Assignment 1: Molecular Mechanics (PART 2 25 points)

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1 Chemistry Fall 2015 Dr. Jean M. Standard September 2, 2015 Assignment 1: Molecular Mechanics (PART 2 25 points) In this assignment, you will perform some additional molecular mechanics calculations using the Avogadro software package. One of the primary objectives of this assignment is to examine in more detail some examples from the current literature. The Avogadro software package will be employed in this assignment. As before, you may access Avogadro on the Macintosh computers located in Julian Hall Room 216, or on your own personal computer. To use Avogadro on the Macs in JH 216, log in with your ULID and password. The Avogadro software package may be started by clicking on its icon in the Dock. THIS PORTION OF ASSIGNMENT 1 IS DUE WEDNESDAY, SEPTEMBER 16, PART A (13 points) Asphaltenes and the Pentane Effect In this part of the assignment, you will explore in more detail the some of the asphaltene structures discussed in the article by D. D. Li and M. L. Greenfield [Energy & Fuels, 2011, 25, ]. 1. Modeling the asphaltene core Consider the core building block of the asphaltene structure shown in Figure 1, which consists of two joined naphthalene rings. Figure 1. Core asphaltene structure a. In the article in Energy & Fuels, the "pentane effect" is discussed as a potential source of strain in some of the asphaltene structures proposed in the literature. In your own words, explain the pentane effect. You may include sketches if you feel it necessary. Include in your discussion whether or not the core section of asphaltene shown in Figure 1 would be expected to exhibit the pentane effect. b. Use Avogadro to build the core section of asphaltene. You may want to use two naphthalene fragments and join them, much in the same way that you joined two benzene fragments to form biphenyl in part 1 of Assignment 1.

2 2 Minimize the energy of the core asphaltene structure using the MMFF94 force field to obtain an optimized geometry. You may choose to use the "Auto Optimization" tool,, to more easily determine that the energy has reached convergence to ~0.01 kj/mol. Report the final energy that you obtained in kj/mol. c. Measure and report the torsional angle for the carbons numbered as shown in Figure 2. The value of this angle provides one measure of the planarity of the core of the asphaltene structure. Is the molecule planar (or very nearly)? Does this result validate your discussion regarding the presence or absence of the pentane effect in this system? Figure 2. Torsional angle for core asphaltene structure 2. Modeling ethyl-substituted asphaltenes Next, consider the two ethyl-substituted asphaltene structure shown in Figure 3, Model A and Model B. Notice that the structures differ only in the placement of the ethyl substituent Model A Model B Figure 3. Ethyl-substituted asphaltene structures. a. Use Avogadro to build Models A and B. Optimize the geometry of both structures to ~0.01 kj/mol using the "Auto Optimization" tool and the MMFF94 force field. Move the side chain around a bit to make sure you find the lowest energy conformer in each case. Report the final energy for each structure in kj/mol. In addition, measure and report the torsional angle ( as shown). b. From your results in part 2a, discuss whether ethyl-substituted Model A and B exhibit the pentane effect. Provide some rationale for your conclusions. Please note: although Models A and B are not conformers, and therefore it would generally not be advisable to compare their molecular mechanics energies, they are structural isomers with the same number of atoms, atom types, and bonds; therefore, it is more reasonable to make specific energy comparisons. c. To further analyze Models A and B, you will investigate the magnitude of the various parts of the total energy for each. To do this, select "Extensions Molecular Mechanics Calculate Energy" from the menu at the top of the screen. The total energy displayed should match closely the value you reported in part 2a.

3 3 Click on the "Messages" tab at the bottom of the screen. Scroll through the Messages listing to find and record the component energies. For the MMFF94 force field, these will be listed as Bond Stretching, Angle Bending, Stretch-Bending (an extra term in MMFF94 not included in many basic force fields), Torsional, Out-of-Plane Bending (another extra term), Van der Waals (same as Nonbonded Interactions), and Electrostatic. Note that MMFF94 assigns partial charges to some of the atoms in polar covalent bonds, so the electrostatic term may be non-zero. Tabulate the values of the force field components for both Models A and B. Note that the components are listed in units of kcal/mol. Also compute and tabulation the differences between the energies of each of the force field components for Models A and B. Compare and contrast the sizes of the force field components for the two model structures. Include in your discussion how you think the values of the force field components support your findings regarding the pentane effect. 3. Modeling asphaltene structures from the literature Finally, consider the original (7A) and modified (7B) phenol-based asphaltene structure shown in Figure 7 of the Energy & Fuels article (reproduced below). Notice that these structures differ only in the placement of two of the alkyl sidechains, denoted by arrows. (From D. D. Li and M. L. Greenfield Energy & Fuels, 2011, 25, ) a. Use Avogadro to build structures 7A and 7B from the literature article. Be very careful to position all the sidechains properly. You might want to build the common framework of the two structures first; that is, build everything except the two alkyl groups shown by the arrows. Optimize the common framework, making sure to move the side chains around during the auto-optimization process in order to try to find the lowest possible energy conformer, and save the structure. Then open the structure in Avogadro and add the additional alkyl groups on to the saved framework structure to create compounds 7A and 7B.

4 4 Optimize the geometry of both structures 7A and 7B using the "Auto Optimization" tool and the MMFF94 force field (it will take a little while; be patient). Again, make sure to move the side chains around in order to ensure that you find a low-energy conformer. Report the final energy for each structure in kj/mol. In addition, measure and report the torsional angle (use the same angle as shown in Figure 3, on the opposite side of the molecule from the OH group). b. Which of the two structures, 7A or 7B, would you expect to exhibit the pentane effect? Include a sketch of that structure, denoting the regions of the molecule where the pentane effect is expected. Compare the torsional angles of the two structures, 7A and 7B. Which one is more planar? Discuss whether or not the torsional angle results are in agreement with your arguments in regard to the pentane effect. Compare the planarity (or lack thereof) to the results presented in the Energy & Fuels article (see Figures 8, 9, and related discussion). Are your results in agreement with regard to which of the structures is more planar than the other? c. Compare the energy for each of the two structures (7A and 7B) that you obtained. Which is higher in energy? What is the energy difference? Do your results confirm the idea that the molecule that exhibits the pentane effect is higher in energy? What is the energy difference reported in the Energy & Fuels article for structures 7A and 7B? Are your results in agreement with this energy difference? Discuss. d. What force field was used in the Energy & Fuels article for the calculations of structures 7A and 7B? Find a literature article that describes the Energy & Fuels force field and provide equations listing the specific components. Compare and contrast the components included in the MMFF94 force field with the one used in the article.

5 5 PART B (12 points) Hydrogen Bonding and Water Structures In this part of the assignment, you will explore the use of molecular mechanics force fields for the description of hydrogen bonding. In particular, you will examine the ability of the MMFF94 and UFF force fields to represent water dimer and trimer structures. You will compare your results with data found in S. S. Xantheas and T. H. Dunning, J. Chem. Phys. 1993, 99, and in F. N. Keutsch R. J. Saykally, Proc. Nat. Acad. Sci. 2001, 98, Modeling the water dimer When two water molecules interact through a hydrogen bond, the observed experimental structure is shown in Figure 4, taken from Xantheas & Dunning. Figure 4. Experimental structure of the water dimer. a. Use Avogadro to build an initial structure for the water dimer. You may start with the available fragment water molecule, orient it in a fashion similar to the water molecule shown on the right in the figure. Use the Select menu at the top of the window to "Select None". Then, insert another water fragment and orient it in a similar fashion to the one shown on the left. Clear any selections before carrying out the next step. Minimize the energy of the water dimer structure using the MMFF94 force field to obtain an optimized geometry. You may use the "Auto Optimization" tool,, to more easily determine that the energy has reached convergence to ~0.01 kj/mol. Report the final energy that you obtained in kj/mol (you will need it in part 3). b. Measure and report the geometrical parameters of the MMFF94 water dimer (bond lengths and angles). Make sure to measure the O-O distance between the water molecules. In addition, make sure to measure the OH---O angle, which gives the degree of linearity of the hydrogen bond. Compare your MMFF94 results to the literature results where possible, focusing particularly on comparisons with the available experimental results reported in Xantheas & Dunning or Keutsch & Saykally, but you may also want to compare with the relatively high level quantum mechanical results (labeled MP2/aug-cc-pVTZ in Xantheas & Dunning). c. Build a new copy of the water dimer using Avogadro and repeat part 1a, this time using the UFF force field. Minimize the energy of the water dimer structure using the UFF force field to obtain an optimized geometry. You may use the "Auto Optimization" tool,, to more easily determine that the energy has reached convergence to ~0.01 kj/mol. Report the final energy that you obtained in kj/mol.

6 6 Make a sketch of, or capture an image of, the UFF water dimer structure and include it in your report. Compare and contrast this structure to the experimental one and the one obtained by MMFF94. Discuss which force field appears to be better for representing hydrogen bonding. [Note: to capture a screen image from Avogadro, select "File Export Graphics". You may then save a screen shot of the structure in a common graphics file format. Alternately, you may use Command-Shift-4 and capture a portion of the screen as a png file. Then, if you are using a Mac in JH 216, you may transfer the file to a flash drive and then to a personal computer.] 2. Modeling the water trimer When three water molecules interact through hydrogen bonding, the expected structure of the water trimer is shown in Figure 5, taken from Xantheas & Dunning. Figure 5. Experimental structure of the water trimer. a. Use Avogadro to build an initial structure for the water trimer. You may start with the available fragment water molecules as you did in part 1 to construct an initial structure. Minimize the energy of the water trimer structure using the MMFF94 force field to obtain an optimized geometry. You may use the "Auto Optimization" tool,, to more easily determine that the energy has reached convergence to ~0.01 kj/mol. Report the final energy that you obtained in kj/mol. b. Measure and report the geometrical parameters of the MMFF94 water trimer (bond lengths and angles). Make sure to measure those geometrical parameters explicitly reported in Xantheas and Dunning. Compare your MMFF94 results to the literature results where possible, focusing particularly on comparisons with the available experimental results in Xantheas & Dunning as well as Keutsch & Saykally, but you may again want to compare with the quantum mechanical results (labeled MP2/aug-cc-pVDZ in Xantheas and Dunning). c. Provide an overall assessment of the ability of the MMFF94 force field for representation of the water trimer structure. Would you suggest the use of this force field for the study of larger water clusters?

7 7 3. Modeling the water 20-mer Large water clusters are thought to be important in atmospheric chemistry, playing a role in condensation and droplet formation. In this part of the project, you will investigate whether or not a molecular mechanics force field is able to model the structure and energy of a symmetric water cluster consisting of 20 water molecules, shown in Figure 6. Clusters like the one shown in Figure 6 have been employed to model atmospheric processes. For example, the 20- mer below was employed by Francisco and coworkers [Q. Shi, S. D. Belair, J. S. Francisco, and S. Kais, Proc. Nat. Acad. Sci. 2003, 100, ] to study uptake of hydroperoxy radicals in liquid-like and solid-like enviroments. Figure 6. The structure of a symmetric water 20-mer from quantum mechanical calculations. a. First, you will need to download the starting structure (obtained from a quantum mechanical calculation) of the water 20-mer. From a browser, go to the course web site ( and click on the link for Course Handouts. Under the listing for September 2, you should find a link called "Water 20-mer structure". When you click on that link, the cartesian coordinates of the cluster will appear in your browser window. Save the coordinates to the Desktop in plain text format (or 'page source' format) using the name "20-mer.xyz". b. Start the Avogadro program and open the water 20-mer using "File Open" from the menu at the top of the window. Make sure that the "Files of type:" menu at the bottom of the file selection window is set to "Common molecule formats". Select the "20-mer.xyz" file, and the initial structure of the water 20-mer should appear in the Avogadro window. Note that the hydrogen bonds will not be displayed. Minimize the energy of the water 20-mer structure using the MMFF94 force field to obtain an optimized geometry. You may use the "Auto Optimization" tool,, to more easily determine that the energy has reached convergence to ~0.01 kj/mol. Report the final energy that you obtained in kj/mol.

8 8 c. Select one water pentamer in the 20-mer cluster. Measure and report the five O-O distances around the edge of pentamer. Compute an average O-O distance. Compare the range of individual values as well as the average with the results you obtained for the water dimer and also the water trimer using MMFF94. Are there any trends that you observed with respect to cluster size? Xantheas & Dunning discuss trends observed in quantum mechanical calculations of water clusters up to hexamer; see Fig. 10 and associated text. How do your findings compare with Xantheas & Dunning's results for O-O distance versus cluster size? d. The dissociation energy (D) of a water cluster containing n water molecules is defined to be the difference in energy between n individual water molecules and the energy of the cluster, D = n E H 2 O ( ) E ( H 2 O) n ( ), (1) where E H 2 O ( ) is the energy of an individual water molecule and E ( H 2 O) n ( ) is the energy of the n-molecule cluster. Using the MMFF94 energies you obtained for the water dimer, trimer, and 20-mer, compute and report the dissociation energy of each cluster in kj/mol. You will need the MMFF94 energy of a single optimized water molecule, which you may calculate anew using Avogadro; alternately, you may use the value you found in Assignment 1 Part 1. In order to compare the dissociation energies on a consistent basis, it is useful to compute the energy per hydrogen bond, E HB, which is defined as the dissociation energy divided by the number of hydrogen bonds, n HB, in the cluster, E HB = D n HB. (2) Using Eq. (2), compute the energy per hydrogen bond E HB in kj/mol for the water dimer, trimer, and 20-mer from your MMFF94 results. Discuss any trends observed as a function of cluster size. The paper by Francisco and coworkers reports quantum mechanical results for the energy per hydrogen bond for the water dimer and 20-mer. Compare your results to the quantum mechanical results and discuss the agreement. To what physical effect do Francisco and coworkers attribute the size-dependence of the hydrogen bond energy? e. Compare and contrast the agreement you found between the MMFF94 results for the trimer with those of the 20-mer. Based on your study of the water 20-mer, has your assessment about the ability of the MMFF94 force field to study larger water clusters changed?