Difference between revisions of "Intro WebMO 1"

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'''''Exercise 1 - Study of H-X-H Bond Angles'''''
 
'''''Exercise 1 - Study of H-X-H Bond Angles'''''
  
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''Exploring the structure of CH<sub>4</sub>''
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===Structure of CH<sub>4</sub>===
 
:- Click “New Job”, then “Create New Job”. The Build Molecule window opens,  
 
:- Click “New Job”, then “Create New Job”. The Build Molecule window opens,  
 
:- Click on the Periodic Table icon (2nd down the left side). Choose “C” by clicking on it.
 
:- Click on the Periodic Table icon (2nd down the left side). Choose “C” by clicking on it.
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:::Record the value of the H-C-H bond angle ___________° (109.4712 literature). Check the other H-C-H bond angles.
 
:::Record the value of the H-C-H bond angle ___________° (109.4712 literature). Check the other H-C-H bond angles.
  
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Scroll down and review the information under Calculated Quantities.
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::Scroll down and review the information under Calculated Quantities; these will be discussed more later.
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When finished, click the Job Manager link under Actions (to the left of the molecule display).
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:- Click the Job Manager link under Actions to return to the Job Manager window.
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To delete files, click the box to the left of the desired file and choose Delete on the menu.
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To continue on to the next exercise, choose New Job > Create New Job.
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===Structure of NH<sub>3</sub>===
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Structure of NH3
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:- Repeat the above procedure for ammonia, NH<sub>3</sub>.
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Build NH3 using the above procedure.
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:- Record the value of the N-H bond length __________Å (~0.999 Å, 1.012 Å literature).
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Use Job Name H3N PM3 Geom Opt, and perform the geometry optimization as before (PM3).
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:- Record the value of the H-N-H bond angle __________° (~107.8 °, 106.67 ° literature).
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Record the value of the N-H bond length __________Å (~0.999 Å, 1.012 Å literature).
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:- Scroll down and review the information under Calculated Quantities.
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Record the value of the H-N-H bond angle __________° (~107.8 °, 106.67 ° literature).
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::*Click on the magnifying glass next to the reported Dipole Moment, then rotate the molecule to see the vector.
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Scroll down and review the information under Calculated Quantities. Click on the magnifying
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:- Return to Job manager.
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glass next to the reported Dipole Moment, then rotate the molecule to see the vector.
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Return to Job manager, and choose New Job > Create New Job.
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===Structure of H2O===
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Structure of H2O
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:- Repeat the above procedure for water, H<sub>2</sub>O.
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Build H2O using the above procedure.
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:- Record the value of the O-H bond length __________Å (~0.951 Å, 0.959 Å literature).
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Use Job Name H2O PM3 Geom Opt, and perform the geometry optimization as before (PM3).
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:- Record the value of the H-O-H bond angle __________° (~107.7 °, 103.9 ° literature).
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Perform the PM3 geometry optimization as above.
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Check out the Dipole Moment, as done above with NH<sub>3</sub>.
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Record the value of the O-H bond length __________Å (~0.951 Å, 0.959 Å literature).
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:- Return to Job Manager.
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Record the value of the H-O-H bond angle __________° (~107.7 °, 103.9 ° literature).
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Check out the Dipole Moment, as with NH3 above.
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===Report===
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Return to Job Manager.
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:1) What conclusions can you make concerning the size of the central atom X and the X-H
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1. What conclusion(s) can you make concerning the H-X-H bond angle and the number of
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bond length?
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:2) What conclusion(s) can you make concerning the H-X-H bond angle and the number of
 
unshared (lone) pairs of electrons around the central atom X?
 
unshared (lone) pairs of electrons around the central atom X?
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2. What conclusions can you make concerning the size of the central atom X and the X-H
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bond length?
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'''END'''

Latest revision as of 15:25, 9 April 2020

The following activities is a modification of this...

Exercise 1 - Study of H-X-H Bond Angles

Structure of CH4

- Click “New Job”, then “Create New Job”. The Build Molecule window opens,
- Click on the Periodic Table icon (2nd down the left side). Choose “C” by clicking on it.
- Click once in the center of the workspace. A dark-gray carbon atom appears. (If you click too many times and have extra atoms, choose Edit > Undo).
- Choose Clean-Up > Comprehensive – Mechanics. This request will add hydrogens and you should now seen methane.
- Experiment with the Rotate, Translate, and Zoom tools (3rd, 4th, 5th icons on left side).

This structure contains idealized bond lengths and angles. A more accurate structure can be found by carrying out an energy minimization using molecular mechanics, semiempirical methods, or ab initio calculations.

- Click the blue “continue” arrow in the lower right side of the Build Molecule window.
(Note: only one computational engine has been enabled, so you do not need to choose the engine, this many change in the future).
- Setup the job using the "Configure Gaussian Job Options" window as shown below:
Screen Shot 2020-04-09 at 9.53.35 AM.png
Before continuing, click on the "Preview" tab, then click, "Generate" to see the input file in a text form. The first line of the input file indicate, in Gaussian 03 language, what type of calculation is being requested. The next set of lines, after the name "CH4" is related to the Z-matrix which describes how the atoms are connected, initial bond lengths, initial bond angles, and then the initial dihedral angles (more on this later). This input file can be edited (more on this later).
- Now, click on the blue “continue” arrow. This will advance you back to the "Job Manager" window where you will see your job running.
  • To kill or stop a job, you would click on the red “X” under Actions on the right side.
  • you may "Refresh" (every ~10 seconds) until you see that your job is Complete.
- Click on the hyperlinked name (CH4) to open the “View Job” window.
- Choose the "Adjust" arrow (4th icon down on left)...
  • Click on one of the H atoms to highlight, then click on the C atom to highlight, and the bond length is displayed just below the molecule.
Record the value of the C-H bond length --> ___________Å (1.091 Å literature). Check the other C-H bond lengths to verify symmetry.
  • Click on one of the H atoms, then C atom, followed by another H atom. The bond angle is displayed just below the molecule.
Record the value of the H-C-H bond angle ___________° (109.4712 literature). Check the other H-C-H bond angles.
Scroll down and review the information under Calculated Quantities; these will be discussed more later.
- Click the Job Manager link under Actions to return to the Job Manager window.

Structure of NH3

- Repeat the above procedure for ammonia, NH3.
- Record the value of the N-H bond length __________Å (~0.999 Å, 1.012 Å literature).
- Record the value of the H-N-H bond angle __________° (~107.8 °, 106.67 ° literature).
- Scroll down and review the information under Calculated Quantities.
  • Click on the magnifying glass next to the reported Dipole Moment, then rotate the molecule to see the vector.
- Return to Job manager.

Structure of H2O

- Repeat the above procedure for water, H2O.
- Record the value of the O-H bond length __________Å (~0.951 Å, 0.959 Å literature).
- Record the value of the H-O-H bond angle __________° (~107.7 °, 103.9 ° literature).

Check out the Dipole Moment, as done above with NH3.

- Return to Job Manager.

Report

1) What conclusions can you make concerning the size of the central atom X and the X-H

bond length?

2) What conclusion(s) can you make concerning the H-X-H bond angle and the number of

unshared (lone) pairs of electrons around the central atom X?

END

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