7# =Y><9"Xzzz "4xzj *ZChemistry 142 Experiment III Enthalpy of Formation of Methyl tert-Butyl Ether PRE-LAB ASSIGNMENT Reading: Before coming to your discussion section, read: 1. Sections 9.2, 12.3, and 12.4 in Olmstead and Williams 2. Experiment VIII, Molecular Modeling and Structure, Part 2 from CH141. 2. The remainder of this experiment in this manual. Purpose: Calculate the Hf of methyl tert-butyl ether using molecular mechanics. INTRODUCTION Methyl tert-butyl ether (MTBE), Figure 1a, is added to gasoline to enhance the octane rating. This ether is now being used in urban areas as a replacement for benzene to decrease air pollution. The decrease in air pollution is in part because MTBE is less volatile than benzene, which decreases the total volatile organic hydrocarbon emission from automobiles. Benzene is also toxic.While MTBE is less toxic and less volatile than benzene, it has the difficulty of being more water soluble. The fate of organic molecules in the environment is determined in part by their solubility in water. For example, a leaking underground gasoline tank introduces organics into surface and ground water. The long term damage done to the environment is determined by the solubility of the organic contaminants in the water1. Soluble organics can travel long distances and allow the spread of contamination over wide areas. Less soluble organics quickly evaporate and cause less of a problem. Minimizing environmental problems often involves such compromises. In the case of MTBE the compromise is between volatility and water solubility. In finding compounds that minimize environmental risks, many candidates must be screened for their properties. Chemical Abstracts Service now has registered over 10 million substances. Screening this many compounds for efficacy and environmental risk is a tremendous problem. The time and cost of doing the necessary laboratory experiments to determine the properties of 10 million compounds is impossible. Instead we must often rely on computer calculations to fill in the missing information. The enthalpy of formation of MTBE is not available in standard tabulations. However, the enthalpy of formation is necessary to determine the enthalpy of combustion for MTBE, which is one of the most important properties of a gasoline additive. In this experiment we will use molecular mechanics to estimate the enthalpy of formation of MTBE. When using a computational method to predict a property, it is best to have tried the method on known compounds first to determine the uncertainty of the calculation. The enthalpy of methyl n-butyl ether, Figure 1b, is tabulated in Lange's Handbook2, so methyl n-butyl ether will make a good test case.  a. methyl tert-butyl ether b. methyl n-butyl ether Figure 1. Two isomers of butyl methyl ether. Enthalpy of Formation The internal energy of formation of a compound in the gas phase is the sum of the bond energy, the steric energy, the vibrational energy, and the kinetic energy of the molecule as a whole. The internal energy is then converted to the enthalpy of formation. Since H=E+(PV), and PV=nRT for an ideal gas, we add RT to convert from internal energy to enthalpy. The enthalpy of formation is then approximated as3: Hf = bond energy + steric energy + vibrational energy + kinetic energy + RT (1) Each of these energies is discussed below. Remember that we introduced the concept of steric energy in the laboratory on hydrogen peroxide, first semester. Bond Energy You are familiar with bond energy calculations from first semester General Chemistry. The energy of a molecule is assumed to be an additive function of the energy of individual bonds. The bond energy calculations in molecular mechanics are done slightly differently than the method you used last semester, using bond increments. Again the bond energies are assumed to be additive. However, the contributions are taken not only for each bond, but increments are added for certain structures, such as different carbon linkages. For example, the bond energy calculation for acetaldehyde from the MM2 program is given below, with energies in kcal. # Bond or Structure Each Total 3 C-H ALIPHATIC -3.205 -9.615 1 C=O -25.00 -25.000 1 C-H ALDEHYDE -2.500 -2.500 1 C-C SP3-SP2 C=O -3.000 -3.000 1 ME-CARBONYL -2.000 -2.000 bond energy = -42.115 kcal/mol   Acetaldehyde The bond energy is -42.115 kcal/mol or -176.2 kJ/mol. Steric Energy Molecular mechanics calculates the steric energy of a molecule. The steric energy is the energy due to the geometry or conformation of a molecule. Energy is minimized in nature, and the conformation of a molecule that is favored is the lowest energy conformation. The steric energy of a molecule includes the stretching or compressing of bonds beyond their equilibrium lengths, the bending of bond angles beyond their equilibrium angles, the dihedral effects of twisting about single bonds, the Lennard-Jones attractions or repulsions of atoms that come close together, and the electrostatic interactions between partial charges in a molecule due to polar bonds: steric energy = bond stretch + angle bend + stretch-bend + dihedral + Lennard-Jones + electrostatic (2) The bond stretch energy represents the energy required to stretch or compress a bond, Figure 2. The angle bend energy is the energy required to bend a bond from its equilibrium angle, Figure 3.   Figure 2. Bond Stretching Figure 3. Angle Bending The stretch-bend interaction energy takes into account the observation that when a bond is bent, the two associated equilibrium bond lengths increase (Figure 4). When intramolecular forces stretch, compress, or bend a bond from its equilibrium length and angle, the molecule resists these changes. When the bonds cannot relax back to their equilibrium positions, the steric energy of the entire molecule is increased. Figure 4. Stretch-Bend InteractionDihedral Energy: Two possible conformations of ethane are shown in Figure 5. The eclipsed conformer is higher in energy than the staggered form. The increase in dihedral energy of the eclipsed form is caused by the repulsion of the electrons in the C-H bonds on different ends of the molecule. In the staggered form, the bonds are further apart thus reducing the electron-electron repulsion between the bonds.  Figure 5. Eclipsed and staggered ethane.Lennard-Jones or Van der Waal's Energy: When two atoms are far apart, an attraction is felt. When two atoms are very close together, a strong repulsion is present. Attractions lower the energy of a molecule, while repulsions raise the energy of a molecule. The Van der Waal's interaction is commonly modeled by the Lennard-Jones equation. We often use the terms Van der Waal's and Lennard-Jones interchangeably. Electrostatic Energy: Atoms in molecules have partial electric charges, which are caused by the polarity of the bond to the atom. Like-partial charges repel and opposite-partial charges attract. These attractions and repulsions are called electrostatic interactions. Different computer programs use different combinations of these six terms. For example, the QUANTA/CHARMm program doesn't include the stretch-bend term. For this exercise we will use the MM2 program, which does include the stretch-bend term. Vibrational Energy We have not yet considered molecular vibrations. In principle, every vibration contributes to the enthalpy. In practice the contributions are often small so they can be ignored. A special case of molecular vibrations are internal rotations. Internal rotations around single bonds are often quite easy, so that internal rotations do contribute to the enthalpy of formation. The contribution of the internal rotations for methyl groups is included automatically in the bond energy calculation discussed above. So methyl group contributions are included. Any other internal rotations in the molecule are usually ignored, as we will do in this lab. Kinetic Energy Kinetic energy terms must be added to account for the energy of translation and rotation of the molecule. The energy of translation (x, y, z motion of the center of mass of the molecule ) is 3/2RT. The rotational energy of a non-linear molecule is also 3/2RT ( 1/2RT for each rotational axis). The total kinetic energy contribution for a nonlinear molecule is 3RT. Summary In summary then Equation 1 is given as: Hf = bond energy + steric energy + vibrational energy + kinetic energy + RT (1) Hf = bond energy + steric energy + 0 + 3RT + RT (3) or at 298.2K: Hf = bond energy + steric energy + 2.4 kcal/mol (4) Methyl n-Butyl Ether We will use methyl n-butyl ether as a test case of the quality of our MM2 calculation. The steric energy from MM2 is 4.2939 kcal/mol. The enthalpy of formation (heat of formation) is -65.72 kcal/mol. In kJ/mol, -65.72 kcal/mol x 4.184 J/cal = -278.0 kJ/mol. The literature value2 of the enthalpy of formation of gaseous methyl n-butyl ether is -264 kJ/mol. The MM2 calculated value of -278 kJ/mol is 5% low, which is a quite respectable margin of error. We can now expect similar accuracy from our calculations Procedure We will use the "QUANTA" program on our Silicon Graphics workstations, to produce our model of MTBE, and the program MM2 to calculate the enthalpy of formation. Energy minimization using CHARMm, like we did first semester, and MM2 are very similar. The force fields are a little different, but the calculations do the same thing. A. Input a rough structure for MTBE. Using the following procedure you will construct a computer model of the MTBE molecule. 1. Pull down the Applications menu, slide right on "Builders," and choose "2D Sketcher." This process opens the ChemNote application. 2. Click on the single bond icon in the bonds palette. The single bond is the horizontal line in the middle left-hand portion of the screen. 3. Position the cursor near the middle of the screen. Hold down the left mouse button and drag the bond a short ways to the right. The default atom type is carbon, therefore the single bond is assumed to have a carbon atom at each end. Now continue to drag single bonds to form the skeleton of MTBE as shown at right. We must now change one carbon to an oxygen. 4. Click on the oxygen icon in the atoms palette in the upper left portion of the screen. 5. Click the left button on the mouse with the cursor over the point where the oxygen is to be. ChemNote is picky about where you click, if an oxygen atom doesn't appear, try moving the mouse and clicking the left mouse button again. The molecule should now appear as show at right. Don't worry about the H atoms on the carbons, ChemNote will add them for you. If your molecule does  not look like that above, pull down the File menu and choose "New", answer "No" to "Save changes first?", and start over. 6. Next save your molecule as a file and return to QUANTA by pulling down the File menu and choosing "Return to Molecular Modeling." The system responds by asking if you wish to "Save changes first?" Click on "Yes." The File Librarian dialog is displayed. First change to the small_molecules/ folder by clicking on small_molecules in the file list. If you can't see the small_molecules/ entry, use the scroll bar to the right of the file list by clicking in the dark blue area beneath the red scroll bar. Now type in a file name for your structure. File names should not contain any spaces or punctuation. For example, MTBE followed by your initials would be a good file name, but remember not to use spaces. 7. QUANTA then calculates the sum of the partial charges on the atoms in your molecule. The sum should be zero, but is often not because the program just uses a table of approximate values for each atom. The actual desired charge on the molecule is entered in the blue edit field; for MTBE the total charge should be zero. Any difference between the calculated charge and the desired charge is smoothed over the atoms in the molecule. Choose the "CT, CH1E,CH2E, CH3E, C5R, C6R, C5RE, C6RE, and HA types" smoothing option and choose OK. (The smoothing you chose is over all carbon atoms and non-polar hydrogens.) 8. If a molecule was in the QUANTA window when you started, you will be asked how you want to display your molecule. Choose "Use the new molecule ____ only." B. Minimize the structure (i.e. find the lowest energy conformation) and calculate the enthalpy of formation using MM2. 1. Pull down the Calculate menu, and choose MM2. 2. Choose "Setup calculation..." from the new MM2 palette. Make sure the following two options are highlighted and only these two: Use MM2 Dipoles Do optimize 3. Click "Finish" to return to the main MM2 palette. Choose "Run and Wait" to do the MM2 calculation. The File Manager dialog box will appear. Type in the name for your MM2 files and click "Save." You can use the same file name as before. 4. The MM2 results will be listed in the "Text Port" in the lower left corner of the screen. Record the final steric energy, and the enthalpy (heat) of formation. Use the following table in your lab book. The data for n-butyl methyl ether is taken from Table II. (The "bond" term listed in the Text Port is the bond stretch contribution to the steric energy.) 6. When you are finished, you must choose "Finish" in the MM2 palette before you can do anything else in QUANTA. Report 1. List the steric energy and enthalpy of formation of MTBE. Convert your results to kJ/mol ( 1 cal = 4.184 kJ ). 2. Compare the steric energy of methyl n-butyl ether and methyl tert-butyl ether. tert-Butyl compounds should have higher steric energy than n-butyl because of the "bulkiness" of the tert-butyl group. That is, the close proximity of the atoms in tert-butyl groups makes it harder for the atoms to keep out of each other's way. Is this true? 3. Since MTBE is used as a gasoline additive, its combustion should release considerable energy. The additive shouldn't give a penalty in the amount of energy available from the gasoline. Use the enthalpy of formation of MTBE to calculate the enthalpy of combustion of MTBE. 4. The enthalpy of combustion of a few of the compounds found in gasoline is given in the table below. Compare the enthalpy of combustion of MTBE from question 3 with these values. ( 2,2,4-trimethylpentane is called iso-octane. The octane rating of iso-octane is set to 100, while the octane rating of the straight chain isomer, n-octane, is set to 0. The octane rating of benzene is 106.) Table. Enthalpy of Combustion for Some Compounds Found in Gasoline.4 CompoundFormulaHcomb ( kJ/mol) n-pentaneC5H12-3532.4 benzeneC6H6-3299.6 n-hexaneC6H14-4191.1 n-heptaneC7H16-4849.3 2,2,4-trimethylpentaneC8H18-5491.8 n-octaneC8H18-5507.2 Literature Cited 1. G. A. Robbins, S. Wang, J. D. Stuart, Anal.Chem.. 1993, 65, 3113. 2. J. A. Dean, Lange's Handbook of Chemistry, 14ed., McGraw-Hill, New York, NY. 3.This formula also assumes that there is only one low energy conformation of the molecule. If there are several low energy conformations, each must be accounted for in Equation 1. 4. D. R. Lide, Ed. CRC Handbook of Chemistry and Physics, 71st. Ed., CRC Press, Boca Raton, FL. D81-85. 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710 l cp f np 1190 690 M 1190 710 l 710 710 l 700 700 l 710 690 l cp f np 1591 175 M 1609 185 l 1369 601 l 1351 591 l cp f gr count origstk sub{P}rp end chemsave restore ,  Helvetica .+='Od CHMDSTRGEU  x (XP6dd@  O `    d HelveticaOverseers Graphs from DWKWDBNMSWD=$bέ$vJh=AMU]no{| & 9 b c    Ag EF#$pqtuUVIq """A @x @}, @xd @hL @G @=` @ J"A"B""""##4$N$O%6%7%C&&'#'/))+p+q++,>,B1232H2R4~4445k5l5566777V7Z::::::::::::;;;;;;;;!;F;G;H;J;a;b;c;e;s;;;;;;;;;< @ @@    Q<==9=T=U=X=Y @ @@NOPcdmn TU      @ABh?@DG\]^@Aprstȵ $ Ph$@ 8Q 8  $ $ $ $K$  $ $ $ >tvwxRUWHI """"<"="""""### #5%7%8%9%C&&''''(&('誤蜔$ >$ >$ >$ >$$ $ $ $ $ d   a  $ P$@h0('))))))+p+r+s++..111126272i2j22333445k5l555556D6_7ܾιyyqqi$ $ $ $ H$ H$ H$ H$ H$ H$ H$ $ > $ >$ >B$ > P$@D >&789~:S:T:::::::::::::;;;;;;";*;+;E;K;S;T;`;f;n;o;p;q;r;s;;;<<=8=9=V=W=XԸԕԇԇԇԇԇ낂}xx$ P  pP" p@@@ P& p@@@   t $$ $ $ /=X=Y$ cBoston 10 Point,Flush left,Geneva 10 Point,Geneva 12 Point,Justified,Point,NC12J,Geneva 10 PointTimesGen10Gen12NWCEN12?