Jump to content

Rep:Mod:JoeC

From ChemWiki

Molecular Modelling report

NH3

The molecule is NH3.

The calculation method is RB3LYP.

The basis set is 6-31G(d.p).

The final energy E(RB3LYP) is -56.55776873 a.u.

The RMS gradient is 0.00000485 a.u.

The point group for the molecule is C3v.

The N-H bond length in ammonia is 1.01798 angstrom.

The H-N-H bond angle in ammonia is 37.129 degrees. 

         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
test molecule

The optimisation file is liked to here

Vibrations for ammonia molecule

From the 3N-6 rule we would expect 6 modes of vibration for ammonia as there are 4 nuclei. The vibration modes 2/3 and 5/6 are degenerate. The vibration modes 1,2 and 3 are bending vibrations. The modes 4,5 and 6 are bonding stretches. Vibration mode 4 is highly symmetric. The umbrella mode is mode 1. 4 bands would be visible in an experimental spectrum of gaseous ammonia.

In ammonia the nitrogen has a charge of -1.125 and the hydrogen nuclei have a charge of 0.375. Nitrogen is expected to have the more negative charge as it is the more electronegative atom.










H2

The molecule is H2.

The calculation method is RB3LYP.

The basis set is 6-31G(d.p).

The final energy E(RB3LYP) is -1.17853936 a.u.

The RMS gradient is 0.00000017 a.u.

The point group for the molecule is D*H.

The H-H bond length in H2 is 0.74279 angstrom. 

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
test molecule

The optimisation file is liked to here

Vibrations for H2 molecule















N2

The molecule is N2.

The calculation method is RB3LYP.

The basis set is 6-31G(d.p).

The final energy E(RB3LYP) is -109.52412868 a.u.

The RMS gradient is 0.00000060 a.u.

The point group for the molecule is D*h.

The N-N bond length in ammonia is 1.10550 angstrom. 

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=-3.401023D-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
test molecule

The optimisation file is liked to here

Vibrations for N2 molecule















Energy for the reaction of N2 + 3H2 -> 2NH3

   E(NH3)= -148492.433112 kJ/mol
   2*E(NH3)= -296984.8662 kJ/mol
   E(N2)= -287555.6217542 kJ/mol
   E(H2)= -3094.25532539 kJ/mol
   3*E(H2)= -9282.765976 kJ/mol
   ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -146.4784698 kJ/mol

From the energies of the reactants and products and the ΔE it is clear that the product has a more negative energy and is hence more stable than the reactants. When the calculated value is compared to the literature value of -45.90 kJ/mol.for the formation of gaseous ammonia. the discrepancy is likely due to the oversimplification of our molecular modelling system. [1]

SiH4

The molecule is SiH4.

The calculation method is RB3LYP.

The basis set is 6-31G(d.p).

The final energy E(RB3LYP) is -291.88802760 a.u.

The RMS gradient is 0.00000002 a.u.

The point group for the molecule is Td.

The Si-H bond length in silane is 1.48485 angstrom.

The H-Si-H bond angle in silane is 109.471 degrees. 

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=-2.456424D-14
 Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.4849         -DE/DX =    0.0                 !
 ! R2    R(1,3)                  1.4849         -DE/DX =    0.0                 !
 ! R3    R(1,4)                  1.4849         -DE/DX =    0.0                 !
 ! R4    R(1,5)                  1.4849         -DE/DX =    0.0                 !
 ! 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                 !
 --------------------------------------------------------------------------------
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
test molecule

The optimisation file is liked to here

Vibrations for SiH4 molecule

As predicted by the 3N-6 rule we can see that there are 9 different modes of vibration. Modes 1,2,3 4,5 and 7,8,9 are all degenerate with modes 1-5 being bond bends and 6-9 being stretches. There is no change in the dipole moment of during the 6th mode of vibration as it is highly symmetric and thus no IR frequencies are recorded. There are 2 distinct IR absorption so 2 bands on an experimental IR spectrum is expected.

IR spectrum for SiH4 molecule
The charge on the Silicon is 0.629 and the charge on each hydrogen is -0.157


This is the molecular orbital that corresponds to the non bonding core 2s orbital of the silicon atom and is deep in energy at -5.28056 a.u.
This is the molecular orbital that corresponds to the third deepest in energy orbital set. It is the set of 3 degenerate 2p non-bonding orbitals around Si. It is deep in energy at -3.63858 a.u.
This is the sigma bonding molecular orbital that corresponds to the first bonding MO. It is a combination of the silicon 3s and hydrogen 1s orbitals to create sigma MOs. This is the lowest energy bonding MO marginally higher in energy in energy at -0.54726 a.u.
This is sigma the bonding molecular orbital that corresponds one of the degenerate silicon 3p valence orbitals combined with the hydrogen 1s orbitals. It is higher in energy at -0.35184 a.u.
This is the sigma* anti bonding molecular orbital that corresponds one of the degenerate silicon 3p valence orbitals combined with the hydrogen 1s to form an orbital. This MO is the LUMO of the molecule. It is marginally higher in energy in energy at 0.5053 a.u. making it positive in energy

Is NaCL ionic

From generating The molecular orbitals of NaCl the electron distribution can be visualized and hence we can determine if the atom is ionic.

The molecule is NaCl.

The calculation method is RB3LYP.

The basis set is 6-31G(d.p).

The energy E(RB3LYP) is -622.56029785 a.u.

The point group is C*V

the RMS gradient is 0.00000003 a.u.

The optimisation file is liked to here

pictures of the calculated HOMO and other high energy occupied MOs showing no electron distribution around the (pink) Na atom thereby showing the ionic nature


test molecule










References

  1. ↑ This is the literature value reference.
Retrieved from "https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:JoeC&oldid=817209"