Learning to Use Scigress Wagner, Eugene P. (revised May 15, 2018)

Transcription

1 Learning to Use Scigress Wagner, Eugene P. (revised May 15, 2018) Abstract Students are introduced to basic features of Scigress by building molecules and performing calculations on them using semi-empirical quantum calculation methods. The results of these calculations will be used to discuss various molecular properties and chemical phenomena. Once students have mastered building and running calculations on molecules, they will be asked to apply these skills to explain some aspects of select chemical reactions. Introduction Visualizing molecular structure has become an essential and integral part of understanding and predicting chemical reactions and physical properties, especially fields such as molecular biochemistry, drug design, and nanotechnology. Although simple representations of molecules like Lewis structures and model kits are helpful toward this endeavor, computational chemistry, also referred to as molecular modeling, has become a very powerful tool in visualizing and investigating molecular structure and phenomena. The computer allows scientists to perform quick quantum mechanical calculations on electron energies and distributions, which are then used to determine many molecular properties including molecular orbitals, molecular arrangements (conformations), dipole moments, and reaction profiles. Why water and oil do not mix, why do some medications work better than others, and how likely is a reaction to occur are examples of important questions that can be investigated through molecular modeling. In fact, you will have an opportunity to investigate these questions in future lab experiments. The purpose of this document is to provide you with an introduction to the fundamentals on how to use Scigress molecular modeling software, investigate molecular structure, and use it to answer chemical questions. To get started, go to the Start menu, navigate to the Programs folder, then the ScigressSuite folder, and click on Scigress. You will be prompted to create a project folder, where all your molecular structure files will be saved. It is suggested that you save this folder to your desktop, then use a USB drive to transfer the entire project folder at the end of today s lab session. Once you create this folder, your drawing palette should open. If not, go to the File menu and choose New Object, then select Blank, naming it as you wish. Since we will build methane first, name your file CH4. Figure 1. Molecule manipulations Your Drawing Palette will have a toolbar similar to those pictured in Figure 1. Each button is labeled with its function. Across the top of the Drawing Palette is a Menu Bar. Each menu is explained below (from left to right). Element drop down menu: Allows you to select an element to draw with. Common and recently used elements are listed in the drop down menu. If you would like to use an element that is not listed, you can click on Periodic Table and select the element you wish to use. Hybridization drop down menu: Displays the hybridization of a selected atom. You can change the hybridization of the selected atom using this menu as well. (1)

2 Charge: Allows you to change the charge of a selected atom or group of atoms. By default, the atoms are uncharged. Clicking the up arrow makes the charge more positive and clicking the down arrow makes the charge more negative. Note that if you select a group of atoms and change the charge, you will add the same unit of charge to all of the atoms in the group. Bond Type drop down menu: Changes the bond type or bond order of a selected bond. The default bond type is single. Now let s set things up so that you can build your first molecule, methane (CH 4). Click on the View menu select Show Electrons. This will allow you to see the valence electrons for each atom. This will help you match your computer drawn molecule to your Lewis structure. Sometimes the electron pairs do not match VSEPR predictions but the number of electrons on each atom should match your Lewis structure. To draw your molecule: Click on the drawing pencil tool in the left toolbar Select the element you wish to draw with from the element drop down menu Single click on the drawing palette to draw a single carbon atom To draw a hydrogen atom covalently bonded to the carbon atom, make sure that your bond type is single and select hydrogen from the element drop down menu. Click and drag from the carbon atom and release the mouse button. A hydrogen atom will appear at the end of the single bond you drew. Keep using these steps to build the remainder of your methane molecule. When you initially draw molecules, aim to make them similar to your sketched Lewis structure from the prelab, including all formal charges and bond types. Now, to make the geometry of your methane drawing look closer to what VSEPR predicts, you will need to beautify it. To do this, select your entire molecule. Click on Action menu, select Beautify, then Comprehensive. This adjusts the geometry of your molecule to a VSEPR/Valence Bond geometry. It also satisfies the normal valence of the atoms in the molecule by adding hydrogen atoms. Another, more precise way of beautifying your structure is to minimize the energy using molecular mechanics, which is based on classical physics. This method is simply moving the point charges (atoms) around until in minimizes the interaction energy while still maintaining the bonds. To perform a molecular mechanics minimization, click on the Experiment menu, then select Run. For Category, select chemical sample (Figure 2). For Choose a property, select optimized geometry. For Choose a Procedure, select MM3. Click on the Start button to begin the calculation. A new window will pop up that will show the progress of Figure 2. Calculation selection window. the calculation. Most calculations only take a few seconds. When you are given the message Geometry optimization is complete, you can close this window and the experiment window. Your methane molecule should now have a geometry that has minimized interaction energies and a more idealized geometry. (2)

3 Beautifying the molecule or using MM3 cleans upo the structure nicely. However, it does not provide the best and most accurate bond lengths and angles compared to the experimental values. We need to now Optimize the geometry of your molecule using a higher level of calculations, Semi-empirical, DFT, or ab-initio. We will use a semi-empirical method called PM6 to do this. When we use semi-empirical methods, the computer solves the Schrödinger equation but substitutes experimental parameters for the portions of the quantum mechanical calculations that cannot be mathematically solved. This results in a faster, yet fairly accurate calculation. To run a Geometry Optimization experiment (or any other experiment), click on the Experiment menu, then select Run. A window will appear that is similar to the one shown in Figure 2. To set up the calculation, choose the following options: For Category, select chemical sample. For Choose a property, select optimized geometry. For Choose a Procedure, select MO-G PM6. Click on the Start button to begin the calculation. A new window will pop up that will show the progress of the calculation. Most calculations only take a few seconds. When you are given the message Geometry optimization is complete, you can close this window and the experiment window. Your methane molecule should now have an optimized geometry, based on the parameters of the MO-G PM6 calculation and approximation method. Use the Rotate tool to examine your molecule from all angles. Exercise 1: Orbitals for Simple Polyatomic Molecules One simple model used for polyatomic ions is VSEPR, where we use the overlap of atomic and hybrid orbitals to describe bonding. Here we will explore if our quantum calculations strictly use hybrid orbitals in VESPR, or may be combining it with more advance bonding theories to map out the electron densities. Question 1: Describe the bonding in methane (CH 4), ammonia (NH 3), and water (H 2O) using what you know about VSEPR. Make sure that your description also accounts for lone pairs. Now, let s examine the orbitals for your optimized methane molecule. To view the orbitals, go to the Analyze menu, then Electronic Structure, and choose All molecular orbitals. A window will appear that allows you to monitor the tabulation of molecular orbitals. When the tabulation is complete, close the window. On the left hand side of your screen, under Model Explorer, you will see a Surfaces option. Click on the arrow to view the available orbitals, which are labeled relative to the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). Double click on any label to view the orbital in the workspace, which will be mapped on your structure. After viewing the molecular orbitals for CH 4, build, optimize the geometries (run the same experimental method as for CH 4), and view the molecular orbitals for NH 3 and water. Question 2: Do the orbitals for CH 4, NH 3, and H 2O resemble your VSEPR descriptions for these models? Using the snipping tool or get a screen shot of the molecules and save to a USB drive. These pictures can then be used in your lab report. Discuss your findings. (3)

4 There is a great deal of information provided from the calculations completed by Scigress. Some of it you saw on the window as the calculation progressed. Some information, such as bond angles and lengths can be obtained simply by clicking on an angle (by selecting the three atoms involved while holding the ctrl key) or a bond and looking at the bottom of the screen. There you will see the value corresponding to your selection. Question 3: What are the bond angles in these three molecules? If they are different, explain why this would happen. Finally, other information is available in the actual output file created from the calculations. For example, Which of these molecules is most easily oxidized? To get the ionization energy, you need to go into the output file created from the calculations. Starting with the file location of your project, go to the CH4.io file folder and then open the MO-G Output file in notepad. Scroll through the output file until you find the ionization potential value. Question 4: Record the ionization energies for methane, ammonia and water and then rank order them in terms of ease of oxidation. Discuss your findings and explaining the ordering based on what you know about the physical and chemical properties of these molecules and atoms. Does the ionization energy correlate well with what you would expect? Is the ionization energy actually the oxidation potential? Explain. Exercise 2: Molecular Orbital Calculations for Ethene and Benzene Now let s examine the molecular orbitals of molecules with double bonds. First build, optimize the geometry, and generate the molecular orbitals for ethene (CH 2CH 2). Examine the HOMO and LUMO. Question 5: Get pictures and identify the HOMO and the LUMO. Provide an explanation to their shape and whether you think they are strengthening or weakening the bond and molecular structure. Question 6: What are the energy values of the HOMO and LUMO? What does the sign in from of the energy value indicate? In other words, would electrons in the LUMO make the molecule more or less stable? What wavelength of light corresponds to the energy difference of the two orbitals? Does it seem probable to promote an electron between these energy levels with light? Why? Question 7: The HOMO-2 represents the first bond between the carbons and the HOMO represents the second bond between the two carbons. What are the main differences you see? Which one do you think is strengthening the structure between the two carbons the most? Next, we will take a look at benzene (C 6H 6). Before beginning, make sure you have a valid Lewis structure for C 6H 6. Build, optimize the geometry, and generate the molecular orbitals. This time you want to examine HOMO-4, and LUMO+2. Question 8: Get pictures and identify the HOMO-4 and the LUMO+2. Provide an explanation to their shape and whether you think they are strengthening or weakening the bond(s) and structure. (4)

5 Question 9: What are the similarities between the HOMO-4 for benzene and the HOMO for ethene? What are the similarities between the LUMO+2 for benzene and the LUMO for ethene? Question 10: Look at some of the other LUMOs for benzene as well as the other HOMOs. Is there any general conclusion you can find about the orbital distribution for HOMOs? What about LUMOs? Exercise 3: Enthalpy of Formation We have learned in class that Enthalpy of formation is the amount of energy exchanged in a reaction of creating one mole of a compound from its elements. These literature values can be found in the appendix of your textbook. Scigress can also calculate theses values. In this exercise, let s see how well the calculated Scigress values compare to the literature values for a few acids. Build each molecule in the table below. Make sure to beautify and inspect the molecule for a reasonable structure before continuing. Run the experiment Chemical sample optimized geometry MO-G PM3 in water for each of these aqueous phase acids. After the calculations are complete you should be able to find the enthalpy of formation in the output window. Look up the literature values for each in the back of your textbook and record it and the Scigress calculated value below. Then calculate the error in the Scigress value compared to literature. Acid o Literature H f o Scigress H f % difference H 2SO 4(aq) HCl(aq) HNO 3(aq) H 3PO 4(aq) Question 11: Discuss any trends you find in the data. Are the reactions endo or exothermic? Can you explain why this would be the case. Exercise 4: Study of Rotation Barrier Energy about Carbon-Carbon Bonds Structure of Ethane, CH 3CH 3 Build ethane and then beautify-comprehensive. To make a bond between the carbon atoms, click on the C atom, drag, and release. A second C atom with a bond should appear. Adjust the dihedral angle. Click one of the H atoms. Shift and Click the attached C atom, the other C atom, and one of the H atoms attached to the second C atom to define a dihedral angle. Click Adjust / Dihedral Angle (Action/Geometry Labels/Dihedral Angle). Click Define Geometry Label / Search from -180 to +180 using 24 steps. / close by clicking ok. Click once in workspace away from molecule. (5)

6 Run the experiment, Property of (category): chemical sample conformations, Property: optimized (potential energy) map, Using: (MO-G) PM3 energies (one label). After a few seconds the calculation is finished and two windows appear the left window shows an energy plot as a function of the dihedral angle and the right window shows the molecule. Choose the dropdown window at the bottom of the left window and choose calc_energy. Use the left and right arrow keys to cursor across the energy map and the molecule should rotate to the form that corresponds to the energy selected. Record the greatest and least values of the energy and the associated dihedral angle geometry. Calculate the barrier energy for rotation of the CH 3 groups around a C-C bond. greatest energy kcal mol geometry or dihedral angle - least energy kcal mol -1 geometry or dihedral angle rotation barrier kcal mol -1 Structure of Ethene, CH 2CH 2 Using the same direction above, build ethene, define the dihedral angle. Run the experiment (as above) and record the greatest and least values of the energy and the associated dihedral angle geometry. Calculate the barrier energy for rotation of the CH 2 groups around a C=C bond. greatest energy kcal mol geometry or dihedral angle - least energy kcal mol -1 geometry or dihedral angle rotation barrier kcal mol -1 Compare the relative magnitudes of the rotational energy barrier between the two molecules and provide an explanation. Do the max and min rotation energy values for the two molecules occur at the same angle/geometry? Provide an explanation. (6)