Teacher Notes

Models of Organic Compounds

Guided-Inquiry Kit

Materials Included In Kit

Carbon atoms (black, 4-hole), 25*
Double bond links (long gray connectors), 25*
Hydrogen atoms (white, 1-hole), 50*
Nitrogen atom (blue, 3-hole)*
Oxygen atoms (red, 2-hole), 2*
Single bond links (short gray connectors), 75*
*In the organic model set

Additional Materials Required

Permanent marker
Zipper-lock plastic bags, 4 (for model sets for Parts A–D)

Prelab Preparation

Divide the “building blocks” from the organic model set provided with the kit into four sets for Parts A–D. Place each set into a separate zipper-lock, plastic bag and label each bag with a permanent marker.

  • Part A: 8 C atoms, 20 H atoms and 26 single bond links
  • Part B: 8 C atoms, 16 H atoms, 20 single bond links and 8 double bond links
  • Part C: 6 C atoms, 6 H atoms, 9 single bond links and 6 double bond links
  • Part D: 3 C atoms, 7 H atoms, 2 O atoms, 1 N atom, 11 single bond links and 2 double bond links

Safety Precautions

Follow all normal classroom safety guidelines.


Store the organic model set for future use.

Lab Hints

  • To obtain additional building blocks for the organic models used in this activity, see the “Organic Small Group Model Set” (Catalog No. AP5453) available from Flinn Scientific, Inc.
  • This is a paper-and-pencil activity—two class sessions are recommended for its completion. Students may work on the different parts of the activity in any order. Rotate the model sets for Parts A–D among the groups in 10–12 minute intervals. Having students work collaboratively in groups of four or five will allow students to brainstorm and bounce ideas back and forth. This is the heart of the guided inquiry process in which students use reasoning skills and critical thinking to actively “construct” their knowledge of the subject matter.
  • The optimum learning environment for guided inquiry is one in which the students teach each other and learn from one another. It is helpful to assign or have students select roles within each group to ensure that all students participate in the process. The manager keeps the group “on task” and checks that all members of the group participate in each activity. The recorder writes down the answers and explanations for each question, along with any observations or questions that arise as the students work through the activity. The presenter may be asked to answer oral questions posed to the group as the teacher monitors progress during the guided inquiry activity. The reflector observes the group dynamics and verifies that all members of the group remain “in the loop” and understand the key concepts that have been developed.

Teacher Tips

  • In general, guided-inquiry activities are most successful if students understand that the activity replaces the lecture. Students are more likely to take responsibility for learning when they are actively engaged in the process of “constructing knowledge.” Guided-inquiry activities simulate the scientific method—students look at data, search for patterns or relationships, and try to identify guiding principles that will explain the data.
  • The teacher’s role in guided-inquiry activities is very important. The atmosphere in the classroom must be conducive to independent learning. The teacher facilitates learning by monitoring students, keeping them on track, and reviewing progress at key junctures. In this activity, for example, the teacher may want to call a “time-out” after step 5 in Part A (the definition of isomers). Call on several groups to give their definitions and then ask students to explain or defend their definition or to modify their definition based on new information that they have heard.
  • Most students will have studied the structures of amino acids, proteins and DNA in their biology classes. Review the structures and properties of biological molecules and relate them to the principles learned in this lab.
  • Have students research the composition, properties, and uses of the various hydrocarbon fractions (e.g., natural gas, gasoline, kerosene) that are obtained from petroleum and investigate the processes that are involved in petroleum refining.

Correlation to Next Generation Science Standards (NGSS)

Science & Engineering Practices

Developing and using models
Constructing explanations and designing solutions

Disciplinary Core Ideas

MS-PS1.A: Structure and Properties of Matter
HS-PS1.A: Structure and Properties of Matter
HS-PS1.B: Chemical Reactions

Crosscutting Concepts

Scale, proportion, and quantity

Performance Expectations

MS-PS1-1. Develop models to describe the atomic composition of simple molecules and extended structures.
HS-PS1-2. Construct and revise an explanation for the outcome of a simple chemical reaction based on the outermost electron states of atoms, trends in the periodic table, and knowledge of the patterns of chemical properties.
HS-PS1-1. Use the periodic table as a model to predict the relative properties of elements based on the patterns of electrons in the outermost energy level of atoms.

Answers to Prelab Questions

  1. Review and define the following terms and concepts related to chemical bonding: (a) valence electrons; (b) Lewis electron dot structures; (c) covalent bond; (d) molecular geometry.
    1. Valence electrons are the electrons in the outermost (highest energy), partially filled electron energy levels in the electronic ground state of an atom. The valence electrons are the electrons that are typically involved in chemical bond formation when elements combine with each other to form compounds. The number of valence electrons affects the types of bonds that an element will form and also the number of covalent bonds that an element will form in a covalent compound.
    2. Lewis electron dot structures are used to indicate the valence electrons around an atom.
    3. A covalent bond is the net attractive force between two atoms that share electrons in a molecule.
    4. Molecular geometry refers to the three-dimensional shape or structure of a molecule. The shape of the molecule depends on the number of bonding and nonbonding pairs of electrons around the central atom in a molecule.
  2. The structural formula of a molecule shows all of the atoms in the structure and the order in which they are connected by covalent bonds. Add hydrogen atoms as needed to each atom in the following structural formulas so that each atom has a closed shell electron configuration and zero charge.

Answers to Questions

Part A. Models of Alkanes—Structural Isomers

  1. Build a model of methane, CH4, the chief component of natural gas, and draw a diagram that illustrates the three-dimensional structure of the molecule. What is the molecular geometry around the carbon atom in methane?

    Methane has a tetrahedral geometry around the central carbon atom. The ideal H—C—H bond angle is 109.5°.

  2. Build models of ethane, C2H6, and propane, C3H8, and write out their structural formulas.
  3. Observe the models: Do the C—C single bonds in ethane and propane rotate freely? Explain.

    The hydrogen atoms on adjacent carbon atoms in ethane can “slide” past each other as the C—C bond turns or rotates.

  4. There are two possible structures for butane, C4H10. Build models of both structures and draw their structural formulas.
  5. The two possible structural formulas for butane represent isomers. Write a definition of isomers that describes the relationship between these two molecules.

    Isomers are molecules or compounds that have the same molecular formula but different structural formulas.

  6. Without building models, draw out the possible structural formulas for three isomers of pentane, C5H12.
  7. Alkanes are hydrocarbons—compounds containing only carbon and hydrogen atoms—in which all of the C—C bonds are single bonds. What is the general formula for an alkane, where n is the number of carbon atoms?


Part B. Models of Alkenes—Geometric Isomers
  1. Alkenes are hydrocarbons—compounds containing only carbon and hydrogen atoms—that have at least one C=C double bond in their structures. Build models of (a) ethene (C2H4) and (b) propene (C3H6), and draw their structural formulas.
  2. Describe the shape or molecular geometry around the C=C double bond in an alkene. What is the H—C—H bond angle in ethene?

    The molecular geometry around the C=C double bond is planar—the two carbon atoms and the atoms attached to them all lie in a single plane. The H–C–H bond angle is 120°.

  3. Unlike C—C single bonds, C=C double bonds do not rotate. Draw a diagram showing the overlap of the orbitals responsible for the sigma and pi bonds, respectively, in a C=C double bond. Use the orbital diagram to explain why the C=C double bond does not freely rotate.

    “Turning” the C=C double bond would destroy the overlap of the p-orbitals in the pi bond. Extra energy (beyond room temperature) must be “added” for the atoms to rotate along the double bond axis.

  4. Butene (C4H8) has one C=C double bond in the structure. Draw three possible structural formulas for alkenes having the formula C4H8. These three molecules represent isomers (see step 5 in Part A).
  5. The structural formula for 2-butene can be abbreviated CH3—CH=CH—CH3. Because of the lack of free rotation about the C=C double bond (see step 3), there are two possible structures for this compound. Build models and draw structural formulas for two possible arrangements of the CH3— groups relative to each other in 2-butene.
  6. The two structures for 2-butene shown in step 5 are called geometric isomers. What is the same and what is different about geometric isomers?

    Geometric isomers have the same molecular formula and the same structural formula, but different arrangements of atoms in space around a C=C double bond.

  7. What is the general formula of an alkene, where n is the number of carbon atoms? Hint: See the formulas of ethene, propene and butene. Why do you think alkenes are called unsaturated and alkanes are called saturated hydrocarbons?

    Alkenes are called “unsaturated” because they contain fewer than the maximum number of hydrogen atoms possible for the number of carbon atoms in the molecule. Alkanes are “saturated” because they cannot add any more hydrogen atoms to their structures.

Part C. Aromatic Compounds and Resonance
  1. Benzene, C6H6, is the parent compound of a class of compounds called aromatic compounds that are very common in nature. The carbon “skeleton” for benzene is shown. Add hydrogen atoms and double bonds, as necessary, to complete the structure of benzene.
  2. Build a model of benzene and describe its shape or molecular geometry (e.g., planar, tetrahedral). Are all of the bond angles in benzene identical?

    Benzene is a planar molecule—all of the atoms lie in a single plane. All of the bond angles are identical.

  3. The structural formula of benzene shown in step 1 has alternating single (C—C) and double (C=C) bonds. It has been found, however, all of the carbon–carbon bonds in benzene are identical. This fact may be explained in terms of resonance. Define resonance and draw two resonance forms for benzene.

    Resonance occurs in a molecule when it is possible to write two or more valid Lewis structures for the molecule. The actual structure of benzene is the average of the two possible Lewis structures.

  4. Because all of the carbon atoms in benzene are identical, there are three possible structural formulas for dichlorobenzene (C6H4Cl2), in which two of the hydrogen atoms in benzene have been replaced by chlorine atoms. Draw structural formulas for the three isomers of dichlorobenzene.
  5. How many different structures are possible for trichlorobenzene (C6H3Cl3)? Explain.

    There are three possible isomers. Many of the structures that might look different are actually the same molecule because of the fact that all of the carbon atoms in a benzene “ring” are identical due to resonance.

Part D. Polar Organic Compounds and Biological Molecules
  1. Alcohols are organic compounds containing an —OH group attached to a carbon atom. Draw the structural formula of ethyl alcohol, C2H5OH.
  2. Ethyl alcohol is a polar compound that is miscible with water. As the number of carbon atoms in an alcohol increases, the solubility of the alcohol in water decreases. Thus, octyl alcohol, C8H17OH, is practically insoluble in water. What characteristics of the C8H17— group make octyl alcohol insoluble in water?

    In octyl alcohol, the polar —OH group “competes” with the nonpolar chain of eight carbon atoms. Octyl alcohol is thus insoluble in water because the long hydrocarbon chain predominates.

  3. Build a model of the amino acid alanine, whose formula is shown below. Note: The —CO2H group has the following bonding arrangement of atoms:
  4. Hold the alanine model so the —CH3 and —CO2H groups are in the positions shown in Structure A. Fill in the circles to show the positions of the other two groups (—H and —NH2) attached to the central (C*) carbon.
  5. Complete Structure B so that it represents the mirror image of Structure A. Is it possible to rotate the model of Structure A In your hands so that it matches the mirror-image structure of B? What would you have to do to the some of the bonds in Structure A to make it match Structure B?

    No matter how you turn or rotate Structure A, it will not “match” the arrangement of atoms shown in Structure B. You would have to physically “break” two of the bonds in Structure A and then switch their positions in order to make it match Structure B.

  6. Structures A and B represent enantiomers, which are defined as non-superimposable mirror images of each other. What does it mean to say that enantiomers are non-superimposable? Why do you think this property of molecules is sometimes called “handedness?”

    Enantiomers cannot be placed on top of one another and made to “match” their mirror image by any combination of rotating or turning the molecules (see Question 5). Our hands are examples of non-superimposable mirror images.

Part E. Organic Functional Groups

Table 1 shows the structures of common organic functional groups. The symbol R is used to represent various rings or chains of carbon atoms attached to the functional group.

Table 1. Structures of Organic Compounds and Functional Groups
The following examples illustrate the great variety of functional groups present in natural products.
Circle and label the organic functional groups in the following natural and consumer products.
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  2. {12541_Answers_Figure_21}
  3. {12541_Answers_Figure_22}
  4. {12541_Answers_Figure_23}


This activity was adapted from Flinn ChemTopic™ Labs, Vol. 19, Chemistry of Organic Compounds; Cesa, I., Editor; Flinn Scientific: Batavia, IL (2006).

Student Pages

Models of Organic Compounds


There are more than nine million organic compounds and more than five million organic reactions associated with them. What factors are responsible for the enormous number of organic compounds? What features make all of these compounds different? Building organic molecules using models can help us understand the remarkable diversity of organic compounds.


  • Covalent bonding
  • Single bonds
  • Double bonds
  • Triple bonds
  • Sigma and pi bonding
  • Structural formula
  • Isomers
  • Functional groups


Attaching the word organic to food and consumer items has become a mark of quality, to signify that something is natural and pure. Organic chemistry is the study of compounds that contain carbon—their structures, properties, and reactions. The name reflects the historical roots of this branch of chemistry. In the early 19th century, organic chemistry was a brand new science devoted to the study of compounds called natural products, which were isolated from plants and animals. Natural products included foods and medicines, soaps and perfumes, preservatives and cosmetics, spices and seasonings, etc. These compounds were originally called “organic” because it was thought that compounds obtained from living organisms required some sort of “vital” or animating force for their existence. Although this notion was discarded in 1828, when the first organic compound was synthesized in the lab, the exciting discoveries of the molecular basis of life in the 20th century more than justify the title “organic” chemistry.

Carbon is unique among the elements because of the large number and diverse structures of compounds that it forms. Several factors help explain why carbon forms so many different compounds:

  • Carbon forms strong and stable bonds with other carbon atoms. The ability of carbon to form strong C–C bonds of almost infinite chain length is called catenation.
  • Chains of carbon atoms can “close in” on themselves to form rings in addition to chains. Many different ring sizes are possible, but five-, six- and seven-membered rings are the most common.
  • The electronegativity of carbon (2.5) is in the middle of the range of values for all elements (0.7–4.0). This means that carbon forms covalent bonds with both nonmetals and metals, everything from aluminum to zirconium.
  • The valency of carbon is four—carbon forms four covalent bonds to achieve a closed shell electron configuration (a stable octet). This is the maximum number of bonds a second row element will form.
  • Because of their small size, carbon atoms form strong multiple bonds (double bonds and triple bonds) to other carbon atoms as well as to nitrogen, oxygen and sulfur atoms. The strength of pi bonds in double and triple bonds depends on the size of the atoms.
All organic compounds contain carbon, as well as hydrogen atoms attached to the carbon “skeleton” in predictable numbers. In most chemical reactions, the C—C skeleton does not change. Typically, organic reactions involve either C=C double or C≡C triple bonds in a molecule, or carbon atoms attached to “heteroatoms,” such as oxygen, nitrogen or chlorine. Organic compounds are classified into functional group classes based on their structures and properties. A functional group is defined as a specific arrangement of atoms, such as —OH or —NH2, that is responsible for the types of reactions a compound will undergo. Functional groups are the reactive groups in a molecule. They undergo characteristic chemical reactions, such as oxidation or dehydration, and also give compounds similar physical properties. The study of organic functional groups provides the underlying structure for the science of organic chemistry. Knowing the chemistry of different functional groups allows chemists to explain and predict the reactions a compound will undergo and also to create new compounds.

Experiment Overview

The purpose of this activity is to discover the basic structures of organic compounds by building molecules “from the ground up” using models. The models will be used to draw structural formulas of organic compounds, determine the general formulas of hydrocarbons, and develop the concept of isomers. The activity, which is divided into five parts, is designed for small groups of students working together. Each part of the activity is a self-contained unit, and different groups will start with different sections as the model sets needed for Parts A, B, C and D rotate among the groups. (Part E does not require a model set.)


Alkanes (Part A)*
Alkenes (Part B)*
Aromatic Compounds (Part C)*
Polar Compounds (Part D)*
*Organic “building blocks” or model sets

Prelab Questions

  1. Review and define the following terms and concepts related to chemical bonding: (a) valence electrons; (b) Lewis electron dot structures; (c) covalent bond; (d) molecular geometry.
  2. The structural formula of a molecule shows all of the atoms in the structure and the order in which they are connected by covalent bonds. Add hydrogen atoms as needed to each atom in the following structural formulas so that each atom has a closed shell electron configuration and zero charge.

Safety Precautions

Please observe all normal classroom safety guidelines.

Student Worksheet PDF


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