View source for Od416


== '''NH3 Optimisation''' ==


What is the molecule? '''NH3'''

What is the calculation method? '''RB3LYP'''

What is the basis set? '''6-31G(d,p)'''

What is the final energy E(RB3LYP) in atomic units (au)? '''-56.55776873'''  

What is the RMS gradient? '''0.00000485'''

What is the point group of your molecule? '''C3V'''

Bond Length: '''1.01798 au'''

Bond Angle: '''105.741 degrees'''


'''Item Table'''

                  Item               Value     Threshold  Converged?
  Maximum Force            0.000004     0.000450     YES
  RMS     Force            0.000004     0.000300     YES
  Maximum Displacement     0.000070     0.001800     YES
  RMS     Displacement     0.000033     0.001200     YES
  Predicted change in Energy=-5.785197D-10
  Optimization completed.
     -- Stationary point found.
                            ----------------------------
                            !   Optimized Parameters   !
                            ! (Angstroms and Degrees)  !
  --------------------------                            --------------------------
  ! Name  Definition              Value          Derivative Info.                !
  --------------------------------------------------------------------------------
  ! R1    R(1,2)                  1.018          -DE/DX =    0.0                 !
  ! R2    R(1,3)                  1.018          -DE/DX =    0.0                 !
  ! R3    R(1,4)                  1.018          -DE/DX =    0.0                 !
  ! A1    A(2,1,3)              105.7412         -DE/DX =    0.0                 !
  ! A2    A(2,1,4)              105.7412         -DE/DX =    0.0                 !
  ! A3    A(3,1,4)              105.7412         -DE/DX =    0.0                 !
  ! D1    D(2,1,4,3)           -111.8571         -DE/DX =    0.0                 !
  --------------------------------------------------------------------------------
  GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad


'''Log File'''


[[File:ODUAN_NH3.LOG]]


'''Static Image'''


[[File:oduan3_nh3_image.png|150px]]


'''Jmol Image ''' 

  <jmol><jmolApplet>

  <title>NH3</title>

  <color>black</color>

 <size>200</size>

  <uploadedFileContents>ODUAN_NH3.LOG</uploadedFileContents>

  </jmolApplet></jmol>

'''Display Vibrations File''' 

[[File:Oduan_displayvibrations_nh3.png|300px]]


'''Display Vibrations Questions'''

how many modes do you expect from the 3N-6 rule? '''3 modes because there are 3 atoms and 3(3) - 6 = 3'''

which modes are degenerate (ie have the same energy)? '''modes 2 and 3; modes 5 and 6'''

which modes are "bending" vibrations and which are "bond stretch" vibrations?

'''mode 1 is bending'''

'''mode 2 is bending'''

'''mode 3 is bending'''

'''mode 4 is stretching'''

'''mode 5 is stretching'''

'''mode 6 is stretching'''

which mode is highly symmetric?

'''mode 4 is highly symmetric'''

one mode is known as the "umbrella" mode, which one is this?

'''mode 1 is the umbrella mode'''

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

'''there would be 3 bands on an an experimental spectrum of gaseous ammonia'''


'''Charge Distributions'''

The N atom has a -1.125 charge and the H atom has a +0.375 charge

== '''N2 Optimisation''' ==

What is the molecule? '''N2'''

What is the calculation method? '''RB3LYP'''

What is the basis set? '''6-31G(d,p)'''

What is the final energy E(RB3LYP) in atomic units (au)? '''-109.52412868'''

What is the RMS gradient? '''0.00000001'''

What is the point group of your molecule? '''D∞h'''

Bond Length: '''1.10550 au'''

Bond Angle: '''180 degrees'''


'''Item Table'''

         Item               Value     Threshold  Converged?
 Maximum Force            0.000000     0.000450     YES
 RMS     Force            0.000000     0.000300     YES
 Maximum Displacement     0.000000     0.001800     YES
 RMS     Displacement     0.000000     0.001200     YES
 Predicted change in Energy=-9.123258D-16
 Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.1055         -DE/DX =    0.0                 !
 --------------------------------------------------------------------------------
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad


'''Log File'''

[[File:ODUAN_N2.LOG]]

'''Static Image'''


[[File:oduan_n2_image.png|150px]]


'''Jmol Image ''' 

  <jmol><jmolApplet>

  <title>N2</title>

  <color>black</color>

 <size>200</size>

  <uploadedFileContents>ODUAN_N2.LOG</uploadedFileContents>

  </jmolApplet></jmol>


'''Display Vibrations File'''

[[File:Oduan_displayvibrations_n2.png]]

none are negative

== '''H2 Optimisation''' ==

What is the molecule? '''H2'''

What is the calculation method? '''RB3LYP'''

What is the basis set? '''6-31G(d,p)'''

What is the final energy E(RB3LYP) in atomic units (au)? '''-1.17853936'''

What is the RMS gradient? '''0.00000001'''

What is the point group of your molecule? '''D∞h'''

Bond Length: '''0.74279 au
'''
Bond Angle: '''180 degrees'''


'''Item Table'''

          Item               Value     Threshold  Converged?
  Maximum Force            0.000000     0.000450     YES
  RMS     Force            0.000000     0.000300     YES
  Maximum Displacement     0.000000     0.001800     YES
  RMS     Displacement     0.000001     0.001200     YES
  Predicted change in Energy=-1.167770D-13
  Optimization completed.
     -- Stationary point found.
                            ----------------------------
                            !   Optimized Parameters   !
                            ! (Angstroms and Degrees)  !
  --------------------------                            --------------------------
  ! Name  Definition              Value          Derivative Info.                !
  --------------------------------------------------------------------------------
  ! R1    R(1,2)                  0.7428         -DE/DX =    0.0                 !
  --------------------------------------------------------------------------------
  GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad


'''Log File'''

[[File:ODUAN_H2.LOG]]


'''Static Image'''

[[File:oduan_h2_image.png|150px]]


'''Jmol Image ''' 

  <jmol><jmolApplet>

  <title>H2</title>

  <color>black</color>

 <size>200</size>

  <uploadedFileContents>ODUAN_H2.LOG</uploadedFileContents>

  </jmolApplet></jmol>

'''Display Vibrations File'''

[[File:oduan_displayvibrations_h2.png]]

== '''Reactivity Questions''' ==

E(NH3)= -56.55776873 au

2*E(NH3)= -113.11553746 au

E(N2)=  -109.52412868 au

E(H2)= -1.17853936 au

3*E(H2)=  -3.53561808 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=

-113.11553746 - (-109.52412868 -3.53561808) = '''-0.05579070 au = -146.47848285 kj/mol'''

'''the product (NH3) is more stable than the reactants (H2 and N2)'''

== '''F2 Optimisation''' ==

What is the molecule? '''F2'''

What is the calculation method? '''RB3LYP'''

What is the basis set? '''6-31G(d,p)'''

What is the final energy E(RB3LYP) in atomic units (au)? '''-199.49825218'''

What is the RMS gradient? '''0.00007365'''

What is the point group of your molecule? '''D∞h'''

Bond Length: '''1.4028 au'''

Bond Angle: '''180 degrees'''

'''Item Table'''

             Item               Value     Threshold  Converged?
  Maximum Force            0.000128     0.000450     YES
  RMS     Force            0.000128     0.000300     YES
  Maximum Displacement     0.000157     0.001800     YES
  RMS     Displacement     0.000221     0.001200     YES
  Predicted change in Energy=-2.131104D-08
  Optimization completed.
     -- Stationary point found.
                            ----------------------------
                            !   Optimized Parameters   !
                            ! (Angstroms and Degrees)  !
  --------------------------                            --------------------------
  ! Name  Definition              Value          Derivative Info.                !
  --------------------------------------------------------------------------------
  ! R1    R(1,2)                  1.4028         -DE/DX =    0.0001              !
  --------------------------------------------------------------------------------
  GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

'''Log File'''

[[File:ODUAN_F2.LOG]]

'''Static Image'''


[[File:oduan_f2_image.png|150px]]


'''Jmol Image ''' 

  <jmol><jmolApplet>

  <title>F2</title>

  <color>black</color>

 <size>200</size>

  <uploadedFileContents>ODUAN_F2.LOG</uploadedFileContents>

  </jmolApplet></jmol>


'''Display Vibrations File'''

[[File:oduan_displayvibrations_f2.png]]

'''Charge Distribution Info:'''

Both F atoms have a 0.000 charge (molecule is non-polar)

'''Vibration Info:'''

This molecule has 1 vibrational mode as predicted by the 3N - 5 rule for linear molecules (3*2-5 = 1). It is a symmetric stretch with the frequency 1065.09

== '''F2 Orbital Pictures and Discussion''' ==

[[File:oduan_f2_orbital_pic1.png]]

The above orbital is a bonding 1σ orbital created by the constructive overlap of the 1s atomic orbital on each F atom. The MO is deep in energy. The MO is occupied. This MO is not directly involved in bonding.


[[File:oduan_f2_orbital_pic2.png]]

The above orbital is an antibonding 1σ* orbital created by the destructive overlap of the 1s atomic orbital on each F atom. The MO is deep in energy. The MO is occupied. This MO is not directly involved in bonding. This MO effectively "cancels out" the 1σ orbital.

[[File:oduan_f2_orbital_pic3.png]]

The above orbital is a bonding 2σ orbital created by the constructive, head-on overlap of the 2p atomic orbital on each F atom. The MO is deep in energy. The MO is occupied. This MO is responsible for the single bond between the F atoms.

[[File:oduan_f2_orbital_pic4.png]]

The above orbital is an bonding 2π orbital created by the sideways, constructive overlap of the 2p atomic orbital on each F atom. The MO is deep in energy. The MO is occupied. This bonding orbital contributes positively to the overall stability of the atom.

[[File:oduan_f2_orbital_pic5.png]]

The above orbital is an antibonding 2π* orbital created by the sideways, destructive overlap of the 2p orbital on each F atom. The MO is the HOMO. The MO is occupied. Electrons from this molecule will interact with the LUMO of another atom in reactions to potentially form new bonds.

== '''Independent Work''' ==

For my independent work I decided to run an analysis on ClF3. 

What is the molecule? '''ClF3'''

What is the calculation method? '''RB3LYP'''

What is the basis set? '''6-31G(d,p)'''

What is the final energy E(RB3LYP) in atomic units (au)? '''-759.44149573'''  

What is the RMS gradient? '''0.00000553'''

What is the point group of your molecule? '''C3V'''

Bond Length: '''1.75684 au'''

Bond Angle: '''120 degrees'''


'''Item Table'''

         Item               Value     Threshold  Converged?
 Maximum Force            0.000011     0.000450     YES
 RMS     Force            0.000007     0.000300     YES
 Maximum Displacement     0.000049     0.001800     YES
 RMS     Displacement     0.000032     0.001200     YES
 Predicted change in Energy=-8.249258D-10
 Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.7568         -DE/DX =    0.0                 !
 ! R2    R(1,3)                  1.7568         -DE/DX =    0.0                 !
 ! R3    R(1,4)                  1.7568         -DE/DX =    0.0                 !
 ! A1    A(2,1,3)              120.0            -DE/DX =    0.0                 !
 ! A2    A(2,1,4)              120.0            -DE/DX =    0.0                 !
 ! A3    A(3,1,4)              120.0            -DE/DX =    0.0                 !
 ! D1    D(2,1,4,3)            180.0            -DE/DX =    0.0                 !
 --------------------------------------------------------------------------------
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

'''Log File'''


[[File:ODUAN_CLF3.LOG]]


'''Static Image'''


[[File:oduan_clf3_image.png|150px]]


'''Jmol Image ''' 

  <jmol><jmolApplet>

  <title>ClF3</title>

  <color>black</color>

 <size>200</size>

  <uploadedFileContents>ODUAN_CLF3.LOG</uploadedFileContents>

  </jmolApplet></jmol>

'''Display Vibrations File''' 

[[File:Oduan_displayvibrations_clf3.png]]

'''Vibrational Information''' 

Mode 1 is bending (scissor)

Mode 2 is bending (rocking)

Mode 3 is bending (umbrella)

Mode 4 is symmetric stretching

Modes 5 and 6 are asymmetric stretching

Modes 5 and 6 are degenerate

'''Charge Information''' 

The Cl atom has a + 0.898 charge 

The F atoms have a -0.338 charge