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Teaching with CAChe Exercises on Molecular Modeling in Chemistry

Crispin Wong and James Currie, eds. Pacific University

Teaching with CAChe Molecular Modeling in Chemistry

Crispin Wong and James Currie Editors Pacific University Forest Grove, Oregon

Copyright statement © 2001 Fujitsu Limited. All rights reserved. This document may not be used, sold, transferred, copied or reproduced, in any manner or form, or in any medium, to any person other than with the prior written consent of Fujitsu Limited. Published by Fujitsu Limited. All possible care has been taken in the preparation of this publication. Fujitsu Limited does not accept liability for any inaccuracies that may be found. Fujitsu Limited reserves the right to make changes without notice both to this publication and to the product it describes.

CAChe Workbook

Forward

1

In 1990, we first started to incorporate molecular modeling into our curriculum using CAChe®. It was a difficult process because computers were too slow, and we had few computers to work with. We struggled to send 25 student assignments through a single coprocessor board running in an early Mac II. Students had to take turns using the single machine to complete assignments using CAChe. Despite its limitations, CAChe was a new instrument in our repertoire that permitted insight into molecular behavior. The computing climate quickly changed. The PowerPC chips gave desktop computers the speed required for modeling, and CAChe truly moved to the desktop. We got serious about technology, built modern computer laboratories, and secured enough CAChe licenses to conduct projects for laboratory sized groups of students. Our curriculum developed as did our capability. We added activities to organic chemistry, major projects in physical chemistry, and a series of exercises to advanced inorganic chemistry. Last of all, we tackled the complex logistics of modeling in large general chemistry sections. We all discovered that computer modeling was a great thinking tool. Each time we modeled a new system, no matter how simple, we discovered something new, or at least gained unexpected insight into the system. The fun began when we found unpredicted results; the results often pointed out our own misconceptions about the underlying chemistry. Presently, we site license CAChe software. The site license has made CAChe accessible to faculty and students; CAChe is available on all department and campus computer lab machines. Faculty and students can use CAChe on their personal computers, whether it be a Macintosh® or Windows® machine. CAChe has become a normal tool which we rarely think of as an unusual feature of our program. The addition of molecular modeling into our curriculum was more feasible than many other settings. Our classes were relatively small, and we had flexibility in scheduling non-class time for individual students. The chemistry department was philosophically together on using modeling where it was an effective and appropriate tool and not just as a technology gimmick. The slow rate of adoption for modeling in some colleges as a standard part of their curriculum is surprising. However, we had a relatively low barrier to the introduction of modeling projects. And there was always someone in the department who would help us over the steep learning curve. Since these are circumstances that some chemistry departments do not share, an important goal of this workbook is to provide a jump start into modeling technology. For

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CAChe Workbook

Forward

those who already use molecular modeling, we hope to stimulate the sharing of ideas. The experiments in this workbook feature areas in our curriculum where we have found modeling to be effective. We have rewritten some experiments to fit a more general environment than ours. For example, our students do a final independent project at the end of general chemistry. The sunscreen project is one independent project but we have adapted it to a more structured, traditional format for this workbook. We have tried to provide complete details so others can see at least one model for implementing modeling exercises. However, we urge you to consult the references, especially to the laboratory portions of the exercises. We did not attempt to give details on safety, waste disposal or even the logistics of how implement these exercises. On another note, our department is nearly all Macintosh but we try to support students who use Windows. We provided equivalent instructions for both environments in this workbook. However, sometimes the procedures for Windows were more complex and in one experiment, could not be executed on a Windows platform. There are many exciting activites that involve molecular modeling. Teaching with CAChe offers a cross section of activities in several disciplines of chemistry. It is our sincere hope that this workbook will convince more faculty that computer aided chemistry (CAChe) should be a normal part of any chemistry curriculum. James Currie Chemistry Department Pacific University

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CAChe Workbook

Table of C ontents Part 1: General Chemistry Experiment 1

Calculating the Geometry of Molecules and Ions . . . . . . . . . . . . . . . . . 1-1

Experiment 2

Kinetics of Substitution Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-17

Experiment 3

Sunscreen and Ultraviolet Absorption . . . . . . . . . . . . . . . . . . . . . . . . . . 3-29

Part 2: Organic Chemistry Experiment 4

Evaluations of Conformations of Menthone and Isomenthone . . . . . . . 4-1

Experiment 5

The Evelyn Effect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7

Experiment 6

Prediction of Aromatic Substitution Rates and Positions . . . . . . . . . . . 6-19

Part 3: Physical Chemistry Experiment 7

Investigating the Resonance Stabilization of Benzene . . . . . . . . . . . . . 7-1

Experiment 8

Vibrational Analysis of Halogen Hydrides . . . . . . . . . . . . . . . . . . . . . . 8-7

Experiment 9

Investigation of the Rotational Barrier in N-N-dimethylacetamide. . . . 9-15

Part 4: Inorganic Chemistry Experiment 10

Polarities of Small Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1

Experiment 11

Structures of Molecules Which Exceed the Octet Rule. . . . . . . . . . . . . 11-5

Experiment 12

Comparison of Gas Phase Acidities of Binary Hydrogen Compounds . 12-9

Experiment 13

Crystal Lattices and Close Packing Sites. . . . . . . . . . . . . . . . . . . . . . . . 13-13

Experiment 14

Identification and Execution of Symmetry Operations . . . . . . . . . . . . . 14-21

Experiment 15

The Relationship Between Infrared Spectra and Molecular Geometry . 15-27

CAChe Workbook

iii

General Chemistry Experiment -

Experiment 16

Molecular Orbitals of Simple Molecules . . . . . . . . . . . . . . . . . . . . . . . . 16-35

Experiment 17

Molecular Orbitals of Diatomic Molecules of Second Period Elements 17-41

Experiment 18

Molecular Orbitals of Octahedral Transition Metal Complexes . . . . . . 18-45

Experiment 19

Relative Ligand Field Strengths. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19-51

Experiment 20

Stereoselectivity of Chiral Chelating Ligands in Metal Complexes . . . 20-57

Exercises for Windows Experiment 21

Exercises for Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21-2

Exercises for Macintosh Experiment 22

Exercises for Macintosh. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22-1

Index Index

iv

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . I-1

CAChe Workbook

Part 1: General Chemistry Experiment 1: Calculating the Geometry of Molecules and Ions Experiment 2: Kinetics of Substitution Reactions Experiment 3: Sunscreen and Ultraviolet Absorption

1

Calculating the Geometry of Molecules and Ions

1

Contributed by Kevin Johnson and James Currie, Pacific University

Overview In this experiment you will use CAChe to create computer representations of molecules and ions and to optimize their structures. Recommended Exercises Complete Pre-lab Assignment: Molecular Modeling before beginning the experiment.

Background One of the important achievements in chemistry is our ability to predict the bulk properties of a compound based on what we know of the microscopic structure of molecules and ions. Molecular geometry provides much of the information upon which these predictions are made.

O H H Lewis Dot Structure

From lectures you have learned to use several models to describe molecules. For example Lewis dot structures delineate connectivity and bonding relationships between atoms of a molecule or ion and can predict bond energies and bond lengths. However, Lewis dot structures do not predict shape. The most basic theory that predicts geometry is the valence-shell electron-pair repulsion (VSEPR) model. The VSEPR model is based on O the premise that the electron pairs around a central atom of a molecule arrange themselves in space to H minimize the repulsive interaction between H regions of negative charge. This model generates the five basic electron pair geometries: linear, VSEPR Tetrahedral Geometry trigonal planar, tetrahedral, trigonal-bipyramidal, and octahedral. The molecular geometry then follows from the connections to other atoms via bonding pairs and from non-bonding electron pairs yielding eleven possible molecular geometries. To qualitatively predict variations in bond angles associated with double bonds or non-bonding pairs, the theory allows for these electron pairs to fill a larger volume of space, and thus distort the predicted molecular geometry toward smaller bond angles. While Lewis dot structures predict bonding and VSEPR theory successfully predicts molecular geometry, neither theory takes into account the relationship between atomic orbitals and electrons in bonds. Valence-bond

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CAChe Workbook

General Chemistry Experiment 1 - Calculating the Geometry of Molecules and Ions

theory approaches this by describing bonding as the overlap of atomic orbitals from two bonded atoms and explains molecular geometry using hybridized atomic orbitals. A more comprehensive model of molecular bonding applies the Schrödinger equation to the electrons and nuclei that make up a molecule. This forms the basis 4 Oxygen sp3 Hybrid Orbitals of molecular orbital (M.O.) theory. For any but the simplest of molecules, M.O. theory requires application of quantum computational methods discussed below.

H2O Molecular Orbital

As scientists we use theories and models to describe natural processes that give rise to observable phenomena. Given a choice between competing theories, that which is least complex yet still satisfactorily answers a given problem is preferable. Thus if we are interested in identifying the shape of a molecule and any expected distortions, VSEPR theory will suffice. However, if we are interested in quantitatively predicting values for bond angles and bond lengths, we must resort to a more sophisticated theory and use computational methods based on M.O. theory. Computational Methods All computational methods are based on the postulate that molecules take the form with the lowest (i.e. most stable) energy. Computational chemistry software works by calculating the energy of a given molecular geometry, then adjusting the atom positions toward lower energy configurations. This process, called optimization, is iterated until a minimum energy configuration is achieved. Computational methods vary in the procedures used for calculating energy and geometry optimization. The two main types of computational methods, classical and quantum, differ in how the energy of a given geometry is calculated. Classical methods such as Mechanics approximate bonds as “springs” and atoms as “balls” and use classical physics to calculate molecular energy. Quantum methods, such as those in MOPAC, numerically solve the Schrödinger equation using either ab initio or semi-empirical calculations. Ab initio methods calculate energy from approximated atomic orbitals and are very computationally intense. Semi-empirical calculations are limited to valence electrons and make assumptions about the atomic orbitals of atoms based on experimental – or empirical – evidence, and therefore require less computation. You will be using semi-empirical calculations for this experiment.

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CAChe Workbook

Modeling Section Exercise 1: With the Instructor Find the CAChe folder on the hard drive; open it and double click on the program Workspace (Windows) or Editor (Macintosh). When the Workspace/Editor opens you will have an empty, untitled window. Build Ammonia NH3 1. Select the Atom tool.

 TIP For most actions, you can click on Edit | Undo to undo the last command.



(Windows) Click on the Atom tool icon.



(Macintosh) Select Tool | Atom tool.

Atom tool

2. Select a N atom. ❏

(Windows) Click on the arrow button in the Element type box at the left of the style bar. A drop-down list of elements is displayed. Select a NNitrogen atom. The hybridization is sp3; look in the Hybridization box to verify that the N atom is sp3.



(Macintosh) Select Atom | N-sp3.

3. Click once near the center of the window. A N atom appears where you clicked. 4. Select a H atom in the same manner as the N atom. 5. Place the atom tool over the center of the N atom. Click and drag away from the atom, then release. This creates a H atom bonded to the N atom. 6. Repeat this two more times to create two more H atoms bonded to the N atom. In the future you may need to: Insert Atoms Not on the Atom List 1. Open the periodic table. ❏

(Windows) Click on the arrow button in the Element Type box and choose Periodic Table...



(Macintosh) Select Atom | Periodic Table.

2. Click on the symbol of the atom you need. Connect Atoms 1. Choose the Select tool. The cursor appears as an arrow. ❏

(Windows) Click on the Select tool icon.



(Macintosh) Click on Tool | Select tool.

2. Click on one atom then hold the Shift key and click on the second atom to select both. 3. Select Edit | Connect Atoms. This forms a bond between the two selected atoms.

CAChe Workbook

1-3

General Chemistry Experiment 1 - Calculating the Geometry of Molecules and Ions

Delete Atoms 1. Choose the Select tool. 2. Click on the atom you want to delete. Make sure that only the atom or atoms you want to delete are selected. 3. Press the Delete button on the keyboard or select (Windows) Edit | Delete or (Macintosh) Edit | Clear.

Rotate

Translate, Rotate, and Zoom 1. Change the position of the molecule by translating, rotating, and zooming. Experiment with each of these three modes. ❏

(Windows) Select the icons on the tool palette. Click and drag the cursor in the molecule window to perform the action corresponding to the icon.



(Macintosh) Translate: Press the Command () key and Option key together. The cursor appears as a hand. Click and drag the mouse to move the molecule around on the screen.

Translate Zoom

Rotate: Press the Command () key and Shift key together. In the window there is a circle around the molecule and the cursor will be an arrow. Click and drag the cursor to rotate the molecule. Zoom: Press the Command () key and Control key together. The cursor appears as a magnifying glass. Click and drag the magnifying glass to zoom in or out on the molecule.  NOTE The Beautify commands apply simple VSEPR rules to the molecular geometry. A Comprehensive Beautify command automatically adds hydrogen atoms to complete the valence shell of an atom. In building NH3, if you omit the hydrogen atoms the Beautify command would add them.

Fix the Geometry 1. Notice that the geometry of the NH3 molecule you created is not correct. ✎

According to the VSEPR rules, what shape should it be?

2. Choose the Select tool. 3. Select the entire molecule by clicking inside the window but not on the molecule. 4. Select Beautify | Comprehensive. ✎

Is the molecule now in the shape you expect for NH3?

5. Use the Rotate mode of the cursor to look at the three dimensional shape of the molecule.

 TIP When selecting atoms, make sure that the cursor is in the center of the atom.

Measure the Bond Lengths and Angles 1. Click on a H atom and hold down the Shift key while you click on a N atom. This selects both atoms. 2. Choose Adjust | Atom Distance. A Set Atom Distance/Atom distance dialog box appears; it shows the separation between the atoms in Ångstroms. 3. Click Cancel after you record the distance in your lab notebook.

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CAChe Workbook

4. Select three atoms that form an angle in order: the end, the center, and the other end atom. In this case, you will select H-N-H. Be sure to select them in the correct order. 5. Choose Adjust | Bond Angle. A Set Bond Angle/Bond angle dialog box appears; it shows the angle between the atoms in degrees. 6. Record the H-N-H angle measurement it in your lab notebook. ✎

Is this result consistent with your VSEPR prediction?



Does it account for the lone-pair on the nitrogen atom in ammonia?

Save the Molecule 1. Select File | Save. A dialog box appears. 2. Name the file “NH3”, and make sure that it is in the correct folder/ location. (Your instructor should specify a designated place). Click Save, but keep the molecule window open.  NOTE The Windows platform uses MOPAC to perform calculations when you run an experiment using the standard method.

Optimize the Structure Windows 1. Select Experiment | New. The Experiment box opens. The program is automatically set to do the optimization calculation. 2. Click Start. This brings up a window that displays the progress of the calculation. When the calculation is complete, the dialog box displays “Calculation Done.” The structure is now optimized. 3. Close the dialog box and return to the Workspace. Do NOT select the Beautify command after optimizing the structure. It will return the molecule to the previous VSEPR geometry. 4. Measure and record in your lab notebook the bond lengths and bond angles. Macintosh 1. Choose Application | MOPAC. The Editor quits and the MOPAC program starts. The parameter box opens. The program is automatically set to do the optimization calculation. 2. Select Run. A dialog box appears that displays the progress of the calculation. When the calculation is complete the dialog box displays “Calculation Done.” 3. Return to the Editor by selecting Applications | Editor. Do NOT select the Beautify command after optimizing the structure. It will return the molecule to the previous VSEPR geometry. 4. Measure and record in your lab notebook the bond lengths and bond angles.

CAChe Workbook

1-5

General Chemistry Experiment 1 - Calculating the Geometry of Molecules and Ions

Exercise 2: On Your Own 1. Build and optimize a CH2Cl2 molecule. 2. Record the predicted bond lengths and angles after beautifying the structure and after optimizing the structure.

Exercise 3: With the Instructor Build a Nitrate Ion (NO3-) 1. Open the Editor/Workspace and select File | New. An empty window appears. 2. Place a N atom with three connected O atoms in the window. 3. Add the formal charges on the appropriate atoms. ❏

(Windows) Select the atom. In the Charge text box type the charge for the atom, or press the up arrow button or down arrow button to display charge values in increasing or decreasing order, respectively.



(Macintosh) Select the Atom tool. Hold down the Option key and click on an atom. A dialog box appears with the periodic properties; the charge field is highlighted. Type the formal charge of the atom and click OK.

4. Repeat this process for all atoms with nonzero formal charges. 5. Optional: Turn on the atom labels. ❏

(Windows) Select View | Atom Attributes. Click on the Label tab. Click the box next to Atomic Symbol and Charge.



(Macintosh) Select View | Atom Shape. The View Atom Shape box appears. Check the box next to the “Atom label consisting of” and choose “Element and charge.” Click OK. The atom symbol and charge are displayed on the molecule.

6. Change the order of the appropriate bonds. The number of bars between the atoms represents the bond order.

 NOTE If the Beautify command adds extra hydrogens, then either the formal charge or the bond order is incorrect.



(Windows) Select the arrow button in the Bond Type box and choose the bond type.



(Macintosh) Choose the Select tool. Hold down the Command () key while clicking and holding on a bond. A menu appears on the screen. Select the type of bond.

7. Select Beautify | Comprehensive. 8. Measure the bond lengths and angles. ✎

Are these results consistent with what you expect for the nitrate ion?

9. Save the structure with the file name “NO3-.” 10. Optimize the structure using MOPAC.

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CAChe Workbook

11. Return to the Workspace/Editor to measure and record the optimized bond lengths and angles. ✎

How is the structure different before optimizing compared to after optimizing?

Exercise 4: On Your Own 1. Build and optimize the structure for CO32−. 2. Record the predicted bond lengths and angles after beautifying and after optimizing the structure. ✎

Are these results what you expected?

Assigned Molecule 1. Build and optimize the structure that your instructor assigned to you. 2. Record the predicted bond lengths and angles after beautifying and after optimizing the structure. 3. Orient the molecule into a good position. Press (Windows) Control + f or (Macintosh) f to center the molecule in the window. Zoom to fill the window with the molecule. 4. Print a copy of the optimized molecule file and staple it to your worksheet. View Orbitals Windows 1. Close any open files in the Workspace. 2. Open the file Carbon.csf from the location specified by your instructor. 3. Select View | Show Surfaces. A dialog box appears; it contains a list of molecular orbitals for the molecule that is open. 4. Highlight Carbon.MO1 and click OK. 5. Record what type of atomic orbital the molecule has. 6. Select View | Show Surfaces. Select Carbon.MO2, and deselect Carbon.MO1. Click OK. Record the type of atomic orbital it has. 7. View Carbon.MO3 and Carbon.MO4 in the same manner. Record the type of atomic orbital. You should rotate the molecule to make sure you see the correct type of orbital. Only select one surface at a time because it is difficult to view the orbitals simultaneously. ✎

What do you notice about the directions of the three p-orbitals?

8. Close the carbon file and open the phosphorus file.

CAChe Workbook

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General Chemistry Experiment 1 - Calculating the Geometry of Molecules and Ions

9. View the surface files Phosphorus.MO1 to Phosphorus.MO9 in the same manner as the carbon files. Record the atomic orbital subshell for each file. Remember to rotate the molecules to view the orbitals fully. 10. Close all the files. Macintosh 1. Open the Visualizer. Make sure that the Editor is closed because the programs will not run simultaneously. 2. Open Atoms | Carbon.MO1 in the folder specified by your instructor. 3. Look at the molecule and record what type of atomic orbital it has. 4. Open the files Carbon.MO2, Carbon.MO3 and Carbon.MO4. Record the type of atomic orbital for each molecule. Rotate the molecule to make sure you see the correct orbital. ✎

What do you notice about the directions of the three p-orbitals?

5. Open and look at the files Phosphorus.MO1 to Phosphorus.MO9. Record the atomic orbital subshell for each file. Remember to rotate the molecules to view the orbital in a better position. 6. Close all the files. View Interesting Molecules Windows 1. Open the folder Small Molecules from the location your instructor specifies. 2. Open the H2 molecule. 3. Select View | Show Surfaces. Highlight H2.MO1 in the list. Click OK. 4. Select View | Show Surfaces. Select the H2.MO2 surface and deselect the H2.MO1 surface. You can also view both surfaces together by highlighting them both. One H2 file is the bonding and the other H2 file is the antibonding. Identify which orbital is the σ and which is the σ∗. 5. Open the C2H4 molecule and view the surfaces C2H4.MO4 to C2H4.MO6 in the same way as the H2 molecule. 6. Identify the σ and π orbitals. 7. Open the C2H2 molecule. Examine the orbital files C2H2.MO3 to C2H2.MO5. Record the σ and π orbitals. 8. Open the CO32- molecule. View the surface file CO32-.MO7. Recall that you can draw the carbonate ion with three resonance structures, where the double bond is between the central carbon atom and each of the three oxygen atoms. This molecular orbital of the carbonate ion is a π−orbital. ✎

What is the term for a π−orbital that extends beyond two atoms?

9. Close the Small Molecules folder and open the Big Molecules folder.

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CAChe Workbook

10. Open and examine the three molecules in the folder. ❏

Buckyball is an allotrope of carbon with the molecular formula C60; it was discovered in the 1980s.



DNA is the molecule that contains genetic codes for living organisms.



Taxol is an anti-cancer drug derived from the Pacific Yew tree.

Macintosh 1. Open the folder Small Molecules from the location your instructor specifies. 2. Open the files H2.MO1 and H2.MO2. One H2 file is the antibonding and the other H2 file is the bonding. Identify which orbital is the σ and which is the σ∗. 3. Open the files C2H4.MO4 to C2H4.MO6. 4. Identify and record the σ and π orbitals. 5. Examine the orbital files C2H2.MO3 to C2H2.MO5 for the molecule C2H2. Record the σ and π orbitals. 6. Open the file CO3-2.MO7. Recall that you can draw the carbonate ion with three resonance structures, where the double bond is between the central carbon atom and each of the three oxygen atoms. This molecular orbital of the carbonate ion is a π−orbital. ❏

What is the term for a π−orbital that extends beyond two atoms?

7. Quit the Visualizer. 8. Close the Small Molecules folder and open the Big Molecules folder. 9. Open and examine the three molecules in the folder. ❏

Buckyball is an allotrope of carbon with the molecular formula C60; it was discovered in the 1980s.



DNA is the molecule that contains genetic codes for living organisms.



Taxol is an anti-cancer drug derived from the Pacific Yew tree.

Report Guidelines Fill out the report form and turn it into your instructor.

CAChe Workbook

1-9

General Chemistry Experiment 1 - Calculating the Geometry of Molecules and Ions

Instructor Notes We use this experiment half way through the first semester of general chemistry. It is an introduction to CAChe and a good way to visualize molecular geometry. The directions are explicit and require no previous knowledge of CAChe. The students complete a pre-lab worksheet before coming to class. We encourage students to keep notes in their lab notebook, documenting the experiment as if they are doing a wet lab. A lab report worksheet is distributed at the end of the lab session. During the lab, we follow a format where we do one exercise with the students, and then they do one exercise on their own. You can choose whether or not to follow that format. The default settings in MOPAC are usually set to do an optimization. However, you may want to double check the settings on the machines you will be using. The difference between PM3 and AM1 calculations should not be noticeable on simple molecules. Our computers are set for a PM3 default optimization, but you can choose which parameter to use. Before the lab, we created the molecular orbital files for the students to view with MOPAC. You can generate the molecular orbitals and molecules, or you can download the files from the website http://www.chem.pacificu.edu/cache. Typical Results Answers to the Pre-lab assignment: A) Ammonia NH3: Shape : Trigonal Pyramidal, H-N-H bond angle 109.5˚ (107˚). B) Dichloromethane CH2Cl2: Shape: Tetrahedral, H-C-H bond angle: 109.5˚, Cl-C-Cl bond angle: 109.5˚, H-C-Cl bond angle: 109.5˚. C) Nitrate ion NO3-: Shape: Trigonal Planar, O-N-O bond angle: 120˚. D) Carbonate ion CO32-: Shape: Trigonal Planar, O-C-O bond angle: 120˚. Answers to Lab Report: NH3: N-H bond length: 0.999-1.000 Å, H-N-H bond angle: 107.98˚-108.16˚. CH2Cl2: C-H bond length: 1.102 Å, C-Cl bond length: 1.756-1.760 Å, H-CH bond angle: 108.714˚, Cl-C-Cl bond angle: 108.021˚, H-C-Cl bond angle: 109.85-110.20˚. NO3-: N-O bond length: 1.239 Å, O-N-O bond angle: 119.99-120.02˚. CO32-: C-O bond length: 1.29 Å, O-C-O bond angle: 119.88-120.13˚

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CAChe Workbook

Individual assignment: Molecule/Ion

Bond length(s)

Bond angle(s)

SiCl4

2.042 Å

109.47˚

AsF5

1.685 Å

90.00˚

1.661 Å

120.00˚

2.120 Å

90.00˚

2.230 Å

95.11˚

SO3

1.384 Å

120.00˚

SF42+

1.425 Å

109.47˚

SOCl2

S-Cl 2.057 Å

116.29˚

S-O 1.407 Å

127.42˚

PCl52-

CAChe Workbook

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General Chemistry Experiment 1 - Calculating the Geometry of Molecules and Ions

C-Cl 1.737 Å

124.20˚

C-O 1.198 Å

111.60˚

ClO2-

1.606 Å

111.21˚

SO32-

1.640 Å

106.16˚

I3-

2.727 Å

179.23˚

PCl4+

2.025 Å

109.47˚

SeBr3-

2.390 Å

119.96˚

SeBr3+

2.417 Å

100.02˚

COCl2

Orbitals Atoms

1-12



Carbon: Carbon.MO1: s, Carbon.MO2: p, Carbon.MO3: p, Carbon.MO4: p.

• •

Phosphorous: MO2: s, MO2: p, MO3: p, MO4: p, MO5: d, MO6: d, MO7: d, MO8: d, MO9: d.

CAChe Workbook

Molecules

• • • •

CAChe Workbook

H2: MO1: σ, ΜΟ2: σ*. C2H4: MO4: σ, MO5: σ, MO6: π. C2H2: MO3: σ, MO4: π, MO5: π. CO32-: MO7: delocalized π.

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General Chemistry Experiment 1 - Calculating the Geometry of Molecules and Ions

Pre-lab Assignment- Molecular Modeling Name: _________________________________ Draw Lewis dot structures and label the nonzero formal charges on atoms for the following four molecules and ions. Predict the shape and bond angles for each. If more than one resonance structure exists draw all possible resonance structures. Record your answers to these questions in your lab notebook. You will need to use them during the lab experiment. A) Ammonia NH3

Shape:

H-N-H bond angle:

B) Dichloromethane CH2Cl2

Shape:

H-C-H bond angle: Cl-C-Cl bond angle: H-C-Cl bond angle

C) Nitrate ion NO3-

Shape:

O-N-O bond angle:

D) Carbonate ion CO32-

Shape:

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O-C-O bond angle:

CAChe Workbook

Lab Report- Molecular Modeling Name: _________________________________ Record all molecular geometry measurements for MOPAC optimized structures. A. Class assignments: NH3

N-H bond length:

H-N-H bond angle:

CH2Cl2

C-H bond length:

H-C-H bond angle:

C-Cl bond length:

Cl-C-Cl bond angle: H-C-Cl bond angle:

NO3-

N-O bond length:

O-N-O bond angle:

CO32-

C-O bond length:

O-C-O bond angle:

B. Individual assignment: Assignment:

Shape:

List bond lengths:

List bond angles:

CAChe Workbook

1-15

General Chemistry Experiment 1 - Calculating the Geometry of Molecules and Ions

C. Orbitals Atoms: Label each file name with the orbital subshell; s, p, or d.

Molecules: Label each file name with the molecular orbital type: σ, σ∗, π, or delocalized π.

Carbon

H2

File

Subshell

File

Carbon.MO1

H2.MO1

Carbon.MO2

H2.MO2

Carbon.MO3

Subshell

C2H4

Carbon.MO4 File Phosphorous File

C2H4.MO4 C2H4.MO5

Subshell

Phosphorous.MO1 Phosphorous.MO2

Subshell

C2H4.MO6 C2H2

Phosphorous.MO3 File

Phosphorous.MO4

C2H2.MO3

Phosphorous.MO5

C2H2.MO4

Phosphorous.MO6

C2H2.MO5

Phosphorous.MO7 Phosphorous.MO8 Phosphorous.MO9

Subshell

CO32File

Subshell

CO3-2.MO7

1-16

CAChe Workbook

2

Kinetics of Substitution Reactions

2

Contributed by James Currie and Kevin Johnson, Pacific University

Overview In this experiment, you use computer modeling to look at examples of substitution reactions involving halogen atoms on a central carbon atom. You model a series of three substitution reactions where either the entering halogen (E) or the leaving halogen (L) is held constant and the other halogen is varied to be Cl, Br, or I.

Recommended Exercises Complete Substitution Kinetics Pre-Lab Report before beginning the experiment.

Background A substitution reaction is simply a replacement reaction in which one atom or group of atoms replaces another atom or group of atoms. A substitution reaction can occur several ways, but in this activity we will be looking at a nucleophilic substitution. E

-

+

C

L

E C

+

L

-

In a nucleophilic substitution reaction, a substance capable of donating a pair of electrons (called the nucleophile) forms a bond to an atom at the expense of a bond to an existing atom or group. We depict a nucleophilic reaction using arrows to show the movement of electrons during bond formation or breakage.

Enthalpy

As with any reaction, there is a change in enthalpy associated with a substitution reaction. The two substances must collide with Ea sufficient energy to pass over a starting barrier known as the activation material ∆Hrx energy (Ea). The structure at the highest energy point on the reaction product pathway is the activated complex or Reaction progress transition state. The energy diagram (right) shows a reaction coordinate for a simple single step reaction such as a nucleophilic substitution. 2-17

CAChe Workbook

General Chemistry Experiment 2 - Kinetics of Substitution Reactions

In this activity, we are going to use computer modeling to find the lowest energy pathway -40 that the molecules take as they move from -50 reactants to products. Using an energy map to -60 find the lowest energy pathway is like using a -30 -40 -50 topographic map to find the easiest route -60 across a mountain range. The energy map will -70 be a contour map with enthalpy contours -80 instead of elevation. Converting the route from 3D contour map to a 2D pathway showing enthalpy as a function of reaction progress (time) gives us the reaction pathway usually found in textbooks. We will be able to look at the enthalpy of the starting molecules and products to determine the heat of reaction. We should be able to find the transition state (the highest energy point on the reaction path) and the activation energy. -30

Activation energies are a principal factor in determining a rate of reaction. The Arrhenius equation relates the rate constant (k) to the activation energy (Ea), temperature (T), the gas constant R and a constant specific for the reaction (A).

k = Ae

– E a ⁄ ( RT )

If you know the activation energy, you can find the rate constant using the Arrhenius equation. For two similar reactions (where A is the same for both), the relative rates are approximately given by:

k1 ⁄ k2 = e

( E a – E a ) ⁄ ( RT ) 1

2

Studying relative rates allows us to understand why some reactions are faster than others. In this experiment, you can use the above equations to compare the relative rates of the different halogen substitution reactions.

Modeling Section Your instructor will assign you either a constant entering halogen (E) or a constant leaving halogen (L). You should model three different reactions holding you assigned group constant and varying the other group with Cl, Br and I. 1. Open the CAChe Workspace/Editor. 2. Select the Atom tool. 3. Select a carbon atom from the Element type/Atom menu. 4. Click once in the workspace to deposit a single carbon atom. Figure A

2-18

5. Select Beautify | Comprehensive with the Select tool. This converts the single carbon atom to a properly built methane molecule (Fig. A).

CAChe Workbook

6. (Optional) Turn on the atom labels. ❏

(Windows) Select View | Atom Attributes. In the Atom Attributes dialog box, click on the Label tab. Select Atomic Symbol.



(Macintosh) Select View | Atom Shape. A View Atom Shape box will open. In the Atom Label consisting of: list, select Element and Charge.

7. Add the leaving halogen (L) to the molecule.

Figure B



(Windows) Select the hydrogen screen right of the carbon atom using the Select tool. Go to the Atom menu and click on Periodic Table and double click on the leaving halogen atom. The hydrogen atom should change color to represent the halogen (green for Cl, red for Br, or violet for I) (Fig. B).



(Macintosh) Select the Atom tool and then select Atom | Periodic Table. The Periodic Table opens. Click on the leaving halogen atom and then click on OK to return to the workspace. Hold down the Command key () and click on the hydrogen atom lying in the plane screen right of the carbon atom. The atom changes color to represent the new atom (green for Cl, red for Br, or violet for I) (Fig. B).

Figure C

8. Return to the Select tool and select the entire molecule. 9. Select Beautify | Comprehensive (Fig. C). 10. Go to the Periodic Table in the Atom menu. 11. Select the second halogen atom (entering halogen E) and change the charge to -1.

leaving halogen

entering halogen Figure D

CAChe Workbook



(Windows) Select the halogen you need. Click OK. Change the charge to -1 by clicking on the down arrow in the Charge box.



(Macintosh) Select the halogen atom type. Type the charge to -1 in the charge box on the Periodic Table. Click OK.

12. Click on the carbon and hold down the mouse button as you draw away from the carbon in the opposite direction to the first halogen atom (Fig.D). DO NOT BEAUTIFY THE MOLECULE AGAIN.

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General Chemistry Experiment 2 - Kinetics of Substitution Reactions

Building an Energy Map

C—Cl distance

You now need to set up a search that 2.9 varies the two halogen distances and -30 2.7 -40 computes the energy at each point. -50 2.5 -60 The search label produces a three 2.3 dimensional equivalent to a contour -30 -40 -50 map (see example at right). In this 2.1 -60 case the contours represent enthalpy. -70 1.9 -80 The resulting map is called a 1.7 potential energy surface. The 1.5 reaction pathway is the path through 1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0 C—Br distance the valley over the lowest possible energy barrier and on to the products. The search of bond distances is intended to find this lowest energy pathway from reactants to products. For a C--Cl bond a reasonable search would be between 1.55 and 3.00Å in 40 steps. For the larger Br or I atoms, we should search between 1.60 and 3.00Å in 40 steps. To setup a search label 1. Click on one of the halogen atoms and while holding the Shift key down, click on the carbon atom. When selecting the atoms ALWAYS select the halogen atom first. 2. Select Adjust | Atom Distance. In the Atom Distance box that appears, click Define Geometry Label | Search and enter the appropriate distances and steps. 3. Repeat this process for the other halogen atom. 4. Save this molecule in the appropriate location using your name as the file name. Since you have built this molecule with too many bonds on the carbon, you get a warning message, but ignore this warning and continue. 5. (Macintosh) Quit the Editor. To produce the potential energy surface Windows 1. Select Experiment | New. The Experiment dialog box opens. 2. Select chemical sample conformations in the pull down menu in the “Property of” line. Select optimized map from the pull down menu in the Property line, and use PM3--Kinetics in the last pull down menu. 3. Click Start. The calculation begins in a separate window. It takes a few minutes to complete the calculations. When the calculations complete, two windows open: the energy map on the left and the molecule on the right. The initial view displays a wide range of energies, so you need to narrow the focus.

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4. Select View | Graph Attributes. The Graph Attributes window opens. 5. Select Attributes under the z-axis (calc_energy). The Axis Attributes box opens. Click on the Range tab. Change the maximum to -50. Macintosh 1. Double click on the Grid settings icon in the CAChe folder window to bring up the MOPAC application. 2. Open the molecule from the File menu and click OK. The calculation begins, requiring a few minutes to compute the energy for each of the 1681 grid points. When the calculation finishes, there is a file labeled as “your name.MAP” in the same folder that you saved the molecule. Double click to open this file in the Visualizer. When the file opens there are two windows: the map on the left and the molecule on the right. The initial view displays a wide range of energies, so you have to narrow the focus.

3. Select View | Define Map. A Define Map window opens. 4. Click on the Set Attributes button for the Z axis (calc_energy). 5. Change the energy Maximum to -50 and click OK. Click OK to close the Define Map dialog. To view the energies 1. Rotate and examine the potential energy map and the molecule (click in the appropriate window to make it active). ❏

(Windows) Select the Rotate tool icon. Click and rotate the map.



(Macintosh) Hold down the Command () and Shift keys together. Click and rotate the map with the mouse.

2. Click on the potential energy surface at various points and note the positions of the atoms that correspond to the point. 3. Click at the minimum point on one side of the transition state. To determine if it is the starting or ending point, look at the molecule and note which carbon-halogen bond is shorter. If C--L is shorter, it is the starting point. If C--E is the shorter bond, it is the ending point.

CAChe Workbook

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General Chemistry Experiment 2 - Kinetics of Substitution Reactions

4. Record the energy and bond distance for each carbon-halogen bond in the starting, transition and ending state. For the bond distance, the labels on each carbon-halogen bond tells you the length. The shortest carbon-halogen bond length (C--L or C--E) is the “bonded” halogen at that particular point. ❏

(Windows) To find the energy, select calc_energy from the pull down menu at the bottom of the molecule window. The energy appears in the box next to the menu.



(Macintosh) The energy is displayed at the top of the molecule window.



Why is the transition state sometimes called the saddle point?

5. (Optional) To enlarge the molecule for easier reading of the labels, use the zoom tool. ❏

(Windows) Click on the Zoom tool icon.



(Macintosh) Hold down the Command () and Option keys together and move the mouse up to enlarge.

6. Repeat this process with the remaining two reactions keeping the assigned halogen constant.

Report Guidelines Fill out the lab report worksheet and hand in to your instructor.

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Instructor Notes We do this modeling experiment during second semester general chemistry after completing the text chapter on kinetics. Students should be reminded that a mechanism is determined experimentally but modeling is useful in formulating a hypothesis. We do a wet kinetics lab on the bromination of acetone in the next lab session. This exercise assumes that the mechanism is SN2. A helpful analogy is to relate the abstract concept of a reaction coordinate to a topographical map and its relationship to observed terrain. We introduce the experiment with slides of actual topographical maps showing mountain passes and juxtaposing the topographic maps with reaction coordinates. We also stop students during their work to discuss what they are seeing on the computer model. The ability to rotate the 3D potential energy surfaces sideways to make them look like a 2D reaction coordinate is also useful. We assign each student either a constant Cl, Br, I nucleophile (E) or a constant Cl, Br, I leaving group (L). With their assigned group constant, the students model three reactions using Cl, Br and I as the variable group. There are six possible reaction sets. For example, one possible set is a constant E=Cl, where the variables are L=Cl, Br, I. It is very important that students follow the directions for building their molecules. This type of optimized search is prone to failure if certain atom positions approach a straight line. We prevent this problem by building the molecule in a defined order and by using the ‘maintain orientation’ option. This option creates dummy atoms as reference points which are included in the numbering. To ensure that the settings are correct on our Macintosh computers, we have students start the calculation by double-clicking on a MOPAC settings file, called Grid Settings. We prepare this file with the specific settings for a PM3 grid search using BFGS optimizer, the ‘maintain orientation’ option and no other options or keywords. On Windows computers, the optimized search experiment can be duplicated and then modified to have these specific settings. Before the lab session, you should make this experiment option and name it PM3-Kinetics. We suggest using 40 points for each search label because it gives a smoother map. The activation energies for the I/Cl and I/Br reactions are very small and difficult to see well with too few points. A 41x41 search only takes about 2 minutes on a newer iMac. Students might want to expand the potential energy map even further than suggested both by changing map axes and by scaling the window so they can see the energy change more clearly.

CAChe Workbook

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General Chemistry Experiment 2 - Kinetics of Substitution Reactions

Typical Results The following represents data that is relatively easy to obtain for students. (E=entering halogen, L= leaving halogen) Data for Methyl Halides E

L

∆Hf(sm)

∆Hf(ts)

∆Hf(prod)

∆H‡

C— E(Å)

C— L(Å)

Cl

Cl

-74.60

-64.70

-74.60

9.90

2.28

2.29

Br

Br

-72.60

-69.50

-72.60

3.10

2.46

2.39

I

I

-63.60

-58.40

-63.60

5.20

2.60

2.60

Cl

Br

-65.35

-64.62

-81.10

0.73

2.41

2.11

Br

I

-62.04

-61.36

-74.13

0.68

2.60

2.33

Cl

I

-55.01

-54.90

-84.00

0.11

2.54

2.17

Further Discussion Each instructor will need to consider whether to encourage discussion about some of the more complex issues. An interesting topic for more advanced discussions is the effect steric hindrance has on molecules. What if the starting halide was chloroethane instead of chloromethane? Would you expect a higher or lower Ea? What about for 2-chloropropane? Pictures of each substance are shown below.

Just as in the real reactions, the reaction models are a bit tricky as the substitution increases. Blank spaces in the table represent modeling problems that do not work well as one large potential energy surface calculation. For these, the regions near the transition state and energy wells need to be done separately to avoid “side reactions.” Simulations modeled in a solvent give more interesting and true to reality surfaces but at the expense of much longer computation times. Students in general chemistry usually do not have the experience to appreciate the subtle difference.

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CAChe Workbook

Data for Ethyl halides E L ∆Hf(sm) ∆Hf(ts) ∆Hf(prod) ∆H‡ C— E(Å) C--L(Å) Cl Cl Br Br I

I

Cl Br

-80.83

-78.04

-81.17

3.0

2.46

2.39

-66.23

-63.20

-66.23

3.0

2.66

2.60

-78.06

-72.74

-86.61

5.4

2.42

2.26

-64.70

-61.27

-86.73

3.4

2.26

2.49

Br I Cl I

Data for 2-Propyl halides E L ∆Hf(sm) ∆Hf(ts) ∆Hf(prod) ∆H‡ C— E(Å) C— L(Å) Cl Cl Br Br I

I

Cl Br

-89.07

-80.02

-94.13

9.0

2.42

2.33

Br I Cl I

CAChe Workbook

2-25

General Chemistry Experiment 2 - Kinetics of Substitution Reactions

Substitution Kinetics Report Name: _____________________________________ Fill in the data below using the potential energy surfaces that you computed using CAChe MOPAC. From the data, calculate the predicted heat of reaction for each of the processes. For comparison calculate the heats of reaction using the bond enthalpy data in the text. E=entering halogen L=leaving halogen

E

L

∆Hf reactants kcal/mol

∆Hf transition state

∆Hproducts kcal/mol

1. Considering the energy map, which reactions are endothermic and which are exothermic?

Ea forward kcal

Ea reverse kcal

∆Hrx (CAChe) kcal/mol

∆Hrx (text) kcal/mol

Plot the above energies on the graph below.

2. Fill out the table below. Considering the C—E and C—L distance, and the position of the transition state on the surface relative to the reactants and products, do the transition states look more like the reactants or products? E

L

C--E distance

C--L distance

Reactants or Products?

3.What are the relative rates constants for the three reaction you calculated? Let the slowest be 1.0. Calculate these using the Arrhenius equation. Assume the prefactor remains constant and T = 298K, and use R=1.987 cal/mol-K. E

2-26

L

Relative Rate

CAChe Workbook

Substitution Kinetics Pre-Lab Report Name: _____________________________________ The chemical reaction below was studied using Computer Aided Chemistry (CAChe). The following energies were calculated: starting materials:-78.1 kcal/mol transition state:-72.7 kcal/mol products-86.6 kcal/mol These values were plotted on the graph below: What is the heat of reaction for the forward process? ______________ kcal/mol Reverse process? ______________kcal/mol What is activation energy (Ea) for the forward process?_______________kcal/mol Reverse process? ______________kcal/mol

Now assume the activation energy was 8.0 kcal/mol, and the starting and ending energies were the same as above. Draw the resulting reaction coordinate on the graph below. What would be the energy of the transition state? ________________kcal/mol

Would the reaction rate be faster or slower than the previous reaction?________________________

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General Chemistry Experiment 2 - Kinetics of Substitution Reactions

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3

Sunscreen and Ultraviolet Absorption

3

Contributed by Crispin Wong and James Currie, Pacific University

Overview Recently, a cosmetic company hired you to help them develop a sunscreen mixture for a new line of products. To accomplish this task, you will model molecules and the ultraviolet (UV) spectra of sunscreen chemicals with CAChe. Using the spectra you generated, you will design a sunscreen. In the third part of the experiment, you will research other commercial sunscreens and analyze them using a UV spectrophotometer. Recommended Exercises Complete Exercises I, II, III, IV, V, VI, VII, and IX before beginning this experiment.

Background

CH3O

OH

O

Figure 1: The conjugated system in oxybenzone, a common sunscreen chemical, helps absorb ultraviolet light.

3-29

Everyday we are exposed to the sun's harmful ultraviolet rays. Awareness about the damage sun exposure causes has increased over the years and a push for sun protection has emerged. One such safety precaution is the use of sunscreen. Most sunscreens utilize chemicals that have chains of alternating single and double bonds resulting in delocalized π bonds. These are called conjugated systems and they are responsible for absorbing harmful ultraviolet light. Ultraviolet light is subdivided into three different ranges: UVA (320-400 nm), UVB (290-320 nm) and UVC (100290 nm). UVC light is harmful, but most of it is absorbed by atmospheric gases and the ozone layer before reaching the earth's surface. Figure 2 shows the absorptions of atmospheric gases and ozone in the UVC range. Continued Figure 2: UVC radiation is absorbed mostly by atmospheric depletion of the ozone layer gases and ozone. Most of the UVB and UVA radiation could eventually increase UVC reach the earth and our skin, relatively unfiltered. radiation.

CAChe Workbook

General Chemistry Experiment 3 - Sunscreen and Ultraviolet Absorption

UVA and UVB wavelengths can penetrate the atmosphere; we try to avoid exposure to these rays. UVA radiation causes immediate redness on skin that disappears after a few hours. It acts through oxygen free radicals and may be linked to skin cancer. UVB is responsible for the more detrimental delayed sunburn and/or tanning. Tanning is a result of UVB light stimulating melanocytes in your skin which produce the dark colored pigment, melanin. UVB radiation acts directly on biological molecules, causing mutations that are potentially cancerous. A Sun Protection Factor (SPF) quantifies sunscreen efficacy against UV rays. SPF value = MED (protected skin)/MED (unprotected skin) The minimal erythema dose (MED) is the minimum dose of UV energy that produces lasting redness on skin. Protected skin is defined as 2 mg/cm2 of sunscreen covering the skin. This could equate to as much as 1 fluid oz. over your whole body. SPF was intended to measure a sunscreen’s ability to block UVB light, which is the primary cause of delayed sunburns. The more noticeable effects of UVB mask the effects of UVA rays, and so SPF does not represent UVA blockage well. Researchers are developing a system to measure UVA protection, such as the protection factor A (PFA). PFA is based on the minimal response dose (MRD), which is the smallest UVA dose that produces redness or tanning on skin.

Part I: Model Sunscreen Chemicals

 NOTE Physical blockers like zinc oxide and titanium dioxide are opaque compounds that reflect all wavelengths of light.

The cosmetic company Make-Me-Pretty is developing a line of products that touts its ability to block UVA and UVB light. They have hired you to lead the research and development for these new products. The product must contain transparent chemicals; physical blockers such as zinc oxide and titanium dioxide will not be considered. To make this task efficient and successful, it is essential to keep your budget to a minimum. One relatively inexpensive tool that aids in developing hypotheses and plans is computer modeling. Modeling allows you to compile and compare information with ease. In this situation, you can model the UV spectra for various sunscreen chemicals. Before you order expensive chemicals to test in the laboratory, you can use the modeled UV spectra to decide which chemicals you want to include in the sunscreen mixture for the cosmetic products. As time allows, you may also want to research the available sunscreen chemicals. Information such as how chemicals affect the skin or how much of a chemical the FDA allows in a product, may be pertinent to your task. In this first section, you will model sunscreen chemicals using CAChe. Consult your instructor to find out which chemicals are available for this experiment and which ones you will model on the computer.

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CAChe Workbook

1. Build a molecule for each of the assigned sunscreen chemicals in the Workspace/Editor. 2. Save the molecules and close the molecules in the Workspace/Editor. 3. Locate and open the program ProjectLeader on the computer. When ProjectLeader opens, a table appears on the screen with the first column labeled “chemical sample”. 4. Double click in the first cell under the “chemical sample” column. ❏ (Windows) An Open dialog box appears. Locate the molecule file and highlight it. Click on Open. The dialog box closes and the structure

appears in the cell. ❏ (Macintosh) A “Select a chemical sample” dialog box opens Locate the molecule file and highlight it. Click on Add. The dialog box closes

and the file name appears in the cell. 5. Repeat step 4 until you have entered all of the molecules in the chemical sample column. 6. Double click in the second column heading cell. ❏ (Windows) An Enter Property dialog box opens. Click on the circle next to Property of. In the pull down menu next to it, highlight UV/vis spectra. Click Next. Highlight excitation energy in the Kind of property list. Click Next. Highlight excitation E at MM/INDO1 geometry. ❏ (Macintosh) A Select Column Header dialog box opens. In the first column select Property of and highlight UV/vis spectra. In the Property column, highlight excitation energy and in the Using column highlight excitation E @ MM/INDO1 geometry.

7. Click OK to close the dialog box. Columns B and C say “UV/vis Spectra” and “excitation energy (cm-1)” respectively. The UV/vis spectra column contains wavelengths (nm) where there are high absorbance values. Excitation energy is the wavelength expressed in a different form (cm-1). 8. Highlight the cells in the second and third columns and select Evaluate | Cells. It may take a while for the calculations to complete. When the calculations finish, wavelengths appear in column two and the corresponding energies in column three. 9. Save the Project in a designated location.

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General Chemistry Experiment 3 - Sunscreen and Ultraviolet Absorption

10. Open the molecule and UV spectra. ❏ (Windows) Return to the Workspace. Open one of the sunscreen

molecules. The molecule should appear in one window, and the molecule’s UV spectrum should appear in a UV-visible Transitions window. If the UV spectrum does not appear select View | UV-visible Transitions. ❏ (Macintosh) Open the Visualizer; then open one of the sunscreen

molecules. A window with the molecule appears. Select Analyze | Electronic Spectra. The UV spectrum opens in a new window. 11. Adjust the scale of the UV/vis graph. The range you want to look at for UVA/UVB absorption is between 250-400 nm. ❏ (Windows) Double click on the x-axis or the y-axis. A View Axis

Attributes dialog box appears. Change the Wavelength Range (x-axis) to go from 250 to 400 nm. Adjust the Intensity Range (y-axis) to best represent the data. Click OK. ❏ (Macintosh) Double click on the x-axis. The Axis Parameters box

opens. Type in 250 in the “Left” box and 400 in the “Right” box. Set the increment to 10 or 15, whichever you prefer. Click OK. Double Click on the y-axis to open the Axis Parameters dialog box. Adjust the range to best represent the data. Close the dialog box when you have finished adjusting the axis. 12. Examine the UV spectrum. ✎ At what wavelength does the chemical have a maximum absorbance (λ

max)? ✎ Is this in the UVA or UVB range?

13. Open another sunscreen molecule and its UV spectrum as you did in step 10. The UV spectrum appears in the same grid as the UV spectrum of the other open molecule. Examine the new UV spectrum, and compare both spectra in the window. You may need to readjust the y-axis. If you continue to open the UV spectra of different molecules, you can view their spectra simultaneously. To remove a spectrum from the grid, close the corresponding molecule window.

Part II: Design a Sunscreen Now that you have modeled the UV spectra of compounds that appear in sunscreens, think about the wavelengths of light that they absorb. There are compounds that are better at blocking UVA, and compounds that block UVB more. A good sunscreen will block both types of ultraviolet light. Your next assignment is to design a sunscreen. Your employer, Make-MePretty, has asked you to find a combination of three or less chemicals that can

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CAChe Workbook

accomplish the goal of blocking both types of ultraviolet light. In addition to recommending a combination of chemicals, you also need to recommend a ratio for the chemicals you choose. Use the UV spectra that you modeled in Part I to look at chemical combinations that will cover the UVA/UVB range. Notice that some chemicals have stronger absorbance than others. Take this into account when you are finding a recommended ratio. 1. Find a combination of chemicals that cover the ultraviolet wavelengths using the UV spectra displayed in the Visualizer. Note the maximum absorbance of each chemical and predict the absorbance curve of the mixture. 2. Verify the chemical combination in the lab using the UV Spectrophotometer. Stock solutions of the sunscreen chemicals (10 mg in 100 mL of absolute ethanol) have been prepared for you. Your instructor will show you how to use the UV Spectrophotometer in your lab.  TIP The optimal absorbance range for UV spectra is 0.500 to 1.500. Absorbances over 2.000 are generally distorted and absorbances that are too low can not be separated from regular noise.

3. Use a micropipet or calibrate a dropper to measure out small amounts of the chemicals into a 5 mL volumetric flask. Because of the varying absorbances of each chemical, the amount of chemicals you put in should add up to anywhere between 0.5 mL and 2.0 mL. For example, if you want to mix chemical A (strong absorber) and chemical B (weak absorber) in a 1:2 ratio, 0.5 mL of chemical A and 1.0 mL of chemical B (1.5 mL total chemicals) in 5 mL ethanol will probably be sufficient. 4. Fill the 5 mL volumetric flask to the fill line with absolute ethanol and swirl the mixture. 5. Run the sample in the UV spectrophotometer. Be sure that you zero the machine before you take the sample. Also, rinse out the cuvet with ethanol before inserting the sample to avoid contamination. 6. If the absorbance is too high when you take a reading with the UV spectophotometer, decrease the amount of chemicals. If the spectrum is weak, increase the amount of chemicals in the mixture. In either case, remix the solution from scratch. Do not add more ethanol or chemicals to the existing solution because you want the chemical proportions to remain intact. It may take a few tries to get the concentration right. Consult your instructor if you have problems finding a good concentration for your UV spectrophotometer.

CAChe Workbook

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General Chemistry Experiment 3 - Sunscreen and Ultraviolet Absorption

Part III: Compare Commercial Sunscreens There are many sunscreens on the market today. Your job now is to compare the UV spectra of different sunscreens--potential competition for your company’s products. You can examine a number of aspects related to UV absorption, SPF, and different chemicals. Below is a list of possible options to explore. The choices are not limited to this list, so you can be creative and test new ideas. ❏ Different SPF sunscreens manufactured by the same company ❏ The same SPF sunscreens manufactured by different companies. ❏ Different SPF sunscreens manufactured by different companies. ❏ Different chemical combinations in same SPF sunscreens. ❏ Tanning lotions vs. sunscreen lotions. ❏ Aged sunscreens vs. new sunscreens.

Make the extracts for the sunscreens you want to compare. Run the spectra on a UV spectrophotometer. To make comparisons easier you might want to print out the UV absorbances on the same graph. Make Sunscreen Extracts 1. Weigh out 0.10 g of sunscreen into a 250 mL beaker. 2. Measure 100 mL of water in a graduated cylinder and add it to the beaker. 3. Stir the sunscreen/water mixture until it is a uniform white suspension. Make sure that sunscreen is not sticking to the side and bottom of the beaker. If you can, use a magnetic stir bar to mix the solution up for 5-10 min. or until it is a uniform white. 4. Pipet 1.0 mL of the sunscreen mixture into a 50 mL beaker. 5. Measure out 9.0 mL of absolute ethanol and add it to the 50 mL beaker. 6. Swirl the ethanol/sunscreen mix for about a minute. 7. Run a UV analysis on the sample. If it is too concentrated, dilute the sample with more ethanol. Make sure you keep track of the dilution factor. It is important to take into account the dilution factor when comparing UV spectra. If they do not have the same dilution constant, you need to correct for concentration to depict the true absorbance relationship between the sunscreens.

Report Guidelines Consult your instructor about the report requirements.

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Instructor Notes In second semester general chemistry, we dedicate the last three lab sessions to unique group projects. The sunscreen lab is one possible project. Students are able to exercise a greater degree of autonomy in researching an aspect of chemistry. This experiment has purposely been designed to be flexible; you can choose which parts you want to highlight in your lab. It could be a more complex project, where students assemble a report complete with research and experimental results. On the opposite end, the lab could be pared down to a simple computer exercise generating UV spectra. This lab is designed for flexibility but in any case, let the students know which parts they should and should not do. Since this experiment is an independent group project, our students research sunscreen chemicals and find the corresponding structures. However, this may not be conducive to large labs or a short period of time. Structures of common sunscreen chemicals are included on page p 3-36. You can hand out this sheet to aid students in their modeling. There are a number of ways to go about modeling the structures. Depending on what chemicals you can obtain, the students may model only those chemicals. Each student can build one structure and share with others, or they can build their own set. We had difficulty modeling octocrilene with the suggested MM/INDO1 parameter. It works best to optimize octocrilene in MOPAC followed by a UV calculation in ZINDO. On a Macintosh you can run the calculations individually, first in MOPAC followed by a Configuration Interaction (Spectra) calculation in ZINDO. On a PC, you may want to create a new experiment where the first calculation is a MOPAC optimization followed by a UV visible transitions calculation using ZINDO at current geometry. Parts II and II assume students have access to an UV spectrophotometer. In some cases, allowing a large amount of students to use the machine is not feasible. Alternative solutions may range from grouping students together to use the UV spec, to running different spectra, then copying and handing them out to students. At the end of the project, the students create posters clearly displaying information they collected. They are also required to write a detailed report, covering their results and conclusions.

CAChe Workbook

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General Chemistry Experiment 3 - Sunscreen and Ultraviolet Absorption

Structure

Name (s)

CAS number

CN

Octocrilene, 2-ethylhexyl 26197-30-4 cyano-3,3-diphenylacrylate.

O O

Octyl methoxycinnamate, 2-Ethylhexyl 4-methoxycinnamate

CH3O O

5466-77-3

O

CH3O

Oxybenzone, Benzophenone 3, 2-Hydroxy-4-meth- 131-57-7 oxybenzophenone

OH

O

OCH3

OH

Avobenzone, Parsol 1789, 4-tert-Butyl-4’-methoxydibenzoylmethane

70356-09-1

Octyl salicylate, 2-Ethylhexyl salicylate

118-60-5

O

OH O O

OH

Homosalate, 3,3,5-trimeth118-56-9 ylcyclohexyl salicylate

O O

Padimate O, Octyl Dimethyl-PABA, Octyl Dimethylaminobenzoate, 21245-02-3 2Ethylhexyl 4-dimethylaminobenzoate

N O O

O OH

PABA, p-aminobenzoic acid (not used anymore)

150-13-0

NH 2

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Part 2: Organic Chemistry Experiment 4: Evaluations of Conformations of Menthone and Isomenthone Experiment 5: The Evelyn Effect Experiment 6: Prediction of Aromatic Substitution Rates and Positions

4

Evaluations of Conformations of Menthone and Isomenthone

4

Contributed by James Currie, Pacific University

Overview In the laboratory, you will determine the experimental percent composition of a menthone and isomenthone equilibrium mixture. In the second part of this experiment, you will use CAChe to evaluate the relative stability of the best conformation for each of the two geometric isomers. Recommended Exercises Complete Exercises I, II, III, VI, and VI before beginning this experiment.

Background Menthone and isomenthone are in equilibrium under acidic conditions. Since there are two chiral centers and only one is changing during the equilibrium, menthone and isomenthone are diasteromers of each other. The change in chirality changes the cis, trans geometry. A careful look at the structures shows that menthone is trans and isomenthone is cis. Although the double bond distorts the chair form of the cyclohexane ring, groups are still in positions that approximate axial and equatorial. For the cis isomenthone, one group must be axial and the other equatorial. The isopropyl or the methyl group can assume either position but the ring flips to permit the larger isopropyl group to always be equatorial. As a result, the isopropyl position is equilibrating but the net effect is the methyl shifting from the equatorial position in menthone to the axial position in isomenthone.

H

+

O

H 3C

O

H 3C

CH CH3

H 3C O

4-1

CH

H 3C O

CH3

(-)-menthone

(+)-isomenthone

Optical Rotation = -30

Optical Rotation = +92

CAChe Workbook

Organic Chemistry Experiment 4 - Evaluations of Conformations of Menthone and Isomenthone

CH3

Since the molecules are chiral we can determine the equilibrium composition by using a polarimeter to measure the optical rotation of the mixture. The specific rotation is calculated from the observed rotation using Equation 1. Because we know the specific rotations of the pure isomers we can determine the isomer ratio from the observed rotation of the mixture. You can use Equation 2 to find the mole fraction of menthone in the mixture.

CH3 acid O

CH3

CH CH3

-30˚

O CH3

CH CH3

α   [ α ] = -------- l • c

where l=length (dm) and c= conc. (g/mL) in 10 mL

Equation 1

+92˚ [ α ] = [ α A ] ⋅ X A + [ αB ] ( 1 – X A )

where αΑ and αB = specific rotations of the pure isomers and xA = mole fraction of A

Equation 2

Laboratory Section For additional details about the procedure, hazards, and waste disposal, consult the text. Mix 3 mL of (-)-menthone with 5.0 mL of glacial acetic acid and 5.0 mL of 1M HCL. Reflux for 30 minutes and then let the mixture cool to room temperature. Bring the pH of the solution to 10 using 3M NaOH. Extract the mixture with two portions of diethyl ether. Dry the ether extracts with magnesium sulfate and evaporate the ether in a pre-weighed vial. To measure the optical rotation, mix all of the product in 10 mL absolute ethanol for a 1 dm tube or 25 mL for a 2 dm tube. Take the optical rotation reading of the product and a blank. Find the specific rotation of the mixture and the mole fraction of menthone.

Modeling Section 1. Build menthone and isomenthone in their best conformations. You may want to start with the cyclohexane fragment. Be sure the hybridization of each atom is correct. 2. (Optional) View the R or S designation on the chiral centers. Menthone is R, S or S, R and isomenthone is R, R or S, S. ❏

(Windows) Select View | Atom Attributes. The Atom Attributes box opens. Click on the Label tab and select Chirality for Asymmetric Carbons.



(Macintosh) Select View | Chiral Centers.

3. Save each molecule you build as menthone or isomenthone.

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4. Set up a dihedral search label between -180 and +180 using 48 steps for the H-C-C-H angle. Select the isopropyl H first (see diagram to the right). This will find the optimal position for the isopropyl group. 5. Compute an optimized conformation search.

 TIP Windows: If you cannot find the map file, look for file types that end in “.map,” not “.csf.” They are labeled as energy.map in the filename.map folder.



(Windows) Select the experiment settings chemical sample conformation, optimized map and MM (MM2) parameter.



(Macintosh) Select exhaustive search and optimized map in Mechanics using MM2 parameters.

H-C-C-H Dihedral Angle.

6. View the resulting map. There are two windows displayed: the map in the left window and the molecule in the right. ❏

(Windows) The map opens in the workspace after the computations are complete.



(Macintosh) Select Applications | Visualizer. Open the molecule.map file. It is saved in the same location as the molecule.

7. Use the left and right arrow keys in the map window to move along the energy path. Note the lowest energy position for the isopropyl group. 8. Save the lowest energy conformation from the menthone map as “last name.menthone” (e.g. Smith.menthone), and the lowest energy conformation from the isomenthone map as “last name.isomenthone” (e.g. Smith.isomenthone). ❏

(Windows) Select the molecule window. Click File | Save as chemical sample.

 TIP Hit i at any time to return the molecule to its initial position.



(Macintosh) Select the molecule window. Click File | Save as.

9. Click in the molecule window and rotate the molecule. Compare the amount of eclipsing or direct atom contact as the group rotates. 10. View the molecule with the full van der Waals radius. Notice that in the higher energy conformations the hydrogens appear to be touching. ❏

(Windows) Click on View | Space Filling.



(Macintosh) Click on View | Atom Shape. The Atom Shape dialog box opens. Change the van der Waals radius to 1.00.

11. Return to the ball and stick mode. ❏

(Windows) Click on View | Ball and Stick.



(Macintosh) Change the van der Waals radius to 0.20.

12. Close the map file. (Macintosh) Exit the Visualizer.

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Organic Chemistry Experiment 4 - Evaluations of Conformations of Menthone and Isomenthone

Optimize the Structures 13. Open each molecule, one at a time, in the Editor/Workspace.

 NOTE A Molecular Mechanics calculation produces relative energies compared to a molecule of the same composition but with ideal bond angles, distances and through space interactions. Thus the results are the net strain in the molecule.

14. Perform a geometry optimization. ❏

(Windows) This is an optimized geometry experiment with MM(MM2) parameter s.



(Macintosh) Select Applications | Mechanics and perform a geometry optimization with MM2 parameters.

15. Note the energies and the distribution of steric strain after each Mechanics calculation. 16. Copy the table from Mechanics into your report. Typical results from a molecular mechanics calculations on one conformation of isomenthone are shown below. Before copying, hit the “i” key to return them to the proper scale. Shrink the window down to the size of the molecule and orient the molecules in positions that are appropriate for seeing the structure clearly. Chair isomenthone (axial i-pr)

Convergence reached, program stopped normally. stretch = 0.751 angle = 1.471 stretch bend = 0.196 dihedral = 7.005 improp torsion = 0.012 van der Waals = 4.459 electrostatics = 0.000 hydrogen bond = 0.000 The energy of the final structure is 13.8935 kcal/mol. Molecular Mechanics optimized structure can be found in chair-isomenthone.a-ipr.

Report Guidelines Report the actual yield, theoretical yield and percent yield. Also report the specific rotation of the product. Copy and paste the final structures into your word processor document. Also include a discussion of the following topics:

4-4



Locate the major sources of strain in each structure. In this case dihedral and van der Waals strain are likely to be the most important.



From the modeling results, predict which of the two structures is most favored, by how much energy (kcal/mol), and briefly discuss the reasons for the order.



Calculate the actual percentage of menthone and isomenthone based on the experimental specific rotation of the equilibrium mixture.



Compare your experimental results with those obtained through a Mechanics calculation. Which is predicted and which is actually favored?

CAChe Workbook

Instructor’s Notes We use the menthone/isomenthone equilibrium experiment as the first modeling project in organic chemistry. We schedule this project about one third of the way through the first semester. This gives us time to assign a tutorial so we are sure that everyone is adequately prepared in the fundamental modeling tasks. At the same time, students may wish to install the software on their personal computers as permitted with our site license. Since this is our first modeling project, we usually take some class time to run through a sample calculation for a similar molecule using a projection system in the lab. The laboratory portion takes about an hour and a half to isolate the product. Since we have only one polarimeter, students come back on their own time to do the specific rotation measurement. Alternatives such as pooling the product for a group or entire class measurement are reasonable for departments where independent work is not possible. For more details on the laboratory procedure refer to the references at the end of this experiment. Typical Results In the experimental portion, students typically obtain 1-2g of equilibrium mixture. When this is dissolved in a 10 mL volumetric flask it gives rotations of 1-2˚ which translates to ~60-65% menthone. When you use Mechanics to search 48 dihedral angle points, there are two low energy valleys in the rotational potential energy diagram for (-)menthone. The use of fewer points in the search might lead students to conclude that the lowest energy is the local minimum at about 180˚. If the HC-C-H dihedral angle of bond leading to the isopropyl group is chosen, the heat of formation local minima are 12.78 kcal at about 67˚ and 12.81 kcal at about 172˚. Selecting the conformer at 67˚ and optimizing gives an energy of 12.57 kcal. Inverting the chiral center will produce the isomenthone isomer with a heat of formation of 13.89 kcal after optimization. Thus there is a difference of 1.32 kcal in favor of menthone. We can make an estimate of the expected isomer ratio by making a few assumptions. If we assume that the change in entropy during isomerization is very small then ∆Grx≈∆Esteric. Furthermore, we can relate the equilibrium constant (K) to our data (∆Esteric= -1.32 kcal) via the equations: ∆G rx = – RT ln K

Equation 3

[ menthone ]   ∆H ≈ – RT ln ------------------------------------rx  [ isomenthone ]

Equation 4

Solving for the ratio of isomers gives a prediction of 1.4:1 or approximately 90% menthone in the final mixture. The class results of 60-65% menthone are in reasonable agreement.

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Organic Chemistry Experiment 4 - Evaluations of Conformations of Menthone and Isomenthone

If you want to take a bit more time, you can obtain slightly better results using MOPAC (PM3), as seen in the table below. Menthone Isomenthone Energy Energy

∆E

Predicted Menthone%

Mechanics

12.57

13.89

1.32

90%

MOPAC (PM3)

-79.04

-77.88

1.06

86%

References Barry, J. J. Chem. Ed. 1973, 50, 292. Lehman, J.W. Operational Organic Chemistry, 3rd ed.; Prentice Hall: Upper Saddle River, NJ, 1999; 136-142.

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5

The Evelyn Effect

5

Contributed by James Currie, Pacific University

Overview The Evelyn effect refers to the observation that the product composition changes during the course of a reaction. The change in composition suggests that a mechanism preference is changing over time; a change in mechanism conflicts with the basic principles of reaction chemistry. You will do a laboratory experiment to see if you can observe the Evelyn effect and then you will use modeling to explain your results. Recommended Exercises Complete Exercise I, II, III, IV, V, and VI before beginning this experiment.

Background The dehydration of 2-methylcyclohexanol or 4-methylcyclohexanol is a common experiment in organic chemistry laboratories. Analysis of the distilled alkene products is useful in validating Zaitzev’s rule and in deducing the mechanism as E1 or E2. Because of the presence of products that require rearrangement, most chemists assumed that an E1 mechanism was operative. CH3

CH3 OH

2-methylcyclohexanol

H 3PO4

+

CH2 +

1-methylcyclohexene methylencyclohexane 3-methylcyclohexene

CH3

CH3 H 3 PO4

OH 4-methylcyclohexanol

CH3

CH3 +

4-methylcyclohexene

CH3 + 1-methylcyclohexene

3-methylcyclohexene

This assumption came under scrutiny in 1994 when Professor David Todd1 was testing this experiment and interrupted the alkene collection midway to have lunch with the department secretary, Evelyn Jacoby. When he returned, he resumed the distillation but kept the second half products separate from the first. When he analyzed the two fractions, he was surprised to find different alkene ratios. The reaction products and pathways to the products seemed to 1. Todd, D. J. Chem. Ed. 1994, 71, 440.

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Organic Chemistry Experiment 5 - The Evelyn Effect

have changed over time. Dr. Todd called this phenomenon the “Evelyn effect.” The Evelyn effect goes against the fundamental principle in organic chemistry--reactions always go by the lowest energy pathway. The favored product should remain so throughout a reaction run at constant conditions. In cases that have multiple paths due to competing mechanisms with close activation energies, we get complex product mixtures. However, even if multiple products are formed from multiple paths of similar energy, the product distribution should not change in constant conditions. To put this principle in perspective, we can consider an analogy to a more familiar setting. Imagine that there are two mountain routes to a city on the other side of the range. One of these routes may have the lower elevation and therefore be easier to navigate. If these two routes are greatly different in altitude, all the traffic will want to travel via the easiest route. If they are close in altitude, we may expect some flow through the slightly higher route but it should not exceed the lower. The preference for the lower route will not change. In the chemical world, the mountain pass altitude is analogous to the activation energy, the traffic to the concentration, the speed to the temperature, and the route to the reaction mechanism/pathway. The presence of the Evelyn effect appears to violate this basic principle of chemistry in the same way that a mountain pass changing its altitude would violate our common sense view of topography. Reaction details When either 2-methyl- or 4-methylcyclohexanol is heated in the presence of acid, the first step in the mechanism is protonation of the hydroxyl group followed by elimination. If the mechanism is concerted (E2), no rearrangements are possible and a simple product mixtures results. However, if the reaction follows an E1 mechanism, it forms a planar carbocation and rearrangements could lead to many additional products. CH3

CH3 OH

OH 2

H3PO 4

CH 3

+

E2

CH 3 +

bp 110.3˚ E1 - H2O CH3 +

5-8

rearrangement products

CAChe Workbook

bp 104˚

CH 3

CH 3 H 3PO 4

OH

CH 3 E2

+ OH

bp 102.7˚ 2

E1 - H2O CH3 rearrangement products

+

Possible rearrangement products: CH3

bp 110.3˚ CH CH 2

bp 97˚

CH 3

bp 104˚ CHCH3

bp 113-17˚

CH3

CH 2

bp 102.7˚

bp 103˚

CH 2CH 3

CH2CH3

bp 106.3˚

bp 97.8˚

CH 2CH 3

bp 98.3˚

The alkene products are volatile compared to the methylcyclohexanols and we assume that once formed, they distill rapidly from the reaction mixture. This means that the reverse reaction, the addition of water to form isomeric methylcyclohexanols, does not play a role in the ultimate product mix. We can conclude that if rearranged products occur, they come from an intermediate carbocation, by way of an E1 mechanism. Because we assume there is no reverse reaction, we can focus on two issues that will help us understand the Evelyn effect: the presence or absence of rearrangements and the reaction’s obedience to Zaitzev’s rule. We could conclude that rearrangement occurs during the dehydration of 2methylcyclohexanol if we find evidence of methylenecyclohexane or 4methylcyclohexene. Unfortunately a typical gas chromatograph does not separate these closely boiling compounds from one of the expected isomer, 3methylcyclohexene. If we do the reaction with 4-methylcyclohexanol, we still cannot separate any rearranged 3-methylcyclohexene from the expected 4methylcyclohexene, but we can easily see any doubly rearranged 1methylcyclohexene. Usually the presence of any rearranged product is

CAChe Workbook

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Organic Chemistry Experiment 5 - The Evelyn Effect

enough to conclude that a carbocation is involved and the mechanism is E1. As we shall see, such hasty judgments are not wise. If Zaitsev’s rule is followed in the deydration of 2-methylcyclohexanol, we should get a higher yield of the more substituted 1-methylcyclohexene. For an E1 mechanism, stereochemistry of the alcohol does not matter because the intermediate is a planar carbocation. However in an E2, the requirement for anti elimination means that stereochemistry plays a major role. To illustrate this point we will look at the dehydrohalogenation of neomenthyl chloride and its stereoisomer, menthyl chloride. CH 3

CH 3 CH3CH 2 O

-

+

CH3CH 2 OH

Cl

CH 3

CH(CH 3 )2 neomenthyl chloride

CH(CH3) 2

CH(CH3) 2

78%

22%

CH3

CH 3 CH3CH 2 O

-

CH3CH 2 OH

Cl

CH(CH3)2

CH(CH 3 )2 menthyl chloride

100%

Neomenthyl chloride gives the expected preference for the more substituted alkene. Surprisingly, menthyl chloride gives 100% of the least substituted alkene, apparently violating Zaitzev’s rule. To understand this we must look at the stereochemical requirements of the E2 mechanism and how they impact this reaction. An E2 mechanism requires that the two groups being eliminated be antiperiplanar or 180˚ from each other. In a cyclohexane ring two adjacent atoms can only achieve 180˚ if they are both axial. When neomenthyl chloride is in its most stable conformation, the two alkyl groups are equatorial and the chlorine atom is axial. Two hydrogens are anti-periplanar leading to the two possible products. In menthyl chloride, placing the chlorine atom in the axial position forces the isopropyl group into the axial position. Only one hydrogen is anti-periplanar and the elimination of this hydrogen leads to the least substituted alkene. So while the menthyl chloride reaction violates Zaitzev’s rule, it does so because stereochemical restrictions permit only one product. neomenthyl chloride H Cl (CH 3)2CH

H H

H -

CH3CH2O

5-10

CH3

menthyl chloride CH 3 Cl H H H (CH 3)2 CH

H -

CH3CH2 O

CAChe Workbook

It is important to note that stereochemistry affects the outcome of this reaction only if the mechanism is E2. Dehydrohalogenations in strong base are always E2, as is the case with neomenthyl and menthyl chloride. But we can turn this statement around and say that if we see an effect of stereochemistry, then the mechanism cannot be E1 and must be E2. Could stereochemistry be an explanation of the Evelyn effect? Maybe, but not by itself because the Evelyn effect is concerned not with product preferences but rather emphasis in product preferences. The real clue comes from the observation by Professor Todd that the commercial 2-methylcyclohexanol and 4-methylcyclohexanol are actually mixtures of cis and trans isomers. Thus, like menthyl chloride, there could be a difference in the rates of elimination for these two isomers. Indeed two French chemists first reported in 19312 that pure cis-2-methylcyclohexanol reacts much faster than the trans isomer giving greater than 90% of the more substituted 1-methylcyclohexene. Recently, two American chemists3, 4 confirmed the faster reactivity for the cis-2-methylcyclohexanol, placing the cis/trans relative rates at 8.4/1.0, respectively. A look at the stereochemistry of these two isomers explains this rate preference. In its lowest energy conformation, the cis alcohol has the water leaving group in the axial position with anti-periplanar hydrogens to either side. Thus stereochemically, either 1-methylcyclohexene or 3methylcyclohexene are possible with Zaitzev’s rule favoring the former. For the trans alcohol, the leaving group is equatorial in the lowest energy conformation and an anti-periplanar reaction is not possible. However, flipping the ring to the alternate chair form switches all the positions permitting a possible E2 reaction leading to 3-methylcyclohexene. OH 2 CH 3 H

CH3

CH3

+

+

H

H 2O H 2O

CH 3

H CH 3 CH 3

H +

H 2O

H

+

OH 2

only

One could argue that the Evelyn effect occurs simply from a change in product preference during an E2 mechanism as the cis isomer gets used up 2. Vavon, G.; Barbier, M. Bull. Soc. Chem. [4] 1931, 49, 567. 3. Cawley, J.J.; Lindner, P. E. J. Chem. Ed. 1997, 74, 102. 4. Cawley, J. J. J. Chem. Ed. 1999, 76, 58.

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Organic Chemistry Experiment 5 - The Evelyn Effect

and the trans begins to dominate. While this statement might be true, it must not be the whole story because, if it was, there would be no 1methylcyclohexene formed in the later stages. The French chemists found that more than 45% of 1-methylcyclohexene in the products when starting from pure trans-methylcyclohexanol. Now let’s turn our attention to 4-methylcyclohexanol. No matter what the mechanism, only 4-methylcyclohexene can be directly formed. Other products can be formed but only after rearrangement during an E1 mechanism. If we see the Evelyn effect during this reaction, it must be from a changing proportion of E1 and E2 mechanisms. In other words, for 4methylcyclohexanol, the Evelyn effect requires a mixed mechanism. In proposing an explanation for your results, you will need to find an explanation of how the preference for a mechanism can change. The presence of cis and trans isomers is central to the argument. Similar to the previous 2-methylcyclohexanol case, cis-4methylcyclohexanol can undergo a direct E2 elimination. The trans isomer must flip its cyclohexane ring into a higher energy conformation before the anti-periplanar requirement is met. Thus an E2 elimination is harder for the trans isomer. You could speculate that a harder E2 will shift the E1/E2 competition toward E1. If this happens what is the expected effect on the product mixture? Keep in mind that once a carbocation is formed, single or multiple rearrangements can follow. +

CH 3

OH 2

H

CH 3

H H2 O

H2 O H

H H

CH3 H

CH3

H2 O +

5-12

OH2

CAChe Workbook

CH3

Laboratory Section For additional details about the procedure, hazards, and waste disposal, consult a text5. Your instructor will assign either 2-methylcyclohexanol or 4methylcyclohexanol for the dehydration project. Set up a distillation apparatus using an unpacked vertical reflux condenser to reduce the chances of the higher boiling alcohol ending up in the product. Do not run water through the vertical condenser. Add 150 mmol of the alcohol, 5 mL of 85% phosphoric acid, and acid resistant boiling chips (or a magnetic stir bar) to a 50 mL boiling flask. Heat the reaction mixture gently giving the products time to form and ascend up the column. Slowly distill the alkene collecting the products into a 10 mL graduated cylinder. Keep the distillation rate down to about one drop per second. Monitor the temperature to be sure it does not exceed 120˚, the boiling point of the alkene products. After collecting about 8 mL, pour the distillate into a centrifuge tube and cap. Return the graduated cylinder and resume collecting product. After about 6 mL of additional product has been collected, watch carefully for the end of the reaction. Stop the distillation immediately when product ceases to distill over and white fumes or foaming occur in the reaction flask. Transfer the second distillate to another centrifuge tube and cap. Wash each distillate with two 5 mL portions of saturated sodium bicarbonate solution. After each wash, draw off the aqueous layer with a Pasteur pipet. Dry each distillate with calcium chloride. Centrifuge if necessary and decant each fraction into a tared vial for analysis. Record the total mass of product and calculate the percent yield. At a time arranged by your instructor, analyze each fraction by gas chromatography. Products should appear in the order of their boiling points. Alkenes with close boiling points, such as 3-methylcyclohexene and 4methylcyclohexene may not be separated. The first major peak usually is a mixture of these two products and the last major peak is usually the 1methylcyclohexene. Your instructor may ask you to confirm the identification of at least one alkene by “spiking” with an authentic sample. Be sure this analysis is complete before the next laboratory meeting because you will be expected to share your results.

Modeling Section Both 2-methylcyclohexanol and 4-methylcyclohexanol are mixtures of cis and trans isomers. In addition, each of these four isomers can exist in two different chair conformations. To fully explain the Evelyn effect, you will need to model all eight structures that may be involved.

5. Lehman, J. W. Operational Organic Chemistry, 3rd ed. Upper Saddle River, NJ: Prentice-Hall, 1999.

CAChe Workbook

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Organic Chemistry Experiment 5 - The Evelyn Effect

We can make an estimate of the expected isomer ratio by making a few assumptions. If we assume that the change in entropy during a flip to the alternate chair conformation is very small then ∆Grx=∆Esteric, where ∆Esteric is the difference (B-A) in steric energy for the two conformations as calculated by molecular mechanics. Then we can relate the equilibrium constant (K) to our data (∆Esteric) via the equations: ∆Grx = − RT ln K R=1.987 cal/mol-K

Equation 1

[conformationB] [conformationA]

Equation 2

∆Esteric ≈ − RT ln

For example, if conformation A is 1.00 kcal lower energy, then B/A is 0.185 or 15.6% B. If the preference increases to 2.00 kcal, the fraction of B drops to 3.3% and for 3.00 kcal to 0.63%. Thus A quickly becomes a non-participant in the reaction. You do not actually need to do this calculation but you should keep this example in mind when analyzing the modeling results Build each structure and optimize their geometry using Molecular Mechanics (MM2). At the end of each calculation record the calculated energy. Check the stereochemistry of the optimized structures looking for the appropriate anti-periplanar relationships necessary for an E2 reaction. Complete this modeling exercise before the next laboratory meeting because you will be expected to participate in a discussion of your results. Copy and paste the results in a word processor. Remember to orient and resize the molecules in a presentable manner.

Report Guidelines Report the results of your experimental work being sure to include: ✎

a summary of procedure and observations.



yield, theoretical yield, and percent yield.



results of your gas chromatography analysis for each fraction.



a report of the average class results for each starting material. Use those results in your analysis of the mechanism.

Address the following issues in a well organized discussion leading to logically argued conclusions regarding the mechanisms involved. ✎

Does the data for the 2-methylcyclohexanol dehydration confirm Professor Todd’s observation of the Evelyn effect?



Is this effect seen in 4-methylcyclohexanol dehydration?



Is Zaitzev’s rule followed?

Sometimes a small product peak is seen between the major methylcyclohexene peaks. Speculate on the identity of this peak.

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Consider the modeling results for 2-methylcyclohexanol first. For each of the four isomers compare the energies of the two chair conformations. ✎

Which will predominate? By a lot or a little?

For the dominate conformations, note the stereochemistry of the atoms around the hydroxyl group. ✎

Which structures meet the criteria of having an H and OH antiperiplanar for E2?



Which alkene(s), if any, will be formed from an E2 elimination?



Do your results suggest whether cis or trans should react faster?



If another pathway, such as E1, was possible, would it be most competitive for the cis or trans?

Write a detailed chronological scenario describing: ✎

what is happening as the reaction proceeds



when the various species are reacting



which mechanisms are predominating



when shifts in mechanism preference might occur.

Repeat the analysis for 4-methylcyclohexanol. Write out a complete mechanism for the formation of each product that you speculate to be present in the product mixture from BOTH the dehydration of 2-methylcyclohexanol and 4-methylcyclohexanol.

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5-15

Organic Chemistry Experiment 5 - The Evelyn Effect

Instructor’s Notes Typical Results The analysis for this experiment is intimidating and complex but, with time, students can understand it. We spend two weeks on this experiment; during the first week the dehydration are done individually by the students, half doing each isomer. In the interim between the first and second lab, all the gas chromatography and modeling are finished. The second lab is spent discussing the GC and modeling results. We talk in detail about the stereochemical requirements that exist for an E2 mechanism but not for an E1. Gas chromatography analysis. We usually use a fast analysis to so we can accommodate all the students on one dedicated GC during one week. We use an SE30 0.52mm capillary column at 65˚ for 2 min; heat at 50˚/min until 160˚ and hold for 1 min. Total time about 5 min. Even with much lower temperatures, we have never been able to separate the three isomers boiling in the region of 103˚. Typical results from GC analysis are shown in the first row of each fraction. A separate analysis by NMR gave us the percentages we thought they might be useful for your understanding of the experiment. 2-methylcyclohexanol CH 3

CH3

CH 3

bp ˚C

110.3

104

102.7

GC

78%

NMR

60%

GC

60%

NMR

60%

CH2

CH CH2

CH2CH 3

CHCH3

Fraction Method

1

2

5-16

103

12% 9%

4%

0.5%

30% 16.3% 13.8%

1%

97

106

113-17

0.1%

0.6%

0.0%

0.1%

0.6%

0.0%

1.6%

4.3%

0.6%

1.6%

4.3%

0.6%

CAChe Workbook

4-methylcyclohexanol CH 3

Fraction

CH 3

CH 3

CH2

Method

bp ˚C

110.3

104

102.7

1

GC

5.4%

94.6%

2

GC

14.3%

85.7%

103

We have been studying this reaction for a long time and believe the evidence is quite persuasive that both E1 and E2 mechanisms are operative. In 2methylcyclohexanol, the students are not able to separate the 3methylcyclohexene, 4-methylcyclohexene, and methylenecyclohexane and therefore have little evidence of how much rearrangement and E1 mechanism occurs. Without more product information, the Evelyn effect could easily be explained simply by considering the unfavorable stereochemical preferences for the trans isomer and the resulting faster E2 reaction for the cis isomer. The 1-methylcyclopentene is easily observed in the GC during the reactions with 2-methylcyclohexanol but not always correctly identified. If students speculate correctly about its identity, the presence of some E1 is certain. In order to have a really interesting discussion, it is necessary to include 4methylcyclohexanol. The 4-methylcyclohexene is the first formed product from either the cis or the trans isomers. However, the easily observed 1methylcyclohexene can only come about from an E1 mechanism and the varying amount of this product strongly suggests varying amounts of E1 mechanism. On the other hand, in order for cis and trans isomers to show different reactivity, and therefore an Evelyn effect, we must have an E2 mechanism. An alternative mechanism proposed by Cawley does not seem to work for the 4-methylcyclohexanol. The following are the results of a molecular mechanics calculation for the eight structures potentially involved. The first letter (a or e) refers to the axial or equatorial placement of the methyl and the second letter the hydroxyl. 2-Methylcyclohexanol

Steric energy Steric energy 4-Methylcyclohexanol (kcal/mol) (kcal/mol)

e,e trans-2-MeOH

7.93

e,e trans-4-MeOH

7.52

a,a trans-2-MeOH

9.82

a,a trans-4-MeOH

9.86

a,e cis-2-MeOH

9.72

a,e cis-4-MeOH

9.29

e,a cis-2-MeOH

8.47

e,a cis-4-MeOH

8.09

Stereochemically either chair form of the cis isomers have the correct antiperiplanar relationships. On the other hand, only the a,a trans conformations can undergo an E2 elimination and there is about a 2 kcal preference for the e,e conformation. We can speculate that in the trans case, the greater CAChe Workbook

5-17

Organic Chemistry Experiment 5 - The Evelyn Effect

difficulty of producing an E2 mechanism permits the alternative E1 to be more competitive. Thus as the cis isomer is consumed and trans begins to predominate, we see increasing amounts of E1. If a good discussion takes place during the second lab, many students will turn in well reasoned reports with logical conclusions. Nearly all students write passable reports and show considerable understanding of this complex reaction. References See footnotes.

5-18

CAChe Workbook

6

Prediction of Aromatic Substitution Rates and Positions

6

Contributed by James Currie, Pacific University

Overview In this exercise you will use CAChe to model key structures in electrophilic aromatic substitution. Two methods (intermediate heat of reaction (∆Hrx) and partial charges on the starting material) are evaluated for predicting relative rates of reaction and substitution position preferences. Recommended Exercises Complete Exercise I, II, III, IV, V, VI, and VIII before beginning this experiment.

Background An electrophilic substitution, such as a nitration, is a two step reaction in which the first step is the formation of a carbocation intermediate. The thermodynamic property that determines the products is the activation energy (Ea) leading to each competing intermediate. It is possible to model the starting material and the transition state leading to the carbocation intermediate. However, modeling transition states is a tedious, complex task that is not necessary for qualitative understanding. Instead you will model the heat of reaction (∆Hrx) of the first step. This is the energy required (change in heat of formation, ∆Hf) to go from the starting material to the intermediate carbocation. Since the transition state should look a lot like the intermediate, this energy should be a good predictor of the Ea. G

G

G NO2

+

-H

H

G

+

NO2

NO2

G NO 2

G

+

-H

+

NO 2 H

6-19

NO 2

CAChe Workbook

Organic Chemistry Experiment 6 - Prediction of Aromatic Substitution Rates and Positions

Furthermore, the difference in energy between the meta and para intermediates should be nearly identical to the differences in energy between the corresponding transition states. By comparing the ∆Hrx for each formation of the intermediates with the ∆Hrx for unsubstituted benzene you can estimate the relative activation or deactivation of each site. A sample set of data is given below. Table 1 chemical sample

∆Hf

∆Hf (NO2+)

Partial Charge

∆Hf

∆Hrx

benzene

23.46

208.40

-0.102

229.16

-2.70

benzoic acid

-66.16

208.40

meta

-.0118

145.78

3.54

para

-0.069

147.88

5.64

You can see from the data in Table 1 that benzoic acid has a higher ∆Hrx for both meta and para substitution than benzene. The Ea for both meta and para is also higher. Thus the carboxylic acid group has deactivated both positions of the benzoic acid toward substitution. You can compute the corresponding data for a different substituent. Use the value given for the ∆Hf (NO2+) in calculating the ∆Hrx for each intermediate. ∆H rx = ∆H f ( intermediate ) – [ ∆H f ( substrate ) + ∆H f ( N O 2+ ) ]

To help gain a qualitative understanding of the directing effects of a substituent and the relative rate of reaction, you will also evaluate the distribution of charge on a substituted benzene and compare the results with benzene itself. Table 1above gives the results for benzoic acid. Notice that the partial charges are more negative on the meta than on the para position. You can relate these results to the reaction by considering that the electrophile (NO2+) will choose to attack the most negative site. Alternatively, you can consider that the charge distribution impacts the energy of the two possible carbocation intermediates. Thus looking at partial charges in the starting material is just another way of viewing the intermediate stability. The advantages of considering partial charges are that CAChe can display partial charges graphically for direct visual comparison, and only the starting material needs to be considered.

6-20

CAChe Workbook

Modeling Section You will be assigned a starting functional group. Choose two other functional groups that have different activating effects.  TIP

Building the Structure

For fast building, retrieve a benzene ring from the Fragment Library.

1. Open the Workspace/Editor and build a benzene molecule. 2. Connect the non-hydrogen atoms to the benzene molecule in the correct places with the atom tool. 3. Correct the hybridization and bond type using the Select tool.

 TIP



(Windows) Select an atom or bond. Go to the Hybridization or Bond type box located in the Style bar. Click on the arrow, the menu appears. Select the correct hybridization or bond type.



(Macintosh) Select an atom or bond. Hold down the Command key while clicking on the atom or bond. Select the appropriate hybridization or bond type from the pop-up menu.

4. Select Beautify | Comprehensive.

Beautifying the structure gives the molecule the correct angles and number of hydrogens. If your molecule is not correct, go back and check bond type and atom charge.

5. Select the atoms (hold down the shift key for multiple selections) you want partial charges for (the two meta and the one para). 6. Save the structure using your last name followed by the functional group for the file name, for example “Smith-CO2H.”

A molecule with three atoms selected for partial charges.

7. Select a nitro group (NO2+) from the Functional Group list in the Fragment Library. 8. Deposit the nitro group in the workspace near the carbon you will connect it to. 9. Select the nitrogen of the nitro group and the meta carbon of the benzene ring. Select Edit | Connect Atoms to connect the nitro group and the benzene ring. 10. Add the positive charge on the appropriate carbon. G



(Windows) Select the appropriate atom. Click the up or down arrow on the Charge box in the Style bar to adjust the charge.



(Macintosh) Hold the Option key while clicking on an atom with the Atom tool. Adjust the characteristics and close.

sp 2 O N

O Notice theHcharges on the atoms in a meta-nitro addition to a benzene molecule.

CAChe Workbook

11. Correct the bond types in the same manner as step 3. 12. Select File | Save as and save the intermediate molecules as before, but with the m or p, for example, “Smith-m-CO2H.”

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Organic Chemistry Experiment 6 - Prediction of Aromatic Substitution Rates and Positions

13. Build the other molecule in the same manner as the first only place the nitro group in the para position. 14. (Macintosh) Quit the Editor. ProjectLeader 15. Open the ProjectLeader template “Nitration.” 16. Save the file in the same location as your molecules. Use your last name as the file name. 17. Double click on the first cell in the column labeled “Aromatic substrate.” In the dialog box that appears, locate the folder your molecule is stored in. Highlight the molecule you want to put in the table. Click on Add. 18. Repeat step 17 to insert meta and para intermediates in the cells located in the columns labeled Intermediate meta and para. 19. Select all the cells by clicking and dragging across the cells with the mouse. Click on Evaluate | Cells. This computes the optimal geometry, the heat of formation, and the partial charges on the selected atoms. Each structure takes a few minutes. The ∆Hrx cells will remain empty because they depend on other numbers in the table. 20. Evaluate the ∆Hrx column for each substance in the table. 21. Open the molecules by (Windows) shift clicking or (Macintosh) double clicking on each structure cell and inspect the result of the geometry optimization after the calculations are finished. If the structures do not appear correct, fix and re-evaluate them. 22. Repeat this process for two other starting molecules with different activating effects.

Report Guidelines For your report, give the results of the calculations in tables similar to Table 1 in the Background. Using the partial charges, discuss a qualitative view of their impact on the products Keep this brief and simple since this is only a view of the starting material.

6-22



From the partial charges, what is the preferred substitution orientation of the three starting materials?



Do the partial charges suggest activation or deactivation?

CAChe Workbook

Discuss in more detail the ∆Hrx for the formation of para and meta intermediates.

CAChe Workbook



What does the data suggest about the preferred orientation?



Compare your two ∆Hrx to that of benzene (see Table 1) for each substrate. Does your data suggest that your group is an activating or deactivating group?



If you can, compare these data with the orientation and relative rate discussion in a text. Are any of the results contrary to your expectations?



Compare the magnitude of your preferences with those for the experimental results of benzoic acid. Experimental results for benzoic acid are 82% meta and 1% para. What is the likely percentage of meta and para in your cases?

6-23

Organic Chemistry Experiment 6 - Prediction of Aromatic Substitution Rates and Positions

Instructor Notes This experiment serves as an alternative to a wet lab on aromatic nitration. Depending on the time available in class, you should discuss the quality of computational results and the utility of modeling. The students model three different aromatic nitrations. We assign one functional group to individual students. They can choose the other two functional groups. However, they should choose groups that have opposite activating effects. For example, if a student is assigned a carboxyl group, they should model an activating group and a borderline activating/deactivating group. We use a template with Project Leader to simplify the calculations. This allows us to focus on the results and not so much on the procedures. Below are pictures of the template we use in Project Leader taken from a Macintosh. The PC version of Project Leader looks very similar and works in the same manner. The template column headings are as follows:

Column Heading

Description

aromatic substrate

chemical sample

∆Hf (kcal/mol)

∆Hf at PM3 geometry

atom

selected atoms

partial charge

partial charge at PM3 geometry

meta

chemical sample

∆Hf (kcal/mol)

∆Hf at PM3 geometry

∆Hrx = F-(B+208.4)

algebraic equation

para

chemical sample

∆Hf (kcal/mol)

∆Hf at PM3 geometry

∆Hrx = I-(B+208.4)

algebraic equation

In the Nitration template, you must evaluate the starting material cells before evaluating the intermediates. The calculation will expand number of rows in the table because it will add the carbon atoms you are evaluating in the atom column. This is why it is important to select the atoms when you build the starting material in the Workspace/Editor. Below is the Project leader template before any calculations are done.

6-24

CAChe Workbook

After the starting material cells are evaluated the table should look like the picture below. Enter in the intermediate structures in the same rows the corresponding starting material.

When you evaluate the intermediate cells it will fill in the ∆Hf. You need to evaluate the ∆Hrx separately because it needs the ∆Hf to do the calculation. After all the calculations have been done, the table should look like the following table.

Typical Results Below is a sample of results. Chemical Sample

Hf (kcal/mol)

OH

-21.671

CH3 Benzene

23.454

I

44.74

CHO

-10.647

SO3H NO2

CAChe Workbook

14.113

-96.21

14.536

Position

average partial Charge

Hf (kcal/mol)

Hrx (kcal/mol)

meta

-0.062

187.28

0.55

para

-0.144

171.07

-15.66

meta

-0.098

218.44

-4.07

para

-0.109

213.28

-9.24

-0.102

229.16

-2.70

meta

-0.096

251.06

-2.08

para

-0.099

245.24

-7.90

meta

-0.119

199.92

2.17

para

-0.070

201.00

3.24

meta

-0.039

117.02

4.83

para

-0.132

123.42

11.23

meta

-0.124

236,74

13,80

para

-0.039

242.28

19.35

6-25

Organic Chemistry Experiment 6 - Prediction of Aromatic Substitution Rates and Positions

6-26

CAChe Workbook

Part 3: Physical Chemistry Experiment 7: Investigating the Resonance Stabilization of Benzene Experiment 8: Vibrational Analysis of Halogen Hydrides Experiment 9: Investigation of the Rotational Barrier in N-N-dimethylacetamide

7

Investigating the Resonance Stabilization of Benzene

7

Contributed by Kevin E. Johnson, Pacific University

Overview In this experiment, you will use both experimental and computational methods to determine the enthalpic contribution to the resonance stabilization of benzene by comparing the enthalpy of formation (∆Hf°) of several compounds. Recommended Exercises Complete Exercise I, II, III, IV, V, and VI before beginning this experiment.

Background The classic example of resonance is the simplest aromatic compound, benzene (C6H6). A Lewis structure predicts alternating double and single bonds around the six carbon ring. Yet it is known that the bond lengths are all equal at 1.397Å, intermediate between the length of a C-C single bond (1.537Å) and a C=C double bond (1.335Å). This is ascribed to bond resonance, where the _ bonding predicted by the Lewis structure is delocalized throughout the six carbon cyclic structure. Thus, the resulting bonds are all equivalent.

= In addition to this structural component, the resonance delocalization of the _ bonds results in an energetic stabilization, or resonance energy. This is a measurable decrease in the molecule's energy as compared to the hypothetical cyclohexatriene, with fixed alternating single and double bonds. The resonance stabilization of benzene is thus the difference between the enthalpies of formation for benzene and cyclohexatriene. ∆Hf˚(resonance) = ∆Hf˚(benzene) - ∆Hf˚(cyclohexatriene) While it is not possible to experimentally measure the formation energy of cyclohexatriene, its heat of formation (∆Hf°(298)) can be predicted using both experimental and computational methods.

7-1

CAChe Workbook

Physical Chemistry Experiment 7 - Investigating the Resonance Stabilization of Benzene

The first analysis is made by calculating the ∆Hf° for the series of six carbon cyclic compounds, and comparing the trend in ∆Hf° predicted by cyclohexane, cyclohexene, and 1,3-cyclohexadiene to benzene to predict the ∆Hf° of cyclohexatriene.

A second method uses the atom and bond equivalence of 1,5,9trans,trans,cis-cyclododecatriene, C12H18 (CDDT). CDDT is not aromatic and therefore does not include the resonance stabilization of benzene. Because of this, the ∆Hf° of CDDT equals the sum of the ∆Hf° for cyclohexane and cyclohexatriene.

+

=

The first and second methods can be accomplished both experimentally and computationally. A third purely computational method involves calculating energies for molecules with locked geometry. The ∆Hf° for cyclohexatriene can be calculated by locking the alternating double and single bonds. The ∆Hf° can then be used to calculate the resonance stabilization of benzene.

Laboratory Section Using oxygen-bomb calorimetry measure the heats of combustion for cyclohexane, cyclohexene, 1,3-cyclohexadiene, benzene, and CDDT. With the quantity you obtain from calorimetry, calculate the heats of formation. Use literature values for the heats of formation of the products CO2 and H2O. With these data, you can predict for the ∆Hf° of the hypothetical cyclohexatriene and compare it with the measured ∆Hf° of benzene. The difference of the two numbers will give you the resonance stabilization of benzene. Literature Values Use a literature source to lookup the ∆Hcomb° and ∆Hf° values for the compounds you measure. Suggested on-line resource: http://webbook.nist.gov/

7-2

CAChe Workbook

Modeling Section Comparison of ∆Hf°  NOTE Remember to choose either AM1 or PM3 for your MOPAC calculations. Both give reasonable results, but you should be consistent and use the same parameter with each calculation.

Build the series of six carbon cyclic compounds and CDDT. Use Project Leader to calculate the enthalpy of formation and to simplify the organization of results. Also consider that the modeling calculations are for isolated molecules, and comparison with experimental results should account for the phase change from liquid to vapor. Modeling hypothetical cyclohexatriene While only hypothetical, you can model cyclohexatriene and compare the calculated ∆Hf˚ to that of benzene. Try various approaches to model the hypothetical compound by fixing atomic positions or bond lengths in the cyclic C6H6 compound. Be critical of the MOPAC results. Decide which method gives you good results and stick to that method.

 TIP To lock bonds, select the bond you wish to lock, followed by Adjust | Lock.

One way to generate a starting point for calculations is to place a benzene fragment and use the Beautify command to alter the bond lengths. Either lock atom positions, or bond lengths to maintain the cyclohexatriene geometry during MOPAC calculations. You may choose to lock the C-C bonds or the C=C bonds or both. After each MOPAC calculation, always check the resulting structure to verify that the bond lengths correspond to expectations. Use the ∆Hf˚ data from only those structures that keep the expected geometry. Another starting point for calculations that does not start with a biased benzene geometry, is to retrieve a cyclohexane fragment. Delete one hydrogen atom per carbon atom, change alternate bonds to double bonds, and lock the single bond lengths. In order to optimize this restricted structure, the MOPAC calculation may require a change in optimization method (BFGS is more successful than EF for example). Always check the resulting geometry after each MOPAC calculation. Record the ∆Hf° for the various calculation methods, remember to use only the numbers that produced the correct geometry. Compare these ∆Hf˚ to that of benzene to estimate the resonance stabilization enthalpy.

Report Guidelines ✎ Report the values from the experimental, literature, and computational

investigations of ∆Hf° for the six carbon cyclic compounds and CDDT. ✎ Use and explain the trends observed for the six carbon cyclic

compounds to estimate the resonance stabilization energy of benzene. A graphical presentation may be useful. ✎ Analyze the data from CDDT in comparison to cyclohexane and

benzene, recognizing that the bonding and atom elements of CDDT amount to the sum of cyclohexane and cyclohexatriene.

CAChe Workbook

7-3

Physical Chemistry Experiment 7 - Investigating the Resonance Stabilization of Benzene

✎ Compare direct calculations of the ∆Hf° of cyclohexatriene with

optimized benzene. ✎ Summarize the conclusions for each method of calculating the

resonance stabilization of benzene. Also, discuss the relative benefits of each method.

7-4

CAChe Workbook

Instructor Notes The first project of our physical chemistry/thermodynamics laboratory course is this computational and experimental investigation of resonance stabilization. The experimental component introduces not only the technique of oxygen bomb calorimetry, but also statistical handling of data and error analysis. Students work in pairs and each group is expected to provide for the class one set of data for all the measured compounds. The class then analyzes the collective results to make a conclusion using the experimental data. The experimental procedure requires very careful attention to individual measurements of sample mass and temperature rise in order to obtain the precision necessary to accurately predict the stabilization energy of benzene. Literature values of ∆Hf suggest a stabilization enthalpy of –33 kJ/mol while organic textbooks quote –36 kJ/mol. Student results from our labs are in the range of –50 kJ/mol. The computational component of the experiment is intended to introduce students to the use of computational methods to complement experimental work. I encourage students to explore the potential of the CAChe tools to solve this problem. A straight-forward calculation of heats of formation for the assigned compounds and trend analysis is the first step. I encourage students to investigate the effect of parameter choice when working in pairs. One member uses PM3 and the other AM1 to critically assess which may be the better tool for this study. Typical Results

Chemical sample

C6H12

0

-38.3

-30.9

-29.49

C6H10

1

-4.1

1.4

-1.08

C6H8

2

19.2

22.1

25.4

C6H6

3

22.0

23.4

19.81

Cyclohexatriene

3

44.8

45.2

C12H18

3

16.0

18.3

Analysis Method

CAChe Workbook

# double AM1 ∆Hf° PM3 ∆Hf° Literature bonds (kcal/mol) (kcal/mol)

21.91

Stabilization Energy

Trend Analysis

-27.8

-27.1

-33.4

C12H18-C6H12

-32.3

-25.8

-31.6

Cyclohexatriene

-22.9

-21.7

7-5

Physical Chemistry Experiment 7 - Investigating the Resonance Stabilization of Benzene

The trend analysis simply takes the linear equation determined by the three unconjugated C6 cyclic compounds and predicts a ∆Hf˚ cyclohexatriene with three unconjugated double bonds. The difference between the predicted value and benzene is the stabilization energy. The ∆Hf˚ of cyclohexatriene can also be predicted by taking the difference between CDDT and cyclohexane. That value compared with benzene provides another route to calculating the stabilization energy. The purely computational method of calculating a molecule with restricted geometry is best accomplished by locking the single bond length in the unoptimized benzene molecule. The results of this computational method are the furthest from the literature values. These results may not be so surprising considering the experimental methods only predict an energy for the cyclohexatriene based on parameterization of real compounds. Overall the AM1 parameters are somewhat better than PM3. However, both yield systematic errors in the calculations of these compounds. An important point for students to realize is that these semi empirical computational methods are not likely to produce values that exactly match experimental or literature results. Instead they can be used to make reasonable comparisons between compounds with similar structural and elemental properties. References Halpern, A. M. Experimental Physical Chemistry: A Laboratory Textbook, 2nd ed.; Prentice Hall: New York, 1997; pp 139-143.

7-6

CAChe Workbook

8

Vibrational Analysis of Halogen Hydrides

8

Contributed by Kevin E. Johnson, Pacific University

Overview In this project you will model and measure the vibrational spectra of four halogen hydrides, HCl, DCl, HBr, and DBr. In addition, you will generate a potential energy curve for the hydrogen-halogen bond. Because CAChe on a Windows platform is unable to calculate information for various isotopes, this is a MACINTOSH ONLY experiment. Recommended Exercises Complete Exercises I, II, III, IV, VI, and VIII before beginning this experiment.

Background The simplest approximation of the interatomic potential energy curve for a covalent bond is a harmonic potential. A quantum mechanical treatment of this potential generates eigenfunctions with equally spaced quantized energy levels, with separation νe. Real bond potentials have quantized states that decrease in spacing with higher energy, and ultimately lead to dissociated atoms or a broken bond. Figure 1 illustrates the potential calculated using the best-known empirical function, the Morse potential.

Figure 1: The Morse Potential

8-7

CAChe Workbook

Physical Chemistry Experiment 8 - Vibrational Analysis of Halogen Hydrides

Morse Potential: V(R) = interatomic potential energy −a R−R V ( R) = De 1 − e ( e ) 



2



R = interatomic distance, Re = equilibrium bond distance De = well depth, a = constant

The parameters of the Morse potential can be related to vibrational levels as follows:

νe = µ=

νe = vibrational frequency

a De π 2µ

µ = reduced mass

m1 m2 m1 + m2

xe =

hν e 4 De

xe = anharmonicity constant

[

E vib ( v) = hν e (v +

(v = 0,1, 2,K)

1 2

) − x e (v + 12 )2 + L]

Evib (v) = vibrational energy levels v = vibrational quantum number

The expected vibrational transitions can therefore be calculated as follows. The fundamental vibrational absorption: ∆E(v=1←0) = Evib(1) - Evib(0) = hνe[1-2xe] The first overtone: ∆E(v=2←0) = Evib(2) - Evib(0) = hνe[2-6xe] In addition, the dissociation energy, which is the energy required to break the bond starting at the lowest vibrational level, can be calculated as follows: D0 = De - Evib(0) = De - hν e 1 − 1 x ( 2 e)

2

Vibrational energies are usually expressed as wavenumbers:

νƒ =

ν c

c = speed of light

A more complete discussion of vibrational spectroscopy and interatomic potential energy curves can be found in most physical chemistry textbooks.

8-8

CAChe Workbook

Laboratory Section You can generate gaseous halogen hydrides in a variety of chemical methods. One method is the reaction of a mixture of H2O and D2O with either PCl3 or PBr3. Dry the gaseous products of HCl and DCl through CaCl2 and the HBr and DBr over CaBr2. It is essential that you do not dry the bromide hydrides using CaCl2, as the halogen will exchange on the solid drying agent. Collect the dry gas in a gas IR cell. With the best resolution possible on the instrument, measure the gas phase rotational-vibrational spectra of HCl, DCl, HBr, and DBr. The spectra for the chloride hydrides will be split due to the 35Cl and 37Cl isotopes. Both the chloride and bromide spectra will include hydrogen and deuterium bands. It is also possible to observe the first overtone vibrational series with sufficient signal strength. For each isotopic combination you can analyze the R and P branches together to determine molecular quantities. This analysis is well described in several references. Literature Values Use a literature source to look up values for Re, νe and xe for the compounds you measure. Suggested on-line resource: http://webbook.nist.gov/

Modeling Section Direct Calculation of Vibrational Spectra 1. Build an HCl molecule in the Editor. Beautify and save the molecule. 2. Run an appended calculation in MOPAC: optimization followed by a force calculation. Choose either AM1 parameters or PM3 parameters, but record your choice and be consistent. Try both parameter sets to determine which produces better results. The optimization method will also affect the output. Select Optimize geometry and the parameter (AM1 or PM3). Click on Details. In the Details dialog box, change the optimization settings to: Minimize gradient by: NLLSQ, Optimize geometry by: BFGS, and the Precise option. Click OK to close the box. Select Append, followed by Vibrational Spectrum (FORCE). Run the calculation 3. View the resulting vibrational spectra by opening the molecule in the Visualizer. Select View | Vibrational Spectra. To ascertain the exact value of the calculated fundamental vibrational transition energy, select Select | Via Internals. In the resulting Internals window select the following: Object Class: vibrational_level and Property: Energy. The value appears in the far right column. Units are in wave numbers (cm-1).

CAChe Workbook

8-9

Physical Chemistry Experiment 8 - Vibrational Analysis of Halogen Hydrides

Calculate Isotope Energies In order to calculate the vibrational transition energies for specific isotopes, a MOPAC input file must be generated and edited. 1. Set up a calculation with the HCl or HBr molecule as before, but instead of running the calculation, choose Option | Create MOPAC Input. This file saves to the same location of the molecule file. Open the Input file in a text editor. Immediately after the element designation, enter the isotopic mass in atomic mass units (amu). See the following example for 1H35Cl: H1.0078 ( Cl34.9688(

2) 1)

2. Save the edited file and open it in MOPAC. The standard MOPAC options disappear in the MOPAC window. Run the calculation. Read the calculated vibrational level from the Internals data as before and record. 3. Run the isotope calculations for all combinations of 1H, 2H, 35Cl, 37Cl, 79Br, and 81Br. Modeling the Interatomic Potential In addition to calculating the fundamental vibrational transition energies, it is also possible to use MOPAC to calculate a potential energy curve for the halogen hydrides. 1. Create a search label (Adjust | Atom Distance) for the H-X bond length in the Editor. The range should cover approximately one half the equilibrium bond distance (see value at the top of the Atom Distance box) to 3 times the bond distance. Choose a reasonable number of steps (50 is more than enough). Save the file.  NOTE An optimized search is not necessary since only two atoms are involved and the bond distance is fixed for each point of the calculation.

2. Run a search calculation using MOPAC. Open the molecule file and choose either AM1 or PM3 parameters. Set Calculation Type: Rigid Search…. It is essential that you set the Multiplicity to Biradical, otherwise MOPAC will calculate the dissociation as two ions rather than as neutral atoms. Before running the calculation be sure that the option for saving the MOPAC Log file is selected. The calculation will create a .map file. You can view the map using the Visualizer. With the map, you can record the energy as a function of bond length by stepping through the calculated potential curve and writing down the corresponding energy for each step. The same data is also available in the MOPAC Log file in the format: Final heat of formation =

x kcal/mol

However, the bond distance data is not included in the log file. The final heats of formation are the only numbers needed; delete any other extraneous information in the file.

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3. Use either the map or the MOPAC log file to tabulate energy as function of bond length and enter it into a spreadsheet file or other data analysis program. Fit the data to the Morse potential. (One method is to use the Solver function in Microsoft® Excel.) The fit parameters should include De, Re and a. From the fit parameters, you can calculate the vibrational energy levels, transitions, and dissociation energy.

Report Guidelines Report the values from the experimental, literature, and computational investigations of the vibrational levels in the halogen hydrides. A plot of the Morse potential from computed and measured data should be included for each compound. Also, compare the various methods and parameters for calculations with the experimentally measured values.

CAChe Workbook

8-11

Physical Chemistry Experiment 8 - Vibrational Analysis of Halogen Hydrides

Instructor Notes This computational exercise is designed to accompany a standard diatomic infrared spectroscopy experiment. The listed references give excellent suggestions toward the experimental component of this project. The MOPAC-generated vibrational spectra for diatomic molecules have limited value. The calculated results yield only the fundamental vibrational transition with no rotational components. However, rotational constants can be calculated using the bond distance of the optimized structure. In addition, the calculation only evaluates the harmonic contribution to the vibrational energy and does not include any anharmonicity. It is possible to make some prediction of the anharmonic components of the diatomic vibrational spectra by calculating the interatomic potential and fitting the resulting data to a Morse potential. Typical Results The following illustrates results from a PM3 parameter calculation:

The fit yields the following Morse parameters: Re (Å) De (kcal/mol) 1.27

456

a (Å-1) 1.75

Analysis of these results produces the following derived molecular constants: νe (cm-1) 2841

νe xe (cm-1) ν (1. In the Kind of analysis box click on Algebraic Equation. 3. Select Next>. Click in the Equation box. Enter “Change=D-B,” which tells Project Leader to subtract the number in column B from the number in column D 4. Click OK. The project table should look like the following:

5. Select the empty cells in column B and then Evaluate | Cells. 6. Repeat for the empty cells in column D. You do not need to wait for the first group to finish before selecting the second group. When all the calculations are finished, select the empty cells in column E and evaluate. The value for change (column E) gives the increase in energy for an axial halogen compared to an equatorial halogen.

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Using the Procedure Editor Some experiments in this workbook requires special procedure options. The best way to do this is to duplicate an existing experiment, alter it and save it as a new experiment. It is easy to alter the default procedures; be aware of this when you are creating new experiments. For more information on using the Procedure Editor, consult your CAChe User Guide manual. 1. Open a new experiment in the Workspace. 2. Select the options that are closest to what you need for your experiment 3. Select Edit. The Procedure Editor application opens. In the Procedure Editor, a CAChe Experiment Environment window with two columns, opens. In the left column is a tree view of the experiment environment.

4. Locate the folder where the experiment is located, and double click on the folder. For example, open Environment/Workspace/chemical sample/ optimized geometry. Double click on the optimized geometry folder. The contents of the folder should open in the folder tree and in the window on the right. 5. Select the experiment closest to the one that you need in the window to the right. 6. Select Edit | Copy, followed by Edit | Paste. A copy of the experiment appears as “experimentname[2].” 7. Rename the experiment copy, by clicking on the experiment name once and typing in a new name.

CAChe Workbook

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Exercises for Windows

8. Double click on the experiment copy. A Procedure dialog box opens. Highlight the call in the Procedure steps list. 9. Select the Delete button in the Procedure window. The call disappears. If you were to edit the current procedure call, instead of deleting it, it changes the settings of other experiments that call the same procedure. 10. Click on the New button to create a new procedure call. A drop-down list of CAChe computational applications appears. Select the applications you wish to run.The laboratory experiments in this workbook require MOPAC calls. When you select MOPAC, a new call appears and a MOPAC settings box opens. 11. Select all the options you need. 12. Select OK. 13. Create sequential calls, as needed. For instance, if you are appending a calculation. 14. Close the procedure box. A box opens asking you to save changes. Select Yes. The experiment is altered; it appears as an experiment option in the Workspace.

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Exercises for Macintosh

22

Exercises for Macintosh

22

I. Building Basics 1. Double click on the Editor icon on your hard drive. The Editor opens, containing an empty untitled window referred to as the workspace. 2. Select Tool | Atom. Your cursor turns into the atom tool and an “Atom” menu option appears next to the Tool menu. In the Tool menu there are three tools used in building molecules: Atom - Use to add new atoms or to modify current atoms Fragment - Use to select molecule fragments or functional groups from the fragment library to be added to the workspace Select - Use to select atoms, bonds, or molecules, followed by execution of various operations. 3. Select Atom | C - sp3. This selects a sp3 hybridized carbon. The active atom is listed at the top of the atom menu.  TIP For most actions, you can click on Edit | Undo to undo your last command.

4. Click once in the workspace to deposit a single carbon (C) atom. Do not double click unless you want multiple atoms. 5. Click on the existing C atom, hold the button down and drag away (click-drag). Release the mouse button. Another C atom appears connected to the first C atom with a single bond. Add three more C atoms by doing a click-drag. You should have a string of five C atoms. 6. Select Atom | O - sp3. 7. Click-drag from the C next to the end. A red oxygen atom is connected to the C atom. 8. Select Tool | Select. Your cursor changes into an arrow (the Select tool). 9. Click in the workspace but not on any atoms or bonds. This selects all atoms and bonds in a molecule. 10. Select Beautify | Comprehensive. If the skeleton structure was built correctly, the correct number of hydrogen atoms are present and the angles are proper for sp3 hybridization.

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Exercises for Macintosh

The Beautify menu has the following correction abilities: Valence - Adds hydrogens to make the correct number of total bonds. For a neutral carbon, that number is four; for a neutral oxygen it is two; a neutral nitrogen three and a positively charged nitrogen is four. Configuration - Changes the hybridization to match the number and type of bond. For example, an atom with four attachments or electron pairs is sp3, with three attachments is sp2 and with two is sp. Rings - Attempts to give ring structures the proper shape. 11. Click File | Save. Save the molecule with the name “2-pentanol” in the appropriate location.

II. Viewing the Structure Open the file “2-pentanol” from Part I in the Editor. Translate, Rotate, and Zoom 1. Change the position of the molecule by translating, rotating, and zooming. Experiment with each of these three modes. Translate: Press the Command () key and Option key together. The cursor appears as a hand. Click and drag the mouse to move the molecule around on the screen. Rotate: Press the Command () key and Shift key together. In the window there is a circle around the molecule and your cursor is an arrow. Click and drag your cursor to rotate the molecule. Movement inside the circle produces rotation around the X and Y axes while movement outside the circle allows rotation around the Z axis. Zoom: Press the Command () key and Control key together. The cursor appears as a magnifying glass. Click and drag the magnifying glass up or down to zoom in or out on the molecule. Several keys are very useful for repositioning the atom: Press f to center and scale the molecule to fit the window. If only one atom is selected, the structure is centered around the selected atom but no scaling is done. Press i to return the molecule to the initial scale and orientation. 2. Enter the Select tool mode.

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3. Select View | Atom Shape. The View Atom Shape dialog box opens. The options in the View Atom Shape box allow you to change the way the atoms and bonds are displayed.

4. Click in the circle next to Element and Charge. The circle fills in black; this means the option is selected. Click OK. The element letter and charge appear on each atom. Viewing with labels enables easy inspection of charges. On the other hand the structures are more suitable for formal reports without the labels. 5. Select View | Atom Shape. Locate the Scale: box. The default view is usually scaled to 0.2 times the van der Waals radius. To view the atoms at their true size, set this number to be 1.0. This mode is known as the spacefilling view. Experiment with the different view options.

Scale = 0.2

Scale = 1.0

6. Return the molecule to 0.2 atom scaling before continuing with other exercises.

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Exercises for Macintosh

III. Modifying structures Begin with the “2-pentanol” file from Exercise I, and change the structure to: O CH 3 CH2CH 2 CCH3

1. Hold down the Command key and click on the carbon (C)-oxygen (O) bond using the Select tool. A pop-up menu appears. Select Double and release the mouse button. The C-O bond is now double. The sp3 hybridization is wrong for atoms with double bonds.

2. Hold down the Command key and click on the carbon atom connected to the O atom. A pop-up menu appears. Select sp2 - trigonal plane and release mouse button. The carbon bond is now sp2.

 NOTE In this case Beautify would have corrected the hybridization for us but this exercise was intended to show how to change the hybridization.

3. Repeat this process for the oxygen atom and set it also for sp2. 4. Select Beautify | Comprehensive. 5. Save this structure. You will use it later in the tutorial.

IV. Further modifications In this section we will use several methods to add or change atoms. These methods are generally interchangeable. Start with the structure “2-pentanol” and modify it in the following manner: 1. Select Tool | Atom. 2. Select Atom | Periodic Table… A Periodic Table opens in a dialog box.

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3. Click on the element bromine (Br) to select it. Look at the Charge: box, make sure that the variable is 0 indicating a neutral atom. Look at the Config: box and make sure the hybridzation is sp3. 4. Click OK to return to the workspace. The atom tool is programmed to drop a Br atom wherever you click. 5. Hold down the Command key and click on the hydrogen (H) atom to replace it with a Br atom. Shortcut: With the Atom tool hold down the Option key and click on a H atom you want to replace. The periodic table appears. Click on Br and then OK. When you return the atom will have been replaced by the Br. 6. Replace the neutral O atom with a positively charged O. With the Atom Tool, hold down the Option key and click on the O atom. The periodic table appears with O selected. Change the charge to +1 and click OK. The O in the molecule is +1. 7. Select Beautify | Comprehensive. The missing H is added and the bond distances and angle are corrected.

8. Select in order, the H atom connected to the O atom, followed by the O atom and then the C atom attatched to the O. 9. Select Adjust | Bond Angle. A Bond Angle dialog box opens, displaying the bond angle in degrees. You can label, record or adjust the angle. In this case, you will label the angle. Select Define Geometry Label, and then Unlock Geometry. Unlock geometry allows the angle to change as you modify the structure. Click Done. The label appears on the bond angle. In the same manner, you can label the atom distance by selecting two bonded atoms and select Adjust | Atom Distance. 10. Select File | Save as. The Save as command leaves the last saved version of the file intact and saves the current molecule as a different file. Name the file “modifications.”

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Exercises for Macintosh

V. Using the Fragment Library Build:

 NOTE The Fragment Library is a collection of common compounds, ions, functional groups, etc. that you can insert into your Editor document.

NO 2

1. Select File | New to open a new Editor document. 2. Select Tool | Fragment to retrieve the Fragment tool. 3. Select Fragment | Fragment Library…A box appears with two columns: categories and fragments. 4. Click on Cyclic in the Categories column. A list of Fragments appear in the Fragments column. Select cyclopentane. Click OK.

5. Click once in the workspace to deposit a cyclopentane fragment into your document.  TIP To rotate the molecule, press the Command key and the Shift key. At the same time hold down the mouse button and move the cursor.

6. Rotate the molecule so you can see all the C–C bonds. 7. Change Two C–C single bonds to C=C double bonds. With the Select tool, press the Command key and click on the bond you want to change. A pop-up menu appears. Select Double. Repeat for other double bond. 8. Select Beautify | Comprehensive. 9. Retrieve the Fragment tool. 10. Select Fragment | Fragment Library…. Select Functional groups from the Categories list. Find the nitro group in the Fragments list and highlight it. Click OK. 11. Click in the workspace to the side of the ring to deposit the nitro group. 12. Return to the Select tool. 13. Select one of the double bonded C atoms adjacent to the CH2, hold down the Shift key and click (shift-click) on the nitrogen atom. Both atoms are selected.

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14.Select Edit | Connect atoms. This command creates a bond between the selected atoms. 15.Click in the workspace but not on any atoms or bonds. All atoms are selected. 16.Select Beautify | Comprehensive. 17.Save the molecule as “nitrocyclo” in the appropriate folder.

VI. Computing Properties Molecular Mechanics

 NOTE You can also open Mechanics directly from your hard drive and open your molecule (File | Open) in Mechanics.

Molecular Mechanics is a computational application that treats molecules like balls connected by springs. Optimizations depend on the bond types and atom hybridizations. Since simple classical physics is used for the optimization no information about electronic properties or reactivity is determined. 1. Open the molecule “nitrocyclo” in the Editor. 2. Select Applications | Mechanics. This command transfers the open molecule into Mechanics. The Mechanics default setting is Optimize Structure. Click Run.

A calculation window appears and information about the progress of the optimization scrolls in the window. When the calculation ends, the window displays the amounts of each type of steric strain and the overall steric energy.

CAChe Workbook

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Exercises for Macintosh

.

3. Select Applications | Editor to return to the Editor. The molecule is open in the Editor. MOPAC  NOTE You can also open MOPAC directly from your hard drive and open your molecule (File | Open).

22-8

If you want information on the electronic properties of a molecule, use an application that uses a quantum mechanical approach. MOPAC is such a program and you can use it to find properties such as heats of formation, orbital energies and shapes, and the distribution of electrons. 1. Select Applications | MOPAC. This command sends your molecule from the Editor and opens it in MOPAC.

CAChe Workbook

The default setting is to Optimize the structure. Many experiments require calculations other than an optimization. Click on the menus to view a list of available options. Here is a list of menus you should become familiar with: ❏ Calculation type: There are a number of options to choose from. Some

common calculations types include: optimize geometry (optimizes the geometry of the molecule), optimized search (creates an energy map), and vibrational spectrum (FORCE) (generates IR spectrum). In this particular exercise, select Optimize geometry. ❏ Multiplicity: Some molecules require multiplicities other than singlet.

The CAChe experiments from this manual will specify when a different multiplicity is needed. For this exercise, leave the multiplicity as Singlet. ❏ Parameters: Some experiments give better results with one parameter

over another. Most experiments specify a parameter. If it does not specify a parameter, use the default setting. For this experiment use PM3. ❏ Details: When you click on Details a separate dialog box opens. This

box gives you more specific options regarding your calculation. The experiments from this workbook will specify which options you should select. If it does not specify options, use the defaults. For this exercise, use the default settings. Click Done to return to the MOPAC window. 2. Click Run. A separate calculation window opens, with MOPAC calculations scrolling through it. When the calculations end, MOPAC reports a heat of formation. Other properties are also calculated and stored in the molecule file. 3. Select Applications | Editor. This command opens your molecule “nitrocyclo” in the Editor.

CAChe Workbook

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Exercises for Macintosh

Tabulator Now that we have electronic information, we can compose pictures of the molecule surface and individual molecular orbitals (MOs) using the Tabulator application. 1. Select Applications | Tabulator. This command sends the open Editor document (“nitrocyclo”) to the Tabulator.

 NOTE A warning message may pop up when you try to run the density calculation telling you that it will write over output files. Click OK and continue with the calculation.

Default settings are set to evaluate six of the molecular orbitals. Click Run.The program finishes quickly and saves surface descriptions of the MOs. MO files are saved in the same location as the original molecule and with the same name as the molecule only with the endings MO1, MO2, MO3, etc. As a second surface example:

 NOTE If you double click on a molecule icon the molecule automatically opens in the Editor. Selecting Applications | Visualizer closes the Editor and opens your molecule in the Visualizer.

2. Select Evaluate isosurface(s) for: Electron Density. 3. Select to Color by: Frontier Density. Click in the circle next to electrophilic. The circle fills in black, indicating that it is selected. Click Run. The surface file is saved in the same location as your molecule. 4. Select Application | Visualizer. This command opens your molecule in the Visualizer.

VII. Visualizing Properties  NOTE Only one graphical display application can be open at once; you can not run the Editor and Visualizer simultaneously.

22-10

We will now look at some of the properties that we calculated in MOPAC and evaluated in the Tabulator. If you are not already in the Visualizer, open this application and open the molecule “nitrocyclo.” 1. Select File | Open Surface. A dialog box opens containing the folder where your molecular orbital files are stored.

CAChe Workbook

2. Locate the surface with the ending .EFonD and select it. Click Open. Your molecule is displayed with a surface colored to show the areas of maximum electrophilic reactivity. Red areas indicate where electrophiles (H+, NO2+, Br+...) have the highest reactivity. 3. Select File | Close Surface. A dialog box opens. Select the .EFonD surface and click Close. 4. Select File | Open surface.

Highest Occupied MO for nitrocyclopentadiene

5. Locate the surface with the ending .MO21 and select it. Click Open. You are viewing the highest occupied molecular orbital. It is a π-orbital as indicated by the maximum electron density above and below the plane of the atoms.

VIII. Energy Maps A change in a molecule’s potential energy occurs whenever a bond angle or distance is altered. If this energy is plotted against the changing property, we get a potential energy coordinate or map. If the energy change during a reaction is plotted against the physical change taking place, we get a potential energy map the we usually refer to as a reaction coordinate. Find the energy change as we rotate the dihedral angle. CH 3CH 2

O C

HH

C CH3

1. Open the file “2-pentanol” from exercises I, II, and III. 2. Select the O atom. Shift-click on the C atom attached to the O. Shift-click on the next two C atoms with two H atoms bonded to it (see diagram to the right). All four atoms are selected.

4 CH 3 CH2

3 C

HH

2 C

1 O CH 3

3. Select Adjust | Dihedral Angle. 4. Click Define Geometry Label and Search between -180 and +180 using 24 steps. 5. Click Done. A search label reading 0.00˚ appears on the molecule.

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Exercises for Macintosh

We can now calculate the energy for each of the angles specified by the label. 6. Select Applications | MOPAC. In the MOPAC window, select the Calculation type: Optimized Search. A dialog box opens. Click in the circle next to Reaction Coordinate. Click Done to return to the MOPAC window. 7. Click Run. When the calculation is done it save the map file in the same location as your molecule with the same name as the molecule only with the ending .map. 8. Select Applications | Visualizer. 9. Open the .Map file in the Visualizer. 10. Click on the reaction coordinate line in the left window and observe the corresponding changes in the molecule. Enlarge and rotate so you can see the changes. In some experiments you may need to adjust the axes. To do this, select View | Define Map. The Define Map box opens. Click on Set Attributes for the axis you want to change. Change the values as needed.

IX. ProjectLeader ProjectLeader can automate the calculation process. This application is especially useful when the same calculation must be done on numerous molecules. 1. Build the four molecules below. H

H H

H

H

H

H

H H H

H H

Cl

H

H H

H

H

H

H H

H

H

H Br

H

H

H H

H H

H

H

H

H

H Cl

H

H H

H

H

H

H

H H H Br

The quickest way to do this is to start with a cyclohexane fragment (Tool | Fragment, followed by Fragment | cyclohexane-chair).

2. Replace an equatorial H atom with a Cl atom. Beautify the structure and save the molecule as “equatCl.” 3. Select the carbon atom with the Cl attached and then select Adjust | Invert Chiral. 4. Beautify the structure and select File | Save as. Save the document as “axial Cl.”

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5. Replace the Cl atom with a Br atom. Beautify the structure and save as “axialBr.”  TIP To convert an equatorial halogen to axial halogen, click on the carbon atom with the halogen, followed by Adjust | Invert Chiral.

6. Repeat step 3 only using Br. Beautify the structure and save as “equatBr. ProjectLeader 7. Open the ProjectLeader application on your hard drive. 8. Double-click in the first cell below the Chemical Sample heading. A dialog box containing a list of file locations opens. Browse to the location of your files. Select the “equatCl” file and click Add. 9. Repeat this operation in the next cell below and add the file “equatBr.” 10. Double-click in the top cell in the second column (column B). The Select Column Header box opens; there are three columns displayed. In the dialog box select Kind: Property of | Chemical sample, Property: heat of formation, and Using: standard procedure. Click OK. 11. Double-click in the top cell in the third column (column C). In the Select Column Header dialog box select the following options: Kind: Chemical sample, Create using: Editor, View using: Editor. Click OK. 12. Double-click in the first cell below the new Chemical Sample heading in column C. 13. Select the “axialCl file” and click Add. 14. Repeat this operation in the next cell below and add the file “axialBr.” 15. Double-click in the top cell in the fourth column (column D). In the Select Column Header dialog box select the following options: Kind: Property of | Chemical sample, Property: heat of formation, Using: standard procedure. 16. Click OK. A dialog box opens asking you to select the source of the energy calculation. Select Column C. We now have a project to calculate the heats of formation for four molecules. We want to find the difference in the energies of molecules with equatorial halogens to those with axial halogens. To do this, we need to create a simple formula. 1. Double-click in the top cell in fifth column (column E). In the Select Column Header dialog box select the following options: Kind: Analysis | Equation, Analysis type: Algebraic.

CAChe Workbook

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Exercises for Macintosh

2. Click OK. An Equation Builder dialog box opens. Enter “Change=D-B” Click OK. The completed project should look like the following:

3. Select the empty cells in column B and then Evaluate | Cells. 4. Repeat for the empty cells in column D. You do not need to wait for the first group to finish before selecting the second group. When all the calculations are finished, select the empty cells in column E and evaluate. The final project should look as below:

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Index

Index A Acidities 12-9 Acids binary 12-11 Activation energy (Ea) 2-17, 6-19 Adjust menu 21-7, 22-5 Amide bonds 9-15 Aromatic substitution reaction 6-19 Arrhenius equation 2-18, 9-19 Atom attributes 21-5 Atom labels 21-5, 22-3 Atom shape options 22-2 Atom tool 21-3, 22-1 Atomic orbital (AO) 17-43 Axes adjust 21-12, 22-11 Axis of rotation (Cn) 14-21

Center molecule 21-4, 22-2 Character table 15-27 Charge change 21-6, 22-4 Chiral chelating ligands 20-57 Chirality 20-57 invert 21-12, 22-12 Classical computational method 1-2 Close packing layers 13-20 sites 13-13 Conformations anti 5-10 Conjugated system 3-29 Coordination compounds 20-57 Crystal lattice 13-13 boundaries 13-18 NaCl 13-17, 13-20 Cubic close packing (ccp) 13-14, 13-18

lone pair 10-1, 11-5 low spin 18-47 Electrophile 6-20 Electrophilic substitution reaction 6-19 Electrophilic susceptibility 21-10, 22-9 Elimination 5-8 Energetic barrier 9-15 Energy map 2-20 generate 21-11, 22-10 Enthalpies of formation 12-9 Equation define 21-13, 22-12 Equilibrium 5-13 Evelyn effect 5-7 Experiments edit 21-15

D

Face centered cubic 13-15 Fragment library 21-7, 22-5 Fragment tool 22-1

B Bases 12-9 Beautify how to 21-3, 22-1 Beautify menu 21-4, 22-2 Bomb calorimetry 7-2 Bond angle 10-1, 10-3 distance 10-1, 12-11 Bond label angle 21-7, 22-5 distance 21-7, 22-5 Bond polarity 10-1 Bond type change 21-6, 22-4

C Calculation type 22-8 Calorimetry bomb 7-2 Carbocation 6-19

CAChe Workbook

Dehydration 5-7 Delocalized π-bonds 3-29, 7-1 Details change 22-8 Diatomic molecules 17-41, 17-42 Dihedral angle 21-11, 22-10 Dipole moment 10-1, 10-3 Distillation 5-13 d-orbital 11-6, 18-45, 19-52

E E1 5-7 E2 5-7 Effective nuclear charge 17-43 Electronegativity 10-1, 10-3, 17-43 Electrons bond pair 11-5

F

G Gas chromatography 5-13, 5-16 Gas phase proton affinity 12-9 Geometry 1-1, 11-5 Geometry label 21-11, 22-10 Group theory 15-27

H Heat of formation (∆Hf°) 7-1 Heat of reaction (∆Hrx) 6-19, 6-20 Heats of combustion 7-2 Hexagonal close packing (hcp) 13-13, 13-14 HOMO 18-47, 19-52, 19-53 Hückel 9-21

I-1

Index

Hybridization 9-16 change 21-3, 22-4

MOPAC 21-8, 22-8 Morse potential 8-7 Multiplicity change 21-15, 22-8

I Identity (E) 14-21 Improper rotation or rotation-reflection (Sn) 14-22 Improper torsion 9-17 Infrared spectra (IR) 15-27 Interatomic potential energy curve 8-7 Internal rotation 9-16 Inversion (i) 14-24 Ionic compound 13-14 Irreducible representation 15-28, 15-29

K

N Nitration 6-19 Nuclear magnetic resonance (NMR) 9-15, 9-16 Nucleophilic substitution reaction 2-17

O Octahedral 11-6, 18-45 Octahedral hole 13-14, 13-19 Octet rule 11-5 Optimize geometry 21-8, 22-7

Kinetics 2-17

P L Lewis dot structures 1-1 Ligand field splitting energy (∆o) 18-46, 19-52 Ligand field strength 19-51 Linear (molecule) 11-6 Linear combination of atomic orbitals (LCAO) 16-35 LUMO 18-47, 19-52, 19-53

M Metal complex 20-57 Molecular Mechanics 21-8, 22-7 Molecular orbital (MO) 11-6, 16-35, 17-41, 17-43, 18-45 antibonding 16-35 bonding 16-35 nonbonding 16-35, 18-45 tabulate 21-10, 22-9 theory 16-35 view 21-10, 22-9

I-2

Parameters change 21-9, 22-8 Partial charge 6-19, 10-3, 12-9, 12-11 π-bonding 18-45, 19-53 Peptide bond 9-16 Periodic table 21-6, 22-4 Plane of symmetry or reflection (σ) 14-22 Point group 14-21, 15-29 C2v 15-27, 15-33 C3v 15-33 Polarity 10-1 Potential energy surface 2-20 Procedure Editor 21-15 ProjectLeader 21-12, 22-11 Property class 21-9

Q Quantum computational method 1-2

R Raman spectroscopy 15-27 Rate constant 2-18 of reaction 2-18 Reaction coordinate 2-23 generate 21-11, 22-10 Rearrangement 5-9 Reducible representation 15-28 Reflect molecule mirror plane 14-22 Resonance stabilization 7-1 Rotate 21-4, 22-2 Rotational barrier 9-15, 9-16

S σ-bonding 18-45, 19-52 Schrödinger equation 1-2 Second period elements 17-41, 17-43 Select tool 21-3, 22-1 Semi-empirical calculations 1-2 SN2 2-23 Spectrochemical series 19-52, 19-54 Stereoselectivity 20-57 Style bar 21-1 Substitution aromatic 6-19 electrophilic 6-19 nucleophilic 2-17 Symmetry 15-27, 15-29, 15-30 Symmetry operations 14-21

T Tabulator 22-9 Tetrahedral 11-6 Tetrahedral hole 13-14, 13-19 Thermodynamics 7-5 Tool menu 22-1 Tool palette 21-1 Toolbar 21-1 Transition metal complex 18-45 Transition state 6-19

CAChe Workbook

Translate 21-4, 22-2 Trigonal bipyramidal 11-6, 15-33 Trigonal planar 11-6

U Ultraviolet (UV) spectra 3-29 Ultraviolet light 3-29 User interface Windows 21-1

V van der Waals scale 21-5, 22-3 Vibrational spectra 8-7 Vibrational spectroscopy 8-8 VSEPR 1-1, 11-5

W Windows user interface 21-1

Z Zaitzev’s rule 5-7 Zoom 21-4, 22-2

CAChe Workbook

I-3

Index

I-4

CAChe Workbook

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