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Mod:Hunt Research Group: Using SMD on ILs

2020-01-28T12:10:27Z

Rr1210: /* Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref name="abmethod">http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] ===

{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.5
|<ref name="Bernales" />
|From SMD-GIL
|-
|epsinf
|2.04
|<ref name="Bernales" />
|From SMD-GIL
|-
|SurfaceTensionAtInterface
|61.24
|<ref name="Bernales" />
|From SMD-GIL
|-
|HBondAcidity (α)
|0.275
|
|Calculated using <ref name="abmethod" />
|-
|HBondBasicity (β)
|0.070
|
|Calculated using <ref name="abmethod" />
|-
|CarbonAromaticity
|0.231
|
|From stoichiometry
|-
|ElectronegativeHalogenicity
|0.308
|
|From stoichiometry
|-
| colspan="4" |<code>eps=11.5 epsinf=2.04 HBondAcidity=0.275 HBondBasicity=0.070 SurfaceTensionAtInterface=61.24 CarbonAromaticity=0.231 ElectronegativeHalogenicity=0.308</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2020-01-15T13:14:55Z

Rr1210: /* Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref name="abmethod">http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] ===

{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.5
|<ref name="Bernales" />
|From SMD-GIL
|-
|epsinf
|2.04
|<ref name="Bernales" />
|From SMD-GIL
|-
|SurfaceTensionAtInterface
|61.24
|<ref name="Bernales" />
|From SMD-GIL
|-
|HBondAcidity (α)
|0.275
|
|Calculated using <ref name="abmethod" />
|-
|HBondBasicity (β)
|0.35
|
|Calculated using <ref name="abmethod" />
|-
|CarbonAromaticity
|0.231
|
|From stoichiometry
|-
|ElectronegativeHalogenicity
|0.308
|
|From stoichiometry
|-
| colspan="4" |<code>eps=11.5 epsinf=2.04 HBondAcidity=0.275 HBondBasicity=0.35 SurfaceTensionAtInterface=61.24 CarbonAromaticity=0.231 ElectronegativeHalogenicity=0.308</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2020-01-15T13:13:56Z

Rr1210:

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref name="abmethod">http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] ===

{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.5
|
|From SMD-GIL
|-
|epsinf
|2.04
|
|From SMD-GIL
|-
|SurfaceTensionAtInterface
|61.24
|
|From SMD-GIL
|-
|HBondAcidity (α)
|0.275
|
|Calculated using <ref name="Bernales" />
|-
|HBondBasicity (β)
|0.35
|
|Calculated using <ref name="Bernales" />
|-
|CarbonAromaticity
|0.231
|
|From stoichiometry
|-
|ElectronegativeHalogenicity
|0.308
|
|From stoichiometry
|-
| colspan="4" |<code>eps=11.5 epsinf=2.04 HBondAcidity=0.275 HBondBasicity=0.35 SurfaceTensionAtInterface=61.24 CarbonAromaticity=0.231 ElectronegativeHalogenicity=0.308</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2020-01-15T13:12:14Z

Rr1210: /* Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] ===

{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.5
|
|From SMD-GIL
|-
|epsinf
|2.04
|
|From SMD-GIL
|-
|SurfaceTensionAtInterface
|61.24
|
|From SMD-GIL
|-
|HBondAcidity (α)
|0.275
|
|Calculated using <ref name="Bernales" />
|-
|HBondBasicity (β)
|0.35
|
|Calculated using <ref name="Bernales" />
|-
|CarbonAromaticity
|0.231
|
|From stoichiometry
|-
|ElectronegativeHalogenicity
|0.308
|
|From stoichiometry
|-
| colspan="4" |<code>eps=11.5 epsinf=2.04 HBondAcidity=0.275 HBondBasicity=0.35 SurfaceTensionAtInterface=61.24 CarbonAromaticity=0.231 ElectronegativeHalogenicity=0.308</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2020-01-15T13:10:07Z

Rr1210: /* Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] ===

{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.5
|
|From SMD-GIL
|-
|epsinf
|2.04
|
|From SMD-GIL
|-
|SurfaceTensionAtInterface
|61.24
|
|From SMD-GIL
|-
|HBondAcidity (α)
|0.275
|
|Calculated using
|-
|HBondBasicity (β)
|0.35
|
|Calculated using
|-
|CarbonAromaticity
|0.231
|
|From stoichiometry
|-
|ElectronegativeHalogenicity
|0.308
|
|From stoichiometry
|-
| colspan="4" |<code>eps=11.5 epsinf=2.04 HBondAcidity=0.275 HBondBasicity=0.35 SurfaceTensionAtInterface=61.24 CarbonAromaticity=0.231 ElectronegativeHalogenicity=0.308</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2020-01-15T13:08:02Z

Rr1210: /* Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] ===

{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.5
|
|
|-
|epsinf
|2.04
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.275
|
|
|-
|HBondBasicity (β)
|0.35
|
|
|-
|CarbonAromaticity
|0.231
|
|
|-
|ElectronegativeHalogenicity
|0.308
|
|
|-
| colspan="4" |<code>eps=11.5 epsinf=2.04 HBondAcidity=0.275 HBondBasicity=0.35 SurfaceTensionAtInterface=61.24 CarbonAromaticity=0.231 ElectronegativeHalogenicity=0.308</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2020-01-15T13:04:04Z

Rr1210:

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] ===

{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2020-01-15T13:03:07Z

Rr1210:

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Bismuth halometallate ionic liquid, parameterised for [C2C1Im][BiCl4] ===

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group:freq script

2019-05-02T13:17:37Z

Rr1210:

*Save the following as script_name.py wherever you want.
*Follow the instructions to run
*Feel free to improve!

<pre>
import os
import glob
import sys

############
#HOW TO RUN#
############

#go to the folder with frequency log files in
#this script currently doesn't work if there are .log file present which don't contain frequency analysis, you will have to change it yourself if you want that.
#this script outputs various data from the frequency files to the terminal including relative values, which are calculated relative to the reference_file.log
#run as follows:

#python path/to/script.py reference_file.log

##################################################################

#setting the reference file, this file is the 0 level for all relative values

ref_file = sys.argv[1]
print "ref_file = " + (ref_file)

#making a list of all .log files in current directory

log_files = []
for log_file in glob.glob('*.log'):
if log_file != ref_file:
log_files.append(log_file)

print "list of files: "
print log_files

#defining the strings which will be searched for in each file

e_elec_string = 'SCF Done'
zpe_string = 'Zero-point correction='
e_string = 'Sum of electronic and thermal Energies='
h_string = 'Sum of electronic and thermal Enthalpies='
g_string = 'Sum of electronic and thermal Free Energies='
freq_string = 'Low frequencies ---'
im_freq_string = 'imaginary frequencies (negative Signs)'
conver_string = 'Stationary point found.'

#fetching all data for the reference file

f = open(ref_file, 'r')

low_freqs_list = []
conver = 'no'
im_freq_num = '0'

for line in f:
if e_elec_string in line:
ref_e_elec_au = line[(len(e_elec_string)+15):(len(e_elec_string)+35)]
ref_e_elec_au = float(ref_e_elec_au)
if zpe_string in line:
ref_zpe_au = line[(len(zpe_string)+1):(len(zpe_string)+37)]
ref_zpe_au = float(ref_zpe_au)
if e_string in line:
ref_e_au = line[(len(e_string)+1):(len(e_string)+35)]
ref_e_au = float(ref_e_au)
if h_string in line:
ref_h_au = line[(len(h_string)+1):(len(h_string)+35)]
ref_h_au = float(ref_h_au)
if g_string in line:
ref_g_au = line[(len(g_string)+1):(len(g_string)+35)]
ref_g_au = float(ref_g_au)
if freq_string in line:
low_freqs = line[(len(freq_string)+1):]
low_freqs = low_freqs.split()
low_freqs_list = low_freqs_list + low_freqs;
if conver_string in line:
conver = 'yes'
if im_freq_string in line:
im_freq_num = line[7:12]
im_freq_num = str(int(im_freq_num))

f.close()

#assigning/calculating all data fields to print for the reference file

ref_low_freqs = []
for low_freq in low_freqs_list:
low_freq = str(int(round(float(low_freq))))
ref_low_freqs.append(low_freq)
low_freqs_string = ",".join(ref_low_freqs)
ref_e_elec_kj = str(ref_e_elec_au*2625.5)
ref_zpe_kj = str(ref_zpe_au*2625.5)
ref_e_kj = str(ref_e_au*2625.5)
ref_h_kj = str(ref_h_au*2625.5)
ref_ts_au = ref_h_au - ref_g_au
ref_ts_kj = str(ref_ts_au*2625.5)
ref_g_kj = str(ref_g_au*2625.5)

#printing header and reference rows

print "Filename,E_elec,DE_elec,zpe,Dzpe,E,DE,H,DH,TS,TDS,G,DG,Low freqencies,,,,,,,,,Converged?,# of imaginary frequencies"
print ref_file+','+ref_e_elec_kj+',0.00,'+ref_zpe_kj+',0.00,'+ref_e_kj+',0.00,'+ref_h_kj+',0.00,'+ref_ts_kj+',0.00,'+ref_g_kj+',0.00,'+low_freqs_string+','+conver+','+im_freq_num

#doing the other files

for log_file in log_files:

##resetting the variables
low_freqs_list = []
conver = 'no'
im_freq_num = '0'
e_elec_au = 'ERROR'
de_elec_au = 'ERROR'
zpe_au = 'ERROR'
dzpe_au = 'ERROR'
e_au = 'ERROR'
de_au = 'ERROR'
h_au = 'ERROR'
dh_au = 'ERROR'
ts_au = 'ERROR'
ts_au = 'ERROR'
tds_au = 'ERROR'
g_au = 'ERROR'
dg_au = 'ERROR'

##fetching all data for the file

f = open(log_file, 'r')
file_name = log_file

for line in f:
if e_elec_string in line:
e_elec_au = line[(len(e_elec_string)+15):(len(e_elec_string)+35)]
e_elec_au = float(e_elec_au)
if zpe_string in line:
zpe_au = line[(len(zpe_string)+1):(len(zpe_string)+37)]
zpe_au = float(zpe_au)
if e_string in line:
e_au = line[(len(e_string)+1):(len(e_string)+35)]
e_au = float(e_au)
if h_string in line:
h_au = line[(len(h_string)+1):(len(h_string)+35)]
h_au = float(h_au)
if g_string in line:
g_au = line[(len(g_string)+1):(len(g_string)+35)]
g_au = float(g_au)
if freq_string in line:
low_freqs = line[(len(freq_string)+1):]
low_freqs = low_freqs.split()
low_freqs_list = low_freqs_list + low_freqs;
if conver_string in line:
conver = 'yes'
if im_freq_string in line:
im_freq_num = line[7:12]
im_freq_num = str(int(im_freq_num))

##assigning/calculating all data fields to print for the file

e_elec_kj = str(e_elec_au*2625.5)
de_elec_kj = str(round(((e_elec_au - ref_e_elec_au)*2625.5),2))
zpe_kj = str(zpe_au*2625.5)
dzpe_kj = str(round(((zpe_au - ref_zpe_au)*2625.5),2))
e_kj = str(e_au*2625.5)
de_kj = str(round(((e_au - ref_e_au)*2625.5),2))
h_kj = str(h_au*2625.5)
dh_kj = str(round(((h_au - ref_h_au)*2625.5),2))
ts_au = h_au - g_au
ts_kj = str(ts_au*2625.5)
tds_kj = str(round(((ts_au - ref_ts_au)*2625.5),2))
g_kj = str(g_au*2625.5)
dg_kj = str(round(((g_au - ref_g_au)*2625.5),2))
low_freqs = []
for low_freq in low_freqs_list:
low_freq = str(int(round(float(low_freq))))
low_freqs.append(low_freq)
low_freqs_string = ",".join(low_freqs)

##printing file row

print file_name+','+e_elec_kj+','+de_elec_kj+','+zpe_kj+','+dzpe_kj+','+e_kj+','+de_kj+','+h_kj+','+dh_kj+','+ts_kj+','+tds_kj+','+g_kj+','+dg_kj+','+low_freqs_string+','+conver+','+im_freq_num
f.close()

</pre>

Mod:Hunt Research Group:freq script

2019-05-02T08:20:06Z

Rr1210:

*Save the following as script_name.py wherever you want.
*Follow the instructions to run
*Feel free to improve!

<pre>
import os
import glob
import sys

############
#HOW TO RUN#
############

#go to the folder with frequency log files in
#this script currently doesn't work if there are .log file present which don't contain frequency analysis, you will have to change it yourself if you want that.
#this script outputs various data from the frequency files to the terminal including relative values, which are calculated relative to the reference_file.log
#run as follows:

#python path/to/script.py reference_file.log

##################################################################

#setting the reference file, this file is the 0 level for all relative values

ref_file = sys.argv[1]
print "ref_file = " + (ref_file)

#making a list of all .log files in current directory

log_files = []
for log_file in glob.glob('*.log'):
log_files.append(log_file)

print "list of files: "
print log_files

#removing the reference file from the list

if ref_file in log_files:
log_files.remove(log_file)
print "log_files list without ref_file: "
print log_files
else:
print "No log_file matches ref_file, script terminating."
exit()

#defining the strings which will be searched for in each file

e_elec_string = 'SCF Done'
zpe_string = 'Zero-point correction='
e_string = 'Sum of electronic and thermal Energies='
h_string = 'Sum of electronic and thermal Enthalpies='
g_string = 'Sum of electronic and thermal Free Energies='
freq_string = 'Low frequencies ---'
im_freq_string = 'imaginary frequencies (negative Signs)'
conver_string = 'Stationary point found.'

#fetching all data for the reference file

f = open(ref_file, 'r')

low_freqs_list = []
conver = 'no'
im_freq_num = '0'

for line in f:
if e_elec_string in line:
ref_e_elec_au = line[(len(e_elec_string)+15):(len(e_elec_string)+35)]
ref_e_elec_au = float(ref_e_elec_au)
if zpe_string in line:
ref_zpe_au = line[(len(zpe_string)+1):(len(zpe_string)+37)]
ref_zpe_au = float(ref_zpe_au)
if e_string in line:
ref_e_au = line[(len(e_string)+1):(len(e_string)+35)]
ref_e_au = float(ref_e_au)
if h_string in line:
ref_h_au = line[(len(h_string)+1):(len(h_string)+35)]
ref_h_au = float(ref_h_au)
if g_string in line:
ref_g_au = line[(len(g_string)+1):(len(g_string)+35)]
ref_g_au = float(ref_g_au)
if freq_string in line:
low_freqs = line[(len(freq_string)+1):]
low_freqs = low_freqs.split()
low_freqs_list = low_freqs_list + low_freqs;
if conver_string in line:
conver = 'yes'
if im_freq_string in line:
im_freq_num = line[7:12]
im_freq_num = str(int(im_freq_num))

f.close()

#assigning/calculating all data fields to print for the reference file

ref_low_freqs = []
for low_freq in low_freqs_list:
low_freq = str(int(round(float(low_freq))))
ref_low_freqs.append(low_freq)
low_freqs_string = ",".join(ref_low_freqs)
ref_e_elec_kj = str(ref_e_elec_au*2625.5)
ref_zpe_kj = str(ref_zpe_au*2625.5)
ref_e_kj = str(ref_e_au*2625.5)
ref_h_kj = str(ref_h_au*2625.5)
ref_ts_au = ref_h_au - ref_g_au
ref_ts_kj = str(ref_ts_au*2625.5)
ref_g_kj = str(ref_g_au*2625.5)

#printing header and reference rows

print "Filename,E_elec,DE_elec,zpe,Dzpe,E,DE,H,DH,TS,TDS,G,DG,Low freqencies,,,,,,,,,Converged?,# of imaginary frequencies"
print ref_file+','+ref_e_elec_kj+',0.00,'+ref_zpe_kj+',0.00,'+ref_e_kj+',0.00,'+ref_h_kj+',0.00,'+ref_ts_kj+',0.00,'+ref_g_kj+',0.00,'+low_freqs_string+','+conver+','+im_freq_num

#doing the other files

for log_file in log_files:

##resetting the variables
low_freqs_list = []
conver = 'no'
im_freq_num = '0'
e_elec_au = 'ERROR'
de_elec_au = 'ERROR'
zpe_au = 'ERROR'
dzpe_au = 'ERROR'
e_au = 'ERROR'
de_au = 'ERROR'
h_au = 'ERROR'
dh_au = 'ERROR'
ts_au = 'ERROR'
ts_au = 'ERROR'
tds_au = 'ERROR'
g_au = 'ERROR'
dg_au = 'ERROR'

##fetching all data for the file

f = open(log_file, 'r')
file_name = log_file

for line in f:
if e_elec_string in line:
e_elec_au = line[(len(e_elec_string)+15):(len(e_elec_string)+35)]
e_elec_au = float(e_elec_au)
if zpe_string in line:
zpe_au = line[(len(zpe_string)+1):(len(zpe_string)+37)]
zpe_au = float(zpe_au)
if e_string in line:
e_au = line[(len(e_string)+1):(len(e_string)+35)]
e_au = float(e_au)
if h_string in line:
h_au = line[(len(h_string)+1):(len(h_string)+35)]
h_au = float(h_au)
if g_string in line:
g_au = line[(len(g_string)+1):(len(g_string)+35)]
g_au = float(g_au)
if freq_string in line:
low_freqs = line[(len(freq_string)+1):]
low_freqs = low_freqs.split()
low_freqs_list = low_freqs_list + low_freqs;
if conver_string in line:
conver = 'yes'
if im_freq_string in line:
im_freq_num = line[7:12]
im_freq_num = str(int(im_freq_num))

##assigning/calculating all data fields to print for the file

e_elec_kj = str(e_elec_au*2625.5)
de_elec_kj = str(round(((e_elec_au - ref_e_elec_au)*2625.5),2))
zpe_kj = str(zpe_au*2625.5)
dzpe_kj = str(round(((zpe_au - ref_zpe_au)*2625.5),2))
e_kj = str(e_au*2625.5)
de_kj = str(round(((e_au - ref_e_au)*2625.5),2))
h_kj = str(h_au*2625.5)
dh_kj = str(round(((h_au - ref_h_au)*2625.5),2))
ts_au = h_au - g_au
ts_kj = str(ts_au*2625.5)
tds_kj = str(round(((ts_au - ref_ts_au)*2625.5),2))
g_kj = str(g_au*2625.5)
dg_kj = str(round(((g_au - ref_g_au)*2625.5),2))
low_freqs = []
for low_freq in low_freqs_list:
low_freq = str(int(round(float(low_freq))))
low_freqs.append(low_freq)
low_freqs_string = ",".join(low_freqs)

##printing file row

print file_name+','+e_elec_kj+','+de_elec_kj+','+zpe_kj+','+dzpe_kj+','+e_kj+','+de_kj+','+h_kj+','+dh_kj+','+ts_kj+','+tds_kj+','+g_kj+','+dg_kj+','+low_freqs_string+','+conver+','+im_freq_num
f.close()

</pre>

Rep:Mod:GJ2118mm2

2019-04-01T10:09:07Z

Rr1210:

== NH3 Molecule ==
=== NH3 Optimisation Results ===

molecule name: Ammonia

calculation method: RB3LYP

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

final energy E(RB3LYP) : -56.55776861

the point group of your molecule : C3V

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>AMMONIA-OPTIMISATION.log</uploadedFileContents>
</jmolApplet></jmol>

=== Summary of results from the Items ===

<pre>
Item Value Threshold Converged?
Maximum Force 0.000195 0.000450 YES
RMS Force 0.000091 0.000300 YES
Maximum Displacement 0.000444 0.001800 YES
RMS Displacement 0.000343 0.001200 YES

</pre>

=== Further Information on the Molecule ===
These values are optimised Values.

Bond length : 1.01798 atomic units

Angle Between bonds : 105.741o
Charge :
Hydrogen atom : 0.375
Nitrogen Atom : -1.125

{| class="wikitable" border="1"
|+ Vibrations for Ammonia Molecule
! Measured factor !! Reading !! Reading
|-
| '''Wavenumber cm-1''' ||1089.5366 || 1693.9474
|-
|'''Symmetry''' || A1|| E
|-
| '''Intensity''' || 145.3814 || 13.5533
|-
|'''Image''' || images || images
|}

We would expect 6 modes of vibration according to 3N-6 rule.

we would expect to see two bands in a spectrum of gaseous ammonia.

== H2 Molecule ==
=== H2 Optimisation Results ===

molecule name: Hydrogen

calculation method: RB3LYP

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

final energy E(RB3LYP) : -1.1592802

the point group of your molecule : D*H

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>HYDROGEN OPTIMISATION.log</uploadedFileContents>
</jmolApplet></jmol>

<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

</pre>

=== Further Information on the Molecule ===
These values are optimised Values.

Bond Length : 0.6 atomic units

Angle Between bonds : 180o

{| class="wikitable" border="1"
|+ Vibrations for Hydrogen Molecule
! heading !! heading
|-
| '''Wavenumber cm-1''' || 4465.6824
|-
|'''Symmetry''' || SGG
|-
| '''Intensity''' || 0
|-
|'''Image''' || images
|}

== N2 Molecule ==
=== N2 Optimisation Results ===

molecule name: Nitrogen

calculation method: RB3LYP

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

final energy E(RB3LYP) : -109.52412868

the point group of your molecule : D*H

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>username_molecule_1.log</uploadedFileContents>
</jmolApplet></jmol>

<pre>

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

</pre>

=== Further Information on the Molecule ===
These values are optimised Values.

Bond Length : 1.10550 atomic units

Angle Between bonds : 180o

{| class="wikitable" border="1"
|+ Vibrations for Nitrogen Molecule
! Measured factor !! Reading
|-
| '''Wavenumber cm-1''' || 2457.3283
|-
|'''Symmetry''' || SGG
|-
| '''Intensity''' || 0
|-
|'''Image''' || images
|}

=== '''Haber Bosch Process''' ===

E(NH3)= -56.55776861 a.u
2*E(NH3)= -113.1155372 a.u
E(N2)= -109.52412868 a.u
E(H2)= -1.1592802 a.u
3*E(H2)= −3.4778406 a.u
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= −0.11356792 a.u

ΔE = −298.2 KJ/mol

== CH4 Molecule ==
=== CH4 Optimisation Results ===

molecule name: Methane

calculation method: RB3LYP

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

final energy E(RB3LYP) : -40.52275298

the point group of your molecule : T

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>username_molecule_1.log</uploadedFileContents>
</jmolApplet></jmol>

<pre>

Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES

</pre>

=== Further Information on the Molecule ===
These values are optimised Values.

Bond Length : 1.07000 atomic units

Angle Between bonds : 109.471o

Charge :

hydrogen : 0.118
carbon : -0.470

{| class="wikitable" border="1"
|+ Vibrations for Methane Molecule
! Measured factor !! Reading
|-
| '''Wavenumber cm-1''' ||1356.2043
|-
|'''Symmetry''' || T1
|-
| '''Intensity''' || 14.1008
|-
|'''Image''' || images
|}

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

All of your jmols are broken and they are all captioned "test molecule", they should have captions reflecting the content.

==NH3 0/1 ==

Have you completed the calculation and given a link to the file?

No log file link.

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

No, it is broken.

Have you included the bond lengths and angles asked for?

YES, though you have used too many decimals points in reporting them.

Have you included the “display vibrations” table?

No

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

No

Did you do the optional extra of adding images of the vibrations?

No

Have you included answers to the questions about vibrations and charges in the lab script?

No you did not answer most questions.

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

No, you did not include log files.

==Crystal structure comparison 0/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

No

Have you compared your optimised bond distance to the crystal structure bond distance?

No

==Haber-Bosch reaction energy calculation 0.5/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

No

== Your choice of small molecule 0/5 ==

Have you completed the calculation and included all relevant information?

No log file.

Have you added information about MOs and charges on atoms?

No

== Independence 0/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

no independent work included.

Rep:Mod:rr12104

2019-03-29T10:54:07Z

Rr1210:

= NH3: optimisation, frequency, NBO =
<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000071 0.001800 YES
RMS Displacement 0.000034 0.001200 YES
Predicted change in Energy=-5.828500D-10
Optimization completed.
-- Stationary point found.
</pre>

{| class="wikitable"
!Molecule
|NH3
|-
!Calculation method
|RB3LYP
|-
!Basis set
|6-31G(d,p)
|-
!Energy /au
|<nowiki>-56.55776863</nowiki>
|-
!RMS gradient
|0.00000478
|-
!Point group
|C3V
|}

N-H bond distance: 1.018Å

N-H bond angle: 105.743°

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:NH3_OPTF_POP.LOG| Log file]]

== Vibrations ==

[[File:Rr1210_display_vibrations.PNG]]

{| class="wikitable"
|-
!wavenumber cm-1
|1092
|1695
|1695
|3458
|3586
|3586
|-
!symmetry
|A1
|E
|E
|A1
|E
|E
|-
!intensity arbitrary units
|145
|14
|14
|1
|0
|0
|-
!image
| [[File:NH3_1090.png|100px]]
| [[File:NH3_1694_1.png|100px]]
| [[File:NH3_1694_2.png|100px]]
| [[File:NH3_3461.png|100px]]
| [[File:NH3_3589_1.png|100px]]
| [[File:NH3_3589_2.png|100px]]
|}

'''How many modes do you expect from the 3N-6 rule?'''

N=4 so 3N-6 is 6 vibrational modes.

'''Which modes are degenerate (ie have the same energy)?'''

modes at 1695 (2 and 3) and 3585 (5 and 6) cm-1 are degenerate

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

bending are 1092 and 1695 cm-1 modes (1,2 and 3), stretching are 3458 and 3586 cm-1 modes (4, 5 and 6), thus stretches are higher in energy than bends

'''Which mode is highly symmetric?'''

the totally symmetric mode in at 3458 cm-1 (mode 4)

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

the umbrella mode is the mode at 1092 cm-1 (mode 1)

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

The vibration has to cause the dipole has to change to be IR active. Also there are 2 degenerate vibrations which will cause only one peak. Therefore we will see 2 peaks, one very intense one at 1091 cm-1 (mode 1) and one very weak one 1694 cm-1 (degenerate modes 2 and 3).

== Charges ==

Charge on N = -1.125
Charge on H = +0.375

N is more electronegative than H so I would expect to be slightly negatively charged and H to be slightly positively charged.

=Reaction and Energy=

== N2: optimisation, frequency, NBO ==
<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 0.000000 0.001200 YES
Predicted change in Energy=-9.718076D-17
Optimization completed.
-- Stationary point found.
</pre>

{| class="wikitable"
!Molecule
|N2
|-
!Calculation method
|RB3LYP
|-
!Basis set
|6-31G(d,p)
|-
!Energy /au
|<nowiki>-109.52412907</nowiki>
|-
!RMS gradient
|0.00000001
|-
!Point group
|DinfH
|}

N-N bond distance: 1.10550Å

<jmol><jmolApplet>
<title>N2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Rr1210_n2_optf_pop.mol2</uploadedFileContents>
</jmolApplet></jmol>

[[Media:N2_OPTF_POP.LOG| Log file]]

[[File:Rr1210_display_vibrations_n2.PNG]]

{| class="wikitable"
|-
!wavenumber cm-1
|2458
|-
!symmetry
|SGG or Σg+
|-
!intensity arbitrary units
|0
|-
!image
| to be added
|}

== H2: optimisation, frequency, NBO ==
<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=-1.150392D-13
Optimization completed.
-- Stationary point found.
</pre>

{| class="wikitable"
!Molecule
|H2
|-
!Calculation method
|RB3LYP
|-
!Basis set
|6-31G(d,p)
|-
!Energy /au
|<nowiki>-1.17853934</nowiki>
|-
!RMS gradient
|0.00000017
|-
!Point group
|DinfH
|}

H-H bond distance: 0.743Å

<jmol><jmolApplet>
<title>H2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Rr1210_h2_optf_pop.mol2</uploadedFileContents>
</jmolApplet></jmol>

[[Media:H2_OPTF_POP.LOG| Log file]]

[[File:Rr1210_display_vibrations_h2.PNG]]

{| class="wikitable"
|-
!wavenumber cm-1
|4466
|-
!symmetry
|SGG or Σg+
|-
!intensity arbitrary units
|0
|-
!image
| to be added
|}

== Structure Comparison ==
[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DAYGEP&DatabaseToSearch=Published DAYGEP]
N-N distances in the complex are 1.119(4) and 1.126(4)Å and N-N distance in the computed molecule is 1.106Å
The computed gas-phase N-N distance is shorter than the experimental solid state structure N-N distance. In the solid state the N2 molecule is coordinated to a metal, thus some of the bond electron-density will be used to form the M-N2 bond and not in the N-N bond. In the solid state there can also be crystal packing effects, and in this case trans effects from the ligands opposite the N2. The computational result is evaluated in the gas phase, and the N2 is an isolated molecule with no external influences. The bond distance could be changed slightly by using an improved computational method. The error in both the crystal structure and the calculation must also be considered, an error of 0.01 in the computed structure means we must consider the crystal structure and computed molecule distances as equivalent within computational error.

= Energies =

E(NH3)= -56.55776863au

2*E(NH3)= -113.11553726au

E(N2)= -109.52412907au

E(H2)= -1.17853934au

3*E(H2)= -3.53561802au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.055790170au, -140.90 kJ/mol

The energy decreases from the gases to the ammonia product so the product is more stable.

= Detailed CO2 MOs explanation =

https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:CO2_MO_explanation

= 10/10 student wikis from 2019 =

https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Yc16318

https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:01349769

https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:dialekticnomaterialisticen

= HOW TO MARK THE LAB =

Note: all google docs/sheets links are view only, make yourself a copy to edit them.

1. Make a google sheet (copy this [https://docs.google.com/spreadsheets/d/1oPOROiKgelTazIq93YMha39urK0Xfrb6h9lcNkVUD-c/edit?usp=sharing example one]) and add the students names from the main list you will be sent. (If you don't get sent a list you can copy and paste the names from blackboard.)

2. Mark each wiki and give feedback using [https://docs.google.com/document/d/17tthqlAuJQbF1UogDzJv3R327fQ5pxu2-NPIZ76lMPc/edit?usp=sharing this template] and [https://docs.google.com/document/d/1ovyfa7ywXH9dsRNmPuXfm9ZJFXTaWvpFINGam8tdeYs/edit?usp=sharing these model answers] added at the end of the students wiki. The first few wikis you should mark with all the markers together to set standards. While marking always ask the other markers if you are unsure on a grade, to make sure you are the same.

3. Type the marks into the google sheet as you go along.

4. Moderation meeting each week with Tricia, use the google sheet to calculate the average for the week and the average for each marker. Grab the links for the best and worst wikis so she can see them.

5. After moderation release the grades via blackboard learn, here is a video showing how: https://www.youtube.com/watch?v=T69nU7FykUs
Go to grade centre, needs marking, and filter for the IMM2 lab, then click on a student. Type their grade in the attempt box and click submit. The page will change automatically to the next students submission.

Rep:Mod:rr12104

2019-03-29T10:14:10Z

Rr1210:

Rep:Mod:ns618

2019-03-29T10:06:56Z

Rr1210:

'''Optimzed NH3'''
<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986278D-10
Optimization completed.
-- Stationary point found.</pre>
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation Method'''
|RB3LYP
|-
|'''Basis Set'''
|6-31G(d,p)
|-
|'''Final Energy E(RB3LYP)'''
|<nowiki>-56.55776873 a.u.</nowiki>
|-
|'''RMS Gradient'''
|0.00000485 a.u.
|-
|'''Point Group'''
|C3V
|}
N-H Bond Length : 1.01798 angstrom

H-N-H Bond Angle : 105.741 degrees

<jmol><jmolApplet>
<title>optimized NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NS618 NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:Vibration display.png]]

{| class="wikitable"
|'''Wavenumber (/cm)'''
|1089.5366
|1693.9474
|-
|'''Symmetry'''
|A1
|E
|-
|'''intensity (arbitrary units)'''
|145.3814
|13.5533
|-
|}

<pre>
Charge on N-atom = -1.125
Charge on H-atom = +0.375

Expected charge on N-atom is -3 and on H-atom is +1
</pre>
'''Optimzed 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
Optimization completed.
-- Stationary point found.
</pre>
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation Method'''
|RB3LYP
|-
|'''Basis Set'''
|6-31G(d,p)
|-
|'''Final Energy E(RB3LYP)'''
|<nowiki>-1.17853936 a.u.</nowiki>
|-
|'''RMS Gradient'''
|0.00000017 a.u.
|-
|'''Point Group'''
|D*H
|}

H-H Bond Length : 0.74279 angstrom

<jmol><jmolApplet>
<title>optimized NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NS618 H2 OPTF.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:Vibration display2.png]]

{| class="wikitable"
|'''Wavenumber (/cm)'''
|4465.6824
|-
|'''Symmetry'''
|SGG
|-
|'''intensity (arbitrary units)'''
|0
|-
|}

<pre>
Charge on H-atom = 0

Expected charge on H-atom is 0
</pre>

'''Optimzed 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=-3.383850D-13
Optimization completed.
-- Stationary point found.

</pre>
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation Method'''
|RB3LYP
|-
|'''Basis Set'''
|6-31G(d,p)
|-
|'''Final Energy E(RB3LYP)'''
|<nowiki>-109.52412868 a.u.</nowiki>
|-
|'''RMS Gradient'''
|0.00000060 a.u.
|-
|'''Point Group'''
|D*H
|}

H-H Bond Length : 1.10550 angstrom

<jmol><jmolApplet>
<title>optimized NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NS618 N26 OPTF.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:Vibration display3.png]]

{| class="wikitable"
|'''Wavenumber (/cm)'''
|2457.3283
|-
|'''Symmetry'''
|SGG
|-
|'''intensity (arbitrary units)'''
|0
|-
|}

<pre>
Charge on N-atom = 0

Expected charge on N-atom is 0
</pre>

'''Optimzed P4'''
<pre>
Item Value Threshold Converged?
Maximum Force 0.000002 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-4.333417D-11
Optimization completed.
-- Stationary point found.
</pre>
{| class="wikitable"
|'''Molecule'''
|P4
|-
|'''Calculation Method'''
|RB3LYP
|-
|'''Basis Set'''
|6-31G(d,p)
|-
|'''Final Energy E(RB3LYP)'''
|<nowiki>-1365.33522654 a.u.</nowiki>
|-
|'''RMS Gradient'''
|0.00000144 a.u.
|-
|'''Point Group'''
|C1
|}

P-P Bond Length : 1.95272, 2.18213, 2.10909 angstrom

P-P-P Bond Angle : 151.102, 61.101, 57.797 degrees

<jmol><jmolApplet>
<title>optimized NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NS618 P4 OPTF.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:Vibration display5.png]]

{| class="wikitable"
|'''Wavenumber (/cm)'''
|87.9479
|152.7457
|337.3398
|-
|'''Symmetry'''
|A
|A
|A
|-
|'''intensity (arbitrary units)'''
|0.1973
|0.1116
|4.0377
|-
|}

<pre>
Charge on P-atom = -0.129, -0.30, +0.79, +0.79

Expected charge on P-atom is 0
</pre>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

NO - you have not used headings at all in the way that a table of contents was generated. All your jmols are labelled as 'optimised NH3" which is only true for one of them.

==NH3 0/1 ==

Have you completed the calculation and given a link to the file?

NO - You missed to include a link to the .log file of your finished calculation. This reduces the achievable mark for this section by 1.

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES - but it is missing most of the vibrations.

Did you do the optional extra of adding images of the vibrations?

NO

Have you included answers to the questions about vibrations and charges in the lab script?

NO - you missed to answer all questions regarding the vibrations.

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

NO - You missed to include a link to the .log file of your finished calculation. This reduces the achievable mark for this section by 1.

==Crystal structure comparison 0/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

NO

Have you compared your optimised bond distance to the crystal structure bond distance?

NO

==Haber-Bosch reaction energy calculation 0/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

NO

Have you reported your answers to the correct number of decimal places?

NO

Do your energies have the correct +/- sign?

NO

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

NO

== Your choice of small molecule 0.5/5 ==

Have you completed the calculation and included all relevant information?

NO - You missed to include a link to the .log file of your finished calculation. This reduces the achievable mark for this section by 1.

Have you added information about MOs and charges on atoms?

You only stated information about and vibrations without trying to analyse them. You stated the charges of the P atoms. You only stated the charge you would have expected but gave no comparison or explanation why the computed charges are different. This is probably because the geometry of your P4 molecule is not looking like it is in reality. Yours is planar but it should be a tetrahedron.

== Independence 0/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

NO - No independent work has been identified.

= Moderation =

The marking of this wiki has been moderated by Tricia Hunt and the grade confirmed. You did complete a few tasks, and we hope the lab was useful/enjoyable to you and taught you something about computational chemistry!

A note on your grade: Unfortunately in this case the pieces of work were thinly spread across different sections of the lab, so in most cases there was simply too little work present in each section to achieve the minimum standard required to award any marks. A similar level of work applied to just one section of the mark scheme may well have resulted in more marks.

Rep:Mod:ach2718

2019-03-28T12:40:34Z

Rr1210:

== NH3 Molecule ==
===Summary===
{|class="wikitable" border="1"
|'''N-H bond length''' || 1.02Å
|-
| '''H-N-H Bond Angle''' || 106°
|-
|'''Calculation Method''' || RB3LYP
|-
|'''Basis set''' || 6-31G(d,p)
|-
|'''Final Energy E(RB3LYP) in au''' || -56.4439719
|-
|'''RMS Gradient'''|| 0.00000485
|-
|'''Point Group''' || C3v
|}

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES

===Jmol image and link to optimised structure file===
<jmol><jmolApplet>
<title>NH3 dynamic image</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACH2718_NH3_OPT_3.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:ACH2718_NH3_OPT_3.LOG| here]]

===Vibration Information===

[[File:ach2718_nh3_vibrations_info.PNG]]

{|class="wikitable" border="1"
|+ Table for NH3
! '''Wavenumber''' cm-1 !! Symmetry !! '''Intensity''' au !! Image of Vibration !! Video of Vibration
|-
| 1090 || A1 || 145 || [[File:ach2718_nh3_vibrationalmode1.PNG|100px]] || Click for the video [[Media:Ach2718_nh3_vibfilm1.gif| here]]
|-
| 1694 || E || 14 || [[File:ach2718_nh3_vibrationalmode2.PNG|100px]] || Click for the video [[Media:Ach2718_nh3_vibfilm2.gif| here]]
|-
| 1694 || E || 14 || [[File:ach2718_nh3_vibrationalmode3.PNG|100px]] ||Click for the video [[Media:Ach2718_nh3_vibfilm3.gif| here]]
|-
| 3461 || A1 || 1 || [[File:ach2718_nh3_vibrationalmode4.PNG|100px]] || Click for the video [[Media:Ach2718_nh3_vibfilm4.gif| here]]
|-
| 3590|| E || 0 || [[File:ach2718_nh3_vibrationalmode5.PNG|100px]] || Click for the video [[Media:Ach2718_nh3_vibfilm5.gif| here]]
|-
| 3590 || E || 0 || [[File:ach2718_nh3_vibrationalmode6.PNG|100px]] || Click for the video [[Media:Ach2718_nh3_vibfilm6.gif| here]]
|}

From the 3N-6 rule, you would expect 6 vibrational modes, which there are for NH3 molecule, being a non linear molecule. However, there are only four distinct wavenumber values and therefore both modes at 1694 and both vibrational modes at 3590 are degenerate. Since the two degenerate modes at 3590 have an IR intensity of 0 you would expect to see 3 bands in the IR spectrum.
Bending vibrational modes are often lower in frequency than stretching, and NH3 follows this trend. The lowest three frequencies are bending and the highest three frequencies are stretches. From the image it is clear that vibrational mode four, at 3561 cm-1 with symmetry label A1, is the only symmetric stretch, the highly symmetric mode. An important bending mode ammonia undergoes is that known as the umbrella mode, which is mode the mode at 1090 cm-1 with the symmetry label A1.

===Charge Analysis===

[[File:ach2718_nh3_chargeanalysis.PNG| 400px]]

The nitrogen in ammonia is shown in red and has a negative charge due to the lone pair of electrons not shown in the image. The negative charge on the nitrogen is enhanced by the fact it is electronegative, and therefore attracts the electrons in the covalent bond with hydrogen towards itself and therefore away from the hydrogen. This gives the hydrogen, shown in red, the partial positive charge we can see. The overall charge of the molecule is zero and therefore the positive and negative charges must cancel each other out.

== N2 Molecule ==
===Summary===
{|class="wikitable" border="1"
|'''N-N Bond Length'''||1.11 Å
|-
|'''N-N Bond Angle''' || 180°
|-
|'''Calculation Method'''||RB3LYP
|-
|'''Basis Set'''||6-31G(d,p)
|-
|'''Final Energy E(RB3LYP) in au''' || -109.5241287
|-
|'''RMS Gradient in au'''|| 0.00000060
|-
|'''Point Group'''|| D∞h
|}

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

===Jmol image and link to optimised structure file===
<jmol><jmolApplet>
<title>N2 Molecule image</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACH2718_N2_OPTIMISATION4.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:ACH2718_N2_OPTIMISATION3.LOG| here]]

=== Vibration Information===
[[File:Ach2718_n2_vibration_window.PNG]]

{|class="wikitable" border="1"
|+ Table for N2
! '''Wavenumber''' cm-1 !! Symmetry !! '''Intensity''' au !! Image of Vibration
|-
| 2457 || SGG || 0 || [[File:Ach2718_n2_image.PNG|120px]]
|}

Because this is a linear molecule, the number of vibrational modes expected is 3N-5, giving us the one seen above. The only mode is a stretching mode and there is no change in dipole, therefore no infrared radiation is absorbed by the molecule, so no signal is seen in infrared spectrometry.

=== Charge Analysis===
[[File:Ach2718_n2_chargeanalysis.PNG| 400px]]

As expected there is no charge on either molecule as N2 is a diatomic molecule and both nitrogens clearly have the same electronegativity, therefore neither pulls electrons within the bond. Due to this the bond is purely covalent, there is no ionic character at all.

== Mono Metallic Transition Metal complex==

'''Name''': Hydrido-dinitrogen-tris(triphenylphosphine)-cobalt

'''Unique identifier''':PPHCHN11

'''Dinitrogen bond length in complex''': 1.11Å
In the optimised calculated structure, the length of a diatomic nitrogen molecule is also 1.11Å. Therefore the bond lengths in the complex and the N2 are equal to 3 significant figures. It is expected that a more detailed analysis would show that the bond length in the complex is longer due to the metal weakening the bond. This is expected because in the coordinate bond electron density from the N-N bond is donated to the metal. However back donation could occur in certain complexes resulting in a stronger bond with shorter bond length in the complex.

The link for this molecule on CCDC is found here:-
https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=PPHCHN11&DatabaseToSearch=Published

== H2 molecule ==
===Summary===

{|class="wikitable" border="1"
|'''H-H Bond Length'''|| 0.74Å
|-
|'''Bond Angle'''|| 180°
|-
|'''Calculation Method'''|| RB3LYP
|-
|'''Basis set'''|| 6-31G(d,p)
|-
|'''Final Energy E(RB3LYP) in au'''|| -1.1785394 au
|-
|'''RMS Gradient in au'''|| 0.00000017
|-
|'''Point Group''' || D∞h
|}

Item Value Threshold Converged?
Maximum Force 0.000039 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000052 0.001800 YES
RMS Displacement 0.000073 0.001200 YES

===Jmol image and link to optimised file===
<jmol><jmolApplet>
<title>H2 optimisation</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACH2718_H2_OPTIMISATION2.LOG</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:ACH2718_H2_OPTIMISATION2.LOG| here]]

===Vibration Information===

[[File:Ach2718_h2_vibrationimage.PNG]]

{|class="wikitable" border="1"
|+ Table for H2
! '''Wavenumber''' cm-1 !! Symmetry !! '''Intensity''' au !! Image of Vibration
|-
| 4466 || SGG || 0 || [[File:Ach2718_h2_vibrationvector.PNG|150px]]
|}

H2 is also a linear molecule and therefore we expect one vibrational mode. It is again a symmetric vibration and therefore there is no change in dipole, and so no signal in the infrared spectrum.

=== Charge analysis===

[[File:Ach2718_h2_chargeanalysis.PNG]]

As H2 is another diatomic molecule with no electronegativity difference, it has no dipole and the bond is purely covalent.

== Haber-Bosch Process==

'''E(NH3)'''= -56.5577687 au

'''2*E(NH3)'''= -113.1155375 au

'''E(N2)'''= -109.5241287 au

'''E(H2)'''= -1.1785394 au

'''3*E(H2)'''= -3.5356181 au

'''ΔE=2*E(NH3)-[E(N2)+3*E(H2)]'''= -0.0557907 au

'''''ΔE = -146.5kJmol-1'''''

Ammonia is more stable than hydrogen and nitrogen gas which can be seen in the negative overall enthalpy change of -146.5 kJmol-1.

==HCN==
===Summary ===
{| class="wikitable" border="1"
| '''C-H bond length''' || 1.068 Å
|-
| '''C-N Bond length''' || 1.16 Å
|-
| '''Calculation Method''' || RB3LYP
|-
| '''Basis set''' || 6-31G(d,p)
|-
| '''Final Energy E(RB3LYP) in au''' || -93.4245813
|-
| '''RMS Gradient in au''' || 0.00017
|-
| '''Point Group''' || C∞v
|}

Item Value Threshold Converged?
Maximum Force 0.000370 0.000450 YES
RMS Force 0.000255 0.000300 YES
Maximum Displacement 0.000676 0.001800 YES
RMS Displacement 0.000427 0.001200 YES

===Jmol image and link to optimised file===

<jmol><jmolApplet>
<title>HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACH2718_HCN_OPTIMISATION1.LOG</uploadedFileContents>
<script>frame 1.8</script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:ACH2718_HCN_OPTIMISATION1.LOG| here]]

===Vibration information===

[[File:ACH2718_HCN_VIBRATIONINFO.PNG]]

{|class="wikitable" border="1"
|+ Table for HCN
! '''Wavenumber''' cm-1 !! Symmetry !! '''Intensity''' au !! Image of Vibration !! Click for video of vibration
|-
| 766 || PI || 35 || [[File:ach2718_hcn_vibimage1.PNG|200px]] || Click for video [[Media:Ach2718_hcn_vibrationfilm1.gif|here]]
|-
| 766 || PI || 35 || [[File:ach2718_hcn_vibimage2.PNG|200px]] || Click for video [[Media:Ach2718_hcn_vibrationfilm2.gif|here]]
|-
| 2215 || SG || 2 || [[File:ach2718_hcn_vibimage3.PNG|200px]]|| Click for video [[Media:Ach2718_hcn_vibrationfilm3.gif|here]]
|-
| 3480 || SG || 57 || [[File:ach2718_hcn_vibimage4.PNG|200px]]|| Click for video [[Media:Ach2718_hcn_vibrationfilm4.gif|here]]
|}

Due to this being a linear molecule, we would expect 3N-5=4 vibrational modes. The two bending modes at 766 cm-1 with symmetry label PI are degenerate. As expected, the two bending vibrations are lower in wavenumber than the two stretching vibrational modes. The molecule does not have a centre of inversion so modes can be Raman active as well as infrared active. The two degenerate modes have a change of dipole moment which results in an infrared intensity of 35.

The stretching mode at 2215 cm-1 with symmetry label SG has only got an infrared intensity of 2. This is due to the nitrogen and hydrogen atom stretching symmetrically in opposite directions from the central carbon atom. The mode has an infrared intensity greater than zero because there is a triple bond between the nitrogen and the central carbon atom while there only is a single bond between the hydrogen atom and the central carbon atom. Due to the greater bond strength of the triple bond compared to the single bond, the hydrogen atom will be further away from the carbon atom than the nitrogen atom. Therefore the dipole moment will be slightly different to the equilibrium dipole moment.

The stretching mode at 3480 cm-1 with symmetry label SG has an infrared intensity of 57. The mode is highly infrared active because it is an asymmetric stretch as shown in the video. The dipole moment changes by a large extent due to the H-C bond distance being much longer in the stretch than the C-N bond distance in the stretch.

=== Charge Analysis ===

[[File:Ach2718_hcn_chargeanalysis.PNG]]

As expected the nitrogen has the negative charge due to the fact it is slightly more electronegative, and has still one lone pair on it, increasing its negative charge. The hydrogen has a slight positive charge only due to the small electronegativity difference between the carbon and hydrogen. This therefore means the molecule is polar.

===Molecular Orbitals===

{| class="wikitable" border="1"
! Molecular Orbital !! Energy !! Image !! Main AO contributions !! Bonding contribution
|-
| 1st Molecular Orbital || -14.36 || [[File:Ach2718_hcn_lowenergy.PNG|100px]] || Nitrogen 1s || non bonding
|-
| 5th Molecular Orbital || -0.38|| [[File:Ach2718_hcn_mo5.PNG| 100px]] || Hydrogen 2s and 1s, Nitrogen 2s, 2pz, 3s and 3pz, Carbon 2pz and 2s || bonding
|-
| HOMO|| -0.36 || [[File:Ach2718_h2_homo.PNG| 100px]] || Nitrogen 2p and 3p, Carbon 2p and 3p || bonding
|-
| LUMO || -0.019 || [[File:Ach2718_hcn_lumo.PNG| 100px]] || Nitrogen 2p and 3p, Carbon 2p and 3p || anti-bonding
|-
| 10th Molecular Orbital || 0.52 || [[File:Ach2718_hcn_mo101.PNG| 100px]] || Hydrogen 2s and 1s, Nitrogen 2s, 2pz and 3s and 3pz, Carbon 2pz and 2s || anti-bonding
|}

The lowest energy MO has the main contribution from the Nitrogen 1s AO. There is almost no contribution from any other AOs which means that it is non bonding. In the picture it can be seen that there is no electron density shared between 2 atoms.

The 5th lowest MO has main contributions from the Hydrogen 2s and 1s, the Nitrogen 2s, 2pz, 3s and 3pz and the Carbon 2pz and 2s AOs where z is the direction along the bonds of the molecule. It is a σ bonding MO which can be seen from the diagram as there is electron density shared across all three atoms. The contribution of the nitrogen and hydrogen AOs are in phase with each other but out of phase with the carbon contribution.

The HOMO has main contributions from the Nitrogen 2p and 3p and the Carbon 2p and 3p AOs. The HOMO is degenerate with the 6th lowest MO. It is a π bonding MO which is seen clearly in the diagram by the large electron density above and below the central z axis through the bonds.

The LUMO has main contributions from the Nitrogen 2p and 3p and the Carbon 2p and 3p AOs. The LUMO is degenerate with the 9th lowest MO. It is the corresponding π anti-bonding MO to the HOMO. The diagram clearly shows the typical π antibonding shape with contributing AOs being out of phase above and below the central axis repelling each other.

The 10th lowest MO has main contributions from the Hydrogen 2s and 1s, the Nitrogen 2s, 2pz, 3s and 3pz and the Carbon 2pz and 2s AOs where z is the direction along the bonds of the molecule. It is the corresponding σ anti bonding MO to the 5th lowest energy MO. 3 phase boundaries are seen in the diagram making it much higher in energy than the 5th lowst MO.

This analysis was obtained using AO contributions to the MOs calculated by Gaussian. However, the AO contributions calculated do not perfectly represent the AOs present in the actual atoms.

== Ethyne C2H2 ==

===Summary===

{| class="wikitable" border="1"
| '''C-C bond length''' || 1.20 Å
|-
| '''C-H Bond length''' || 1.07 Å
|-
| '''Calculation Method''' || RB3LYP
|-
| '''Basis set''' || 6-31G(d,p)
|-
| '''Final Energy E(RB3LYP) in au''' || -77.3295039
|-
| '''RMS Gradient in au''' || 0.00526
|-
| '''Point Group''' || D∞h
|}

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000023 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

===Jmol image and link to optimised file ===
<jmol><jmolApplet>
<title>Ethene</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACH2718_C2H2_OPTIMISATION1.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:ACH2718_C2H2_OPTIMISATION1.LOG| here]]

== Use of hydrogen cyanide to form ethyne and diatomic nitrogen==

'''2HCN → N2 + C2H2'''

'''E(N2)'''= -109.5241287 au

'''E(C2H2)'''= -77.3295039 au

'''E(HCN)'''= -93.4245813 au

'''2*E(HCN)'''= -186.8491626 au

'''ΔE=E(N2) + E(C2H2) - 2*E(HCN)'''= -0.00447 au

'''''ΔE = -11.7kJmol-1'''''

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 0.5/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, most answers are correct. However there are only 2 visible peaks in the spectra of NH3, due to the low intensity of the other 2 peaks. (See infrared column in vibrations table.)

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 5/5 ==

Have you completed the calculation and included all relevant information?

YES, well done on the high level of detail in your vibrational analysis!

Have you added information about MOs and charges on atoms?

YES, again very detailed and well explained analysis well done!

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did an extra calculation on ethyne and you analysed the energetics of a relevant reaction independently, well done.

Rep:Mod:ROBFINN

2019-03-28T12:23:22Z

Rr1210:

==NH3 Molecule==
===Summary===
{| class="wikitable" border="1"
| Calculation Method || RB3LYP
|-
| Basic set || 6-31G(d,p)
|-
| Final Energy / au || -56.55776873
|-
| RSM Gradient || 0.00000485
|-
| Point Group || C3V
|-
| N-H bond distance / Å || 1.01798
|-
| H-N-H bond angle / ° || 105.741
|}
===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986260D-10
Optimization completed.
-- Stationary point found.
</pre>
===Jmol Image===
<jmol><jmolApplet>
<title> NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RGFINN_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:RGFINN_NH3_OPTF_POP.LOG| here]]
===Frequency Analysis===
[[File:RGFINN_NH3_VIBRATIONS.png]]

{| class="wikitable" border="1"
! wavenumber / cm-1 !! intensity / arbitrary units !! image
|-
| 1090 || 145 || [[File:RGFINN_NH3_VIB1.png |250px]]
|-
| 1694 || 14 || [[File:RGFINN_NH3_VIB2.png|250px]]
|-
| 1694 || 14 || [[File:RGFINN_NH3_VIB3.png|250px]]
|-
| 3461 || 1 || [[File:RGFINN_NH3_VIB4.png|250px]]
|-
| 3590 || 0 || [[File:RGFINN_NH3_VIB5.png|250px]]
|-
| 3590 || 0 || [[File:RGFINN_NH3_VIB6.png|250px]]
|}
From the 3N-6 rule, six modes would be expected. Mode 2 and 3, and 5 and 6 are degenerate. Modes 1, 2 and 3 are bending vibrations. Modes 4, 5 and 6 are stretching vibrations. Mode 4 is highly symmetrical. Mode 1 is the umbrella mode. You would expect to see two bands in an experimental spectrum of gaseous ammonia. Mode four is symmetrical, so won't produce a dipole moment so won't be seen. Modes 2&3 and 5&6 are degenerate so will appear as two peaks. Mode 5&6 have an intensity of zero so won't be seen.

===Charge Analysis===
[[File:RGFINN_NH3_CHARGE.png|centre]]
The charge on the nitrogen is -1.125 and the charge on the hydrogen is +0.375. This is due to nitrogen being more electronegative than hydrogen, so nitrogen has a higher tendency to attract the electron density from the covalent bond, making the nitrogen more negative.

==H2 Molecule==
===Summary===
{| class="wikitable" border="1"
| Calculation Method || RB3LYP
|-
| Basic set || 6-31G(d,p)
|-
| Final Energy / au || -1.17853936
|-
| RSM Gradient || 0.00000017
|-
| Point Group || Dinfh
|-
| H-H bond distance / Å || 0.74279
|}

===Item Table===
<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
Optimization completed.
-- Stationary point found.
</pre>
===Jmol Image===
<jmol><jmolApplet>
<title> H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RGFINN_H2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:RGFINN_H2_OPTF_POP.LOG| here]]
===Frequency Analysis===
[[File:RGFINN_H2_VIBRATIONS.png]]

{| class="wikitable" border="1"
! wavenumber / cm-1 !! intensity / arbitrary units
|-
| 4466 || 0
|}
Linear molecules use the rule 3N-5. Therefore, we can see there should only be one vibrational mode.
===Charge Analysis===
[[File:RGFINN_H2_CHARGE.png|centre]]
The charge on both hydrogens is zero, as they have the same electronegativity.

==N2 Molecule==
===Summary===
{| class="wikitable" border="1"
| Calculation Method || RB3LYP
|-
| Basic set || 6-31G(d,p)
|-
| Final Energy / au || -109.52412868
|-
| RSM Gradient || 0.00000060
|-
| Point Group || Dinfh
|-
| N-N bond distance / Å || 1.10550
|}

===Item Table===
<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=-3.400991D-13
Optimization completed.
-- Stationary point found.
</pre>
===Jmol Image===
<jmol><jmolApplet>
<title> N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RGFINN_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:RGFINN_N2_OPTF_POP.LOG| here]]

===Frequency Analysis===
[[File:RGFINN_N2_VIBRATIONS.png]]

{| class="wikitable" border="1"
! wavenumber / cm-1 !! intensity / arbitrary units
|-
| 2457 || 0
|}
Linear molecules use the rule 3N-5. Therefore, we can see there should only be one vibrational mode.
===Charge Analysis===
[[File:RGFINN_N2_CHARGE.png|centre]]
The charge on both nitrogens is zero, as they have the same electronegativity.

==trans-bis(1-(diethylphosphino)-N-((diethylphosphino)methyl)-N-(2,6-difluorobenzyl)methanamine)-bis(dinitrogen)-chromium [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=aqezih&DatabaseToSearch=Published| AQEZIH]]==
[[https://pubs.rsc.org/en/Content/ArticleLanding/2016/CC/C6CC03449G#!divAbstract| Jonathan D. Egbert, Molly O'Hagan, Eric S. Wiedner, R. Morris Bullock, Nicholas A. Piro, W. Scott Kassel, Michael T. Mock, Chemical Communications, 2016, 52, 9343, DOI: 10.1039/C6CC03449G]]
[[File:AQEZIH.png|centre]]
N-N bond distance is equal to 1.127 Å.
The crystal structure has a longer N-N bond length when compared to the computational distance. This implies that the bond is weaker. This could be due to the central chromium being electron withdrawing, which makes the bond weaker and consequently longer. The crystal structure is also a solid, so more electron withdrawing groups could interact with the N-N bond, spreading electron density over more atoms, making the bond weaker and longer.

==Haber-Bosch Process==
{| class="wikitable" border="1"
! Molecule !! Energy / au
|-
| NH3 || -56.55777
|-
| N2 || -109.52413
|-
| H2 || -1.17854
|}

N2 + 3H2 → 2NH3

ΔE = [2xE(NH3)] - [E(N2) + 3xE(H2)]
= [-113.11554] - [-109.52413 - 3.53562]
= -0.05579 au
= -146.5 kJ/mol

The reaction is exothermic, therefore the product (ammonia) is more stable as energy is released during the reaction.
==CH4 Molecule==
===Summary===
{| class="wikitable" border="1"
| Calculation Method || RB3LYP
|-
| Basic set || 6-31G(d,p)
|-
| Final Energy / au || -40.52401404
|-
| RSM Gradient || 0.00003263
|-
| Point Group || Td
|-
| C-H bond distance / Å || 1.09197
|-
| H-C-H bond angle / ° || 109.471
|}
===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES
Predicted change in Energy=-2.256043D-08
Optimization completed.
-- Stationary point found.
</pre>
===Jmol Image===
<jmol><jmolApplet>
<title> CH4 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RGFINN_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.8</script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:RGFINN_CH4_OPTF_POP.LOG| here]]

===Frequency Analysis===
[[File:RGFINN_CH4_VIBRATIONS.png]]

{| class="wikitable" border="1"
! wavenumber / cm-1 !! intensity / arbitrary units
|-
| 1356 || 14
|-
| 1356 || 14
|-
| 1356 || 14
|-
| 1579 || 0
|-
| 1579 || 0
|-
| 3046 || 0
|-
| 3162 || 25
|-
| 3162 || 25
|-
| 3162 || 25
|}
From the 3N-6 rule, nine modes would be expected. Mode 1&2&3, and 4&5, and 7&8&9 are degenerate. Modes 1, 2, 3, 4 and 5 are bending vibrations. Modes 6, 7, 8 and 9 are stretching vibrations. Mode 6 is highly symmetrical. You would see two peaks for methane. Modes 1&2&3 and 7&8&9 are degenerate so will produce two peaks. The rest of the modes have zero intensity so won't be seen.

===Charge Analysis===
[[File:RGFINN_CH4_CHARGE.png|centre]]
The charge on the carbon is -0.930 and the charge on the hydrogen is +0.233. This is due to carbon being more electronegative than hydrogen, so carbon has a higher tendency to attract the electron density from the covalent bond, making the carbon more negative.

===Molecular Orbitals===
====HOMO====
[[File:RGFINN_CH4_MO5.png|centre|200px]]
[[File:RGFINN_CH4_MO4.png|centre|200px]]
[[File:RGFINN_CH4_MO3.png|centre|200px]]
These three molecular orbitals are degenerate with an energy of -0.38831 au. These are the highest occupied molecular orbital in the molecule, and are each occupied by two electrons with opposite spins. These are bonding orbitals and form σ bonds. Each MO has contribution from 1s atomic orbital from hydrogen and a 2p atomic orbital from carbon, which also forms an antibonding σ MO. This does contribute to the bond order of the molecule.

====LUMO====
[[File:RGFINN_CH4_MO6.png|centre|200px]]
This is the lowest unoccupied molecular orbital in the molecule, with an energy of 0.11824 au. It is unoccupied. The 2s AO of carbon and the 1s AO of hydrogen combind to form this MO and a σ MO. It is an antibonding orbital. This doesn't contribute to the bond order of the molecule.

====Carbon 1s====
[[File:RGFINN_CH4_MO1.png|centre|200px]]
This MO is contributed to by the 1s AO in carbon, with an energy of -10.16707 au. Due to it's highly negative energy, it doesn't contribute to the bonding.

====1σ====
[[File:RGFINN_CH4_MO2.png|centre|200px]]
This id the first σ molecular orbital with an energy of -0.69041 au. This is occupied with two electrons with opposite spins and is a bonding orbital. The 2s AO from carbon and the 1s AO from hydrogen contribute to this. This does contribute to the bond order of the molecule.

====7σ* 8σ* 9σ*====
[[File:RGFINN_CH4_MO7.png|centre|200px]]
[[File:RGFINN_CH4_MO8.png|centre|200px]]
[[File:RGFINN_CH4_MO9.png|centre|200px]]
These are three degenerate σ* molecular orbitals. They are unoccupied and each have an energy of 0.17677 au. A 2p AO from carbon and a 1s AO from hydrogen combind to form each MO. This doesn't contribute to the bond order of the molecule.
==Independent Cl2 Molecule==

===Summary===
{| class="wikitable" border="1"
| Calculation Method || RB3LYP
|-
| Basic set || 6-31G(d,p)
|-
| Final Energy / au || -920.34987886
|-
| RSM Gradient || 0.00002511
|-
| Point Group || Dinfh
|-
| Cl-Cl bond distance / Å || 2.04174
|}

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000043 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000121 0.001800 YES
RMS Displacement 0.000172 0.001200 YES
Predicted change in Energy=-5.277255D-09
Optimization completed.
-- Stationary point found.
</pre>
===Jmol Image===
<jmol><jmolApplet>
<title> Cl2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RGFINN_CL2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:RGFINN_CL2_OPTF_POP.LOG| here]]

===Frequency Analysis===
[[File:RGFINN_CL2_VIBRATIONS.png]]

{| class="wikitable" border="1"
! wavenumber / cm-1 !! intensity / arbitrary units
|-
| 520 || 0
|}
Linear molecules use the rule 3N-5. Therefore, we can see there should only be one vibrational mode.
===Charge Analysis===
[[File:RGFINN_CL2_CHARGE.png|centre]]
The charge on both chlorines is zero, as they have the same electronegativity.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES, overall a very good wiki well done!

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, and overall your explanations are correct, clear and well presented, well done! The aspect you could have improved upon would be to explain that the LUMO and the 1 sigma MOs are bonding/antibonding counterparts. And the same for the HOMOs and the 7,8,9 sigma star MOs.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You calculated Cl2 independently well done!

Rep:Mod:01492350

2019-03-28T12:16:13Z

Rr1210:

=Molecular Modelling 2=
==NH3 (Ammonia)==
Calculation Method: RB3LYP

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

Final Energy E(RB3LYP): -56.55777 a.u. (atomic units)

RMS Gradient: 4.85 x 10-6 a.u. (atomic units)

Point Group: C3V

<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>ME1218_NH3_OPT1.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Bond Length (N-H):1.02 Å

Bond Angle (H-N-H):105.7°

The optimisation file is linked to [[Media:ME1218_NH3_OPT1.LOG| here]]

[[File:01492350 Screenshot-Vibrations-NH3.png|thumb|left|The 'Display Vibrations' window in Gaussian of the optimised NH3.]]

{| class="wikitable"
|+ Vibrational modes of NH3
| '''Wavenumber''' (cm-1) || 1089.5366 || 1693.9474 || 1693.9474 || 3461.2932 || 3589.8170 || 3589.8170
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' (arbitrary units) || 145.3814 || 13.5533 || 13.5533 || 1.0608 || 0.2711 || 0.2711
|-
| '''Image'''|| [[File:01492350 Screenshot-Vibrations-NH3-image1.png|200px|.]] || [[File:01492350 Screenshot-Vibrations-NH3-image2.png|200px|.]] || [[File:01492350 Screenshot-Vibrations-NH3-image2.png|200px|.]] || [[File:01492350 Screenshot-Vibrations-NH3-image3.png|200px|.]] || [[File:01492350 Screenshot-Vibrations-NH3-image4.png|200px|.]] || [[File:01492350 Screenshot-Vibrations-NH3-image4.png|200px|.]]
|}

Charges on atoms:

N=-1.125

H=0.375

[[File:01492350 NH3 Charges.png|thumb|left|The charge distribution of NH3.]]

One would expect the charge on the nitrogen to be more negative than the hydrogen(s) since nitrogen is more electronegative. Nitrogen therefore, withdraws electron density from the hydrogens making the hydrogens slightly positively charged (and making itself negatively charged).

===Questions===

Using the 3N-6 rule, one would expect the NH3 molecule to have 6 vibrational modes (as value of N=4 for ammonia).

The 1693.95 cm-1 vibrational modes and 3589.82 cm-1 vibrational modes are degenerate; for each, there are two vibrational modes with that energy.

The 3461.29 cm-1 and 3589.82 cm-1 modes are bond stretching vibrations whereas the 1089.54 cm-1 and 1693.95 cm-1 modes are bending vibrations.

The vibrational mode with frequency 3461.29 cm-1 is highly symmetric.

The vibrational mode with frequency 1089.54 cm-1 is known as the 'umbrella mode'.

In an experimental spectrum of gaseous ammonia, there would be 2 bands observed. This is because, including degeneracy, there would be 4 signals. However, as the intensity is so low for 3589.82 cm-1 and 3461.29 cm-1 (around 0 and 1 respectively), these would not be observed.

==H2 (Hydrogen)==
Calculation Method: RB3LYP

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

Final Energy E(RB3LYP): -1.17854 a.u. (atomic units)

RMS Gradient: 1.7 x 10-7 a.u. (atomic units)

Point Group: D∞H

<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

</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>ME1218_H2_OPT1.LOG</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

Bond Length (H-H):0.74 Å

The optimisation file is linked to [[Media:ME1218_H2_OPT1.LOG| here]]

[[File:01492350 Screenshot-Vibrations-H2.png|thumb|left|The 'Display Vibrations' window in Gaussian of the optimised H2.]]

{| class="wikitable"
|+ Vibrational modes of H2
| '''Wavenumber''' (cm-1) || 4465.6824
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' (arbitrary units) || 0.0000
|-
| '''Image'''|| [[File:01492350 Screenshot-Vibrations-H2-image1.png|200px|.]]
|}

Charges on atoms:

H=0.000

[[File:01492350 H2 Charges.png|thumb|centre|The charge distribution of H2.]]

==N2 (Nitrogen)==
Calculation Method: RB3LYP

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

Final Energy E(RB3LYP): -109.52413 a.u. (atomic units)

RMS Gradient: 6 x 10-7 a.u. (atomic units)

Point Group: D∞H

<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

</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>ME1218_N2_OPT1.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

Bond Length (N-N):1.11 Å

The optimisation file is linked to [[Media:ME1218_N2_OPT1.LOG| here]]

[[File:01492350 Screenshot-Vibrations-N2.png|thumb|left|The 'Display Vibrations' window in Gaussian of the optimised N2.]]

{| class="wikitable"
|+ Vibrational modes of N2
| '''Wavenumber''' (cm-1) || 2457.3283
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' (arbitrary units) || 0.0000
|-
| '''Image'''|| [[File:01492350 Screenshot-Vibrations-N2-image1.png|200px|.]]
|}

Charges on atoms:

N=0.000
[[File:01492350 N2 Charges.png|thumb|The charge distribution of N2.]]

====Nitrogen Orbitals - independence mark====

The HOMO molecular orbital is the 3σg. This is made up of the 2pz atomic orbitals of each nitrogen atom. The LUMO molecular orbital is the 1π*g. This is made up of two 2px or two 2py atomic orbitals. It is an antibonding orbital.

[[File:01492350 N2 Orbital HOMO.PNG|thumb|left|The HOMO of N2.]]
[[File:01492350 N2 Orbital LUMO.PNG|thumb|centre|The LUMO of N2.]]

====Nitrogen mono-metallic transition metal complex====

Unique Identifier: BARTOF

Bond Length (N-N) in BARTOF complex:1.11218 Å

Bond Length (N-N) in optimised structure:1.10550 Å

<jmol><jmolApplet>
<title>BARTOF Complex</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>BARTOF.search2.cif</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BARTOF&DatabaseToSearch=Published

[[File:01492350 BARTOF Mercury.PNG|thumb|The 3D representation of the N2 mono-metallic transition metal complex 'BARTOF' in Mercury.]]

[[File:01492350 BARTOF.png|thumb|centre|The structure of the N2 mono-metallic transition metal complex 'BARTOF' in Conquest.]]

The bond distance in the computational model of N2 is lower than that found in the crystal structure of BARTOF. This is because the transition metal (Fe in this case) withdraws electron density from the nitrogen atom in the BARTOF complex. This weakens the bond between the nitrogen atoms so the bond distance is elongated. There may be errors in the computational calculations made which may mean the values differ (and do reflect those in real life).

====Haber Process====

E(NH3)=-56.55776873 a.u.
2*E(NH3)=-113.1155375 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)]=-0.05579 a.u.
ΔE=-146.8 kJ mol-1 (energy to convert N2 (g) and H2 (g) into NH3 (g))

Therefore, as the value for ΔE is negative (exothermic), the NH3 is more stable.

==HCN (Hydrogen Cyanide)==
Calculation Method: RB3LYP

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

Final Energy E(RB3LYP): -93.42458 a.u. (atomic units)

RMS Gradient: 1.7 x 10-4 a.u. (atomic units)

Point Group: C∞V

<pre>

Item Value Threshold Converged?
Maximum Force 0.000370 0.000450 YES
RMS Force 0.000255 0.000300 YES
Maximum Displacement 0.000676 0.001800 YES
RMS Displacement 0.000427 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>HCN</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>ME1218_HCN_OPT1.LOG</uploadedFileContents>
<script>frame 1.8</script>
</jmolApplet></jmol>

Bond Length (C-N):1.16 Å

Bond Length (C-H):1.07 Å

The optimisation file is linked to [[Media:ME1218_HCN_OPT1.LOG| here]]

[[File:01492350 Screenshot-Vibrations-HCN.png|thumb|left|The 'Display Vibrations' window in Gaussian of the optimised HCN.]]

{| class="wikitable"
|+ Vibrational modes of HCN
| '''Wavenumber''' (cm-1) || 766.7352 || 766.7352 || 2214.7397 || 3479.9336
|-
| '''Symmetry''' || PI || PI || SG || SG
|-
| '''Intensity''' (arbitrary units) || 35.2959 || 35.2959 || 2.0451 || 57.3217
|-
| '''Image'''|| [[File:01492350 Screenshot-Vibrations-HCN-image1.png|200px|.]] || [[File:01492350 Screenshot-Vibrations-HCN-image2.png|200px|.]] || [[File:01492350 Screenshot-Vibrations-HCN-image3.png|200px|.]] || [[File:01492350 Screenshot-Vibrations-HCN-image4.png|200px|.]]
|}

The HCN molecule has four vibrational modes. Using the 3N-5 rule (for linear molecules), one would expect there to be 4 vibrational modes. There is one set of degenerate vibrational modes (with wavenumber 766.7352 cm-1.

The 2214.7397 cm-1 and 3479.9336 cm-1 modes are bond stretching vibrations whereas the 766.7352 cm-1 degenerate modes are bending vibrations.

In an experimental spectrum of 2 bands would be observed. This is because, including degeneracy, there would be 3 signals. However, as the intensity is so low for 2214.7397 cm-1 (only 2.0451), this would not be observed.

Charges on atoms:

C=0.073

N=-0.308

H=0.234

[[File:01492350 Screenshot-charges-HCN.PNG|thumb|left|The charge distribution of HCN.]]

In the HCN molecule, the nitrogen (N) atom is the most electronegative. Therefore, the nitrogen atoms withdraws electron density from the carbon atom (C). Hence, the nitrogen has the most negative charge. Carbon is more electronegative than hydrogen so withdraws electron denisty from the hydrogen leading to a less positive charge on the carbon and a more positive charge on the hydrogen.

===HCN Orbitals===

{| class="wikitable"
|+ Molecular Orbitals of HCN
| '''Molecular Orbital Type''' || 1π* (LUMO) antibonding || 1π (HOMO) bonding || 5σ bonding || 4σ* anti-bonding || 3σ bonding
|-
|'''Occupied with elctrons?'''|| No || Yes || Yes || Yes || Yes
|-
| '''Atomic Orbitals''' || The 3px/y and 2px/y from N and those from C contribute significantly || The 2px/y from the N, 2px/y from the C contribute significantly || 2pz from N and from C contribute significantly along with the 2s orbital of H || The 2s and 3s from the N, 2pz from C and 1s from H contribute significantly|| The 2s and 3s from the N contribute singificantly along with the 2s from the C
|-
| '''Energy''' (a.u.) || 0.01929 || -0.35939 || -0.38064 || -0.60777 || -0.91995
|-
| '''Image'''|| [[File:01492350 HCN Orbital LUMO.PNG|200px|.]] || [[File:01492350 HCN Orbital HOMO.PNG|200px|.]] || [[File:01492350 HCN Orbital 3.PNG|200px|.]] || [[File:01492350 HCN Orbital 4.PNG|200px|.]] || [[File:01492350 HCN Orbital 5.PNG|200px|.]]
|}

The LOG file was used to evaluate the atomic orbital contributions to each molecular orbital in the HCN molecule. The % contribution from each AO is listed in the LOG file. The atomic orbitals that make up molecular orbitals are not so definitive and clear-cut. Instead, some atomic orbital will contribute a small percentage towards the MO. For example, in the 4σ* anti-bonding molecular orbital, there is a 15% contribution from 2s (N) and 15% contribution from 3s (N). Therefore, it cannot be said that the nitrogen only gives the 2s towards this molecular orbital.

There are degenerate orbitals (with the same energy). These are the 1π* and 1π. The 1π* and 1π orbitals are made up of px or py atomic orbitals. These have the same energy. The overlap between px orbitals or py orbitals is equivalent and forms a π bond with electron denisty above/ below the plane of the molecule. The overlap between pz orbitals, however, is greater and forms along the plane. This forms a σ bond.

There are 2π bonds and a σ bond between the carbon and the nitrogen atoms. There is only a σ bond between the hydrogen and the carbon. Other orbitals like 1σ and 2σ* are deep in energy (with energies of -14.36 a.u. and -10.25 a.u. respectively) so won't have an effect on bonding. Therefore, they do not need to be considered.

==CO (Carbon monoxide) - independence mark==
Calculation Method: RB3LYP

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

Final Energy E(RB3LYP): -113.30945 a.u. (atomic units)

RMS Gradient: 1.83 x 10-5 a.u. (atomic units)

Point Group: C∞V

<pre>

Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000018 0.001200 YES

</pre>

<jmol><jmolApplet>
<title>CO</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>ME1218_CO_OPT1.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

Bond Length (C-O):1.14 Å

The optimisation file is linked to [[Media:ME1218_CO_OPT1.LOG| here]]

[[File:01492350 Screenshot-Vibrations-CO.png|thumb|left|The 'Display Vibrations' window in Gaussian of the optimised CO.]]

{| class="wikitable"
|+ Vibrational modes of CO
| '''Wavenumber''' (cm-1) || 2209.1389
|-
| '''Symmetry''' || SG
|-
| '''Intensity''' (arbitrary units) || 67.9587
|-
| '''Image'''|| [[File:01492350 Screenshot-Vibrations-CO-image 1.png|200px|.]]
|}

Charges on atoms:

C=0.506

O=-0.506

[[File:01492350 CO Charges.PNG|thumb|left|The charge distribution of CO.]]

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, you have looked into the MOs especially with a lot of detail, well done. The one point I would disagree with is that if the 4 sigma star MO has contributions from the C 2pz then the node is at the C atom and not between the atoms so there are bonding interactions between the C and N and the C and H atoms, not antibonding.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You looked at the N2 MOs and calculated CO independently, well done!

Rep:Mod:01492350

2019-03-28T12:14:47Z

Rr1210:

Rep:Mod:Yc16318

2019-03-28T12:07:35Z

Rr1210:

= NH3 Molecule =

== Summary Information ==

=== Summary of NH3 Molecule ===
{| class="wikitable" border="1"
|+ NH3 Optimisation
|-
| '''Molecule Name''' || NH3
|-
| '''Calculation Method''' || RB3LYP
|-
| '''Basis Set''' || 6-31G(d,p)
|-
| '''E(RB3LYP)''' || -56.55776873 au
|-
| '''RMS Gradient Norm''' || 0.00000485 au
|-
| '''Point Group''' || C3v
|}

N-H Bond Distance: 1.02Å (±0.01Å)

H-N-H Bond Angle: 106° (±1°)

=== Item Table ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986282D-10
</pre>

=== Jmol File ===
<jmol><jmolApplet>
<script>frame 1.16</script>
<title>Optimised NH3 Molecule
</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YUANCHEN NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:YUANCHEN NH3 OPT.LOG| here]]

== Frequency Analysis ==

=== A snapshot of the display vibration table ===
[[File:YC16318 Screenshot display vibrations.PNG|400px]]

=== Vibration Modes of the NH3 Molecule ===
{| class="wikitable" border="1"
|+ Vibration Modes of the NH3 Molecule
|'''Mode'''
|1
|2
|3
|-
|'''Wavenumber''' (cm-1) || 1090 || 1694 || 1694
|-
|'''Symmetry'''
|A1
|E
|E
|-
|'''Intensity'''
|145
|14
|14
|-
|'''Image'''
|[[File:Yc16318 vib 1.png|200px]]
|[[File:Yc16318 vib 2.png|200px]]
|[[File:Yc16318 vib 3.png|200px]]
|}

{| class="wikitable" border="1"
|'''Mode'''
|4
|5
|6
|-
|'''Wavenumber''' (cm-1) || 3461 || 3590 || 3590
|-
|'''Symmetry'''
|A1
|E
|E
|-
|'''Intensity'''
|1
|0
|0
|-
|'''Image'''
|[[File:Yc16318 vib 4.png|200px]]
|[[File:Yc16318 vib 5.png|200px]]
|[[File:Yc16318 vib 6.png|200px]]
|}

=== Q & A ===
how many modes do you expect from the 3N-6 rule?

- 3×4-6=6 modes

Which modes are degenerate (i.e. have the same energy)?

- Mode 2 and 3; Mode 5 and 6 (two pairs of modes that are degenerate to each other).

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

- Bending: 1, 2, 3; Bond Stretch: 4, 5, 6

Which mode is highly symmetric?

- Mode 4

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

- Mode 1

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

- 2 bands. 3 bands are expected from mode 1,2,3, but mode 2 and mode 3 are degenerate, thus only two bands are shown. Mode 4 is symmetrical hence not IR active, while mode 5 and 6 have intensities of 0.

== Charge Analysis ==

=== Charge Distribution of the NH3 Molecule ===

[[File:YC16318 charge analysis.PNG]]

The N-atom is expected to carry negative charge and the H-atoms are expected to carry positive charges because nitrogen is more electronegative compared to hydrogen.

= N2 Molecule =
== Summary Information ==
=== Summary of N2 Molecule ===
{| class="wikitable" border="1"
|+ N2 Optimisation
|-
| '''Molecule Name''' || N2
|-
| '''Calculation Method''' || RB3LYP
|-
| '''Basis Set''' || 6-31G(d,p)
|-
| '''E(RB3LYP)''' || -109.52412868 au
|-
| '''RMS Gradient Norm''' || 0.00000060 au
|-
| '''Point Group''' || D∞h
|}

N≡N Bond Distance: 1.11Å (±0.01Å)

=== Item Table ===
<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=-3.401045D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

=== Jmol File ===
<jmol><jmolApplet>
<title> Optimised N2 Molecule</title>
<script>frame 1.10</script>
<color>black</color>
<size>200</size>
<uploadedFileContents>YC16318 N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:YC16318 N2 OPTIMISATION.LOG| here]]

== Frequency Analysis ==

=== A snapshot of the display vibration table ===
[[File:Yc16318 n2 Display vib.PNG|400px]]

=== Vibration Modes of the N2 Molecule ===
{| class="wikitable" border="1"
|+ Vibration Mode of the N2 Molecule
|-
|'''Wavenumber''' (cm-1) || 2457
|-
|'''Symmetry'''
|SGG
|-
|'''Intensity'''
|0
|-
|'''Image'''
|[[File:Yc16318 N2 vib.PNG|200px]]
|}

== Charge Analysis ==

=== Charge Distribution of the N2 Molecule ===
[[File:Yc16318 N2 Charge1.PNG|200px]]

[[File:Yc16318 n2 charge2.PNG|200px]]

The molecule does not have a permanent dipole moment and no charge is allocated to either N atoms (homonuclear)

= H2 Molecule =
== Summary Information ==
=== Summary of H2 Molecule ===
{| class="wikitable" border="1"
|+ H2 Optimisation
|-
| '''Molecule Name''' || H2
|-
| '''Calculation Method''' || RB3LYP
|-
| '''Basis Set''' || 6-31G(d,p)
|-
| '''E(RB3LYP)''' || -1.17853936 au
|-
| '''RMS Gradient Norm''' || 0.00000017 au
|-
| '''Point Group''' || D∞h
|}

H-H Bond Distance: 0.74Å (±0.01Å)

=== Item Table ===
<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
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

</pre>

=== Jmol File ===
<jmol><jmolApplet>
<title>Optimised H2 Molecule</title>
<script>frame 1.12</script>
<color>black</color>
<size>200</size>
<uploadedFileContents>YC16318 H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:YC16318 H2 OPT.LOG| here]]

== Vibration Analysis ==
=== A snapshot of the display vibration table ===
[[File:Yc16318 H2 display vib.PNG|400px]]

=== Vibration Mode of the H2 Molecule ===
{| class="wikitable" border="1"
|+ Vibration Mode of the H2 Molecule
|-
|'''Wavenumber''' (cm-1) || 4466
|-
|'''Symmetry'''
|SGG
|-
|'''Intensity'''
|0
|-
|'''Image'''
|[[File:Yc16318 H2 VIB.PNG|200px]]
|}

== Charge Analysis ==
=== Charge Distribution of the H2 Molecule ===
[[File:YC16318 H2 Charge1.PNG|200px]]

[[File:Yc16318 H2 Charge2.PNG|200px]]

The molecule does not have a permanent dipole moment and no charge is allocated to either h atoms (homonuclear)

= Structure and Reactivity =

== N2 Coordinating in Mono-metallic TM Complex==
Mono-metallic TM Complex Identifier: DEKFUX

The Mono-metallic Ruthenium Complex is linked to [[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=CEUJED&year=2017&spage=12709&volume=23&id=doi:10.1002/chem.201702727&pid=ccdc:1555410| here]]

The original journal can be found at[[https://onlinelibrary.wiley.com/doi/full/10.1002/chem.201702727]]

N≡N Bond Length: 1.09 Å (±0.01Å)

Structure of The Ruthenium Complex

[[File:Yc16318 complex.PNG]]

The bond length found in the structure is slightly shorter than the one obtained through Gaussian (N≡N Bond Distance=1.11 Å). This could be due to:

1. The N-N triple bond is strengthened when the molecule is coordinated to the Ruthenium because the metal centre donates electron density to the triple bond

2. experimental error (only small deviation)

3. the Bond Length Gaussian found is a local minimum instead of the overall minimum

4. Ideally, the N≡N bond found in the metal complex should be longer than that in N2 molecule as coordinating to the metal centre would decrease the electron density in the N≡N bond thus weakens the bond.

== Haber-Bosch process ==
E(NH3)= -56.5577687 au

2×E(NH3)= -113.1155374 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3×E(H2)= -3.5356182 au

ΔE=2×E(NH3)-[E(N2)+3×E(H2)]=-0.0557905≈-0.05579 au= -145.4 kJ/mol

The ammonia product is more stable as it has a lower energy and the energy for the reaction is exothermic (ΔE<0)

= CO Molecule =

== Summary Information ==
=== Summary of CO Molecule ===
{| class="wikitable" border="1"
|+ CO Optimisation
|-
| '''Molecule Name''' || CO
|-
| '''Calculation Method''' || RB3LYP
|-
| '''Basis Set''' || 6-31G(d,p)
|-
| '''E(RB3LYP)''' || -113.30945314 au
|-
| '''RMS Gradient Norm''' || 0.00000433 au
|-
| '''Point Group''' || C∞v
|}

C≡O Bond Distance: 1.14Å (±0.01Å)

=== Item Table ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
Predicted change in Energy=-2.221224D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

</pre>

=== Jmol File ===
<jmol><jmolApplet>
<title>Optimised CO Molecule</title>
<script>frame 1.12</script>
<color>black</color>
<size>200</size>
<uploadedFileContents>YC16318 CO OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:YC16318 CO OPT.LOG| here]]

== Vibration Analysis ==
=== A snapshot of the display vibration table ===
[[File:YC16318 CO Dis vib.PNG|400px]]

=== Vibration Mode of the CO Molecule ===
{| class="wikitable" border="1"
|+ Vibration Mode of the CO Molecule
|-
|'''Wavenumber''' (cm-1) || 2209
|-
|'''Symmetry'''
|SG
|-
|'''Intensity'''
|68
|-
|'''Image'''
|[[File:Yc16318 CO vib.PNG|200px]]
|}

== Charge Analysis ==
=== Charge Distribution of the CO Molecule ===
[[File:YC16318 CO Charge.PNG|200px]]

=== Vibration Motion of The CO Molecule ===
[[File:Yc16318 CO VIBGIF.gif]]

The C atom has a positive partial charge while the O atom has a negative partial charge. This is because O is more electronegative than C.

== Molecular Orbitals of The CO Molecule ==

=== Five MOs of CO ===
*How do you tell apart bonding, antibonding and nonbonding?**
{| class="wikitable" border="1"
|Order of the MO
|1
|3
|5
|-
|'''Image'''
|[[File:Yc16318 CO MO1.PNG|180px]]
|[[File:YC16318 CO MO3.PNG|180px]]
|[[File:YC16318 CO MO5.PNG|180px]]
|-
|'''Energy'''
|Deep in energy (core) (-19.25806 au)
|High in energy (-1.15790 au) one magnitude higher than the previous MO (-10.30433 au)
|Relatively high in energy, identical to MO #6 (-0.46742 au)
|-
|'''Bonding, anti-bonding or a mixture?'''
| Neither, the main contribution being the 1s orbital on the O atom
| Bonding, 2s on O contributes to this MO the most (has the largest molecular orbital coefficient). 2pz on C also contributes to the MO to a small extent (hence the green patch on C)
| Bonding, 2px on O contributes to this MO the most, following by 3px on O and 2px on C
|-
|'''What effect will this MO have on bonding?'''
| Do not participate in bonding
| It contributes to the σ bond to some extent
| Pi bond along x-axis
|-
|'''Occupied or unoccupied?'''|| Occupied || Occupied || Occupied
|}

{| class="wikitable" border="1"
|Order of The MO
|7
|8
|-
|'''Image'''
|[[File:YC16318 CO HOMO.PNG|180px]]
|[[File:YC16318 CO LUMO.PNG|180px]]
|-
|'''Energy'''
|HOMO (-0.37145 au)
|LUMO (-0.02178 au)
|-
|'''Bonding, anti-bonding or a mixture?'''
| A mixture, major contribution of this MO is from 3s on the C atom. Other major contributions are from 2s and 2pz on C, and 2pz and 3pz on O
| Anti-bonding, major contribution of this MO is from 2px and 3px on the C atom, and 2px and 3px on the O atom
|-
|'''What effect will this MO have on bonding?'''
| Mostly destabilising effect due to the anti-bonding component
| Destabilising effect
|-
|'''Occupied or unoccupied?'''|| Occupied || Unoccupied
|}

== Independence ==
=== An comparison between the MO theory and Gaussian as means of explaining the C≡O bond ===
[[File:COMOdiagram.png]]

Original diagram can be found here[[http://www.chemtube3d.com/orbitalsCO.htm]]

The MO#1 (1σ) is not shown in the diagram because it is deep in energy and do not interact with the illustrated AOs/MOs, it is suggested by the MO theory that the 1s AOs in both atoms overlap to form bonding 1σ and antibonding 2σ. However, Gaussian suggests that the 1s AOs are core orbitals that barely participate in bonding.

In the MO diagram, MO#3 (3σ) is illustrated as a bonding orbital created by the overlapping of the 2s AOs from both C and O which is also stabilised by the sp hybridisation of 2s and 2p within the O atom and the C atom individually.

MO#5 is shown in the diagram as one of the degenerate 1π orbitals resulted , which also agrees with the computation in Gaussian which indicates that 2px on both C and O contribute to MO#5. However, in addition to the 2px AOs, Gaussian also suggests that 3px on O has a major contribution to this MO as well.

The HOMO (5σ) is stabilised by the overlap of 2pz AOs in both C and O, but destabilised by the out of phase overlap in the sp hybridisation (antibonding), hence it's a mixture, which agrees with the results found in Gaussian. Because O is more electronegative and therefore its orbitals are deeper in energy, the MO orbital formed would resemble AOs in O more. This observation also agrees with Gaussian, which indicates that orbitals on O have higher molecular orbital coefficients.

The LUMO is the antibonding orbital from the overlap between 2p AOs from both C and O that resembles 2p orbital in C more because it is closer in energy to the less electronegative C, which agrees with calculations in Gaussian as well.

==== Conclusion ====
In comparison to the MO theory, the calculations in Gaussian gives more in-depth and accurate information about the MO and the AOs that contribute to a certain MO. Most results found in Gaussian agree with the MO theory relatively well. However, it was found that MO is not formed by overlapping of one or two pairs of AOs from the two bonding atoms. Rather, many AOs, including the ones in higher main energy levels, may contribute to the MO to various extents. Another major difference being Gaussian suggests that the core orbitals (1s) do not participate in bonding whereas the MO theory suggests that the 1s orbitals do overlap, however the stabilising effect of the bonding is cancelled out by the fully occupied antibonding orbital.

=== CO as a ligand in complex molecules ===

==== CO in the mono-metallic Rhenium Pincer complex====

Mono-metallic TM Complex Identifier: DEKFUX

The mono-metallic Rhenium Pincer Complex is linked to [[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=ACSBDA&year=2017&spage=941&volume=73&id=doi:10.1107/S205252061701006X&pid=ccdc:1560700| here]]

The original journal can be found at[[http://scripts.iucr.org/cgi-bin/paper?S205252061701006X]]

C≡O Bond Length: 1.24 Å (±0.01Å)

Structure of The Rhenium Pincer Complex

[[File:Yc16318 CO Complex.PNG]]

The bond length found in the structure is longer than the one obtained through Gaussian (C≡O Bond Distance=1.14 Å). This could be due to:

1. The C≡O molecule coordinates to the metal centre using the lone pair of electron on C

2. The value obtained from experiment may not be accurate due to apparatus error or human error.

3. The Bond Length calculated by Gaussian is only an approximation, therefore may not be accurate. It is limited to the method you choose. It is possible to get more accurate results using a better method that has more parameters.

==== CO in metallic TM complexes====

The average Bond length of C≡O is calculated using Data Analysis in Conquest to be 1.15 Å and the mode is calculated to be 1.18 Å, both are longer than the bond length of C≡O as a molecule. This supports the explanation that C≡O elongates due to the weakening of the triple bond after coordinating to a metal centre.

==== Histogram of C≡O bond length in various complexes ====
[[File:Yc16318 co analysis2.PNG]]

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, very detailed explanations with lots of information which you explained clearly, well done!

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You took a deeper look into the MOs and the theory behind it, well done! You also analysed the bond length of C=O in the context of the crystal structures database, excellent work.

Rep:Mod:nwc18

2019-03-28T10:37:27Z

Rr1210:

== NH3 molecule ==
Calculation Method: RB3LYP

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

Final energy E(RB3LYP): -56.55776873 a.u.

RMS Gradient Norm: 0.00000485 a.u.

Point group: C3V

N-H bond distance: 1.02 Å accurate to 0.01 Å

H-N-H bong angle: 106 ° accurate to 1 °

===Item table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986284D-10
</pre>

===Structure of NH3===
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NWC18 NH3 OPT POP.LOG</uploadedFileContents>
<script>frame x.y</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:NWC18_NH3_OPT_POP.LOG| here]]

===Display Vibration===

[[File:Display_vibration_NH3.PNG]]

===Wavenumber and intensity table===

{| class="wikitable"
!'''Wavenumber'''/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
!'''Symmetry'''
|A1
|E
|E
|A1
|E
|E
|-
!'''Imtensity'''/arbitrary unit
|145
|14
|14
|1
|0
|0
|-
!'''Image'''
|
[[File:Vibration1.1.PNG|100px]]
|
[[File:Vibratio2.1.PNG|100px]]
|
[[File:Vibration3.1.PNG|100px]]
|
[[File:Vibration4.1.PNG|100px]]
|
[[File:Vibration5.1.PNG|100px]]
|
[[File:Vibration6.1.PNG|100px]]
|}

Expect 6 modes from the 3N-6 rule.

The modes with frequency 1694 cm-1 are degenerate and the modes with frequency 3590 cm-1 are degenerate.

Bending vibrations: modes with frequency 1090 cm-1 and 1694 cm-1.

Bond stretch vibrations: modes with frequency 3461 cm-1 and 3590 cm-1.

The mode with frequency 3461 cm-1 is highly symmetric.

The mode with frequency 1090 cm-1 is the umbrella mode.

2 bands would be expected in an experimental spectrum of of gaseous ammonia.

===Charge===

Nitrogen=-1.125

Hydrogen= 0.375

The nitrogen atom is negatively charged whilst all three hydrogen atoms are positively charged because nitrogen is more electronegative than hydrogen.

== N2 molecule ==
Calculation Method: RB3LYP

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

Final energy E(RB3LYP): -109.52412868 a.u.

RMS Gradient Norm: 0.00000060 a.u.

Point group: D∞H

N,N triple bond distance: 1.11 Å accurate to 0.01 Å

===Item Table===

<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=-3.401042D-13
</pre>

===Structure of N2 ===

<jmol><jmolApplet>
<title>N2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NWC18_N2_OPT_POP.LOG</uploadedFileContents>
<script>frame x.y</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:NWC18_N2_OPT_POP.LOG| here]]

===Display Vibration===

[[File:Display_vibration_N2.PNG]]

===Wavenumber and intensity table===

{| class="wikitable"
!'''Wavenumber'''cm-1
!'''Symmetry'''
!'''Imtensity'''arbitrary unit
!'''Image'''
|-
|2457
|SGG
|0
|[[File:Vibration_n2.PNG|150px]]
|}

===Charge===

both N atoms=0

This is because both atoms have the same electronegativity so no dipole as no difference in electronegativity.

== H2 molecule ==
Calculation Method: RB3LYP

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

Final energy E(RB3LYP): -1.17853936 a.u.

RMS Gradient Norm: 0.00000015 a.u.

Point group: D∞H

H-H bond distance: 0.74 Å accurate to 0.01 Å

===Item Table===

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.062231D-14
</pre>

===Structure of H2===

<jmol><jmolApplet>
<title>H2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NWC18_H2_OPT_POP.LOG</uploadedFileContents>
<script>frame x.y</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:NWC18_H2_OPT_POP.LOG| here]]

===Display Vibration===

[[File:Display_vibration_H2.PNG]]

===Wavenumber and intensity table===

{| class="wikitable"
!'''Wavenumber'''cm-1
!'''Symmetry'''
!'''Imtensity'''arbitrary unit
!'''Image'''
|-
|4466
|SGG
|0
|[[File:vibration_h2.PNG|150px]]
|}

===Charge===

both H atoms=0

This is because both atoms have the same electronegativity so no dipole as no difference in electronegativity.

==mono-metallic TM complex that coordinates N2==

unique identifier=VEJROU

link to the structure of VEJROU[[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=EJICFO&year=2017&spage=3769&id=doi:10.1002/ejic.201700569&pid=ccdc:1547287]]

computed N,N triple bond distance=1.11 Å

experimental N,N triple bond distance in complex=1.20 Å

VEJROU is an Iron-Dinitrogen complex that catalyse the conversion of nitrogen gas into silylamine similar to the nitrogen fixation process.<ref name="VEJROU" /> This is essential as most nitrogen exist in the gas form in air but is required by most organisms as a nutrient. Hence, processes like nitrogen fixation allows the naturally ocurring nitrogen gas to be converted and used by organisms and so initiates the nitrogen nutrient cycle.
The computational and experimental value of the N,N bond length are very similar despite the experimental value being determined from a dinitrogen metal complex other than nitrogen gas. This is because the N2 -metal interaction is weak as the central iron ion has only a charge of +2 and has a coordination number of 6. However, the small increase in bond length in the complex will be due to the positively charged iron(II) ion distorting and attracting the electron cloud of the bonding nitrogen atom and hence reducing the strength of the N,N triple bond.

== Haber-Bosch reaction energy calculation ==
E(NH3)= -56.55777 a.u.

2*E(NH3)= -113.11554 a.u.

E(N2)= -109.52413 a.u.

E(H2)= -1.17854 a.u.

3*E(H2)= -3.53562 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579 a.u.= -146.5 kJ/mol

The reaction is exothermic meaning energy was transferred to the surroundings when hydrogen and nitrogen gas react to form ammonia gas. Therefore, the ammonia product is more stable than the gaseous reactants.

== ClF5 molecule ==
Calculation Method: RB3LYP

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

Final energy E(RB3LYP): -958.98366366 a.u.

RMS Gradient Norm: 0.00012016 a.u.

Point group: C4V

Cl-F bond distance: 1.65 Å (apical)and 1.70 Å (basal) accurate to 0.01 Å

F-Cl-F bong angle: 86 ° (apical) and 90 ° (basal) accurate to 1 °

===Item Table===
Item Value Threshold Converged?
Maximum Force 0.000398 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001404 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
Predicted change in Energy=-3.987469D-07
===Structure of ClF5===
<jmol><jmolApplet>
<title>ClF5</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NWC18 CLF5 OPT POP.LOG</uploadedFileContents>
<script>frame x.y</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:NWC18_CLF5_OPT_POP.LOG| here]]
===Display Vibration===
[[File:Display_vibration_CLF5_1.PNG]]
===Wavenumber and intensity table===
{| class="wikitable"
!'''Wavenumber'''/cm-1
|259
|280
|280
|374
|452
|452
|471
|522
|560
|733
|805
|805
|-
!'''Symmetry'''
|B2
|E
|E
|B1
|E
|E
|A1
|B2
|A1
|A1
|E
|E
|-
!'''Imtensity'''/arbitrary unit
|0
|0
|0
|0
|0
|0
|28
|0
|7
|75
|404
|404
|-
!'''Image'''
|
[[File:Vibration1.2.PNG|70px]]
|
|
|
[[File:Vibration3.2.PNG|70px]]
|
|
|
[[File:Vibration5.2.PNG|70px]]
|
[[File:Vibration6.2.PNG|70px]]
|
[[File:Vibration7.2.PNG|70px]]
|
[[File:Vibration8.2.PNG|70px]]
|
|
|}

All B symmetries are not IR active because there is no dipole moment. This is because the vibration of the flourine molecules allows the dipoles to cancel out.

Expect 12 modes from the 3N-6 rule.

The modes with frequency 280 cm-1, 452cm-1and 805cm-1 are degenerate with each of the same frequency..

Bending vibrations: modes with frequency 259 cm-1, 280 cm-1, 347 cm-1,452 cm-1 and 471 cm-1.

Bond stretch vibrations: modes with frequency 522 cm-1, 560 cm-1, 733 cm-1 and 805 cm-1.

The mode with frequency 560 cm-1 and 733 cm-1 are highly symmetric.

4 bands would be expected in an experimental spectrum of of gaseous ammonia.

===Charge===
Chlorine= 1.998

Fluorine= -0.335 (apical) and -0.416 (basal)

Fluorine atoms are negatively charged whilst chlorine atoms are poistively charged because fluorine is more electronegative (the most electronegative) than chlorine.

===Molecular Orbital===
Hybridisation of the chlorine atom in ClF5 = sp3d2

The molecular structure of ClF5 = square pyramidal

This structure is due the lone pair of electrons on the chlorine atom repelling the 5 singly bonded fluorine atoms more than the bonding pairs repel each other.

The apical bond and basal bonds are similar in bond energy and so bond length. This is because the bond angle between two opposite basal bonds is 171 ° which is close to the crossover point where the trend in bond energy reverse.<ref name="modiagram" />

{| class="wikitable"
!'''MO 1.σ

(lowest molecular orbital)
!'''MO 2.σ*

(valence bond orbital)
!'''MO 3.σ*

(valence bond orbital)
!'''MO 4.σ*Homo

(valence bond orbital)
!'''MO 5.σ*Lumo
|-
|[[File:MO_1.PNG|150px]]
|[[File:MO_28a.PNG|100px]]
|[[File:MO_29.PNG|100px]]
|[[File:MO_HOMO.PNG|100px]]
|[[File:MO_LUMO.PNG|100px]]
|}

MO 1.σ:The overlap of the 1s orbitals cannot be seen as the orbitals are too small and low in energy(-101.96235 a.u.). Hence, this will not be involved in bonding.

MO 2 and 3.σ*: The p orbitals overlap to form both σ and π bonds. There are three p orbitals on the fluorine atoms which contributes to the σ* MO but the 3pz orbital has the greatest contribution to the σ* MO. This is because σ antibonding orbitals are higher in energy than bonding orbitals and π antibonding orbitals in the same set due to the lower density of electron between the nuclei. The two σ* (MO 2 and 3) are degenerate.

HOMO: This is an anitbonding MO with the s orbital of chlorine and p orbitals of the fluorines being the main contributor. This is the highest occupied molecular orbital invovled in bonding.

LUMO: This is a σ* orbital with both antibonding and bonding characters. The py orbitals on the basal fluorines and the pz orbitals of the chlorine and apacal fluorine are the main contributions towards the MO. The pz orbitals of the apacal fluorine and chlorine are antibonding whilst the py orbitals of the basal fluorine shows bonding character towards the pz orbital of the chlorine (as shown in the LUMO MO diagram). This is not involved in bonding.
==Independent mark:O2 molecule==
Calculation Method: RB3LYP

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

Final energy E(RB3LYP): -150.25742434 a.u.

RMS Gradient Norm: 0.00007502 a.u.

Point group: D∞H

O-O bond distance: 1.22 Å accurate to 0.01 Å

===Item Table===

<pre>
Item Value Threshold Converged?
Maximum Force 0.000130 0.000450 YES
RMS Force 0.000130 0.000300 YES
Maximum Displacement 0.000080 0.001800 YES
RMS Displacement 0.000113 0.001200 YES
Predicted change in Energy=-1.033738D-08
</pre>

===Structure of O2===

<jmol><jmolApplet>
<title>O2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NWC18_O2_OPT_POP.LOG</uploadedFileContents>
<script>frame x.y</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:NWC18_O2_OPT_POP.LOG| here]]

===Display Vibration===

[[File:Display_vibration_O2.PNG]]

===Wavenumber and intensity table===

{| class="wikitable"
!'''Wavenumber'''cm-1
!'''Symmetry'''
!'''Imtensity'''arbitrary unit
!'''Image'''
|-
|1643
|SGG
|0
|[[File:vibration_o2.PNG|150px]]
|}

===Charge===

both O atoms=0

This is because both atoms have the same electronegativity so no dipole as no difference in electronegativity.

== References ==
<references>
<ref name="VEJROU">Imayoshi,R.,Nakajima,K.,Takaya,J.,Iwasawa,N.,Nishibayashi,Y.(2017) Synthesis and Reactivity of Iron- and Cobalt-Dinitrogen Complexes Bearing PSiP-Type Pincer Ligands toward Nitrogen Fixation. ''European Journal of Inorganic Chemistry''. 2017(32),3769-3778. Available from:https://doi.org/10.1002/ejic.201700569 [Accessed 19th March 2019].</ref>

<ref name="modiagram">Rossi,A,R.,Hoffmann,R.(1974) Transition Metal Pentacoordination. ''Inorganic Chemistry''. 1975,14(2),365-374. Available from:https://pubs.acs.org/doi/pdf/10.1021/ic50144a032 [Accessed 21th March 2019].</ref>
</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 3.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, your charges explanation is good and you have made a good attempt at explaining the MOs (which are quite complicated for this molecule!). For a complicated molecule like this it is often not possible to label an entire MO as sigma or pi, or even bonding or antibonding. Instead you can talk about the individual interactions present for example in MO2 you could say that there are sigma type antibonding interactions between the neighbouring F atoms, and that this MO reduces the F-F bonding character.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did an extra calculation on O2 well done!

Rep:Mod:YC15218

2019-03-28T09:03:29Z

Rr1210:

== NH3 ==
=== Optimisation ===
==== Summary Information ====

Molecule name: NH3

Calculation method: RB3LYP

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

Final energy E(RB3LYP) in atomic units (au): -56.55776873

The point group of molecule: C3V

==== Optimisation Information ====

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986277D-10
Optimization completed.
 -- Stationary point found.
 ----------------------------
 ! Optimized Parameters !
 ! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>OPTIMIZED_NH3_YEXUANCHENG.LOG</uploadedFileContents>
<script>frame x.y</script>
</jmolApplet></jmol>

Optimised N-H bond distance: 1.02Å
Optimised H-N-H bond angle: 106°

Link to Completed NH3 Optimisation: [[Media:OPTIMIZED_NH3_YEXUANCHENG.LOG|Optimized NH3 ]]

=== Vibrations and Charges ===
==== Display Vibrations Table ====
[[File:yc15218_nh3_vibration.png]]

==== Table of Vibrations and Intensities ====
{| class="wikitable" border="1"
|+ NH3 vibration information
|-
|wavenumber cm-1
|1090
|1694
|1694
|3460
|3590
|3590
|-
|symmetry
|A1
|E
|E
|A1
|E
|E
|-
|intensity in arbitrary units
|145
|14
|14
|1
|0
|0
|-
|image
|[[File:NH3_vibration_1_yc15218.png|250px]]
|[[File:NH3_vibration_2_yc15218.png|250px]]
|[[File:NH3_vibration_3_yc15218.png|250px]]
|[[File:NH3_vibration_4_yc15218.png|250px]]
|[[File:NH3_vibration_5_yc15218.png|250px]]
|[[File:NH3_vibration_6_yc15218.png|250px]]
|}

==== Q&A ====
Q:How many modes do you expect from the 3N-6 rule?

A:6 modes are expected(3*4-6).

Q:Which modes are degenerate (ie have the same energy)?

A:Modes with wavenumbers of 1694 are degenerate. Modes with wavenumbers of 3590 are degenerate.

Q:Which modes are "bending" vibrations and which are "bond stretch" vibrations?

A:Modes with wavenumbers of 1090 and 1694 are "bending" vibrations. Modes with wavenumbers of 3460 and 3590 are "bond stretch" vibrations.

Q:Which mode is highly symmetric?

A:The mode with wavenumber of 3640.

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

A:The mode with wavenumber of 1090.

Q:How many bands would you expect to see in an experimental spectrum of gaseous ammonia?

A:4 bands are expected.

==== NBO Charges ====
Charge on N-atom: -1.125

Charge on H-atoms:0.375

Nitrogen is expected to have a negative charge and hydrogens are expected to have positive charges since nitrogen has greater electronegativity than hydrogen.

== N2 ==
=== Optimisation ===
==== Summary Information ====

Molecule name: N2

Calculation method: RB3LYP

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

Final energy E(RB3LYP) in atomic units (au): -109.52412868

The point group of molecule: D*H

==== Optimisation Information ====
<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=-3.401159D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>OPTIMIZED_N2_YEXUANCHENG.LOG</uploadedFileContents>
<script>frame x.y</script>
</jmolApplet></jmol>

Optimised N-N bond distance: 1.11Å

Link to Completed N2 Optimisation: [[Media:OPTIMIZED_N2_YEXUANCHENG.LOG|Optimized N2 ]]

=== Vibrations and Charges ===
==== Display Vibrations Table ====

[[File:yc15218_n2_vibration.png]]

==== Table of Vibrations and Intensities ====
{| class="wikitable" border="1"
|+ N2 vibration information
|-
|wavenumber cm-1
|2457
|-
|symmetry
|SGG
|-
|intensity in arbitrary units
|0
|-
|image
|[[File:N2_vibration_yc15218.png|300px]]
|}

==== NBO Charges ====
Both nitrogen atoms have charge of zero which is what I expect since N2 is a homoatomic molecule.

== H2 ==
=== Optimisation ===
==== Summary Information ====

Molecule name: H2

Calculation method: RB3LYP

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

Final energy E(RB3LYP) in atomic units (au): -1.17853936

The point group of molecule: D*H

==== Optimisation Information ====
<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
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>OPTIMIZED_H2_YEXUANCHENG.LOG</uploadedFileContents>
<script>frame x.y</script>
</jmolApplet></jmol>

Optimised H-H bond distance: 0.74Å

Link to Completed H2 Optimisation: [[Media:OPTIMIZED_H2_YEXUANCHENG.LOG|Optimized H2 ]]

=== Vibrations and Charges ===
==== Display Vibrations Table ====

[[File:yc15218_h2_vibration.png]]

==== Table of Vibrations and Intensities ====
{| class="wikitable" border="1"
|+ H2 vibration information
|-
|wavenumber cm-1
|4466
|-
|symmetry
|SGG
|-
|intensity in arbitrary units
|0
|-
|image
|[[File:H2_vibration_yc15218.png|300px]]
|}

==== NBO Charges ====
Both hydrogen atoms have charge of zero which is what I expect since H2 is a homoatomic molecule.

== Structure and Reactivity ==

=== Information of the Mono-metallic TM Complex that Coordinates with N2 ===
Bis(dinitrogen)-dihydrido-bis(tricyclohexylphosphine)-ruthenium

Identifier: YECMIF

N-N distances:1.104(3)Å and 1.101(3)Å

These distances are smaller than the computational distance which is 1.11Å.

This may be explained by the interaction between nitrogens and the remaining part of the crystal such as hydrogen-bonding which would cause the bond distance to be smaller.

Also, when running the optimisation, the fully optimised structure is achieved which may differ from the one in reality.

=== Energy for the Haber-Bosch Process ===
E(NH3)= -56.55777 au

2*E(NH3)= -113.11554 au

E(N2)=-109.52413 au

E(H2)=-1.17854 au

3*E(H2)=-3.53562 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579 au

ΔE=-146.5 kJ/mol

The ammonia product is more thermodynamically stable.

== HCN ==
=== Optimisation ===
==== Summary Information ====

Molecule name: HCN

Calculation method: RB3LYP

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

Final energy E(RB3LYP) in atomic units (au): -93.42458132

The point group of molecule: C*V

==== Optimisation Information ====

<pre>

Item Value Threshold Converged?
Maximum Force 0.000370 0.000450 YES
RMS Force 0.000255 0.000300 YES
Maximum Displacement 0.000676 0.001800 YES
RMS Displacement 0.000427 0.001200 YES
Predicted change in Energy=-2.062470D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.157 -DE/DX = 0.0004 !
! R2 R(2,3) 1.0686 -DE/DX = 0.0004 !
! A1 L(1,2,3,-2,-1) 180.0 -DE/DX = 0.0 !
! A2 L(1,2,3,-3,-2) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

</pre>

<jmol><jmolApplet>
<title>HCN</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>OPTIMIZED_HCN_YEXUANCHENG.LOG</uploadedFileContents>
<script>frame x.y</script>
</jmolApplet></jmol>

Optimized C-N bond distance: 1.16Å

Optimized C-H bond distance: 1.07Å

Optimized H-C-N bond angleː 180°

Link to Completed HCN Optimisation: [[Media:OPTIMIZED_HCN_YEXUANCHENG.LOG|Optimized HCN ]]

=== Vibrations and Charges ===
==== Display Vibrations Table ====
[[File:yc15218_hcn_vibration.png]]

==== Table of Vibrations and Intensities ====
{| class="wikitable" border="1"
|+ HCN vibration information
|-
|wavenumber cm-1
|767
|767
|2215
|3480
|-
|symmetry
|PI
|PI
|SG
|SG
|-
|intensity in arbitrary units
|35
|35
|2
|57
|-
|image
|[[File:HCN_vibration_1_yc15218.png|300px]]
|[[File:HCN_vibration_2_yc15218.png|300px]]
|[[File:HCN_vibration_3_yc15218.png|300px]]
|[[File:HCN_vibration_4_yc15218.png|300px]]
|}

==== NBO Charges ====
Charge on N-atom: -0.308

Charge on C-atom: 0.073

Charge on H-atom: 0.234

Nitrogen is expected to have a negative charge and carbon and hydrogen are expected to have positive charges since nitrogen has greater electronegativity than the others.

=== Molecular Orbitals ===

{| class="wikitable" border="1"
|+ MO of HCN
|-
|Energy in au
| -14.36050
| -0.60777
| -0.38064
| -0.35939
| -0.01929
|-
|Description
|The 1s orbital of nitrogen contributes to this MO and it does not form any overlap with other orbitals due to large energy difference. It is deep in energy and occupied by a pair of electrons.
|This sigma bonding MO is contributed by the 2s orbital of nitrogen and the 2s orbital of carbon. It is below the HOMO/LUMO energy region and occupied by a pair of electrons. It has stabilizing effect on bonding.
|This sigma bonding MO is contributed by the overlap bewteen 2p orbital of nitrogen, the 2s orbital of carbon and the 1s orbital of hydrogen. It is just below the HOMO/LUMO energy region. It has stabilizing effect on bonding.
|One 2p orbital from carbon and one 2p orbital from nitrogen contribute to this pi bonding orbital. It is the highest occupied molecular orbital (HOMO), occupied by a pair of electrons. There are two MOs at this energy which differ in orientation. They both have stabilizing effect on bonding.
|One 2p orbital from carbon and one 2p orbital from nitrogen contribute to this pi antibonding orbital. It is the lowest unoccupied molecular orbital (LUMO).There are two MOs at this energy which differ in orientation.
|-
|image
|[[File:HCN_MO_1_yc15218.png|300px]]
|[[File:HCN_MO_2_yc15218.png|300px]]
|[[File:HCN_MO_3_yc15218.png|300px]]
|[[File:HCN_MO_4_yc15218.png|300px]]
|[[File:HCN_MO_5_yc15218.png|300px]]
|}

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 0.5/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, most answers are correct. However there are only 2 visible peaks in the spectra of NH3, due to the low intensity of the other 2 peaks. (See infrared column in vibrations table.)

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

No you gave the identifier but you did not include a link or valid reference to the CCDC.

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 3/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, you included all the information and your explanations of the nitrogen charge and MO1 were particularly good. You could have improved by explaining why C and H have different charges. The MO explanations could have been improved by breaking down the specific interactions, for example the second MO shown increases the C-H bonding but decreases the N-C bonding. You also could have mentioned that the LUMO has no impact on the bonding in the molecule since it is unoccupied.

== Independence 0/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

No independent work located.

Rep:Mod:yqc01506162

2019-03-28T08:54:12Z

Rr1210:

=NH3 molecule=

==Summary information==

{| class="wikitable" border="1"

! Calculation method !! RB3LYP
|-
! Basis set !! 6-31G(d,p)
|-
! Final energy E(RB3LYP) in au !! -56.55776873
|-
! RMS gradient norm in au !! 0.00000485
|-
! Point group !! C3V
|}

==Item section==
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

==Jmol of NH3==
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YQC18_NH3_OPTF_POP.LOG</uploadedFileContents>

</jmolApplet></jmol>

The optimisation file is liked to [[File:YQC18_NH3_OPTF_POP.LOG| here]]

==Key structural information==

N-H bond distance= 1.02 +/- 0.01Å

H-N-H bond angle= 106 +/- 1°

==Display vibrations table==

[[File:display vibration NH3.png]]

==Table of vibration and intensities==

{| class="wikitable" border="1"
! wavenumber(cm-1) !! 1090 !! 1694 !! 1694!! 3461 !! 3590 !! 3590
|-
! symmetry !! A1 !! E !! E !! A1 !! E !! E
|-
! intensity(arbitary units) !! 145 !! 13.6 !! 13.6 !! 1.06 !! 0.271 !! 0.271
|-
! image !! [[File:NH3 vibration 1.png|150px]] !! [[File:NH3 vibration 2.png|150px]] !! [[File:NH3 vibration 3.png|150px]] !! [[File:NH3 vibration 4.png|150px]] !! [[File:NH3 vibration 5.png|150px]] !! [[File:NH3 vibration 6.png|150px]]
|}

1. 6 modes are expected from 3N-6 rule

2. Modes with wavenumbers both being 1694 cm-1 are degenerate. Modes with wavenumbers both being 3590 cm-1 are also degenerate.

3. Modes with wavenumber 1090, 1694 and 1694 cm-1 are bending vibrations. Modes with wavenumbers 3461, 3590 and 3590 cm-1 are "bond stretch" vibrations.

4. Mode with wavenumber 3461 cm-1 is highly symmetric.

5. Mode with wavenumber 1090 cm-1 is the "umbrella mode"

6. I would expect to see 2 bands in an experimental spectrum of gaseoous ammonia.

==NBO charges==

[[File:NBO NH3.png|300px]]

The charge on N atom is -1.125 and charge on H atom is 0.375. I would expect negative charge on N and positive charge on H. This is because N is more electronegative than H hence pulls electron density towards H.

=N2 and H2 molecules=

==N2 molecule==

===Summary information===

{| class="wikitable" border="1"
! Calculation method !! RB3LYP
|-
! Basis set !! 6-31G(d,p)
|-
! Final energy E(RB3LYP) in au !! -109.52412868
|-
! RMS gradient norm in au !! 0.00000060
|-
! Point group !! D∞h
|}

===Item section===

<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
</pre>

===Jmol of N2===

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YQC_N2_OPTF_POP.LOG</uploadedFileContents>

</jmolApplet></jmol>

The optimisation file is liked to [[File:YQC_N2_OPTF_POP.LOG| here]]

===Key structural information===

Optimised N-N bond length= 1.11 +/- 0.01 Å

Optimised N-N bond angle= 180 +/- 1°

===Display vibration table===

[[File:display vibration N2.png]]

===Table of vibrations and intensities===

{| class="wikitable" border="1"
! wavenumber(cm-1) !! 2457
|-
! symmetry !! SGG
|-
! intensity(arbitary units) !! 0.00
|-
! image !! [[File:N2 vibration.png|150px]]
|}

===NBO charges===

[[File:NBO N2.png|300px]]

The charge on both N atom is 0.000

==H2 molecule==

===Summary information===

{| class="wikitable" border="1"
! Calculation method!! RB3LYP
|-
! Basis set !! 6-31G(d,p)
|-
! Final energy E(RB3LYP) in au !! -1.17853936
|-
! RMS gradient norm in au !! 0.00000017
|-
! Point group !! D∞h
|}

===Item section===

<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
</pre>

===Jmol of H2===

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YQC_H2_OPTF_POP.LOG</uploadedFileContents>

</jmolApplet></jmol>

The optimisation file is liked to [[File:YQC_H2_OPTF_POP.LOG| here]]

===Key stuctural information===

Optimised H-H bond length = 0.74 +/- 0.01 Å

Optimised H-H bond angle = 180 +/- 1°

===Display vibration table===

[[File:display vibration H2.png]]

===Table of vibration and intensities===

{| class="wikitable" border="1"
! wavenumber(cm-1) !! 4466
|-
! symmetry !! SGG
|-
! intensity(arbitary units) !! 0.00
|-
! image !! [[File:H2 vibration.png|150px]]
|}

===NBO charges===

[[File:NBO H2.png|300px]]

The charge on both N atom is 0.000.

==A mono-metallic TM complex that coordinates N2==

{| class="wikitable" border="1"
! molecule name !! (Dinitrogen-N)-(2-(1-(2,6-di-isopropylphenylimino)ethyl)-6-(1-(2,6-di-isopropylphenyl)amidoehenyl)pyridine-N,N'N'')-iron
|-
! unique identifier !! COGBIK
|-
! N-N bond distance obtained(Å) !! 1.11
|-
! N-N bond distance in the complex(Å) !! 1.14
|-
! structure !! [[File:COGBIK.png]]
|-
! Link to the structure !! https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=COGBIK&DatabaseToSearch=Published
|}

The N-N bond distance in the complex is longer than computational distance.

Experimental reason: After accepting electrons from N, Fe becomes very negative and stabilizes by donating 3d electrons into pi-antibonding orbitals on N atom. This shortens Fe-N bond hence elongates N-N bond. This is called 'synergic effect'.

Computational reason: Computational analysis errors

=Haber-Bosch reaction energy calculation=

E(NH3)= -56.5577687 a.u

2*E(NH3)= -113.1155375 a.u

E(N2)= -109.5241287 a.u

E(H2)= -1.1785394 a.u

3*E(H2)= -3.5356181 a.u

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -146.5 kJ/mol

The ammonia product is more stable

=My choice of small molecule: HCN=

==Summary table==

{| class="wikitable" border="1"
! Calculation method !! RB3LYP
|-
! Basis set !! 6-31G(d.p)
|-
! Final energy E(RB3LYP) in au !! -93.42458132
|-
! RMS gradient norm in au !! 0.00017006
|-
! Point group !! C∞v
|}

==Item section==

<pre>
Item Value Threshold Converged?
Maximum Force 0.000370 0.000450 YES
RMS Force 0.000255 0.000300 YES
Maximum Displacement 0.000676 0.001800 YES
RMS Displacement 0.000427 0.001200 YES
</pre>

==Jmol of HCN==

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

</jmolApplet></jmol>

The optimisation file is liked to [[File:YQC_HCN_OPTF_POP.LOG| here]]

==Key strucutral information==

Optimised C-H bond length= 1.07 +/- 0.01 Å

Optimised C-N bond length = 1.16 +/- 0.01 Å

Optimised H-C-N bond angle = 180 +/- 1°

==Display vibrations table==

[[File:display vibration HCN.png]]

==Table of vibrations and intensities==

{| class="wikitable" border="1"
! wavenumber(cm-1) !! 2215 !! 767 !! 767 !! 3480
|-
! symmetry !! SG !! PI !! PI !! SG
|-
! intensity(arbitary units) !! 2.05 !! 35.3 !! 57.3
|-
! image !! [[File:HCN vibration 1.png|150px]] !! [[File:HCN vibration 2.png|150px]] !! [[File:HCN vibration 3.png|150px]] !! [[File:HCN vibration 4.png|150px]]
|}

==NBO charges==

[[File:NBO HCN.png|300px]]

The charge on N atom is -0.308

The charge on C atom is 0.073

The charge on H atom is 0.234

==Molecular orbitals==

1. [[File:HCN MO 1.png|300px|thumb|center|MO 1]]

1s atomic orbital from nitrogen contributes to the MO. The MO is non-bonding. The MO is deep in energy. The MO is occupied and has no effect on bonding.

2. [[File:HCN MO 2.png|300px|thumb|center|MO 3]]

2s atomic orbitals from carbon,nitrogen and 1s atomic orbital from hydrogen contribute to the MO. The MO is bonding. The MO is deep in energy. The MO is occupied and stabilizes the bonding.

3. [[File:HCN MO 9.png|300px|thumb|center|MO 4]]

2s atomic orbitals from hydrogem and nitrogen and 2pz atomic orbital from carbon contribute to the MO. The MO is bonding. The MO is deep in energy. The MO is occupied and destabilizes the bonding.

4.[[File:HCN MO 5.png|300px|thumb|center|MO 6]]

2py atomic orbitals from carbon and nitrogen contribute to the MO. The MO is bonding. The MO is in the LUMO. The MO is occupied and stabilizes the bonding.

5.[[File:HCN MO 6.png|300px|thumb|center|MO 8]]

2py atomic orbitals from carbon and nitrogen contribute to the MO. The MO is antibonding. The MO is in the HOMO. The MO is unoccupied and therefore has no effect on bonding.

=Independent work: Cl2 molecule=

==Summary table==

{| class="wikitable" border="1"
! Calculation method !! RB3LYP
|-
! Basis set !! 6-31G(d.p)
|-
! Final energy E(RB3LYP) in au !! -920.34987886
|-
! RMS gradient norm in au !! 0.0000251
|-
! Point group !! D∞h
|}

==Item section==

<pre>
Item Value Threshold Converged?
Maximum Force 0.000043 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000121 0.001800 YES
RMS Displacement 0.000172 0.001200 YES
</pre>

==Jmol of Cl2==

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YQC_CL2_OPTF_POP.LOG</uploadedFileContents>

</jmolApplet></jmol>

The optimisation file is liked to [[File:YQC_CL2_OPTF_POP.LOG| here]]

==Key structural information==

Optimised Cl-Cl bond length= 2.04 +/- 0.01 Å

Optimised Cl-Cl bond angle= 180 +/- 1°

==Display vibrations table==

[[File:display vibration cl2.png]]

==Table of vibration and intensities==

{| class="wikitable" border="1"
! Wavenumber(cm-1) !! 520
|-
! Symmetry !! SGG
|-
! Intensity(arbitary units) !! 0.00
|-
! image !! [[File:cl2 vibration.png|150px]]
|}

==NBO charges==

[[File:NBO CL2.png|300px]]

The charge on both Cl atom is 0.000.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, however you have left all the jmol captions as the default “test molecule” this gives the reader no information.

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 2.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, you have included the relevant information well done! Your explanations of MOs 1 and 3 are very good and clearly explained! On the charges you could have improved by explaining why each atom has a different charge in terms of the relative electronegativities of the elements. For MO 4 the C-H bond is strengthened but the N-C bond is weakened. You also seem to be confused on the terms HOMO and LUMO, have a look back in your lecture notes for those terms or show your tutor your wiki and ask them.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did an extra calculation on Cl2 well done!

Rep:Mod:aec18

2019-03-28T08:43:53Z

Rr1210:

== NH3 Ammonia Molecule ==

=== Optimised molecule information ===
{| class="wikitable" border="1"
|+ NH3
| Calculation method || RB3LYP
|-
| Basis set || 6-31G(d.p)
|-
| Final energy (RB3LYP) || -56.5577687 a.u.
|-
| Point group || C3v
|-
| RMS gradient || 0.00000485
|-
| Bond distance || 1.02Å
|-
| Bond angle || 106°
|}

The optimisation file is liked to[[Media:AEC18 NH3 OPTIMISATION.LOG| here]]

=== Item Table ===
<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986282D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !
-------------------------------------------------------------------------------- </pre>

===Jmol dynamic image===
<jmol><jmolApplet>
<title>Ammonia</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>AEC18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3 Vibrations===

[[File:aec18_NH3_vibrations.jpg]]

{| class="wikitable" border="1"
|+ Bond vibrations
|-
| Wavenumber (cm-1) || 1090 || 1693 || 1693 || 3461 || 3590 || 3590
|-
| Symmetry || A1 || E || E || A1 || E || E
|-
| Intensity (arbitrary units) || 145 || 13.6 || 13.6 || 1.06 || 0.27 || 0.27
|-
| Image || [[File:AEC18_NH3_VIBRATIONS1.jpg]] || [[File:AEC18_NH3_VIBRATIONS2.jpg]] || [[File:AEC18_NH3_VIBRATIONS3.jpg]] || [[File:AEC18_NH3_VIBRATIONS4.jpg]] || [[File:AEC18_NH3_VIBRATIONS5.jpg]] || [[File:AEC18_NH3_VIBRATIONS6.jpg]]
|}

=== Questions ===

How many modes do you expect from the 3N-6 rule?

6 modes of vibration can be expected from this molecule.

Which modes are degenerate (ie have the same energy)?

The two vibrations of wavelength 1693 and 3590 are degenerate.

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

Bending = 1089cm-1, 1693cm-1, 1693cm-1
Bond stretch = 3461cm-1, 3589cm-1, 3589cm-1

Which mode is highly symmetric?

1089cm-1 and 3461cm-1 modes are highly symmetric.

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

1089cm-1 is the 'umbrella' mode.

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

2 bands can be expected:

[[File:aec18_nh3_spectrum.jpg]]

=== Atomic charges ===

As shown on image:

H atoms = 0.375

N atom = -1.125

This is as expected as the nitrogen atom is the more electronegative of the two and so will carry the negative charge.

[[File:aec18_NH3_charges.jpg]]

== N2 Nitrogen Molecule ==

=== Optimisation information ===
{| class="wikitable" border="1"
|+ N2
| Calculation method || RB3LYP
|-
| Basis set || 6-31G(d.p)
|-
| Final energy (RB3LYP) || -109.5241287 a.u.
|-
| Point group || DinfH
|-
| RMS gradient || 0.00000060
|-
| Bond distance || 1.11Å
|}

The optimisation file is liked to[[Media:AEC18_N2_OPTIMISATION.LOG| here]]

=== Item table ===
<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=-3.400954D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------</pre>

=== Jmol dynamic image===
<jmol><jmolApplet>
<title>Nitrogen</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>AEC18_N2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== N2 Vibrations ===

[[File:aec18_N2_vibrations.jpg]]

{| class="wikitable" border="1"
|+ Bond vibrations
|-
| Wavenumber (cm-1) || 2457
|-
| Symmetry || SGG
|-
| Intensity (arbitrary units) || 0.00
|-
| Image || [[File:AEC18_N2_VIBRATIONS_2457.jpg]]
|}

=== Atomic Charges ===

[[File:aec18_n2_charges.jpg]]

== H2 Hydrogen Molecule ==

=== Optimisation information===
{| class="wikitable" border="1"
|+ H2
| Calculation method || RB3LYP
|-
| Basis set || 6-31G(d.p)
|-
| Final energy (RB3LYP) || -1.1785394 a.u.
|-
| Point group || DinfH
|-
| RMS gradient || 0.00000017
|-
| Bond distance || 0.74Å
|}

The optimisation file is liked to[[Media:AEC18_H2_OPTIMISATION.LOG| here]]

=== Item table===
<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
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------</pre>

===Jmol dynamic image===
<jmol><jmolApplet>
<title>Hydrogen molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>AEC18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== H2 vibrations===
[[File:AEC18_H2_VIBRATIONS.jpg]]

{| class="wikitable" border="1"
|+ Bond vibrations
|-
| Wavenumber (cm-1) || 4466
|-
| Symmetry || SGG
|-
| Intensity (arbitrary units) || 0.000
|-
| Image || [[File:AEC18_H2_VIBRATIONS_4466.jpg]]
|}

===Atomic Charges===
[[File:aec18_H2_charges.jpg]]

== Transition metal complex (containing N2) ==

The mono-metallic TM complex containing N2 has the code VEJSOV. It can be found here: [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VEJSOV&DatabaseToSearch=Published]

The TM Complex N-N bond length = 1.1165 Å

Optimised N2 molecule bond length = 1.11 Å

[[File:AEC18_TM_COMPLEX.jpg]]

The N-N bond length in the TM complex is slightly longer than the optimised N-N bond length for N2 and so can therefore be considered as slightly weaker. This is because for N2 the electrons are uniformly shared within the triple bond, making it stronger as there is little electron distortion in the bond between the two atoms. For the TM complex, one of the nitrogen atoms is also bonded to a Co atom and so the electron distribution within the N-N bond is less as some of these electrons are now distorted towards the N-Co bond. This therefore makes the N-N bond weaker and so longer which explains the observations above.

Although the value worked out for the N-N bond length in my N2 optimised molecule is similar to the experimental value calculated for the TM complex using Mercury, errors must be taken into account. These include both computational and experimental errors. To decrease computational errors a better method could have been used, such as CCSD instead of B3LYP which is what I used.

==Transition metal complex (containing H2)==

The mono-metallic TM complex containing H2 has the code CEJDEA. It can be found here: [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=CEJDEA&DatabaseToSearch=Published]

The TM Complex N-N bond length = 0.7552 Å

Optimised H2 molecule bond length = 0.74Å

[[File:AEC18_TM_H2.jpg]]

As previously suggested, the increased bond length in the TM complex is due to the other atom bonded to the two hydrogen's (tungsten in this case), resulting in the lengthening of the H-H bond as electron density in the bond is less. There is a greater effect for the lengthening of the hydrogen bond than the nitrogen bond (see previous) as the H-H bond is a single bond rather than a triple bond and so the effect caused by another atom on this bond is greater.

== Haber process calculations ==

The energy required for the reaction Nx2 + 3Hx2 -> 2NHx3 can be determined using the final energy values previously calculated.

(Energies quoted are in a.u. unless otherwise specified).

E(NH3)=-56.5577687

2*E(NH3)=-113.1155374

E(N2)= -109.5241286

E(H2)= -1.17853936

3*E(H2)=-3.53561808

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.1155374 - [-109.5241286 + (-3.53561808)]
ΔE= -113.1155374 + 113.05974668 = -0.05579072

ΔE= -0.05579 a.u. = -146.5 kJ/mol

The energy for converting hydrogen and nitrogen into ammonia is -146.5 kJ/mol. The combined energies of the reactants is higher (less negative) than the energy of the ammonia product and so the ammonia product is the more stable. The reaction is exothermic which further supports this theory.

== Molecule of my choice: CH4 ==

===Optimisation information===
{| class="wikitable" border="1"
|+ CH4
| Calculation method || RB3LYP
|-
| Basis set || 6-31G(d.p)
|-
| Final energy (RB3LYP) || -40.5240140 a.u.
|-
| RMS gradient || 0.0000320
|-
| C-H Bond distance || 1.09Å
|-
| Bond angle || 109°
|}

The optimisation file is liked to[[Media:AEC18_CH4_OPTIMISATION.LOG| here]]

===Item table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES
Predicted change in Energy=-2.256038D-08
Optimization completed.
-- Stationary point found. ----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.092 -DE/DX = -0.0001 !
! R2 R(1,3) 1.092 -DE/DX = -0.0001 !
! R3 R(1,4) 1.092 -DE/DX = -0.0001 !
! R4 R(1,5) 1.092 -DE/DX = -0.0001 !
! A1 A(2,1,3) 109.4712 -DE/DX = 0.0 !
! A2 A(2,1,4) 109.4712 -DE/DX = 0.0 !
! A3 A(2,1,5) 109.4712 -DE/DX = 0.0 !
! A4 A(3,1,4) 109.4712 -DE/DX = 0.0 !
! A5 A(3,1,5) 109.4712 -DE/DX = 0.0 !
! A6 A(4,1,5) 109.4712 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -120.0 -DE/DX = 0.0 !
! D2 D(2,1,5,3) 120.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) -120.0 -DE/DX = 0.0 !
! D4 D(3,1,5,4) 120.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

===Jmol dynamic image===

<jmol><jmolApplet>
<title>Methane</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>AEC18_CH4_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

===CH4 Vibrations===

[[File:AEC18_CH4_VIBRATIONS.jpg]]

{| class="wikitable" border="1"
|+ Bond vibrations
|-
| Wavenumber (cm-1) || 1356 || 1356 || 1356 || 1579 || 1579 || 3046 || 3162 || 3162 || 3162
|-
| Symmetry || T2 || T2 || T2 || E || E || A1 || T2 || T2 || T2
|-
| Intensity (arbitrary units) || 14.10 || 14.10 || 14.10 || 0.00 || 0.00 || 0.00 || 25.33 || 25.33 || 25.33
|}

[[File:aec18_ch4_spectrum.jpg]]

===Atomic charges===

H atom charge = 0.233

C atom charge = -0.930

[[File:aec18_ch4_charges.jpg]]

This is as expected as the carbon atom is the more electronegative of the two and therefore will carry the negative charge.

===Molecular Orbitals===

{| class="wikitable" border="1"
|+ Molecular Orbitals
|-
|MO || 1 || 2 || 3 || 4 (similar to 5) || 6
|-
|Image || [[File:AEC18_CH4_MO1.jpg]] || [[File:AEC18_CH4_MO2.jpg]] || [[File:AEC18_CH4_MO3_2.jpg]] || [[File:AEC18_CH4_MO4.jpg]] || [[File:AEC18_CH4_MO6.jpg]]
|-
|Description || The first molecular orbital above shows the 1s orbital of carbon. The energy of the MO is -10.16707 a.u. which is the lowest of all the molecular orbitals, therefore making this the most stable MO. This is very deep in energy therefore it is unlikely to be involved in bonding. || The MO labelled 2 above shows the 1s and 2s orbitals of the carbon interacting with the 1s orbital of each hydrogen atom. These are all bonding interactions. The energy of this MO is -0.69041 a.u. making it a lot less stable than the previous orbital. || MO's 3,4,5 are degenerate (energy = -0.38831 a.u.) as each involves one of the three different p orbitals in carbon. MO number 3 involves the 2Py (and some contribution from 3Py) orbital of carbon interacting with the 1s and 2s orbital of each H atom. || Similarly, MO numbers 4 and 5 are degenerate but involve the 2Pz and 2Px orbital respectively. Each is a bonding molecular orbital. || Finally the MO labelled 6 is the LUMO (lowest unoccupied molecular orbital). It is the only antibonding orbital shown above and involves the 3s orbital of carbon in an antibonding interaction with each hydrogen 2s atom.
|}

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, overall a well structured wiki, however a lot of your images are oversized preventing the reader from viewing the figures in context as they fill so much of the screen!

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES, well done for good explanations and looking up a crystal structure for both molecules.

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 3.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, overall you have some good explanations on the charges and some of the MOs, especially MOs 1 and 2. For MO 3 and 4 you could have mentioned that these MOs increase the bonding between the H atoms and the C atom. MO 6 is actually the antibonding counterpart to MO2, it has the same atomic contributions, but the phase of the C 2s AO is reversed. The H atoms primarily contribute 1s AOs not 2s AOs to the LUMO.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You looked up two crystals well done!

Rep:Mod:yb3818 complabs

2019-03-28T08:35:26Z

Rr1210:

== NH3 molecule ==
The diagram shows NH3 (or ammonia) created using GaussView

Calculation method: RB3LYP
Basis set: 6-31G(d,p)

The final energy of the optimised molecule: -56.55776873 a.u.

RSM Gradient: 0.00000485 a.u.

Point group of the molecule: C3v

N-H bond length: 1.02Å

H-N-H bond angle: 106°

{| class="wikitable" border="1"
|+ Optimisation information
|-
! Item !! Value !! Threshold !! Converged?
|-
| Maximum Force || 0.000005 || 0.00450 || YES
|-
| RMS Force || 0.000003 || 0.000300 || YES
|-
| Maximum Displacement || 0.000012 || 0.001800 || YES
|-
| RMS Displacement || 0.000008 || 0.001200 || YES
|-
|}

<jmol><jmolApplet>
<title>Optimised Ammonia molecule</title>
<color>black</color>
<size>200</size>
<script>frame 1.16</script>
<uploadedFileContents>YB3818_NH3_MOLECULE.LOG</uploadedFileContents>
</jmolApplet></jmol>
The optimisation file is liked to [[Media:YB3818_NH3_MOLECULE.LOG| here]]

Vibrational data for ammonia:

[[File:Vibrational data YB3818.PNG]]

{| class="wikitable" border="1"
|+ Information about ammonia vibrations
! wavenumber/ cm-1 !! 1090 !! 1694 !! 1694!! 3461!! 3590!! 3590
|-
| symmetry || A1 || E || E || A1 || E || E
|-
| IR intensity || 145 || 14 || 14 || 1 || 0 || 0
|-
| image || align="center"|[[File:Vib_1089.54_ammonia_yb3818.PNG |150px]] ||align="center"|[[File:Vib_1693.95-1_yb3818.PNG |150px]] || align="center"|[[File:vib_1693.95-2_yb3818.PNG |150px]] || align="center"|[[File:vib_3461.29_yb3818.PNG |150px ]] || align="center"|[[File:vib_3590_1_yb3818.PNG|150px ]] || align="center"|[[File:vib_3590_2_yb3818.PNG|150px]]
|}

Ammonia molecule is expected to have 6 vibrational nodes (3N-6 rule, where N is the number of atoms in the molecule). There are two vibrational nodes that appear at 1694 cm-1 and two vibrational nodes at 3590 cm-1. Two vibrational nodes that occur at the same wavenumber are considered to be degenerate. 5 vibrations represent "bond stretches"(1694,3461 and 3590 cm-1) and mode at 1090 cm-1 represents "bending" mode. The latter mode is commonly known as "umbrella" mode. Out of six modes, only four vibrations can be detected by spectrometer. However, since there are two pairs of degenerate modes, only two peaks appear in an experimental spectrum of ammonia. For 3590 cm-1 the intensity is zero, therefore it is not seen.

Charges of atoms in ammonia molecule:

[[File:Charges yb3818 nh3.PNG |200px]]

We would expect nitrogen to be negatively charged and all of the three hydrogen atoms positively charged. Nitrogen is more electronegative and therefore pulls electron density away from hydrogen atoms.

== N2 molecule ==

N2 molecule was created in GaussView using RB3LYP method and 6-31G(d,p) as a basis set. The final energy of the optimised molecule was found to be -109.52412868 a.u. Molecule has D∞H point group. The length of a triple bond between nitrogen atoms is found to be 1.11 Å to 3 sig.fig. Since nitrogen molecule is diatomic, the bond angle appears to be 0°.

{| class="wikitable" border="1"
|+ Optimisation information
|-
! Item !! Value !! Threshold !! Converged?
|-
| Maximum Force || 0.000001 || 0.004500 || YES
|-
| RMS Force || 0.000001 || 0.000300 || YES
|-
| Maximum Displacement || 0.000000 || 0.001800 || YES
|-
| RMS Displacement || 0.000000 || 0.001200 || YES
|-
|}

<jmol><jmolApplet>
<title>Optimised Nitrogen gas molecule</title>
<color>black</color>
<size>200</size>
<script>frame 1.16</script>
<uploadedFileContents>YB3818 N2.LOG</uploadedFileContents>
</jmolApplet></jmol>
The optimisation file is liked to [[YB3818 N2.LOG |here]]

The following data about vibrations of N2 molecule was obtained:

[[File:N2-vibdata.PNG]]

From the table above nitrogen gas molecule has only one vibration at 2457 cm-1 as expected - for any linear molecule there are 3N-5 vibrational modes. This vibration represents N-N bond stretching. The bond is symmetrical, no change in dipole moment is observed and, therefore, the molecule is IR inactive (IR intensity is found to be 0). Table below summarises all of the information:

{| class="wikitable" border="1"
|+ Nitrogen gas vibrations
|-
! wavenumber/ cm-1 !! 2457
|-
| symmetry || SGG
|-
| IR intensity || 0
|-
| image || align="center"|[[File:Vib_picn2_yb3818.PNG |150px]]
|-
|}

N2 molecule is homo-nuclear diatomic molecule and we would expect to have no charges on nitrogen atoms. GaussView has shown no charges on any of the nitrogen atoms. The picture below shows charge distribution. Both atoms appear black doe to the even charge distribution.

[[File:Charge_n2_yb3818.PNG |200px]]

== H2 molecule ==

H2 molecule was created in GaussView using RB3LYP method and 6-31G(d,p) as a basis set. The final energy of the optimised molecule was found to be -1.17853936 a.u. Molecule has D∞H point group. The length of a bond between hydrogen atoms is found to be 0.743 Å to 3 sig.fig. Since hydrogen molecule is diatomic, the bond angle appears to be 0°.

{| class="wikitable" border="1"
|+ Optimisation information
|-
! 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
|-
|}

<jmol><jmolApplet>
<title>Optimised Hydrogen gas molecule</title>
<color>black</color>
<size>200</size>
<script>frame 1.16</script>
<uploadedFileContents>YB3818_H2.LOG</uploadedFileContents>
</jmolApplet></jmol>
The optimisation file is liked to [[YB3818_H2.LOG |here]]

The following data about vibrations of H2 molecule was obtained:

[[File:Vibdata_h2_yb3818.PNG]]

From the table above hydrogen gas molecule has only one vibration at 4466 cm-1 as expected - for any linear molecule there are 3N-5 vibrational modes. This vibration represents H-H bond stretching. The bond is symmetrical, no change in dipole moment is observed and, therefore, the molecule is IR inactive (IR intensity is found to be 0). Table below summarises all of the information:

{| class="wikitable" border="1"
|+ Hydrogen gas vibrations
|-
! wavenumber/ cm-1 !! 4466
|-
| symmetry || SGG
|-
| IR intensity || 0
|-
| image || align="center"|[[File:Vib_4466_yb3818.PNG |200px]]
|-
|}

H2 molecule is homo-nuclear diatomic molecule and we would expect to have no charges on hydrogen atoms. GaussView has shown no charges on any of the hydrogen atoms. The picture below shows charge distribution. Both atoms appear black doe to the even charge distribution.

[[File:H2_charges_yb3818.PNG |200px]]

== Mono-metalic Transition Metal complex with H2 ==
bis(Tri-isopropylphosphine)-(dihydrogen-H,H')-nitrosyl-dibromo-rhenium has a unique identifier HIVYAM.

[[File:Metal compound yb3818.PNG]]

The CCDS file of this molecule is liked to [[Media:Organom1_yb3818.cqs| here]]

In the crystal structure H-H bond appears to be 1.11 Å. The bond length obtained after optimisation is 0.743 Å. The bond length is longer in the complex, because the central atom of Rhenium pulls electron density of the bond towards itself, making the H-H bond weaker.
We are using Quantum mechanics to compute the bond length which is just approximation and differ to what happens in reality.

== Harber-Bosch ==
Reaction:
N2+3H2 -> 2NH3

E(NH3)= -56.5577687 a.u.

2*E(NH3)= -113.1155374 a.u.

E(N2)= -109.5241287 a.u.

E(H2)= -1.1785394 a.u.

3*E(H2)= -3.5356182 a.u.

ΔE=2*E(NH3)-[E(N2)+3*3*E(H2)]=-0.0557905 a.u.

ΔE in kJ/mol: ΔE=-0.0557905*2625.5=-146.4779578=-146.5 kJ/mol ( to 1 d.p.)

Therefore, the energy of converting hydrogen and nitrogen gas into ammonia gas is -146.5 kJ/mol. The reaction is exothermic meaning that the product (ammonia) is more thermodynamically more stable than reactants (nitrogen and hydrogen gas).

== CH4 molecule ==
=== Optimisation: ===

CH4 molecule was created in GaussView using RB3LYP method and 6-31G(d,p) as a basis set. The final energy of the optimised molecule was found to be -40.52401404 a.u. Molecule has TD point group. The length of C-H is found to be 1.09 Å and the bond angle is 109°.

{| class="wikitable" border="1"
|+ Optimisation information
|-
! Item !! Value !! Threshold !! Converged?
|-
| Maximum Force || 0.000063 || 0.00450 || YES
|-
| RMS Force || 0.000034 || 0.000300 || YES
|-
| Maximum Displacement || 0.000179 || 0.001800 || YES
|-
| RMS Displacement || 0.000095 || 0.001200 || YES
|-
|}

<jmol><jmolApplet>
<title>Optimised methane molecule</title>
<color>black</color>
<size>200</size>
<script>frame 1.16</script>
<uploadedFileContents>CH4_YB3818.LOG</uploadedFileContents>
</jmolApplet></jmol>
The optimisation file is liked to [[Media:CH4_YB3818.LOG| here]]

===Vibrations===

The following data about vibrations of CH4 molecule was obtained:

[[File:Vibrations_yb3818.PNG]]

{| class="wikitable" border="1"
! wavenumber / cm-1 !! symmetry !! IR intensity !! image
|-
| 1356 || T2 || 14 || [[File:YB3818_1VIBCH4.PNG|250px]]
|-
| 1356|| T2 || 14 || [[File:YB3818_2CH4.PNG|250px]]
|-
| 1356 || T2 || 14 || [[File:YB3818_CH4VIB.PNG|250px]]
|-
| 1578 ||E || 0 || [[File:YB3818_4VIB.PNG|250px]]
|-
| 1578 || E || 0 || [[File:YB3818_5.PNG|250px]]
|-
| 3046 || A1 || 0 || [[File:YB3818_6.PNG|250px]]
|-
| 3162|| T2 ||25 || [[File:YB3818_7.PNG|250px]]
|-
| 3162|| T2 || 25 || [[File:YB3818_8.PNG|250px]]
|-
| 3162|| T2 || 25 || [[File:YB3818_9.PNG|250px]]
|}

For any non-linear molecule there are 3N-6 vibrational modes.Therefore, we would predict to see 9 vibrations and this is what is shown in the table above. Modes 4,5 and 6 have zero intensity, therefore they are not seen in IR spectrum. 1,2 and 3 are degenerate as well as 7,8 and 9, therefore only two absorption are seen in IR spectrum of CH4.

=== Charge: ===
[[File:Yb3818 vhargesch4.PNG]]

Carbon is more electronegative than hydrogen, therefore we would expect a negative charge on carbon since it pulls electron density towards itself.

== MO's diagrams for methane molecule ==
The first 9 molecular orbitals were looked at, where three bonding and three antibonding orbitals were found to be degenerate. Here is some information about 5 different orbitals.

===1s orbital===

[[File:MO_1_yb3818.PNG |250px]]

This molecular orbital has -10.16707 a.u. From the picture this is 1s carbon atomic orbital, as there is no hydrogen contribution is seen. This AO does not participate in the bonding as it is deep in energy and it is occupied by two electrons.

=== 1σ orbital ===

[[File:MO_2_yb3818.PNG |250px]]

This molecular orbital has energy of -0.69041 a.u. 1s orbital of hydrogen atom and 2s carbon orbital are mostly contribute to this MO. This orbital is occupied by two electrons. It is low enough in energy to be a bonding orbital and it contributes to the bond order.

=== 2σ,3σ,4σ ===

[[File:MO 4 yb3818.PNG |250px]]

The picture displays 3σ orbital. 2σ,3σ and 4σ are all degenerate but they have different orientation in space. The energy of the three molecular orbitals are found to be -0.38831 a.u. The contribution to each orbital comes mostly from 3s hydrogen orbital and one 2p carbon orbital in x,y and z orientation. All three orbitals contribute to the bond order and each one of them is occupied by 2 electrons. 4σ orbital is a HOMO orbital of the molecule.

=== 5σ* ===

[[File:MO_6_yb3818.PNG |250px]]

This picture shows 5σ orbital with the energy of +0.11824. The energy is positive and therefore, this molecular orbital is an antibonding orbital. Contribution to its energy comes mostly from 2s carbon atomic orbital and 1s hydrogen atomic orbital. This orbital is unoccupied and it does not contribute to the bond order. This orbital is a LUMO orbital of the mo

=== 6σ*,7σ*,8σ* ===
[[File:MO 8 yb3818.PNG |250px ]]

This picture shows 8σ* orbital. 6σ*,7σ* and 8σ* are all degenerate but they have different orientation in space. The energy of these orbitals is found to be +0.17677 a.u. The energy is high and these orbital is an antibonding orbital.This orbital is unoccupied by electrons and does not contribute to the bond order.

== Independent work ==
HCN molecule information:

===Optimisation information===

HCN molecule was created in GaussView using RB3LYP method and 6-31G(d,p) as a basis set. The final energy of the optimised molecule was found to be -93.42458132 a.u. Molecule has C∞v point group. The length of C-H is found to be 1.07 Å and triple bond between carbon and nitrogen is 1.16 Å and the bond angle is 180°.

{| class="wikitable" border="1"
|+ Optimisation information
|-
! Item !! Value !! Threshold !! Converged?
|-
| Maximum Force || 0.000370 || 0.00450 || YES
|-
| RMS Force || 0.000255 || 0.000300 || YES
|-
| Maximum Displacement || 0.000731 || 0.001800 || YES
|-
| RMS Displacement || 0.000459 || 0.001200 || YES
|-
|}

<jmol><jmolApplet>
<title>Optimised HCN molecule</title>
<color>black</color>
<size>200</size>
<script>frame 1.16</script>
<uploadedFileContents>YB3818_HCN1.LOG</uploadedFileContents>
</jmolApplet></jmol>
The optimisation file is liked to [[Media:YB3818_HCN1.LOG| here]]

===Vibrations===

The following data about vibrations of N2 molecule was obtained:

[[File:Vibrationaldata hcn yb3818.PNG]]

{| class="wikitable" border="1"
! wavenumber / cm-1 !! symmetry !! intensity !! image
|-
| 767 || PI || 35 || [[File:Hcn_1_vib_yb3818.PNG|250px]]
|-
| 767 || PI || 35 || [[File:Vib_yb3818_2.PNG|250px]]
|-
| 2214 || SG || 2 || [[File:Yb3818_3_hcn.PNG|250px]]
|-
| 3480 || SG || 57 || [[File:Vib_4_hcn_yb3818.PNG|250px]]
|}

For any linear molecule the total number of vibrational modes is 3N-5 (whewre N-number of molecules) HCN molecule should, therefore, have 4 vibrational modes and it is seen from the table above. All four vibrations appear in IR-spectrum, however the first two absorption will overlap since these two vibrations are degenerate; the thirs vibration has a low intensity and might be hard to spot on IR-spectrum.

=== Charge: ===

[[File:Hcn yb3818 charges.PNG]]

Nitrogen is more electronegative than carbon than hydrogen, which means nitrogen will pull electron density towards itself. We would expect Nitrogen atom to be negatively charged, whereas hydrogen should be positively charged. Carbon charge is expected to be in between these two values. By computing the charges, we can see that carbon atom is just slightly positively charged and hydrogen and nitrogen are, indeed, positively and negatively charged particles respectfully.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 0 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, good explanations overall which are clearly communicated well done! To improve you could have mentioned that the LUMO is antibonding counterpart to the bonding MO 2: the same AOs contribute but with opposite phases rather than the same phase. The same for the sigma * and sigma MOs.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You calculated and analysed HCN well done!

Rep:Mod:hb918

2019-03-28T08:26:55Z

Rr1210:

==''' NH3 Molecule '''==

=== NH3 Summary ===
{| class="wikitable" border="1"
|+
! Feature !! Result
|-
| N-H Bond Distance || 1.02 Å
|-
| H-N-H Bond Angle || 106o
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d.p)
|-
| Final Energy E(RB3LYP)|| -56.6 au
|-
| RMS Gradient || 0.00000485 au
|-
| Point Group of the Molecule || C3v
|}

==== Optimisation of NH3 ====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

==== Jmol Image of NH3 ====
<jmol><jmolApplet>
<title>Optimised Ammonia</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>HB918_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

The optimisation file is linked[[Media:HB918_NH3_OPTF_POP.LOG| here]]

=== Vibrations and Vibrational Modes ===
[[File:hb918_displayvibrations.png]]

==== NH3 Vibrations ====
{| class="wikitable" border="1"
|+
! Wavenumber (cm-1) !! Symmetry !! Intensity (arbitrary units) !! Image
|-
| 1090 ||A1 ||145 || [[File:hb918_vibration1.png]]
|-
| 1694 ||E ||14|| [[File:hb918_vibration2.png]]
|-
| 1694 ||E ||14 || [[File:hb918_vibration3.png]]
|-
| 3461 ||A1 ||1 || [[File:hb918_vibration4.png]]
|-
| 3590 ||E ||0 || [[File:hb918_vibration5.png]]
|-
| 3590 ||E ||0 || [[File:hb918_vibration6.png]]
|}

• Based on the 3N-6 rule, we would expect that there are 6 vibrational modes (3(4) - 6 = 6).

• The data shows that there are 2 sets of degenerate vibrational modes. These occur at 1694cm-1 and 3590cm-1.

• The vibrations at 1090cm-1 and 1694cm-1 are bending modes and the vibrations at 3461cm-1 and 3590cm-1 are stretching modes.

• The vibrational mode at 3461cm-1 is highly symmetric.

• The mode at 1090cm-1 is known as the "umbrella" mode.

• In an experimental spectrum of gaseous ammonia we would expect to see 2 bands because the vibrational modes at 3461cm-1 and 3590cm-1 have very low intensities. The 2 visible bands in the spectrum would be produced from the vibrational modes at 1090cm-1 and 1694cm-1.

=== Charge Analysis ===

[[File:hb918_nh3_nbo.png]]

'''This image shows the NBO charge distribution for NH3'''

The N-atom has a charge of -1.125 D and the H-atoms have a charge of +0.375 D. We expect the N-atom to have a negative charge because it is the most electronegative atom in NH3 and this shows that the electron density mostly resides on the N-atom in the molecule.

==''' N2 Molecule '''==

=== N2 Summary ===
{| class="wikitable" border="1"
|+
! Feature !! Result
|-
| N-N Bond Distance || 1.11 Å
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d.p)
|-
| Final Energy E(RB3LYP)|| -109.5 au
|-
| RMS Gradient || 0.00013888 au
|-
| Point Group of the Molecule || D*h
|}

==== Optimisation of N2 ====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000241 0.000300 YES
Maximum Displacement 0.000075 0.001800 YES
RMS Displacement 0.000106 0.001200 YES

</pre>

==== Jmol Image of N2 ====
<jmol><jmolApplet>
<title>Optimised Nitrogen</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>HB918_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

The optimisation file is linked[[Media:HB918_N2_OPTF_POP.LOG| here]]

=== Vibrations and Vibrational Modes of N2 ===
[[File:hb918_n2_displayvibrations.png]]

==== N2 Vibrations ====
{| class="wikitable" border="1"
|+
! Wavenumber (cm-1) !! Symmetry !! Intensity (arbitrary units) !! Image
|-
| 2457 ||SGG ||0 || [[File:hb918_vibration1_n2.png]]
|}

• To calculate the expected number of vibrational modes for a linear molecule, we use the 3N - 5 rule. This gives an answer of 3(2) - 5 = 1 vibrational mode. This vibrational mode is found at 2457cm-1.

=== Charge Analysis ===

[[File:hb918_n2_nbo.png]]

'''This image shows the NBO charge distribution for N2'''

The charge on each N-atom is 0 D. We would expect the N-atoms to have a charge of 0 D because this molecule does not have a dipole as the electronegativity of each N-atom is the same, so there is equal charge distribution across the molecule.

=== N2 Mono-Metallic TM Complex ===

==== Mono-Metallic TM Complex 2D Structure ====

N2 can bind to a metal ion in order to form a TM complex. The structure below is an example of a mono-metallic TM complex where the central cobalt ion coordinates to N2. This structure has an IUPAC name of (bis(2-(dicyclohexylphosphino)phenyl)(methyl)silyl)-dinitrogen-(trimethylphosphino)-cobalt. The unique identifier for this structure is VEJSEL. More information about this structure can be found [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=vejsel&DatabaseToSearch=Published here]]

[[File:hb918_vejselconquest.png]]

==== Mono-Metallic TM Complex 3D Structure ====

<jmol><jmolApplet>
<title>3D VEJSEL</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Hb918_VEJSEL.mol2</uploadedFileContents>
</jmolApplet></jmol>

This shows the 3D structure of the molecule. The N-atoms are depicted in blue.

==== Bond Properties ====

In the structure above, the N-N triple bond length obtained from Avogadro is found to be 1.13 Å. Using Gaussian, the bond length in an optimised N2 molecule is 1.11 Å. This difference in bond length shows that the VEJSEL N-N triple bond is weaker than expected. This is due to the fact that one of the N-atoms is coordinated to a cobalt metal ion and Co withdraws electron density slightly from the N2 triple bond and therefore also lowers the energy of this bond. This results in a longer bond length because the atoms are less tightly bound together. A difference in the bond lengths can also be due to the difference between computational and experimental methods for determining bond length. Computational methods involve the optimisation of the bond lengths to a fixed distance that places the molecule in the lowest energy state. Furthermore computational methods consider molecules in the gaseous state whereas experimentally the structure would be used in the solid state to determine bond length by X-ray diffraction.

=== Haber-Bosch Process ===

The Haber-Bosch process combines N2 and H2 to form ammonia. The overall reaction is given by the equation '''N2 + 3H2 → 2NH3'''.

E(NH3) = -56.55776873 au

2*E(NH3) = -113.115537 au

E(N2) = - 109.52412866 au

E(H2) = -1.17853934 au

3*(H2) = - 3.53561802 au

ΔE = 3*(H2) - (E(N2) + 3*(H2)) = -0.0557990 au

ΔE = -0.0557990 * 2625.5 = -146.500222 kJmol-1

ΔE = -146.5 kJmol-1

The energy change shows that this is an exothermic reaction because is it a negative energy change. Therefore the product (NH3) is more stable than the reactants (H2 and N2)

==''' H2 Molecule '''==

=== H2 Summary ===
{| class="wikitable" border="1"
|+
! Feature !! Result
|-
| H-H Bond Distance || 0.74 Å
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d.p)
|-
| Final Energy E(RB3LYP)|| -1.18 au
|-
| RMS Gradient || 0.00005659 au
|-
| Point Group of the Molecule || D*h
|}

==== Optimisation of H2 ====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000098 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000129 0.001800 YES
RMS Displacement 0.000182 0.001200 YES

</pre>

==== Jmol Image of H2 ====
<jmol><jmolApplet>
<title>Optimised Hydrogen</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>HB918_H2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

The optimisation file is linked[[Media:HB918_H2_OPTF_POP.LOG| here]]

=== Vibrations and Vibrational Modes of H2 ===
[[File:hb918_h2_displayvibrations.png]]

==== H2 Vibrations ====
{| class="wikitable" border="1"
|+
! Wavenumber (cm-1) !! Symmetry !! Intensity (arbitrary units) !! Image
|-
| 4464 ||SGG ||0 || [[File:hb918_h2_vibration1.png]]
|}

• Again, to calculate the expected number of vibrational modes for a linear molecule, we use the 3N - 5 rule. This gives an answer of 3(2) - 5 = 1 vibrational mode. This vibrational mode is found at 4464cm-1.

=== Charge Analysis ===

[[File:hb918_h2_nbo.png]]

'''This image shows the NBO charge distribution for H2'''

Each H-atom has a charge of 0 D. This is because there is no dipole in the molecule, so there is an even charge distribution across the 2 H-atoms.

==''' (Own Choice) CH4 Molecule '''==

=== CH4 Summary ===
{| class="wikitable" border="1"
|+
! Feature !! Result
|-
| C-H Bond Distance || 1.07 Å
|-
| H-C-H Bond Angle || 109o
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d.p)
|-
| Final Energy E(RB3LYP)|| -40.5 au
|-
| RMS Gradient || 0.00003263 au
|-
| Point Group of the Molecule || TD
|}

==== Optimisation of CH4 ====

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES

</pre>

==== Jmol Image of CH4 ====
<jmol><jmolApplet>
<title>Optimised Methane</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>HB918_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

The optimisation file is linked[[Media:HB918_CH4_OPTF_POP.LOG| here]]

=== Vibrations and Vibrational Modes ===
[[File:hb918_ch4_displayvibrations.png]]

==== CH4 Vibrations ====
{| class="wikitable" border="1"
|+
! Wavenumber (cm-1) !! Symmetry !! Intensity (arbitrary units) !! Image
|-
| 1356 ||T2 ||14 || [[File:hb918_ch4_vibration1.png]]
|-
| 1356 ||T2 ||14|| [[File:hb918_ch4_vibration2.png]]
|-
| 1356 ||T2 ||14 || [[File:hb918_ch4_vibration3.png]]
|-
| 1579 ||E ||0 || [[File:hb918_ch4_vibration4.png]]
|-
| 1579 ||E ||0 || [[File:hb918_ch4_vibration5.png]]
|-
| 3046 ||A1 ||0 || [[File:hb918_ch4_vibration6.png]]
|-
| 3162||T2 ||25 || [[File:hb918_ch4_vibration7.png]]
|-
| 3162 ||T2 ||25 || [[File:hb918_ch4_vibration8.png]]
|-
| 3162 ||T2 ||25 || [[File:hb918_ch4_vibration9.png]]
|}

•Using the 3N - 6 rule, we would predict that there are 3(5) - 6 = 9 vibrational modes.

•The 3 vibrations at 1356 (cm-1) are degenerate, the 2 vibrations at 1579 (cm-1) are degenerate, and the 3 vibrations at 3162 (cm-1) are degenerate.

=== Charge Analysis ===

[[File:hb918_ch4_nbo.png]]

'''This image shows the NBO charge distribution for CH4'''

The C-atom has a charge of -0.93 D and the H-atoms have a charge of 0.233 D. We expect the carbon atom to have a negative charge because it is the most electronegative atom in CH4 and this shows that the electron density mostly resides on the C-atom in the molecule.

==== CH4 Molecular Orbitals ====
{| class="wikitable" border="1"
|+
! Image !! Energy !! Description
|-
| [[File:hb918_ch4_mo1.png| 150px]] || -10.16707 || This orbital is the 1s orbital located on the carbon atom. It is much lower in energy than the other orbitals as it is tightly bound to carbon and it is very stable. It is deep in energy. As it is the 1s orbital, the electrons in this orbital are found very close to the nucleus which is the reason for its stability. This orbital is filled with 2 electrons, both electrons are from carbon.
|-
| [[File:hb918_ch4_mo2.png| 150px]] || -0.69041 || This orbital is the lowest energy bonding MO between the 2s orbital of carbon and the 1s orbital of hydrogen. As it is a bonding MO and it is filled with 2 electrons, it is involved in chemical bonding.
|-
| [[File:hb918_ch4_mo4.png| 150px]] || -0.38831 || This orbital is another filled bonding MO, it is one of 3 degenerate bonding MOs. It is formed from the combination of the 2p orbital on carbon and the 1s orbital of hydrogen. Each MO is perpendicular to each other. Only one is shown in the image. One of these is also the HOMO as each of these 3 degenerate MOs is filled with 2 electrons and this is the highest energy level occupied in CH4.
|-
| [[File:hb918_ch4_mo6.png| 150px]] ||0.11824 || This is an empty antibonding MO. It is the lowest energy unoccupied MO and therefore it is the LUMO. As this antibonding orbital is unfilled, it has no effect on the chemical bonding within the molecule.
|-
| [[File:hb918_ch4_mo8.png| 150px]] || 0.17677 || This is another empty antibonding MO. It is the antibonding MO formed from destructive interference of the carbon 2p and hydrogen 1s orbitals. There are 3 of these with the same energy and they are degenerate and perpendicular to each other. This is higher in energy than the HOMO/LUMO region. It is unfilled and has no effect on the chemical bonding within the molecule.
|}

=='''(Independent Work) HCN Molecule'''==

=== HCN Summary ===
{| class="wikitable" border="1"
|+
! Feature !! Result
|-
| C-N Bond Distance || 1.16 Å
|-
| C-H Bond Distance || 1.07 Å
|-
| H-C-N Bond Angle || 180o
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d.p)
|-
| Final Energy E(RB3LYP)|| -93.4 au
|-
| RMS Gradient || 0.00017006 au
|-
| Point Group of the Molecule || C*V
|}

==== Optimisation of HCN ====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000370 0.000450 YES
RMS Force 0.000255 0.000300 YES
Maximum Displacement 0.000676 0.001800 YES
RMS Displacement 0.000427 0.001200 YES

</pre>

==== Jmol Image of HCN ====
<jmol><jmolApplet>
<title>Optimised HCN</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>HB918_HCN_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

The optimisation file is linked[[Media:HB918_HCN_OPTF_POP.LOG| here]]

=== Vibrations and Vibrational Modes ===
[[File:hb918_hcn_diplayvibrations.png]]

==== HCN Vibrations ====
{| class="wikitable" border="1"
|+
! Wavenumber (cm-1) !! Symmetry !! Intensity (arbitrary units) !! Image
|-
| 767 ||PT ||35 || [[File:hb918_hcnvib1.png]]
|-
| 767 ||PT ||35|| [[File:hb918_hcnvib2.png]]
|-
| 2215 ||SG ||2 || [[File:hb918_hcnvib3.png]]
|-
| 3480 ||SG ||57 || [[File:hb918_hcnvib4.png]]
|}

• Using the 3N-5 rule we woudl expect there for be 3(3) - 5 = 4 vibrational modes.

•The vibrational modes at 767 cm-1 are degenerate and they are bending modes.

•The modes at 2215 cm-1 and 3480 cm-1 are stretching modes.

=== Charge Analysis ===

[[File:hb918_hcn_nbo.png]]

'''This image shows the NBO charge distribution for HCN'''

The H-atom has a charge of 0.234 D, the C-atom has a charge of 0.073 D, and the N-atom has a charge of -0.308 D. We expect the N-atom to have the most negative charge because it is the most electronegative atom in the molecule. We expect the C-atom to be less positively charged than the H-atom because C is more electronegative than H. Electron density mostly resides on the N-atom

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, overall this is a well structured wiki. However a lot of your images are very oversized and prevent the reader from seeing them with the other information on the page for context.

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, overall good explanations on both MOs and charges. The MO discussion is also very well formatted, with appropriately sized images allowing the reader to compare the MOs. To improve the discussion you could have explained that the LUMO is the antibonding counterpart to MO2, and included its atomic contributions. Well done for recognising that unoccupied MOs do not effect the bonding.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did an extra calculation and charge analysis on HCN, well done!

Rep:Mod:adb3418

2019-03-28T08:18:14Z

Rr1210:

=NH3=
N-H bond length=1.02 A

H-N-H angle=1060

{|class="wikitable" border="1"
!Item !! Value !! Threshold !! Converged?
|-
| Maximum Force || 0.000004 || 0.000450 || YES
|-
| RMS Force || 0.000004 || 0.000300 || YES
|-
| Maximum Displacement || 0.000072 || 0.001800 || YES
|-
| RMS Displacement || 0.000035 || 0.001200 || YES
|}

==Calculation method==
RB3LYP

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

==Final energy E(RB3LYP)==
-56.5577687 a.u.

==Dipole moment==
1.85 Debye

==Point group==
C3V

==JSmol==
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OPTIMISATION_ADB3418.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Display options==
[[FILE:Betterpaint.png|centre]]

==Vibration analysis==
{|class="wikitable" border="1"class="wikitable" border="1"
|'''Mode number'''||1||2||3||4||5||6
|-
|'''Wavenumber''' ( cm-1 )||1090||1694||1694||3461||3590||3590
|-
|'''Symmetry'''||A1||E||E||A1||E||E
|-
|'''Intensity''' (arbitrary units)||145||14||14||1||0||0
|-
|'''Image'''||[[File:Nvib1-adb3418.png|200x200px]]||[[File:Nvib2_adb3418.png|200x200px]]||[[File:Vib3adb3418.png|200x200px]]||[[File:Nvib4_adb3418.png|200x200px]]||[[File:Nvib5_adb3418.png|200x200px]]||[[File:Nvib6_adb3418.png|200x200px]]
|}

==Answered questions==
Applying the 3N-6 rule, I would expect 6 vibration modes.
The modes that are degenerate are modes 2 (1694 cm-1) and 3 (1694 cm-1), as well as modes 5 (3590 cm-1) and 6 (3590 cm-1).
The bond stretch vibration modes are 4,5 and 6. The bending vibration modes are 1,2 and 3.
The mode that is highly symmetrical is mode 4.
The umbrella mode is mode 1 at 1090 cm-1.
I would expect to see only 2 bands in the IR spectrum of ammonia due to the fact that there are degenerate vibration modes and some of the have very low intensity due to very small change in dipole moment. I would expect to see bands at 1090 and 1694 cm-1.

==Charge analysis==
I would expect a partial positive charge on hydrogen atoms and a partial negative charge on nitrogen based on the fact that nitrogen is more electronegative than hydrogen. The results yielded by Gaussian are consistent with my predictions:
charge on H = +0.375
charge on N = -1.125

[[File:Chargesep_adb3418.png|300x300px]]

==LOG file==
[[Media:NH3_OPTIMISATION_ADB3418.LOG]]

=N2=

N-N bond length=1.11 A

{|class="wikitable" border="1"
|-
! 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
|}

==Calculation type==
RB3LYP

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

==Final energy E(RB3LYP)==
-109.5241287 a.u.

==Dipole moment==
0.00 Debye

==Point group==
D∞h

==JSmol==
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NIT_OPT_ADB3418.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Display options==
[[File:Picn_adb3418.png|centre]]

==Vibration analysis==
{| class="wikitable" border="1"
|-
|'''Frequency''' (cm-1)||2457
|-
|'''Symmetry'''||SGG
|-
|'''Intensity'''||0
|-
|'''Image'''||[[File:Vibw_adb3418.png|200x200px]]
|}
The vibration is not visible in IR because it induces no change in dipole.

==Charge analysis==
Because it is a homonuclear diatomic molecule, N2 does not exhibit partial charges on the constituent atoms. Electron density is equally shared.

==LOG file==
[[Media:NIT_OPT_ADB3418.LOG]]

=H2=

H-H bond length=0.74 A

{| class="wikitable" border="1"
|-
!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
|}

==Calculation type==
RB3LYP

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

==Final energy E(RB3LYP)==
-1.1785394 a.u.

==Dipole moment==
0.00 Debye

==Point group==
D∞h

==JSmol==
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>H2_OPT_ADB3418.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Display options==
[[File:Pich_adb3418.png|centre]]

==Vibration analysis==
{| class="wikitable" border="1"
|-
|'''Frequency''' (cm-1)||4466
|-
|'''Symmetry'''||SGG
|-
|'''Intensity'''||0
|-
|'''Image'''||[[File:Hvib_adb3418.png|200x200px]]
|}
The vibration is not visible in IR because it induces no change in dipole.

==Charge analysis==
Because it is a homonuclear diatomic molecule, H2 does not exhibit partial charges on the constituent atoms. Electron density is equally shared.

==LOG file==
[[Media:H2OP.LOG]]

=H2 in a mono-metallic transition metal complex=
The compound that I selected is HINBOV, trichloro-bis(cyclohexylisocyanido)-bis(dimethylphenylphosphine)-rhenium(III) 1,2-dichlorobenzene solvate which coordinates H2.
The H-H bond is 0.84 A, which is longer than the calculated H-H bond ( 0.74 A ) in gaseous hydrogen molecule. This deviation is due to the fact that Ru draws electron density from H-H bond in the Ruthenium complex, weakening it and thus making it longer. The values may also be different due to computational errors in our method. To reduce the errors, we could use a more accurate method.
[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HINBOV&DatabaseToSearch=Published]

=Haber-Bosch process=

{|class="wikitable" border="1"
|E(NH3)=-56.5577687 || a.u.
|-
|2*E(NH3)=-113.115537|| a.u.
|-
|E(N2)=-109.5241287 || a.u.
|-
|E(H2)=-1.1785394 || a.u.
|-
|3*E(H2)=-3.5356182 || a.u.
|}
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]
ΔE=-146.5 kJ/mol

From calculation consideration, the stablest molecule is N2, followed by NH3 and the least stable molecule is H2. Therefore, the gaseous reactants are stabler than the product. Also, according to these calculations, Haber-Bosch process is exothermic, thus the formation of ammonia is favoured.

=CH4=

C-H bond=1.09 A

H-C-H angle=1100

{|class="wikitable" border="1"
|-
! Item !! Value !! Threshold !! Converged?
|-
| Maximum Force || 0.000063 || 0.000450 || YES
|-
|RMS Force || 0.000034 || 0.000300 || YES
|-
|Maximum Displacement || 0.000179 || 0.001800 || YES
|-
|RMS Displacement || 0.000095 || 0.001200 || YES
|}
==Calculation method==
RB3LYP

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

==Final energy E(RB3LYP)==
-40.5240140 a.u.

==Dipole moment==
0.00 Debye

==Point group==
Td

==JSmol==
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>METHANE_ADB3418.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Display options==
[[FILE:Picc+adb3418.png |centre]]

==Vibration analysis==
{|class="wikitable" border="1"class="wikitable" border="1"
|'''Mode number'''||1||2||3||4
|-
|'''Wavenumber''' ( cm-1 )||1356||1356||1356||1579
|-
|'''Symmetry'''||T2||T2||T2||E
|-
|'''Intensity''' (arbitrary units)||14||14||14||0
|-
|'''Image'''||[[File:Mevib1_adb3418.png|200x200px]]||[[File:Mevib2_adb3418.png|200x200px]]||[[File:Mevib3_adb3418.png|200x200px]]||[[File:Mevib4_adb3418.png ‎|200x200px]]
|}
{|class="wikitable" border="1"class="wikitable" border="1"
|'''Mode number'''||5||6||7||8||9
|-
|'''Wavenumber''' ( cm-1 )||1579||3046||3162||3162||3162
|-
|'''Symmetry'''||E||E||A1||T2||T2
|-
|'''Intensity''' (arbitrary units)||0||0||0||25||25
|-
|'''Image'''||[[File:Mevib5_adb3418.png|200x200px]]||[[File:Mevib6_adb3418.png|200x200px]]||[[File:Mevib7_adb3418.png|200x200px]]||[[File:Mevib8_adb3418.png|200x200px]]||[[File:Mevib9_adb3418.png|200x200px]]
|}

==Charge analysis==
Because it is a non-polar molecule by virtue of the connectivity of the atoms and the very small difference in electronegativities, methane does not present a dipole moment.

==Molecular orbitals of CH4==

{|class="wikitable" border="1"
!Molecular orbital !! 1!! 2!! 3!! 4!!5
|-
|'''Energy''' (a.u.)||-10.16707 (deep in energy)||-0.69041||-0.38831 (HOMO)||0.11824 (LUMO) ||0.17677 (LUMO+1)
|-
|-
|'''Type of orbital'''||Bonding||Bonding||Bonding||Antibonding||Antibonding
|-
|'''Constituent atomic orbitals'''||2s of carbon||2s of carbon + 1s of hydrogen || 2p of carbon + 1s of hydrogen|| out-of-phase 2s of carbon + 1s of hydrogen||out-of-phase 2p of carbon + 2s of hydrogen
|-
|'''Ocuppied?'''||Yes||Yes||Yes||No||No
|-
|'''Contributes to'''||Non-bonding||Bonding||Bonding||Bonding||Antibonding
|-
|'''Shape'''||[[File:Loworb_adb3418.PNG|200x200px]]||[[File:Forb_adb3418.PNG|200x200px]]||[[File:Forb2_adb3418.PNG|200x200px]]||[[File:Tr_adb3418.PNG|200x200px]]||[[File:Ant2orb_adb3418.PNG|centre|200x200px]]
|}

==LOG file==
[[Media:METHANE_ADB3418.LOG]]

=Investigation of a reaction=
In the process of oil drilling, methane gas is released from pockets of natural gas. Because it is a greenhouse gas that is 86 times more powerful than CO2 over the course of 20 years, it is usually burned in a process called "flaring"<ref>https://www.sierraclub.org/sierra/green-life/let-it-burn-congress-allows-flaring-venting-methane-gas</ref>. Methane is a very abundant and cheap source of fuel. It is of great interest to find an efficient method of converting methane into a liquid fuel like methanol. Current protocols of oxidising methane to methanol use high temperatures, O2 and nitrogen oxides as catalysts<ref>https://www.sierraclub.org/sierra/green-life/let-it-burn-congress-allows-flaring-venting-methane-gas</ref>. It is also elusive to prevent further oxidation to CO2. In this section, I want to explore a reaction that has been done in literature before<ref> Peipei Xiao et al. “Selective oxidation of methane to methanol with H2O2 over an Fe-MFI zeolite catalystusing sulfolane solvent”. In:Chem. Commun.55 (20 2019), pp. 2896–2899.doi:10.1039/C8CC10026H.url:http://dx.doi.org/10.1039/C8CC10026H.4
</ref> and that can generate methanol from methane. The reaction can be summarised as follows:
CH4 + H2O2 ---> CH3OH + H2O
We can apply the same method as the one used for the Haber-Bosch process. We build each molecule in Gaussian, optimise it and extract the energy parameter. Thus, to estimate the ΔE for this reaction, we deduce the formula:
ΔE=E(CH3OH)+E(H2O)-E(CH4)-E(H2O2)
The values calculated by Gaussian are the following:

{|class="wikitable" border="1"
|-
|E(CH3OH)=-115.7239644 ||a.u.
|-
|E(H2O)=-76.4197374 || a.u.
|-
|E(CH4)=-40.5240140 || a.u.
|-
|E(H2O2)=-151.5431915|| a.u.
|}
Thus, plugging the numbers in (and converting to kJ/mol) gives a ΔE of '''-200.8 kJ/mol'''. According to these calculations, oxidation of methane by hydrogen peroxide is an exothermic reaction. This means that, enthalpically
(energetically), this reaction is favourable. Using enthalpies of formation from literature<ref>https://www.thoughtco.com/common-compound-heat-of-formation-table-609253</ref>, we can obtain a literature value of ΔH for this reaction. Thus, ΔH was calculated to be '''-261.6 kJ/mol'''. The difference in values might arise from the fact that the calculation method used assumes this reaction happens in vacuum (it assumes the components are in vacuum). Also, this method is not very accurate and other methods could be used to obtain better results. However, the calculated energy is only part of the picture. Such a reaction cannot happen in the absence of a catalyst. Entropy should also be considered when assessing how favourable a chemical reaction is.

==LOG files==
{|class="wikitable" border="1"
|-
|Methanol||[[Media:METHANOLTRY_adb3418.LOG]]
|-
|Hydrogen peroxide||[[Media:H2O2TRY_adb3418.LOG]]
|-
|Water||[[Media:H2O_adb3418.LOG]]
|-
|Methane||[[Media:METHANE_ADB3418.LOG]]
|}

=References=

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, overall a good structure, however you have used a few too many subheadings which really break up the page and make it hard work for the reader to see the data in context. Also you have left all your jmol captions the same - test molecule - this isn’t a good caption and doesn’t help the reader understand the figure.

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, well done for mentioning dipole moment.

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, overall accurate and succinct description, well done! One part which isn't quite right is that MOs 4 and 5 do not contribute to the overall bonding of the molecule - this is because they are unoccupied so have no impact on the positions of electrons in the molecule.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You wrote an extra minireport on generating methanol from methane, you used the literature and did extra calculations and analysis, well done this section was really good!

Rep:Title=Mod:mb7418introtomolecularmodel

2019-03-28T08:06:16Z

Rr1210:

=Title=

'''NH3 molecule'''

{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3LYP
|-
|Basis set
|6-31G(d.p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-56.5577687</nowiki>
|-
|RMS gradient (au)
|0.00000485
|-
|Point group
|C3V
|}

N-H bond distance = 1.02Å (2 d.p)

H-N-H bond angle = 106° (0 d.p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MEHNAZ BASIR NH3 OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MEHNAZ BASIR NH3 OPTIMISED.LOG| here]]

[[File:Mehnaz basir ss NH3 display vibrations.png|800px]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity (arbitrary)
!Type of vibration
!Image of vibration
|-
|1
|1090
|A1
|145
|Bend
|[[File:Mb7418 NH3 1ss.png|150px]]
|-
|2
|1694
|E
|14
|Bend
|[[File:Mb7418 NH3 2ss.png|150px]]
|-
|3
|1694
|E
|14
|Bend
|[[File:Mb7418 NH3 3ss.png|150px]]
|-
|4
|3461
|A1
|1
|Stretch
|[[File:Mb7418 NH3 4ss.png|150px]]
|-
|5
|3590
|E
|0
|Stretch
|[[File:Mb7418 NH3 5ss.png|150px]]
|-
|6
|3590
|E
|0
|Stretch
|[[File:Mb7418 NH3 6ss.png|150px]]
|}

In the NH3 molecule, Nitrogen atom has a charge of -1.125 and all the Hydrogen atoms have a charge of 0.375. I would expect the Nitrogen atom's charge to be more negative in comparison. the reason for this is because Nitrogen is more electronegative in comparison to the Hydrogen atoms. Hence it'll have a higher electron density thus making it more negative.

6 modes are expected from the (3N-6) rule. The modes 2 and 3 are degenerate. 5 and 6 are also degenerate to each other. Modes 1, 2 and 3 are bending vibrations whilst modes 4, 5 and 6 are bond stretch vibrations. The mode which is highly symmetrical is 4. The umbrella mode is 1. 2 bands are expected to be seen in an experimental spectrum of gaseous ammonia due to there being two degenerate pairs. In addition, modes 5 and 6 have an intensity of 0.

'''N2 molecule'''
{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-109.5241287</nowiki>
|-
|RMS Gradient Norm (au)
|0.00000365
|-
|Point Group
|D*H
|}

N≡N bond distance = 1.11Å (2 d.p)

N2 is a linear molecule.

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000002 0.001800 YES
RMS Displacement 0.000003 0.001200 YES
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>N2 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MEHNAZ BASIR N2 OPTIMISED.txt</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MEHNAZ BASIR N2 OPTIMISED.txt| here]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity (arbitrary)
|-
|1
|2457
|SGG
|0
|}

[[File:Mb7418 n2 ss.png|800px]]

Both Nitrogen molecules have no charge. The reason for this is because they are the same element, hence they have the same electronegativities. So the molecule is non polar as the charge is distributed evenly along both atoms.

'''H2 molecule'''

{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3YLB
|-
|Basis set
|6-31G(d.p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-1.1785394</nowiki>
|-
|RMS Gradient Norm (au)
|0.00000017
|-
|Point Group
|D*H
|}

H-H bond distance = 0.74Å (2 d.p)

<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
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>H2 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MEHNAZ BASIR H2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MEHNAZ BASIR H2.LOG| here]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity
|-
|1
|4466
|SGG
|0
|}

[[File:Mb7418 h2 ss.png|800px]]

Both Hydrogen atoms have a charge distribution of 0. This shows it's a non polar molecular as it has no difference in charge.

'''Structure and reactivity of H2'''

Unique identifier = CEFCAS

[[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=ACIEF5&year=2005&spage=7227&volume=44&id=doi:10.1002/anie.200502297&pid=ccdc:275803]]
{| class="wikitable"
!Molecule
!H-H bond (Å)
|-
|H2
|0.74
|-
|CEFCAS
|1.48
|}
The H-H bond in the H2 molecule is shorter compared to the H-H bond in the metal complex. The reason for this is because the hydrogen atom is bonded to both the transition metal and another hydrogen. The bond density in the H-H bond becomes smaller compared to the bond density in the H-TM (TM = transition metal) bond. This causes the H-H bond to become longer. In addition, the bonds may be different due to computational errors. This can be fixed by using a different method.

'''Haber-Bosch reaction energy calculation for NH3'''

E(NH3)= -56.5577687 au

2*E(NH3)= -113.1155374 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356182 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557905 au = -146.5(1 d.p) kJ/mol

The exothermic reaction is favoured. The forward reaction is exothermic. Hence there will be a higher production of ammonia in this reaction because ammonia is more stable.

'''CH4 molecule'''
{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3LYP
|-
|Basis set
|6-31G(d.p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-40.5240140</nowiki>
|-
|RMS Gradient Norm (au)
|0.00003263
|-
|Point Group
|TD
|}

C-H bond distance = 1.07Å (2 d.p)

H-C-H bond angle = 109° (0 d.p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>CH4 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MEHNAZ BASIR CH4.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MEHNAZ BASIR CH4.LOG| here]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity (arbitrary)
!Type of vibration
!Image of vibration
|-
|1
|1356
|T2
|14
|Bend
|[[File:Mb7418 CH4 1.png|150px]]
|-
|2
|1356
|T2
|14
|Bend
|[[File:Mb7418 CH4 2.png|150px]]
|-
|3
|1356
|T2
|14
|Bend
|[[File:Mb7418 CH4 3.png|150px]]
|-
|4
|1579
|E
|0
|Bend
|[[File:Mb7418 CH4 4.png|150px]]
|-
|5
|1579
|E
|0
|Bend
|[[File:Mb7418 CH4 5.png|150px]]
|-
|6
|3046
|A1
|0
|Stretch
|[[File:Mb7418 CH4 6.png|150px]]
|-
|7
|3162
|T2
|25
|Stretch
|[[File:Mb7418 CH4 7.png|150px]]
|-
|8
|3162
|T2
|25
|Stretch
|[[File:Mb7418 CH4 8.png|150px]]
|-
|9
|3162
|T2
|25
|Stretch
|[[File:Mb7418 CH4 9.png|150px]]
|}

The carbon atom has a charge distribution of -0.930 and all the hydrogen atoms have a charge distribution of 0.233. The reason why the carbon atom is more negative is because it has a higher electronegative value compared to hydrogen. hence the electrons in the carbon-hydrogen bond will be more attracted to the carbon. Therefore, the carbon atom has a higher electron density compared to the hydrogens atoms. Thus it is more negative.

9 modes are expected from the (3N-6) rule. The modes 1, 2 and 3 are degenerate which each other. Mode 4 and 5 are degenerate to each other. Modes 7, 8 and 9 are also degenerate to each other. Mode 6 is highly symmetrical. 2 bands are expected to see in an experimental spectrum of gaseous methane.

'''Haber-Bosch reaction energy calculation for CH4'''

C + 2H2 → CH4

E(H2)= -1.1785394 au

2*E(H2)= -2.3570788 au

E(C)= -37.77600769 au

E(CH4)= -40.5240140 au

ΔE=E(CH4)-[E(C)+2*E(H2)]= -0.39092751 au = -1026.4 kJ/mol

[[https://socratic.org/questions/what-is-the-standard-enthalpy-of-formation-of-methane-given-that-the-average-c-h]]

{| class="wikitable" border="1"
|+ Molecular orbitals of CH4
! MO 1 !! MO 2 !! MO 3!! MO 5 !! MO 6
|-
| [[File:CH4 MO1 mb7418.png|150px]] || [[File:CH4 MO2 mb7418.png|150px]] || [[File:CH4 MO3 mb7418.png|150px]]|| [[File:CH4 MO5 mb7418.png|150px]] || [[File:CH4 MO6 mb7418.png|150px]]
|-
| This MO is occupied. This MO shows contribution from a 1s orbital on the central carbon. This orbital is not involved in bonding, this is because the energy of the MO is very deep -10.16707 a.u (5dp). || This MO is occupied. This MO is the 2s orbital on carbon bonding with the 1s orbitals on all four hydrogen atoms. This is not antibonding. There is a sigma interaction, no pi interactions. || This MO is occupied. This MO is a 2px atomic orbital on the central carbon atom, bonding to all the 1s hydrogen atoms. However, hydrogen atoms 2 and 5 are in the same phase bonding to each other. This is true for hydrogens 3 and 4. In addition to this, hydrogen 2 and 5 are antibonding to 3 and 4 s orbitals. MO's 3,4 and 5 are degenerate (same energies), simply because they either have a px, py or pz interacting with the hydrogens 1s orbital.|| this MO is occupied. This MO has interactions similar to previous MO, just it uses a 2pz orbital on carbon interacting with hydrogens 1s. This MO is the HOMO, it is lower in energy than the LUMO. This is involved in bonding with sigma interactions. || This MO is the LUMO. It is higher in energy than HOMO. It is not involved in bonding because it is unoccupied. There is anti bonding interaction between the 3s orbital on the carbon to the surrounding hydrogens 1s orbitals. We see two different phases. In addition to this, the 1s orbitals on all the hydrogen are in the same phase and they have a bonding interaction. This MO is not involved in bonding.
|}

'''Independence - O2'''
{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3LYP
|-
|Basis set
|6-31G(d.p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-150.2574243</nowiki>
|-
|RMS Gradient Norm (au)
|0.00007502
|-
|Point group
|D*H
|}

O=O bond distance = 1.22Å (2 d.p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000130 0.000450 YES
RMS Force 0.000130 0.000300 YES
Maximum Displacement 0.000080 0.001800 YES
RMS Displacement 0.000113 0.001200 YES
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>O2 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MB7418 O2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MB7418 O2.LOG| here]]

[[File:Mb7418 O2 ss.png|800px]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity (arbitrary)
!Type of vibration
|-
|1
|1643
|SGG
|0
|Stretch
|}

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, overall it is good, however you didn't use the built in headings which allow the wiki to auto-generate a table of contents, this is very useful to the reader of a long wiki page with lots of data.

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, very good explanations well done. Note that MO6 is actually the antibonding counterpart to the bonding MO2.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did an extra calculation on O2 well done!

Rep:Title=Mod:mb7418introtomolecularmodel

2019-03-28T08:05:48Z

Rr1210:

'''NH3 molecule'''

{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3LYP
|-
|Basis set
|6-31G(d.p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-56.5577687</nowiki>
|-
|RMS gradient (au)
|0.00000485
|-
|Point group
|C3V
|}

N-H bond distance = 1.02Å (2 d.p)

H-N-H bond angle = 106° (0 d.p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MEHNAZ BASIR NH3 OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MEHNAZ BASIR NH3 OPTIMISED.LOG| here]]

[[File:Mehnaz basir ss NH3 display vibrations.png|800px]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity (arbitrary)
!Type of vibration
!Image of vibration
|-
|1
|1090
|A1
|145
|Bend
|[[File:Mb7418 NH3 1ss.png|150px]]
|-
|2
|1694
|E
|14
|Bend
|[[File:Mb7418 NH3 2ss.png|150px]]
|-
|3
|1694
|E
|14
|Bend
|[[File:Mb7418 NH3 3ss.png|150px]]
|-
|4
|3461
|A1
|1
|Stretch
|[[File:Mb7418 NH3 4ss.png|150px]]
|-
|5
|3590
|E
|0
|Stretch
|[[File:Mb7418 NH3 5ss.png|150px]]
|-
|6
|3590
|E
|0
|Stretch
|[[File:Mb7418 NH3 6ss.png|150px]]
|}

In the NH3 molecule, Nitrogen atom has a charge of -1.125 and all the Hydrogen atoms have a charge of 0.375. I would expect the Nitrogen atom's charge to be more negative in comparison. the reason for this is because Nitrogen is more electronegative in comparison to the Hydrogen atoms. Hence it'll have a higher electron density thus making it more negative.

6 modes are expected from the (3N-6) rule. The modes 2 and 3 are degenerate. 5 and 6 are also degenerate to each other. Modes 1, 2 and 3 are bending vibrations whilst modes 4, 5 and 6 are bond stretch vibrations. The mode which is highly symmetrical is 4. The umbrella mode is 1. 2 bands are expected to be seen in an experimental spectrum of gaseous ammonia due to there being two degenerate pairs. In addition, modes 5 and 6 have an intensity of 0.

'''N2 molecule'''
{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-109.5241287</nowiki>
|-
|RMS Gradient Norm (au)
|0.00000365
|-
|Point Group
|D*H
|}

N≡N bond distance = 1.11Å (2 d.p)

N2 is a linear molecule.

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000002 0.001800 YES
RMS Displacement 0.000003 0.001200 YES
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>N2 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MEHNAZ BASIR N2 OPTIMISED.txt</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MEHNAZ BASIR N2 OPTIMISED.txt| here]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity (arbitrary)
|-
|1
|2457
|SGG
|0
|}

[[File:Mb7418 n2 ss.png|800px]]

Both Nitrogen molecules have no charge. The reason for this is because they are the same element, hence they have the same electronegativities. So the molecule is non polar as the charge is distributed evenly along both atoms.

'''H2 molecule'''

{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3YLB
|-
|Basis set
|6-31G(d.p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-1.1785394</nowiki>
|-
|RMS Gradient Norm (au)
|0.00000017
|-
|Point Group
|D*H
|}

H-H bond distance = 0.74Å (2 d.p)

<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
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>H2 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MEHNAZ BASIR H2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MEHNAZ BASIR H2.LOG| here]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity
|-
|1
|4466
|SGG
|0
|}

[[File:Mb7418 h2 ss.png|800px]]

Both Hydrogen atoms have a charge distribution of 0. This shows it's a non polar molecular as it has no difference in charge.

'''Structure and reactivity of H2'''

Unique identifier = CEFCAS

[[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=ACIEF5&year=2005&spage=7227&volume=44&id=doi:10.1002/anie.200502297&pid=ccdc:275803]]
{| class="wikitable"
!Molecule
!H-H bond (Å)
|-
|H2
|0.74
|-
|CEFCAS
|1.48
|}
The H-H bond in the H2 molecule is shorter compared to the H-H bond in the metal complex. The reason for this is because the hydrogen atom is bonded to both the transition metal and another hydrogen. The bond density in the H-H bond becomes smaller compared to the bond density in the H-TM (TM = transition metal) bond. This causes the H-H bond to become longer. In addition, the bonds may be different due to computational errors. This can be fixed by using a different method.

'''Haber-Bosch reaction energy calculation for NH3'''

E(NH3)= -56.5577687 au

2*E(NH3)= -113.1155374 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356182 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557905 au = -146.5(1 d.p) kJ/mol

The exothermic reaction is favoured. The forward reaction is exothermic. Hence there will be a higher production of ammonia in this reaction because ammonia is more stable.

'''CH4 molecule'''
{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3LYP
|-
|Basis set
|6-31G(d.p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-40.5240140</nowiki>
|-
|RMS Gradient Norm (au)
|0.00003263
|-
|Point Group
|TD
|}

C-H bond distance = 1.07Å (2 d.p)

H-C-H bond angle = 109° (0 d.p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>CH4 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MEHNAZ BASIR CH4.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MEHNAZ BASIR CH4.LOG| here]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity (arbitrary)
!Type of vibration
!Image of vibration
|-
|1
|1356
|T2
|14
|Bend
|[[File:Mb7418 CH4 1.png|150px]]
|-
|2
|1356
|T2
|14
|Bend
|[[File:Mb7418 CH4 2.png|150px]]
|-
|3
|1356
|T2
|14
|Bend
|[[File:Mb7418 CH4 3.png|150px]]
|-
|4
|1579
|E
|0
|Bend
|[[File:Mb7418 CH4 4.png|150px]]
|-
|5
|1579
|E
|0
|Bend
|[[File:Mb7418 CH4 5.png|150px]]
|-
|6
|3046
|A1
|0
|Stretch
|[[File:Mb7418 CH4 6.png|150px]]
|-
|7
|3162
|T2
|25
|Stretch
|[[File:Mb7418 CH4 7.png|150px]]
|-
|8
|3162
|T2
|25
|Stretch
|[[File:Mb7418 CH4 8.png|150px]]
|-
|9
|3162
|T2
|25
|Stretch
|[[File:Mb7418 CH4 9.png|150px]]
|}

The carbon atom has a charge distribution of -0.930 and all the hydrogen atoms have a charge distribution of 0.233. The reason why the carbon atom is more negative is because it has a higher electronegative value compared to hydrogen. hence the electrons in the carbon-hydrogen bond will be more attracted to the carbon. Therefore, the carbon atom has a higher electron density compared to the hydrogens atoms. Thus it is more negative.

9 modes are expected from the (3N-6) rule. The modes 1, 2 and 3 are degenerate which each other. Mode 4 and 5 are degenerate to each other. Modes 7, 8 and 9 are also degenerate to each other. Mode 6 is highly symmetrical. 2 bands are expected to see in an experimental spectrum of gaseous methane.

'''Haber-Bosch reaction energy calculation for CH4'''

C + 2H2 → CH4

E(H2)= -1.1785394 au

2*E(H2)= -2.3570788 au

E(C)= -37.77600769 au

E(CH4)= -40.5240140 au

ΔE=E(CH4)-[E(C)+2*E(H2)]= -0.39092751 au = -1026.4 kJ/mol

[[https://socratic.org/questions/what-is-the-standard-enthalpy-of-formation-of-methane-given-that-the-average-c-h]]

{| class="wikitable" border="1"
|+ Molecular orbitals of CH4
! MO 1 !! MO 2 !! MO 3!! MO 5 !! MO 6
|-
| [[File:CH4 MO1 mb7418.png|150px]] || [[File:CH4 MO2 mb7418.png|150px]] || [[File:CH4 MO3 mb7418.png|150px]]|| [[File:CH4 MO5 mb7418.png|150px]] || [[File:CH4 MO6 mb7418.png|150px]]
|-
| This MO is occupied. This MO shows contribution from a 1s orbital on the central carbon. This orbital is not involved in bonding, this is because the energy of the MO is very deep -10.16707 a.u (5dp). || This MO is occupied. This MO is the 2s orbital on carbon bonding with the 1s orbitals on all four hydrogen atoms. This is not antibonding. There is a sigma interaction, no pi interactions. || This MO is occupied. This MO is a 2px atomic orbital on the central carbon atom, bonding to all the 1s hydrogen atoms. However, hydrogen atoms 2 and 5 are in the same phase bonding to each other. This is true for hydrogens 3 and 4. In addition to this, hydrogen 2 and 5 are antibonding to 3 and 4 s orbitals. MO's 3,4 and 5 are degenerate (same energies), simply because they either have a px, py or pz interacting with the hydrogens 1s orbital.|| this MO is occupied. This MO has interactions similar to previous MO, just it uses a 2pz orbital on carbon interacting with hydrogens 1s. This MO is the HOMO, it is lower in energy than the LUMO. This is involved in bonding with sigma interactions. || This MO is the LUMO. It is higher in energy than HOMO. It is not involved in bonding because it is unoccupied. There is anti bonding interaction between the 3s orbital on the carbon to the surrounding hydrogens 1s orbitals. We see two different phases. In addition to this, the 1s orbitals on all the hydrogen are in the same phase and they have a bonding interaction. This MO is not involved in bonding.
|}

'''Independence - O2'''
{| class="wikitable"
!Key information
!
|-
|Calculation method
|RB3LYP
|-
|Basis set
|6-31G(d.p)
|-
|Final energy, E(RB3LYP) (au)
|<nowiki>-150.2574243</nowiki>
|-
|RMS Gradient Norm (au)
|0.00007502
|-
|Point group
|D*H
|}

O=O bond distance = 1.22Å (2 d.p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000130 0.000450 YES
RMS Force 0.000130 0.000300 YES
Maximum Displacement 0.000080 0.001800 YES
RMS Displacement 0.000113 0.001200 YES
</pre>

'''Project molecule'''

<jmol><jmolApplet><script>frame x.y</script>
<title>O2 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MB7418 O2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:MB7418 O2.LOG| here]]

[[File:Mb7418 O2 ss.png|800px]]

{| class="wikitable"
!Mode
!Wavenumber (cm-1)
!Symmetry
!Intensity (arbitrary)
!Type of vibration
|-
|1
|1643
|SGG
|0
|Stretch
|}

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, overall it is good, however you didn't use the built in headings which allow the wiki to auto-generate a table of contents, this is very useful to the reader of a long wiki page with lots of data.

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, very good explanations well done. Note that MO6 is actually the antibonding counterpart to the bonding MO2.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did an extra calculation on O2 well done!

Rep:Mod:IAB

2019-03-28T07:59:10Z

Rr1210:

= Ignacy Bartnik's Wiki Page =

== NH3 Molecule ==

=== Results of Gaussian calculations ===
{| class="wikitable"
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-56.5577687 a.u.</nowiki>
|-
|RMS Gradient Norm
|0.00000485 a.u.
|-
|Point Group
|C3V
|-
|N-H bond length
|1.02 Å
|-
|H-N-H bond angle
|106°
|}

==== Final results table from .log file ====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986274D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

==== .log File of NH3 Molecule ====
[[File:IAB18_NH3_OPTIMISATION.LOG]]

==== Interactive model of NH3 Molecule ====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IAB18_NH3_OPTIMISATION.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

=== NH3 Vibrations ===

==== Screen Shot of calculated Vibrations ====
[[File:IAB_NH3_Vibrations_screen.png]]

==== Calculated Vibrations of NH3 ====
{| class="wikitable"
|'''Mode'''
|1
|2
|3
|4
|5
|6
|-
|'''wavenumber''' 
cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|'''symmetry'''
|A1
|E
|E
|A1
|E
|E
|-
|'''intensity''' 
arbitrary units
|145
|14
|14
|1
|0
|0
|-
|'''image'''
|[[File:IAB NH3 image1.png|120px]]
|[[File:IAB NH3 image2.png|120px]]
|[[File:IAB NH3 image3.png|120px]]
|[[File:IAB NH3 image4.png|120px]]
|[[File:IAB NH3 image5.png|120px]]
|[[File:IAB NH3 image6.png|120px]]
|}

Modes 2 and 3 are degenerated with respect to each other and modes 5 and 6 are also degenerated with respect to each other.
6 modes of vibrations would be expected of NH3 using the 3N-6 rule and indeed 6 modes were calculated.
Modes 1, 2, and 3 are bending vibration modes, while modes 4, 5, and 6 and bond stretching vibration modes.
Mode 4 is highly symmetric.
2 bands would be expected in an IR spectrum, corresponding to absoptions for 1 and 2 & 3. 2 & 3 would be indistinguishable as they are degenerate, vibrational mode 4 does not have a change in dipole, so it would not be visible in an IR spectrum and mode 5 & 6 have a very low intensity so they could be seen in a very delicate spectrometer but most of the time, they too would be undetectable.
Vibration mode 1 is the so called umbrella motion vibration.

==== Charge Distribution of NH3 ====
{| class="wikitable"
!Atom
!N
!H
|-
|Charge (elementary charge)
|<nowiki>-1.125</nowiki>
|0.375
|}
It would be expected for the nitrogen to have a negative charge and hydrogen to have a partial positve charge as the nitrogen is more electronegative and indeed, this is also found in the calculations.

== N2 Molecule ==

=== Results of Gaussian calculations ===
{| class="wikitable"
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-109.5241287 a.u.</nowiki>
|-
|RMS Gradient Norm
|0.00000060 a.u.
|-
|Point Group
|D*H
|-
|N-N bond length
|1.11 Å
|-
|N-N bond angle
|180°
|}

==== Final results table from .log file ====
<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=-3.401096D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

==== .log File of N2 Molecule ====
[[File:IAB18_N2_OPTIMISATION.LOG]]

==== Interactive model of N2 Molecule ====
<jmol><jmolApplet>
<title>N2 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IAB18_N2_OPTIMISATION.LOG</uploadedFileContents>
<script>frame 1.11</script>
</jmolApplet></jmol>

=== N2 Vibrations ===

==== Screen Shot of calculated Vibrations ====
[[File:IAB_N2_Vibrations_screen.png]]

==== Calculated Vibrations of N2 ====
{| class="wikitable"
|'''Mode'''
|1
|-
|'''wavenumber''' 
cm-1
|2457
|-
|'''symmetry'''
|SGG
|-
|'''intensity''' 
arbitrary units
|0
|-
|'''image'''
|[[File:IAb N2 image1.png|200px]]
|}

For the N2 molecule, only 1 mode of vibration would be expected from the 3N-5 rule (not 3N-6 as it is a linear molecule), and indeed only 1 vibrational mode is predicted by the calculations. Since there is only one mode, there is no degeneracy possible. The one mode is a bond stretch vibration. It would not be IR active as it does not change the dipole of the molecule, so N2 would not be visible in an IR spectrum.

====== Charge Distribution of N2 ======
{| class="wikitable"
!Atom
!N
|-
|Charge (elementary charge)
|<nowiki>0</nowiki>
|}

It would be expected that there is equal charge distribution over the whole N2 molecule as it is a elementary diatomic molecule, meaning it is purely covalent and both the nitrogens are identical in their electronegativity. Therefore, their electron attraction cancels each other out completely. This is also what was calculated, resulting in no charge on the individual atoms and no dipole.

== H2 Molecule ==

=== Results of Gaussian calculations ===
{| class="wikitable"
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-1.1785394 a.u.</nowiki>
|-
|RMS Gradient Norm
|0.00000017 a.u.
|-
|Point Group
|D*H
|-
|H-H bond length
|0.74 Å
|-
|H-H bond angle
|180°
|}

==== Final results table from .log file ====
<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
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

==== .log File of H2 Molecule ====
[[File:IAB18_H2_OPTIMISATION.LOG]]

==== Interactive model of H2 Molecule ====
<jmol><jmolApplet>
<title>H2 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>H2struvcture.xyz</uploadedFileContents>
</jmolApplet></jmol>

=== H2 Vibrations ===

==== Screen Shot of calculated Vibrations ====
[[File:IAB_H2_Vibrations_screen.png]]

==== Calculated Vibrations of H2 ====
{| class="wikitable"
|'''Mode'''
|1
|-
|'''wavenumber''' 
cm-1
|4466
|-
|'''symmetry'''
|SGG
|-
|'''intensity''' 
arbitrary units
|0
|-
|'''image'''
|[[File:IAB H2 image1.png|200px]]
|}

For the H2 molecule, only 1 mode of vibration would be expected from the 3N-5 rule (not 3N-6 as it is a linear molecule), and indeed only 1 vibrational mode is predicted by the calculations. Since there is only one mode, there is no degeneracy possible. The one mode is a bond stretch vibration. It would not be IR active as it does not change the dipole of the molecule, so H2 would not be visible in an IR spectrum. In this aspect the H2 molecule is very similar to the N2 molecule.

====== Charge Distribution of H2 ======
{| class="wikitable"
!Atom
!H
|-
|Charge (elementary charge)
|<nowiki>0</nowiki>
|}

It would be expected that there is equal charge distribution over the whole H2 molecule as it is a elementary diatomic molecule, meaning it is purely covalent and both the hydrogens are identical in their electronegativity. Therefore, their electron attraction cancels each other out completely. This is also what was calculated, resulting in no charge on the individual atoms and no dipole.

== Bond Length of N2 in mono-metallic transition metal complex ==

<jmol><jmolApplet>
<title>Interactive model of MABVER Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MABVER.sd</uploadedFileContents>

</jmolApplet></jmol>
<ref name="LazyDog" />

{| class="wikitable"
!Complex
!N-N bond length(Å)
|-
|MABVER
|<nowiki>1.08</nowiki><ref name="LazyDog" />
|}

The transition metal complex with N2 can be found here [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=MABVER&DatabaseToSearch=Published]

The bond length of the N2 in the MABVER complex is shorter than the calculated bond length of N2 . This is not expected as the N2 would donate some of its electrons from its bonding orbitals to the metal (as it has none in non-bonding orbitals), and then there would be some overlap of its non bonding orbitals and the metal electrons orbitals, so the N2 bond should be weaker resulting in a longer bond. However, this is not necessarily true, and it is possible that if the whole complex and not just N2 was calculated, the same bond length would be found. Even if it was not, this can still be explained by the fact that a simplified theory is being used to reduce compute time, and it also does not incorporate packing effects, which could well result in a shorter bond length as well.

==Calculating the energy of Haber Bosch Process==

{| class="wikitable"
!
!E(NH3)
!2*E(NH3)
!E(N2)
!E(H2)
!3*E(H2)
!ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=
|-
|Energy (au)
|<nowiki>-56.5577687</nowiki>
|<nowiki>-113.1155375</nowiki>
|<nowiki>-109.5241287</nowiki>
|<nowiki>-1.1785394</nowiki>
|<nowiki>-3.5356181</nowiki>
|<nowiki>-0.0557907</nowiki>
|-
|Energy (kJ mol -1)
|<nowiki>-148492.4</nowiki>
|<nowiki>-296984.8</nowiki>
|<nowiki>-287555.6</nowiki>
|<nowiki>-3094.3</nowiki>
|<nowiki>-9282.8</nowiki>
|<nowiki>-146.5</nowiki>
|}

In terms of energy, N2 is most stable, NH3 is less stable and H2 is least stable. Even though N2 is very stable, the reaction of 3H2 + N2 → 2NH3 is energetically favorable, as NH3 is also quite stable and H2 has a reltively low stability.

== CN- Molecule ==

=== Results of Gaussian calculations ===
{| class="wikitable"
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-92.8245315 a.u.</nowiki>
|-
|RMS Gradient Norm
|0.00000704 a.u.
|-
|Point Group
|CinfV
|-
|C-N bond length
|1.18 Å
|-
|C-N bond angle
|180°
|}

==== Final results table from .log file ====
<pre>

Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000005 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-6.650397D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1841 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

==== .log File of CN- Molecule ====
[[File:IAB18 CN- OPTIMISATION.LOG]]

==== Interactive model of CN- Molecule ====
<jmol><jmolApplet>
<title>CN- molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IAB18 CN- OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== CN- Vibrations ===

==== Screen Shot of calculated Vibrations ====
[[IMAGE:IAB CN- Vibrations screen.png]]

==== Calculated Vibrations of CN- ====
{| class="wikitable"
|'''Mode'''
|1
|-
|'''wavenumber''' 
cm-1
|2139
|-
|'''symmetry'''
|SG
|-
|'''intensity''' 
arbitrary units
|8
|-
|'''image'''
|[[File:IAB CN- image1.png|200px]]
|}

For the CN- molecule, only 1 mode of vibration would be expected from the 3N-5 rule (not 3N-6 as it is a linear molecule), and indeed only 1 vibrational mode is predicted by the calculations. Since there is only one mode, there is no degeneracy possible. The one mode is a bond stretch vibration. Unlike the other diatomics analysed on this wiki page, the CN- would be IR active as it does change its dipole of the molecule with the vibration, as it has an overall dipole and the distance between the charges changes as it vibrates.

====== Charge Distribution of CN- ======
{| class="wikitable"
!Atom
!C
!N
|-
|Charge (elementary charge)
|<nowiki>-0.246</nowiki>
|<nowiki>-0.754</nowiki>
|}

It would be expected that there is an unequal charge distribution that is overall negative for the CN- molecule as it is a simple diatomic with a negative charge. Indeed, the calculations show that both the nitrogen and carbon have negative charges, with the nitrogen having more of the negative charge, which again agrees with expectations as nitrogen is more electronegative and more electron rich, starting in its elemental state with a lone pair.

=== MOs of CN- ===

{| class="wikitable"
|'''Arbitrary MO number'''
|1
|2
|3
|4
|5
|-
|'''image'''
|[[File:IAB CN- MO image1.png|300px]]
|[[File:IAB CN- MO image2.png|300px]]
|[[File:IAB CN- MO image3.png|300px]]
|[[File:IAB CN- MO image4.png|300px]]
|[[File:IAB CN- MO image5.png|300px]]
|-
|'''MO number as seen in gaussian'''
|1
|6
|7
|8
|10
|-
|'''Energy''' 
au
|<nowiki>-14.00393</nowiki>
|<nowiki>-0.01696</nowiki>
|<nowiki>0.01857</nowiki>
|<nowiki>0.35435</nowiki>
|<nowiki>0.59206</nowiki>
|-
|'''Occupied?'''
|Occupied
|Occupied
|Occupied
|Unoccupied
|Unoccupied
|-
|'''Bonding?''' 
|Bonding
|Bonding
|Bonding
|Anti bonding
|Anti bonding
|-
|'''AO contribution''' 
|According to a traditional MO diagram, this orbital consists of 1s AOs of C and N combinding to make a σ bonding orbital, but gaussian predicts that this will be practically just the 1s nitrogen AO which is also what it displays in the image.
|According to a traditional MO diagram, this orbital consists of 2p AOs of C and N combinding to make a π bonding orbital. According to the calculations,2px orbitals of both the N and C are the major contributors while the 3px also play a role. The other AOs do not play a relevant role. Both C and N contribute more or less equally.
|According to a traditional MO diagram, this orbital consists of 2p AOs of C and N combinding to make a σ bonding orbital. According to the calculations, the major positively contributing AOs are the 3s orbital from the carbon and the 2pz from the nitrogen. The negative contributers are the carbon 3pz and 2pz.
|According to a traditional MO diagram, this orbital consists of 2p AOs of C and N combinding to make a π* anti-bonding orbital. According to the calculations,3py orbitals of both the N and C are the major contributors while the 2py also play a role. The other AOs do not play a relevant role. Both C and N contribute equally.
|According to a traditional MO diagram, this orbital consists of 2p AOs of C and N combinding to make a σ* anti-bonding orbital. According to the calculations, the nitrogen 3s orbital has a large positive contribution while the carbon 3s has an equal but negative contribution and then, the C 3pz also has a large negative contribution. This is very interesting as for the 4th MO, the traditional understanding fit very well with the calculations, while here it does not. This is probably partly due to the "traditional understanding" being referenced being quite simplistic and also, gaussian not being as reliable in calculating energetically high unoccupied MOs.
|-
|'''General comment?''' 
|This is an orbital that is increadibly deep in energy and will therefore being practically completely inert. Nitrogen is more electronegative, so it makes sense that it will be the major contributor to the MO, although it is suprising to see just how much of the MO is due to the N and how little the C contributes.
|This orbital is one level below the HOMO, so it is not as relevant for reactions, but could still concievable affect them. It is bonding and occupied, so it contributes to the bonding. It is well predicted by a traditional MO diagram, with the 2p orbitals being the largest contributing AOs. It is also degenerate with what gaussian would call MO 5, as that one is just shifted by 90° as it is made of px orbitals instead of py.
|This is a very relevant orbital as it is the HOMO. It is occupied and bonding so it adds to the C-N bond. It is quite high in energy, and accessible, so it will participate in reactions whenever the molecule acts as a nucleophile. This is the orbital that will "attack" the LUMO of whatever it is reacting with. It is worthy to note that this σ orbital is higher in energy than the corresponding π orbitals, which only happens for atoms with low atomic numbers (the π/σ switch occurs for only a few compounds).
|This is an unoccupied bond so it does not play a role in the bond of the molecule. However, it is the LUMO, degenerate with what gaussian labeled MO number 9, which is the other π* anti-bonding orbital. That one was not included as it is the same, just shifted 90° as it is made of px orbitals instead of py. Both of these orbitals might seem quite important, as being the LUMO, they will take part in reactions where CN- acts as an electrophile, but CN- rarely acts as an electrophile, so they are not as important. It is interesting that the 3p orbitals contribute more than the 2p orbitals. This is further evidence for it being unoccupied and being quite high in energy.
|This is an unoccupied bond so it does not play a role in the bond of the molecule. Additionally, there are two other energetically lower unoccupied orbital, so it is also unlikely to take part in things lewis acid base reactions, as there the LUMO orbital will be more relevant.
|-
|}

=== Independence Mark: CN- bond length ===

For my independece mark, I decided to investigate the literature value of CN- bond lengths, but because it is an ion, I decided to look at it bonded in a transition metal complex. I looked at 3 different complexes, taken from here [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=AVARUM&DatabaseToSearch=Published] [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEHMIP&DatabaseToSearch=Published] [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=FILDEL01&DatabaseToSearch=Published]

<jmol><jmolApplet>
<title>Interactive model of AVARUM Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>AVARUM.mol2</uploadedFileContents>

</jmolApplet></jmol>
<ref name="LazyDog2" />

<jmol><jmolApplet>
<title>Interactive model of DEHMIP Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DEHMIP.mol2</uploadedFileContents>

</jmolApplet></jmol>
<ref name="LazyDog3" />

<jmol><jmolApplet>
<title>Interactive model of FILDEL01 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>FILDEL01.mol2</uploadedFileContents>

</jmolApplet></jmol>
<ref name="LazyDog4" />

{| class="wikitable"
!Complex
!Average C-N bond length(Å)
|-
|AVARUM
|<nowiki>1.12</nowiki><ref name="LazyDog2" />
|-
|DEHMIP
|<nowiki>1.15</nowiki><ref name="LazyDog3" />
|-
|FILDEL01
|<nowiki>1.14</nowiki><ref name="LazyDog4" />
|-
|}

All of these bond lengths are shorter than the 1.18 Å bond length calculated in gaussian for the ion in a vacuum. This is again, similar to what was observed for the N2 molecule. CN- and N2 are isoelectronic and have all their electrons in bonding orbitals, so when they bond to something else, like in the transition metal complexes, their bond should become weaker and therefore longer, however the opposite is observed in the examples shown above. It is impossible to tell if this is due to too many approximations in the calculation made with gaussian, or if it due to the packing effects from just this information. However, a literature value was found to be 1.14 Å <ref name="LazyDog5" />, suggesting that it is not the packing effects that make the bond length shorted in the transition metal complexes, but that it is the gaussian calculations which wrongly predict a longer bond than is found in nature. The fact that gaussian, with the method of calculation that was used, does not meet reality exactly, should not be suprising as it is a computationally much simplified method, again, to enable performing it on a regular PC by students, and requiring hours and days of CPU time. If a different method of calculations was used, it well maybe that the correct bond length would be calculated, but then students would not be able to perform these calculations on regular PCs.

<references>
<ref name="LazyDog"> S.M.P.R.M.Cunha, M.F.C.G.da Silva, A.J.L.Pombeiro, Inorganic Chemistry, 2003, 42, 2157, DOI: 10.1021/ic026176e </ref>

<ref name="LazyDog2"> Zong-xin Pi, Jian-Hong Bi, Hua-Ze Dong, Asian Journal of Chemistry, 2015, 27, 2729, DOI: 10.14233/ajchem.2015.17812 </ref>

<ref name="LazyDog3"> Maria-Gabriela Alexandru, Diana Visinescu, Sergiu Shova, Francesc Lloret, Miguel Julve, Inorganic Chemistry, 2017, 56, 12594, DOI: 10.1021/acs.inorgchem.7b02050 </ref>

<ref name="LazyDog4"> Mohammed A. Abbas, Colin D. McMillen, Julia L. Brumaghim, Inorganica Chimica Acta, 2017, 468, 308, DOI: 10.1016/j.ica.2017.07.003 </ref>

<ref name="LazyDog5"> F. H. Allen, O. Kennard, D. G. Watson, L. Brammer, A. G. Orpen. Tables of bond Lengths determined by X-Ray and Neutron Diffraction. Part 1. Bond Lengths in Organic Compounds. J. Chem. Soc. Perkin Trans. II 1987, S1-S19. </ref>

</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, good explanations and sentence structure well done!

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES, you lost the half mark for giving the bond angle - invalid for a diatomic.

Have you added information about MOs and charges on atoms?

YES, good job on the MO analysis, very detailed explanations! On MO 1 there is not much C contribution because MO 2 contains the C 1s, the AOs are too localised to interact and forming a bonding anti-bonding pair so instead you get two MOs, each with just one AO.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You looked up some crystal structures and analysed the different C-N bond lengths, well done!

Rep:Mod:XS2218

2019-03-24T18:58:40Z

Rr1210:

=='''NH3 Molecule'''==
===''Summary information''===

'''Molecular Name''':NH3

'''Calculation Method''':RB3LYP

'''Basis Set''':6-31G(d,p)

'''Final Energy E(RB3LYP)''':-56.55776873 a.u.

'''RMS Gradient Norm''':0.00000485 a.u.

'''Point group''':C3V

===''Optimisatio''n===
<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986282D-10
Optimization completed.
-- Stationary point found.</pre>

<jmol><jmolApplet>
<script>frame 1.16</script>
<title>optimised NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>XS2218_PHUNT_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''N-H Bond distance''':1.02Å

'''H-N-H Bond angle''':106°

The optimisation file is liked to [[Media:XS2219_PHUNT_NH3_OPTF_POP.LOG| here]]

===''Vibration''s===
====Vibration Displays====
[[File:XS2218_VIBRATION_Screenshot.png‎]]

====Vibration Table====
{|class="wikitable" border=1
| style="text-align: center;"|'''wavenumber'''/cm-1 || style="text-align: center;"|1090|| style="text-align: center;"|1694|| style="text-align: center;"|3462|| style="text-align: center;"|3590
|-
| style="text-align: center;"|'''Symmetry'''
| style="text-align: center;"|A1
| style="text-align: center;"|E
| style="text-align: center;"|A1
| style="text-align: center;"|E
|-
| style="text-align: center;"|'''Intensity'''/a.u.
| style="text-align: center;"|145
| style="text-align: center;"|14
| style="text-align: center;"|1
| style="text-align: center;"|0
|-
| style="text-align: center;"|'''Image'''
|[[File:XS2218_vibration_Screenshot_(2).png]]
|[[File:XS2218_vibration_Screenshot_(3).png]]
|[[File:xs2218_vibration_nh3_Screenshot_(34).png]]
|[[File:xs2218_vibration_nh3_Screenshot_(35).png]]
|}

====Questions====
how many modes do you expect from the 3N-6 rule? '''''6'''''

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

which modes are "bending" vibrations and which are "bond stretch" vibrations? '''''bending:1,2,3 bond stretch;4,5,6'''''

which mode is highly symmetric? '''''4'''''

one mode is known as the "umbrella" mode, which one is this? '''''1'''''

how many bands would you expect to see in an experimental spectrum of gaseous ammonia? '''''2'''''

===''Atomic Charges''===
'''N''':-1.123

'''H''':0.375

''We would expect N to be negatively charged as N is more electronegative, it draws electrons on H towards itself and H is expected to be positively charged.
''

=='''N2 Molecule'''==
===''Summary information''===

'''Molecular Name''':N2

'''Calculation Method''':RB3LYP

'''Basis Set''':6-31G(d,p)

'''Final Energy E(RB3LYP)''':-109.52412868 a.u.

'''RMS Gradient Norm''':0.00000060

'''Point group''':D*H

===''Optimisatio''n===
<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=-3.400985D-13
Optimization completed.
-- Stationary point found. </pre>

<jmol><jmolApplet>
<script>frame 1.10</script>
<title>optimised N2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>XS2218_PHUNT_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''N-N Bond distance''':1.11Å

'''N-N Bond angle''':180°

The optimisation file is liked to [[Media:XS2218_PHUNT_N2_OPTF_POP.LOG| here]]

===''Vibrations''===
====Vibration Displays====
[[File:xs2218_vibration_n2_Screenshot_(4).png‎]]

====Vibration Table====
{|class="wikitable" border=1
| style="text-align: center;"|'''wavenumber'''/cm-1 || style="text-align: center;"|2457
|-
| style="text-align: center;"|'''Symmetry'''
| style="text-align: center;"|SGG
|-
| style="text-align: center;"|'''Intensity'''/a.u.
| style="text-align: center;"|0
|-
| style="text-align: center;"|'''Image'''
|[[File:xs2218_vibration_n2_Screenshot_(5).png]]
|}

===''Atomic Charges''===
'''N1''':0

'''N1''':0

''We would expect both N to be neutral as they have the same electronegativity.''

=='''H2 Molecule'''==
===''Summary informatio''n===

'''Molecular Name''':H2

'''Calculation Method''':RB3LYP

'''Basis Set''':6-31G(d,p)

'''Final Energy E(RB3LYP)''':-1.17853936 a.u.

'''RMS Gradient Nomr''':0.00000017 a.u.

'''Point group''':D*H

===''Optimisation''===
<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
Optimization completed.
-- Stationary point found.</pre>

<jmol><jmolApplet>
<script>frame 1.12</script>
<title>optimised H2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>XS2219_PHUNT_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''N-N Bond distance''':0.74 Å

'''N-N Bond angle''':180°

The optimisation file is liked to [[Media:XS2219_PHUNT_H2_OPTF_POP.LOG| here]]

===''Vibrations''===
====Vibration Displays====
[[File:xs2218_vibration_h2_Screenshot_(6).png‎]]

====Vibration Table====
{|class="wikitable" border=1
| style="text-align: center;"|'''wavenumber'''/cm-1 || style="text-align: center;"|4466
|-
| style="text-align: center;"|'''Symmetry'''
| style="text-align: center;"|SGG
|-
| style="text-align: center;"|'''Intensity'''/a.u.
| style="text-align: center;"|0
|-
| style="text-align: center;"|'''Image'''
|[[File:xs2218_vibration_h2_Screenshot_(7).png]]
|}

===''Atomic Charges''===
'''H1''':0

'''h1''':0

''We would expect both h to be neutral as they have the same electronegativity.''

==Mono-metallic TM complex==
'''Refcode''': DOFBUX

'''Compound name''':(1,3-bis((Di-t-butylphosphino)methyl)-2,3-dihydro-1H-1,3,2-benzodiazaborole)-dinitrogen-cobalt

'''Link''':[https://www.ccdc.cam.ac.uk/structures/Search?Compound=(1,3-bis((Di-t-butylphosphino)methyl)-2,3-dihydro-1H-1,3,2-benzodiazaborole)-dinitrogen-cobalt&DatabaseToSearch=Published]

'''N-N bond distance''':1.12 Å

''The N-N bond distance in this crystal structure is different from the computational distance,it is slightly longer. This is because the computational distance is obtained from an optimised N2 structure which has the lowest energy, whereas in the crystal structure, the N-N is next to Co which is electropositive so it pushes the electrons to the N, electron-repulsion causes the bond to become longer.
''

==Habor-Bosch Process==

'''''N2 + 3H2 -> 2NH3'''''

E(NH3)=-56.5577687 a.u.

2*E(NH3)=-113.1155374 a.u.

E(N2)=-109.5241287 a.u.

E(H2)=-1.1785394 a.u.

3*E(H2)= -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -146.5 kJ/mol

''The ammonia product is more stable than the gaseous reactants, this is an exothermic reaction''

=='''CO Molecule'''==
===''Summary information''===

'''Molecular Name''':CO

'''Calculation Method''':RB3LYP

'''Basis Set''':6-31G(d,p)

'''Final Energy E(RB3LYP)''':-113.30945314 a.u.

'''RMS Gradient Norm''':0.00001828 a.u.

'''Point group''':C*V

===''Optimisation''===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000018 0.001200 YES
Predicted change in Energy=-3.956716D-10
Optimization completed.
-- Stationary point found.
</pre>

<jmol><jmolApplet>
<script>frame 1.10</script>
<title>optimised CO</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>XS2218_PHUNT_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''CO Bond distance''':1.14Å

'''CO Bond angle''':180°

The optimisation file is liked to [[Media:XS2218_PHUNT_CO_OPTF_POP.LOG| here]]

===''Vibrations''===
====Vibration Displays====
[[File:xs2218_vibrationdisplay_co_Screenshot_(28).png ]]

====Vibration Table====
{|class="wikitable" border=1
| style="text-align: center;"|'''wavenumber'''/cm-1 || style="text-align: center;"|2209
|-
| style="text-align: center;"|'''Symmetry'''
| style="text-align: center;"|SSG
|-
| style="text-align: center;"|'''Intensity'''/a.u.
| style="text-align: center;"|68
|-
| style="text-align: center;"|'''Image'''
|[[File:xs2218_vibration_co_Screenshot_(27).png]]
|}

''1 band is expected to see on the spectrum.''

===''Atomic Charges''===
'''C''':0.506

'''O''':-0.506

''We would expect O to be negatively charged as O is more electronegative, it draws electrons on C towards itself and so C is expected to be positively charged.
''

===''Molecular Orbitals''===
[[File:xs2218_mo_co_Screenshot_(29).png]]
This is the LUMO, 1π* anti-bonding orbital. 2p AOs on C and O contribute to this MO.

[[File:xs2218_mo_co_Screenshot_(30).png]]
This is the HOMO. It is a mixture of 2s and 2p AOs and occupied by 2 electrons.

[[File:xs2218_mo_co_Screenshot_(31).png]]
This is the 1π bonding orbital, 4 electrons from 2p orbitals on C and O contribute to this MO. It is slightly deeper in energy than HOMO.

[[File:xs2218_mo_co_Screenshot_(32).png]]
This is the 4σ orbital. It is a mixture of 2s and 2p AOs and occupied by 2 electrons. It is also quite deep in energy.

[[File:xs2218_mo_co_Screenshot_(33).png]]
This is the 3σ bonding orbital. 2 electrons from 2s orbitals on C and O contribute to this MO. It is deep in energy.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 3/5 ==

Have you completed the calculation and included all relevant information?

YES, you gave a bond angle which is invalid for a diatomic however.

Have you added information about MOs and charges on atoms?

YES, the information is present and you have done some correct analysis well done! To improve you could have written more detail in your MO explanations. For example explaining the impact of each MO on the overall bonding in the molecule, e.g. the LUMO has no effect even though it is antibonding because it is unoccupied.

== Independence 0/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

Rep:Mod:01576020dp3618

2019-03-24T18:53:39Z

Rr1210:

==Introduction==
Gaussian was used to optimize the structures of several molecules using the RB3LYP calculation method and the 6-31G(d,p) basis set. Another calculation method was also used to explore its effects on the obtained results. The findings are discussed below. NH3, N2, H2, CO and SF4 were studied using the aforementioned program. Molecular orbitals of the latter molecule were also studied and discussed. Comparison to other studies of these molecules can also be found below.

==NH3 molecule==
===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || NH3
|-
| File name || dp3618_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 || 0.00000485 a.u.
|-
| Dipole Moment || 1.8466 Debye
|-
| Point group || C3V
|}

N-H bond lengths: 1.02 Å

H-N-H bond angles: 106°

"Item" table:
<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986275D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>DP3618 NH3 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 NH3 OPTF POP.LOG| here]]

===Vibrational analysis===

[[File: DP3618 screenshot DisplayVibrations.png]]

{| class="wikitable" border="1"
|+ Vibrational modes of the NH3 molecule
! !! Vibration 1 !! Vibration 2 !! Vibration 3 !! Vibration 4 !! Vibration 5 !! Vibration 6
|-
| '''Wavenumber''' [cm-1] || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''IR Intensity''' || 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image''' || [[File: DP3618 screenshot vibration1.png|200 px]] || [[File: DP3618 screenshot vibration2.png|200 px]] || [[File: DP3618 screenshot vibration3.png|200 px]] || [[File: DP3618 screenshot vibration4.png|200 px]] || [[File: DP3618 screenshot vibration5.png|200 px]] || [[File: DP3618 screenshot vibration6.png|200 px]]
|-
|}

There are 3N-6 expected vibrational modes in a non-linear molecule. Since our molecule consists of 4 atoms, we would expect 6 vibrational modes to exist and that is confirmed by the quantum calculation.

There are 2 degenerate vibrational modes with a wavenumber of 1693.95 cm-1 and 2 degenerate modes with a wavenumber of 3589.82 cm-1.

Two types of vibrations exist; "bending" and "stretching". Vibrations with wavenumbers 1089.54 cm-1 and the two with 1693.95 cm-1 fall in the former category, whilst the other 3 fall in the latter. This is in agreement with the generally accepted fact that bending vibrations have smaller frequencies/wavenumbers than stretching vibrations.<ref name="vibrations" />

The stretching mode with the wavenumber 3461.29 cm-1 is highly symmetric.

The symmetric bending mode (1089.54 cm-1) is known as the "umbrella" mode.

Based on the calculated wavenumbers of the different vibrations, we would expect to see 3 bands in the experimental spectrum of gaseous ammonia (Vibration 4 is highly symmetric and therefore not IR active), but two of them are degenerate, so we only see 2 bands.

Predicted IR spectrum:

[[File: DP3618 screenshot ir.png|450 px]]

===Charge analysis===
Taking into account the electronegativities of the constituent atoms of ammonia, we would expect the nitrogen atom to be negatively charged and the 3 hydrogen atoms to be positively charged. Since ammonia is neutral overall, the sum of the individual charges on atoms should be 0. This is confirmed by the results of the calculation.

The charge on the nitrogen atom is -1.125 and the charge on each of the hydrogen atoms is 0.375.

[[File: DP3618 screenshot charges.png|300px]]

==N2 molecule==

===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || N2
|-
| File name || dp3618_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 || 0.00000158 a.u.
|-
| Dipole Moment || 0.0000 Debye
|-
| Point group || D∞h
|}

N-N bond length: 1.11 Å

"Item" table:
<pre>
Item Value Threshold Converged?
Maximum Force 0.000003 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
Predicted change in Energy=-2.352265D-12
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

<jmol><jmolApplet>
<title>N2molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP3618 N2 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 N2 OPTF POP.LOG| here]].

===Vibrational analysis===

[[File: DP3618 screenshot DisplayVibrations n2.png]]

{| class="wikitable" border="1"
|+ Vibrational mode of the N2 molecule
! !! Vibration 1
|-
| '''Wavenumber''' [cm-1] || 2457
|-
| '''Symmetry''' || SGG
|-
| ''' IR Intensity''' || 0
|-
| '''Image''' || [[File: DP3618 screenshot vibration1 n2.png|200 px]]
|-
|}

There are 3N-5 expected vibrational modes in a linear molecule. Since our molecule consists of 2 atoms, we would expect 1 vibrational mode to exist and that is confirmed by the quantum calculation.

The vibrational mode is the "stretching" type and is symmetric.

There is no change in dipole moment and the molecule shows no bands in the IR spectrum, this is also predicted by our calculation (IR Intensity = 0).

===Charge analysis===
This molecule consists of two identical atoms with same electronegativities. We expect a purely covalent bond with charge 0 on both atoms. This is exactly what we see from the results of the calculation.

[[File: DP3618 screenshot charges n2.png|300 px]]

==H2 molecule==

===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || H2
|-
| File name || dp3618_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 || 0.00000204 a.u.
|-
| Dipole Moment || 0.0000 Debye
|-
| Point group || D∞h
|}

H-H bond length: 0.74 Å

"Item" table:
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000005 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.634290D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

<jmol><jmolApplet>
<title>H2molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP3618 H2 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 H2 OPTF POP.LOG| here]].

===Vibrational analysis===

[[File: DP3618 screenshot DisplayVibrations h2.png]]

{| class="wikitable" border="1"
|+ Vibrational mode of the H2 molecule
! !! Vibration 1
|-
| '''Wavenumber''' [cm-1] || 4466
|-
| '''Symmetry''' || SGG
|-
| ''' IR Intensity''' || 0
|-
| '''Image''' || [[File: DP3618 screenshot vibration1 h2.png|200 px]]
|-
|}

There are 3N-5 expected vibrational modes in a linear molecule. Since our molecule consists of 2 atoms, we would expect 1 vibrational mode to exist and that is confirmed by the quantum calculation.

The vibrational mode is the "stretching" type and is symmetric.

There is no change in dipole moment and the molecule shows no bands in the IR spectrum, this is also predicted by our calculation (IR Intensity = 0).

===Charge analysis===
This molecule consists of two identical atoms with same electronegativities. We expect a purely covalent bond with charge 0 on both atoms. This is exactly what we see from the results of the calculation.

[[File: DP3618 screenshot charges h2.png|300 px]]

==Structure and Reactivity==
===N2 molecule in a mono-metallic complex===
An example of a mono-metallic TM complex coordinating an N2 molecule.
Its crystal structure identifier is VEJROU. The structure was reported [https://onlinelibrary.wiley.com/doi/full/10.1002/ejic.201700569 here].

Structure of the complex:

[[File: DP3618 screenshot complex.png|300 px]]

N-N bond distance in this complex is 1.20 Å, which is longer than the calculated N-N distance in the gas phase (1.11 Å). Some electron density which was used purely for bonding between the two nitrogens in the gas phase is now used to bond one nitrogen to the transition metal. There is less electron density between the nitrogens now, the bonding is weaker and longer. Since end-on N2 complexes are linear around the nitrogen, π backbonding can occur. In this case the d orbital of the metal atom can donate electron density into the π* orbital of the N2. The extend of this phenomena is dependent on the metal atom. If it is relatively electropositive, this effect is more significant, whereas in the case of more electronegative metals, such as Fe in our case, this is not so substantial.<ref name="backbonding" />

The values might also differ because of computational errors, these could be reduced by using a more accurate computational method. One should note, though, that there is also some error in the experimental data, due to instrumental or random errors.

===Energy of N2(g) + 3 H2(g) -> 2 NH3(g) reaction===
{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| 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.
|-
|}

In the gas phase, the product of the above reaction is more stable than the reactants by 146.5 kJ/mol.

==SF4 molecule==

===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || SF4
|-
| File name || dp3618_sf4_optf_pop
|-
| File type || .log
|-
| Calculation Type || FREQ
|-
| Calculation Method || RB3LYP
|-
| Basis set || 6-31G(d,p)
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -797.45952418 a.u.
|-
| RMS Gradient Norm || 0.00016003 a.u.
|-
| Dipole Moment || 0.8894 Debye
|-
| Point group || C2v
|}

Labeled picture of the molecule:

[[File: DP3618 screenshot sf4label.png|300 px]]

S-F(2 or 5) bond length: 1.67 Å

S-F(3 or 4) bond length: 1.59 Å

F(3)-S-F(4) bond angle: 102°

F(2)-S-F(5) bond angle: 171°

"Item" table:
<pre>
Item Value Threshold Converged?
Maximum Force 0.000245 0.000450 YES
RMS Force 0.000136 0.000300 YES
Maximum Displacement 0.001150 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
Predicted change in Energy=-5.227194D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.672 -DE/DX = 0.0002 !
! R2 R(1,3) 1.5946 -DE/DX = -0.0002 !
! R3 R(1,4) 1.5946 -DE/DX = -0.0002 !
! R4 R(1,5) 1.672 -DE/DX = 0.0002 !
! A1 A(2,1,3) 87.3127 -DE/DX = 0.0 !
! A2 A(2,1,4) 87.3127 -DE/DX = 0.0 !
! A3 A(3,1,4) 101.9122 -DE/DX = 0.0001 !
! A4 A(3,1,5) 87.3127 -DE/DX = 0.0 !
! A5 A(4,1,5) 87.3127 -DE/DX = 0.0 !
! A6 L(2,1,5,3,-1) 174.6253 -DE/DX = 0.0001 !
! A7 L(2,1,5,3,-2) 186.6353 -DE/DX = -0.0001 !
! D1 D(2,1,4,3) 86.6823 -DE/DX = 0.0 !
! D2 D(3,1,5,4) -102.0679 -DE/DX = -0.0001 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad</pre>

<jmol><jmolApplet>
<title>SF4molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP3618 SF4 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.18</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 SF4 OPTF POP.LOG| here]].

===Vibrational analysis===

[[File: DP3618 screenshot DisplayVibrations sf4.png]]

{| class="wikitable" border="1"
|+ Vibrational modes of the SF4 molecule
! !! Vibration 1 !! Vibration 2 !! Vibration 3 !! Vibration 4 !! Vibration 5 !! Vibration 6 !! Vibration 7 !! Vibration 8 !! Vibration 9
|-
| '''Wavenumber''' [cm-1] || 189 || 330 || 435 || 488 || 496 || 585 || 809 || 851 || 866
|-
| '''Symmetry''' || A1 || B1 || A2 || A1 || B2 || A1 || B2 || B1 || A1
|-
| '''IR Intensity''' || 0 || 10 || 0 || 20 || 2 || 3 || 509 || 150 || 101
|-
| '''Image''' || [[File: DP3618 screenshot vibration1 sf4.png|150 px]] || [[File: DP3618 screenshot vibration2 sf4.png|150 px]] || [[File: DP3618 screenshot vibration3 sf4.png|150 px]] || [[File: DP3618 screenshot vibration4 sf4.png|150 px]] || [[File: DP3618 screenshot vibration5 sf4.png|150 px]] || [[File: DP3618 screenshot vibration6 sf4.png|150 px]] || [[File: DP3618 screenshot vibration7 sf4.png|150 px]] || [[File: DP3618 screenshot vibration8 sf4.png|150 px]]
|| [[File: DP3618 screenshot vibration9 sf4.png|150 px]]
|-
|}

There are 3N-6 expected vibrational modes in a non-linear molecule. Since our molecule consists of 5 atoms, we would expect 9 vibrational modes to exist. There are two vibrational modes with an expected IR intensity of 0 and there are no degenerate vibrational modes, so we would expect to see 7 peaks in an IR spectrum.

===Charge analysis===
This molecule consists of two types of atoms. Fluorine is more electronegative than sulphur, so we expect it to have slight negative charge. The charges on the two types of F atoms will probably be slightly different because of different bond lengths. This is exactly what we see from the results of the calculation.

Charge on sulphur is 1.983, charge on the closer two fluorines (3 and 4 in the above labelled picture) is -0.455 and on the two further apart (2 and 5) it is -0.537.

[[File: DP3618 screenshot charges sf4.png|300 px]]

===Molecular orbital analysis===
'''MO 2'''

[[File: DP3618 screenshot MO2 sf4.png|300 px]]

As can be concluded by looking at the visualisation of the orbital, the F atom s orbitals most likely contribute most to this molecular orbital (MO). This can be checked by inspecting the Molecular Orbital Coefficients in the .log file of the calculation. For this MO, the contribution of the S s atomic orbitals (AOs) is negligible, just as we would expect. Simmilarly, the other two F atom AOs do not contribute much towards this MO. The two 1s orbitals from two F atoms contribute most towards this MO, which is reflected in the size and shape of the orbital. This MO is very deep in energy and is therefore not involved in bonding.

'''MO 7'''

[[File: DP3618 screenshot MO7 sf4.png|300 px]]

This orbital mostly has contributions from the sulphur AOs. It is almost entirely a 2px orbital, with very minor contribution from the other orbitals. It is also deep in energy, therefore it is a non-bonding orbital.

'''MO 10'''

[[File: DP3618 screenshot MO10 sf4.png|300 px]]

This orbital is very interesting because it has relatively equal contributions from all atoms in the molecule. Another thing we notice when looking at the MO Coefficients is that this MO is almost entirely composed of 2s and 3s orbitals of all atoms. It is a bonding orbital.

'''MO 18'''

[[File: DP3618 screenshot MO18 sf4.png|300 px]]

This MO has practically zero contribution from the s AOs. It is an antibonding orbital of the 2p and 3p fluorine AOs. Antibonding can also be noted by looking at the visualisation. There are 2 nodal planes going through the bonds.

'''MO 22'''

[[File: DP3618 screenshot MO22 sf4.png|300 px]]

A MO composed of many AOs, mostly 2p and 3p AO of the fluorines and also 3p and 4pz AOs from the sulphur atom. This is a bonding orbital.

'''MO 26'''

[[File: DP3618 screenshot MO26 sf4.png|300 px]]

Another very diverse MO, with substantial amount of anti-bonding character. It has many contributions from s and p orbitals of all atoms in the molecule. This MO is important because it is the highest occupied molecular orbital (HOMO).

'''MO 27'''

[[File: DP3618 screenshot MO27 sf4.png|300 px]]

This is another anti-bonding orbital with many contributions from different AOs. It is the lowest unoccupied molecular orbital (LUMO) of this molecule. Since this is the lowest-lying MO, any electrons donated to this molecule will first occupy this orbital.

There is a gap in the MO energies between the 9th and the 10th. All MOs up to the 9th have energy lower than -6 a.u. These are non-bonding orbitals, which could also be concluded by looking at the visualisation of the orbitals since all of these are very localised to individual atoms. The 10th MO, on the other hand, is spread out over the whole molecule and has an energy value of -1.3 a.u. This orbital is therefore the lowest bonding orbital.

==Independent work==
===Comparison of our results with other studies===
An interesting study was carried out by Hay on the electronic structures of different sulphur compounds, including SF4, which was studied here.<ref name="calcstudy" /> That study took a different approach than ours, but the results are rather similar. The MO energies for example, are consistently slightly lower in our case, but all the trends coincide. There is a ~65 a.u. difference between the lowest and the second lowest orbital. These are followed by two pairs of degenerate orbitals. There is another substantial energy gap between the 5th and the 6th orbital. These similarities continue throughout the MOs.

Another study performed by Oberhammer et al. focused on the structure of chalcogen tetrahalides in the gas phase.<ref name="structurestudy" /> Their bond length results are in great agreement with our findings. The S-F bond lengths were 1.67 Å and 1.59 Å in our case and ~1.65 Å and ~1.55 Å in their. There was, however a difference in bond angles. Whilst ours were 102° and 171°, theirs were 87.5° and 101.5°. This is definitely something that should be further explored in the future.

===Using different computational methods===
NH3, N2 and H2 were also optimised using a different calculation method to explore what effect a different computational method would have on the outcome of the optimisation. The RCCSD-FC calculation method was suggested by a demonstator. There are very few differences between the two optimisations, probably owing to the simplicity of the molecules studied.

'''NH3 molecule'''
The energy of the optimised structure was slightly higher in this second case at -56.39854662 a.u. The dipole was slightly higher, being 1.8637 D here. The N-H bond distance was 1.01 Å, which is slightly shorter than in the case of the RB3LYP calculation method. The H-N-H bond angle was the same at 106°. Vibrational frequencies were consistently higher by 40-80 cm-1. The full .log file can be viewed [[Media:DP3618 NH3CCSD OPTF POP.LOG| here]].

'''N2 molecule'''
In this case the energy of the second optimised structure was slightly higher at -109.25579376 a.u. N-N bond distance was the same as in the initial calculation. The vibrational frequency was slightly lower with 2411 cm-1. The full .log file can be viewed [[Media:DP3618 N2CCSD OPTF POP.LOG| here]].

'''H2 molecule'''
Again, the energy of the optimised structure was slightly higher in the additional calculation, this time being -1.16515738 a.u. Bond length was the same, but the vibrational frequency was slightly higher: 4504 cm-1. The full .log file can be viewed [[Media:DP3618 H2CCSD OPTF POP.LOG| here]].

It is evident from the paragraphs above that the two methods used are very similar. They can therefore be used interchangeably in systems similar to the ones studied here. Perhaps the molecules used were not complex enough to invoke greater discrepancies in the results obtained.

===CO molecule===

===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || CO
|-
| File name || dp3618_co_optf_pop
|-
| File type || .log
|-
| Calculation Type || FREQ
|-
| Calculation Method || RB3LYP
|-
| Basis set || 6-31G(d,p)
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -113.30945314 a.u.
|-
| RMS Gradient Norm || 0.00001828 a.u.
|-
| Dipole Moment || 0.0599 Debye
|-
| Point group || C∞v
|}

C-O bond length: 1.14 Å

"Item" table:
<pre>
Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000011 0.001800 YES
RMS Displacement 0.000018 0.001200 YES
Predicted change in Energy=-3.956716D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad</pre>

<jmol><jmolApplet>
<title>CO molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP3618 CO OPTF POP.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 CO OPTF POP.LOG| here]].

===Vibrational analysis===

{| class="wikitable" border="1"
|+ Vibrational mode of the H2 molecule
! !! Vibration 1
|-
| '''Wavenumber''' [cm-1] || 2209
|-
| '''Symmetry''' || SG
|-
| ''' IR Intensity''' || 68
|-
| '''Image''' || [[File: DP3618 screenshot vibration1 co.png|200 px]]
|-
|}

===Charge analysis===
This molecule consists of two atoms with different electronegativities. We expect a dipole moment and two charges of opposite signs on carbon and oxygen. This is exactly what we see from the results of the calculation.

[[File: DP3618 screenshot charges co.png|300 px]]

==References==
<references>
<ref name="vibrations">Harwood, L. M., Claridge, T. D. W. (Eds.). (1997). Introduction to Organic Spectroscopy (pp.22-33). New York, Oxford University Press Inc.</ref>
<ref name="backbonding">Holland PL. Metal-dioxygen and metal-dinitrogen complexes: where are the electrons?. Dalton Trans. 2010;39(23):5415-25.</ref>
<ref name="calcstudy">Jeffrey Hay, P. (1977). Generalized valence bond studies of the electronic structure of SF2, SF4, and SF6. 99. 1003-1012.</ref>
<ref name="structurestudy">Oberhammer H., Shlykov S. A., Gas phase structures of chalcogen tetrahalides MX4 with M=S, Se, Te and X=F, Cl, Br, I. Dalton Trans. 2010; 39: 2838-2841.</ref>
</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, overall very good however captions should always describe the item - captioning all of your jmols "molecule" is not helpful for the reader!

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, overall very good effort with your explanations, well done. There are a couple of errors in your MO analysis, for example MO 18 is actually a bonding orbital of the F4 fragment (non bonding between S and F). The bonding interactions are through space between adjacent F atoms. There are nodal planes but these are along bonds, nodal planes indicating antibonding interactions are usually across the bonds.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did extra calculations, analysis and comparison to the literature, well done!

Rep:Mod:ch6518y1imm2

2019-03-24T18:44:31Z

Rr1210:

==Ammonia NH3==
====Structure====
{| class="wikitable" border="1"
|+ Optimisation of of NH3
! Calculation Method !! Basis Set !! Final Energy E / a.u. !! Point Group
|-
| RB3LYP || 631G(d,p) || -56.55776873 || C3V
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>



<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>400</size>
<uploadedFileContents>CH6518_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 7</script>
</jmolApplet></jmol>

Optimised N-H bond length (Angstrom): 1.02 ± 0.01

Optimised H-N-H bond angle (Degrees): 106 ± 1

Charge on N: +0.375

Charge on H: -1.125

(Dipole Moment: 1.8466 Db)

Opt file [[Media:CH6518_NH3_OPTF_POP.LOG| here]]

====Vibrational Modes====

[[File:Ch6518_nh3_vibrations.PNG]]

{| class="wikitable" border="1"
|+ Vibrational Modes of NH3
! Wavenumber / cm-1 !! Symmetry !! Intensity !! Bend or Stretch !! Image
|-
| 1090 || A1 || 145.4 || rowspan="3" | Bend || [[File:Ch6518_nh3_1090.png|x150px]]
|-
| 1694 || E || 13.6 || [[File:Ch6518_nh3_1694_1.png|x150px]]
|-
| 1694 || E || 13.6 || [[File:Ch6518_nh3_1694_2.png|x150px]]
|-
| 3461 || A1 || 1.1 || rowspan="3" | Stretch || [[File:Ch6518_nh3_3461.png|x150px]]
|-
| 3590 || E || 0.3 || [[File:Ch6518_nh3_3590_1.png|x150px]]
|-
| 3590 || E || 0.3 || [[File:Ch6518_nh3_3590_2.png|x150px]]
|}

Number of expected vibrational modes: <math>3N-6=3*4-6=6</math>

Two pairs of degenerate vibrational modes, one pair at 1694 cm-1, the other at 3590 cm-1.

The vibrations at 1090 cm-1 and 3461 cm-1 are highly symmetric.

The 1090 cm-1 is known as the "umbrella" mode due to its resemblance to an opening and closing umbrella.

In an IR spectrum of gaseous ammonia, four bands would be predicted since there are vibrational modes at four different frequencies.

==Haber-Bosch Process==

===Molecular Nitrogen N2===
====Structure====
{| class="wikitable" border="1"
|+ Optimisation of of N2
! Calculation Method !! Basis Set !! Final Energy E / a.u. !! Point Group
|-
| RB3LYP || 631G(d,p) || -109.52412868 || D∞h
|}

<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
</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>black</color>
<size>400</size>
<uploadedFileContents>CH6518_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 4</script>
</jmolApplet></jmol>

Optimised N≡N bond length (Angstrom): 1.11 ± 0.01

Charge on each N: 0

(Dipole moment: 0 Db)

The molecule [https://onlinelibrary.wiley.com/doi/full/10.1002/chem.201702727 (dinitrogen)-(2,2',2' '-(phosphanetriyl)tris(1-(diphenylphosphanyl)-3-methyl-1H-indole))-ruthenium tetrahydrofuran solvate] (refcode DEKFUX) has a reported N≡N bond length of 1.086(6) Angstrom. In dinitrogen complexes, one of the nitrogens donates its lone pair, which exists in an sp orbital, to the metal to form a dative covalent bond. Consequently, the electron density around the donor nitrogen decreases, causing it to attract the electrons in the N≡N pi-bond more strongly since the effective nuclear charge they experience increases. Because the electrons move closer to the bonded nitrogen, so too does the second nitrogen; this results in a shorter equilibrium bond length. In pure diatomic molecular nitrogen gas, both atoms are electronically equal, but when coordinated with a metal there is an imbalance in electron density.

Opt file [[Media:CH6518_N2_OPTF_POP.LOG| here]]

====Vibrational Modes====

[[File:Ch6518_n2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ Vibrational Modes of N2
! Wavenumber / cm-1 !! Symmetry !! Intensity !! Bend or Stretch !! Image
|-
| 2457 || SGG || 0.0 (IR inactive) || Stretch || [[File:Ch6518_n2.png|x150px]]
|}

Number of expected vibrational modes: <math>3N-5=3*2-5=1</math>

===Molecular Hydrogen H2===
====Structure====
{| class="wikitable" border="1"
|+ Optimisation of of H2
! Calculation Method !! Basis Set !! Final Energy E / a.u. !! Point Group
|-
| RB3LYP || 631G(d,p) || -1.17853936 || D∞h
|}

<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
</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>black</color>
<size>400</size>
<uploadedFileContents>CH6518_H2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 5</script>
</jmolApplet></jmol>

Optimised H-H bond length (Angstrom): 0.74 ± 0.01

Charge on each H: 0

(Dipole moment: 0 Db)

Opt file [[Media:CH6518_H2_OPTF_POP.LOG| here]]

====Vibrational Modes====

[[File:Ch6518_h2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ Vibrational Modes of H2
! Wavenumber / cm-1 !! Symmetry !! Intensity !! Bend or Stretch !! Image
|-
| 4466 || SGG || 0.0 (IR Inactive) || Stretch || [[File:Ch6518_h2.png|x150px]]
|}

Number of expected vibrational modes: <math>3N-5=3*2-5=1</math>

===Energy Calculations===
<math>E(NH_3)=-56.55777 </math>

<math>2*E(NH_3)=-113.11554 </math>

<math>E(N_2)=-109.52413 </math>

<math>E(H_2)=-1.17854 </math>

<math>3*E(H_2)=-3.53562 </math>

<math>\Delta E=2*E(NH_3)-[E(N_2)+3*E(H_2)]= -113.11554-(-109.52413-3.53562)=-0.0557905 a.u. =-146.5 kJ mol^{-1} </math>

Hence ΔE = -146.5 kJ mol-1 < 0

So the reaction is exothermic, and thus the ammonia product is more stable than the reactants. However, entropy greatly favours the reverse reaction.

==Sulfur Tetrafluoride SF4==
====Structure====
{| class="wikitable" border="1"
|+ Optimisation of of SF4
! Calculation Method !! Basis Set !! Final Energy E / a.u. !! Point Group
|-
| RB3LYP || 631G(d,p) || -797.45952460 || C2v
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000148 0.000450 YES
RMS Force 0.000065 0.000300 YES
Maximum Displacement 0.000570 0.001800 YES
RMS Displacement 0.000281 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>SF4</title>
<color>black</color>
<size>400</size>
<uploadedFileContents>CH6518_SF4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 7</script>
</jmolApplet></jmol>

Optimised S-Fax bond length (Angstrom): 1.67 ± 0.01

Optimised S-Feq bond length (Angstrom): 1.59 ± 0.01

Optimised Fax-S-Fax bond angle (Degrees): 171 ± 1

Optimised Feq-S-Feq bond angle (Degrees): 102 ± 1

Optimised Fax-S-Feq bond angle (Degrees): 87 ± 1

Charge on S: +1.983

Charge on Fax: -0.537

Charge on Feq: -0.455

(Dipole moment: 0.8849 Db)

Opt file [[Media:CH6518_SF4_OPTF_POP.LOG| here]]

====Vibrational Modes====

[[File:Ch6518_sf4_vibrations.PNG]]

{| class="wikitable" border="1"
|+ Vibrational Modes of SF4
! Wavenumber / cm-1 !! Symmetry !! Intensity !! Bend or Stretch !! Image
|-
| 189 || A1 || 0.5 || rowspan="5" | Bend || [[File:Ch6518_sf4_189.png|x150px]]
|-
| 330 || B1 || 9.9 || [[File:Ch6518_sf4_330.png|x150px]]
|-
| 435 || A2 || 0.0 (IR inactive) || [[File:Ch6518_sf4_435.png|x150px]]
|-
| 488 || A1 || 20.5 || [[File:Ch6518_sf4_488.png|x150px]]
|-
| 496 || B2 || 2.1 || [[File:Ch6518_sf4_496.png|x150px]]
|-
| 584 || A1 || 2.7 || rowspan="4" | Stretch || [[File:Ch6518_sf4_584.png|x150px]]
|-
| 807 || B2 || 508.8 || [[File:Ch6518_sf4_807.png|x150px]]
|-
| 852 || B1 || 149.9 || [[File:Ch6518_sf4_852.png|x150px]]
|-
| 867 || A1 || 100.8 || [[File:Ch6518_sf4_867.png|x150px]]
|}

Number of expected vibrational modes: <math>3N-6=3*5-6=9</math>

====Molecular Orbitals====

{| class="wikitable" border="1"
|+ Molecular Orbitals of SF4
! Orbital Number !! Energy / eV !! Orbital type !! Occupied? !! Image
|-
| 9 || -6.17183 || Non-bonding || Yes || [[File:Ch6518_sf4_mo9.PNG|x300px]]
|-
| 10 || -1.32222 || Bonding || Yes || [[File:Ch6518_sf4_mo10.png|x300px]]
|-
| 13 || -1.17960 || Primarily bonding || Yes || [[File:Ch6518_sf4_mo13.PNG|x300px]]
|-
| 14 || -0.78968 || Primatily antionding || Yes || [[File:Ch6514_sf4_mo14.PNG|x300px]]
|-
| 26 (HOMO) || -0.34280 || Primarily bonding || Yes || [[File:Ch6518_sf4_mo26.PNG|x300px]]
|-
| 27 (LUMO) || -0.07939 || Primarily antibonding || No || [[File:Ch6518_sf4_mo27.PNG|x300px]]
|}

Orbitals 1-9 are very deep in energy and are therefore inaccessible; these are made from the core electrons of the constituent atoms. However, subsequent MOs are much higher-lying, with all MOs above the 14th having E > -1 eV.
Overall the molecule has no pi bonds, therefore for every filled bonding orbital with pi character there must be an equal amount of pi antibonding character.
Due to the number of atomic orbitals contributing to the molecular orbitals, none of the higher-lying orbitals can be considered to be purely bonding or purely antibonding. The electron distribution for the orbitals may lie between one pair of atoms, but produce a node between another pair.
S-character can be observed in the shape of orbital 14, whilst the large rear lobe(s) of orbitals 26 and 27 (the HOMO and LUMO) indicate contribution from a d orbital.

==Independence Task - other small molecules==

===Carbon Monoxide CO===
====Structure====
{| class="wikitable" border="1"
|+ Optimisation of of CO
! Calculation Method !! Basis Set !! Final Energy E / a.u. !! Point Group
|-
| RB3LYP || 631G(d,p) || -113.30945314 || C∞v
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>CO</title>
<color>black</color>
<size>400</size>
<uploadedFileContents>CH6518_CO_OPTF_POP.LOG</uploadedFileContents>
<script>frame 7</script>
</jmolApplet></jmol>

Optimised C-O bond length (Angstrom): 1.14 ± 0.01

Charge on C: +0.506

Charge on O: -0.506

(Dipole moment: 0.0599 Db)

Opt file [[Media:CH6518_CO_OPTF_POP.LOG| here]]

====Vibrational Modes====

[[File:Ch6518_co_vibrations.PNG]]

{| class="wikitable" border="1"
|+ Vibrational Modes of CO
! Wavenumber / cm-1 !! Symmetry !! Intensity !! Bend or Stretch !! Image
|-
| 2209 || SG || 68.0 || Stretch || [[File:Ch6518_co.png|x150px]]
|}

Number of expected vibrational modes: <math>3N-5=3*2-5=1</math>

===Cyanide CN-===
====Structure====
{| class="wikitable" border="1"
|+ Optimisation of of CN-
! Calculation Method !! Basis Set !! Final Energy E / a.u. !! Point Group
|-
| RB3LYP || 631G(d,p) || -92.82453153 || C∞v
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000005 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>CN-</title>
<color>black</color>
<size>400</size>
<uploadedFileContents>CH6518_CN-_OPTF_POP.LOG</uploadedFileContents>
<script>frame 7</script>
</jmolApplet></jmol>

Optimised C-N bond length (Angstrom): 1.18 ± 0.01

Charge on C: -0.246

Charge on N: -0.754

(Dipole moment: 0.5236 Db)

Opt file [[Media:CH6518_CN-_OPTF_POP.LOG| here]]

====Vibrational Modes====

[[File:Ch6518_cn_vibrations.PNG]]

{| class="wikitable" border="1"
|+ Vibrational Modes of CN-
! Wavenumber / cm-1 !! Symmetry !! Intensity !! Bend or Stretch !! Image
|-
| 2139 || SG || 7.8 || Stretch || [[File:Ch6518_cn.png|x150px]]
|}

Number of expected vibrational modes: <math>3N-5=3*2-5=1</math>

===Hydrogen Cyanide HCN===
====Structure====
{| class="wikitable" border="1"
|+ Optimisation of of HCN
! Calculation Method !! Basis Set !! Final Energy E / a.u. !! Point Group
|-
| RB3LYP || 631G(d,p) || -93.42458132 || C∞v
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000370 0.000450 YES
RMS Force 0.000255 0.000300 YES
Maximum Displacement 0.000676 0.001800 YES
RMS Displacement 0.000427 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>HCN</title>
<color>black</color>
<size>400</size>
<uploadedFileContents>CH6518_HCN_OPTF_POP.LOG</uploadedFileContents>
<script>frame 7</script>
</jmolApplet></jmol>

Optimised C-N bond length (Angstrom): 1.07 ± 0.01

Optimised H-C bond length (Angstrom): 1.16 ± 0.01

Charge on H: +0.234

Charge on C: +0.073

Charge on N: -0.308

(Dipole moment: 2.8933 Db)

Opt file [[Media:CH6518_HCN_OPTF_POP.LOG| here]]

====Vibrational Modes====

[[File:Ch6518_hcn_vibrations.PNG]]

{| class="wikitable" border="1"
|+ Vibrational Modes of HCN
! Wavenumber / cm-1 !! Symmetry !! Intensity !! Bend or Stretch !! Image
|-
| 767 || PI || 35.3 || rowspan="2" | Bend || [[File:Ch6518_hcn_767_1.png|x150px]]
|-
| 767 || PI || 35.3 || [[File:Ch6518_hcn_767_2.png|x150px]]
|-
| 2215 || SG || 2.0 || rowspan="2" | Stretch || [[File:Ch6518_hcn_2215.png|x150px]]
|-
| 3480 || SG || 57.3 || [[File:Ch6518_hcn_3480.png|x150px]]
|}

Number of expected vibrational modes: <math>3N-5=3*3-5=4</math>

Pair of degenerate vibrational modes at 767 cm-1

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 0.5/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, most answers are correct. However there are only 2 visible peaks in the spectra of NH3, due to the low intensity of the other 2 peaks. (See infrared column in vibrations table.)

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 3/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, you added all the necessary information, well done! To improve you could have explain the charges in terms of electronegativity, and added more details on the individual MOs such as which AOs are contributing to each. The explanation of the MOs overall was good though.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did several extra calculations, with analysis, well done!

Rep:Mod:THISISMYDOMAIN272

2019-03-24T18:37:56Z

Rr1210:

= NH3 molecule =

<jmol><jmolApplet>
<script>frame 1.16</script>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZNAJEEB4318_NH3_OPTIN_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

== NH3 calculation results ==

Calculation method = RB3LYP

Basis set = 6-31G(d.p)

Final energy E(RB3LYP) = -56.55777 ±0.00001 a.u.

RMS gradient = 0.00000485 a.u.

Point group of molecule = C3V

N-H bond distance = 1.02±0.01Å

H-N-H bond angle = 106±1°

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986269D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

== NH3 vibration results ==

[[File:zn4318_Displayvib_nh3.png]]

{| class="wikitable" border="1"
|+ NH3 Vibrations table
! !! Frequency 1!! Frequency 2!! Frequency 3!! Frequency 4!! Frequency 5!! Frequency 6
|-
| Wavenumber/cm-1 || 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| Symmetry || A1|| E|| E|| A1|| E|| E
|-
| Intensity/a.u. || 145.4|| 13.6|| 13.6||1.1|| 0.3|| 0.3
|-
|Image || [[File:Zn4318_nh3_f1.png|80px]]|| [[File:Zn4318_nh3_f2.png|80px]]|| [[File:Zn4318_nh3_f3.png|80px]]|| [[File:Zn4318_nh3_f4.png|80px]]|| [[File:Zn4318_nh3_f5.png|80px]]|| [[File:Zn4318_nh3_f6.png|80px]]

|}

=== NH3 vibration results Q and A ===

Based on the 3N-6 rule, as N=4 for NH3, 6 vibrational modes are expected. This matches the simulation with frequencies 2 and 3 and frequencies 5 and 6 being degenerate. Frequencies 1, 2 and 3 are bond bending modes whilst frequencies 4, 5 and 6 are bond stretching modes. Frequency 4 is highly symmetric, with frequency 1 seeming to be the umbrella mode. 2 bands would be expected to be seen in an experimental spectrum, being frequency 1 and an overlap of 2 and 3. This is because frequencies 2 and 3 are degenerate in energy so would produce a peak of equal intensity and wavenumber, appearing as a single band rather than 2.

== NH3 charge analysis ==

[[File:Zn4318_nh3_charge.png]]

The Nitrogen and Hydrogen were calculated to have charges of -1.125 and 0.375 respectively. This matches what would be expected, as Nitrogen is more electronegative than Hydrogen, so would have a more negative charge. Each Hydrogen is in an identical environment so should each have equal charges, as depicted in the simulation.

The Gaussian optimisation file used is [[Media:ZNAJEEB4318_NH3_OPTIN_POP.LOG| here]]

= N2 molecule =

<jmol><jmolApplet>
<title>N2 molecule</title>
<script>frame 1.10</script>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZN4318_N2_OPTIN_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

== N2 calculation results ==

Calculation method = RB3LYP

Basis set = 6-31G(d.p)

Final energy E(RB3LYP) = -109.52413±0.00001a.u.

RMS gradient = 0.00000060 a.u.

Point group of molecule = D∞h

N≡N bond distance = 1.11±0.01Å

N≡N bond angle = 180±1°

<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=-3.401033D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

== N2 vibration results==

[[File:Zn4318_N2_displayvib.png]]
{| class="wikitable" border="1"
|+ N2 Vibrations table
! !! Frequency 1
|-
| Wavenumber/cm-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity/a.u. || 0
|-
|Image || [[File:Zn4318_n2_f1.png]]
|}

As this is a linear molecule, the 3N-5 rule applies here. As there are 2 atoms in the molecule, N=2 so there should be 1 vibrational mode. This is equal to the number of calculated modes. Frequency 1 is a symmetric stretch that would not be expected to appear in an IR spectrum, but would in a Raman spectrum.

== N2 charge analysis==

[[File:Zn4318_n2_charge.png]]

Both Nitrogen's were calculated as being neutral, which is expected as they are equal in electronegativities so would be a non-polar molecule.

==N2 Comparison to mono-metallic TM complex==

[[File:Zn4318_n2_monometallic.png]]

In [[https://www.researchgate.net/publication/250818551_A_tris-dinitrogne_complex_Preparation_and_crystal_structure_of_mer-MoN23PPrn_2Ph3| CILSEV]] from Conquest, the N≡N bonds are 1.092Å (N1≡N2), 1.124Å(N3≡N4) and 1.104Å (N5≡N6) respectively for mer-tris(Dinitrogen)-tris(di-n-propyl-phenylphosphine)-molybdenum whilst the calculated N≡N via B3LYP is 1.11Å. The N1≡N2 and N5≡N6 bonds are 0.019Å and 0.13Å shorter than the computational value due to the reduced orbital overlap between Mo and both N1 and N5. This is caused by the bulky phosphine groups which repel the 2 nitrogen ligands together and cause deviations in the expected bond angles and lengths of the complex. The N3≡N4 bond is 0.014Å larger than the calculated value, which can be attributed to the calculation having few iterations of relatively low resolution as well as the phophine group possibly lengthening the N3≡N4 bond. This can be improved by using a more accurate computational method which is more suited for mono-metallic complexes to get a better estimate for the bond length. The N3≡N4 bond is also expected to be slightly larger due to the transition metal withdrawing electron density from the N3≡N4 ligand, decreasing the N3≡N4 bond electron density and therefore increasing the bond length.

The Gaussian optimisation file for N2 is [[Media:ZN4318_N2_OPTIN_POP.LOG| here]]

= H2 molecule =

<jmol><jmolApplet>
<title>H2 molecule</title>
<script>frame 1.12</script>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZN4318_H2_OPTIN_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

== H2 calculation results==

Calculation method = RB3LYP

Basis set = 6-31G(d.p)

Final energy E(RB3LYP) = -1.17854±0.00001 a.u.

RMS gradient = 0.00000017 a.u.

Point group of molecule = D∞h

H-H bond distance = 0.74±0.01Å

H-H bond angle = 180±1°

<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000005 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.939322D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

== H2 vibration results==

[[File:Zn4318_h2_displayvib.png]]
{| class="wikitable" border="1"
|+ H2 Vibrations table
! !! Frequency 1
|-
| Wavenumber/cm-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity/a.u. || 0
|-
|Image || [[File:Zn4318_h2_f1.png]]
|}

As this is a linear molecule, the 3N-5 rule applies here. As there are 2 atoms in the molecule, N=2 so there should be 1 vibrational mode. This is equal to the number of calculated modes. Frequency 1 is a symmetric stretch that would not be expected to appear in an IR spectrum, but would in a Raman spectrum.

==H2 charge analysis==

[[File:Zn4318_h2_charge.png]]

Both Hydrogen's were calculated as being neutral, which is expected as they are equal in electronegativities so would be a non-polar molecule.

The Gaussian optimisation file for H2 is [[Media:ZN4318_H2_OPTIN_POP.LOG| here]]

= Haber-Bosch process energy calculation =

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.1155375 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)] ≈ -0.05579 Hartree ≈ -146.5 kJmol-1

The ammonia product is more stable as it is lower in energy than the reagants, as shown in how the ΔE<0 which depicts an exothermic reaction.

= Project molecule, CO ==

<jmol><jmolApplet>
<script>frame 1.10</script>
<title>CO molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZN4318_CO_OPTIN_POP_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

== CO calculation results==

Calculation method = RB3LYP

Basis set = 6-31G(d.p)

Final energy E(RB3LYP) = -113.30945±0.00001 a.u.

RMS gradient = 0.00000433 a.u.

Point group of molecule = C ∞V

C≡O bond distance = 1.14±0.01Å

C≡O bond angle = 180±1°

<pre>

Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
Predicted change in Energy=-2.221214D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

== CO vibration results==

[[File:Zn4318_co_displayvib.png]]
{| class="wikitable" border="1"
|+ CO Vibrations table
! !! Frequency 1
|-
| Wavenumber/cm-1 || 2209
|-
| Symmetry || SG
|-
| Intensity/a.u. || 68
|-
|Image || [[File:Zn4318_co_f1.png]]
|}

As this is a linear molecule, the 3N-5 rule applies here. As there are 2 atoms in the molecule, N=2 so there should be 1 vibrational mode. This is equal to the number of calculated modes. Frequency 1 is a symmetric stretch that would not be expected to appear in an IR spectrum, but would in a Raman spectrum.

== CO charge analysis==

[[File:Zn4318_co_charge.png]]

The Carbon and Oxygen were calculated to have charges of 0.506 and -0.506 respectively. This is as predicted as Oxygen is more electronegative than Carbon, so would be expected to be more negatively charged than Carbon. This would also imply that they should have equal magnitudes of charge as they are the only 2 atoms in the molecule.

The Gaussian optimisation file used is [[Media:ZN4318_CO_OPTIN_POP_2.LOG| here]]

== CO molecular Orbital analysis==

{| class="wikitable" border="1"
|+ CO Molecular Orbitals table
! !! MO 8!! MO 7!! MO 6!! MO 5!! MO 4
|-
| Energy/Hartree AO || -0.02178|| -0.37145|| -0.46742 || -0.46742|| -0.57004
|-
| Carbon Bonding AO || 2px|| 2pz|| 2py|| 2px|| 2s
|-
| Oxygen Bonding AO || 2px|| 2pz|| 2py|| 2px || 2s
|-
| Description || π*g is the LUMO || σ*g is the HOMO || πu|| πu|| σu
|-

|Image || [[File:Zn4318_co_mo_8.png|85px]]|| [[File:Zn4318_co_mo_7.png|85px]]|| [[File:Zn4318_co_mo_6.png|85px]]|| [[File:Zn4318_co_mo_5.png|85px]]|| [[File:Zn4318_co_mo_4.png|85px]]

|}

MOs 5 and 6 are 2 degenerate MOs as they are the overlap of different p AO but at different orientations, being in the x and then the y plane. MO 7 is the highest occupied molecular orbital and would act as a nucleophile from the Carbon as it has a greater charge density than the Oxygen. MO 8 is the lowest unoccupied molecular orbital with the carbon having a more diffuse spread of electron density, so would be more likely to be attacked by a nucleophile.
MO's 7 and 8 are antibonding orbitals whilst MO's 4, 5 and 6 are bonding orbitals.

=Independence mark, calculating the N2 bond length via a different computational method =

<jmol><jmolApplet>
<script>frame 1.10</script>
<title>N2 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZN4318_N2_OPTIN_POP_CAM.LOG</uploadedFileContents>
</jmolApplet></jmol>

== N2 calculation results==

Calculation method = RCAM-B3LYP

Basis set = 6-31G(d.p)

Final energy E(RCAM-B3LYP) = -109.47916±0.00001 a.u.

RMS gradient = 0.00000012 a.u.

Point group of molecule = D∞V

C≡O bond distance = 1.10±0.01Å

C≡O bond angle = 180±1°

<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 0.000000 0.001200 YES
Predicted change in Energy=-1.203893D-14
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1008 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

== N2 vibration results==

[[File:Zn4318_n2_displayvib_cam.png]]
{| class="wikitable" border="1"
|+ N2 Vibrations table
! !! Frequency 1
|-
| Wavenumber/cm-1 || 2511
|-
| Symmetry || SGG
|-
| Intensity/a.u. || 0
|-
|Image || [[File:Zn4318_n2_f1_cam.png]]
|}

This is a linear molecule, so the 3N-5 rule applies here. As there are 2 atoms in the molecule, N=2 so there should be 1 vibrational mode. This is equal to the number of calculated modes. Frequency 1 is a symmetric stretch that would not be expected to appear in an IR spectrum, but would in a Raman spectrum.

== N2 charge analysis==

[[File:Zn4318_n2_charge_cam.png]]

Both Nitrogen's were calculated as being neutral with CAM-B3LYP, which is expected as they are equal in electronegativities so would be a non-polar molecule.

==Comparing B3LYP and CAM-B3LYP results for N2==

Comparing the 2 vibrational values, B3LYP=2457cm-1 whilst RCAM-B3LYP=2511cm-1. The experimental value for N2 is 2330cm-1 as shown [[Media:Zn4318_n2_bondlength_lit.pdf| here]]. This shows that B3LYP and CAM-B3LYP have percentage uncertainties of 5.3% and 7.5% respectively. This suggests that B3LYP is more accurate at calculating frequencies than CAM-B3LYP.

Comparing the bond lengths, B3LYP=1.11Å whilst RCAM-B3LYP=1.10Å. The experimental value for N2 is 1.0975Å[http://www.wiredchemist.com/chemistry/data/nitrogen-compounds]]. This shows that B3LYP and CAM-B3LYP have percentage uncertainties of 0.11% and 0.023% respectively. This shows that CAM-B3LYP is more accurate than B3LYP when calculating bond lengths.

Both charge distributions calculated were the same, being 0 on each Nitrogen.

===Using the N2 bond length from CAM-B3LYP to compare with the monometallic complex===
[[File:Zn4318_n2_monometallic.png]]

The CAM-B3LYP length of 1.10Å compared to the 3 N≡N of 1.092Å (N1≡N2), 1.124Å(N3≡N4) and 1.104Å (N5≡N6) from [[https://www.researchgate.net/publication/250818551_A_tris-dinitrogne_complex_Preparation_and_crystal_structure_of_mer-MoN23PPrn_2Ph3| CILSEV]] shows that the calculated value is now also shorter than N5≡N6. This is likely due to how, whilst N5≡N6 and N1≡N2 are shortened by the large phoshine groups, the effect of the transition metal withdrawing electron density from the N≡N is greater. This causes each N≡N in the monometallic structure to be longer than expected.
This is different to the conclusion made via the B3LYP calculation as the bond length of 1.11Å was larger than both N1≡N2 and N5≡N6, suggesting that the shortening by the large phosphine groups was greater than the lengthening cased by the transition metal.

The Gaussian optimisation file used is [[Media:ZN4318_N2_OPTIN_POP_CAM.LOG| here]]

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES, However you have given a bond angle of 180, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

Have you added information about MOs and charges on atoms?

YES, overall good explanations, nicely laid out, well done! You could have added a bit more detail on the MOs for example why does the C contribute more strongly to the HOMO and LUMO?

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did an extra calculation on N2 and looked at a further literature comparison of the bond length well done!

Sn518

2019-03-24T18:29:58Z

Rr1210:

===NH3 Molecule===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986275D-10
Optimization completed.
-- Stationary point found.
</pre>
[[SN518_NH3_OPT_1.LOG|NH3]]
<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SN518_NH3_OPT 1.LOG</uploadedFileContents>
</jmolApplet> <script>frame 1:16</script> </jmol>

==== Molecule Summary ====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation Method'''
|RB3LYP
|-
|'''Basis Set'''
|6-31G(d.p)
|-
|'''Final Energy E(RB3LYP)(au)'''
|<nowiki>-56.55777 </nowiki>
|-
|'''RMS Gradient(au)'''
|4.85x 10-6
|-
|'''Point Group'''
|C3v
|}

'''Bond Length:''' 1.02Å '''H-N-H Bond Angle''': 105.7°

==== Vibrations ====
[[File:Vibrations NH3 screenshot 1.PNG|300px]]

{| class="wikitable"
|'''Vibrational Mode'''
|1 || 2 || 3 || 4 || 5 || 6
|-
|'''Wavenumber (cm-1)'''
|1090 ||1694 ||1694 ||3461 ||3590 ||3590
|-
|'''Symmetry'''
|A1 || E || E || A1 || E || E
|-
|'''Intensity (arbitrary units)'''
|145 ||14 ||14 || 1 ||0 || 0
|-
|'''Vibration Image'''
|[[File:Vibration 1 nh3.PNG|150px]] ||[[File:Vibration 2 nh3.PNG|150px]]||[[File:Vibration 3 nh3.PNG|150px]]||[[File:Vibration 4 nh3.PNG|150px]]||[[File:Vibration 5 nh3.PNG|130px]]||[[File:Vibration 6 nh3.PNG|150px]]
|-
|}

The expected number of vibrational modes for NH3 is 3N-6= 3(4)-6= 6.
The degenerate modes are of wavenumber 1694 cm-1, and of wavenumber 3590cm-1.
Modes with frequencies of 1090cm-1and the two modes of 1694cm-1 are bending modes whereas frequencies of 3461cm-1, and 3590 cm-1 are the bond stretching vibrations.
The vibrational frequency of 3461cm-1with A1 symmetry is the highly symmetric mode.
The umbrella mode appears to be the second vibrational mode (6) with wavenumber 3590cm-1.
Two bands would be expected in an experimental spectrum of gaseous ammonia from the modes with frequency 1090cm-1 and 1694cm-1, but as two modes have peaks at 1696cm-1,they will overlap.

==== Charge Analysis ====
[[File:NH3 charge analysis colour.PNG|250px]]

The nitrogen atom would be expected to be slightly negative as it is an electronegative atom whereas the H atom would be slightly positive. This correlates to the image shown above as the overall charge cancels out as a NH3 molecule does not possess any charge.

==N2 Molecule==
<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=-3.400949D-13
Optimization completed.
-- Stationary point found.
</pre>
[[N2 MOLECULE OPT VERSION 1.LOG|N2]]
<jmol><jmolApplet>
<title> N2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>N2 MOLECULE OPT VERSION 1.LOG</uploadedFileContents>
</jmolApplet> <script>frame 1:10</script> </jmol>

==== Molecule Summary ====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation Method'''
|RB3LYP
|-
|'''Basis Set'''
|6-31G(d.p)
|-
|'''Final Energy E(RB3LYP)(au)'''
|<nowiki>-109.52513</nowiki>
|-
|'''RMS Gradient(au)'''
|6.00x 10-7
|-
|'''Point Group'''
|D∞h
|}

'''Bond Length:''' 1.11Å

==== Vibrations ====
[[File:Vibrations N2 screenshot 1.PNG|300px]]

{| class="wikitable"
|'''Vibrational Mode'''
|1
|-
|'''Wavenumber (cm-1)'''
|2457
|-
|'''Symmetry'''
|SGG
|-
|'''Intensity (arbitrary units)'''
|0
|-
|'''Vibration Image'''
|[[File:Vibration 1 n2.PNG|150px]]
|-
|}

==== Charge Analysis ====
[[File:N2 charge analysis colour.PNG|250px]]

The charge is shown in the image as 0.00 as both nitrogen atoms have the same electronegativity, therefore the atoms could not be coloured by charge as a neutral charge is a black colour and the writing would be illegible as it is also black.

==== N2 Molecular Orbitals (Independence Mark) ====
HOMO is shown in the left image and is a 3σg orbital formed by contributions from the 2pz orbitals from each N atom in a N2 molecule. Whereas the LUMO is shown in the right image and is a 1π* orbital formed by contributions from 2px and 2py orbitals from both the N atoms.

[[File:N2 Homo M Orbital.PNG|300px]] [[File:N2 Lumo M Orbital.PNG|300px]]

==H2 Molecule==
<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
Optimization completed.
-- Stationary point found.
</pre>
[[H2 MOLECULE OPT 1 SN.LOG|H2]]
<jmol><jmolApplet>
<title> H2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>H2 MOLECULE OPT 1 SN.LOG </uploadedFileContents>
</jmolApplet> <script>frame 1:12</script> </jmol>

==== Molecule Summary ====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation Method'''
|RB3LYP
|-
|'''Basis Set'''
|6-31G(d.p)
|-
|'''Final Energy E(RB3LYP)(au)'''
|<nowiki>-1.17854</nowiki>
|-
|'''RMS Gradient(au)'''
|1.7x 10-7
|-
|'''Point Group'''
|D∞h
|}

'''Bond Length:''' 0.74Å

==== Vibrations ====
[[File:Vibrations H2 screenshot 1.PNG|300px]]

==== Charge Analysis ====
[[File:H2 charge analysis colour.PNG|250px]]

Just like the N2 molecule, the charge is shown in the image as 0.00 as both hydrogen atoms have the same electronegativity. Thus, the neutral charge would be shown by the atoms being black.

== Mono-Metallic TM Complex: Phenylamido-(dinitrogen)-tetrakis(trimethylphosphine)-rhenium(i) ==
[[File:Bibjax structure 1.PNG|250px]]
[[CCDC Link]]

The structure found was Phenylamido-(dinitrogen)-tetrakis(trimethylphosphine)-rhenium(i) with the CSD refcode: BIBJAX. The N-N bond distance was 1.10Å.The crystal structure and N-N computational lengths are the same values to one decimal place which can be explained by the fact that there may not be much interaction between the transition metal and the nitrogen atoms. Nevertheless, it maybe the case that the errors are not reflected in the computational calculations and so both values appear to be identical.

==Haber-Bosch Reaction Energy Calculation==

E(NH3)=-56.55777 au

2*E(NH3)=-113.11554 au

E(N2)=-109.52413 au

E(H2)=-1.17854 au

3*E(H2)=-3.53562 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.05579au
ΔE= -146.5 kJ mol-1

As the energy for this reaction: N2 + 3H2 -> 2NH3 is -146.5 kJ mol-1 and therefore negative, the reaction is an exothermic process and so the ammonia product is more stable than the gaseous product.

==CO Molecule==
<pre>
Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000018 0.001200 YES
Predicted change in Energy=-3.956716D-10
Optimization completed.
-- Stationary point found.
</pre>
[[SN518 CO OPT 1.LOG|CO]]
<jmol><jmolApplet>
<title> CO Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents> SN518 CO OPT 1.LOG</uploadedFileContents>
</jmolApplet> <script>frame 1:10</script> </jmol>

==== Molecule Summary ====
{| class="wikitable"
|'''Molecule'''
|CO
|-
|'''Calculation Method'''
|RB3LYP
|-
|'''Basis Set'''
|6-31G(d.p)
|-
|'''Final Energy E(RB3LYP)(au)'''
|<nowiki>-113.30945</nowiki>
|-
|'''RMS Gradient(au)'''
|1.83x 10-5
|-
|'''Point Group'''
|C∞v
|}

'''Bond Length:''' 1.14Å

==== Vibrations ====
[[File:Vibration 1 CO.PNG|300px]]

{| class="wikitable"
|'''Vibrational Mode'''
|1
|-
|'''Wavenumber (cm-1)'''
|2209
|-
|'''Symmetry'''
|SG
|-
|'''Intensity (arbitrary units)'''
|68
|-
|'''Vibration Image'''
|[[File:Vibratoin 1 CO screenshot.PNG|250px]]
|-
|}

==== Charge Analysis ====
[[File:CO charge analysis colour.PNG|300px]]

The charge on CO is neutral as the values of the charges cancel out.

==== CO Molecular Orbitals ====

{| class="wikitable"
|'''Molecular Orbital Type'''
| 3σ || 4σ* || 1π || 5σ (HOMO)|| 1π* (LUMO)
|-
|'''Energy of Orbitals (au)'''
| -1.15791 || -0.57004 ||-0.46743 ||-0.37145 ||-0.02177
|-
|'''Molecular Orbital'''
|[[File:3 sigma CO.PNG|150px]] || [[File:4 sigma star CO.PNG|150px]] ||[[File:1 pi 1.PNG|150px]] || [[File:HOMO 5 sigma CO.PNG|150px]] ||[[File:LUMO 1 pi star CO.PNG|150px]]
|-
|'''Combination of AOs)'''
|One 2s AO from both C and O || One 2s AO from both C and O to form antibonding orbitals|| 2px from C and 2px from O || 2pz from C and 2pz from O || 2px from C and 2px from O to form antibonding orbitals
|-
|}
All the orbitals here are occupied except the 1π* orbital which is the LUMO.
In the CO molecule, the oxygen atom is more electronegative than the carbon atom and so the electrons are expected to occupy the orbitals that are predominantly of the oxygen atom. As oxygen is quite electronegative (3.4), its energy levels are deeper in energy (more negative) and so the system is more stable and the electrons are harder to remove.
There are two 1π orbitals formed by the contribution of the 2px and 2py orbitals on C and O which are degenerate and there are in fact two 1π* antibonding orbitals again for the same reason. Therefore, in CO there are two π bonds and one σ bond.
The 1π, 5σ and 1π* are a mixture of the 2p orbitals and thus the 5σ orbital is higher in energy than the 1π orbital. Both the HOMO and LUMO are not that different in terms of their energy values.

===O2 Molecule (Independence Mark)===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000130 0.000450 YES
RMS Force 0.000130 0.000300 YES
Maximum Displacement 0.000080 0.001800 YES
RMS Displacement 0.000113 0.001200 YES
Predicted change in Energy=-1.033738D-08
Optimization completed.
-- Stationary point found.
</pre>
[[SN518 O2 OPT 1 SN.LOG|O2]]
<jmol><jmolApplet>
<title> O2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents> SN518 O2 OPT 1 SN.LOG</uploadedFileContents>
</jmolApplet> <script>frame 1.10 </script> </jmol>

==== Molecule Summary ====
{| class="wikitable"
|'''Molecule'''
|O2
|-
|'''Calculation Method'''
|RB3LYP
|-
|'''Basis Set'''
|6-31G(d.p)
|-
|'''Final Energy E(RB3LYP)(au)'''
|<nowiki>-150.25742</nowiki>
|-
|'''RMS Gradient(au)'''
|7.50x 10-5
|-
|'''Point Group'''
|D∞h
|}

'''Bond Length:''' 1.22Å

==== Vibrations ====
[[File:Vibrations O2 screenshot 1.PNG|300px]]

{| class="wikitable"
|'''Vibrational Mode'''
|1
|-
|'''Wavenumber (cm-1)'''
|1643
|-
|'''Symmetry'''
|SGG
|-
|'''Intensity (arbitrary units)'''
|0
|-
|'''Vibration Image'''
|[[File:Vibration 1 O2 sn518.PNG|250px]]
|-
|}

==== Charge Analysis ====
[[File:O2 charge analysis colour.PNG|300px]]

The two oxygen atoms have the same electronegativities and therefore pull the same amount of electron density. Thus the charge cancels out and the molecule is neutral.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, good explanations well done! You could have mentioned that the 1pi MO has a larger contribution from O than C, as you explained due to the different electronegativities causing the AOs of O to be lower than those of C. You can see the opposite effect in the LUMO.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You calculated O2 and you did deeper analysis on the MOs of N2, well done!

Rep:Title=Mod:KartikMudgalComputationalNH3Analysis

2019-03-24T18:22:47Z

Rr1210:

==NH3 Molecule==

====Molecule Information====

{| class="wikitable" border="1"
|+ Optimised NH3 Molecule
! Name of Molecule !! Ammonia
|-
! Calculation Method !! RB3LYP
|-
! Basis Set !! 6-31G(d,p)
|-
! Final Energy E(RB3LYP) in atomic units (a.u.)!! -56.55776873
|-
! RMS Gradient !! 0.00000485
|-
! Point Group !! C3V
|-
! N-H Bond Length (Å)!! 1.01798
|-
! H-N-H Bond Angle (°)!! 105.74115
|}

<jmol><jmolApplet>
<title>Optimised Ammonia</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>K MUDGAL NH3 OPTIMISATION-1ST LAB RUN.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:K MUDGAL NH3 OPTIMISATION-1ST LAB RUN.LOG| here]]

"Item Table"

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986269D-10
Optimization completed.
-- Stationary point found.

</pre>

===Animating The Vibrations===

[[File:Picture of Display Vibrations Menu of Optimised NH3 (Kartik Mudgal).PNG]]

{| class="wikitable" border="1"
|+ "Table of data for each vibration"
! Wavenumber (cm-1) !! Symmetry !! Intensity
|-
| 1090 || A1 || 145
|-
| 1694 || E || 14
|-
| 1694 || E || 14
|-
| 3461 || A1 || 1
|-
| 3590 || E || 0
|-
| 3590 || E || 0
|}

===Questions on Vibrations===

From the 3N-6 rule, one would expect to see 6 vibrational modes. The degenerate modes are the modes with 1694 cm -1 and 3590 cm -1 wavenumbers. The bending vibrational modes are at 1090 cm -1 & 1694 cm -1. The stretching vibrational modes are at 3590cm -1 & 3461cm- -1. The highly symmetric modes are 3461 cm -1 and 1090 cm -1. The umbrella mode is 1090 cm -1. In the experimental spectrum of gaseous ammonia, one would expect to see 2 bands.

===Picture of Charge Distrubution on Optimised NH3===

[[File:Picture of charge distrubution of Optimised NH3 (Kartik Mudgal).PNG]]

The nitrogen would hold a negative charge whilst the hydrogen would be positive. This is because nitrogen has a greater electronegativity, hence it withdraws a greater amount of electron denisty and forms a partial negative charge on the nitrogen. A partial positive charge would resultantly be formed on the hydrogen, thus forming a neutral molecule overall.

==N2 Molecule==

====Molecule Information====

{| class="wikitable" border="1"
|+ Optimised N2 Molecule
! Name of Molecule !! Nitrogen
|-
! Calculation Method !! RB3LYP
|-
! Basis Set !! 6-31g(D,P)
|-
! Final Energy E(RB3LYP) in atomic units (a.u.) !! -109.52412868
|-
! RMS Gradient !! 0.02473091
|-
! Point Group !! D∞h
|-
! Nitrogen Bond Length (Å)!! 1.11
|-
! Nitrogen Bond Angle (°)!! No bond angle present
|}

<jmol><jmolApplet>
<title>Optimised Nitrogen</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KARTIK MUDGAL N2 OPTIMISATION-1ST RUN.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:KARTIK MUDGAL N2 OPTIMISATION-1ST RUN.LOG| here]]

"Item Table"

<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=-3.401074D-13
Optimization completed.
-- Stationary point found.

</pre>

===Animating The Vibrations===

[[File:Picture of Display Vibrations Menu of Optimised N2 (Kartik Mudgal).PNG]]

{| class="wikitable" border="1"
|+ "Table of data for each vibration"
! Wavenumber (cm-1) !! Symmetry !! Intensity
|-
| 2457 || SGG || 0
|}

===Questions on Vibrations===

N2 has one vibrational mode which is a symmetric mode. This vibrational mode is not IR active as there is no change in overall dipole moment.

===Picture of Charge Distrubution on Optimised N2===

[[File:Charge Analysis of Optimised N2.PNG]]

==H2 Molecule==

====Molecule Information====

{| class="wikitable" border="1"
|+ Optimised H2 Molecule
! Name of Molecule !! Hydrogen
|-
! Calculation Method !! RB3LYP
|-
! Basis Set !! 6-31G(d,p)
|-
! Final Energy E(RB3LYP) in atomic units !! -1.17853936
|-
! RMS Gradient !! 0.00000017
|-
! Point Group !! D∞h
|-
! H-H Bond Length (Å)!! 0.74279
|-
! H-H Bond Angle (°)!! No bond angle Present
|}

<jmol><jmolApplet>
<title>Optimised Hydrogen</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KARTIK MUDGAL H2 OPTIMISED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:KARTIK MUDGAL H2 OPTIMISED STRUCTURE.LOG| here]]

"Item Table"

<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
Optimization completed.
-- Stationary point found.

</pre>

===Animating The Vibrations===

[[File:Picture of Display Vibrations Menu of Optimised H2 (Kartik Mudgal).PNG]]

{| class="wikitable" border="1"
|+ "Table of data for each vibration"
! Wavenumber (cm-1) !! Symmetry !! Intensity
|-
| 4466 || SGG || 0
|}

===Questions on Vibrations===

H2 has one vibrational mode which is a symmetric mode. This vibrational mode is not IR active as there is no change in overall dipole moment.

===Picture of Charge Distrubution on Optimised H2===

[[File:Charge Analysis of Optimised H2.PNG]]

==Structure and Reactivity==

Unique Identifier for the Complex: ABASUR

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=ABASUR&DatabaseToSearch=Published Link to Complex in CCDC]

H-H bond length (Å): 1.00

Difference in H-H Bond Length between the crystal Structure and computational value (Å): 0.25721

The bond length of the H-H bond in the transition metal complex is 1.00 Å. The bond length is shorter in the gaseous H2 molecule than in the transition metal complex (Dihydrogen-(dihydrogen bis(3,5-bis(trifluoromethyl)pyrazolyl)-borate-H,N)-bis(tri-isopropylphosphine)-ruthenium ). This is because in the transition metal complex, Ru-H bonds are also formed with each hydrogen. The dz2 orbital of ruthenium overlaps with the bonding orbital of the H2 bond, thus withdrawing electron density from the bonding orbital to increase the bond length of the H-H bond in the complex. The dxy orbital of ruthenium also overlaps with the anti-bonding orbital to partially weaken the bond and thus further increase the bond length of the H-H bond as well. Hence the H-H bond length in the transition metal complex is longer than in the gaseous molecule.

It is also important to note that because we are using computational methods to analyse our molecular structures, there are going to be error which occur due to the limitations of this computational method. Using a better computational method which takes more parameters into consideration would yield a greater accuracy.

==Energies of the Haber-Bosch Process==

E(NH3)= -56.55777 a.u.

2*E(NH3)= -113.11554 a.u.

E(N2)=-109.52413 a.u.

E(H2)=-1.17854 a.u.

3*E(H2)=-3.53562 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.05579 a.u.

ΔE= -146.47848 kJ/Mol

As this is an exothermic reaction, the product formed is more energetically stable than the reactant. Therefore, the ammonia product is 146.48 kJ/Mol (2dp) more stable than the gaseous reactants (N2 and H2)

==CO Molecule==

====Molecule Information====

{| class="wikitable" border="1"
|+ Optimised CO Molecule
! Name of Molecule !! Carbon Monoxide
|-
! Calculation Method !! RB3LYP
|-
! Basis Set !! 6-31G(d,p)
|-
! Final Energy E(RB3LYP) in atomic units!! -113.30824232
|-
! RMS Gradient !! 0.03370421
|-
! Point Group !! C∞V
|-
! C-O Bond Length (Å)!! 1.13794
|-
! C-O Bond Angle (°)!! No Bond Angle present
|}

<jmol><jmolApplet>
<title>Optimised Carbon Monoxide</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>K MUDGAL CO OPTIMISATION-1ST LAB RUN.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:K MUDGAL CO OPTIMISATION-1ST LAB RUN.LOG| here]]

"Item Table"

<pre>

Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
Predicted change in Energy=-2.221225D-11
Optimization completed.
-- Stationary point found.

</pre>

===Animating The Vibrations===

[[File:Picture of Display Vibrations Menu of Optimised CO (Kartik Mudgal)1.PNG]]

{| class="wikitable" border="1"
|+ "Table of data for each vibration"
! Wavenumber (cm-1) !! Symmetry !! Intensity
|-
| 2209.01 || SG || 67.96
|}

===Questions on Vibrations===

CO has one stretching vibrational mode which is IR active as it results in a change in overall dipole moment. Hence one band should appear in its IR spectrum.

===Picture of Charge Distrubution on Optimised CO===

[[File:Charge Analysis of Optimised CO.PNG]]

The oxygen has a greater electronegativity than the carbon, thus withdrawing a greater amount of electron density and resulting in a partial negative charge forming on the oxygen. The carbon would hold a partial positive charge.

====Molecular Orbitals of CO ====

{| class="wikitable" border="1"
|+ Analysis of chosen Molecular Orbitals of CO
! !! MO 1 !! MO 2 !! MO 3 !! MO 4 !! MO 5
|-
| Image of Molecular Orbital || [[File:Kartik Mudgal (CO) (ENERGY 1) Analysis.PNG|150px]] || [[File:Kartik Mudgal (CO) (ENERGY 4) Analysis.PNG|150px]] || [[File:Kartik Mudgal (CO) (ENERGY 6) Analysis.PNG|150px]] || [[File:Kartik Mudgal (CO) LUMO Analysis.PNG|150px]] || [[File:Kartik Mudgal (CO) HOMO Analysis.PNG|150px]]
|-
| Analysis of Molecular Orbital || This is a non- bonding orbital which is very deep in energy and occupied. The 1S atomic orbital of the oxygen contributes mainly to this molecular orbital. However, this isn't involved in bonding due to being tightly held in by the oxygen atom. || This is a bonding orbital which is partially deep in energy. The contribution mainly occurs from the 2s orbital on the carbon and the 2p orbital on the oxygen. Being occupied, it also resultantly has an effect on the overall bonding of the molecule. || Here, the majority of the contribution to the molecular orbital is from the 2p orbital on each atom, forming a pi bond. It forms an occupied bonding orbital which isn't very deep in energy. || This is the LUMO and therefore high in energy. The contribution to this molecular orbital mainly occurs from the 2p orbitals on each atom which are out of phase to form an anti-bonding orbital. This is unoccupied (hence not having any contribution towards the bonding of the molecule). || This is the HOMO and therefore high in energy. The contributions mainly occur from the two p-orbitals of each atom (evident considering there are nodes on each atom in this bonding orbital). The orbitals are in phase and thus overlap to form a bonding orbital which is occupied.
|}

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, overall very good explanations. For MO2 you could have been more clear that the effect on the overall bonding of the molecule is to increase the bonding. (You say it has an effect but you leave the reader to infer what the effect is, it may seem obvious but you should state exactly what you mean in scientific writing.)

== Independence 0/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

No independent work found.

Rep:Mod:scm4918

2019-03-24T18:15:28Z

Rr1210:

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

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

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

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

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

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

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that The 2 electrons in the H2 bond must be diffused between 3 atoms and therefore lead to a weaker, more dispersed bond. Another reason is that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.

===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

2*E(NH3) = -113.1155375 a.u.

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

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

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of carbon monoxide you would expect to see one band since the single stretching vibration produces a change in dipole moment.

===Atomic Charges===
The charge on the O-atom was found to be -0.506 and 0.506 on the C-atom. This matches the expectation since Oxygen is a more electronegative atom than Carbon and therefore draws electron density towards itself resulting in a relative negative charge.

===Molecular Orbitals===
{| class="wikitable" border="1"
|+ Molecular Orbitals of CO
! MO number
|4
|5
|7
|8
|10
|-
! energy /a.u.
| -0.57004
| -0.46742
| -0.37145
| -0.02178
|0.26241
|-
! image
|[[File:Scm4918_co_mo4.png|200px]]
|[[File:Scm4918_co_mo5.png|200px]]
|[[File:Scm4918_co_mo7.png|200px]]
|[[File:Scm4918_co_mo8.png|200px]]
|[[File:Scm4918_co_mo10.png|200px]]
|}
The 4th MO arises from the antibonding overlap of the 2sAOs.
The 5th MO arises from the bonding overlap of two pAOs oriented perpendicular to the bond.
The 7th MO arises from the bonding overlap of two pAOs oriented along the bond, this is the '''HOMO'''.
The 8th MO arises from the antibonding overlap of two pAOs oriented perpendicular to the bond, this is the '''LUMO'''.
The 10th MO arises from the antibonding overlap of two pAOs oriented along the bond (this orbital is also unoccupied).

A good reason for this molecules stability is the fact that only the bonding pAO based MOs are occupied.

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

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

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 0.5/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES, you have included too many d.p. though, for this method you should report angles to the nearest degree and bond lengths in A to 2 d.p.

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, most answers are correct. However there are only 2 visible peaks in the spectra of NH3, due to the low intensity of the other 2 peaks. (See infrared column in vibrations table.)

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 3/5 ==

Have you completed the calculation and included all relevant information?

YES, you did include a bond angle which is invalid though.

Have you added information about MOs and charges on atoms?

YES, Your explanations are very good but the MO section is a bit short. More details would have increased your mark. The sentence on the molecule's stability is excellent well done!

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

You calculated P4, well done!

Do some deeper analysis on your results so far

MM2athena

2019-03-24T18:07:15Z

Rr1210:

== NH3 Molecule ==

{| class="wikitable"
|Molecule Name
|NH3
|-
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|final energy E(RB3LYP) in atomic units (au)
|<nowiki>-56.55776873</nowiki>
|-
|Point Group
|C3V
|}

=== '''Item Table''' ===
<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

This is my link [https://wiki.ch.ic.ac.uk/wiki/images/e/e4/ATHINAMASOURA_AM12618_PHUNT_NH3_OPTF_POP.LOG ]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ATHINAMASOURA_AM12618_PHUNT_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

N-H bond length : 1.02 Å error: 0.01 Å

H-N-H bond angle : 106o error: 1°

=== Vibrational analysis ===

[[File:AM2 Display Vibrations NH3.PNG]]

{| class="wikitable"
|'''wavenumber''' 
cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|'''symmetry'''
|A1
|E
|E
|A1
|E
|E
|-
|'''intensity''' 
arbitrary units
|145
|14
|14
|1
|0
|0
|-
|'''image'''
|[[File:1.PNG|160px]]
|[[File:2.PNG|180px]]
|[[File:3.2.PNG|180px]]
|[[File:4.2.PNG|170px]]
|[[File:5.PNG|190px]]
|[[File:6.2.PNG|150px]]
|}
* Number of modes expected using 3N-6 rule : 6
* Degenerated Modes : 2 modes of wavenumber 1694cm-1 and 2 of wavenumber 3590 cm-1
* "bending" vibrations: 1090 cm-1 , 1694 cm-1 (both of them)
* "bond stretch" vibrations: 3461cm-1 and 3590 cm-1 (both of them)
* Highly symmetric mode: 3461 cm-1
* Umbrella mode: 1090 cm-1
* Expected number of bands in experimental spectrum of gaseous ammonia: In the IR spectrum we need to see a change in dipole moment so we would expect 3 but we see only 2 ( 1090 cm-1 , 1694 cm-1) because 2 of the modes are degenerated. The ones with intensity 0 are not show and also the vibrational mode of wavenumber 3461 cm-1 does not have a change in dipole moment(it is symmetrical)

=== '''Charge Distribution''': ===

Nitrogen (N) is more electronegative and pulls electron density away from than Hydrogen (H) therefore the expected charge on Nitrogen will be negative and the one on Hydrogen positive. Since there are three H atoms present and the molecule is neutral, the charge on the Nitrogen will be three times the charge of each hydrogen atom

Expectation is in agreement with our calculations.

According to calculations charge on Nitrogen is -1.125 and charge on a hydrogen atom is +0.375

[[File:Charge distribution on NH3 molecule am12618.PNG|300px]] [[File:2Charge distribution on NH3 molecule am12618.PNG|300px]]

== N2 Molecule==

{| class="wikitable"
|Molecule Name
|N2
|-
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|final energy E(RB3LYP) in atomic units (au)
|<nowiki>-109.52412868</nowiki>
|-
|Point Group
|D*H
|}

=== '''Item Table''' ===
<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
</pre>

This is my link [https://wiki.ch.ic.ac.uk/wiki/images/2/2d/AthinaMasoura_am12618_PHunt_N2_optf_pop.LOG]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>AthinaMasoura_am12618_PHunt_N2_optf_pop.LOG</uploadedFileContents>
</jmolApplet></jmol>

Bond Length: 1.11 Å error: 0.01 Å

Bond Angle: 180o error 1o

=== Vibrational analysis ===

[[File:AM2 Display Vibrations N2.PNG]]

{| class="wikitable"
!'''wavenumber''' 
cm-1
!2457
|-
|'''symmetry'''
|SGG
|-
|'''intensity''' 
arbitrary units
|0
|-
|'''image'''
|[[File:N2 vibrational mode.PNG|200px]]
|}
* Number of modes expected using 3N-5 rule : 1
* Degenerated Modes : 0
* "bending" vibrations: 0
* "bond stretch" vibrations: 2457 cm-1
* Highly symmetric mode: 2457 cm-1
* Umbrella Mode: -
* Expected number of bands in experimental spectrum :0 (no dipole moment)

=== '''''Charge Distribution''''': ===
The Homonuclear diatomic molecule is neutral and since it is consisted of two Nitrogen(N) atoms, each one of them has charge of zero

Expectation is in agreement with our calculations.

According to calculations charge on each Nitrogen atom is 0

[[File:2Charge distribution on N2 molecule am.PNG]]

=== Mono-metallic Transition Metal complex ===

From Research at ConQuest, one transition metal complex that containes H2 is the one linked here [[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=ORGND7&year=2017&spage=3654&volume=36&id=doi:10.1021/acs.organomet.7b00632&pid=ccdc:1530725]]

Unique Identifier : YECMOL

The distance between the two Nitrogen atoms in the metal complex is 1.108 Å. When the bond distance of two nitrogen atoms was calculated it was found to be 1.10550 Å ( with all d.p). The small difference present indicates that the bond between the 2 nitrogens in the metal complex is longer than the bond we calculated in the optimised structure. This is because the electron density at the N≡N homonuclear diatomic molecule is distributed evenly between the two atoms whereas in the complex, the electron density is pulled away from the bond between the nitrogens and goes towards the bond of the one nitrogen with the transition metal. This makes the bond of N≡N weaker therefore longer than the one in the N≡N molecule.
Comparing the optimised bond distance to the crystal structure bond distance in 2 d.p. though, we can see that they are exactly the same. We should therefore take into account errors which possibly occured from the computational calculation method. If the bond distance of N≡N was determined experimentally it would have been more accurate and probably shorter. To get a bigger difference between the bond lengths one way would be to optimise the optimised molecule, and then repeat the procedure. This time we could improve the accuracy by using a better computational method (not RB3LYP) that has more parameters to optimise.

[[File:Transition Metal complex YECMOL withbonddistance.PNG]]

==H2 Molecule==
{| class="wikitable"
!Molecule Name
!H2
|-
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|final energy E(RB3LYP) in atomic units (au)
|<nowiki>-1.17853936</nowiki>
|-
|Point Group
|D*H
|}

=== '''Item Table''' ===
<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
</pre>

This is my link [https://wiki.ch.ic.ac.uk/wiki/images/f/fc/AthinaMasoura_am12618_PHunt_h2_optf_pop.LOG]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>AthinaMasoura_am12618_PHunt_h2_optf_pop.LOG</uploadedFileContents>
</jmolApplet></jmol>

Bond Length: 0.75 Å (2 d.p) error: 0.01 Å

Bond Angle: 180o error: 1o

=== Vibrational analysis ===

[[File:AM2 Display Vibrations H2.PNG]]

{| class="wikitable"
!'''wavenumber''' 
cm-1
!4466
|-
|'''symmetry'''
|SGG
|-
|'''intensity''' 
arbitrary units
|0
|-
|'''image'''
|[[File:Vibrational Mode of H2.PNG|200px]]
|}
* Number of modes expected using 3N- rule : 1
* Degenerated Modes : 0
* "bending" vibrations: 0
* "bond stretch" vibrations: 4466 cm-1
* Highly symmetric mode: 4466 cm-1
* Umbrella mode: -
* Expected number of bands in experimental spectrum: 0 (no dipole moment)

=== '''Charge Distribution''': ===
The homonuclear diatomic molecule is neutral and since it is consisted of two Hydrogen(H) atoms, each one of them has charge of zero

Expectation is in agreement with our calculations.

According to calculations charge on each hydrogen atom is 0

[[File:Charge distribution H2.PNG]]

=== Mono-metallic Transition Metal complex ===

From Research at ConQuest, one transition metal complex that containes H2 is the one linked here [[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=ORGND7&year=2007&spage=4498&volume=26&id=doi:10.1021/om700480t&pid=ccdc:664160]]

Unique Identifier: CILXAX

[[File:Transition metal complex.PNG]]

The exact bond distance calculated for the H-H bond was 0.74279 Å. The bond distance of the same bond in the transition metal complex is 0.753 Å. The small difference present indicates that the bond between the 2 hydrogens in the metal complex is longer than the bond we calculated in the optimised structure. This is because the electron density at the H-H homonuclear diatomic molecule is distributed evenly between the two atoms whereas in the complex, the electron density is pulled away from the bond between the H atoms and goes towards the bonds that these hydrogens form with the transition metal . This makes the bond of H-H weaker therefore longer than the one in the H-H molecule.
Comparing the optimised bond distance to the crystal structure bond distance in 2 d.p. though, we can see that they are exactly the same. We should therefore take into account errors which possibly occured from the computational calculation method. To get a bigger difference between the bond lengths one way would be to optimise the optimised molecule, and then repeat the procedure. This time we could improve the accuracy by using a better computational method (not RB3LYP) that has more parameters to optimise. This would result in a larger difference between the bond lengths of the two ( H-H, and transition metal complex of H-H)

==Haber-Bosch process==
'''N2 + 3H2 -> 2NH3'''

E(NH3)= -56.55776873 au (7 d.p.)= - 148492.421 kJmol-1

2*E(NH3)= -113.1155375 au (7 d.p.)=-296984.8437 kJmol-1

E(N2)=-109.52412868 au (7 d.p.)= - 287555.5998 kJmol-1

E(H2)= -1.17853936 au (7 d.p.)=-3094.25509 kJmol-1

3*E(H2)= -3.53561808 au ( 7 d.p.)= - 9282.765269 kJmol-1

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au

ΔE=-146.5 (1 d.p) kJmol-1

The products are lower in energy than the reactants ( Energy has a more negative value) therefore they are more stable. The reaction towards the products is more thermodynamically feasible because ΔG is negative.

== ClF3==

{| class="wikitable"
|Molecule Name
|Clf3
|-
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|final energy E(RB3LYP) in atomic units (au)
|<nowiki>-759.46531688</nowiki>
|-
|Point Group
|CS
|}

=== '''Item Table''' ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000232 0.001800 YES
RMS Displacement 0.000142 0.001200 YES

</pre>

This is my link [https://wiki.ch.ic.ac.uk/wiki/images/5/58/ATHINAMASOURA2_AM12618_PHUNT_CLF3_OPTF_POP.LOG]

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ATHINAMASOURA2_AM12618_PHUNT_CLF3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:Molecule labels.PNG|200px]]

Bond Lengths: 1.73 Å (Cl-F3), 1.73 Å (Cl-F4), 1.65 Å (Cl-F2) (in 2 d.p) error: 0.01 Å

Bond Angles : 87o (F2-Cl-F3) , 87o (F2-Cl-F4), 174 o (F3-Cl-F4) (O d.p) error: 1o

The bond angles seem absurd because the correct structure of the molecule is T-shaped because the 2 lone pairs on Chlorine are in the equatorial position. Therefore the bond angles should have been 90 between F-Cl-F and 180. The difference is because the angles were calculated using computational methods. Therefore there are possible errors that might occur. To get the correct values of angles one way would be to optimise the optimised molecule, and then repeat the procedure. This time a more accurate calculation method could be used (not RB3LYP) that has more parameters to solve.

However, if one searches for all the possible angles of this molecule there are many values found on the web. For example [[http://www.chemtube3d.com/VSEPRShapeClF3.html]].

Also according to other sources for example [[https://chem.libretexts.org/Courses/University_of_California_Davis/UCD_Chem_002A/UCD_Chem_2A/Text/Unit_IV%3A_Electronic_Structure_and_Bonding/09%3A_Chemical_Bonding_I%3A_Basic_Concepts/9.07%3A_The_Shapes_of_Molecules]] the shape is T-shape but due to the lone pair repulsions the F–Cl–F angle is less than 180°.

=== Vibrational analysis ===

[[File:AM2 Display Vibrations ClF3.PNG]]

{| class="wikitable"
!'''wavenumber''' 
cm-1
!305
|309
|401
|541
|736
|753
|-
|'''symmetry'''
|A'
|A''
|A'
|A'
|A'
|A'
|-
|'''intensity''' 
arbitrary units
|14
|18
|2
|3
|38
|370
|-
|'''image'''
|[[File:Vibrational mode clf3 1.PNG|150px]]
|[[File:Vibrational mode clf3 2.PNG|155px]]
|[[File:Vibrational mode clf3 3.PNG|150px]]
|[[File:Vibrational mode clf3 4.PNG|150px]]
|[[File:Vibrational mode clf3 5.PNG|170px]]
|[[File:Vibrational mode clf3 6.PNG|150px]]
|}

* Number of modes expected using 3N-6 rule : 6
* Degenerated Modes : 0
* "bending" vibrations: 305 cm-1 , 309 cm-1 , 401 cm-1
* "bond stretch" vibrations: 541 cm-1, 736 cm-1 , 753 cm-1

=== '''Charge Distribution:''' ===

Fluorine atoms are more electronegative than the Chlorine atom therefore they withdraw electron density away from it. Also the 2 fluorine atoms have about the same distance from the centre atom therefore they will have the same charge and the other one a bit different one. All of their charges are negative. The sum of all the charges on atoms should be negative therefore chlorine has a positive charge with magnitude equal to the sum of the negative charges on fluorine atoms.

Expectation is in agreement with our calculations.

According to calculations charge on Chlorine is + 1.125

Charge of each fluorine atoms that has a bond distance 1.73 Å from the chlorine atom : -0.454

Charge of fluorine atom of bond distance 1.65 Å : -0.316

[[File:Charge distribution1.PNG|300px]] [[File:Charge distribution2.PNG|270px]]

=== Molecular Orbitals ===

The Orbitals shown are the solutions to the Schrödinger equation [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year1/10_mos_n2.html]

{| class="wikitable"
!Molecular Orbital
!1
!9
!10
!13
!15
|-
|Character of MO
|The energy of MO is -101.79317 au. This means that the orbitals of Cl, F1, F2, and F3 are very deep in energy. The electrons are very close to the nucleus-They are very deep in core, so the orbitals are not involved in bonding.
|The energy of the MO is -1.28165 au. Here we can visualize the s orbitals of all the atoms (as spheres) overlapping. The MO is bonding so all the s orbitals overlap together to form bonds.

The MO is occupied
|The energy of the MO is -1.17371 au. What is shown is the p orbitals (parallel) of F3 and Cl overlapping.The same p atomic orbital of Cl is overlapping with a p orbital of F4. These are all bonding orbitals, whereas the s orbital of F2 is antibonding to the s orbital of chlorine.Consequently the MO is a mixture of bonding and antibonding. ( we can see a nodal plane- electrons are not along the bond)

The MO is occupied
|The energy of the MO is -0.59476 au. Here, a p orbital of the F3 overlaps with the p orbital of Chlorine. The p orbitals are parallel. Also, that p orbital of Cl overlaps with one p orbital of F4 that is parallel to it. These are all bonding orbitals.There are sigma interactions along the bonds. However there is an antibonding orbital between the s orbital of the F2 atom and the p orbital of Cl. Consequently the MO is a mixture of bonding and antibonding. ( we can see a nodal plane- electrons are not along the bond).

The MO is occupied
|The energy of the MO is -0.53821 au. Here all the parallel p atomic orbitals of all the atoms overlap with each other resulting in a bonding MO. We see a nodal plane because of the nodal plane present in the p orbitals when there is change of phase.

The MO is occupied
|-
|Image
|[[File:AM MO 1.PNG|300px]]
|[[File:2AM MO 9.PNG|300px]]
|[[File:2AM MO 10.PNG|320px]]
|[[File:2AM MO 13.PNG|300px]]
|[[File:2AM MO 15.PNG|320px]]
|}

[[File:HOMO LUMO AM.PNG]]

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, overall good, but you have left all the jmol captions as the default “test molecule” this gives the reader no information.

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES, good detailed explanation, well done!

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES, in general most molecules are not shaped exactly perfect. This is often due to a principle call Jahn-Teller distortion, you will learn more about this later!

Have you added information about MOs and charges on atoms?

YES, very good effort with your explanations, well done for explaining the impact of the interactions between the AOs on the bonding in the molecule. MO 10 is actually s orbitals, not p, and MO13 is all p orbitals. The F-Cl interactions are bonding, there are no nodes across the bonds, the node is at the F atom because it has a p orbital.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You looked up and added extra details from the literature, well done!

Rep:Mod:SJL1218

2019-03-24T17:56:37Z

Rr1210:

== NH3 Molecule ==

==== NH3 Optimisation Summary ====
{| class="wikitable"
|Molecule
|NH3
|-
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-56.55776873</nowiki>
|-
|RMS Gradient Norm
|0.00000485
|-
|Point Group
|C3V
|}

=== NH3 Items List, Model and Structural Information ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986271D-10
Optimization completed.
-- Stationary point found.
</pre>

<jmol><jmolApplet>
<title>Ammonia</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SJL1218_NH3_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

N-H bond distance: 1.02Å

H-N-H bond angle: 106°

[[SJL1218_NH3_OPT_POP.LOG| link to .log file]]

=== NH3 Vibrations and Atomic Charges ===
'''Vibrational Modes'''

[[File:Sjl1218_nh3_displayvibs.PNG]]
{| class="wikitable"
|Wavenumber cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity (arbitary units)
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:Sjl1218_nh3_1090v.PNG|150px]]
|[[File:Sjl1218_nh3_1694v.PNG|150px]]
|[[File:Sjl1218_nh3_1694vv.PNG|150px]]
|[[File:Sjl1218_nh3_3461v.PNG|150px]]
|[[File:Sjl1218_nh3_3590v.PNG|150px]]
|[[File:Sjl1218_nh3_3590vv.PNG|150px]]
|}

==== NH3 Vibrations Questions ====
'''How many modes do you expect from the 3N-6 rule?'''

3(4 atoms)-6 = 6 vibrational modes.

'''Which modes are degenerate?'''

Two modes with wavenumber 1694cm-1 and two modes with wavenumber 3590cm-1 are degenerate.

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

Bending modes: 1090cm-1, 1694cm-1.

Vibrational modes: 3461cm-1, 3590cm-1.

'''Which mode is highly symmetric?'''

Vibrational mode 3461cm-1 is highly symmetric

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

Bending mode 1090cm-1

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

4 bands

'''Atomic Charges'''

[[File:Sjl1218_nh3_atomiccharge.PNG]]

Nitrogen Charge: -1.125C

Hydrogen Charge: 0.375C

Nitrogen is expected to have a negative charge because it is more electronegative, and hydrogen to be positive because it it less electronegative.

== N2 and H2 Molecule ==

=== N2 Optimisation Summary ===
{| class="wikitable"
|Molecule
|N2
|-
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-109.52412868</nowiki>
|-
|RMS Gradient Norm
|0.00000003
|-
|Point Group
|D*H
|}

=== N2 Items List, Model and Structural Information ===
<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 0.000000 0.001200 YES
Predicted change in Energy=-1.075650D-15
Optimization completed.
-- Stationary point found.
</pre>

<jmol><jmolApplet>
<title>Nitrogen</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SJL1218_N2_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

N-N bond distance: 1.11Å

[[SJL1218_N2_OPT_POP.LOG| link to .log file]]

=== N2Vibrations and Atomic Charges ===
'''Vibrational Modes'''

[[File:Sjl1218_n2_displayvibs.PNG]]

{| class="wikitable"
|Wavenumber cm-1
|2457
|-
|Symmetry
|SGG
|-
|Intensity (arbitary units)
|0
|-
|Image
|[[File:Sjl1218_n2_2457v.PNG|200px]]
|}
'''Atomic Charges'''

[[File:Sjl1218_n2_atomiccharge.PNG]]

Nitrogen Charge: 0C

Same atom so there are no electronegative differences.

=== H2 Optimisation Summary ===
{| class="wikitable"
|Molecule
|H2
|-
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-1.17853936</nowiki>
|-
|RMS Gradient Norm
|0.00002276
|-
|Point Group
|D*H
|}

=== H2 Items List, Model and Structural Information ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000039 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000052 0.001800 YES
RMS Displacement 0.000073 0.001200 YES
Predicted change in Energy=-2.043043D-09
Optimization completed.
-- Stationary point found.
</pre>

<jmol><jmolApplet>
<title>Hydrogen</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SJL1218_H2_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

H-H bond distance: 0.72Å

[[SJL1218_H2_OPT_POP.LOG| link to .log file]]

=== H2 Vibrations and Atomic Charges ===
'''Vibrational Modes'''

[[File:Sjl1218_h2_displayvibs.PNG]]

{| class="wikitable"
|Wavenumber cm-1
|4466
|-
|Symmetry
|SGG
|-
|Intensity (arbitary units)
|0
|-
|Image
|[[File:Sjl1218_h2_4466v.PNG|200px]]
|}
'''Atomic Charges'''

[[File:Sjl1218_h2_atomiccharge.PNG]]

Hydrogen Charge: 0C

Same atom so there are no electronegative differences.

=== N2 Conquest Search ===

Mono-metallic TM complex that coordinates N-N

Formula: C44H54N4P4RuW

Name: (1,1'-bis(Diethylphosphino)ruthenocene-P,P')-bis(dinitrogen-N)-bis(diphenyl(methyl)phosphino)-tungsten

Unique Identifier: CUHVAD

link to CCDC: [[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=ORGND7&year=2009&spage=4741&volume=28&id=doi:10.1021/om900298g&pid=ccdc:759201]]

[[File:sjl1218_n2_complex.PNG|300px]]

N-N bond distance in diatomic N2: 1.11Å

N-N bond distances in C44H54N4P4RuW: 1.14Å and 1.16Å<ref name="N-NBond" />

The N-N bond in tungsten transition metal complex has a longer and weaker bond than on its own as a molecule. This is due to the electron withdrawal property of the tungsten cation; electron density shifts from the N-N domain to the centre of the complex. Thus, the bond order of the N-N bond decreases, suggesting that the bond is weakened and increases in length. The experimental value will be the exact value whereas the bond length found using Gaussian is only an approximation, not taking into account any ionic character or other factors involved.

== The Haber-Bosch process ==
'''N2 + 3H2 → 2NH3'''

E(NH3)= -56.5577687 a.u.(7 d.p)

2*E(NH3)= -113.1155375 a.u. (7 d.p)

E(N2)= -109.5240412 a.u. (7 d.p)

E(H2)= -1.1785394 a.u. (7 d.p)

3*E(H2)= -3.5356181 a.u. (7 d.p)

ΔE= 2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 a.u. (6 d.p)

ΔE= -146.5 kJ mol-1

The products are more stable because the reaction is exothermic so ammonia will end up with lower energy.

== Choice of Small Molecule- CO ==

=== CO Optimisation Summary ===
{| class="wikitable"
|Molecule
|CO
|-
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-113.30945314</nowiki>
|-
|RMS Gradient Norm
|0.00000202
|-
|Point Group
|C*V
|}

=== CO Items List, Model and Structural Information ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-4.844559D-12
Optimization completed.
-- Stationary point found.
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SJL1218_CO_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

C-O bond distances: 1.14Å

[[SJL1218_CO_OPT_POP.LOG| link to .log file]]

=== CO Vibrations and Atomic Charges ===
'''Vibrational Modes'''

[[File:Sjl1218_co_displayvibs.PNG]]
{| class="wikitable"
|Wavenumber cm-1
|2209
|-
|Symmetry
|SG
|-
|Intensity (arbitary units)
|68
|-
|Image
|[[File:Sjl1218_co_2209v.PNG|150px]]
|}
'''Atomic Charges'''

[[File:sjl1218_co_atomiccharge.PNG]]

Carbon Charge: 0.506C

Oxygen Charge: -0.506C

Oxygen has a negative charge because it is more electronegative than carbon.

=== CO Molecular Orbitals ===
{| class="wikitable"
|Molecular Orbital
|3σg
|4σ*u
|1πu
|5σg 
|1π*g 
|-
|Images
|[[File:sjl1218_mo_3sigma.PNG|150px]]
|[[File:sjl1218_mo_4sigma.PNG|150px]]
|[[File:sjl1218_mo_1pi.PNG|150px]]
|[[File:sjl1218_mo_5sigma.PNG|150px]]
|[[File:sjl1218_mo_1pi_star.PNG|150px]]
|-
|Atomic Orbitals that contribute
|Carbon 2s

Oxygen 2s
|Carbon 2s/2p

Oxygen 2s/2p

(s-p mixing)
|Carbon 2p

Oxygen 2p
|Carbon 2s/2p

Oxygen 2s/2p

(s-p mixing)
|Carbon 2p

Oxygen 2p
|-
|Type of MO bonding
|Bonding
|Antibonding
|Bonding
|Bonding
|Antibonding
|-
|Depth of energy
|E= -1.16eV (in the HOMO/LUMO region)
|E= -0.57eV (in the HOMO/LUMO region)
|E= -0.47eV (in the HOMO/LUMO region)
|E= -0.37eV (in the HOMO/LUMO region)
|E= -0.02eV (in the HOMO/LUMO region)
|-
|Occupancy
|Occupied
|Occupied
|Occupied
|Occupied
|Unoccupied
|-
|Effect MO has on bonding
|Large effect on bonding. Formed from 2s AOs which are large and overlaps effectively.
|Large effect on bonding. Formed from s-p mixed AOs which are large and overlaps between the atoms effectively. Higher in energy than 3σ because this is an antibonding MO.
|Large effect on bonding. 2p-2p AOs are close in energy thus forming a strong contribution to the overall bonding.
|Significant effect on bonding. This orbital is the HOMO contributed from s-p mixed AOs forming a strong overlap.
|Significant effect on bonding. This orbital is the LUMO formed from 2p-2p AOs that are close in energy, hence strong interaction.
|}

== CH4 Molecule ==

{| class="wikitable"
|Molecule
|NH3
|-
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-40.52401404</nowiki>
|-
|RMS Gradient Norm
|0.00003263
|-
|Point Group
|TD
|}

=== CH4 Items List, Model and Structural Information ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES
Predicted change in Energy=-2.256043D-08
Optimization completed.
-- Stationary point found.
</pre>

<jmol><jmolApplet>
<title>Methane</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SJL1218_CH4_OPT_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

C-H bond distance: 1.09Å

H-C-H bond angle: 109°

[[SJL1218_CH4_OPT_POP.LOG| link to .log file]]

=== CH4 Vibrations and Atomic Charges ===
'''Vibrational Modes'''

[[File:Sjl1218_ch4_displayvibs.PNG]]
{| class="wikitable"
|Wavenumber cm-1
|1356
|1356
|1356
|1579
|1579
|3046
|3162
|3162
|3162
|-
|Symmetry
|T2
|T2
|T2
|E
|E
|A1
|T2
|T2
|T2
|-
|Intensity (arbitary units)
|14
|14
|14
|0
|0
|0
|25
|25
|25
|-
|Image
|[[File:Sjl1218_ch4_1358v.PNG|150px]]
|[[File:Sjl1218_ch4_1358vv.PNG|150px]]
|[[File:Sjl1218_ch4_1358vvv.PNG|150px]]
|[[File:Sjl1218_ch4_1579v.PNG|150px]]
|[[File:Sjl1218_ch4_1579vv.PNG|150px]]
|[[File:Sjl1218_ch4_3046v.PNG|150px]]
|[[File:Sjl1218_ch4_3162v.PNG|150px]]
|[[File:Sjl1218_ch4_3162vv.PNG|150px]]
|[[File:Sjl1218_ch4_3162vvv.PNG|150px]]
|}

'''Atomic Charges'''

[[File:sjl1218_ch4_atomiccharge.PNG]]

Carbon Charge: -0.930C

Hydrogen Charge: 0.233C

Carbon has a negative charge because it is more electronegative than hydrogen.

<references>
<ref name="N-NBond">M.Yuki, T.Midorikawa, Y.Miyake, Y.Nishibayashi CCDC 759201: Experimental Crystal Structure Determination, 2010.</ref>
</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 0.5/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, most answers are correct. However there are only 2 visible peaks in the spectra of NH3, due to the low intensity of the other 2 peaks. (See infrared column in vibrations table.)

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, very good explanations overall. However the LUMO does not have an effect on the bonding within the molecule as it is unoccupied so does not effect the electrons or interactions in the molecule. In a reaction it could become at least partially occupied so it would have an impact on reactivity.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

You calculated CH4, well done!

Do some deeper analysis on your results so far

Rep:Mod:01509348

2019-03-24T17:49:42Z

Rr1210:

== NH3 ==

===NH3 optimisation===
{| class="wikitable" border="1"
|+ NH3 summary
| molecule || NH3
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d,p)
|-
| E(RB3LYP) ||-56.55776873a.u.
|-
|RMS Gradient Norm || 0.00000485a.u.
|-
| Point Group ||C3V
|}
{| class="wikitable" border="1"
|+ additional information of NH3
| bond length of NH || 1.11 Å
|-
| bond angle of H-N-H || 106 degree
|}

=== bond length of NH ===
1.11 Å

=== bond angle of H-N-H ===
106 degree
===item table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES

</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YINGTINGJIA NH3 OPTF POP GJF.LOG</uploadedFileContents>
<script>frame 1.17 </script>

</jmolApplet></jmol>

The optimisation file is liked to [[Media:YINGTINGJIA NH3 OPTF POP GJF.LOG| here]]

[[File:Screen shot of display vibrations.PNG]]

{| class="wikitable" border="1"
|+ vibrations
|-
| wavenumbercm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
|symmetry || A1 || E || E || A1 || E || E
|-
| intensity arbitrary units || 146 || 14 || 14 || 1 || 0 || 0
|-
|screen shot of vibration mode ||[[File:Yingting.JiaNH3 MODE1.PNG|250px|]] || [[File:Yingting Jia NH3 2.PNG|250px|]] || [[File:YingtingJia NH3 3.PNG|250px|]] || [[File:Yingting.JiaNh34.PNG|250px|]]|| [[File:Yingting JiaNH3 5.PNG|250px|]] ||[[File: YingtingJiaNH3 6.PNG|250px|]]
|-

|}
{| class="wikitable" border="1"
|+ NH3 questions
|-
| number of vibration modes || 3
|-
| degenerate || 1694cm-1,3590 cm-1
|-
| bending || 1090cm-1,1694cm-1,1694cm-1
|-
| stretching || 3461cm-1,3590cm-1,3590cm-1
|-
| highly symmetric || 3461cm-1
|-
|umbrella || 1090cm-1
|-
|number of bands in an experimental spectrum of gaseous ammonia || 2
|}

===Charge of atoms in NH3===
{| class="wikitable" border="1"
|+
! atom !! charge
|-
| N || -1.125
|-
| H || 0.375
|}
charge expected for N is negative as N is much more electronegative than H, so it draws majority of electron density, giving a negative charge. whereas H shows partial positive, giving a positive charge.

==N2==
===N2 optimisation===
{| class="wikitable" border="1"
|+ summary of N2
|-
| molecule || N2
|-
|Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d,p)
|-
| E(RB3LYP) || -109.52412868a.u.
|-
| RMS Gradient Norm || 0.00000365a.u.
|-
| Point Group ||D*H
|}

===bond length of NN ===
1.10550 Å
===item table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000002 0.001800 YES
RMS Displacement 0.000003 0.001200 YES
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YINGTINGJIA N2 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.13 </script>

</jmolApplet></jmol>
The optimisation file is liked to [[Media:YINGTINGJIA N2 OPTF POP.LOG| here]]
[[File:screen shot of display vibration of N2.PNG]]

{| class="wikitable" border="1"
|+ vibrations of N2
|-
| wavenumbercm-1 || 2457
|-
|symmetry || SGG
|-
| intensity arbitrary units || 0
|-
|}

{| class="wikitable" border="1"
|+ N2 questions
|-
| number of vibration mode || 1
|-
| degenerate || only has one frequency of 2457 cm-1
|-
| bending || N/A
|-
| stretching || 2457
|-
| highly symmetric || 2457
|-
|umbrella || N/A
|-
|number of bands in an experimental || N/A
|}

===Charge of atoms in N2===
{| class="wikitable" border="1"
|+
! atom !! charge
|-
| N || 0.000
|-
| N || 0.000
|}
the charge on both N atoms should be zero since there is no electronegativity in N2, no permanent dipole, even distribution of electron density
===mono-metallic TM complex that coordinates N2===
{| class="wikitable" border="1"
|+
|-
|unique identifier || DAYSUR
|-
|compound name ||mer-Chloro-dinitrogen-(methylisocyanide)-tris(trimethylphosphite)-rhenium(i)
|-
| distance in crystal structure || 1.04 Å
|-
| computational distances || 1.11 Å
|}
The bond length crystal structure is different from computational distance. This is due to the fact that there is interaction(coordination) between the NN bond and the functional groups in the crystal structure. The dithiophosphinato ligand which is trans to N2 ligand is a better electron-donor which shortens Re-N and N-N.[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DAYSUR&DatabaseToSearch=Published]] <ref name="DAYSUR"/>

==H2 ==
===H2 optimisation===
{| class="wikitable" border="1"
|+ H2 summary
| molecule || H2
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d,p)
|-
| E(RB3LYP) ||-1.17853936a.u.
|-
|RMS Gradient Norm ||0.00012170a.u.
|-
| Point Group ||D*H
|}
===bond length of HH ===
0.74 Å
===Item table ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000211 0.000450 YES
RMS Force 0.000211 0.000300 YES
Maximum Displacement 0.000278 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YINGTINGJIAT H2 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.15 </script>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:YINGTINGJIAT H2 OPTF POP.LOG| here]]
[[File:Screen shot of display vibration of H2.PNG]]
{| class="wikitable" border="1"
|+ vibrations of H2
|-
| wavenumbercm-1 || 4461
|-
|symmetry || SGG
|-
| intensity arbitrary units || 0
|-
|}
{| class="wikitable" border="1"
|+ H2 questions
|-
|number of mode || 1
|-
| degenerate || only has one frequency of 4461 cm-1
|-
| bending || N/A
|-
| stretching || 4461 cm-1
|-
| highly symmetric || 4461cm-1

|-
|umbrella || N/A
|-
|number of bands in an experimental spectrum || N/A
|}

===Charge of atoms in H2===
{| class="wikitable" border="1"
|+
! atom !! charge
|-
| H || 0.000
|-
| H || 0.000
|}
the charge expected for both H2 atoms should be zero as there is no difference in electronegativity, no permanent dipole, electron density distributed evenly.

==energy for Haber-Bosch process==
E(NH3)=-56.55776873a.u
2*E(NH3)=-113.1155375a.u

E(N2)=-109.52412868a.u

E(H2)= -1.17853936a.u.

3*E(H2)= -3.5356179a.u

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.05579074a.u=-146.5 kJ/mol
Therefore, energy for converting hydrogen and nitrogen gas into ammonia gas is -146.5 kJ/mol, product is more stable as reaction is exothermic, so product is lower in energy.

==CO molecule==
CO optimisation
{| class="wikitable" border="1"
|+ CO summary
| molecule || CO
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d,p)
|-
| E(RB3LYP) ||-113.30945314 a.u.
|-
|RMS Gradient Norm ||0.00000433 a.u.
|-
| Point Group ||C*V
|}
{| class="wikitable" border="1"
|+ additional information of CO
| bond length of CO || 1.14 Å
|}
===ITEM TABLE===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES

</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YINGTING JIA CO OPTF POP.LOG</uploadedFileContents>
<script>frame 1.11</script>
</jmolApplet></jmol>
The optimisation file is liked to [[Media:YINGTING JIA CO OPTF POP.LOG| here]]

[[File:JYT Screen shot of display vibration of CO.PNG]]

{| class="wikitable" border="1"
|+ vibrations of CO
|-
| wavenumbercm-1 || 2209
|-
|symmetry || SG
|-
| intensity arbitrary units || 68
|-
|}
{| class="wikitable" border="1"
|+ CO questions
|-
|number of vibration mode || 1
|-
| degenerate || only has one frequency of 2209 cm-1
|-
| bending || N/A
|-
| stretching || 2209 cm-1
|-
| highly symmetric || 2209 cm-1
|-
|umbrella || N/A
|-
|number of bands in an experimental spectrum || 1
|}

===Charge of atoms in CO===
{| class="wikitable" border="1"
|+
! atom !! charge
|-
| C || 0.506
|-
| O ||-0.506
|}
O is more electronegative than C, so O drags electron density to itself, showing a negative charge. C is electropositive, so it has a positive charge.
===mono-metallic TM complex that coordinates CO===
{| class="wikitable" border="1"
|+
|-
|unique identifier || ACOJEK
|-
|compound name ||fac-tricarbonylchloridobis(4-hydroxypyridine)rhenium(i) pyridin-4(1H)-one solvate
|-
| distance in crystal structure || 1.152(5) Å,1.156(8) Å, 1.333(7) Å
|-
| computational distances || 1.13 Å
|}
Distance in crystal structure is longer than computational distance this is because of the interaction between the CO bond and rest of ligands in the crystal structure. when C binds to Re atom, it is destabilised since the electrons can not delocalised to have resonance form, causing the lengthen of CO distance.[[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=ACSECI&year=2017&spage=1551&volume=73&id=doi:10.1107/S2056989017013512&pid=ccdc:1575682]] <ref name="ACOJEK"/>

==O2==
===O2 optimisation===
{| class="wikitable" border="1"
|+ O2 summary
| molecule || O2
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d,p)
|-
| E(RB3LYP) || -150.25250603 a.u.
|-
|RMS Gradient Norm ||0.00007502 a.u.
|-
| Point Group ||D*H
|}

==CO2==
CO2 optimisation
{| class="wikitable" border="1"
|+ CO2 summary
| molecule || CO2
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d,p)
|-
| E(RB3LYP) ||-188.58093945 a.u.
|-
|RMS Gradient Norm ||0.00001154 a.u.
|-
| Point Group ||D*H
|}
===bond length of C=O in CO2 ===
1.17Å

===item table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YINGTING JIA CO2 OPTF.LOG</uploadedFileContents>
</jmolApplet></jmol>
The optimisation file is liked to [[Media:YINGTING JIA CO2 OPTF.LOG| here]]
[[File:Jyt screen shot of CO2.PNG]]

===Charge of atoms in CO2===
{| class="wikitable" border="1"
|+
! atom !! charge
|-
| C || 1.022
|-
| O ||-0.511
|}

==Energy of reaction involves CO==

2CO+O2-> 2CO2

E(CO)=-113.30945314 a.u.

E(O2)=-150.25250603 a.u.

2*E(CO)=-226.6189063 a.u.

E(CO2)=-188.58093945 a.u.

2*E(CO2)=-377.1618789 a.u

ΔE=2*E(CO2)-(2*E(CO2)+E(O2))=-0.29046659 a.u= -762.6kJ/mol

product CO2 is more stable than reactants as the reaction is exothermic. So product CO2 is lower in energy.

==molecular orbitals of CO==

{| class="wikitable" border="1"
|+ Molecular orbitals of CO
! No. !! energy!! picture!! explanation
|-
| 1|| -19.25806a.u || [[File:Screen shot of CO 1.PNG|250px]] || this is formed from the two 1s core AOs of C and O overlapping in phase.The energy of this MO is -19.25806a.u, which is much deeper than MO formed from the valence shell AOs. this is due to the fact that 1s AO are held tightly to the nuclei, which causes very poor overlap. The 1s orbital of O is deeper in energy, which means that it has a greater contribution to the MO than 1s in C atom, therefore, it appears to be larger in the MO orbital.
|-
|3 || -1.15790 a.u || [[File:Screen shot of CO 3.PNG|250px]] || this is a bonding sigma molecular orbital formed from two 2s valence AOs from C and O overlapping in phase. this time the overlap is much stronger as the shape of MO appears to be one extended surface. In addition, the energy of this MO is -1.15790 a.u which is much higher. it is interesting to note that in C and O the 2s and 2p orbitals are close in energy , which leads to s-p mixing. so the energy of this sigma MO is actually decreased due to the increase in bonding character caused by positive combination.
|-
|5 || -0.46742a.u || [[File:Correct screen shot of CO5.PNG|250px]] || this is a bonding pi molecular orbital formed from 2Px valence AOs from C and O overlapping in phase. the energy of this MO is -0.46742a.u, which is exactly same as the pi bonding MO formed from overlapping of two Py orbitals of C and O. this is because that the Px and Py AOs are degenerate, so the MOs formed from them are degenerate. in addition, C has greater contribution to this MO than O as this MO is closer in energy to 2Px of C.
|-
|7 HOMO|| -0.37145a.u || [[File:COrrect screen shot of CO HOMO.PNG|250px]] ||this is a bonding sigma molecular orbital formed from 2Pz valence AOs from C and O overlapping in phase, the energy of this MO is -0.37145a.u. this is the highest occupied molecular orbital of CO molecule and is fully occupied. the energy of this MO is actually increased as there is a decrease in bonding character due to negative combination caused by s-p mixing. moreover, the energy of this MO is closer to 2Pz of C, which indicates that C has a greater contribution to the formation of this MO. However, it is noticeable that the electron density between two atoms is relatively small, which indicates that the bonding character is not very large.
|-
|8 LUMO|| -0.02178 a.u) || [[File:Correct screen shot of CO lumo.PNG|250px]] ||This is a anti-bonding pi molecular orbital formed from 2Px valence AOs from C and O overlapping out of phase, the energy of this MO is -0.02178 a.u. this is the lowest unoccupied molecular orbital of CO molecule. C in this case has a greater contribution to this MO. therefore, when there is a molecule wants to attach to CO molecule, it will always attach from C. for example, when CO binds to metal as a ligand, it would always binds through C to make a metal complex.
|-
|}

==Reference==
<references>
<ref name="DAYSUR">M. Fernanda N. N. Carvalho, Armando J. L. Pombeiro, Ulrich Schubert, Olli Orama, Christopher J. Pickett and Raymond L. Richards J. Chem. Soc., Dalton Trans., (1985,0, 2079-2084)</ref>
<ref name="ACOJEK">S. Argibay-Otero, R. Carballo, E.M. Vázquez-López, Acta Crystallographica Section E: Crystallographic Communications, 2017, 73, 1551, DOI: 10.1107/S2056989017013512</ref>
</references>

==Independence==
===CH4 optimisation===
{| class="wikitable" border="1"
|+ CH4 summary
| molecule || CH4
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d,p)
|-
| E(RB3LYP) ||-40.52401404 a.u.
|-
|RMS Gradient Norm || 0.00003263 a.u.
|-
| Point Group ||TD
|}

{| class="wikitable" border="1"
|+ additional information of CH4
| bond length of CH || 1.09 Å
|-
| bond angle of HCH || 109 degree
|}

===item table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES

</pre>
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YINGTING JIA-CHE FINAL.LOG</uploadedFileContents>
<script>frame 1.9 </script>

</jmolApplet></jmol>

The optimisation file is liked to [[Media:YINGTING JIA-CHE FINAL.LOG| here]]

{| class="wikitable" border="1"
|+ vibrations of CH4
|-
| wavenumbercm-1 || 1356 || 1356 || 1356 || 1579 || 1579 || 3046|| 3162 || 3162|| 3162
|-
|symmetry || T2 || T2 || T2 || E || E || A1 || T2 || T2 || T2
|-
| intensity arbitrary units || 14 || 14 || 14 || 0 || 0 || 0 ||25|| 25|| 25

|}
[[File:Yingting JiaCH4 VIBRATIONS.PNG]]

===Charge of atoms in CH4===
{| class="wikitable" border="1"
|+
! atom !! charge
|-
| C || -0.470
|-
| H || 0.118
|}

===H2O===
===H2O optimisation===
{| class="wikitable" border="1"
|+ H2O summary
| molecule || H2O
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G(d,p)
|-
| E(RB3LYP) ||-76.41973740 a.u.
|-
|RMS Gradient Norm || 0.00006276 a.u.
|-
| Point Group ||C2V
|}

===Energy of reaction involves CH4===

CH4+H2O-> CO+3H2

E(CH4)=-40.52401404 a.u.

E(H2O)=-76.41973740 a.u.

E(CO)=-113.30945314 a.u.

E(H2)=-1.17853936a.u.

3*E(H2)=-3.53561808a.u
ΔE=(E(CO)+3*E(H2))-(E(CH4)+E(H2O))=0.09868022a.u.=259.1kJ/mol

the reactants are more stable than products. reaction is endothermic, reactants are lower in energy.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, overall very good, however you have left all the jmol captions as the default “test molecule” this gives the reader no information.

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, excellent explanations on the MOs, well done!

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

You did extra calculations, and an extra energy comparison, and an extra literature comparison, well done!

CHEMIMM2P

2019-03-24T17:41:43Z

Rr1210:

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name="CObondlength" />,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.

<references>
<ref name="CObondlength"> Gilliam, O. R.; Johnson, C. M.; Gordy, W. (1950). "Microwave Spectroscopy in the Region from Two to Three Millimeters". Physical Review. 78 (2): 140–144. Bibcode:1950PhRv...78..140G. doi:10.1103/PhysRev.78.140.</ref>
</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES, however you have written a lot of explanations in the "pre" boxes, it makes the text run off the screen so you can't read it.

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, well done. Please note electron-negative is not a word, you mean electronegative.

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 2.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES. You could have included more detail in your descriptions of the MOs however, such as which atom is contributing which AO to the MO, and whether the interactions are bonding or antibonding.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

You checked a result against the literature, well done!

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far

Rep:Mod:RumanAhmedsNH3Stuff

2019-03-24T14:28:48Z

Rr1210:

= NH3 =

=== Molecule ===

<jmol><jmolApplet>
<title>Optimised Ammonia</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RUMAN AHMED NH3 OPTIMISE POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Molecule Information ====

Molecule Name: Ammonia

Calculation Method: RB3LYP

Basis Set: 6-31G(d.p)

Final Energy: E(RB3LYP) = -56.55776873 au

RMS Gradient: 0.00000485 au

Point Group: C3v

Bond Length: 1.01798 +- 0.01A

Bond Angle: 105.741 +- 1°

'''The optimisation file can be accessed by clicking [[Media:RUMAN AHMED NH3 OPTIMISE POP.LOG| here]]'''

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986274D-10
Optimization completed.
 -- Stationary point found.

</pre>

=== Vibrations ===

[[File:RumansDisplayVibrationsNotYours.PNG]]

{| class="wikitable" border="3"

! Wavenumber !! Symmetry !! Intensity (au)
|-
| 1090 || A1 || 145
|-
| 1694 || E || 14
|-
| 1694 || E || 14
|-
| 3461 || A1 || 1
|-
| 3590 || E || 0
|-
| 3590 || E || 0
|}

==== Questions on Vibrations ====

1) Modes expected from 3N-6 rule: 3*4-6=6

2) Degenerate Modes: Modes with wavenumbers 1694cm-1 and modes with wavenumbers 3590cm-1

3) Bending Vibrations: 1090cm-1 and 1694cm-1 Bond Stretches: 3461cm-1 and 3590cm-1

4) Highly Symmetric Modes: 3461cm-1 and 1090cm-1

5) Umbrella Mode: 1090cm-1

6) 2 bands

=== Charge Analysis ===

Charge on each H: +0.375

Charge on N: -1.125

Overall Charge on Ammonia: 0

The expected charge values for each Hydrogen would be '''above 0 and below +1''', and ''each Hydrogen would have the same charge value''. The expected charge value on the Nitrogen would be '''-3 multiplied by the charge value of 1 Hydrogen, below 0 and above -3.''' This is because the N-H bond is polar, due to the Nitrogen being highly electronegative when compared to Hydrogen, so electron density in the N-H bond is withdrawn by the Nitrogen. Because the electron density isn't fully withdrawn, the charge values on each Hydrogen would be greater than 0, but less than 1. And the charge value of the Nitrogen would be -3 multiplied by the charge on a single Hydrogen atom in the molecule.

= N2 =

=== Molecule ===

<jmol><jmolApplet>
<title>Optimised Nitrogen</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RUMANAHMEDN2OPTIMISEPOP.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Molecule Information ====

Molecule Name: Nitrogen

Calculation Method: RB3LYP

Basis Set: 6-31G(d.p)

Final Energy: E(RB3LYP) = -109.52412868 au

RMS Gradient: 0.02473091 au

Point Group: DinfH

Bond Length: 1.10550 +- 0.01A

Bond Angle: There is no bond angle because it is a diatomic molecule.

'''The optimisation file can be accessed by clicking [[Media:RUMANAHMEDN2OPTIMISEPOP.LOG| here]]'''

<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=-3.401012D-13
Optimization completed.
-- Stationary point found.

</pre>

=== Vibrations ===

[[File:RumansN2VibrationsNotYours.PNG]]

{| class="wikitable" border="3"
! Wavenumber !! Symmetry !! Intensity (au) !
|-
| 2457 || SSG || 0
|}

N2 has a single band and is IR inactive.

=== Charge Analysis ===

Charge on each Nitrogen atom: 0

Overall Charge on N2: 0

Expected charge on each Nitrogen: 0

Expected charge across entire molecule: 0

The two atoms in N2 are the same; both are Nitrogen. Because of this, they have equal electronegativities and the bond will not be polar.

= H2 =

=== Molecule ===

<jmol><jmolApplet>
<title>Optimised Hydrogen</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RUMANAHMEDH2OPTIMISEPOP.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Molecule Information ====

Molecule Name: Hydrogen

Calculation Method: RB3LYP

Basis Set: 6-31G(d.p)

Final Energy: E(RB3LYP) = -1.17853936 au

RMS Gradient: 0.00000017 au

Point Group: DinfH

Bond Length: 0.74279 +- 0.01A

Bond Angle: There is no bond angle because it is a diatomic molecule.

'''The optimisation file can be accessed by clicking [[Media:RUMANAHMEDH2OPTIMISEPOP.LOG| here]]'''

<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
Optimization completed.
-- Stationary point found.

</pre>

=== Vibrations ===

[[File:RumansH2VibrationsNotYours.PNG]]

{| class="wikitable" border="3"
! Wavenumber !! Symmetry !! Intensity (au) !
|-
| 4466 || SSG || 0
|}

H2 has a single band and is IR inactive.

=== Charge Analysis ===

Charge on each Hydrogen atom: 0

Overall Charge on H2: 0

Expected charge on each Hydrogen: 0

Expected charge across entire molecule: 0

The two atoms in H2 are the same; both are Hydrogen. Because of this, they have equal electronegativities and the bond will not be polar.

=== ConQuest/CCDC ===

Unique Identifier for complex: GIKGOW01

Link to complex: [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=GIKGOW01&DatabaseToSearch=Published this is the link]

H-H bond in complex: 0.9080 A

Difference in bond lengths: H-H bond in complex is 0.16521 A longer.

The H-H bond in the metal complex is longer due to the Rhenium bonded to one of the Hydrogens in the H-H bond. The Re-H bond withdraws electron density from the H-H bond, weakening the bond. The weakening of the bond causes the bond to elongate.

=== Energies ===

E(NH3)= -56.5577687 au

2*E(NH3)= -113.1155375 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356181 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
= -146.4784829 KJ/mol (au value multiplied by 2625.5)

'''All values are to 7 dp'''

The value for ΔE is highly negative, indicating that the reaction is highly exothermic, so energy is released. Therefore, the Ammonia gas is ~146.5 KJ/mol more stable than the reactants.

= CO =

=== Molecule ===

<jmol><jmolApplet>
<title>Optimised Carbon Monoxide</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RUMANCOOPTIMISEPOP.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Molecule Information ====

Molecule Name: Carbon Monoxide

Calculation Method: RB3LYP

Basis Set: 6-31G(d.p)

Final Energy: E(RB3LYP) = -113.30945313 au

RMS Gradient: 0.00010485 au

Point Group: C*v

Bond Length: 1.13786 +- 0.01A

Bond Angle: There is no bond angle because it is a diatomic molecule.

'''The optimisation file can be accessed by clicking [[Media:RUMANCOOPTIMISEPOP.LOG| here]]'''

<pre>

Item Value Threshold Converged?
Maximum Force 0.000182 0.000450 YES
RMS Force 0.000182 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
Predicted change in Energy=-1.301714D-08
Optimization completed.
-- Stationary point found.

</pre>

=== Vibrations ===

[[File:RumansCOVibrationsNotYours.PNG]]

{| class="wikitable" border="3"
! Wavenumber !! Symmetry !! Intensity (au) !
|-
| 2210 || SG || 70
|}

CO has a single band and is IR active.

=== Charge Analysis ===

Charge on Carbon: +0.506

Charge on Oxygen: -0.506

Overall Charge on Carbon Monoxide: 0

Expected charge on Carbon: 0 < Q1 < +1

Expected charge on Oxygen: -Q1 ( -1 < Q2 < 0)

Expected charge across entire molecule: 0

Oxygen has a higher electronegativity than carbon, so electrons within the C-O triple bond will be withdrawn by the oxygen, causing the Carbon to be slightly positively charged, and the Oxygen to become slightly negatively charged.

=== Molecular Orbital Information ===

==== HOMO ====

[[File:COHOMOStuff.PNG|300px]]

This is the HOMO of Carbon Monoxide. It shows mainly p orbital character. It is an occupied antibonding orbital with sigma* interactions, mainly contributed to by the 2pz orbitals from both Carbon and Oxygen.

==== LUMO ====

[[File:COLUMOStuff.PNG|300px]]

This is the LUMO of Carbon Monoxide. It shows mainly p orbital character. It is an unoccupied antibonding pi* orbital, and is mainly contributed to by the 2px orbital from Carbon and the 2px orbital from Oxygen, both of which are out of phase. The 2px orbital from Oxygen is very bloated, which could be due to s interactions with the 2px orbital, making it larger than a typical p orbital.

==== 6th MO ====

[[File:CO2pBondingStuff(6).PNG|300px]]

This is the 6th Molecular Orbital in Carbon Monoxide. It shows p orbital character. It is an occupied bonding pi orbital, and is contributed to by the 2py orbitals from both Carbon and Oxygen, both of which are in phase.

==== 1st MO ====

[[File:CO1sBondingStuff(1).PNG|300px]]

This is the 1st Molecular Orbital of Carbon Monoxide. It shows s orbital character. It is occupied, and it's very deep in energy, therefore it cannot take part in bonding. It is almost solely contributed to by the 1s orbital from Oxygen.

==== 4th MO ====

[[File:CO(4)Stuff.PNG|300px]]

This is the 4th Molecular Orbital of Carbon Monoxide. It shows mainly s character. It is an occupied bonding orbital, and is mainly contributed to by the 2s orbital of Carbon and the 2s orbital of Oxygen, however there is a significant amount of contribution from the 2px orbitals of both Carbon and Oxygen too.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, overall good explanations. Some of your MO explanations are incorrect however, for example for MO4 I don't see any p character on the carbon atom. Also the carbon is the grey atom and the oxygen the red one, you seen to have mixed them up in some calculations.

== Independence 0/1 ==

If you have finished everything else and have spare time in the lab you could:
Check one of your results against the literature, or
Do an extra calculation on another small molecule, or
Do some deeper analysis on your results so far

No independent work found.

Rep:Mod: Sa13018

2019-03-24T14:12:40Z

Rr1210:

='''NH3 Molecule'''=

<jmol><jmolApplet>
<title>test molecule (NH3)</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SA13018 NH3 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

==General==
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986293D-10
</pre>

<pre>
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -56.55776873 a.u.
Dipole Moment 1.5008 Debye
Point Group C3V
</pre>

<pre>
N-H bond distance = 1.02 a.u
H-N-H bond angle = 106
</Pre>

==Vibration analysis==

[[File:sa13018_nh3_display_vibrations.png|240x240px|thumb|A Gaussview of the display vibrations of NH3|centre]]
{|
|+
|-
!'''wavenumber''' cm^-1
| 1090 || 1694||1694 ||3461 || 3590||3590
|-
!'''symmetry'''
|A1 || E|| E||A1 || E || E
|-
!'''intensity'''(arbitary units)
|145||14||14 || 1 || 0||0
|-
!'''Image'''
|[[File:sa13018_nh3_vib_1.png|153x153px]]||[[File:sa13018_nh3_vib_2.png|200x200px]]||[[File:sa13018_nh3_vib_3.png|153x153px]]||[[File:sa13018_nh3_vib_4.png|153x153px]]||[[File:sa13018_nh3_vib_5.png|153x153px]]||[[File:sa13018_nh3_vib_6.png|153x153px]]
|}

<pre>
Number of modes= 6
Degenerate modes= modes at 1694, and 3590 cm^-1
bending vibrations= 1090,1694
stretching vibrations= 3461,3590
highly symmetric = 3461, and also 1090 (not as symmetric as 3461)
umbrella mode= 1090
bands in gaseous ammonia= 3
The number of bands is 3, as there are 2 that don't result in a change in dipole moment, and so do not show an IR peak. There are then 2 degenerate peaks; they will show the same wavenumber, and so there are only 3 visibile bands in gaseous ammonia. For condensed it might be different, considering the effect of disorder.
</pre>

==Charge output==
<pre>
Charge on N = -1.125
Charge on H = 0.375
This seems like a likely charge distribution, considering the electronegativity of Nitrogen is much greater than Hydrogen, resulting in a greater electron density around the nitrogen, and an overall much greater charge (x3).
</pre>

='''N2 molecule'''=

==General==

<jmol><jmolApplet>
<title>test molecule (N2)</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SA13018 N2 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000145 0.000450 YES
RMS Force 0.000145 0.000300 YES
Maximum Displacement 0.000045 0.001800 YES
RMS Displacement 0.000064 0.001200 YES
Predicted change in Energy=-6.585141D-09
</pre>

<pre>
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -109.52412867 a.u.
Dipole Moment 0.0000 Debye
Point Group D*H
</pre>

==Vibration analysis==

<pre>
N-N bond length= 1.11 a.u
N-N bond angle= n/a. There are only 2 atoms, so no valid bond angle.
</pre>

[[File:sa13018_n2_display_vibrations.png|219x219px|thumb|A Gaussview of the display vibrations of N2]]
{|
|+
|-
!'''wavenumber''' cm^-1
|2457
|-
!'''symmetry'''
|SGG
|-
!'''intensity'''(arbitary units)
|0
|-
!'''Image'''
|[[File:sa13018_n2_vib_1.png|153x153px]]
|}[[File:sa13018_n2_charge_output.png|150x150px|thumb|A Gaussview of the charge distribution of N2|left]]

<pre>
Vibrational modes expected from 3N-5 = 1
Degenerate modes = n/a
bending vibrations = n/a
bond stretch vibrations = 2457
highly symmetric stretch = 2457
umbrella mode = n/a
how many bands= zero; no change of dipole in the stretch
</pre>

==TM co-ordination==
<pre>
N2 is co-ordinated to an iridium complex, in <nowiki>''</nowiki>bis((adamantan-1-ylmethyl)(diisopropyl)phosphine)-(dinitrogen)-hydrido-iridium<nowiki>''</nowiki>. The unique identifier for this is ANAZEV, and the article for the molecule can be found here: <nowiki>https://pubs.acs.org/doi/10.1021/ja1037808</nowiki>.

The NN bond length in this molecule is 1.108 Å. This is almost identical to the bond length for the calculated computational length of 1.11. This implies that the computational calculation works and has found the correct stationary point for the optimised bond length. However, there is still a chance of some error; there is a possibility that the bond length could be shorter in reality than the computed distance, as the computed distance could be the result of a local minimum potential energy rather than the global minimum. If the bond length is shorter in reality, it would imply that the bond length of the co-ordinated NN bond is greater than computed. This would make sense as the electron density of the NN bond could be reduced by coordination, resulting in an overall longer bond.
The link to the CCDC structure is this:https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=ANAZEV&DatabaseToSearch=Published
</pre>

==Charge output==
<pre>
There is no charge on the atoms, as the electronegativities are equal.
</pre>

[[File:sa13018_anazev.png|150x150px|thumb|Bis-((adamantan-1-ylmethyl)(diisopropyl)phosphine)-(dinitrogen)-hydrido-iridium|left]]

='''H2 molecule'''=

==General==

<jmol><jmolApplet>
<title>test molecule (H2)</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SA13018 H2 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000066 0.000300 YES
Maximum Displacement 0.000087 0.001800 YES
RMS Displacement 0.000123 0.001200 YES
Predicted change in Energy=-5.726834D-09
</pre>

<pre>
H-H bond length= 0.74 a.u
H-H bond angle= n/a. There are only 2 molecules.
</pre>

<pre>
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -1.17853935 a.u.
Dipole Moment 0.0000 Debye
Point Group D*H
</pre>

==Vibration analysis==

[[File:sa13018_h2_display_vibrations.png|150x150px|thumb|A Gaussview of the display vibrations of H2]]
{|
|+
|-
!'''wavenumber''' cm^-1
|4464
|-
!'''symmetry'''
|SGG
|-
!'''intensity'''(arbitary units)
|0
|-
!'''Image'''
|[[File:sa13018_h2_vib_1.png|152x152px]]
|}

<pre>
Vibrational modes expected from 3N-5 = 1
Degenerate modes = n/a
bending vibrations = n/a
bond stretch vibrations = 4464
highly symmetric stretch = 4464
umbrella mode = n/a
how many bands= zero; no change of dipole in the stretch
</pre>

==Charge output==

[[File:sa13018_h2_charge_output.png|150x150px|thumb|A Gaussview of the charge distribution of H2|left]]

<pre>
There is no charge on the atoms, as the electronegativities are equal.
</pre>

='''The Haber Process'''=
<pre>
E(NH3)=-56.55776873 a.u
2*E(NH3)= -113.11553746 a.u
E(N2)=-109.52413 a.u
E(H2)=-1.17854 a.u
3*E(H2)= -3.53562 a.u
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= 0.05578746 a.u
This is equal to -146.5 kJ/mol
The process of converting N2 and 3H2 to 2NH3 is exothermic, and this implies that the more stable is the NH3 product over the reactants.
</pre>

='''Project molecule (ClF3)'''=

<jmol><jmolApplet>
<title>test molecule (ClF3)</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SA13018 CLF3 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

==General==

<pre>
Item Value Threshold Converged?
Maximum Force 0.000050 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000204 0.001800 YES
RMS Displacement 0.000134 0.001200 YES
Predicted change in Energy==-1.250231D-08
</pre>

<pre>
Cl-F(1) bond length= 1.65 a.u
Cl-F(4) bond length= 1.73 a.u
F4-Cl-F2 bond angle= 174
F4-Cl-F3 bond angle= 87
</pre>

<pre>
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -759.46531688 a.u.
Dipole Moment 0.8386 Debye
Point Group C2V
</pre>

==Vibration analysis==

[[File:sa13018_clf3_display_vibrations.png|153x153px|thumb|A Gaussview of the display vibrations of ClF3|left]]
{|
|+
|-
!'''wavenumber''' cm^-1
| 305 || 309||401||541|| 736||752
|-
!'''symmetry'''
|A1 || B1||B2||B2 || A1 || A1||
|-
!'''intensity'''(arbitary units)
|14||18||1 || 541 || 736||752
|-
!'''Image'''
|[[File:sa13018_clf3_vib_1.png|153x153px]]||[[File:sa13018_clf3_vib_2.png|153x153px]]||[[File:sa13018_clf3_vib_3.png|153x153px]]||[[File:sa13018_clf3_vib_4.png|153x153px]]||[[File:sa13018_clf3_vib_5.png|153x153px]]||[[File:sa13018_clf3_vib_6.png|153x153px]]
|}

<pre>
Vibrational modes expected from 3N-6= 6
Degenerate modes = n/a
bending vibrations = 305,309,401
bond stretch vibrations = 541,736,752
highly symmetric stretch = 541
umbrella mode = 309
how many bands= 5
There are 5 different vibrational modes that result in a change in dipole moment, so would cause 5 bands to appear in gaseous sample. The condensed state would not show this many, as there is more disorder to account for, and this would result in overlap between the closely lying bands.
</pre>

==Molecular Orbital Analysis==

{| class="wikitable"
!
!
!
!
|-
!
|[[File:sa13018_clf3_mo_3.png|356x356px|thumb|A Gaussview of the [3] MO of ClF3, showing the 1s electrons of the F2 and F4, which are degenerate in energy.|centre]]
|[[File:sa13018_clf3_mo_2.png|200x200px|thumb|A Gaussview of the [2] Molecular orbital of ClF3. This shows the 1s orbital of the F3 molecule, and is lower in energy than the adjacent F2 and F4 molecules' 1s MO energies (which are degenerate). This is interesting as you would expect the opposite when you increase the size of the orbitals, as the increased electron density of the region would push electrons away from the molecule in larger orbitals. Here, this is causing the electrons to go closer to the nucleus, thus reducing the overall energy of the electrons in that orbital.|left]]
!
|-
!
|[[File:sa13018_clf3_mo_9.png|356x356px|thumb|A Gaussview of the [9] MO of ClF3. This shows the first case of a molecular orbital in this molecule both spatially and energetically large enough to span the whole molecule; the 3pz orbitals here overlap in a pi- bonding manner, for in-phase orbitals for all the individual atomic orbitals of the molecule.|left]]
|[[File:sa13018_clf3_mo_8.png|356x356px|thumb|A Gaussview of the [8] MO of ClF3. This is shows the 3py atomic orbital of the Cl atom, and is significantly lower in energy than the [9] MO, with an energy difference of almost 6.2 a.u. |centre]]
!
|-
!
|[[File:sa13018_clf3_mo_22_homo.png|356x356px|thumb|A Gaussview of the [22] MO of ClF3. This is the Highest Occupied Molecular Orbital (HOMO) in the molecule, and is a clear pi antibonding orbital across all the atoms. There are 3 nodes across the individual atomic orbital of Cl. In addition to this, the F3 molecule, the middle one, is significantly smaller than the F2 and F4 molecules, as there is repulsion from the high electron density in this region. Thus the orbital is smaller due to less electrons being present in this region. This is the reverse effect to the [2] MO of ClF3, which is held more tightly and is lower in energy.
<ref name="ClF3" />|left]]
|[[File:sa13018_clf3_mo_23_lumo.png|356x356px|thumb|A Gaussview of the [23] MO of ClF3. This is the Lowest Unoccupied Molecular Orbital (LUMO, and it is very interesting! There is both sigma and pi antibonding occuring here, as well as some degree of pi and sigma bonding. This is due to the spatial arrangement of the p orbitals of the F2 and F4 atoms, which are arranged in a way that they can make these interactions. The antibonding is clear to see; there is sigma antibonding due to the clear node defined between F2 ( and F4), and the Cl atoms. The pi antibonding is between the F3 and Cl atoms. However, there is also some '''angled''' pi bonding occurring between the same phases of the F2F4 atoms and the Cl; a very interesting angle of approach. In addition to this, as we ''increase the isovalue, a measure of the electron density per region'', we encounter some angled sigma bonding between the p molecules of the F atoms. It is an incredibly interesting molecular orbital, so therefore it is a real shame that it contributes nothing to the energy of the bonding of the molecule; it is '''Unoccupied'''.|centre]]
!
|}

==Charge output==

[[File:sa13018_clf3_charge_output.png|150x150px|thumb|A Gaussview of the charge distribution of ClF3|left]]

<pre>
The F atoms are more electronegative than Cl, so have the negative charge. Cl has a charge of 1.225, and the individual F atoms have different charges based on position. The F3 middle atom is slightly less charged, with a charge of -0.315 as there is more repulsion of electrons from here due to increased electron density in that region. The outer F atoms have a charge of -0.465.
</pre>

<references>
<ref name="ClF3">This is based on works from this article by Henry Rzepa in the Winnower.https://thewinnower.com/papers/vsepr-theory-a-closer-look-at-chlorine-trifluoride-clf3</ref>
</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES, however you have written lots of text in the "pre" boxes, and you have not inserted line breaks leaving the reader to scroll sideways to read your work. You don't need to use the boxes the default formatting is much better.

Do you effectively use tables, figures and subheadings to communicate your work?

Lots of your tables are not formatted nicely and have extra rows/columns or no lines. Many of your figures are not cropped and one has been crudely coloured around in paint instead.

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 3.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, good detailed explanations, well done. MO9 is made up of s type AOs not p type and the bonding is sigma bonding.

== Independence 0/1 ==

If you have finished everything else and have spare time in the lab you could:
Check one of your results against the literature, or
Do an extra calculation on another small molecule, or
Do some deeper analysis on your results so far

No independent work.

Rep:Mod: Sa13018

2019-03-24T13:54:13Z

Rr1210:

='''NH3 Molecule'''=

<jmol><jmolApplet>
<title>test molecule (NH3)</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SA13018 NH3 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

==General==
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986293D-10
</pre>

<pre>
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -56.55776873 a.u.
Dipole Moment 1.5008 Debye
Point Group C3V
</pre>

<pre>
N-H bond distance = 1.02 a.u
H-N-H bond angle = 106
</Pre>

==Vibration analysis==

[[File:sa13018_nh3_display_vibrations.png|240x240px|thumb|A Gaussview of the display vibrations of NH3|centre]]
{|
|+
|-
!'''wavenumber''' cm^-1
| 1090 || 1694||1694 ||3461 || 3590||3590
|-
!'''symmetry'''
|A1 || E|| E||A1 || E || E
|-
!'''intensity'''(arbitary units)
|145||14||14 || 1 || 0||0
|-
!'''Image'''
|[[File:sa13018_nh3_vib_1.png|153x153px]]||[[File:sa13018_nh3_vib_2.png|200x200px]]||[[File:sa13018_nh3_vib_3.png|153x153px]]||[[File:sa13018_nh3_vib_4.png|153x153px]]||[[File:sa13018_nh3_vib_5.png|153x153px]]||[[File:sa13018_nh3_vib_6.png|153x153px]]
|}

<pre>
Number of modes= 6
Degenerate modes= modes at 1694, and 3590 cm^-1
bending vibrations= 1090,1694
stretching vibrations= 3461,3590
highly symmetric = 3461, and also 1090 (not as symmetric as 3461)
umbrella mode= 1090
bands in gaseous ammonia= 3
The number of bands is 3, as there are 2 that don't result in a change in dipole moment, and so do not show an IR peak. There are then 2 degenerate peaks; they will show the same wavenumber, and so there are only 3 visibile bands in gaseous ammonia. For condensed it might be different, considering the effect of disorder.
</pre>

==Charge output==
<pre>
Charge on N = -1.125
Charge on H = 0.375
This seems like a likely charge distribution, considering the electronegativity of Nitrogen is much greater than Hydrogen, resulting in a greater electron density around the nitrogen, and an overall much greater charge (x3).
</pre>

='''N2 molecule'''=

==General==

<jmol><jmolApplet>
<title>test molecule (N2)</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SA13018 N2 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000145 0.000450 YES
RMS Force 0.000145 0.000300 YES
Maximum Displacement 0.000045 0.001800 YES
RMS Displacement 0.000064 0.001200 YES
Predicted change in Energy=-6.585141D-09
</pre>

<pre>
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -109.52412867 a.u.
Dipole Moment 0.0000 Debye
Point Group D*H
</pre>

==Vibration analysis==

<pre>
N-N bond length= 1.11 a.u
N-N bond angle= n/a. There are only 2 atoms, so no valid bond angle.
</pre>

[[File:sa13018_n2_display_vibrations.png|219x219px|thumb|A Gaussview of the display vibrations of N2]]
{|
|+
|-
!'''wavenumber''' cm^-1
|2457
|-
!'''symmetry'''
|SGG
|-
!'''intensity'''(arbitary units)
|0
|-
!'''Image'''
|[[File:sa13018_n2_vib_1.png|153x153px]]
|}[[File:sa13018_n2_charge_output.png|150x150px|thumb|A Gaussview of the charge distribution of N2|left]]

<pre>
Vibrational modes expected from 3N-5 = 1
Degenerate modes = n/a
bending vibrations = n/a
bond stretch vibrations = 2457
highly symmetric stretch = 2457
umbrella mode = n/a
how many bands= zero; no change of dipole in the stretch
</pre>

==TM co-ordination==
<pre>
N2 is co-ordinated to an iridium complex, in <nowiki>''</nowiki>bis((adamantan-1-ylmethyl)(diisopropyl)phosphine)-(dinitrogen)-hydrido-iridium<nowiki>''</nowiki>. The unique identifier for this is ANAZEV, and the article for the molecule can be found here: <nowiki>https://pubs.acs.org/doi/10.1021/ja1037808</nowiki>.

The NN bond length in this molecule is 1.108 Å. This is almost identical to the bond length for the calculated computational length of 1.11. This implies that the computational calculation works and has found the correct stationary point for the optimised bond length. However, there is still a chance of some error; there is a possibility that the bond length could be shorter in reality than the computed distance, as the computed distance could be the result of a local minimum potential energy rather than the global minimum. If the bond length is shorter in reality, it would imply that the bond length of the co-ordinated NN bond is greater than computed. This would make sense as the electron density of the NN bond could be reduced by coordination, resulting in an overall longer bond.
The link to the CCDC structure is this:https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=ANAZEV&DatabaseToSearch=Published
</pre>

==Charge output==
<pre>
There is no charge on the atoms, as the electronegativities are equal.
</pre>

[[File:sa13018_anazev.png|150x150px|thumb|Bis-((adamantan-1-ylmethyl)(diisopropyl)phosphine)-(dinitrogen)-hydrido-iridium|left]]

='''H2 molecule'''=

==General==

<jmol><jmolApplet>
<title>test molecule (H2)</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SA13018 H2 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000066 0.000300 YES
Maximum Displacement 0.000087 0.001800 YES
RMS Displacement 0.000123 0.001200 YES
Predicted change in Energy=-5.726834D-09
</pre>

<pre>
H-H bond length= 0.74 a.u
H-H bond angle= n/a. There are only 2 molecules.
</pre>

<pre>
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -1.17853935 a.u.
Dipole Moment 0.0000 Debye
Point Group D*H
</pre>

==Vibration analysis==

[[File:sa13018_h2_display_vibrations.png|150x150px|thumb|A Gaussview of the display vibrations of H2]]
{|
|+
|-
!'''wavenumber''' cm^-1
|4464
|-
!'''symmetry'''
|SGG
|-
!'''intensity'''(arbitary units)
|0
|-
!'''Image'''
|[[File:sa13018_h2_vib_1.png|152x152px]]
|}

<pre>
Vibrational modes expected from 3N-5 = 1
Degenerate modes = n/a
bending vibrations = n/a
bond stretch vibrations = 4464
highly symmetric stretch = 4464
umbrella mode = n/a
how many bands= zero; no change of dipole in the stretch
</pre>

==Charge output==

[[File:sa13018_h2_charge_output.png|150x150px|thumb|A Gaussview of the charge distribution of H2|left]]

<pre>
There is no charge on the atoms, as the electronegativities are equal.
</pre>

='''The Haber Process'''=
<pre>
E(NH3)=-56.55776873 a.u
2*E(NH3)= -113.11553746 a.u
E(N2)=-109.52413 a.u
E(H2)=-1.17854 a.u
3*E(H2)= -3.53562 a.u
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= 0.05578746 a.u
This is equal to -146.5 kJ/mol
The process of converting N2 and 3H2 to 2NH3 is exothermic, and this implies that the more stable is the NH3 product over the reactants.
</pre>

='''Project molecule (ClF3)'''=

<jmol><jmolApplet>
<title>test molecule (ClF3)</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SA13018 CLF3 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

==General==

<pre>
Item Value Threshold Converged?
Maximum Force 0.000050 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000204 0.001800 YES
RMS Displacement 0.000134 0.001200 YES
Predicted change in Energy==-1.250231D-08
</pre>

<pre>
Cl-F(1) bond length= 1.65 a.u
Cl-F(4) bond length= 1.73 a.u
F4-Cl-F2 bond angle= 174
F4-Cl-F3 bond angle= 87
</pre>

<pre>
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -759.46531688 a.u.
Dipole Moment 0.8386 Debye
Point Group C2V
</pre>

==Vibration analysis==

[[File:sa13018_clf3_display_vibrations.png|153x153px|thumb|A Gaussview of the display vibrations of ClF3|left]]
{|
|+
|-
!'''wavenumber''' cm^-1
| 305 || 309||401||541|| 736||752
|-
!'''symmetry'''
|A1 || B1||B2||B2 || A1 || A1||
|-
!'''intensity'''(arbitary units)
|14||18||1 || 541 || 736||752
|-
!'''Image'''
|[[File:sa13018_clf3_vib_1.png|153x153px]]||[[File:sa13018_clf3_vib_2.png|153x153px]]||[[File:sa13018_clf3_vib_3.png|153x153px]]||[[File:sa13018_clf3_vib_4.png|153x153px]]||[[File:sa13018_clf3_vib_5.png|153x153px]]||[[File:sa13018_clf3_vib_6.png|153x153px]]
|}

<pre>
Vibrational modes expected from 3N-6= 6
Degenerate modes = n/a
bending vibrations = 305,309,401
bond stretch vibrations = 541,736,752
highly symmetric stretch = 541
umbrella mode = 309
how many bands= 5
There are 5 different vibrational modes that result in a change in dipole moment, so would cause 5 bands to appear in gaseous sample. The condensed state would not show this many, as there is more disorder to account for, and this would result in overlap between the closely lying bands.
</pre>

==Molecular Orbital Analysis==

{| class="wikitable"
!
!
!
!
|-
!
|[[File:sa13018_clf3_mo_3.png|356x356px|thumb|A Gaussview of the [3] MO of ClF3, showing the 1s electrons of the F2 and F4, which are degenerate in energy.|centre]]
|[[File:sa13018_clf3_mo_2.png|200x200px|thumb|A Gaussview of the [2] Molecular orbital of ClF3. This shows the 1s orbital of the F3 molecule, and is lower in energy than the adjacent F2 and F4 molecules' 1s MO energies (which are degenerate). This is interesting as you would expect the opposite when you increase the size of the orbitals, as the increased electron density of the region would push electrons away from the molecule in larger orbitals. Here, this is causing the electrons to go closer to the nucleus, thus reducing the overall energy of the electrons in that orbital.|left]]
!
|-
!
|[[File:sa13018_clf3_mo_9.png|356x356px|thumb|A Gaussview of the [9] MO of ClF3. This shows the first case of a molecular orbital in this molecule both spatially and energetically large enough to span the whole molecule; the 3pz orbitals here overlap in a pi- bonding manner, for in-phase orbitals for all the individual atomic orbitals of the molecule.|left]]
|[[File:sa13018_clf3_mo_8.png|356x356px|thumb|A Gaussview of the [8] MO of ClF3. This is shows the 3py atomic orbital of the Cl atom, and is significantly lower in energy than the [9] MO, with an energy difference of almost 6.2 a.u. |centre]]
!
|-
!
|[[File:sa13018_clf3_mo_22_homo.png|356x356px|thumb|A Gaussview of the [22] MO of ClF3. This is the Highest Occupied Molecular Orbital (HOMO) in the molecule, and is a clear pi antibonding orbital across all the atoms. There are 3 nodes across the individual atomic orbital of Cl. In addition to this, the F3 molecule, the middle one, is significantly smaller than the F2 and F4 molecules, as there is repulsion from the high electron density in this region. Thus the orbital is smaller due to less electrons being present in this region. This is the reverse effect to the [2] MO of ClF3, which is held more tightly and is lower in energy.
<ref name="ClF3" />|left]]
|[[File:sa13018_clf3_mo_23_lumo.png|356x356px|thumb|A Gaussview of the [23] MO of ClF3. This is the Lowest Unoccupied Molecular Orbital (LUMO, and it is very interesting! There is both sigma and pi antibonding occuring here, as well as some degree of pi and sigma bonding. This is due to the spatial arrangement of the p orbitals of the F2 and F4 atoms, which are arranged in a way that they can make these interactions. The antibonding is clear to see; there is sigma antibonding due to the clear node defined between F2 ( and F4), and the Cl atoms. The pi antibonding is between the F3 and Cl atoms. However, there is also some '''angled''' pi bonding occurring between the same phases of the F2F4 atoms and the Cl; a very interesting angle of approach. In addition to this, as we ''increase the isovalue, a measure of the electron density per region'', we encounter some angled sigma bonding between the p molecules of the F atoms. It is an incredibly interesting molecular orbital, so therefore it is a real shame that it contributes nothing to the energy of the bonding of the molecule; it is '''Unoccupied'''.|centre]]
!
|}

==Charge output==

[[File:sa13018_clf3_charge_output.png|150x150px|thumb|A Gaussview of the charge distribution of ClF3|left]]

<pre>
The F atoms are more electronegative than Cl, so have the negative charge. Cl has a charge of 1.225, and the individual F atoms have different charges based on position. The F3 middle atom is slightly less charged, with a charge of -0.315 as there is more repulsion of electrons from here due to increased electron density in that region. The outer F atoms have a charge of -0.465.
</pre>

<references>
<ref name="ClF3">This is based on works from this article by Henry Rzepa in the Winnower.https://thewinnower.com/papers/vsepr-theory-a-closer-look-at-chlorine-trifluoride-clf3</ref>
</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:
Check one of your results against the literature, or
Do an extra calculation on another small molecule, or
Do some deeper analysis on your results so far

Acc2518

2019-03-24T13:50:40Z

Rr1210:

== NH3 molecule ==
=== Optimisation data ===
{| class="wikitable"
|+ NH3 optimisation
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d.p)
|-
|'''Final energy E(RB3LYP)'''
|<nowiki>-56.55776873 (au)</nowiki>
|-
|'''RMS gradient'''
|0.00000485 (au)
|-
|'''Point group'''
|C3V
|-
|'''Bond length (N-H)'''
|1.02 (Å)
|-
|'''Bond angle (H-N-H)'''
|106(°)
|}
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

<jmol><jmolApplet>
<title> NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACC2518 NH3 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>
[[:File:ACC2518 NH3 OPTF POP.LOG|Optimised NH3 .log file (acc2518)]]

=== Vibrations ===
[[File:Acc2518 vibrations screenshot.jpg|The Gaussview "Display Vibrations" window of the optimised ammonia molecule.|350px]]

{| class="wikitable" border="1"
|+ IR vibration data
|-
| '''Wavenumber''' (cm-1) || 1090 || 1694
|-
| '''Symmetry''' || A1 || E
|-
| '''Intensity''' (arbitrary units) || 145 || 14
|-
| '''Image'''|| [[File:acc2518VM1.png|250px]] || [[File:acc2518VM2.png|300px]]
|-
! colspan="3" style="text-align: centre;"|
|-
| '''Wavenumber''' (cm-1) || 1694|| 3461
|-
| '''Symmetry''' || E || A1
|-
| '''Intensity''' (arbitrary units) || 14 || 1
|-
| '''Image'''|| [[File:acc2518VM3.png|250px]] || [[File:acc2518VM4.png|275px]]
|-
! colspan="3" style="text-align: centre;"|
|-
| '''Wavenumber''' (cm-1) || 3590|| 3590
|-
| '''Symmetry''' || E || E
|-
| '''Intensity''' (arbitrary units) || 0 || 0
|-
| '''Image'''|| [[File:acc2518VM5.png|275px]] || [[File:acc2518VM6.png|250px]]
|}

Using the 3N-6 rule, where N represents the number of atoms in a molecule, it is expected that ammonia will have six vibrational modes as shown above. There are two pairs of degenerate modes with a frequency of 1694 (cm-1) and 3590 (cm-1). The modes with a frequency of 1090 (cm-1) and 1694 (cm-1) correspond to bending vibrations and the modes with a frequency 3461 (cm-1) and 3590 (cm-1) correspond to bond stretch vibrations. The bond stretch vibration at 3461 (cm-1) is highly symmetric whilst the stretches with a frequency of 3590 (cm-1) are asymmetric. The bending vibration with a frequency of 1090 (cm-1) is known as the umbrella mode. Three bands would be expected to be seen with the two stretches at 3590 (cm-1) being too low in intensity. The bends with a frequency of 1694 (cm-1) are degenerate and only one band will be observed between the two. Hence the three observed bands would be at 1090 (cm-1), 1694 (cm-1) and 3461 (cm-1).

=== Charge analysis ===
[[File:Acc2518 charge analysis.png|The Gaussview generated atomic charges of ammonia.|250px]]

Nitrogen has a greater electronegativity than hydrogen and hence there is greater electron density distributed around the N atom in ammonia relative to hydrogen. This explains the negative charge on N and the positive charge on H.

==N2 molecule==

===Optimisation data===

{| class="wikitable"
|+ N2 optimisation
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d.p)
|-
|'''Final energy E(RB3LYP)'''
|<nowiki>-109.52412868 (au)</nowiki>
|-
|'''RMS gradient'''
|0.00000060 (au)
|-
|'''Point group'''
|D∞h
|-
|'''Bond length (N-N)'''
|1.11 (Å)
|}

<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
</pre>

<jmol><jmolApplet>
<title> Nitrogen molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACC2518 N2 OPTIMISATION.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>
[[:File:ACC2518 N2 OPTIMISATION.LOG|Optimised N2 .log file (acc2518)]]

===Vibrations===
[[File:Acc2518 N2vibration.png|Nitrogen display vibrations screenshot|350px]]

{| class="wikitable" border="1"
|+ IR vibration data
|-
| '''Wavenumber''' (cm-1) || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' (arbitrary units) || 0
|-
| '''Image'''|| [[File:Acc2518NitrogenVM.png|250px]]
|}
Using the 3N-5 rule for linear molecules, Nitrogen can be expected to have one vibrational mode but this mode has an IR intensity of zero since Nitrogen molecules are IR inactive. This is because they have no overall dipole.

===Charge analysis===
[[File:Acc2518nitrogen charges.png]]

Both nitrogen atoms have the same electronegativity so the charge is neutral on both atoms.

===CCDC search===
'''Unique identifier:''' [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VAMQAE&DatabaseToSearch=Published VAMQAE]

'''Deposition number:''' 1530121

The complex linked above contains nitrogen coordinated to cobalt with a N-N bond distance of 1.08 Å which is slightly shorter than the optimised N-N bond length, displayed above, of 1.11 Å (2.d.p). During the optimisation process for nitrogen, assumptions have to be made for the computational process to be carried out. Each assumption made will increase the uncertainty in measurable quantities such as the bond length. Hence, the computationally determined bond length from the optimisation is a model and may not fully reflect the true bond length or the bond length determined by a computational program considering slightly different assumptions.

It should also be considered that the optimisation gave a prediction for the N-N bond length in a nitrogen molecule whereas the molecule linked above contains a nitrogen molecule that is coordinated into a transition metal complex. A lone pair of electrons on one of the nitrogen atoms has been donated to a cobalt ion, this draws electron density away from the donating nitrogen atom and would therefore slightly increase the positive charge on this atom. This may cause the donating nitrogen atom to attract the electrons in the N-N bond more strongly which would then explain the shorter bond in the transition metal complex compared to the nitrogen molecule.

==H2 molecule==

===Optimisation data===
{| class="wikitable"
|+ H2 optimisation
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d.p)
|-
|'''Final energy E(RB3LYP)'''
|<nowiki>-1.17853936 (au)</nowiki>
|-
|'''RMS gradient'''
|0.00000017 (au)
|-
|'''Point group'''
|D∞h
|-
|'''Bond length (H-H)'''
|0.74 (Å)
|}

<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

</pre>

<jmol><jmolApplet>
<title> Hydrogen molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACC2518 H2 OPTIMISATION.LOG</uploadedFileContents>
<script>frame 1.7</script>
</jmolApplet></jmol>
[[:File:ACC2518 H2 OPTIMISATION.LOG|Optimised H2 .log file (acc2518)]]

===Vibrations===
[[File:Acc2518 H2vibration.png|Hydrogen display vibrations screenshot|350px]]

{| class="wikitable" border="1"
|+ IR vibration data
|-
| '''Wavenumber''' (cm-1) || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' (arbitrary units) || 0
|-
| '''Image'''|| [[File:Acc2518HydrogenVM.png|250px]]
|}
Using the 3N-5 rule for linear molecules, hydrogen can be expected to have one vibrational mode but this mode has an IR intensity of zero since hydrogen molecules, like nitrogen molecules, are IR inactive.

===Charge analysis===
[[File:Acc2518hydrogen charges.png]]

Both hydrogen atoms have the same electronegativity so the charge is neutral on both atoms.

==The Haber-Bosch process==
N2 + 3H2 -> 2NH3

E(NH3)=-56.55776873

 '''2*E(NH3)''' =2*(-56.55776873)=-113.11553746

 '''E(N2)''' =-109.52412868

E(H2)=-1.17853936

 '''3*E(H2)''' =3*(-1.17853936) =-3.53561808

'''ΔE= 2*E(NH3) -[ E(N2) + 3*E(H2) ]'''= -0.05579069 ≈ -0.05579 au (5.d.p)

'''ΔE=-146.5 kJ/mol (1.d.p)'''

ΔE is negative which indicates that the gaseous reactants are less stable than the ammonia product since the reactants are at a higher energy than the product. Although this process is not necessarily entropically favourable with four reactant gaseous molecules forming two gaseous product molecules, the reaction has a significantly negative enthalpy change which reflects the result calculated above.

== Project molecule (NF3) ==

=== Optimisation data ===
{| class="wikitable"
|+ NF3 optimisation
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d.p)
|-
|'''Final energy E(RB3LYP)'''
|<nowiki>-354.07131058 (au)</nowiki>
|-
|'''RMS gradient'''
|0.00010256 (au)
|-
|'''Point group'''
|C3V
|-
|'''Bond length (N-F)'''
|1.38 (Å)
|-
|'''Bond angle (F-N-F)'''
|102(°)
|}
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000612 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>

<jmol><jmolApplet>
<title> NF3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACC2518_NF3_OPTF_POP.LOG </uploadedFileContents>
<script>frame 1.7</script>
</jmolApplet></jmol>
[[:File:ACC2518_NF3_OPTF_POP.LOG|Optimised NF3 .log file (acc2518)]]

=== Vibrations ===
[[File:Acc2518 NF3 vibrations screenshot.png|The Gaussview "Display Vibrations" window of the optimised nitrogen trifluoride molecule.|350px]]

{| class="wikitable" border="1"
|+ IR vibration data
|-
| '''Wavenumber''' (cm-1) || 482 || 482
|-
| '''Symmetry''' || E || E
|-
| '''Intensity''' (arbitrary units) || 1 || 1
|-
| '''Image'''|| [[File:Acc2518 NF3 VM1.png|300px]] || [[File:Acc2518 NF3 VM2.png|300px]]
|-
! colspan="3" style="text-align: centre;"|
|-
| '''Wavenumber''' (cm-1) || 644|| 930
|-
| '''Symmetry''' || A1 || E
|-
| '''Intensity''' (arbitrary units) || 3 || 208
|-
| '''Image'''|| [[File:Acc2518 NF3 VM3.png|300px]] || [[File:Acc2518 NF3 VM4.png|300px]]
|-
! colspan="3" style="text-align: centre;"|
|-
| '''Wavenumber''' (cm-1) || 930|| 1062
|-
| '''Symmetry''' || E || A1
|-
| '''Intensity''' (arbitrary units) || 208 || 40
|-
| '''Image'''|| [[File:Acc2518 NF3 VM5.png|300px]] || [[File:Acc2518 NF3 VM6.png|300px]]
|}

Nitrogen trifluoride has the same number of atoms as ammonia and so six vibrational modes can be predicted from the 3N-6 rule. There are also two pairs of degenerate modes with frequencies of 482 (cm-1) and 930 (cm-1). The modes with a frequency of 482 (cm-1) and 644(cm-1) correspond to bending vibrational modes and the modes with a frequency of 930 (cm-1) and 1062 (cm-1) correspond to stretching vibrational modes. The mode with a frequency of 1062 (cm-1) represents a symmetric stretch whilst the modes with a frequency of 930 (cm-1) represent asymmetric stretches. In contrast to ammonia, the highest frequency bond stretch of nitrogen trifluoride is the symmetric stretch.

Three bands can be expected in the NF3 IR spectrum at frequencies of 644 (cm-1) 930 (cm-1) and 1062 (cm-1). The bends at 482 (cm-1) will be too low in frequency to appear in the spectrum which starts at a frequency of 500 (cm-1). The stretches at 930 (cm-1) are degenerate and hence will only display one band between them. The band as 644 (cm-1) may not be clearly visible due its relative low intensity of 3 arbitrary units.

=== Charge analysis ===
[[File:Acc2518 NF3 charge analysis.png|The Gaussview generated atomic charges of ammonia.|250px]]

Fluorine has a greater electronegativity that nitrogen and therefore there is greater electron density distributed around the three fluorine atoms compared to the nitrogen atom. The three fluorine atoms are treated as equivalent which means that the magnitude of the positive charge on nitrogen is three times the magnitude of the negative charge on a single fluorine atom.

=== Molecular orbitals (MO) ===

The nitrogen atom contributes 7 electrons and each fluorine atom contributes 9 electrons which means that nitrogen trifluoride contains 34 electrons in total and hence 17 electron pairs. In the table below, a molecular orbital number of 1 would denote the molecular orbital that is deepest in energy. Therefore, orbital 17 represents the HOMO and orbital 18 represents the LUMO. All of the molecular orbitals shown below are occupied with the exception of the LUMO.

{| class="wikitable"
!Molecular orbital number
!Image
!Type of molecular orbital
!Energy (au)
!Extra details
|-
|18
|[[File:Acc2518 MO18.png|200px]]
|Antibonding
|0.01947
|There are nodes in the centre of the N-F bonds which indicates that the LUMO is an antibonding orbital with destructive inteference between phases of opposite sign. The nodes in the centre of all four atoms also indicate that this MO was formed from 2p atomic orbitals from both nitrogen and fluorine.
|-
|17
|[[File:Acc2518 MO17.png|200px]]
|Bonding
| -0.35162
| The phase denoted by the green region shows orbital overlap across all three N-H bonds which implies that the HOMO is a bonding orbital. This MO has been formed from 2p orbitals which explains the nodes observed in the centre of the F atoms.
|-
|16
|[[File:Acc2518 MO16.png|200px]]
|Non-bonding
| -0.42224
|There is no electron density along any of the bonds which is the key indicator that this is a non-bonding MO. Since the electron density is localised around the fluorine atoms, this MO appears to show lone electron pairs on these fluorine atoms. There is no electron density being shared between the fluorine atoms which suggests there is destructive interference preventing such an interaction.
|-
|15
|[[File:Acc2518 MO15.png|200px]]
|Bonding
| -0.43590
| As observed in the HOMO, there is electron density along all three bonds which indicates the bonding nature of the MO. However, in contrast to the HOMO, the electron density along the bonds is not in the same phase for each bond. There is also some constructive interference between two of the F atoms which appears to indicate a very partial π character between the two atoms. This also means that this interaction is the product of two 2p atomic orbitals on fluorine overlapping slightly in phase with each other.
|-
|5
|[[File:Acc2518 MO5.png|200px]]
| Bonding
| -1.35870
| This MO contains no nodes at all implying that it is bonding in nature. It is also formed from overlap of 2s orbitals, in phase, on all atoms since the entire molecule is encased in electron density as a result of the constructive interference. It cannot be formed from 1s orbitals which would be far lower in energy and will also only occupy the first 4 MOs since there are 8 1s electrons in NF3.
|}

== Bonus Molecule (CO2) ==

===Optimisation data===

{| class="wikitable"
|+ CO2 optimisation
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d.p)
|-
|'''Final energy E(RB3LYP)'''
|<nowiki>-188.58093945 (au)</nowiki>
|-
|'''RMS gradient'''
|0.00001154 (au)
|-
|'''Point group'''
|D∞h
|-
|'''Bond length (C-O)'''
|1.17 (Å)
|-
|'''Bond angle (C-O-C)'''
|180 (°)
|-
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES

</pre>

<jmol><jmolApplet>
<title> Carbon dioxide molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ACC2518 CO2 OPTF POP.LOG</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>
[[:File:ACC2518 CO2 OPTF POP.LOG|Optimised CO2 .log file (acc2518)]]

===Vibrations===
[[File:Acc2518 CO2vibration.png|Carbon dioxide display vibrations screenshot|350px]]

{| class="wikitable" border="1"
|+ IR vibration data
|-
| '''Wavenumber''' (cm-1) || 640|| 640
|-
| '''Symmetry''' || PIU || PIU
|-
| '''Intensity''' (arbitrary units) || 31 || 31
|-
| '''Image'''|| [[File:Acc2518co2VM1.png|200px]] || [[File:Acc2518co2VM2.png|250px]]
|-
! colspan="3" style="text-align: centre;"|
|-
| '''Wavenumber''' (cm-1) || 1372|| 2436
|-
| '''Symmetry''' || SGG || SGU
|-
| '''Intensity''' (arbitrary units) || 0 || 546
|-
| '''Image'''|| [[File:Acc2518co2VM3.png|350px]] || [[File:Acc2518co2VM4.png|300px]]
|}
Using the 3N-5 rule for linear molecules, carbon dioxide can be expected to have 4 vibrational modes. The modes with a frequency of 640 cm-1 correspond to bends and the modes with frequencies of 1372 cm-1 and 2436 cm-1 correspond to stretches. The two modes with a frequency of 640 cm-1 are degenerate and will only produce one IR band between them. The stretch with a frequency of 1372 will not produce an IR band as the stretch is symmetric and has no overall dipole. The asymmetric stretch at 2436 cm-1 will also produce an IR band to give two IR bands overall.

===Charge analysis===
[[File:Acc2518 CO2charges.png]]

Oxygen has a greater electronegativity than carbon which explains the negative charge on each oxygen atom and the positive charge on the central carbon atom.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, overall a very good wiki with detailed explanations and a nice layout, well done! The explanation of the charges is good and most of the MO discussion is good. In MO17 however the main contribution to the N atom is of s rather than p character. Overall this MO is antibonding between the F and N atoms with pi bonding amongst the F atoms.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:
Check one of your results against the literature, or
Do an extra calculation on another small molecule, or

You calculated CO2 well done!

Do some deeper analysis on your results so far

Rep:Mod:tb1217

2019-03-24T13:38:13Z

Rr1210:

== NH3 ==

=== Summary ===
'''NH3''', commonly referred to as Ammonia is a colourless gas with a pungent odour<ref name="summary" />

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -56.5577687 AU
|-
| '''RMS gradient'''|| 0.00000485 AU
|-
| '''Point Group '''|| C3v
|-
| '''Bond angle H-N-H'''|| 105.7°
|-
| '''Bond distance H-N '''|| 1.02 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:
<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=-5.785197D-10
Optimization completed.
-- Stationary point found.
</pre>

===Viewing NH3===

[[File:Tb1217_nh3_opt.log]]

<jmol><jmolApplet>
<title>NH3</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>Tb1217_nh3_opt.log</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

===Vibrations of NH3===

{| class="wikitable" border="2"

! !! colspan="4" style="text-align: center;"| Value
|-
| '''Wavenumber''' (cm-1)||style="text-align: center;"| 1090|| style="text-align: center;"|1694|| style="text-align: center;"|3460 || style="text-align: center;"|3590
|-
|'''Symmetry'''|| style="text-align: center;"|A1 ||style="text-align: center;"| E || style="text-align: center;"|A1 ||style="text-align: center;"|E
|-
|'''Intensity''' (arbitrary units)||style="text-align: center;"| 145 ||style="text-align: center;"| 13.6 ||style="text-align: center;"|1.06||style="text-align: center;"|0.27
|-
|'''Image'''|| [[File:Tb1217_145.PNG|100px]]||[[File:Tb1217_13.6.PNG|100px]]||[[File:tb1217_nh3_1.06.PNG|100px]] ||[[File:tb1217_Nh3_0.27.PNG|100px]]
|}

[[File:tb1217_vibrations_NH3.png|thumb|center|Display Vibrations of NH3]]

Using the 3N-6 rule, NH3, with N=4, is expected to have 6 modes of vibration.
It has 2 degenerate modes of vibration, 2 with an intensity of 13.6, and 2 with an intensity of 0.27. An IR spectrum has peaks when there is a change in dipole moment for the bonds, where the intensity listed above corresponds to the height of the peak on the spectrum. On the IR spectrum of NH3, 2 bands are expected; one for 1090cm-1 and one for 1694cm-1. The bands for 3460cm-1 and 3590cm-1 are not seen due to there being no overall change in dipole moment.
The vibrations of 1090cm-1 and 1694cm-1 vibrations are bending. The vibrations of 3460cm-1 and 3590cm-1 are bond stretching vibrations.
The modes for 1090cm-1 and 3460cm-1 are both symmetric, where the mode 3460cm-1 mode is highly symmetric as the point group does not move as it does in the mode for 1090-1.

Additionally, the 1090cm-1 mode is known as the umbrella mode due to the way in which the bonds bend.

===Charge Analysis of NH3===
[[File:Tb1217_nh3_charges.PNG|thumb|center|Charges of NH3]]
Nitrogen is more electronegative than Hydrogen, hence has a negative charge and Hydrogen has a positive charge. As Nitrogen is more electronegative, it has a greater pull on the shared pair of electrons hence has a negative charge.

== N2==
=== Summary ===
'''N2''' is a 'colourless, odourless, tasteless' gas and is needed for many biological processes as well as in the production of fertiliser <ref name="N2" />

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -109.5241287 AU
|-
| '''RMS gradient'''|| 0.0000006 AU
|-
| '''Point Group '''|| D∞h
|-
| '''Bond distance H-N '''|| 1.11 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:

<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=-3.383662D-13
Optimization completed.
</pre>

===Viewing N2===

[[File:tb1217_n2.log]]

<jmol><jmolApplet>
<title>N2</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>tb1217_n2.log</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

===Vibrations of N2===

{| class="wikitable" border="2"

! !! colspan="1" style="text-align: center;"| Value
|-
| '''Wavenumber''' (cm-1)||style="text-align: center;"| 2457
|-
|'''Symmetry'''|| style="text-align: center;"|SGG
|-
|'''Intensity''' (arbitrary units)||style="text-align: center;"| 0
|-
|'''Image'''|| [[File:tb1217_n2_vibration.png|150px]]
|}

[[File:tb1217_vibrations_n2.png|thumb|center|Display Vibrations of N2]]

The IR spectrum of N2 has no peaks due as the single vibrational mode that does occur, bond stretching, has no overall change in dipole moment. Hence, there is no peak for the mode which occurs at 2457cm-1.

===Charge Analysis of N2===
[[File:tb1217_n2_charges.png|thumb|center|Charges of N2]]
The molecule is made up of 2 Nitrogen atoms, hence the individual atoms do not have a charge. Furthermore, the molecule itself also does not have a charge.

=== Mono-metallic TM complex of N2===

TRANS-BIS(1,1'-BIS(DIETHYLPHOSPHINO)FERROCENE)-bis(dinitrogen) (structure identifier AGISEP) has a crystal structure and contains a dinitrogen bond of length of 1.14Å. This is longer than the computed length of 1.11Å.

[[File:tb1217_tm.png|thumb|center|TRANS-BIS(1,1'-BIS(DIETHYLPHOSPHINO)FERROCENE)-bis(dinitrogen)]]

The crystal structure has a longer bond length for the dinitrogen triple bond than the value computed. One of the factors as to why this occurs is due to the Tungsten atom which, due to its electronegativity, pulls electron density away from the Nitrogen involved in the N2 bond. This reduces the bond strength and also lengthens the bond, hence making it longer than the computed length of 1.11Å.

''Link to structure'':
https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=AGISEP&DatabaseToSearch=Published

== H2==
=== Summary ===
'''H2''' is also a colourless, tasteless, and odourless gas and is also extremely flammable <ref name="H2" />.

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -1.1785394 AU
|-
| '''RMS gradient'''|| 0.00000017 AU
|-
| '''Point Group '''|| D∞h
|-
| '''Bond distance H-N '''|| 0.74 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:

<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=-1.167770D-13
Optimization completed.
</pre>

===Viewing H2===

[[File:tb1217_h2_optimised.log]]

<jmol><jmolApplet>
<title>H2</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>tb1217_h2_optimised.log</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

===Vibrations of H2===

{| class="wikitable" border="2"

! !! colspan="1" style="text-align: center;"| Value
|-
| '''Wavenumber''' (cm-1)||style="text-align: center;"| 4466
|-
|'''Symmetry'''|| style="text-align: center;"|SGG
|-
|'''Intensity''' (arbitrary units)||style="text-align: center;"| 0
|-
|'''Image'''|| [[File:tb1217_h2_vibration1.png|150px]]
|}

[[File:tb1217_h2_display.png|thumb|center|Display Vibrations of H2]]

Similarly to N2, the IR spectrum of H2 has no peaks as the single vibrational mode that does occur, bond stretching, has no overall change in dipole moment. Hence, there is no peak for the mode which occurs at 4466cm-1.

===Charge Analysis of H2===
[[File:tb1217_h2_charges.png|thumb|center|Charges of H2]]
The molecule is made up of 2 Hydrogen atoms, hence the individual atoms do not have a charge. Furthermore, the molecule itself also does not have a charge.

== Haber-Bosch Process ==

[[File:tb1217_ammonia.png|thumb|center|Haber-Bosch Process reaction]]

The '''Haber-Bosch Process''' is the reaction used to produce fertiliser. N2 and H2 gases react to form ammonia. In the following table, the energies of the reaction has been given:

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Energy of Haber-Bosch Process
! !! Energy (au)
|-
| '''E(NH3)'''|| -56.5577687
|-
| '''2*E(NH3)'''|| -113.1155374
|-
|'''E(N2)'''|| -109.5241287
|-
|'''E(H2)'''|| -1.1785394
|-
|'''3*E(H2)'''||-3.5356182
|}

The total energy for the reaction is 2*E(NH3) - [E(N2)+3*E(H2)] and using the values from above, is calculated as -0.0557905au. Energy differences are reported in kJmol-1 and for this reaction is -146.476645kJmol-1, -146.5kJmol-1 (1dp).
The reaction has a negative energy change, hence the reaction is exothermic and the ammonia product is more stable than the gaseous N2 and H2 as it is of a lower energy than the reactants.

== PF5 ==

=== Summary ===
'''PF5''', phosphorus pentafluoride, is a colourless and toxic gas which adopts a trigonal bipyramidal geometry.

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -840.6763460 AU
|-
| '''RMS gradient'''|| 0.01907AU
|-
| '''Point Group '''|| C3v
|-
| '''Bond angle F-P-F'''|| 90° and 120°
|-
| '''Bond distance P-F '''|| 1.57 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:
<pre>
Item Value Threshold Converged?
Maximum Force 0.000299 0.000450 YES
RMS Force 0.000090 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000268 0.001200 YES
Predicted change in Energy=-2.765727D-07
Optimization completed.
-- Stationary point found.
</pre>

===Viewing PF5===

[[File:TB1217_PF5.LOG]]

<jmol><jmolApplet>
<title>PF5</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>TB1217_PF5.LOG</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

===Vibrations of PF5===

{| class="wikitable" border="2"

! !! colspan="8" style="text-align: center;"| Value
|-
| '''Wavenumber''' (cm-1)||style="text-align: center;"| 172||style="text-align: center;"| 478|| style="text-align: center;"|503|| style="text-align: center;"|544|| style="text-align: center;"|669|| style="text-align: center;"|784|| style="text-align: center;"|997|| style="text-align: center;"|1020
|-
|'''Symmetry'''|| style="text-align: center;"|E'||style="text-align: center;"| E'' || style="text-align: center;"|E' ||style="text-align: center;"|A2''|| style="text-align: center;"|A1'|| style="text-align: center;"|A1'|| style="text-align: center;"|A2''|| style="text-align: center;"|E'
|-
|'''Intensity''' (arbitrary units)||style="text-align: center;"| 0.035||style="text-align: center;"| 0 ||style="text-align: center;"|37.9||style="text-align: center;"|47.3||style="text-align: center;"| 0||style="text-align: center;"| 0||style="text-align: center;"| 363||style="text-align: center;"| 248
|-
|'''Image'''|| [[File:tb12171.PNG|70px]]||[[File:tb12172.PNG|70px]]||[[File:tb12173.PNG|70px]] ||[[File:tb12174.PNG|70px]]|| [[File:tb12175.PNG|70px]]|| [[File:tb12176.PNG|70px]]|| [[File:tb12177.PNG|70px]]|| [[File:tb12178.PNG|70px]]
|}

[[File:tb1217_PF5_vibrations.PNG|thumb|center|Display Vibrations of PF5]]

The IR spectrum of PF5 has 4 peaks at 503cm-1, 544cm-1, 997cm-1, and 1020cm-1.

===Charge Analysis of PF5===
[[File:tb1217_charges_pf5.PNG|thumb|center|Charges of PF5]]
Fluorine is more electronegative than Phosphorus, hence has a negative charge and Phosphorus has a positive charge. As Fluorine is more electronegative, it has a greater pull on the shared pair of electrons hence has a negative charge. There are two different charges for the Fluorine; -0.570 and -0.536. Due to the geometry of the molecule, the Fluorine atoms vary by charge depending on their position in the trigonal bipyramidal shape.

===Molecular Orbitals of PF5===

Below is a table of several occupied molecular orbitals (MO) of PF5 computed using Gaussview.

{| class="wikitable" border="2"
! MO Number !! Image!! !!Energy (a.u) !! Occupied?
|-
| style="text-align: center;"|'''1'''||[[File:Tb1217_mo1.PNG|100px]]|| This is the atomic 1s orbital of the central Phosphorus atom. It is not involved in any of the bonding between the Phosphorus and Fluorine atoms as it is very deep in energy. It is seen that is not involved in the bonding as there is no overlap observed with other orbitals.|| -77.4|| Yes
|-
|style="text-align: center;"| '''7'''||[[File:Tb1217_mo3.PNG|100px]]||Again, this is not a MO as there is no overlap between atomic orbitals. This is the 2s orbital of the central Phosphorus atom and is not involved in the bonding between the orbitals of the atoms. There is also a huge leap in energy from the previous AO as it is now 2s and not 1s, hence not as deep in energy||-6.82||Yes
|-
| style="text-align: center;"|'''11'''||[[File:Tb1217_mo2.PNG|100px]]||For this, the valence s AO's overlap to form this MO, and the overlap is extended to form one surface. The 3s of the Phosphorus atom and the 2s and 3s of the Fluorine atoms overlap to form this MO. The energy of this molecular orbital is much higher than the one of the previous atomic orbitals due to the bonding that occurs. ||-1.33|| Yes
|-
|style="text-align: center;"|'''16'''||[[File:Tb1217_mo5.PNG|100px]]||This is another MO of PF5 with a large charge density around the Phosphorus atom. For this MO, the 3s atomic orbital of the Phosphorus and the 2p atomic orbital of the Fluorine atom are overlapping. ||-0.71 || Yes
|-
|style="text-align: center;"|'''25'''||[[File:Tb1217_mo4.PNG|100px]]||This image shows 3 non-bonding orbital of the 2p orbitals of the Fluorine atoms surrounding the central Phosphorus. ||-0.47|| Yes
|}

== HCN ==

=== Summary ===

'''HCN''', Hydrogen Cyanide, is an extremely flammable and also poisonous substance which exists at room temperature as a liquid. There is a single bond between Hydrogen and the central Carbon, and a triple bond between the Nitrogen and central Carbon. Overall, the molecule adopts a linear geometry.

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -93.4245813AU
|-
| '''RMS gradient'''|| 0.00017006AU
|-
| '''Point Group '''|| C1
|-
| '''Bond distance C-H '''|| 1.07 Å
|-
| '''Bond distance C-N ''' (triple bond)|| 1.16 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:
<pre>
Item Value Threshold Converged?
Maximum Force 0.000370 0.000450 YES
RMS Force 0.000255 0.000300 YES
Maximum Displacement 0.000731 0.001800 YES
RMS Displacement 0.000459 0.001200 YES
Predicted change in Energy=-2.199408D-07
Optimization completed.
-- Stationary point found.
</pre>

===Viewing HCN===

[[File:TB1217_HCN.LOG]]

<jmol><jmolApplet>
<title>HCN</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>TB1217_HCN.LOG</uploadedFileContents>
<script>frame 1.8</script>
</jmolApplet></jmol>

== References ==

<ref name="summary">https://pubchem.ncbi.nlm.nih.gov/compound/ammonia#</ref>

<ref name="N2">http://www.uigi.com/nitrogen.html</ref>

<ref name="H2">https://en.wikipedia.org/wiki/Hydrogen</ref>

<references>
</references>
=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES - overall your wiki is very good well done! Excellent explanations particularly for the first part.

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, good explanation on the charges. The MOs are nicely presented and most of your written explanations are correct, well done. However you have missed out explaining whether interactions are bonding or anti-bonding. For example MO 11 and MO 16 are formed of in phase (same colour, bonding, MO11) and out of phase (different colour, antibonding, MO 16) AOs. You will develop confidence with this concept over your upcoming lecture courses, don't worry!

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

You added lots of extra references, well done.

Do an extra calculation on another small molecule, or

You also calculated HCN, good work.

Do some deeper analysis on your results so far

Rep:Mod:tb1217

2019-03-24T13:37:37Z

Rr1210:

== NH3 ==

=== Summary ===
'''NH3''', commonly referred to as Ammonia is a colourless gas with a pungent odour<ref name="summary" />

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -56.5577687 AU
|-
| '''RMS gradient'''|| 0.00000485 AU
|-
| '''Point Group '''|| C3v
|-
| '''Bond angle H-N-H'''|| 105.7°
|-
| '''Bond distance H-N '''|| 1.02 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:
<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=-5.785197D-10
Optimization completed.
-- Stationary point found.
</pre>

===Viewing NH3===

[[File:Tb1217_nh3_opt.log]]

<jmol><jmolApplet>
<title>NH3</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>Tb1217_nh3_opt.log</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

===Vibrations of NH3===

{| class="wikitable" border="2"

! !! colspan="4" style="text-align: center;"| Value
|-
| '''Wavenumber''' (cm-1)||style="text-align: center;"| 1090|| style="text-align: center;"|1694|| style="text-align: center;"|3460 || style="text-align: center;"|3590
|-
|'''Symmetry'''|| style="text-align: center;"|A1 ||style="text-align: center;"| E || style="text-align: center;"|A1 ||style="text-align: center;"|E
|-
|'''Intensity''' (arbitrary units)||style="text-align: center;"| 145 ||style="text-align: center;"| 13.6 ||style="text-align: center;"|1.06||style="text-align: center;"|0.27
|-
|'''Image'''|| [[File:Tb1217_145.PNG|100px]]||[[File:Tb1217_13.6.PNG|100px]]||[[File:tb1217_nh3_1.06.PNG|100px]] ||[[File:tb1217_Nh3_0.27.PNG|100px]]
|}

[[File:tb1217_vibrations_NH3.png|thumb|center|Display Vibrations of NH3]]

Using the 3N-6 rule, NH3, with N=4, is expected to have 6 modes of vibration.
It has 2 degenerate modes of vibration, 2 with an intensity of 13.6, and 2 with an intensity of 0.27. An IR spectrum has peaks when there is a change in dipole moment for the bonds, where the intensity listed above corresponds to the height of the peak on the spectrum. On the IR spectrum of NH3, 2 bands are expected; one for 1090cm-1 and one for 1694cm-1. The bands for 3460cm-1 and 3590cm-1 are not seen due to there being no overall change in dipole moment.
The vibrations of 1090cm-1 and 1694cm-1 vibrations are bending. The vibrations of 3460cm-1 and 3590cm-1 are bond stretching vibrations.
The modes for 1090cm-1 and 3460cm-1 are both symmetric, where the mode 3460cm-1 mode is highly symmetric as the point group does not move as it does in the mode for 1090-1.

Additionally, the 1090cm-1 mode is known as the umbrella mode due to the way in which the bonds bend.

===Charge Analysis of NH3===
[[File:Tb1217_nh3_charges.PNG|thumb|center|Charges of NH3]]
Nitrogen is more electronegative than Hydrogen, hence has a negative charge and Hydrogen has a positive charge. As Nitrogen is more electronegative, it has a greater pull on the shared pair of electrons hence has a negative charge.

== N2==
=== Summary ===
'''N2''' is a 'colourless, odourless, tasteless' gas and is needed for many biological processes as well as in the production of fertiliser <ref name="N2" />

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -109.5241287 AU
|-
| '''RMS gradient'''|| 0.0000006 AU
|-
| '''Point Group '''|| D∞h
|-
| '''Bond distance H-N '''|| 1.11 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:

<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=-3.383662D-13
Optimization completed.
</pre>

===Viewing N2===

[[File:tb1217_n2.log]]

<jmol><jmolApplet>
<title>N2</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>tb1217_n2.log</uploadedFileContents>
<script>frame 1.10</script>
</jmolApplet></jmol>

===Vibrations of N2===

{| class="wikitable" border="2"

! !! colspan="1" style="text-align: center;"| Value
|-
| '''Wavenumber''' (cm-1)||style="text-align: center;"| 2457
|-
|'''Symmetry'''|| style="text-align: center;"|SGG
|-
|'''Intensity''' (arbitrary units)||style="text-align: center;"| 0
|-
|'''Image'''|| [[File:tb1217_n2_vibration.png|150px]]
|}

[[File:tb1217_vibrations_n2.png|thumb|center|Display Vibrations of N2]]

The IR spectrum of N2 has no peaks due as the single vibrational mode that does occur, bond stretching, has no overall change in dipole moment. Hence, there is no peak for the mode which occurs at 2457cm-1.

===Charge Analysis of N2===
[[File:tb1217_n2_charges.png|thumb|center|Charges of N2]]
The molecule is made up of 2 Nitrogen atoms, hence the individual atoms do not have a charge. Furthermore, the molecule itself also does not have a charge.

=== Mono-metallic TM complex of N2===

TRANS-BIS(1,1'-BIS(DIETHYLPHOSPHINO)FERROCENE)-bis(dinitrogen) (structure identifier AGISEP) has a crystal structure and contains a dinitrogen bond of length of 1.14Å. This is longer than the computed length of 1.11Å.

[[File:tb1217_tm.png|thumb|center|TRANS-BIS(1,1'-BIS(DIETHYLPHOSPHINO)FERROCENE)-bis(dinitrogen)]]

The crystal structure has a longer bond length for the dinitrogen triple bond than the value computed. One of the factors as to why this occurs is due to the Tungsten atom which, due to its electronegativity, pulls electron density away from the Nitrogen involved in the N2 bond. This reduces the bond strength and also lengthens the bond, hence making it longer than the computed length of 1.11Å.

''Link to structure'':
https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=AGISEP&DatabaseToSearch=Published

== H2==
=== Summary ===
'''H2''' is also a colourless, tasteless, and odourless gas and is also extremely flammable <ref name="H2" />.

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -1.1785394 AU
|-
| '''RMS gradient'''|| 0.00000017 AU
|-
| '''Point Group '''|| D∞h
|-
| '''Bond distance H-N '''|| 0.74 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:

<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=-1.167770D-13
Optimization completed.
</pre>

===Viewing H2===

[[File:tb1217_h2_optimised.log]]

<jmol><jmolApplet>
<title>H2</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>tb1217_h2_optimised.log</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

===Vibrations of H2===

{| class="wikitable" border="2"

! !! colspan="1" style="text-align: center;"| Value
|-
| '''Wavenumber''' (cm-1)||style="text-align: center;"| 4466
|-
|'''Symmetry'''|| style="text-align: center;"|SGG
|-
|'''Intensity''' (arbitrary units)||style="text-align: center;"| 0
|-
|'''Image'''|| [[File:tb1217_h2_vibration1.png|150px]]
|}

[[File:tb1217_h2_display.png|thumb|center|Display Vibrations of H2]]

Similarly to N2, the IR spectrum of H2 has no peaks as the single vibrational mode that does occur, bond stretching, has no overall change in dipole moment. Hence, there is no peak for the mode which occurs at 4466cm-1.

===Charge Analysis of H2===
[[File:tb1217_h2_charges.png|thumb|center|Charges of H2]]
The molecule is made up of 2 Hydrogen atoms, hence the individual atoms do not have a charge. Furthermore, the molecule itself also does not have a charge.

== Haber-Bosch Process ==

[[File:tb1217_ammonia.png|thumb|center|Haber-Bosch Process reaction]]

The '''Haber-Bosch Process''' is the reaction used to produce fertiliser. N2 and H2 gases react to form ammonia. In the following table, the energies of the reaction has been given:

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Energy of Haber-Bosch Process
! !! Energy (au)
|-
| '''E(NH3)'''|| -56.5577687
|-
| '''2*E(NH3)'''|| -113.1155374
|-
|'''E(N2)'''|| -109.5241287
|-
|'''E(H2)'''|| -1.1785394
|-
|'''3*E(H2)'''||-3.5356182
|}

The total energy for the reaction is 2*E(NH3) - [E(N2)+3*E(H2)] and using the values from above, is calculated as -0.0557905au. Energy differences are reported in kJmol-1 and for this reaction is -146.476645kJmol-1, -146.5kJmol-1 (1dp).
The reaction has a negative energy change, hence the reaction is exothermic and the ammonia product is more stable than the gaseous N2 and H2 as it is of a lower energy than the reactants.

== PF5 ==

=== Summary ===
'''PF5''', phosphorus pentafluoride, is a colourless and toxic gas which adopts a trigonal bipyramidal geometry.

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -840.6763460 AU
|-
| '''RMS gradient'''|| 0.01907AU
|-
| '''Point Group '''|| C3v
|-
| '''Bond angle F-P-F'''|| 90° and 120°
|-
| '''Bond distance P-F '''|| 1.57 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:
<pre>
Item Value Threshold Converged?
Maximum Force 0.000299 0.000450 YES
RMS Force 0.000090 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000268 0.001200 YES
Predicted change in Energy=-2.765727D-07
Optimization completed.
-- Stationary point found.
</pre>

===Viewing PF5===

[[File:TB1217_PF5.LOG]]

<jmol><jmolApplet>
<title>PF5</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>TB1217_PF5.LOG</uploadedFileContents>
<script>frame 1.12</script>
</jmolApplet></jmol>

===Vibrations of PF5===

{| class="wikitable" border="2"

! !! colspan="8" style="text-align: center;"| Value
|-
| '''Wavenumber''' (cm-1)||style="text-align: center;"| 172||style="text-align: center;"| 478|| style="text-align: center;"|503|| style="text-align: center;"|544|| style="text-align: center;"|669|| style="text-align: center;"|784|| style="text-align: center;"|997|| style="text-align: center;"|1020
|-
|'''Symmetry'''|| style="text-align: center;"|E'||style="text-align: center;"| E'' || style="text-align: center;"|E' ||style="text-align: center;"|A2''|| style="text-align: center;"|A1'|| style="text-align: center;"|A1'|| style="text-align: center;"|A2''|| style="text-align: center;"|E'
|-
|'''Intensity''' (arbitrary units)||style="text-align: center;"| 0.035||style="text-align: center;"| 0 ||style="text-align: center;"|37.9||style="text-align: center;"|47.3||style="text-align: center;"| 0||style="text-align: center;"| 0||style="text-align: center;"| 363||style="text-align: center;"| 248
|-
|'''Image'''|| [[File:tb12171.PNG|70px]]||[[File:tb12172.PNG|70px]]||[[File:tb12173.PNG|70px]] ||[[File:tb12174.PNG|70px]]|| [[File:tb12175.PNG|70px]]|| [[File:tb12176.PNG|70px]]|| [[File:tb12177.PNG|70px]]|| [[File:tb12178.PNG|70px]]
|}

[[File:tb1217_PF5_vibrations.PNG|thumb|center|Display Vibrations of PF5]]

The IR spectrum of PF5 has 4 peaks at 503cm-1, 544cm-1, 997cm-1, and 1020cm-1.

===Charge Analysis of PF5===
[[File:tb1217_charges_pf5.PNG|thumb|center|Charges of PF5]]
Fluorine is more electronegative than Phosphorus, hence has a negative charge and Phosphorus has a positive charge. As Fluorine is more electronegative, it has a greater pull on the shared pair of electrons hence has a negative charge. There are two different charges for the Fluorine; -0.570 and -0.536. Due to the geometry of the molecule, the Fluorine atoms vary by charge depending on their position in the trigonal bipyramidal shape.

===Molecular Orbitals of PF5===

Below is a table of several occupied molecular orbitals (MO) of PF5 computed using Gaussview.

{| class="wikitable" border="2"
! MO Number !! Image!! !!Energy (a.u) !! Occupied?
|-
| style="text-align: center;"|'''1'''||[[File:Tb1217_mo1.PNG|100px]]|| This is the atomic 1s orbital of the central Phosphorus atom. It is not involved in any of the bonding between the Phosphorus and Fluorine atoms as it is very deep in energy. It is seen that is not involved in the bonding as there is no overlap observed with other orbitals.|| -77.4|| Yes
|-
|style="text-align: center;"| '''7'''||[[File:Tb1217_mo3.PNG|100px]]||Again, this is not a MO as there is no overlap between atomic orbitals. This is the 2s orbital of the central Phosphorus atom and is not involved in the bonding between the orbitals of the atoms. There is also a huge leap in energy from the previous AO as it is now 2s and not 1s, hence not as deep in energy||-6.82||Yes
|-
| style="text-align: center;"|'''11'''||[[File:Tb1217_mo2.PNG|100px]]||For this, the valence s AO's overlap to form this MO, and the overlap is extended to form one surface. The 3s of the Phosphorus atom and the 2s and 3s of the Fluorine atoms overlap to form this MO. The energy of this molecular orbital is much higher than the one of the previous atomic orbitals due to the bonding that occurs. ||-1.33|| Yes
|-
|style="text-align: center;"|'''16'''||[[File:Tb1217_mo5.PNG|100px]]||This is another MO of PF5 with a large charge density around the Phosphorus atom. For this MO, the 3s atomic orbital of the Phosphorus and the 2p atomic orbital of the Fluorine atom are overlapping. ||-0.71 || Yes
|-
|style="text-align: center;"|'''25'''||[[File:Tb1217_mo4.PNG|100px]]||This image shows 3 non-bonding orbital of the 2p orbitals of the Fluorine atoms surrounding the central Phosphorus. ||-0.47|| Yes
|}

== HCN ==

=== Summary ===

'''HCN''', Hydrogen Cyanide, is an extremely flammable and also poisonous substance which exists at room temperature as a liquid. There is a single bond between Hydrogen and the central Carbon, and a triple bond between the Nitrogen and central Carbon. Overall, the molecule adopts a linear geometry.

The molecule was optimised using GaussView with the following criteria:

{| class="wikitable" border="2"
|+ Criteria
|-
| '''Calculation Method'''||B3LYP
|-
| '''Basis Set'''||6-31G(d,p)
|}

Optimisation was carried out to calculate the values for the molecule with the optimum position of the nuclei for the electron configuration of the molecule.

Having optimised the molecule, the following values were calculated:

{| class="wikitable" border="1"
! !! Value
|-
| '''E(RB3LYP)'''|| -93.4245813AU
|-
| '''RMS gradient'''|| 0.00017006AU
|-
| '''Point Group '''|| C1
|-
| '''Bond distance C-H '''|| 1.07 Å
|-
| '''Bond distance C-N ''' (triple bond)|| 1.16 Å
|}

The angles have been calculated with an accuracy of 1° and the distance with 0.01Å

Item section of the output:
<pre>
Item Value Threshold Converged?
Maximum Force 0.000370 0.000450 YES
RMS Force 0.000255 0.000300 YES
Maximum Displacement 0.000731 0.001800 YES
RMS Displacement 0.000459 0.001200 YES
Predicted change in Energy=-2.199408D-07
Optimization completed.
-- Stationary point found.
</pre>

===Viewing HCN===

[[File:TB1217_HCN.LOG]]

<jmol><jmolApplet>
<title>HCN</title>
<color>grey</color>
<size>200</size>
<uploadedFileContents>TB1217_HCN.LOG</uploadedFileContents>
<script>frame 1.8</script>
</jmolApplet></jmol>

== References ==

<ref name="summary">https://pubchem.ncbi.nlm.nih.gov/compound/ammonia#</ref>

<ref name="N2">http://www.uigi.com/nitrogen.html</ref>

<ref name="H2">https://en.wikipedia.org/wiki/Hydrogen</ref>

<references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES - overall your wiki is very good well done! Excellent explanations particularly for the first part.

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, good explanation on the charges. The MOs are nicely presented and most of your written explanations are correct, well done. However you have missed out explaining whether interactions are bonding or anti-bonding. For example MO 11 and MO 16 are formed of in phase (same colour, bonding, MO11) and out of phase (different colour, antibonding, MO 16) AOs. You will develop confidence with this concept over your upcoming lecture courses, don't worry!

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

You added lots of extra references, well done.

Do an extra calculation on another small molecule, or

You also calculated HCN, good work.

Do some deeper analysis on your results so far

Rep:Mod:zp2518

2019-03-22T17:01:43Z

Rr1210:

==NH3 molecule==

===summary ===
Calculation MethodːRB3LYP

Basis Setː6-31G(d,p)

Final Energy(RB3LYP)ː-56.5577687 a.u.

RMS Gradientː0.0000049 a.u.

Point GroupːC3V

N-H bond distance = 1.02 Å

H-N-H bond angle = 106°

=== "Item" table ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

The maximum force is below 0.00045 and the converge of the set of values means that the optimisation is completed

===JMol of structure ===
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<script>frame 1.16</script>
<uploadedFileContents>PZOUHANWEN NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked [[Media:PZOUHANWEN NH3 OPTF POP.LOG| here]]

=== Display vibrations table ===
[[File:Pzouhanwen screenshot.png|thumb|left|Display Vibrations]]

=== Table of vibrations and intensities ===
{| class="wikitable" border="1"

| wave number cm-1|| 1090 || 1694|| 3461|| 3590
|-
| symmetry||A1 || E ||A1 || E
|-
| intensity arbitrary unit|| 145 || 14 || 1 || 0
|-
| image || [[File:pzouhanwen screenshot v1.png|150px]] || [[File:pzouhanwen screenshot v2.png|150px]]|| [[File:pzouhanwen screenshot v3.png|150px]]|| [[File:pzouhanwen screenshot v4.png|150px]]
|}

The vibrations at 1694 cm-1 and 3590 cm-1 have two degenerate states respectively, 6 modes of vibrations in total

The difference in the intensity is due to the different in the change of dipole during the vibration . The first mode have the highest intensity among the 6 modes because it has the highest change in the dipole (all H-atoms move to the same side). And the two degenerate vibration, modes 5&6, have the lowest change in dipole among the 6 modes hence the lowest intensity.

=== Question and answer ===

====how many modes do you expect from the 3N-6 rule?====

6.

====which modes are degenerate (ie have the same energy)?====

Modes2&3 , modes5&6.

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

Modes1,2,3 are bending. Modes4,5,6 are bond stretch.

====which mode is highly symmetric?====

Modes 1,4 are highly symmetric.

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

Mode 1.

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

We expect to see four bands, because modes 2&3 and 5&6 are degenerate. But two of the four bands are too low in intensity (1.06&0.27) to be visualise in an real experiment due to the limitation of experimental appliance.

=== NBO charge ===
Charge on the N-atom = -1.125

charge on the H-atom = 0.375

The N-atom are expected to have the negative charge due to its high electronegativity

==H2 molecule==

====summary ====
Calculation MethodːRB3LYP

Basis Setː6-31G(d,p)

Final Energy(RB3LYP)ː-1.1785394 a.u.

RMS Gradientː0.0000002 a.u.

Point GroupːD∞h

H-H bond distance = 0.74 Å

linear structure

=== "Item" table ===
<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

</pre>

The maximum force is below 0.00045 and the converge of the set of values means that the optimisation is completed

===JMol of structure ===
<jmol><jmolApplet>
<title>H2</title>
<color>black</color>
<size>200</size>
<script>frame 1.12</script>
<uploadedFileContents>PZOUHANWEN H2 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked [[Media:PZOUHANWEN H2 OPTF POP.LOG| here]]

=== Display vibrations table ===
[[File:Pzouhanwen screenshot h2.png|thumb|left|Display Vibrations]]

=== Table of vibrations and intensities ===
{| class="wikitable" border="1"

| wave number cm-1|| 4466
|-
| symmetry||SGG
|-
| intensity arbitrary unit|| 0
|-
| image || [[File:pzouhanwen screenshot h2 v.png|190px]]
|}

The intensity of this vibration is zero due to the vibration is symmetric and there's no change in the dipole.

=== NBO charge ===
Charge on both of the H-atoms = 0

The two H-atoms have same electronegativity, the charges are ''cancelled out'' due to the molecule's symmetry, so the NBO charges are 0.

==N2 molecule==

====summary ====
Calculation MethodːRB3LYP

Basis Setː6-31G(d,p)

Final Energy(RB3LYP)ː-109.5241287 a.u.

RMS Gradientː0.0000006 a.u.

Point GroupːD∞h

N-N bond distance = 1.11 Å

Linear structure

=== "Item" table ===
<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
</pre>

The maximum force is below 0.00045 and the converge of the set of values means that the optimisation is completed

===JMol of structure ===

<jmol><jmolApplet>
<title>N2</title>
<color>black</color>
<size>200</size>
<script>frame 1.10</script>
<uploadedFileContents>PZOUHANWEN N2 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked [[Media:PZOUHANWEN N2 OPTF POP.LOG| here]]

=== Display vibrations table ===
[[File:Pzouhanwen screenshot n2.png|thumb|left|Display Vibrations]]

=== Table of vibrations and intensities ===
{| class="wikitable" border="1"

| wave number cm-1|| 2457
|-
| symmetry||A1
|-
| intensity arbitrary unit|| 0
|-
| image || [[File:pzouhanwen screenshot n2 v.png|190px]]

|}

The intensity of this vibration is zero due to the vibration is symmetric and there's no change in the dipole.

=== NBO charge ===
Charge on both of the N-atoms = 0

The two N-atoms have same electronegativity, the charges are ''cancelled out'' due to the molecule's symmetry, so the NBO charges are 0.

==Mono-metallic TM complex that coordinates H2==
DECXOY

Sturcture displayed[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DECXOY&DatabaseToSearch=Published here]]

H-H Bond distance in the structure with identifier DECXOY = 0.9 Å

H-H bond distance gained by computational calculation = 0.74 Å

The computational distances H-H is smaller than that in the structure we gained(DECXOY) which means the H-H bond is shorter and stronger. This can be explained by the difference in the environment of the H-atoms. In the structure, H-atoms are bonded to metal ion and the electronegative TM pull the electron density away form the hydrogens. The electron density diffusion cause the strength of bond between the H-atoms in the structure to be lower, hence longer distance. In addition, in the computational calculation, only parameters are used, while in real experiment, environment should also be taken in to consideration. The effect of this computational failure could be also be an explanation to difference in the H-atoms distance.

==Determining the energy for Haber-Bosch process ==
E(NH3)= -56.5577687 a.u.

2*E(NH3)= 3*-1.17853936 = -113.1155375 a.u.

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853936 a.u.

3*E(H2)= 3*-1.17853936 = -3.53561808 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

=-113.1155375-[-109.52412868+-3.53561808]

=-0.05579064 a.u.

=-146.5 KJ/mol

The energy change have negative sign, so the ammonia product is more stable.

==O2 molecule==

===summary ===
Calculation MethodːRB3LYP

Basis Setː6-31G(d,p)

Final Energy(RB3LYP)ː-150.2574243 a.u.

RMS Gradientː0.0000750 a.u.

Point GroupːD∞h

O=O bond distance = 1.22 Å

linear structure

=== "Item" table ===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000130 0.000450 YES
RMS Force 0.000130 0.000300 YES
Maximum Displacement 0.000080 0.001800 YES
RMS Displacement 0.000113 0.001200 YES

</pre>

The maximum force is below 0.00045 and the converge of the set of values means that the optimisation is completed

===JMol of structure ===

<jmol><jmolApplet>
<title>O2</title>
<color>black</color>
<size>200</size>
<script>frame 1.10</script>
<uploadedFileContents>PZOUHANWEN O2 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:PZOUHANWEN O2 OPTF POP.LOG| here]]

=== Display vibrations table ===
[[File:Pzouhanwen screenshot o2.png|thumb|left|Display Vibrations]]

=== Table of vibrations and intensities ===
{| class="wikitable" border="1"

| wave number cm-1|| 1643
|-
| symmetry||SGG
|-
| intensity arbitrary unit|| 0
|-
| image || [[File:pzouhanwen screenshot o2 v.png|190px]]

|}

The intensity of this vibration is zero due to the vibration is symmetric and there's no change in the dipole.

=== NBO charge ===
Charge on both of the O-atoms = 0

The two O-atoms have same electronegativity, the charges are ''cancelled out'' due to the molecule's symmetry, so the NBO charges are 0.

=== MOs ===
{| class="wikitable" border="1"

| 1s-1s σ bonding orbital || [[File:pzouhanwen moo2 1.png|190px]] || This is non-bonding MO formed by combination of two 1s AO of the oxygen atoms with the same phase. It is deep in energy with the lowest energy level in the structure of oxygen molecule. This MO is occupied by two pair-spin electron and it does not contribute to the bond forming
|-
| 1s-1s σ* orbital||[[File:pzouhanwen moo2 2.png|190px]] || This is an non-bonding MO formed by combination of two 1s AO that out of phase. It is deep in energy with the second lowest energy level in the structure of oxygen molecule. This MO is occupied by two pair-spin electron and it does not contribute to the bond forming
|-
| 2py-2py π* orbital || [[File:pzouhanwen moo2 8.png|190px]] || This is an anti-bonding MO formed by overlapping of two parallel py orbital that out of phase. It is in the HOMO reigion and occupied by two pair-spin electron in the calculated MOs structure. But in theory it is only occupied by one self-spin electron. This difference is due to the failure of calculation.This MO destabilise the O-O bonding
|-
| 2pz-2pz π* orbital || [[File:pzouhanwen_moo2_9.png|190px]] || This is an non-bonding MO formed by overlapping of two parallel pz orbital that out of phase. It is in the LUMO reigion and unoccupied with no contribution to the bond forming in the calculated MOs structure. But in theory it is in the HOMO region and is an anti-bonding orbital with the same energy as the other π2p orbital(degenerate). It also have one self-spin electron in it and destabilise the O-O bonding in theory. This difference is due to the failure of calculation.

|-
| 2px-2px σ* orbital || [[File:pzouhanwen_moo2_10.png|190px]] || This is an non-bonding MO formed by overlapping of two head-to-head px orbital that out of phase. It is higher in energy and unoccupied in the calculated MOs structure. But in theory it is in the LUMO region. This difference is due to the failure of calculation.This MO do not contribute to the O-O bond forming.

|}

==IndependenceːCO2 molecule==

====summary ====
Calculation MethodːRB3LYP

Basis Setː6-31G(d,p)

Final Energy(RB3LYP)ː-188.5809395 a.u.

RMS Gradientː 0.0000115 a.u.

Point GroupːD∞h

C=O bond distance = 1.17 Å

O=C=O bond angle = 180 °

linear structure

=== "Item" table ===
<pre>
Item Value Threshold Converged?
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES

</pre>

The maximum force is below 0.00045 and the converge of the set of values means that the optimisation is completed

===JMol of structure ===

<jmol><jmolApplet>
<title>CO2</title>
<color>black</color>
<size>200</size>
<script>frame 1.10</script>
<uploadedFileContents>PZOUHANWEN CO2 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:PZOUHANWEN CO2 OPTF POP.LOG| here]]

=== Display vibrations table ===
[[File:Pzouhanwen screenshot co2.png|thumb|left|Display Vibrations]]

=== Table of vibrations and intensities ===
{| class="wikitable" border="1"

| wave number cm-1|| 640 || 1372|| 2436
|-
| symmetry||PIU||SGG||SGU
|-
| intensity arbitrary unit|| 31|| 0|| 545
|-
| image || [[File:pzouhanwen screenshot co2 v.png|190px]] || [[File:pzouhanwen screenshot co2 v2.png|190px]] || [[File:pzouhanwen screenshot co2 v3.png|190px]]

|}

The vibration at 640 cm-1 have two degenerate vibration states.

The intensity of second mode of vibration is zero due to the vibration is symmetric and there's no change in the dipole.
The 4th mode of vibration has higher intensity than the 1st and 2nd ones' because the 4th mode vibration have higher change in the dipole.

=== NBO charge ===
Charges on both of the O-atoms and C-atom = 0

The two O-atoms have same electronegativity, the charges are ''cancelled out'' due to the molecule's symmetry as the three-atom molecule have linear shape, so the NBO charges are 0.

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, very good explanations overall, well done!

One area I would improve is when a molecule is unoccupied you call it a non-bonding MO. It is clearer to say for e.g. the LUMO: This MO has antibonding interations between the O atoms, but does not reduce the bonding in the molecule because it is unnoccupied.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

You did an extra calculation, well done.

Do some deeper analysis on your results so far

Rp318NH3

2019-03-22T16:55:15Z

Rr1210:

==NH3==

===Information about the Molecule===

Bond angle(Optimised):105.741o
Bond length (Optimised):1.01798Å

====Table of Optimisation Results of Molecule====
{| class="wikitable" border="1"
|+ NH3 Optimisation Results
|-
|Calculation Method||RB3LYP
|-
|Basis set||6-31G(d,p)
|-
|E(RB3LYP)||-56.5577687 a.u.
|-
|RMS Gradient Norm||0.00000485 a.u.
|-
|Point Group||C3V
|}

====Table Showing the Convergence of Molecule====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

The optimisation file is linked to [[Media:NH3 01516896 IMM2.LOG|here]]
====Model of Molecule====
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3 01516896 IMM2.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrations of Molecule====
[[File:Vibrations_NH3_2_01516896.PNG|thumb|center|Table of Vibrations]]

{| class="wikitable" border="1"
|+ Table of vibration types and wavenumbers
|-
|Wavenumber cm-1||1090||1694||3461||3590
|-
|Symmetry||A1||E||A1||E
|-
|Intensity Arbitrary units||145||14||1||0.2
|}

The 3N-6 rule shows that there are 6 vibrational modes. Vibrational modes at 1694cm-1 and 3590cm-1 are degenerate.Bending vibrations hasve vibrations at lower frequencies than bond stretch vibrations. In this case the bending vibrations are at 1090cm-1 and 1694cm-1 and the bond streching vibrations are at 3461cm-1 and 3590cm-1.There is a highly symmetrical stretch at 3461cm-1. The mode known as the umbrella mode has the vibration frequecy of 1090cm-1. Three peaks are expected in an experimental spectrum of gaseous ammonia. This is because the symmetrical bond stretch peak will ovelap with the other bond strech peak.

====Charge Analysis of Molecule====
{|class="wikitable" border="1"
|+ Charges on Atoms
|-
|H atom||0.375
|-
|N atom||-1.125
|}

Charge expected on N is negative while for H it would be positive. This is because N is more electronegative than H threrfore the electrons oin the bond are drawn toward N more.

==H2==
===Information about the Molecule===
Bond angle (Optimised):180o
Bond length (Optimised):0.600Å

====Table of Optimisation Results of Molecule====
{| class="wikitable" border="1"
|+ H2 Optimisation Results
|-
|Calculation Method||RB3LYP
|-
|Basis set||6-31G(d,p)
|-
|E(RB3LYP)||-1.1785394 a.u.
|-
|RMS Gradient Norm||0.00000017 a.u.
|-
|Point Group||D*H
|}

====Table Showing the Convergence of Molecule====
<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
</pre>

The optimisation file is linked to [[Media:H2 01516896 IMM2.LOG|here]]

====Model of Molecule====
<jmol><jmolApplet>
<title>H2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>H2 01516896 IMM2.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrations of Molecule====
[[File:Vibrations_H2_01516896.PNG|thumb|center|Table of Vibrations]]

H2 does not have a peak in the IR spectrum as the molecule is diatomic therefore there is no change in dipole.
====Charge Analysis of Molecule====
Molecule is a diatomic molecule therefore there is no diference in charge between the two atoms.

==N2==
===Information about the Molecule===
Bond angle (Optimised):180o
Bond length (Optimised):1.106Å

====Table of Optimisation Results of Molecule====
{| class="wikitable" border="1"
|+ N2 Optimisation Results
|-
|Calculation Method||RB3LYP
|-
|Basis set||6-31G(d,p)
|-
|E(RB3LYP)||-109.5241287a.u.
|-
|RMS Gradient Norm||0.00000060 a.u.
|-
|Point Group||D*H
|}

====Table Showing the Convergence of Molecule====
<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
</pre>

The optimisation file is linked to [[Media:N2 01516896 IMM2.LOG|here]]

====Model of Molecule====
<jmol><jmolApplet>
<title>N2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>N2 01516896 IMM2.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrations of Molecule====
[[File:Vibrations_N2_01516896.PNG|thumb|center|Table of Vibrations]]

N2 does not have a peak in the IR spectrum as the molecule is diatomic therefore there is no change in dipole.
====Charge Analysis of Molecule====
Molecule is a diatomic molecule therefore there is no diference in charge between the two atoms.
==== N2 Bond Length from Transition Metal Complex====
A bond length of N2 was found to be 1.131(8)Å from the transition metal complex (bis(2-(dicyclohexylphosphino)phenyl)(methyl)silyl)-dinitrogen-(trimethylphosphino)-cobalt structure VEJSEL<ref name="VEJSEL"/>. Bondlength between computational value and experimental value is very close together (both round down to 1.1Å.

==Haber-Bosch Reaction Calculation==
{| class="wikitable" border="1"
|-
|E(NH3)=-56.5577687
|-
|2*E(NH3)=-113.1155374
|-
|E(N2)=-109.5241287
|-
|E(H2)=-1.1785394
|-
|3*E(H2)=-3.5356182
|-
|ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557905 a.u.
|}
Converting from a.u. to kjmol-1 gives -146.82kjmol-1.
Ammonia product is more stable than the gaseous reactants.

==O2==
===Information about the Molecule===
Bond angle (Optimised):180o
Bond length (Optimised):1.216Å

====Table of Optimisation Results of Molecule====
{| class="wikitable" border="1"
|+ O2 Optimisation Results
|-
|Calculation Method||RB3LYP
|-
|Basis set||6-31G(d,p)
|-
|E(RB3LYP)||-150.2574243 a.u.
|-
|RMS Gradient Norm||0.00007502 a.u.
|-
|Point Group||D*H
|}

====Table Showing the Convergence of Molecule====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000130 0.000450 YES
RMS Force 0.000130 0.000300 YES
Maximum Displacement 0.000080 0.001800 YES
RMS Displacement 0.000113 0.001200 YES

</pre>

The optimisation file is linked to [[Media:O2 01516896 IMM2.LOG|here]]

====Model of Molecule====
<jmol><jmolApplet>
<title>O2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>O2 01516896 IMM2.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrations of Molecule====
[[File:Vibrations_O2_01516896.PNG|thumb|center|Table of Vibrations]]

O2 does not have a peak in the IR spectrum as the molecule is diatomic therefore there is no change in dipole.
====Charge Analysis of Molecule====
Molecule is a diatomic molecule therefore there is no diference in charge between the two atoms.
====Molecular Orbitals====
{| class="wikitable" border="1"
|+ Table of Molecular Orbitals
|-
|Molecular Orbital||Atomic Orbitals in MO||Bonding or Antibonding||Energy/a.u.||Occupied or Unoccupied
|-
|[[File:Molecular_orbitals_O2_01516896_1.PNG|150px]]||1s orbitals from each Oxygen atom||Bonding||-19.30736 MO is deep in energy||Occupied
|-
|[[File:Molecular_orbitals_O2_01516896_2.PNG|150px]]||1s orbitals from each oxygen atom||Antibonding||-19.30712 MO is deep in energy||Occupied
|-
|[[File:Molecular_orbitals_O2_01516896_3.PNG|150px]]||2pz orbitals from each oxygen atom||Bonding||-0.53151||Occupied
|-
|[[File:Molecular_orbitals_O2_01516896_4.PNG|150px]]||2p orbitals from each oxygen atom||Bonding||-0.51526||Occupied
|-
|[[File:Molecular_orbitals_O2_01516896_5.PNG|150px]]||2p orbitals from each oxygen atom||Antibonding||-0.17928||Unoccupied
|}

==References==
<references>
<ref name="VEJSEL"> https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VEJSEL&DatabaseToSearch=Published </ref>
</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 0.5/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES, you have a few too many decimal places though!

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, most answers are correct. However there are only 2 visible peaks in the spectra of NH3, due to the low intensity of the other 2 peaks. (See infrared column in vibrations table.) All peaks can be distinguished from one another.

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

1 or 0 d.p would be more appropriate.

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 3.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, very good information, well done. You could have discussed the MOs in a bit more detail.

== Independence 0/1 ==

If you have finished everything else and have spare time in the lab you could:
Check one of your results against the literature, or
Do an extra calculation on another small molecule, or
Do some deeper analysis on your results so far

No independent work found.

Rep:MOD:JAP10537443

2019-03-22T16:50:10Z

Rr1210:

=Title=

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 106°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is in fact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Below is more NH3 vibrational information:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1 is highly symmetric.

"Umbrella" mode = The mode at 1090cm-1 is known as the "umbrella" mode.

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that N2 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] is a mono-metallic transition metal (TM) complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly greater at 1.12Å <ref name="Bond Distance" /> . They are very similar because the two nitrogen atoms are, like in N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the two nitrogen atoms and so slightly increasing the bond length. Further more, the N triple-bond N bond length of the diatomic, N2, was determined computationally, which uses approximations to predict the bond distance. This is unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference.

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on either H2 atom because both atoms in the diatomic are the same and in the same environment. Hence, they have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribution' on the right:

Haber-Bosch reaction energy calculation

Determining the energy for the Haber-Bosch reaction (N2(g) + 3H2(g) → 2NH3(g)):

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 interesting Molecular Orbitals of Oxygen
|-
| || MO 1 - σ1s || MO 2 - σ*1s || MO 3 - σ2s || MO 4 - σ*2s ||MO 5 - σ*2pz
|-
| '''Image'''|| [[File:JAP18_O2_MO1.jpg|100px]] || [[File:JAP18_O2_MO2.jpg|100px]]|| [[File:JAP18_O2_MO3.jpg|100px]]|| [[File:JAP18_O2_MO4.jpg|100px]]|| [[File:JAP18_O2_MO5.jpg|100px]]
|-
| '''Contributing AOs'''|| The two 1s core AOs on each O-atom|| The two 1s core AOs on each O-atom|| The two 2s valence AOs on each O-atom || The two 2s valence AOs on each O-atom|| The two 2pz valence AOs on each O-atom
|-
| '''MO type'''|| Bonding || Antibonding|| Bonding || Antibonding || Antibonding
|-
| '''MO energy'''|| Deep (-19.31 au) || Deep (-19.31 au) || Fairly high (-1.28 au) || Fairly high (-0.80 au) || High - it is the LUMO (0.21 au)
|-
| '''MO occupancy'''|| Occupied || Occupied || Occupied || Occupied || Unoccupied
|-
| '''MO's contribution to bonding'''|| Very little contribution due to little overlap between AOs as they are tightly held to the respective nuclei || Very little contribution due to little overlap between AOs as they are tightly held to the respective nuclei || Large contribution due to great overlap between AOs - overlap between AOs is so extensive that we only see one extended surface || Large contribution as overlap between AOs is fairly great || No current contribution to bonding as it contains no electrons
|-
|}

Note - the LUMO shown on Gaussian is actually the π*2py MO because the calculated energies of the π*2px and π*2py MOs aren't exactly the same. As a result of a restricted optimsation being used and Gaussian strictly following Hund's rule of maximum multiplicity, 2 electrons occupy the π*2px, resulting in the π*2py being unoccupied. In real life, the two degenerate π*2px and π*2py orbitals are SOMOs (both contain one electron) and the LUMO is the orbital highlighted in the table above - the σ*2pz orbital.

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> Hydrogen Cyanide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted by 'Figure 5 - HCN Charge Distribution' on the right:

References

<references>
<ref name="Bond Distance">Galindo, A.; Gutiérrez, E.; Monge, A.; Paneque, M.; Pastor, A.; Pérez, P.; Rogers, R.; Carmona, E. J. Chem. Soc., Dalton Trans. 1995, 3801-3808.</ref>
</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES, but it helps the reader to use the built in subheadings from which the wiki can automatically generate a table of contents.

==NH3 0.5/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES, most answers are correct. However there are only 2 visible peaks in the spectra of NH3, due to the low intensity of the other 2 peaks. (See infrared column in vibrations table.)

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES, good exaplanation well done!

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, very good explanation about the restricted calculation, well done!

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

You calculated and analysed HCN well done!

Do some deeper analysis on your results so far

Rep:Mod:IND7209

2019-03-22T16:44:54Z

Rr1210:

=Title=

'''NH3 molecule'''

N-H bond length = 1.02

H-N-H bond angle = 106

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55777 a.u.

RMS Gradient Norm = 0.00000485 a.u.

Point Group = C3V

<pre> Item Value Threshold Converged?

Maximum Force 0.000004 0.000450 YES

RMS Force 0.000004 0.000300 YES

Maximum Displacement 0.000072 0.001800 YES

RMS Displacement 0.000035 0.001200 YES

Predicted change in Energy=-5.986301D-10</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RP3218_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:RP3218_NH3_OPTF_POP.LOG]]

The N in the NH3 molecule will have a negative charge, compared to the three Hydrogens as it is more electronegative than the hydrogens, therfore making it more electron withdrawing, hence a negative charge.

[[File:NH3_Chanrge_Distribution.jpg]]

[[File:display_vibrations.jpg]]

{| class="wikitable" border="1"
|-
| '''Wavenumber''' cm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 14 || 14 || 1 || 0.3 || 0.3
|-
| '''Image''' || [[File:NH3_VIBRATION_PHOTO_1.jpg]] || [[File:NH3_VIBRATION_PHOTO_2.jpg]] || [[File:NH3_VIBRATION_PHOTO_3.jpg]] || [[File:NH3_VIBRATION_PHOTO_4.jpg]] || [[File:NH3_VIBRATION_PHOTO_5.jpg]] || [[File:NH3_VIBRATION_PHOTO_6.jpg]]
|}

How many modes do you expect from the 3N-6 rule?

Which modes are degenerate (ie have the same energy)?

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

Which mode is highly symmetric?

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

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

Expected modes = 6

Degenerate modes = The two modes of vibrations at 1694cm-1 are degenerate and the two vibrations at 3590cm-1

"Bending" vibrations = The vibrations at 1090cm-1 , 1694cm-1 and 1694cm-1 are bending modes

"Bond stretch" vibrations = The vibrations at 3461cm-1 , 3590cm-1 and 3590cm-1 are stretching modes

Highly symmetric mode = The highly symmetric mode is at 3461cm-1

"Umbrella" mode = The umbrella mode is the 1090cm-1 vibration

Number of bands in an experimental spectrum of gaseous ammonia = 3

'''N2 molecule'''

N-N bond length = 1.11 Å

N-N bond angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868

RMS Gradient Norm = 0.00000060

Point Group = D*H

<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=-3.401191D-13</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RPABC_N2_OPTIMISE.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:RPABC_N2_OPTIMISE.LOG]]

[[File:N2_display_vibrations.jpg]]

{| class="wikitable" border="1"
|-
| '''Wavenumber''' cm-1 || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:N2_vibration_photo.jpg]]
|}

'''Below is a link for a mono-metallic TM complex that coordinates N2.'''

[[https://www.ccdc.cam.ac.uk/structures/search?sid=ConQuest&coden=001490&year=2016&spage=12181&volume=7&id=doi:10.1038/ncomms12181&pid=ccdc:1447087]]

The bond distance for N2 was 1.11 Å when calculated, whilst the bond distance of the crystal structure in the above link is 1.13 Å <ref name="Distance" />. The similarity is because of the similar bond strength. However the slight difference in distance is due to the withdrawal of electron density towards the Fe atom, reducing the bond order of the N-N bond, therefore making the bond weaker and longer. The bond distance found via the optimisation was an approximation, whilst the distance found via experimental means was different as the N2 molecule was bound to an Fe complex.

My expectations for the charges on the N atoms are zero, as the two Nitrogen atoms have the same electron density and electronegativity, therefore a zero charge.

[[File:Charge_on_N2.jpg]]

'''H2 molecule'''

H-H bond length = 0.74 Å

H-H bond angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853936

RMS Gradient Norm = 0.00000017

Point Group = D*H

<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>

<jmol><jmolApplet>
<title>H2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RPAREKH_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:RPAREKH_H2_OPTF_POP.LOG]]

[[File:H2_display_vibrations.jpg]]

{| class="wikitable" border="1"
|-
| '''Wavenumber''' cm-1 || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:H2_vibration_photo.jpg]]
|}

My expectations for the charges on the H atoms are zero, as the two hydrogen atoms have the same electron density and electronegativity, therefore a zero charge.

[[File:Charge_on_h2.jpg]]

'''Haber-Bosch Process'''

E(NH3)= -56.55777 a.u.

2*E(NH3)= -113.11554 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)]= -0.05580 a.u.

ΔE= -146.5 KJ/mol

The more stable substance is the NH3 as this is an exothermic reaction, therefore the NH3 is at a lower energy state, which means it has a lower energy than both the reactants combined.

'''O2 Molecule'''

O-O bond length = 1.22 Å

O-O bond angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00000974 a.u.

Point Group = SGG

<pre> Item Value Threshold Converged?

Maximum Force 0.000017 0.000450 YES

RMS Force 0.000017 0.000300 YES

Maximum Displacement 0.000010 0.001800 YES

RMS Displacement 0.000015 0.001200 YES

Predicted change in Energy=-1.739381D-10</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RPAREKH_O2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:RPAREKH_O2_OPTF_POP.LOG]]

[[File:O2_display_vibration.jpg]]

{| class="wikitable" border="1"
|-
| '''Wavenumber''' cm-1 || 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:O2_VIBRATION_PHOTO.jpg]]
|}

My expectations for the charges on the H atoms are zero, as the two hydrogen atoms have the same electron density and electronegativity, therefore a zero charge.

[[File:O2_CHRAGE_DISTRIBUTION.jpg]]

{| class="wikitable" border="1"
|-
| '''MO number and type''' || σ1s || σ*1s || σ2s || σ*2s || σ2pz
|-
| '''MO photo''' || [[File:1s-bonding_MO_of_O2.jpg]] || [[File:1s_antibonding_MO_of_O2.jpg]] || [[File:2s-bonding_MO_of_O2.jpg]] || [[File:2s-antibonding_MO_of_O2.jpg]] || [[File:2p-bonding_MO_of_O2.jpg]]
|-
| '''AOs which contribute to MOs''' || Two 1s || Two 1s || Two 2s || Two 2s || Two 2p (2px)
|-
| '''Is MO Bonding, Antibonding or Both?''' || Bonding || Antibonding || Bonding || Antibonding || Bonding
|-
| '''Depth of MO energy in HOMO/LUMO region''' || -19.31 (Very Deep in Energy) || -19.31 (Very Deep in Energy) || -1.28 (Higher in Energy than 1s AOs, this is a valence energy level) || -0.80 (Valence energy level therefore high in Energy than 1s AOs and 2s bonding AO) || -0.53 (Valence energy level therefore high in energy)
|-
| '''Is MO Occupied or Unoccupied?''' || Occupied || Occupied || Occupied || Occupied || Occupied
|-
| '''Effect of MO on Bonding''' || Little. This has only a small contibution to bonding since the AOs are so deep in energy and so hardly overlap at all, also they are held tightly to the nuclei. || Little, for same reason as on left, due to being very low in energy therefore poor overlap. || Large, since the 2s AOs are large hence there is strong overlap, which is why these AOs are valence AOs due to the increase in enrgy compared to the 1s AOs. || Large, for the same reason as on the left. The bonding is so extensive, that it extends throughout the bond, hence a strong overlap. As this is an antibonding orbital, it will be higher in energy therefore less stable than a bonding MO. Due to the increased overlap of orbitals, the energy difference between the bonding and antibonding orbitals is larger. || Large, since this MO is formed via the head-on overlap of two 2pz AOs. The fact that the energy gap between the 2s AOs and 2p AOs of O2 is large, means that s-p mixing does not occur, therefore the shape of this MO is not distorted. In this case the bond order would not be affected if O2 did participate in s-p mixing.
|}

'''CO2'''

C-O bond length = 1.17 Å

O-C-O bond angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -188.58093945 a.u.

RMS Gradient Norm = 0.00001154 a.u.

Point Group = SGG

<pre> Item Value Threshold Converged?

Maximum Force 0.000024 0.000450 YES

RMS Force 0.000017 0.000300 YES

Maximum Displacement 0.000021 0.001800 YES

RMS Displacement 0.000015 0.001200 YES

Predicted change in Energy=-5.259645D-10</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RPAREKH_CO2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:RPAREKH_CO2_OPTF_POP.LOG]]

[[File:CO2_DISPLAY_VIBRATIONS.jpg]]

{| class="wikitable" border="1"
|-
| '''Wavenumber''' cm-1 || 640 || 640 || 1372 || 2436
|-
| '''Symmetry''' || PTU || PTU || SGG || SGU
|-
| '''Intensity''' arbitrary units || 30.7 || 30.7 || 0 || 546
|-
| '''Image''' || [[File:CO2_VIBRATION_PHOTO_1.jpg]] || [[File:CO2_VIBRATION_PHOTO_2.jpg]] || [[File:CO2_VIBRATION_PHOTO_3.jpg]] || [[File:CO2_VIBRATION_PHOTO_4.jpg]]
|}

The two Oxygen atoms in the CO2 molecule will have a negative charge, compared to the Carbon as they are more electronegative than the Carbon, therfore making it more electron withdrawing, hence a negative charge.

[[File:CO2_Charge_Distribution.jpg]]

<references>
<ref name="Distance">(1) Kuriyama, S.; Arashiba, K.; Nakajima, K.; Matsuo, Y.; Tanaka, H.; Ishii, K.; Yoshizawa, K.; Nishibayashi, Y. Nature Communications 2016, 7.</ref>
</references>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 0.5/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

You didn't use the built in subheadings which automatically generate a contents page, this makes it much easier for a reader to navigate.
You have left the jmol captions as the default “test molecule” this gives the reader no information.

==NH3 0.5/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES most answers are correct. However there are only 2 visible peaks in the spectra of NH3, due to the low intensity of the other 2 peaks. (See infrared column in vibrations table.)

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, good explanations, well done!

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

Do an extra calculation on another small molecule, or

You did an extra calculation, well done.

Do some deeper analysis on your results so far