CHEM 350, Fall 2008 Principles of Organic Chemistry I Lab Prof. T. Nalli, WSU
Expt #1 - Molecular Modeling of Alkanes
Assigned Reading/Viewing - Lab Manual, #1, Expt 18a. Hyperchem installation instructions. Hyperchem help tutorials noted on page 3.
Overview
Molecular models can be very helpful for the 3-D visualization of organic molecules. The models can be manipulated (for example, bonds can be rotated) in order to mimic the types of dynamic processes the actual molecules undergo.
Computer molecular modeling programs are not as helpful with the visualization of molecules because the display is two dimensional. However, these programs are capable of predicting quantitative information about the molecule, for example the bond angles, total energy, and distances between atoms.
In this lab you will use molecular models in conjunction with Hyperchem molecular modeling software to discover and learn about some of the most important concepts that allow us to predict the most stable conformation(s) of an organic molecule.
Pre-lab Assignment
Install Hyperchem on your laptop using the instructions available at http://course1.winona.edu/tnalli/f08/hyperchem%20install.html.
Some Important Definitions
Conformation - A particular molecular structure that is arrived at through single bond rotation. Different conformations of a molecule are easily interconverted by single bond rotation(s).
Conformer - A conformation of a molecule that corresponds to a potential energy minimum for the molecule.
Molecular mechanics - A computational method that allows the relative energies of different conformations of a molecule to be approximated. (Note the terms “relative” here! The energy of a structure calculated using molecular mechanics only has meaning when compared to similarly calculated energies for other conformations of the same molecule.) Molecular mechanics is based on the same basic principles that chemists use qualitatively to judge conformation stability.
Geometry Optimization – Also referred to as “Energy Minimization”. Mathematical algorithms are available that vary the bond angles, torsion angles, and bond lengths in a molecule, calculating the energy and continuing until a conformation that corresponds to an energy minimum (i.e., a conformer) is found. These algorithms, by design, try not to change the molecule in a way that increases the energy. For this reason, they are not guaranteed to find the overall lowest energy conformation of a particular structure (the “global minimum”). Read more about global versus local minima in the lab manual reading assignment.
RMS Gradient – In an energy minimization routine, the root mean square (RMS) of the derivative of the energy with respect to the Cartesian coordinates is used as a criterion of when to stop looking for a lower energy and accept the current value as representing the minimum. In theory, the RMS gradient is zero when an energy minimum has been achieved. In practice, the computer will never achieve a value of zero so we set a minimum value for the RMS gradient when we set up a geometry optimization. In simple terms, if we set the RMS gradient to a lower value then the computer will keep looking longer for a “true” minimum.
Strain – Any interaction in a structure that causes it to have a higher energy is called strain. The difference in energy between any particular conformation and the lowest energy conformer of the same molecule is a measure of the amount of strain that conformation possesses.
PROCEDURES
Record all data, observations, and structural drawings directly in the lab notebook as you do this experiment. Make all models both with the Molymod kit and on the computer in Hyperchem. Hyperchem procedures are consistently given in italics throughout this handout.
When using the Molymod kit make sure to use tetrahedral carbon atoms (the black balls with 4 holes!)
General Hyperchem Instructions: Complete “cookbook” instructions on how to use Hyperchem throughout this experiment would be very difficult to put in writing and counterproductive. You need to get a feel for how to use this program both for this lab and for future experiments. Please view all of the tutorials circled in the screenshot below menu before beginning the lab. You will find these under the Hyperchem help menu.
Hyperchem does not have “undo” capabilities. I strongly recommend saving each model first thing after you have successfully constructed it.
When using Hyperchem it will be easier if all of our models look the same. Under the “Display” menu, select Rendering and set Atom Rendering to "balls and cylinders". This will give us ball and stick models that look very much like our Molymod kit models.
Refer to the following figure as necessary to identify the Hyperchem tool icons.
Build Select Free Rotate XY Rotate Translate
Conformations of Ethane
Staggered Ethane. Construct a model of ethane, CH3-CH3. Look straight down the C-C bond and rotate it until the C-H bonds in front exactly bisect the H-C-H angles of the back carbon. You now have a model of the staggered conformation of ethane. This structure can be represented on paper in a number of ways, including wedge-dash formulas and Newman projections (see below).
In Hyperchem, select the Build tool and then click, drag, and release a short distance away in the main window. Under the Build menu select “Add H & Model build”. The resulting ethane model is already in the staggered conformation. The model can be rotated around in space much like the Molymod model by using either the free rotate tool or the XY rotate tool.
Draw structural representations (Newman and wedge/dash) of staggered ethane in your notebook.
Eclipsed Ethane. Rotate the C-C bond 1/6th of a turn (60°) so that all of the C-H bonds are lined up. You now have a model of the eclipsed conformation of ethane.
In Hyperchem you can rotate the C-C bond using the procedure shown in the “Using selection to perform an internal rotation” tutorial. Make a model of eclipsed ethane in Hyperchem using this procedure. (Hint: you will want to free rotate the molecule so that you are looking straight down the C-C bond before you do the bond rotation).
Draw structural representations (Newman and wedge/dash) of eclipsed ethane in your notebook.
Eclipsed vs Staggered Ethane. Observe the two ethane conformations carefully. In which of the two ethane conformations do the sigma electrons of the C-H bonds on one carbon come closer to the sigma electrons of the C-H bonds of the other carbon? Which conformation would you expect to be less stable, the eclipsed or the staggered? (Think of VSEPR theory in attempting to answer this question.)
Plot a graph of potential energy versus the angle between one of the C-H bonds on the front carbon and one of the C-H bonds on the back carbon (the dihedral or torsion angle). Start with the eclipsed conformation (torsion angle = 0°) and go through one full rotation (360°). Indicate on the graph where each conformation would be found.
Hyperchem will allow you to make this graph quantitative by using molecular mechanics to estimate the relative energy of each conformation. First run an energy minimization on your eclipsed ethane model. Under the Compute menu select geometry optimization. Use all of the default parameters and hit OK. Observe carefully what happens to the model and record the energy value displayed in the bottom left corner of the window.
(All energy values in Hyperchem are in units of kcal/mol. Also please note that these values are estimates and all of the digits displayed by Hyperchem are not significant. The energy results are probably only good to ± 0.1 kcal/mol)
Now redo the energy minimization but use a lower value (0.001) for the RMS gradient termination condition. Record what happens in your notebook as well as the energy obtained.
Based on what you just saw do you think it would be a good idea to run future energy minimizations with the RMS gradient set to 0.1? Discuss this with the instructor before going on.
Redetermine the energy of the eclipsed conformation using the following procedure. First lock the model in an exactly eclipsed conformation by using the select tool to select the 4 atoms that define the torsion angle (H-C-C-H). Next, under the Build menu select Constrain Bond Torsion and enter 0° (or cis). Now unselect the selected atoms by clicking with the selection tool anywhere in the main window not on the molecule. Under the Build menu select “Add H & Model build”. Finally run a geometry optimization with the RMS gradient set to 0.001. Record the results in your notebook.
Conformations of Propane
From here on it is assumed that you will record all observations and data from each stage of the experiment in your notebook! (Remember to note energy values after each geometry optimization!) Also for all future geometry optimizations set the RMS gradient to 0.001.
Staggered Propane. Remove a hydrogen from the ethane model and add a CH3 group in its place. You now have a model of propane. Rotate each of the C-C bonds so that both of these bonds are staggered. A wedge/dash formula of the model should look like the figure below.
In Hyperchem use the build tool to add a carbon (click on one of the hydrogens of your ethane model to change it to a carbon atom). Add H and Model Build and then minimize the energy as before. You should end up with the all staggered propane conformation shown above.
Draw a Newman projection that represents this conformation of propane. Represent the extra methyl group simply by "CH3". (Note - the Newman projection should look the same regardless of which C-C bond you sight down.
Eclipsed Propane. Rotate one of the C-C bonds in this model so that it is now eclipsed. It should look like the figure below.
Draw a Newman projection that shows the conformation around the eclipsed bond.
To get to the above model in Hyperchem, you can use selection to perform rotation of the C-C bond (like you did with ethane). Or more preferably, select 4 atoms to define the torsion angle around one of the C-C bonds (i.e., H-C-C-H), constrain the bond torsion to 0° (Build menu), Add H & Model Build, and then run a Geometry Optimization. (You need to unselect atoms in a molecule before geometry optimization otherwise Hyperchem will only adjust the position of the selected atoms.)
Eclipsed vs Staggered Propane. Plot a graph of energy versus torsion angle for one of the C-C bonds in propane. (Assume the other C-C bond stays staggered.) Use the energy values obtained using Hyperchem to label the scale of the y axis on the last graph (The graph should show quantitatively the relative energies of the two conformations.)
How much strain is present in eclipsed propane? In staggered propane?
Conformations of Butane
Remove a hydrogen from one of the end carbons of the propane model and add a CH3 group in its place. You now have a model of butane. Rotate each of the C-C bonds so that they are all staggered and the two end CH3 groups are opposite each other. A wedge/dash formula of the model should look like the figure below. This model represents the anti conformation of butane. We will refer to it as conformation A.
Draw a Newman projection that shows the conformation of the bond between the center two carbons (use "CH3" to represent each of the end carbons).
Now rotate the center C-C bond 60°. This is conformation B. Draw a Newman projection of this conformation.
Rotate the center bond another 60° to give conformation C. This model represents the gauche conformation of butane. Draw a Newman projection of this conformation.
Rotate the center bond another 60°. This is conformation D. Draw a Newman projection that shows the conformation of the bond between the center two carbons.
Rotate the center bond another 60° and draw a Newman projection of the resulting structure. Is this a new conformation of butane or is it the same as one of those already examined?
Rotate the center bond another 60° and draw a Newman projection of the resulting structure. Is this a new conformation of butane or is it the same as one of those already
examined?
Rotate the center bond another 60° and what do you have?
Which of the above conformations do you think is the most stable (lowest energy)? Which should be the least stable? Explain.
In Hyperchem start from scratch and make n-butane using the build tool followed by Add H & Model Build. Minimize the energy of this model as before. Make sure that you are looking at the anti conformation (A) by free rotating it so that you are looking at it from the side like in the above picture and verifying that the four carbons form a zig zag pattern. If this is not the case, start over or use Constrain Bond Torsion to set the C-C-C-C torsion angle to 180° and repeat the model build and energy minimization.
Next use selection to rotate the central C-C bond approximately 60º to get conformation B. Run a geometry optimization and note your results. Does the energy value obtained represent the relative energy of B? If not come up with a procedure to get an energy value for B.
Now make a model of gauche butane, conformation C. Run geometry optimization and record the energy. Also measure the C-C-C-C torsion angle in the minimized gauche butane. Do this by selecting the four carbon atoms in order and noting the message that occurs at bottom left in the Hyperchem window. (Four atoms bonded sequentially always defines a torsion angle)