Building Molecules from Atoms

Grade Level

Prospective and practicing K-8 Teachers; may be adapted for use in elementary classrooms.


Exercises 1-4 take approximately 1 hour.

In the previous two laboratory sessions, we learned that the atoms and molecules being investigated were all around us. In this lab, we are going to begin an exploration of how atoms interact with each other to form molecules. Observations of both different atoms and different molecule formations will be made. In the footsteps of many scientists before us, we will use model building as a technique to make these observations and to discover how these atoms come together to form bonds and create molecules.


To Ponder

1. How many substances have you come into contact with in your lives (for example, wood, steel, plastic, nylon, Teflon, leaf, skin, fingernail, beak, claw, hair, cotton, paper, wool, rayon, cardboard, glue, paste, flour, sugar, salt, pepper)? Dozens? Hundreds? Thousands? Millions?
2. Every substance has its own unique properties, making it different from other substances. How can we understand the many different properties in the many substances we know?
3. Is it really true that all substances are made of just 109 different kinds of atoms? How can there possibly be so many different kinds of substances when there are so few kinds of atoms?
4. Do atoms retain their individual properties when they are joined together to form molecules?
5. Do all molecules of the same type have the same properties?
6. How do the organic molecules characteristic of living things differ from inorganic molecules?



Molecular Modeling Kit including:
Atoms Color  
nitrogen yellow, 3 bonds  
oxygen red, 2 bonds  
carbon black, 4 bonds  
hydrogen white, 1 bond
(colors may vary from kit to kit)
Metal Connectors
long links - for forming double and triple bonds
short links - for forming single bonds



Once you have completed these exercises you should be able to:
1. Understand how molecules form and break apart in living things.
2. Describe the effects of one, two and three bonds on the rotation of atoms.
3. Recognize that forming a bond requires and captures energy, while breaking a bond releases energy.




Atoms are basic building blocks that can combine with one another in an enormous variety of patterns. They link together in regular ways to form molecules


Powerful Idea

A molecule by definition contains more than one atom(e.g. H2 - hydrogen gas, N2 - nitrogen gas, O2 - oxygen gas, H2O - water, CO2.- carbon dioxide gas). Molecules may contain one or more kinds of atoms and may be solids, liquids, or gases at room temperature. Billions of the same kind of molecules together form a homogeneous substance such as water or absolute alcohol. A homogeneous substance is one that contains the same molecules or atoms throughout. Living cells are so small that we typically view them with powerful magnifying devices such as light and electron microscopes. Yet a single living cell contains billions of atoms and molecules. How can scientists study anything that is this tiny?

It is NOT possible to 'see' small molecules like water or sugar by any available means. In fact, only recently has it become possible to 'see' large macromolecules like DNA with electron and scanning electron microscopes. Yet the philosopher Democritus (384-322 BC) first proposed the idea of atoms several hundred years before Christ was born. And John Dalton (1766-1844) produced the basic postulates of the atomic theory two centuries ago. The theory is based upon many sound lines of evidence largely involving:


  • looking at many molecules together,
  • looking indirectly at the effects and behaviors of molecules,
  • looking at models of molecules, and
  • making predictions based upon the theory and testing them in the laboratory.

In this lab, we will use the modeling approach.


Exercise 1

Molecular Structure

Background 1. Some molecules consists of two or more atoms held together by covalent chemical bonds. Covalent Bonds are formed when two atoms share a pair of electrons between them. They are strong bonds that serve to hold atoms tightly together in molecules.

One covalent bond is formed by one pair of shared electrons, one electron from one atom and the other electron from the other atom. In water, for example, there are two single covalent bonds.

Figure 1. Water


A pair of atoms may form more than one covalent bond between them, as in O2 or O=O.

Figure 2. Oxygen

c. The number of covalent bonds formed by a particular small atom is usually equal to the number of electrons it needs to fill its outer orbital. Thus hydrogen forms one bond, oxygen forms two bonds, and carbon forms four bonds.
Question d.

How many covalent bonds are in each of the following molecules?

oxygen gas, O2 __________
water, H2O __________
carbon dioxide, CO2 __________

To Do e.

Draw these molecules to show the covalent bonds between the atoms.

oxygen gas water carbon dioxide

Question f. Where is the biologically usable energy stored in a molecule?


Exercise 2

Modeling Molecules

Use the molecular model kit in order to help you visualize how molecules are put together and what they look like.

To Do 1. Familiarize yourself with the modeling kit. Open the box and sort the pieces into similar piles.
2. The roundish plastic pieces with holes in them represent various types of atoms. Each color represents a different element. The gray links represent covalent bonds. Check the list under Supplies (p. 1) to make sure that you have all the necessary pieces.
Question 3. Examine one of the white hydrogen atoms. How many holes (bonding points) does it have? __________
4. How many holes (bonding points) are in the black carbon atoms? __________
5. How many holes (bonding points) are in the red oxygen atoms? __________
6. How many holes (bonding points) are in the blue nitrogen atoms? __________
Explain 7.

Do these structures correspond to your expectations based on the last lab? Explain.

Background 8. The short links are to be used when bonding two atoms together with one covalent bond. The long links are to be used when bonding the same two atoms together with 2 or 3 covalent bonds.
9. A carbon atom is very versatile and can bond to another carbon atom with a single, double, or triple bond. To see how, take out 6 black carbon atoms and connect them in pairs as follows:
To Do a.

connect one pair of carbon atoms together with one covalent bond (use one short gray link)

Model 1: Carbon - carbon single bond

To Do b.

connect the second pair together with two covalent bonds (use two long gray links)

Model 2: Carbon - carbon double bond

To Do c.

connect the third pair together with three covalent bonds

Model 3: Carbon - carbon triple bond

Question 10.

For each bonded pair, try rotating the atoms around their bonds and also wiggling the atoms with respect to each other. What happens?

Explain 11.

Which arrangement, 1, 2, or 3 shared covalent bonds, places the least constraint on the free motion of atoms?

Question 12.

Which arrangement, 1, 2, or 3 shared covalent bonds, places the greatest constraint on the free motion of atoms?


The greater the constraints on free motion, the less stable the bond and the more likely it will break. Which of these situations, 1) a single bond, 2) a double bond), or 3) a triple bond produces the most constrained, least stable, most reactive molecule?

To Do 14.

Make a model of hydrogen gas, H2. It consists of two hydrogen atoms connected by a single covalent bond. Take two hydrogen atoms and connect them together with a short link.

Model 4: Hydrogen gas

Question a.

What does the link between the two atoms represent? Describe in terms of the structure of the atoms and their shared parts.

Explain b.

Could you connect more than two hydrogen atoms together? Explain, again in terms of the structure of the atoms and their shared parts, why or why not.

To Do 15.

Another simple molecule is oxygen gas, O2. To model oxygen, take two oxygen atoms and covalently bond them together in such a manner that nothing else could be attached to either atom.

Model 5: Oxygen gas

Question a. How many covalent bonds are required to connect two oxygen atoms together?
b. What is this number of covalent bonds between two atoms called?
Describe c.

Describe these bonds with diagrams.

Question d. How many electrons are being shared by the two atoms?


Exercise 3

Molecular Formulas

Background 1. You may have already noticed the relationship between the number of atoms in a molecule and their representation in the molecular formula. Molecules of both hydrogen and oxygen gas have two atoms. Their formulas are H2 and O2. The H stands for hydrogen; the O for oxygen. The subscript number in each formula tells how many of each particular type of atom are in the molecule, 2 hydrogens in hydrogen gas and 2 oxygens in oxygen gas.
Question 2.

The molecular formula for water is H2O. What atoms make up water and how many of each are there?


Water is an inorganic molecule. What is the basis of this classification?

To Do 4.

Construct a model of water. Obtain one oxygen atom and two hydrogen atoms and connect them together. Draw what it looks like in the space below. Note that the bonding angle is larger than 90o

Question 5.

The molecular formula for methane gas is CH4.What atoms make up methane gas and how many of each are there? Methane gas is an organic molecule. Why is it so classified? Where does it occur?

To Do 6.

Construct a model of methane. Draw your model of methane below.


Exercise 4

Types of Bonds

Describe 1.

To review what you learned above, describe how covalent bonds are formed and where they occur.


Electrons are shared equally in a covalent bond joining two atoms of the same element. Name three molecules in which this is the case.

Background 3.

In water, however, the electrons are not shared equally between the atoms because oxygen is highly electronegative. Electronegativity is a measure of the ability of an atom in a molecule to attract electrons to itself. Because oxygen is highly electronegative, the shared electrons in covalent bonds are much more attracted to the oxygen atom than to the hydrogen. Because of this, the oxygen takes on a partial negative charge while the hydrogens take on partial positive charges. These partial charges are indicated with the delta symbol (). This polarity makes water molecules behave like little magnets and accounts for many of the unusual properties of water.

Figure 3. Water molecule

To Do 4. On the sketch of the water molecule above, show the partial positive and partial negative charges.
5. As we noted previously, these partial charges make water molecules behave like little magnets, with the (negative) oxygen of one water molecule attracting the (positive) hydrogen of another water molecule. The attraction between atoms in different molecules due to partial charges in this case is called a hydrogen bond. Hydrogen Bonds are very weak bonds because the atoms are attracted to each other by only partial, not full, charges. Hydrogen bonds are much weaker than covalent bonds - they are readily broken and readily formed anew because no electrons are actually shared. Use dotted lines to draw the hydrogen bonds that might occur among half a dozen water molecules.
To Do 6. Make models of several water molecules and lay them out on your table to demonstrate their hydrogen bonding interactions, using 'dotted' toothpicks to represent hydrogen bonds. The three atoms, H - O ---H, usually lie in a straight line. Show your instructor the arrangement.
Describe 7. Hydrogen bonding among water molecules gives rise to many of the interesting qualities of water we studied earlier. Although each individual hydrogen bond is weak and easily broken, the large number of hydrogen bonds in a substance such as water has a strong cumulative effect. Describe how hydrogen bonding among water molecules accounts for each of the phenomena below.



high specific heat

Describe 8. Many organic molecules have partial charges on various atoms. This is true of wood, paper products, and glass. Describe how hydrogen bonding between water and other substances accounts for the phenomena below.



capillary action

Note: On the other hand, there are many molecules that attract one another and exhibit cohesiveness without hydrogen bonding such as mercury

Background 9. A third type of bond is the ionic bond which forms between two or more ions with opposite charges, typically in salts such as sodium chloride (NaCl), acids such as sulfuric acid (H2SO4), and bases such as sodium hydroxide (NaOH). Rather than share a pair of electrons, an ionic bond is formed when one atom gives one or more electrons to another atom. In NaCl, for example, the sodium (which has just one electron in its outer orbit) gives it electron to chlorine (which has 7 electrons in its outer orbit). In this way, both atoms reach stable electron configurations.
Question a.

What is the charge on the sodium ion which has lost an electron? Explain.


What is the charge on the chloride ion which has accepted an electron? Explain.


What is the charge on the sodium chloride molecule? Explain.

To Do 10.

Ionic bonds are stronger than hydrogen bonds. In a dry sodium chloride (NaCl) crystal, the ions form a latticework held together by ionic bonds. Draw the molecular structure of a salt crystal .

To Do 11.

Salt separates in solutions. Water molecules pack around each ion, forming hydrogen bonds from their partially charged areas to the ion's full charge. Different ends of the water molecule are attracted to positive and negative ions. Draw salt ions in solution below, showing the water and hydrogen bonds.

Background 12.

Hydrogen bonds also play a role in the folding of and in maintaining the shape of large molecules such as DNA, because weak hydrogen bonds form between different partially charged areas of the molecule.

Figure 4. Section of DNA molecule showing hydrogen bonding between nucleotides at different points in the DNA strands.

Background 13. Water is but one of many polar molecules. In fact, any time OXYGEN or NITROGEN is involved (for example, in carbohydrates or proteins or DNA), the molecules are likely to be polar due to the strong attraction of electrons by these two electronegative elements. This polarity helps to make many different molecules water soluble.

Powerful Ideas

14. Summary. There are more than 12 million substances on earth, made from various combinations of approximately 100 different kinds of atoms. The postulates of Dalton's theory still apply today:
a. All matter is made of atoms.
b. All atoms of a given element are identical, both in mass and in properties [except for isotopes]. Atoms of different elements have different masses and different properties.
c. Compounds [molecules] are formed by combination of two or more different atoms which combine in whole numbers (e.g., 1 atom of A, two atoms of B, and four atoms of C).
d. Atoms are the units of chemical change. A chemical reaction involves combination, separation or rearrangement of atoms. Atoms are NOT created, destroyed, divided into parts, or converted into other kinds of atoms during a chemical reaction.

Living things are filled with dynamic, ongoing chemical reactions. Consider the large scale reactions described below and classify them as combination (combining atoms to build larger molecules), separation (breaking molecules down into smaller subunits), or rearrangement (changing the bonds between atoms within a molecule).

digestion __________________
cellular respiration __________________
photosynthesis __________________
DNA synthesis __________________
O2 binds to hemoglobin __________________


Briefly describe how your body obtains the atoms it needs to construct your hair, skin, organs and all the other tissues.

17. Disassemble all of the molecules you have made, return all pieces to the box, and put the box away.



Atkin, Peter. (1987). Molecules.The abstract concept of molecules is related to everyday experiences. The illustrations clarify the explanations.

Salem, Lionel. (1987). Marvels of the Molecule.The author describes the formation and behavior of molecules. Although the concepts are complex, the illustrations and explanations make the book understandable and interesting.

Chemistry Teaching Resources, Umea University, Sweden URL: http://www.anachem.umu.se/eks/pointers.htm


Section D: Structure of Matter

Grade 6-8 (Benchmark 1 of 7)
All matter is made up of atoms, which are far too small to see directly through a microscope. The atoms of any element are alike but are different from atoms of other elements. Atoms may stick together in well-defined molecules or may be packed together in large arrays. Different arrangements of atoms into groups compose all substances.

Grade 6-8 (Benchmark 3 of 7)
Atoms and molecules are perpetually in motion. Increased temperature means greater average energy of motion, so most substances expand when heated. In solids, the atoms are closely locked in position and can only vibrate. In liquids, the atoms or molecules have higher energy, are more loosely connected, and can slide past one another; some molecules may get enough energy to escape into a gas. In gases, the atoms or molecules have still more energy and are free of one another except during occasional collisions.

Grade 6-8 (Benchmark 6 of 7)
There are groups of elements that have similar properties, including highly reactive metals, less-reactive metals, highly reactive nonmetals (such as chlorine, fluorine, and oxygen), and some almost completely nonreactive gases (such as helium and neon). An especially important kind of reaction between substances involves combination of oxygen with something else as in burning or rusting. Some elements don't fit into any of the categories; among them are carbon and hydrogen, essential elements of living matter.