Exploring Transition States and Molecular Properties with Cerius2, Assignments of Health sciences

Download Exploring Transition States and Molecular Properties with Cerius2 and more Assignments Health sciences in PDF only on Docsity! 1 528F03ProblemSet05.doc ChE 528 Problem Set 5 Due Thursday 10/9/2003 1. Go through the Beta version of the Quantum Web Module on the CRE website. Write a paragraph of what you learned. Include a list of four things that you liked and four things that need to be improved. 2. List four approximations that were made in developing the transition state theory and how seriously will each affect the estimate of the frequency factor A? 3. Approximately how much error would be introduced in the H − d 1} H − d 2} Br transition state example given in Laidler if the distances d1 and d2 were off by a factor of 2 or more? How abut if the frequencies were off by 1/2? Which is the most critical measurement for calculating any of the parameters? 4. Calculate the specific reaction rate at 300K for the reaction F +H2 →HF +H using both collision theory and transition state theory. Use Cerius2 (or literature references) to estimate any parameters you may need. We will use in this Cerius2 to study the SN2 reaction: F +H2 →HF +H We will calculate the thermo-physical properties of the reactants and the transition state in order to estimate the partition functions, the rate constant, and the activation energy of this reaction. After following the procedure to load Cerius2, you can follow these steps. (In the following, “click” implies a left click) I. The H2 Molecule: (i) Draw the H2 molecule: 1. In the Visualizer window, click on STICK and change it to BALL & STICK 2. In the Visualizer window, click Build and select 3-D Sketcher 3. In the Sketcher window, choose Sketch with and select H 4. Click once the model window and you will see a hydrogen atom 5. Click again and you will form the H-H molecule You have now constructed the H2 molecule (ii) Optimize the molecule: 1. In the Sketcher window, click and hold CLEAN. You will see that the bond distance changes; this is a preliminary optimization of the structure 2. In the Visualizer window, click on BUILDERS 1 and change it to QUANTUM 1. 3. Click on the MOPAC tab and click Run 2 528F03ProblemSet05.doc 4. Rename your file as “H2” (or anything else you may prefer) in the File Prefix, change the Task to Geometry Opt. and Frequency and the Method to PM3. You may want to run different methods to compare the results. 5. Click on RUN and let the run finish; a graph of the IR spectra of H2 will pop up. Again, because of a graphic bug, you will need to minimize the window and double click on the icon to restore the window. You have now optimized the H2 molecule (iii) Note the results: 1. In the Visualizer window, click on Geometry then Measurements. You can measure the distance by clicking on the button in the pop-up window and clicking on the H and H atoms in the model window What is the H-H bond length? ________________________________________ 2. In the Visualizer window under MOPAC, click on Analyze and choose Files. The last run is usually chosen as the default file. If it is not, select the H2.out file (or whatever name you selected for your file). 3. Note these values shown in this window: What is the Heat of Formation? _____________________________________ What is the Dipole Moment? _____________________________________ 4. In the Visualizer window under MOPAC, click on Analyze and choose Vibrations. With the model window visible select a frequency and left click the Animate button in order to animate the vibrations. To stop the animation, just left click on the same or another frequency. Note the various frequencies: ________________, ____________________ What do these frequencies represent? ________________, _____________ 5. Run the Geometry Opt. and Frequency task again, this time click on More, then check Thermophysical Properties and choose a temperature range from 290 K to 310 K. After the run is over, click Analyze, Files and click on Examine File. You will see the various partition functions, enthalpies and entropies at various temperatures. Note the various properties at 300 K: Heat of formation: ________________ Enthalpy: ________________ Cp: ________________ Entropy: ________________ Zero-point energy: ________________ qtrans = __________________ qrot = __________________ qvib = __________________ You have now calculated the necessary properties of the H2 molecule II. The Transition state F-H-H: (i) Draw the F-H-H transition state: 1. Start a new session 2. In the Sketcher window, choose Sketch with and select H 3. Click on the model window at three points to get the H-H-H structure 4. In the Sketcher window, choose Edit Element and select F 5 528F03ProblemSet05.doc A B E. The threshold velocity increases with increasing rotational quantum number but decreases with increasing vibrational quantum number. True False Explain F. In the Karplus Theory the impact parameter, b, is chosen randomly in a Monte Carlo procedure in the calculation of the reaction cross section. True False Explain G. The minimum kinetic energy (given in terms of the relative velocity) that two molecules (atoms) must have in order to react is equal to the height of the potential energy barrier. True False Explain H. The reaction cross section is a function of the frequency of vibration of the reacting molecule. True False Explain I. For a “head on collision” in which the impact parameter is zero, the reaction probability for a H2 molecule in the v = 0 vibrational state with no rotation is 1.0. True False Explain J. The activation energy is greater than the threshold energy, but less than the barrier height. True False Explain K. The sum of the v = 0 vibrational energy and threshold kinetic energy is the minimum total energy (relative to the classical ground state) necessary for reaction to occur. True False Explain 6 528F03ProblemSet05.doc L. The molecular trajectories were calculated by systematically choosing various values of the impact parameter, rotational and vibrational quantum numbers, and the orientation of the H2 molecule relative to the H molecule and then solving the 12 Hamiltonian Equations numerically. True False Explain M. If the reaction probability calculated from the collision trajectories is found to be the following function of the impact parameter Pr = 2 − b( ) 2π[ ] for b ≤ 2 a.u. Pr = 0 for b > 2 a.u. where b and the number 2 are in atomic units (a.u.). The reaction cross section is (1) 8/3 sq. a.u. ao 2( ) (2) 4/3 sq. a.u. (3) 2 sq. au. (4) 12.56 sq. a.u. (5) None of the above (6) Not possible to calculate from the above information Optional 6. Use Cerius2 to explore the properties of molecules of your choice. Write a paragraph describing all that you could find out about the molecule using Cerius2?