OL Lab 9: Building Models of Organic Compounds

Learning Objectives

The primary goals of this laboratory session are to:

• Construct virtual molecular models to better understand the structure and bonding patterns of organic compounds.

• Develop extended structural formulas for selected organic molecules.

Organic compounds are predominantly carbon-based, often incorporating additional atoms such as hydrogen, oxygen, and nitrogen. The unique bonding ability of carbon, which allows for the formation of four covalent bonds, makes it possible to create a vast array of molecules. This bonding versatility gives rise to countless compounds, many of which serve as essential biomolecules, pharmaceuticals, and industrial chemicals.

In this exercise, students use the online tool MolView to build molecular models and sketch extended structural formulas. Through these visualizations, learners gain insight into how structure dictates function in organic chemistry. Proper modeling also strengthens comprehension of molecular geometry, bond arrangements, and functional groups.

Exploration 1: Building Models of Hydrocarbons

Hydrocarbons, the simplest organic compounds, are composed only of hydrogen and carbon atoms. These molecules can appear in linear, branched, or cyclic structures and are often categorized into saturated (alkanes), unsaturated (alkenes and alkynes), and aromatic forms.

The following hydrocarbons were constructed virtually, and their condensed structural formulas are listed below:

Note: For cyclic and aromatic compounds such as benzene and cyclohexene, structural diagrams are more informative than condensed formulas.

Exploration 2: Identification of Functional Groups

Part 2A: Building Functional Groups

Functional groups are specific atom clusters that define the reactivity and chemical behavior of organic molecules. The following groups were modeled in this exercise:

• Alcohol

• Ether

• Ketone

• Carboxylic Acid

• Aldehyde

• Ester

• Amine

Part 2B: Identification of Functional Groups

The table below summarizes functional groups with their corresponding molecules and condensed structural formulas:

Exploration 3: Building Hydrocarbons Containing Functional Groups

In this section, extended structural models of hydrocarbons and functionalized compounds were created using MolView. Examples include:

• Difluoromethane

• Trichloromethane (chloroform)

• Tetrachloromethane (carbon tetrachloride)

• Propanol

• Ethanoic Acid (acetic acid)

When propanol and ethanoic acid are combined, they undergo esterification to produce propyl ethanoate, an ester often used in fragrances.

Additional compounds modeled include:

• Phenol

• Dimethyl ether (CH3OCH3)

• Propanal (CH3CH2CHO)

• Hexanoic acid (CH3CH2CH2CH2CH2COOH)

• Ethylamine (CH3CH2NH2)

Questions

1. Write the names of a biomolecule (also known as macromolecules) that contain each of the functional groups below.

• Amine – Proteins (contain amino groups in amino acids)

• Aldehyde – Carbohydrates (e.g., glyceraldehyde)

• Carboxylic Acid – Lipids (fatty acids with carboxyl groups)

• Alcohol – Carbohydrates (contain hydroxyl groups in sugars)

2. Find an example of an ester used as a fragrance or flavoring and give the name, condensed structural formula, and flavor of your chosen ester.

One example of an ester is Methyl butanoate, commonly used in artificial fruit flavorings.

• Condensed Structural Formula: CH3CH2CH2COOCH3

• Flavor/Fragrance: Apple-like aroma and taste

3. For each of the following, give the functional group and application.

Reflection

This laboratory experience significantly improved my understanding of organic chemistry concepts, especially the role of functional groups in determining molecular reactivity. By building and examining models, I was able to visualize how atoms are arranged in space and how this impacts their physical and chemical properties.

One valuable takeaway was the recognition of nomenclature systems, including IUPAC naming rules, which emphasize prefixes, suffixes, and functional group priorities. Although constructing models was time-intensive, it provided a strong foundation for identifying organic molecules in real-world contexts, such as analyzing drug compositions, food labels, and safety data sheets.

I also learned that some compounds have multiple naming conventions (common vs. systematic), which can occasionally lead to confusion. For instance, esters can be described either by the alcohol-then-acid naming format or vice versa, depending on context. Despite these challenges, the lab reinforced the importance of molecular visualization in both academic learning and professional applications, particularly in healthcare, pharmaceuticals, and biochemistry research.

References

McMurry, J. (2021). Organic Chemistry (10th ed.). Cengage Learning.

Solomons, T. W. G., Fryhle, C. B., & Snyder, S. A. (2020). Organic Chemistry (12th ed.). Wiley.

Zumdahl, S. S., & Zumdahl, S. A. (2020). Chemistry: An Atoms First Approach (3rd ed.). Cengage Learning.

CHEM 120 Week 5 Lab: Organic Chemistry.