they are so strongly bound in their solid crystals and yet so easily part ways to flow seamlessly with water.

Perception of these things requires thinking on the Molecular Level. This means understanding how to explain the behavior that you can see by thinking about the behavior of atoms and molecules. It means thinking about different size scales at the same time. One way to get an idea of the meaning of the phrase ‘the molecular level’ is to take a look at the Cell Size and Scale page at content/cells/scale/. Visit the page to zoom in and see many different levels of scale. Another useful introduction to this way of thinking is an applet from PhET: States of Matter. Understanding how atoms and molecules behave and how their behavior leads to the world we sense through sight, touch, smell and taste is the goal of chemical education. Perceiving on the Molecular Level deepens one’s appreciation of the intricacy and beauty of the world. It broadens the mind and can even move the spirit.

In this activity you will start on the path to seeing the world the way a chemist does. Chemists—and scientists generally—make sense of the world through the use of models. Models are sometimes physical like the model everyone has likely seen of DNA: little spheres connected with sticks. At other times models are mathematical: in physics motion is modeled using surprisingly simple equations. Today you will construct a model that is constructed using simple drawings of atoms and molecules. You will use these drawings to represent elements, compounds, homogeneous mixtures and heterogeneous mixtures.

Some examples of such models are displayed below.

molecular.modelA.liq-vapor (3K) molecular.modelB.solid-gas (4K) molecular.modelC.2gases (2K)

In these models atoms are drawn as circles. Different atoms are shaded differently so they can be told apart. Atoms that are bonded together in molecules overlap or touch. Notice the three-atom molecule in box A. It has one large atom in the middle and two small atoms bonded to it, one on each side (small-large-small or S-L-S). Another way to draw a molecule with two small and one large atom might be to put one of the small ones in the middle (S-S-L). Clearly this would be a completely different molecule: structure matters.

Identify the descriptions below with the models above:

  1. This model shows a solid element in a heterogenous mixture with a diatomic gaseous element. The two substances are made of different elements.
  2. This model displays a liquid compound in a heterogeneous mixture with the gaseous form of the same compound.
  3. This model depicts a homogeneous mixture of two elements, one of which is a diatomic gas.

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Draw models in boxes large enough to clearly show what is required in the description. Be consistent in how you draw your atoms. Be clear about making different elements look different and provide a key detailing which color is which element and identifying molecules. Be clear about showing how atoms are connected up to form molecules.

  1. ElementColor
    Hydrogen (H)White
    Oxygen (O)Red
    Nitrogen (N)Blue
    Carbon (C)Black
    Sulfur (S)Yellow
    Sodium (Na)Gray
    Chlorine (Cl)Yellow-green
    Use the color code at right to draw the following molecules. Draw one example of each molecule and check with your teacher to be sure you have it right for each one before continuing with this activity.
    NH3, CH4, H2O, NO2, N2O,
    CO, CO2, SO2, SO3, H2S, HCN
  2. Draw a box on your paper, about 6 cm on a side. Fill the box with a model of a solid material, shown at the molecular scale. Choose one of the molecules from the previous question to draw as a solid. Solids can be recognized by the fact that all molecules touch one another and that the molecules are arranged in a regular pattern. Particles in a solid vibrate in place but maintain their positions.
  3. Draw a box on your paper, about 6 cm on a side. Fill the box with a model of a liquid material, shown at the molecular scale. Choose one of the molecules from the first question to draw as a liquid. Liquids can be recognized by the fact that all molecules touch one another and that the molecules are randomly oriented and distributed. Particles in a liquid move around in random directions and are not held in one place.
  4. Draw a box on your paper, about 6 cm on a side. Fill the box with a model of a gas, shown at the molecular scale. Choose a molecule from above. Gases are made of particles with large amounts of space between them. The molecules move very quickly in random directions. Usually, each one is as far away from its neighbor as about 5 times its own diameter.
  5. Draw molecular-level drawings of the following substances and mixtures.
    1. a homogeneous mixture of Ne and Ar gases (these elements are noble gases and occur in nature as monatomic gases, in a homogeneous mixture the particles are equally likely to be found in any part of the mixture)
    2. water (H2O) in the liquid phase homogeneously mixed with ammonia (NH3); there should be more water molecules than ammonia molecules
    3. solid sodium chloride (NaCl) which is made of alternating positive sodium atoms (ions: Na+) and negative chlorine atoms (chloride ions: Cl-).
    1. a liquid homogeneous mixture of Na+ ions, Cl- ions and water; there should be equal numbers of the monatomic ions Cl- and Na+ (this mixture is a model of salt, NaCl, dissolved in water); the water molecules should outnumber the ions.
    2. a gaseous mixture of strong-smelling hydrogen sulfide (H2S) with nitrogen gas (N2) in which the H2S has not fully mixed with the nitrogen; this is a heterogeneous model in which the mixture has zones where one component is more concentrated than the other
  1. Solids are more dense than gases. Draw a model showing the element iodine in both solid and gaseous forms. In words explain how your model explains the difference in density between solids and gases. Iodine exists as a diatomic molecule (I2).
  2. Before asking students to attempt the following question, show this animation about salt dissolving in water from the Middle School Chemistry site of the American Chemical Society.
    Models can be used to show a process as well as matter with no apparent motion. In the style of a newspaper cartoon draw a series of models showing how separate ions of Na+ and Cl- leave the solid phase and dissolve in liquid water. Solid salt can be depicted as in the model below which shows alternating positive and negative ions. Positive ions are physically attracted to the oxygen atom in water molecules and negative ions are attracted to the hydrogen atoms. Try to show all of this in your drawings.
  3. molecular.model-salt.Ar.H2O (4K) Describe the model drawing shown here in a short paragraph. Identify each substance in the mixture. Identify the gas as homo- or hetero-geneous. The solid is an ionic compound and so is a pure substance.
  4. There are no molecules of an ionic compound such as sodium chloride (NaCl). Yet they are still considered compounds and not mixtures. Explain.
  5. Are these models you have been drawing limited in any way? How?
Significant inspiration for this activity is due to an activity written up in an (unknown to me) edition of ChemCom from the American Chemical Society. I used the idea for the activity while writing it up completely in my own words. Some of the questions were borrowed in concept but re-written. Also, I owe my use of the phrase “The Molecular Level” to Prof. Gale Rhodes, emeritus professor of chemistry at the University of Southern Maine. His site is called The Molecular Level.
You can find a useful simulation about the states of matter viewed at the molecular level using a Java applet at the PhET site: States of Matter.
Last Updated: Aug 27, 2015      Home
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