Assignment
CompChem2: Geometry Optimizations
Use WebMO to complete the following exercises. You are encouraged to comment on the additional results provided by WebMO in your answers, if appropriate.
1. Vinyl alcohol conformers (exercise 3.2).
Build vinyl alcohol-0°, vinyl alcohol-180°, and acetaldehyde. When building these molecules, adjust dihedral angles to result in planar, staggered conformations as in the text. Perform a Geometry Optimization, Hartree-Fock 3-21G calculation. add the line “%Mem=16MB” as the first line of the input file to reduce memory usage and speed up the calculation.
Make a table with columns for molecule, number of optimization steps, energy (Hartree), relative energy (kcal/mol). The relative energy should be calculated relative to the global minimum. Note that 1 Hartree = 627.5095 kcal/mol (back inside cover of ECESM). What is the route line in the input file for these jobs? Copy and report the text from the output file indicating that the optimization has converged.
2. Vinyl alcohol transition state (p.77).
Build an approximate transition state for the isomerization of vinyl alcohol-0° and vinyl alcohol-180° as follows. View a geometry optimized vinyl alcohol job that successfully ran, and choose New Job Using This Geometry. Adjust the H-O-C=C dihedral angle to 90°. Perform a Transition State Optimization, Hartree-Fock 3-21G calculation.
Make a table with columns for conformation and relative energy (kcal/mol). Include both stable conformations and the transition state in the table. What is the route line in the input file for this job? What indications are present in the output file to suggest that this optimization differs from the previous optimizations.
3. Silane elimination reaction transition state (exercise 3.7).
In this exercise, the transition state for the reaction SiH4 ® SiH2 + H2 will be found. The same general method as in Exercise 3.7 will be used, except dummy atoms (X) and redundant coordinates will not be included. Also, the semi-empirical PM3 basis set will be used for increased speed, but at the cost of less accuracy.
Build SiH4 and set up a PM3 optimization as a template for this calculation. Before submitting your job, preview the input file and edit the displayed text into the following:
#N PM3/3-21G Opt=QST2
Silane QST2: SiH2 + H2
0 1
Si
H 1
B1
H 1
B2 2 A1
H 1
B3 2 A2 3 D1
H 1
B4 2 A3 3 D2
A3 96.849005
A2 84.283836
A1 110.00006
D2 -99.87710
D1 -81.78112
B4 1.9999999
B3 1.9999997
B2 1.4799991
B1 1.4799999
Silane QST2: SiH4
0 1
Si
H 1
B1
H 1 B2 2 A1
H 1
B3 2 A2 3 D1
H 1
B4 2 A3 3 D2
A3 109.37081
A2 109.30689
A1 110.00006
D2 120.13988
D1 -120.0214
B4 1.4800000
B3 1.4800000
B2 1.4799991
B1 1.4799999
Be very careful to include blank lines where indicated. Submit the job and view the result.
Insert a picture of the transition state for this reaction. Which H atoms are forming hydrogen. What is their bond length. How does their bond angle with Si compare to the other SiH2 bond angle?
Describe how the transition state search algorithm for this exercise differs from the previous exercise. When would you use each algorithm?
4. How could WebMO be improved to assist you with your calculations? Please be as imaginative and thorough as possible with your suggestions and constructive criticism!