ChemWiki - User contributions [en]

ERHW DFT calc

2020-04-23T16:11:36Z

Ewalter: /* NH3BH3 optimisation data */

=='''Level 1 Lab classes: DFT calculations'''==
===Practice simulations and optimisations===
====NH3 optimisation data====

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: C3v

Optimised NH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PHUNT NH3 OPTIMISATION EW.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986279D-10
</pre>

<pre>
Bond distances and bond angles
! 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 !
</pre>

XYZ file
<pre>
4
NH3molecule
N 0.0000 0.0000 0.1192 N
H 0.0000 0.9372 -0.2782 H
H -0.8116 -0.4686 -0.2782 H
H 0.8116 -0.4686 -0.2782 H
</pre>

[[File:Printscreenofvibrations.jpg|1000px|thumb|center|screen shot of vibrational modes]]

====Vibrational modes====

{| class="wikitable" border="1"
|+ Vibrational modes
! !! 1 !! 2 !! 3 !! 4 !! 5 !! 6
|-
| '''wavenumber (cm-1)''' || 1090 || 1694 || 1694 || 3461 || 3590 || 3590 ||
|-
| '''symmetry''' || A1 || E || E || A1 || E || E ||
|-
| '''Intensity''' (arbitrary units) || 145 || 14 || 14 || 1 || 0.3 || 0.3 ||
|-
| '''Diagram''' || [[File:erhw_NH3_vib1.jpg|300px]] || [[File:erhw_NH3_vib2.jpg|300px]] || [[File:erhw_NH3_vib3.jpg|300px]]
||[[File:erhw_NH3_vib4.jpg|300px]] || [[File:erhw_NH3_vib5.jpg|300px]] || [[File:erhw_NH3_vib6.jpg|300px]] ||
|}

====Charge distribution====

[[File:erhw_NH3_chargedistribution.jpg|500px|thumb|center| A screenshot showing the charge distribution in a NH3 molecule.]]

===PF5optimisation data===

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: D3h

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>EW PF5 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000011 0.000300 YES
Maximum Displacement 0.000061 0.001800 YES
RMS Displacement 0.000026 0.001200 YES
Predicted change in Energy=-3.393566D-09
</pre>

<pre>
Bond distances and bond angles
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.5693 -DE/DX = 0.0 !
! R2 R(1,3) 1.597 -DE/DX = 0.0 !
! R3 R(1,4) 1.5693 -DE/DX = 0.0 !
! R4 R(1,5) 1.5693 -DE/DX = 0.0 !
! R5 R(1,6) 1.597 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 90.0 -DE/DX = 0.0 !
! A5 A(3,1,4) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 120.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 90.0 -DE/DX = 0.0 !
! A10 L(3,1,6,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,6,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -90.0 -DE/DX = 0.0 !
! D2 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) 180.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) -120.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 120.0 -DE/DX = 0.0 !
! D6 D(3,1,5,4) 90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) -120.0 -DE/DX = 0.0 !
</pre>

XYZ file
<pre>
6
PF5
1 P1 0.0000 0.0000 0.0000 P
2 F2 0.0000 1.5693 0.0000 F
3 F3 0.0000 0.0000 1.5970 F
4 F4 -1.3590 -0.7846 0.0000 F
5 F5 1.3590 -0.7846 0.0000 F
6 F6 0.0000 0.0000 -1.5970 F
</pre>

=='''Level 2 Lab classes: DFT calculations'''==

===BH3 optimisation data===

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group:

Optimised BH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ERHW_BH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000710 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
Predicted change in Energy=-1.365987D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1928 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1924 -DE/DX = 0.0 !
! R3 R(1,4) 1.1926 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9864 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0146 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.999 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
</pre>

===NH3BH3 optimisation data===

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group:

Optimised NH3BH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ERHW_NH3BH3_REPEAT.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000121 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.000564 0.001800 YES
RMS Displacement 0.000316 0.001200 YES
Predicted change in Energy=-1.705954D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5969 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.8743 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5969 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8689 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8689 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0296 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8689 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0296 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0296 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 180.0 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 60.0 -DE/DX = 0.0 !
! D6 D(2,7,8,6) 180.0 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 60.0 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 180.0 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0 -DE/DX = 0.0 !
</pre>

ERHW DFT calc

2020-04-23T16:08:08Z

Ewalter: /* NH3BH3 optimisation data */

File:ERHW NH3BH3 REPEAT.LOG

2020-04-23T16:07:26Z

Ewalter:

ERHW DFT calc

2020-04-23T16:05:03Z

Ewalter: /* Level 2 Lab classes: DFT calculations */

=='''Level 1 Lab classes: DFT calculations'''==
===Practice simulations and optimisations===
====NH3 optimisation data====

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: C3v

Optimised NH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PHUNT NH3 OPTIMISATION EW.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986279D-10
</pre>

<pre>
Bond distances and bond angles
! 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 !
</pre>

XYZ file
<pre>
4
NH3molecule
N 0.0000 0.0000 0.1192 N
H 0.0000 0.9372 -0.2782 H
H -0.8116 -0.4686 -0.2782 H
H 0.8116 -0.4686 -0.2782 H
</pre>

[[File:Printscreenofvibrations.jpg|1000px|thumb|center|screen shot of vibrational modes]]

====Vibrational modes====

{| class="wikitable" border="1"
|+ Vibrational modes
! !! 1 !! 2 !! 3 !! 4 !! 5 !! 6
|-
| '''wavenumber (cm-1)''' || 1090 || 1694 || 1694 || 3461 || 3590 || 3590 ||
|-
| '''symmetry''' || A1 || E || E || A1 || E || E ||
|-
| '''Intensity''' (arbitrary units) || 145 || 14 || 14 || 1 || 0.3 || 0.3 ||
|-
| '''Diagram''' || [[File:erhw_NH3_vib1.jpg|300px]] || [[File:erhw_NH3_vib2.jpg|300px]] || [[File:erhw_NH3_vib3.jpg|300px]]
||[[File:erhw_NH3_vib4.jpg|300px]] || [[File:erhw_NH3_vib5.jpg|300px]] || [[File:erhw_NH3_vib6.jpg|300px]] ||
|}

====Charge distribution====

[[File:erhw_NH3_chargedistribution.jpg|500px|thumb|center| A screenshot showing the charge distribution in a NH3 molecule.]]

===PF5optimisation data===

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: D3h

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>EW PF5 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000011 0.000300 YES
Maximum Displacement 0.000061 0.001800 YES
RMS Displacement 0.000026 0.001200 YES
Predicted change in Energy=-3.393566D-09
</pre>

<pre>
Bond distances and bond angles
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.5693 -DE/DX = 0.0 !
! R2 R(1,3) 1.597 -DE/DX = 0.0 !
! R3 R(1,4) 1.5693 -DE/DX = 0.0 !
! R4 R(1,5) 1.5693 -DE/DX = 0.0 !
! R5 R(1,6) 1.597 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 90.0 -DE/DX = 0.0 !
! A5 A(3,1,4) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 120.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 90.0 -DE/DX = 0.0 !
! A10 L(3,1,6,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,6,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -90.0 -DE/DX = 0.0 !
! D2 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) 180.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) -120.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 120.0 -DE/DX = 0.0 !
! D6 D(3,1,5,4) 90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) -120.0 -DE/DX = 0.0 !
</pre>

XYZ file
<pre>
6
PF5
1 P1 0.0000 0.0000 0.0000 P
2 F2 0.0000 1.5693 0.0000 F
3 F3 0.0000 0.0000 1.5970 F
4 F4 -1.3590 -0.7846 0.0000 F
5 F5 1.3590 -0.7846 0.0000 F
6 F6 0.0000 0.0000 -1.5970 F
</pre>

=='''Level 2 Lab classes: DFT calculations'''==

===BH3 optimisation data===

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group:

Optimised BH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ERHW_BH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000710 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
Predicted change in Energy=-1.365987D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1928 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1924 -DE/DX = 0.0 !
! R3 R(1,4) 1.1926 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9864 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0146 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.999 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
</pre>

===NH3BH3 optimisation data===

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group:

Optimised NH3BH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ERHW_BH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

ERHW DFT calc

2020-04-23T09:22:55Z

Ewalter: /* BH3 optimisation data */

ERHW DFT calc

2020-04-23T09:09:11Z

Ewalter: /* Level 2 Lab classes: DFT calculations */

File:ERHW BH3 OPTIMISATION.LOG

2020-04-23T09:06:49Z

Ewalter:

ERHW DFT calc

2020-04-23T08:53:01Z

Ewalter: /* Level 2 Lab classes: DFT calculations */

ERHW DFT calc

2020-04-23T08:37:54Z

Ewalter: /* Level 1 Lab classes: DFT calculations */

ERHW DFT calc

2020-04-23T08:37:21Z

Ewalter: /* DFT calculations */

ERHW DFT calc

2020-04-23T08:36:24Z

Ewalter: /* DFT calculations */

=='''DFT calculations'''==
===Practice simulations and optimisations===
====NH3 optimisation data====

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: C3v

Optimised NH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PHUNT NH3 OPTIMISATION EW.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986279D-10
</pre>

<pre>
Bond distances and bond angles
! 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 !
</pre>

XYZ file
<pre>
4
NH3molecule
N 0.0000 0.0000 0.1192 N
H 0.0000 0.9372 -0.2782 H
H -0.8116 -0.4686 -0.2782 H
H 0.8116 -0.4686 -0.2782 H
</pre>

[[File:Printscreenofvibrations.jpg|1000px|thumb|center|screen shot of vibrational modes]]

====Vibrational modes====

{| class="wikitable" border="1"
|+ Vibrational modes
! !! 1 !! 2 !! 3 !! 4 !! 5 !! 6
|-
| '''wavenumber (cm-1)''' || 1090 || 1694 || 1694 || 3461 || 3590 || 3590 ||
|-
| '''symmetry''' || A1 || E || E || A1 || E || E ||
|-
| '''Intensity''' (arbitrary units) || 145 || 14 || 14 || 1 || 0.3 || 0.3 ||
|-
| '''Diagram''' || [[File:erhw_NH3_vib1.jpg|300px]] || [[File:erhw_NH3_vib2.jpg|300px]] || [[File:erhw_NH3_vib3.jpg|300px]]
||[[File:erhw_NH3_vib4.jpg|300px]] || [[File:erhw_NH3_vib5.jpg|300px]] || [[File:erhw_NH3_vib6.jpg|300px]] ||
|}

====Charge distribution====

[[File:erhw_NH3_chargedistribution.jpg|500px|thumb|center| A screenshot showing the charge distribution in a NH3 molecule.]]

===PF5optimisation data===

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: D3h

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>EW PF5 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000011 0.000300 YES
Maximum Displacement 0.000061 0.001800 YES
RMS Displacement 0.000026 0.001200 YES
Predicted change in Energy=-3.393566D-09
</pre>

<pre>
Bond distances and bond angles
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.5693 -DE/DX = 0.0 !
! R2 R(1,3) 1.597 -DE/DX = 0.0 !
! R3 R(1,4) 1.5693 -DE/DX = 0.0 !
! R4 R(1,5) 1.5693 -DE/DX = 0.0 !
! R5 R(1,6) 1.597 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 90.0 -DE/DX = 0.0 !
! A5 A(3,1,4) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 120.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 90.0 -DE/DX = 0.0 !
! A10 L(3,1,6,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,6,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -90.0 -DE/DX = 0.0 !
! D2 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) 180.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) -120.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 120.0 -DE/DX = 0.0 !
! D6 D(3,1,5,4) 90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) -120.0 -DE/DX = 0.0 !
</pre>

XYZ file
<pre>
6
PF5
1 P1 0.0000 0.0000 0.0000 P
2 F2 0.0000 1.5693 0.0000 F
3 F3 0.0000 0.0000 1.5970 F
4 F4 -1.3590 -0.7846 0.0000 F
5 F5 1.3590 -0.7846 0.0000 F
6 F6 0.0000 0.0000 -1.5970 F
</pre>

ERHW DFT calc

2020-04-23T08:34:13Z

Ewalter: /* DFT calculations */

=='''DFT calculations'''==
===Practice simulations and optimisations===
====NH3 optimisation data====

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: C3v

Optimised NH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PHUNT NH3 OPTIMISATION EW.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986279D-10
</pre>

<pre>
Bond distances and bond angles
! 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 !
</pre>

XYZ file
<pre>
4
NH3 molecule
N 0.0000 0.0000 0.1192 N
H 0.0000 0.9372 -0.2782 H
H -0.8116 -0.4686 -0.2782 H
H 0.8116 -0.4686 -0.2782 H
</pre>

[[File:Printscreenofvibrations.jpg|1000px|thumb|center|screen shot of vibrational modes]]

====Vibrational modes====

{| class="wikitable" border="1"
|+ Vibrational modes
! !! 1 !! 2 !! 3 !! 4 !! 5 !! 6
|-
| '''wavenumber (cm-1)''' || 1090 || 1694 || 1694 || 3461 || 3590 || 3590 ||
|-
| '''symmetry''' || A1 || E || E || A1 || E || E ||
|-
| '''Intensity''' (arbitrary units) || 145 || 14 || 14 || 1 || 0.3 || 0.3 ||
|-
| '''Diagram''' || [[File:erhw_NH3_vib1.jpg|300px]] || [[File:erhw_NH3_vib2.jpg|300px]] || [[File:erhw_NH3_vib3.jpg|300px]]
||[[File:erhw_NH3_vib4.jpg|300px]] || [[File:erhw_NH3_vib5.jpg|300px]] || [[File:erhw_NH3_vib6.jpg|300px]] ||
|}

====Charge distribution====

[[File:erhw_NH3_chargedistribution.jpg|500px|thumb|center| A screenshot showing the charge distribution in a NH3 molecule.]]

===PF optimisation data===

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: D3h

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>EW PF5 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000011 0.000300 YES
Maximum Displacement 0.000061 0.001800 YES
RMS Displacement 0.000026 0.001200 YES
Predicted change in Energy=-3.393566D-09
</pre>

<pre>
Bond distances and bond angles
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.5693 -DE/DX = 0.0 !
! R2 R(1,3) 1.597 -DE/DX = 0.0 !
! R3 R(1,4) 1.5693 -DE/DX = 0.0 !
! R4 R(1,5) 1.5693 -DE/DX = 0.0 !
! R5 R(1,6) 1.597 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 90.0 -DE/DX = 0.0 !
! A5 A(3,1,4) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 120.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 90.0 -DE/DX = 0.0 !
! A10 L(3,1,6,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,6,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -90.0 -DE/DX = 0.0 !
! D2 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) 180.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) -120.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 120.0 -DE/DX = 0.0 !
! D6 D(3,1,5,4) 90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) -120.0 -DE/DX = 0.0 !
</pre>

XYZ file
<pre>
6
PF5
1 P1 0.0000 0.0000 0.0000 P
2 F2 0.0000 1.5693 0.0000 F
3 F3 0.0000 0.0000 1.5970 F
4 F4 -1.3590 -0.7846 0.0000 F
5 F5 1.3590 -0.7846 0.0000 F
6 F6 0.0000 0.0000 -1.5970 F
</pre>

ERHW DFT calc

2020-04-22T14:59:33Z

Ewalter: /* DFT calculations */

=='''DFT calculations'''==
===Practice simulations and optimisations===
====NH3 optimisation data====

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: C3v

Optimised NH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PHUNT NH3 OPTIMISATION EW.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986279D-10
</pre>

<pre>
Bond distances and bond angles
! 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 !
</pre>

[[File:Printscreenofvibrations.jpg|1000px|thumb|center|screen shot of vibrational modes]]

====Vibrational modes====

{| class="wikitable" border="1"
|+ Vibrational modes
! !! 1 !! 2 !! 3 !! 4 !! 5 !! 6
|-
| '''wavenumber (cm-1)''' || 1090 || 1694 || 1694 || 3461 || 3590 || 3590 ||
|-
| '''symmetry''' || A1 || E || E || A1 || E || E ||
|-
| '''Intensity''' (arbitrary units) || 145 || 14 || 14 || 1 || 0.3 || 0.3 ||
|-
| '''Diagram''' || [[File:erhw_NH3_vib1.jpg|300px]] || [[File:erhw_NH3_vib2.jpg|300px]] || [[File:erhw_NH3_vib3.jpg|300px]]
||[[File:erhw_NH3_vib4.jpg|300px]] || [[File:erhw_NH3_vib5.jpg|300px]] || [[File:erhw_NH3_vib6.jpg|300px]] ||
|}

====Charge distribution====

[[File:erhw_NH3_chargedistribution.jpg|500px|thumb|center| A screenshot showing the charge distribution in a NH3 molecule.]]

===PF optimisation data===

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: D3h

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>EW PF5 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000011 0.000300 YES
Maximum Displacement 0.000061 0.001800 YES
RMS Displacement 0.000026 0.001200 YES
Predicted change in Energy=-3.393566D-09
</pre>

<pre>
Bond distances and bond angles
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.5693 -DE/DX = 0.0 !
! R2 R(1,3) 1.597 -DE/DX = 0.0 !
! R3 R(1,4) 1.5693 -DE/DX = 0.0 !
! R4 R(1,5) 1.5693 -DE/DX = 0.0 !
! R5 R(1,6) 1.597 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 90.0 -DE/DX = 0.0 !
! A5 A(3,1,4) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 120.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 90.0 -DE/DX = 0.0 !
! A10 L(3,1,6,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,6,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -90.0 -DE/DX = 0.0 !
! D2 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) 180.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) -120.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 120.0 -DE/DX = 0.0 !
! D6 D(3,1,5,4) 90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) -120.0 -DE/DX = 0.0 !
</pre>

ERHW DFT calc

2020-04-22T14:55:32Z

Ewalter: /* DFT calculations */

ERHW DFT calc

2020-04-22T14:53:54Z

Ewalter: /* DFT calculations */

File:EW PF5 OPTIMISATION.LOG

2020-04-22T14:53:01Z

Ewalter:

ERHW DFT calc

2020-04-22T14:52:29Z

Ewalter: /* DFT calculations */

ERHW DFT calc

2020-04-22T11:19:34Z

Ewalter: /* Practice simulations and optimisations */

File:Erhw NH3 chargedistribution.jpg

2020-04-22T11:13:20Z

Ewalter:

ERHW DFT calc

2020-04-22T11:08:03Z

Ewalter: /* Practice simulations and optimisations */

=='''DFT calculations'''==
===Practice simulations and optimisations===
====1. NH3 optimisation====

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: C3v

Optimised NH3 molecule

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PHUNT NH3 OPTIMISATION EW.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986279D-10
</pre>

<pre>
Bond distances and bond angles
! 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 !
</pre>

[[File:Printscreenofvibrations.jpg|1000px|thumb|center|screen shot of vibrational modes]]

{| class="wikitable" border="1"
|+ Vibrational modes
! !! 1 !! 2 !! 3 !! 4 !! 5 !! 6
|-
| '''wavenumber (cm-1)''' || 1090 || 1694 || 1694 || 3461 || 3590 || 3590 ||
|-
| '''symmetry''' || A1 || E || E || A1 || E || E ||
|-
| '''Intensity''' (arbitrary units) || 145 || 14 || 14 || 1 || 0.3 || 0.3 ||
|-
| '''Diagram''' || [[File:erhw_NH3_vib1.jpg|300px]] || [[File:erhw_NH3_vib2.jpg|300px]] || [[File:erhw_NH3_vib3.jpg|300px]]
||[[File:erhw_NH3_vib4.jpg|300px]] || [[File:erhw_NH3_vib5.jpg|300px]] || [[File:erhw_NH3_vib6.jpg|300px]] ||
|}

====1i. Questions====

1. With the 3N-6 rule would expect 6 modes
2. A1 modes are degenerate and have the same energy
3. 4

ERHW DFT calc

2020-04-22T11:04:05Z

Ewalter: /* Practice simulations and optimisations */

File:Erhw NH3 vib6.jpg

2020-04-22T10:59:31Z

Ewalter:

File:Erhw NH3 vib5.jpg

2020-04-22T10:58:51Z

Ewalter:

File:Erhw NH3 vib4.jpg

2020-04-22T10:58:35Z

Ewalter:

File:Erhw NH3 vib3.jpg

2020-04-22T10:58:19Z

Ewalter:

File:Erhw NH3 vib2.jpg

2020-04-22T10:58:04Z

Ewalter:

File:Erhw NH3 vib1.jpg

2020-04-22T10:57:40Z

Ewalter:

ERHW DFT calc

2020-04-22T10:56:28Z

Ewalter: /* DFT calculations */

ERHW DFT calc

2020-04-22T10:20:41Z

Ewalter: /* DFT calculations */

ERHW DFT calc

2020-04-22T10:15:56Z

Ewalter: /* DFT calculations */

File:Printscreenofvibrations.jpg

2020-04-22T10:13:11Z

Ewalter:

ERHW DFT calc

2020-04-22T09:58:41Z

Ewalter: /* DFT calculations */

File:PHUNT NH3 OPTIMISATION EW.LOG

2020-04-22T09:45:11Z

Ewalter: Ewalter uploaded a new version of File:PHUNT NH3 OPTIMISATION EW.LOG

ERHW DFT calc

2020-04-22T09:43:22Z

Ewalter: /* DFT calculations */

=='''DFT calculations'''==
===Practice simulations and optimisations===
====1. NH3 optimisation====

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: C3v

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PHUNT NH3 OPTIMISATION EW.LOG</uploadedFileContents>
</jmolApplet></jmol>

File:PHUNT NH3 OPTIMISATION EW.LOG

2020-04-22T09:05:03Z

Ewalter: Ewalter uploaded a new version of File:PHUNT NH3 OPTIMISATION EW.LOG

File:PHUNT NH3 OPTIMISATION EW.LOG

2020-04-22T08:53:18Z

Ewalter: Ewalter uploaded a new version of File:PHUNT NH3 OPTIMISATION EW.LOG

File:PHUNT NH3 OPTIMISATION EW.LOG

2020-04-22T08:50:13Z

Ewalter:

ERHW DFT calc

2020-04-22T08:49:24Z

Ewalter: /* Practice simulations and optimisations */

=='''DFT calculations'''==
===Practice simulations and optimisations===
====1. NH3 optimisation====

Method: B3LYP

Basis set: 6-31G(d,p)

Calculations: OPTF

Point group: C3v

ERHW DFT calc

2020-04-22T08:48:45Z

Ewalter: Created page with "=='''DFT calculations'''== ===Practice simulations and optimisations=== ====1. NH3 optimisation==== Method: B3LYP Basis set: 6-31G(d,p) Calculations: OPTF Point group:..."

=='''DFT calculations'''==
===Practice simulations and optimisations===
====1. NH3 optimisation====

Method: B3LYP
Basis set: 6-31G(d,p)
Calculations: OPTF

Point group: C3v

File:Word file for Wikipedia practice.docx

2020-04-01T15:53:31Z

Ewalter: