This experiment is a continuation of the earlier experiment on molecular
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1 Molecular Modeling: Experiment 2 Page 115 Bonding and Molecular Structure Experiment 2 This experiment is a continuation of the earlier experiment on molecular structure. In that experiment you used a computer to construct models of molecules, learned to visualize those models, made measurements of bond angles, and began to recognize the factors determining molecular structure. The present experiment builds on the earlier experiment. Our objectives now are: to review the construction of electron dot structures of simple molecules; to review the factors determining molecular structure; to review the idea of formal charge on atoms; to observe the connection between bond length and bond order; to observe the consequences of double bonding; and to understand the notion of molecular polarity. Using the CAChe Software This experiment assumes that you know how to construct a molecule and measure bond angles and bond lengths using the CAChe Molecular Modeling system from Oxford Molecular. You should review the instructions for the software for the basic functions. Instruction in using two other functions of the software setting atom formal charge and determining the hybridization of an atom in a molecule or ion are given in a separate document. The Experiment You should work in pairs, using either the Macintosh or Windows computers. Follow the instructions in each part of the experiment be especially careful to draw the structures you are building and use the plastic molecular models available in the Computer Lab to help you further visualize the structures. Name Score /10 Instructor Comments: The instructions for using the CAChe modeling software are available on the General Chemistry web site at /kotzjc/111lab.html and in this Laboratory Manual. Background Before doing this experiment is is assumed that you are thoroughly familiar with the theories of bonding and molecular structure as outlined in Chapters 9 and 10 of Chemistry & Chemical Reactivity. Specifically, you should be familiar with drawing electron dot structures (Section 9.4) formal charge (Section 9.7) the properties of chemical bonds (bond order and bond length) (Section 9.8) the polarity of bonds and molecules hybridization (Section 10.2) the nature of multiple bonds and the consequences of multiple bond formation (pages )
2 Molecular Modeling: Experiment 2 Page 116 Part I: Drawing Dot Structures, Using VSEPR Theory, and Determining Molecular Polarity Using the CAChe software, construct a model of each of the following molecules having carbon oxygen bonds: a) Sketch the Lewis electron dot structure. (Make sure the item ELECTRONS is checked in the EDIT menu. This must be done in order to display the lone pairs of electrons properly.) b) Construct a model using the CAChe software, measure the C O bond angles in each molecule, and determine the hybridization of the C atom in CO 2, 2 CO, and 3 CO; c) Sketch the three-dimensional structure of each molecule (indicate the angles and hybridization on your sketch of the structure or on the dot structure); d) Using the terms of the VSEPR theory, describe the molecular geometry of each molecule. (In the case of methanol, describe the geometry around both the C and O atoms.) Carbon monoxide, CO (Note: In the case of CO, the formal charges must be set (C = -1 and O = +1) in order to see the lone pairs of electrons displayed properly.) Carbon Dioxide, CO 2
3 Molecular Modeling: Experiment 2 Page 117 Formaldehyde, 2 CO Methanol, 3 CO (To decide if methanol is polar, it is very helpful to build a plastic model of the molecule.) What is the relation between the C atom hybridization and the bond angles around the C atom in your molecules? Are any of the molecules above polar? If so, explain briefly why you would describe them as polar?
4 Molecular Modeling: Experiment 2 Page 118 Part II: Using VSEPR Theory and the Connection Between Bond Length and Bond Order Using the CAChe software, construct a model of each of the molecules below. b) Sketch each structure you have built and measure the unique bond angles in the molecule. (Indicate the angles on your sketch.) c) Using the terms of VSEPR theory, describe the geometry around the C atom in each molecule. d) Indicate on your drawings the hybridization of the C atoms. e) Indicate on your drawings the carbon carbon bond order in each molecule. (Bond order: Is the C C bond single, double, or triple or does it have some fractional order such as 1.5.) Ethane, 3 C C 3 Ethylene, 2 C=C 2
5 Molecular Modeling: Experiment 2 Page 119 Acetylene, C C Benzene, C 6 6 (obtain this structure from the fragment library) ow does the C atom hybridization change in this series of molecules? What is the relation between the geometry around the C atom in these molecules and the C atom hybridization?
6 Molecular Modeling: Experiment 2 Page 120 Part III: Using Formal Charge in Constructing a Model a) Draw electron dot structures for the SO 3 molecule and the SO 2-3 anion. Determine the formal charge of each atom in the molecule or ion and indicate the charge on your sketch. b) Based on your electron dot structures, predict the structure of SO 3 and SO 2-3. b) Construct models of SO 3 and SO 2-3. (Be careful to set the formal charge of each atom. See the separate instructions on the operation.) Sulfur trioxide, SO 3 (Be sure to draw dot structures for all possible resonance structures) The sulfite anion, SO 3 2- ow does the hybridization of the S atom change on adding two electrons to SO 3? Would you predict the three S O bonds in SO 3 to have the same or different lengths? Is the SO 3 molecule predicted to be polar? Does the CAChe structure agree with your prediction? Are there limitations to simple molecular modeling procedures?
7 Molecular Modeling: Experiment 2 Page 121 PART IV: Structures of Simple Molecules of BIochemical Importance In the Fragment Library in the CAChe system you will find a very large number of structures of important molecules. Look for the ones below and give the information requested. Glycine (in Amino Acid fragment library). This is the simplest alpha-amino acid. Sketch its structure, indicate the hybridization of each atom. Be sure to note that there are electric charges on the N atom and one O atom. Glyceraldehyde, C 3 6 O 3 (in the Carbohydrate fragment library). This is the simplest possible carbohydrate [C 3 6 O 3 = C 3 ( 2 O) 3 ]. Sketch its structure and indicate the hybridization of each atom. Is the molecule polar? Epinephrine, C 9 13 NO 3 (in the Drugs-All fragment library). This is a compound used as a bronchodilator and antiglaucoma agent. Sketch its structure, indicating the hybridization of the C and N atoms. Is the molecule polar?
8 Molecular Modeling: Experiment 2 Page 122 Part V: Consequences of Double Bonding Multiple bonds are found in many, many molecules, and they have important structural consequences. ere we look at two molecules and see some of the structural effects. Information on the effect of multiple bonds is found on pages of Chemistry & Chemical Reactivity. See especially Screen 10.8 of the Interactive General Chemistry CD-ROM. Pi (π) bonds are one component of a double or triple bond. You can view a pi bond by opening the file C24.MO6 on the General Chemistry CD-ROM. Go to the CAChe folder, then to ORBITALS, then to MOs, and then to the C24 folder. (A small picture of the orbital is shown here.) In your own words, describe the shape of the pi bond and where it is located in this molecule relative to the C and atoms. (Ignore the colors.) (Note: this file in ONLY available on the Macintosh computers.) The molecules cis- and trans-dichloroethylene are said to be structural isomers. That is, they have the same formula but different structures. Cl Build a model of the trans isomer and indicate the C atom hybridization. C C C C Cl Cl cis-dichloroethylene Cl trans-dichloroethylene ow do the molecules differ? Decide whether each molecule is polar or nonpolar.
9 Molecular Modeling: Experiment 2 Page 123 Cis- and trans-2-butene. 3 C C C C C 3 C C 3 cis-2-butene C 3 trans-2-butene The compound 2-butene has two structural isomers. That is, there are two molecules having the same formula, C 4 8. owever, one has the end C 3 groups one one side of the molecule (cis), whereas the other (trans) has the C 3 groups on opposite sides. Screen 10.8: As one end of the 2-butene molecule rotates relative to the other, the energy of the molecule changes. Notice that as the end of the molecule rotates the energy increases from about 27 kj/mol to over 233 kj/mol. That is, there is a very large energy barrier to be overcome to move one end of the molecule relative to the other. Observe the animations on Screen 10.8, listen carefully to the narration, and answer the following questions: a) As one end of trans-2-butene rotates, what do you observe? When the molecule has an energy at the top of the energy barrier, what is its structure? ow does it differ from the structure of the molecule at the bottom of the energy barrier? b) Why is there a large barrier to rotation in the 2-butene molecule? c) ow does the barrier to rotation in 2-butene compare with that in butane (the other animation on Screen 10.8)? Why is there a large difference in the energy involved and what does this tell you about single bonds relative to double bonds?
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