ChemWiki - User contributions [en]

Blb15 2016-3-7

2016-03-11T17:58:04Z

Blb15: /* Molecular orbitals */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CH2O_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

== Molecular orbitals ==

[[File:BLB15_CH2O_MOs.png]]

MOs 1 and 2 involve the 1s electrons of oxygen and carbon in a nonbonding MO , localized tightly around C and O.

MO 3 is the σ bonding MO from 2s orbitals of C and O:
[[File:BLB15_CH2O_orb_3.jpg]]

MO 4 is the σ* antibonding from MO 2s electrons of the two H:
[[File:BLB15_CH2O_orb_4.jpg]]

MO 5 is the is the bonding combination of 1s with the 2px of C and O:
[[File:BLB15_CH2O_orb_5.jpg]]

MO 6 is the bonding 2py of C and O:
[[File:BLB15_CH2O_orb_6.jpg]]

MO 7 is the bonding 2pz of C and O:
[[File:BLB15_CH2O_orb_7.jpg]]

MO 8 is the HOMO σ*, made from the 1s and 2px
[[File:BLB15_CH2O_orb_8.jpg]]

MO 9 in the LUMO pi* anti-bonding, made from the 2pz
[[File:BLB15_CH2O_orb_9.jpg]]

Blb15 2016-3-7

2016-03-11T17:56:52Z

Blb15: /* Molecular orbitals */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CH2O_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

== Molecular orbitals ==

[[File:BLB15_CH2O_MOs.png]]

MOs 1 and 2 involve the 1s electrons of oxygen and carbon in a nonbonding MO , localized tightly around C and O.

MO 3 is the σ bonding MO from 2s orbitals of C and O:
[[File:BLB15_CH2O_orb_3.jpg]]

MO 4 is the σ* antibonding from MO 2s electrons of the two H:
[[File:BLB15_CH2O_orb_4.jpg]]

MO 5 is the is the combination of 1s with the 2px of C and O:
[[File:BLB15_CH2O_orb_5.jpg]]

MO 6 is the 2py of C and O:
[[File:BLB15_CH2O_orb_6.jpg]]

MO 7 is the 2pz of C and O:
[[File:BLB15_CH2O_orb_7.jpg]]

MO 8 is the HOMO σ*, made from the 1s and 2px
[[File:BLB15_CH2O_orb_8.jpg]]

MO 9 in the LUMO pi*, made from the 2pz
[[File:BLB15_CH2O_orb_9.jpg]]

Blb15 2016-3-7

2016-03-11T17:55:32Z

Blb15: /* Basics */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CH2O_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

== Molecular orbitals ==

[[File:BLB15_CH2O_MOs.png]]

MOs 1 and 2 involve the 1s electrons of oxygen and carbon in a nonbonding MO , localized tightly around C and O.

MO 3 is the σ bonding MO from 2s orbitals of C and O:
[[File:BLB15_CH2O_orb_3.jpg]]

MO 4 is the σ* antibonding from MO 2s electrons of the two H:
[[File:BLB15_CH2O_orb_4.jpg]]

MO 5 is the is the combination of 1s with the 2px of C and O:
[[File:BLB15_CH2O_orb_5.jpg]]

MO 6 is the 2py of C and O:
[[File:BLB15_CH2O_orb_6.jpg]]

MO 7 is the of C and O:
[[File:BLB15_CH2O_orb_7.jpg]]

MO 8 is the HOMO σ*, made from the 1s and 2px
[[File:BLB15_CH2O_orb_8.jpg]]

MO 9 in the LUMO pi*, made from the 2pz
[[File:BLB15_CH2O_orb_9.jpg]]

Blb15 2016-3-7

2016-03-11T17:54:47Z

Blb15: /* Basics */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CH2O POP.log</uploadedFileContents>
</jmolApplet></jmol>
=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

== Molecular orbitals ==

[[File:BLB15_CH2O_MOs.png]]

MOs 1 and 2 involve the 1s electrons of oxygen and carbon in a nonbonding MO , localized tightly around C and O.

MO 3 is the σ bonding MO from 2s orbitals of C and O:
[[File:BLB15_CH2O_orb_3.jpg]]

MO 4 is the σ* antibonding from MO 2s electrons of the two H:
[[File:BLB15_CH2O_orb_4.jpg]]

MO 5 is the is the combination of 1s with the 2px of C and O:
[[File:BLB15_CH2O_orb_5.jpg]]

MO 6 is the 2py of C and O:
[[File:BLB15_CH2O_orb_6.jpg]]

MO 7 is the of C and O:
[[File:BLB15_CH2O_orb_7.jpg]]

MO 8 is the HOMO σ*, made from the 1s and 2px
[[File:BLB15_CH2O_orb_8.jpg]]

MO 9 in the LUMO pi*, made from the 2pz
[[File:BLB15_CH2O_orb_9.jpg]]

File:CH2O POP.LOG

2016-03-11T17:54:10Z

Blb15:

Blb15 2016-3-7

2016-03-11T17:49:22Z

Blb15: /* Molecular orbitals */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

== Molecular orbitals ==

[[File:BLB15_CH2O_MOs.png]]

MOs 1 and 2 involve the 1s electrons of oxygen and carbon in a nonbonding MO , localized tightly around C and O.

MO 3 is the σ bonding MO from 2s orbitals of C and O:
[[File:BLB15_CH2O_orb_3.jpg]]

MO 4 is the σ* antibonding from MO 2s electrons of the two H:
[[File:BLB15_CH2O_orb_4.jpg]]

MO 5 is the is the combination of 1s with the 2px of C and O:
[[File:BLB15_CH2O_orb_5.jpg]]

MO 6 is the 2py of C and O:
[[File:BLB15_CH2O_orb_6.jpg]]

MO 7 is the of C and O:
[[File:BLB15_CH2O_orb_7.jpg]]

MO 8 is the HOMO σ*, made from the 1s and 2px
[[File:BLB15_CH2O_orb_8.jpg]]

MO 9 in the LUMO pi*, made from the 2pz
[[File:BLB15_CH2O_orb_9.jpg]]

Blb15 2016-3-7

2016-03-11T17:46:23Z

Blb15: /* Molecular orbitals */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

== Molecular orbitals ==

[[File:BLB15_CH2O_MOs.png]]

MOs 1 and 2 involve the 1s electrons of oxygen and carbon in a nonbonding MO , localized tightly around C and O.

MO 3 is the σ bonding MO from 2s orbitals of C and O:
[[File:BLB15_CH2O_orb_3.jpg]]

MO 4 is the σ* antibonding from MO 2s electrons of the two H:
[[File:BLB15_CH2O_orb_4.jpg]]

MO 5 is the is the combination of 1s with the 2px of C and O:
[[File:BLB15_CH2O_orb_5.jpg]]

MO 6 is the 2py of C and O:
[[File:BLB15_CH2O_orb_6.jpg]]

MO 7 is the 2pz of C and O:
[[File:BLB15_CH2O_orb_7.jpg]]

MO 8 is the HOMO σ*, made from the 1s and 2px
[[File:BLB15_CH2O_orb_8.jpg]]

MO 9 in the LUMO,
[[File:BLB15_CH2O_orb_9.jpg]]

[[File:BLB15_CH2O_orb_10.jpg]]

[[File:BLB15_CH2O_orb_11.jpg]]

Blb15 2016-3-7

2016-03-11T17:45:40Z

Blb15:

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

== Molecular orbitals ==

[[File:BLB15_CH2O_MOs.png]]

MOs 1 and 2 involve the 1s electrons of oxygen and carbon in a nonbonding MO , localized tightly around C and O.
MO 3 is the σ bonding MO from 2s orbitals of C and O:
[[File:BLB15_CH2O_orb_3.jpg]]
MO 4 is the σ* antibonding from MO 2s electrons of the two H:
[[File:BLB15_CH2O_orb_4.jpg]]
MO 5 is the is the combination of 1s with the 2px of C and O:
[[File:BLB15_CH2O_orb_5.jpg]]
MO 6 is the 2py of C and O:
[[File:BLB15_CH2O_orb_6.jpg]]
MO 7 is the 2pz of C and O:
[[File:BLB15_CH2O_orb_7.jpg]]
MO 8 is the HOMO σ*, made from the 1s and 2px
[[File:BLB15_CH2O_orb_8.jpg]]
MO 9 in the LUMO,
[[File:BLB15_CH2O_orb_9.jpg]]

[[File:BLB15_CH2O_orb_10.jpg]]

[[File:BLB15_CH2O_orb_11.jpg]]

File:BLB15 CH2O orb 11.jpg

2016-03-11T17:21:57Z

Blb15:

File:BLB15 CH2O orb 10.jpg

2016-03-11T17:21:49Z

Blb15:

File:BLB15 CH2O orb 9.jpg

2016-03-11T17:21:36Z

Blb15:

File:BLB15 CH2O orb 8.jpg

2016-03-11T17:21:22Z

Blb15:

File:BLB15 CH2O orb 7.jpg

2016-03-11T17:21:14Z

Blb15:

File:BLB15 CH2O orb 6.jpg

2016-03-11T17:21:05Z

Blb15:

File:BLB15 CH2O orb 5.jpg

2016-03-11T17:20:55Z

Blb15:

File:BLB15 CH2O orb 4.jpg

2016-03-11T17:20:45Z

Blb15:

File:BLB15 CH2O orb 3.jpg

2016-03-11T17:20:36Z

Blb15:

File:BLB15 CH2O MOs.png

2016-03-11T15:59:02Z

Blb15:

Blb15 2016-3-7

2016-03-11T15:55:03Z

Blb15: /* Vibrations */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

Blb15 2016-3-7

2016-03-11T15:54:23Z

Blb15: /* Vibrations */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

Blb15 2016-3-7

2016-03-11T15:54:08Z

Blb15: /* Charge distribution */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]

The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

Blb15 2016-3-7

2016-03-11T15:53:53Z

Blb15: /* Vibrations */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

=== Charge distribution ===
[[File:BLB15_CH2O_charge.jpg]]
The charges are according to expectations, the oxygen wears a positive partial charge, while the carbon and the hydrogens are positive, the carbon being the most positive.

File:BLB15 CH2O charge.jpg

2016-03-11T15:49:42Z

Blb15: Blb15 uploaded a new version of File:BLB15 CH2O charge.jpg

Blb15 2016-3-7

2016-03-11T15:49:08Z

Blb15: /* Simulation of formaldehyde */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
The modes visualised in order 1-6:
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

Blb15 2016-3-7

2016-03-11T15:48:34Z

Blb15:

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

Blb15 2016-3-7

2016-03-11T15:45:50Z

Blb15: /* Basics */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

== N2 ==

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif|thumb|Mode 1]]
[[File:Blb15 ch2o vibr 2.gif|thumb|Mode 2]]
[[File:Blb15 ch2o vibr 3.gif|thumb|Mode 3]]
[[File:Blb15 ch2o vibr 4.gif|thumb|Mode 4]]
[[File:Blb15 ch2o vibr 5.gif|thumb|Mode 5]]
[[File:Blb15 ch2o vibr 6.gif|thumb|Mode 6]]

Blb15 2016-3-7

2016-03-11T15:43:09Z

Blb15: /* H2 */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

== N2 ==

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

Blb15 2016-3-7

2016-03-11T15:42:33Z

Blb15: /* 1 */

= Getting started =
== NH3 ==
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

== H2 ==

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

Blb15 2016-3-7

2016-03-11T15:41:19Z

Blb15: /* 3 */

== 1 ==
=== 2 ===
==== 3 ====
NH3
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

H2

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

Blb15 2016-3-7

2016-03-11T15:40:58Z

Blb15: /* 3 */

== 1 ==
=== 2 ===
==== 3 ====
NH3
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798 -1.95227 0.00000 0.00000 -0.00011 -0.00011 -1.95238
</pre>
<pre> 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=-5.785205D-10
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

H2

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

Blb15 2016-3-7

2016-03-11T15:40:10Z

Blb15: /* Simulation of formaldehyde */

== 1 ==
=== 2 ===
==== 3 ====
NH3
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798 -1.95227 0.00000 0.00000 -0.00011 -0.00011 -1.95238
</pre>
<pre> 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=-5.785205D-10
Optimization completed.
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

H2

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

Blb15 2016-3-7

2016-03-11T15:31:27Z

Blb15: /* Simulation of formaldehyde */

== 1 ==
=== 2 ===
==== 3 ====
NH3
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798 -1.95227 0.00000 0.00000 -0.00011 -0.00011 -1.95238
</pre>
<pre> 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=-5.785205D-10
Optimization completed.
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

H2

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif|150px]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

Blb15 2016-3-7

2016-03-11T15:30:35Z

Blb15:

== 1 ==
=== 2 ===
==== 3 ====
NH3
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798 -1.95227 0.00000 0.00000 -0.00011 -0.00011 -1.95238
</pre>
<pre> 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=-5.785205D-10
Optimization completed.
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

H2

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

Blb15 2016-3-7

2016-03-11T15:27:12Z

Blb15: /* Simulation of formaldehyde */

== 1 ==
=== 2 ===
==== 3 ====
NH3
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798 -1.95227 0.00000 0.00000 -0.00011 -0.00011 -1.95238
</pre>
<pre> 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=-5.785205D-10
Optimization completed.
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

H2

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif|150px]]
[[File:Blb15 ch2o vibr 2.gif|150px]]
[[File:Blb15 ch2o vibr 3.gif|150px]]
[[File:Blb15 ch2o vibr 4.gif|150px]]
[[File:Blb15 ch2o vibr 5.gif|150px]]
[[File:Blb15 ch2o vibr 6.gif|150px]]

Blb15 2016-3-7

2016-03-11T15:22:51Z

Blb15: /* 3 */

== 1 ==
=== 2 ===
==== 3 ====
NH3
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798 -1.95227 0.00000 0.00000 -0.00011 -0.00011 -1.95238
</pre>
<pre> 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=-5.785205D-10
Optimization completed.
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

H2

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.
It does not quite fit the literature value of -92 kJ/mol, the error is due to the simulation process which would be different if we take the real circumstances into account, but that requires a deeper understanding of the software.

= Simulation of formaldehyde =

== Basics ==

=== Vibrations ===

As a nonlinear molecule, the 3N-6 rule applies and can be observed:
[[File:Blb15 ch2o vibr.png]]
[[File:Blb15 ch2o vibr 1.gif]]
[[File:Blb15 ch2o vibr 2.gif]]
[[File:Blb15 ch2o vibr 3.gif]]
[[File:Blb15 ch2o vibr 4.gif]]
[[File:Blb15 ch2o vibr 5.gif]]
[[File:Blb15 ch2o vibr 6.gif]]

File:Blb15 ch2o vibr.png

2016-03-11T15:20:42Z

Blb15: Blb15 uploaded a new version of File:Blb15 ch2o vibr.png

File:Blb15 ch2o vibr 6.gif

2016-03-11T15:18:18Z

Blb15:

File:Blb15 ch2o vibr 5.gif

2016-03-11T15:18:02Z

Blb15:

File:Blb15 ch2o vibr 4.gif

2016-03-11T15:17:43Z

Blb15:

File:Blb15 ch2o vibr 3.gif

2016-03-11T15:17:29Z

Blb15:

File:Blb15 ch2o vibr 2.gif

2016-03-11T15:17:11Z

Blb15:

File:Blb15 ch2o vibr 1.gif

2016-03-11T15:16:51Z

Blb15:

File:Blb15 ch2o vibr.png

2016-03-11T15:08:28Z

Blb15:

File:BLB15 CH2O charge.jpg

2016-03-11T15:07:03Z

Blb15:

Blb15 2016-3-7

2016-03-11T14:04:34Z

Blb15: /* 3 */

== 1 ==
=== 2 ===
==== 3 ====
NH3
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798 -1.95227 0.00000 0.00000 -0.00011 -0.00011 -1.95238
</pre>
<pre> 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=-5.785205D-10
Optimization completed.
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

H2

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>
This means that the ammonia is more stable thermodinamically, the reaction is exothermic.

Blb15 2016-3-7

2016-03-11T13:36:47Z

Blb15: /* 3 */

== 1 ==
=== 2 ===
==== 3 ====
NH3
<pre>
File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V
Bond Angle = 105.741
Bond Length = 1.01798 -1.95227 0.00000 0.00000 -0.00011 -0.00011 -1.95238
</pre>
<pre> 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=-5.785205D-10
Optimization completed.
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.

H2

<pre>
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=-1.164080D-13
</pre>
<pre>
File Name = BLB15 H2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 0.743
</pre>

[[File:Blb15 h2 vibr.png]]

N2

<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401117D-13
</pre>

<pre>
File Name = BLB15 N2 POP
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
Bond Length = 1.11
</pre>

[[File:Blb15 n2 vibr.png]]

<pre>
E(NH3)= -56.55776873 a.u.
2*E(NH3)= -113.11553746 a.u.
E(N2)= -109.52412868 a.u.
E(H2)= -1.17853936 a.u.
3*E(H2)= -3.53561808 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u.= -146.48 kJ/mol
</pre>

Blb15 2016-3-7

2016-03-11T13:19:24Z

Blb15: /* 3 */

File:Blb15 n2 vibr.png

2016-03-11T13:01:27Z

Blb15:

File:Blb15 h2 vibr.png

2016-03-11T13:01:10Z

Blb15:

Blb15 2016-3-7

2016-03-11T12:34:00Z

Blb15:

== 1 ==
=== 2 ===
==== 3 ====
NH3

File Name = BLB15_NH3_OPT_POP
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Point Group = C3V Bond Angle = 105.741 Bond Length = 1.01798 -1.95227 0.00000 0.00000 -0.00011 -0.00011 -1.95238
<pre> 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=-5.785205D-10
Optimization completed.
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>BLB15_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/images/c/ca/BLB15_NH3_OPT_POP.LOG | NH3 log file]]

[[File:Blb15 nh3 vibrations.png]]

The number of six vibrational modes are expectable from the 3N-6 rule for nonlinear molecules (N is the number of atoms in the molecule).
There are two pairs of degenerate modes, one pair of stretch at 1700 cm-1 and one of bending at 3600 cm-1. Additionally, the vibration at 1100 cm-1 is a bend (also known as umbrella), and the 3460 cm-1 is a stretch. Both of the not degenerate ones are very symmetric as they all have a C3 symmetry. Apparently only the lower two frequencies can be observed in IR spectrum due to the higher ones being really weak (13.5 and 145 vs 0.27 and 1.06) meaning that we would observe two peaks.

[[File:BLB15 NH3 charge.jpg]]

The charge distribution is according to expectations, the sum of the charges is zero, the hydrogen atoms are even and the nitrogen wears a relatively big negative charge, that can be expected from the difference in electronegativity values.