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 http://learn.genetics.utah.edu/ 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.

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.

Exercises

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.