----------------------------------------------------------------------

Building Molecules from Atoms

 
Prior Knowledge. Eliciting students' prior knowledge is a very important step in beginning each new lesson. Students' current understandings provide the foundation from which to build new knowledge. See the Instructional Guide for a detailed discussion of the approach we recommend. The 'To Ponder' questions and the table of alternative ideas should help you get started.  

----------------------------------------------------------------------

 

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?

Chances are good that you have personally had contact with thousands or millions of different kinds of substances.

 
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?

This is the power of atomic/molecular theory. Each substance is made of a different kind of molecule, and we can explain the properties of the substance by the behavior of its molecules.

 
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?

This also illustrates the marvelous power of atomic/molecular theory. It is really true that all molecules are made of some combination of atoms, and that there are only 109 different kinds of atoms. When atoms are combined in new ways, the molecules that are formed have properties different from those of other types of molecules.

 
4.

Do atoms retain their individual properties when they are joined together to form molecules?

Some properties are retained but others are not. Water (H2O), for example, has very different properties from H atoms and O atoms. The new properties that arise may be called emergent properties.

 
5.

Do all molecules of the same type have the same properties?

All molecules of the same type share the same properties. The properties of the substance will vary depending upon the current state of the substance (solid, liquid, or gas) and the environment in which it is placed (for example, air, water, oil, sea level, 5000 feet, etc.), but all molecules of the same type will vary in the same ways under these different conditions.

 
6.

How do the organic molecules characteristic of living things differ from inorganic molecules?

Organic molecules are carbon-based. That is, all molecules which contain carbon we deem organic. Inorganic molecules do not contain carbon.

 

----------------------------------------------------------------------

 
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.  

----------------------------------------------------------------------

 

Supplies

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
 

----------------------------------------------------------------------

 

Objectives

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.  

----------------------------------------------------------------------

 

Background

Molecules

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. 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? They solve this problem by:

  • looking at many molecules together,
  • looking indirectly at the effects and behaviors of molecules, and
  • looking at models of molecules.

In this lab, we will use the last approach, modeling.

 

----------------------------------------------------------------------

 

Exercise 1

Molecular Structure

 

Background

1. Some molecules consist 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.  
a.

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

b.

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 __________

Oxygen gas contains one double bond or two covalent bonds all together. Water has two single covalent bonds, and carbon dioxide has two double bonds, or four covalent bonds all together.

 
To Do e.

Can you draw these molecules to show the bonds between the atoms?

 

Question

f.

Where is the biologically usable energy stored in a molecule?

The biologically usable energy stored in molecules is in the bonds between the atoms. When molecules are broken down, energy is released from the bonds as they are broken which may provide energy to drive other reactions or which may provide heat to maintain body temperature.

 

----------------------------------------------------------------------

 

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 round plastic pieces with holes in them represent various types of atoms. The gray links represent covalent bonds. Check to make sure that you have the following pieces:

blue (nitrogen)    long links (for double and triple bonds)
red (oxygen)
black (carbon)    short links (for single bonds)
white (hydrogen)

Note that each color represents a certain element.

 

Question

3.

Examine one of the white hydrogen atoms. How many holes (bonding points) does it have? __________

The hydrogen "atoms" have one hole in them, as hydrogen has one electron it can use to bond other atoms.

 
4.

How many holes (bonding points) are in the black carbon atoms? __________

The carbon "atoms" have four holes in them because each carbon atom can bind with up to four other atoms.

 
5.

How many holes (bonding points) are in the red oxygen atoms? __________

The red oxygen "atoms" have two holes in them. Each oxygen atom can bind with up to two other atoms.

 
6.

How many holes (bonding points) are in the blue nitrogen atoms? __________

The blue nitrogen "atoms" have three holes in them as each nitrogen atom can bind with three other atoms.

 

Explain

7.

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

These structures should correspond to your expectations based on the last lab, especially the orbital diagrams in Lesson 2, Exercise 3 and the number of electrons in the outer shell summarized in Table 3. Atoms will bond other atoms by either sharing, taking, or giving up electrons in such a way as to complete their outer shell.


 

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.

It is important to note that whereas the short and long links are used in this fashion so that the models will fit together, it by no means represents the correct bond lengths. In actuality, single bonds are longer than double bonds which are longer than triple 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 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 (use three long gray links)

Model 3: 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.  

Explain

11.

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

The carbon atoms bonded together by a single bond have the most free motion around the bond.

 

Question

12.

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

The carbon atoms bonded together by a triple bond will have the least free motion around the bonds.

 
13.

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 least stable (most reactive) molecule?

The answer is 3. In this case, the triple bond produces the least stable 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.

The link between the two atoms represents a covalent bond which consists of a pair of shared electrons. Each hydrogen shares one of its electrons with the other hydrogen.

 

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.

As each hydrogen only has one electron to share in the formation of chemical bonds, it is impossible to connect more than two hydrogen atoms to each other.

 
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?

Two covalent bonds are required to connect two oxygen atoms together and completely fill the outer orbital of each atom. They form a double bond between the two atoms.

 
b.

What is this number of covalent bonds between two atoms called?

The number of covalent bonds between these two atoms is called a double bond.

 

Describe

c. Describe these bonds with orbital diagrams.  

Question

d.

How many electrons are being shared by the two atoms?

Each oxygen atom is sharing two electrons with the other oxygen atom.

 

----------------------------------------------------------------------

 

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?

Two atoms of hydrogen and one atom of oxygen make up each water molecule.

 
3.

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

Water is an inorganic molecule because it does not contain carbon.

 

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

Model 6: Water molecule

 

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 because it does contain carbon. Where does it occur?

One atom of carbon and four atoms of hydrogen make up each methane molecule. Methane is what we know as natural gas. Ordinarily, it is both colorless and odorless. The local gas companies add substances which give methane the scent with which we are familiar.

 

To Do

6.

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

Model 7: Methane molecule

 

----------------------------------------------------------------------

 

Exercise 4

Types of Bonds

 

Describe

1.

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

Covalent bonds are formed between atoms when the atoms in question come together and share electrons.

 
2. In covalent bonds, electrons are usually shared equally between atoms and in these cases the bonds have no charge. This is the case in hydrogen, oxygen, and methane gas.  

Background

3.

In water, however, the electrons are not shared equally between the atoms. Oxygen, with 6 negatively charged electrons in its outer shell, has a far greater attraction for electrons than each hydrogen, having just one electron in its outer shell. Therefore, the shared electrons spend much more time orbiting oxygen than orbiting 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 shown below (you first saw this drawing in the water lab).

Figure 3. Water molecule showing partial charges

 

To Do

4. On the sketch of the water molecule you made 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. One reason Hydrogen bonds are very weak bonds is 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. Draw the hydrogen bonds that might occur among half a dozen water molecules.  
 

To Do

6. Make models of several water molecules and demonstrate their hydrogen bonding interactions with _____ toothpicks.  

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 very 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.

cohesion

Because of hydrogen bonds, the water molecules "stick" to each other making water cohesive.

high specific heat

Because of hydrogen bonding, the water molecules require a greater amount of energy to be separated from each other. This is reflected in a higher boiling temperature than that of other molecules of the same mass which do not hydrogen bond.

 

Describe

8.

Many molecules also 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 each of the phenomena below.

adhesion

The partial charges of these molecules allow water to hydrogen bond with any oxygen, nitrogen, or fluorine in them. We can observe this as water "sticks" or adheres to the wood, paper products, or glass.

capillary action

By the same principle above, water will adhere to and be drawn along the surface of any substance with which it can hydrogen bond.

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. Rather than share a pair of electrons, 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?

The charge on the sodium ion is +1.

 
b.

What is the charge on the chloride ion?

The charge on the chloride ion is -1.

 
c.

What is the charge on the sodium chloride molecule?

The charge on the entire molecule is 0 (+1 + -1 = 0).

 

To Do

10.

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

Figure1: Sodium chloride crystal (NaCl)

 

To Do

11.

Salts separate 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 electrochemical interactions.

 

Background

12.

Hydrogen bonds also play a role in the folding of and in maintaining the shape of large molecules such as DNA, because the 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 molecules which contain polar covalent bonds. In fact, any time OXYGEN or NITROGEN is involved in a covalent bond (e.g., in sugars or amino acids or DNA), the bond is likely to be a polar covalent bond due to the extreme attraction of electrons by these two elements. These polar bonds help 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.  
15.

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 separation
cellular respiration separation
photosynthesis combination
DNA synthesis combination
O2 binds to hemoglobin rearrangement

 
16.

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.  

----------------------------------------------------------------------