Molecular Modeling in Organic Chemistry

In this laboratory activity, you will be examining molecular models of various organic compounds. You will pay particular attention to the existence of isomers. Isomers are prevalent in organic compounds due primarily to carbon's ability to make 4 bonds. 

In the first part of this lab, you may visit one or more of the following websites:
http://www.molecularmodels.ca/ - start by clicking on "Molecular Models"
http://www.dcu.ie/~pratta/jmgallery/index.htm - start by clicking on the "Molecular Viewing Gallery (Jmol enabled)
http://preparatorychemistry.com/Bishop_Molecules.htm - start by clicking on "Hydrocarbons" or "Alcohols"

All of the molecular models at the above sites are rendered using Jmol java applets. It will take several seconds to load the Jmol applet the first time, or up to a minute or more if your computer or internet connection is slow. Subsequent models will load much faster. Java is ordinarily enabled on web browsers. In the event it is not, you will need to enable Java and/or download the latest version for your operating system. The free download and instructions may be found at http://java.com/en/download/index.jsp.  

You will be required to turn in answers to the following questions. On the first page, type your name and that of your lab partner. Individual or group reports are allowed. The questions should be typed out (available here). Recall that ChemSketch will even allow you to confirm your IUPAC names, though the Generate Name feature under the tools menu. If you are working from home, ChemSketch is available for download at  http://www.acdlabs.com/resources/freeware/chemsketch/

If you are submitting this assignment electronically, please use a filename convention of Lastname Organic Models Lab or Lastname1 Lastname 2 Organic Models Lab.

Build molecular models and draw molecular structures (condensed structures or line structures are just fine) for each isomer that is possible for each of the molecular formulas given below. Then give the IUPAC name for each. Distinguish between any cis- and trans- isomers that you find.

  1. Five alkanes that have the formula C6H14.
  2. Six alkenes that have the formula C5H10.
  3. Six cycloalkanes that have the formula C5H10.
  4. Three alkynes that have the formula C5H8.
  5. Four alcohols that have the formula C4H10O.
  6. Three ethers that have the formula C4H10O. Use common names for the ethers.

After you complete constructing and naming the compounds above, complete the questions below. You may use condensed structural formulas, if you prefer.

  1. Build molecular models and draw molecular structures for a primary amine, a secondary amine, and a tertiary amine that each have the formula C3H9N.
  2. Select one of the alkenes from #2. Show its reaction with bromine. Draw the structural formula and name the product(s) of the reaction.
  3. Select the simplest alcohol from #5 that could be oxidized to an aldehyde. Draw the structural formula and give the IUPAC name of the aldehyde that would be formed when the alcohol is oxidized.
  4. Select the simplest alcohol from #5 that could be oxidized to a ketone. Draw the structural formula and give the IUPAC name of the ketone that would be formed when the alcohol is oxidized.
  5. Which alcohol in #5 could not be oxidized? Why not?
  6. Which of the products of the reactions in #9 and #10 may be oxidized to an organic acid? Draw the structural formula and give the IUPAC name of the organic acid that would be formed.
  7. Using the organic acid from #12 and the alcohol used in #9, draw the structural formula and give the IUPAC name of the ester that would be formed.

Finally, draw the structural formula (condensed structures or line structures are just fine) for each of the compounds whose names appear below.

  1. 3-ethyl-2-methylpentane
  2. 2-pentanol
  3. cis-2-hexene
  4. 3-heptanone
  5. hexanoic acid
  6. ethyl propyl ether
  7. ethyl propanoate

Submitting Your Assignment

Follow your instructor’s directions for submitting this lab report. Remember to name the file as specified near the beginning of Assignment section (Lastname Organic Models Lab or Lastname1 Lastname2 Organic Models Lab). If you are emailing your report, use the subject line “Chem 1062: Organic Models Lab”. If you worked in pairs and are submitting this assignment on an individual basis, please underline your own name and include your lab partner’s name on the assignment.