ChemWiki - User contributions [en]

Rep:Mod:sy4615

2016-02-19T12:59:47Z

Sy4615:

== Ammonia ==

{| class="wikitable"
!
!NH3
|-
|r(E-X)
|
|-
|θ(X-E-X)
|
|}
<gallery>
[[File:ammonia_3D.png]]
</gallery><gallery>
[[File:SHyan_ammonia_3D.png]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><pre>

nh3 optimisation
File Name SHYANT_NH3_OPTF_POP
File Type .log
Calculation Type FREQ
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
Charge 0
Spin Singlet
E(RB3LYP) -56.55776873 a.u.
RMS Gradient Norm 0.00000323 a.u.
Imaginary Freq
Dipole Moment 1.8465 Debye
Point Group C3V
Job cpu time: 0 days 0 hours 0 minutes 9.0 seconds.

</pre>
[[File:SHyan_ammonia_3D.png|250px]]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SHYANT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[File:Vib.png]]

The charge on the nitrogen atom in ammonia: -1.125
The charge on the hydrogen atom in ammonia: 0.375.
The expected value for charge on nitrogen is about three times more than on hydrogen because the electronegative of nitrogen is also triple the value of hydrogen.

Basic summary for N2

[[File:SHyan_nitrogen_3D.png|250px]]

<pre>

Title Card Required
File Name SHyant_n2_optf_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
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

</pre>
The frequency is 2457.33.

Basic summary for H2

[[File:SHyan_hydrogen_3D.png|250px]]

<pre>

Title Card Required
File Name SHyant_h2_optf_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
Job cpu time: 0 days 0 hours 0 minutes 6.0 seconds.

</pre>
The frequency is 4465.68.

E(NH3)=-56.55776873
2*E(NH3)=-113.11553746
E(N2)=-109.52412868
E(H2)=-1.17853936
3*E(H2)=-3.53561808
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557907

the energy for converting hydrogen and nitrogen gas into ammonia gas is -146.81 kj/mol. It is more stable in the ammonia form than in the reactant mixture.

== Cyanide ==

[[File:SHyan_cynide_3D.png|250px]]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SHYANTT CN- OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>

Title Card Required
File Name SHyantt_cn-_optf_pop
File Type .log
Calculation Type FREQ
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
Charge -1
Spin Singlet
E(RB3LYP) -92.82453153 a.u.
RMS Gradient Norm 0.00000704 a.u.
Imaginary Freq 0
Dipole Moment 0.5236 Debye
Point Group C*V
Job cpu time: 0 days 0 hours 0 minutes 8.0 seconds.

</pre>

[[File:CN-123.png]]

The charge on the nitrogen atom in cyanide ion is -0.754 and the charge on the carbon atom is -0.246

[[File:1sigma.png|350px]]

This is the lowest energy sigma molecular orbital in the molecule, it is at at an energy well of -14.00393 au and are not very involved with chemical bonding.

[[File:3sigma.png|350px]] [[File:4.png|350px]]

These are the 3-sigma bonding MO and the 4-sigma anitibonding MO. They form by combining the 2s valence AOs in carbon and nitrogen atom. The energy of these orbitals are much more higher, therefore they are very involved in the chemical bonding.

[[File:5pi.png|350px]] [[File:6pi.png|350px]]

These are the pi bonding orbitals, they have exactly the same energy of -0.01696 au,because there are two pi AOs on each atom that are perpendicular to the bond.

[[File:7mix.png|350px]]

Formed by mixing of the 5 sigma and the 3 sigma MOs, the 5 sigma orbital goes up in energy and the become the HOMO in the molecules. The mixing also cause the distortion of the shape of the MOs.

Rep:Mod:sy4615

2016-02-19T12:45:05Z

Sy4615:

Rep:Mod:sy4615

2016-02-19T12:26:46Z

Sy4615:

File:7mix.png

2016-02-18T15:40:13Z

Sy4615:

File:6pi.png

2016-02-18T15:39:50Z

Sy4615:

File:5pi.png

2016-02-18T15:39:24Z

Sy4615:

File:4.png

2016-02-18T15:38:54Z

Sy4615: Sy4615 uploaded a new version of File:4.png

File:3sigma.png

2016-02-18T15:38:36Z

Sy4615:

File:1sigma.png

2016-02-18T15:37:50Z

Sy4615:

Rep:Mod:sy4615

2016-02-18T15:30:34Z

Sy4615:

File:CN-123.png

2016-02-18T15:30:02Z

Sy4615:

File:Cn-.png

2016-02-18T15:09:56Z

Sy4615:

Rep:Mod:sy4615

2016-02-18T15:04:57Z

Sy4615:

== Ammonia ==

{| class="wikitable"
!
!NH3
|-
|r(E-X)
|
|-
|θ(X-E-X)
|
|}
<gallery>
[[File:ammonia_3D.png]]
</gallery><gallery>
[[File:SHyan_ammonia_3D.png]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><pre>

nh3 optimisation
File Name SHYANT_NH3_OPTF_POP
File Type .log
Calculation Type FREQ
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
Charge 0
Spin Singlet
E(RB3LYP) -56.55776873 a.u.
RMS Gradient Norm 0.00000323 a.u.
Imaginary Freq
Dipole Moment 1.8465 Debye
Point Group C3V
Job cpu time: 0 days 0 hours 0 minutes 9.0 seconds.

</pre>
[[File:SHyan_ammonia_3D.png|250px]]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SHYANT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[File:Vib.png]]

The charge on the nitrogen atom in ammonia: -1.125
The charge on the hydrogen atom in ammonia: 0.375.
The expected value for charge on nitrogen is about three times more than on hydrogen because the electronegative of nitrogen is also triple the value of hydrogen.

Basic summary for N2

[[File:SHyan_nitrogen_3D.png|250px]]

<pre>

Title Card Required
File Name SHyant_n2_optf_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
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

</pre>
The frequency is 2457.33.

Basic summary for H2

[[File:SHyan_hydrogen_3D.png|250px]]

<pre>

Title Card Required
File Name SHyant_h2_optf_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
Job cpu time: 0 days 0 hours 0 minutes 6.0 seconds.

</pre>
The frequency is 4465.68.

E(NH3)=-56.55776873
2*E(NH3)=-113.11553746
E(N2)=-109.52412868
E(H2)=-1.17853936
3*E(H2)=-3.53561808
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557907

the energy for converting hydrogen and nitrogen gas into ammonia gas is -146.81 kj/mol. It is more stable in the ammonia form than in the reactant mixture.

== Cyanide ==

[[File:SHyan_cynide_3D.png|250px]]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SHYANTT CN- OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>

Title Card Required
File Name SHyantt_cn-_optf_pop
File Type .log
Calculation Type FREQ
Calculation Method UB3LYP
Basis Set 6-31G(d,p)
Charge 0
Spin Doublet
E(UB3LYP) -92.71174738 a.u.
RMS Gradient Norm 0.00000292 a.u.
Imaginary Freq 0
Dipole Moment 1.2679 Debye
Point Group C*V
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

</pre>

File:SHYANTT CN- OPTF POP.LOG

2016-02-18T15:03:31Z

Sy4615:

File:SHyan cynide 3D.png

2016-02-18T14:59:16Z

Sy4615:

Rep:Mod:sy4615

2016-02-18T14:21:48Z

Sy4615:

{| class="wikitable"
!
!NH3
|-
|r(E-X)
|
|-
|θ(X-E-X)
|
|}
<gallery>
[[File:ammonia_3D.png]]
</gallery><gallery>
[[File:SHyan_ammonia_3D.png]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><pre>

nh3 optimisation
File Name SHYANT_NH3_OPTF_POP
File Type .log
Calculation Type FREQ
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
Charge 0
Spin Singlet
E(RB3LYP) -56.55776873 a.u.
RMS Gradient Norm 0.00000323 a.u.
Imaginary Freq
Dipole Moment 1.8465 Debye
Point Group C3V
Job cpu time: 0 days 0 hours 0 minutes 9.0 seconds.

</pre>
[[File:SHyan_ammonia_3D.png|150px]]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SHYANT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[File:Vib.png]]

The charge on the nitrogen atom in ammonia: -1.125
The charge on the hydrogen atom in ammonia: 0.375.
The expected value for charge on nitrogen is about three times more than on hydrogen because the electronegative of nitrogen is also triple the value of hydrogen.

Basic summary for N2

[[File:SHyan_nitrogen_3D.png|150px]]

<pre>

Title Card Required
File Name SHyant_n2_optf_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
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

</pre>
The frequency is 2457.33.

Basic summary for H2

[[File:SHyan_hydrogen_3D.png|150px]]

<pre>

Title Card Required
File Name SHyant_h2_optf_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
Job cpu time: 0 days 0 hours 0 minutes 6.0 seconds.

</pre>
The frequency is 4465.68.

E(NH3)=-56.55776873
2*E(NH3)=-113.11553746
E(N2)=-109.52412868
E(H2)=-1.17853936
3*E(H2)=-3.53561808
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557907

the energy for converting hydrogen and nitrogen gas into ammonia gas is -146.81 kj/mol. It is more stable in the ammonia form than in the reactant mixture.

Rep:Mod:sy4615

2016-02-18T14:18:51Z

Sy4615:

Rep:Mod:sy4615

2016-02-18T14:08:21Z

Sy4615:

File:SHyan hydrogen 3D.png

2016-02-18T14:07:21Z

Sy4615:

File:SHyan nitrogen 3D.png

2016-02-18T14:06:59Z

Sy4615:

Rep:Mod:sy4615

2016-02-18T13:55:53Z

Sy4615:

Rep:Mod:sy4615

2016-02-18T13:39:58Z

Sy4615:

Rep:Mod:sy4615

2016-02-16T14:44:36Z

Sy4615:

File:Vib.png

2016-02-16T14:43:39Z

Sy4615:

Rep:Mod:sy4615

2016-02-16T14:38:31Z

Sy4615:

Rep:Mod:sy4615

2016-02-16T14:08:29Z

Sy4615:

geometry data
{| class="wikitable"
!
!NH3
|-
|r(E-X)
|
|-
|θ(X-E-X)
|
|}
<gallery>
[[File:ammonia_3D.png]]
</gallery><gallery>
[[File:SHyan_ammonia_3D.png]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><gallery>
[[File:SHyant_nh3_optf_pop.gjf]]
</gallery><pre>

nh3 optimisation
File Name SHYANT_NH3_OPTF_POP
File Type .log
Calculation Type FREQ
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
Charge 0
Spin Singlet
E(RB3LYP) -56.55776873 a.u.
RMS Gradient Norm 0.00000323 a.u.
Imaginary Freq
Dipole Moment 1.8465 Debye
Point Group C3V
Job cpu time: 0 days 0 hours 0 minutes 9.0 seconds.

</pre>
[[File:SHyan_ammonia_3D.png|150px]]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SHYANT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

File:SHYANT NH3 OPTF POP.LOG

2016-02-16T14:05:36Z

Sy4615:

File:SHyant nh3 optf pop.chk

2016-02-16T13:58:41Z

Sy4615:

File:SHyant nh3 optf pop.gjf

2016-02-16T13:47:47Z

Sy4615: Sy4615 uploaded a new version of File:SHyant nh3 optf pop.gjf

Rep:Mod:sy4615

2016-02-15T17:14:41Z

Sy4615:

File:SHyan ammonia 3D.png

2016-02-15T16:55:25Z

Sy4615:

File:SHyant nh3 optf pop.gjf

2016-02-15T16:32:23Z

Sy4615:

Rep:Mod:sy4615

2016-02-15T16:29:45Z

Sy4615:

geometry data
{| class="wikitable"
!
!NH3
|-
|r(E-X)
|
|-
|θ(X-E-X)
|
|}
<pre>

nh3 optimisation
File Name SHYANT_NH3_OPTF_POP
File Type .log
Calculation Type FREQ
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
Charge 0
Spin Singlet
E(RB3LYP) -56.55776873 a.u.
RMS Gradient Norm 0.00000323 a.u.
Imaginary Freq
Dipole Moment 1.8465 Debye
Point Group C3V
Job cpu time: 0 days 0 hours 0 minutes 9.0 seconds.

</pre>

Rep:Mod:sy4615

2016-02-15T15:08:24Z

Sy4615:

geometry data
{| class="wikitable"
!
!BH3
!BBr3
!
|-
|r(E-X)
|
|
|
|-
|θ(X-E-X)
|
|
|
|}

Rep:Mod:sy4615

2016-02-15T14:52:23Z

Sy4615:

3rdyearlab

Rep:Mod:sy4615

2016-02-15T14:51:19Z

Sy4615:

<nowiki>Insert non-formatted text here</nowiki>BBr3!

Rep:Mod:sy4615

2016-02-15T14:50:40Z

Sy4615: Created page with "BBr3! {|BBr3|r(E-X)|θ(X-E-X)|}"

BBr3!
{|BBr3|r(E-X)|θ(X-E-X)|}

Main Page

2016-02-15T14:34:58Z

Sy4615:

[[Image:QR_complab.png|right|QR]]
= Title=mode:sy4615 =
This is a communal area for documenting teaching and laboratory courses. To [[admin:add|add to any content on these pages]], you will have to log in using your Imperial College account.
== ChemDraw/Chemdoodle Hints ==
#[[IT:chemdraw|Useful hints for using ChemDraw/ChemDoodle]]

== Student wiki ==
#[[StudentWiki:Contents|Student pages]]

== Tablet Project ==
# [[tablet:tablet|Tablet Pilot Project]]
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# [[mod:3D|3D-printable models]]
# [[mod:stereo|Lecture Theatre Stereo]]

= Laboratories and Workshops =
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=== [[it:it_facillities|Email and IT@www.ch.imperial.ac.uk]]: A summary of available IT resources ===

===First Year Chemical Information Lab 2015 ===
*[[it:intro-2011|Introduction]]
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*[[Measurement_Science_Lab:_Introduction|Measurement Science Lab Course]]

===[[organic:conventions|Conventions in organic chemistry]]===
===[[organic:arrow|Reactive Intermediates in organic chemistry]]===
===[[organic:stereo|Stereochemical models]] ===

== Second Year ==
===Second Year Modelling Workshop ===
*[[Coursework]]
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*[[it:conquest|Conquest searches]]




=== Molecular Dynamics (Physical Chemistry Laboratory) ===
*[[Running MD code in MATLAB|Running MD code in MATLAB]]

== Third Year ==

===Third Year Computational Chemistry Lab ===
*[[mod:intro|Information needed for the course]]


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**[[Mod:phys3|Transition states and reactivity.]]
**[[ThirdYearMgOExpt-1415|MgO experiment]]
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*[[mod:programs|General program instructions:]]
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# [[ebooks:howto|How to get eBooks]]
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# [https://itunes.apple.com/gb/course/id562191620 Pericylic reactions in iTunesU ] (download [https://itunes.apple.com/gb/app/itunes-u/id490217893?mt=8 App] first)
# [https://itunes.apple.com/gb/course/id562191825 Conformational analysis in iTunesU] (download [https://itunes.apple.com/gb/app/itunes-u/id490217893?mt=8 App] first)
# [https://itunes.apple.com/gb/course/id562191342 A library of mechanistic animations in iTunesU] (download [https://itunes.apple.com/gb/app/itunes-u/id490217893?mt=8 App] first)
# [[IT:panopto|How to compress and disseminate Panopto lecture recordings]]
= Material from previous years =
== First year ==
===Introduction to Chemical Programming Workshop 2013===
*[[1da-workshops-2013-14|Workshop script]]
== Third Year ==
===Synthesis and computational lab ===
*[[Mod:organic|Synthesis and computational lab]]


= PG =

# [[rdm:intro|Data management]]