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Rep:Mod:mg4417

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Miren Gami (CID:01206786)

Introduction to Molecular Modelling 2 wiki report

Optimised NH3 molecule

Key Information

Optimisation Summary

Calculation method: RB3LYP

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

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

RMS gradient: 0.00000485 a.u.

Point group: C3V

Geometric Information

Bond angle: 105.741°

Bond length: 1.01798 Å

"Item" table

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= -5.986294D-10

Jmol and LOG file

Optimised ammonia molecule

LOG file

Analysis

Frequency

Display vibrations window for the ammonia molecule.
"Umbrella" mode in ammonia

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

Which modes are degenerate (ie have the same energy)?: 2 and 3; 5 and 6

Which modes are "bending" vibrations and which are "bond stretch" vibrations?: 1,2 and 3 are "bending" vibrations, 4,5 and 6 are "bond stretch" vibrations

Which mode is highly symmetric? 1 and 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

Charge

Charge on N is -1.125

Charge on H is 0.375

Charge distribution for the ammonia molecule.

These charges are as expected. The nitrogen atom is expected to be negatively charged since it is more electronegative than the hydrogen atoms and pulls electron density from them. The hydrogen atoms would therefore be positively charged.

Optimised N2 molecule

Key Information

Optimisation Summary

Calculation method: RB3LYP

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

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

RMS gradient: 0.00000365 a.u.

Point group: D∞H

Geometric Information

Bond angle: 180°

Bond length: 1.10550 Å

"Item" table

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

Predicted change in Energy= -1.248809D-11

Jmol and LOG file

Optimised nitrogen molecule

LOG file

Analysis

Frequency

Display vibrations window for the nitrogen molecule. There is one bond stretch vibration (symmetric).
Bond stretching in the nitrogen molecule

Charge

N2 is a homonuclear diatomic molecule so both atoms have the same electronegativity and the electron density is equally distributed between them. As a result, the atomic charge on either atom is zero.

Optimised H2 molecule

Key Information

Optimisation Summary

Calculation method: RB3LYP

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

Final energy E(RB3LYP): -1.17853930 a.u.

RMS gradient: 0.00012170 a.u.

Point group: D∞H

Geometric Information

Bond angle: 180°

Bond length: 0.74309 Å

"Item" table

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

Predicted change in Energy= -5.852867D-08

Jmol and LOG file

Optimised hydrogen molecule

LOG file

Analysis

Frequency analysis

Display vibrations window for the hydrogen molecule. There is one bond stretch vibration (symmetric).
Bond stretching in the hydrogen molecule

Charge

H2 is a homonuclear diatomic molecule so both atoms have the same electronegativity and the electron density is equally distributed between them. As a result, the atomic charge on either atom is zero.

Haber-Bosch reaction energies

• E(NH3)= -56.55776873 a.u.

• 2*E(NH3)=2*-56.55776873 a.u. = -113.11553746 a.u.

• E(N2)= -109.52412868 a.u.

• E(H2)= -1.17853930 a.u.

• 3*E(H2)=3*-1.17853930 a.u.= -3.5356179 a.u.

• ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579088 a.u.

-0.05579088 a.u.= -146.48 kJ/mol

For 1 mol of NH3: -73.24 kJ/mol

This is an exothermic reaction, the gaseous NH3 is lower in energy than the products and therefore more stable.

Optimised F2 molecule

Key Information

Optimisation Summary

Calculation method: RB3LYP

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

Final energy E(RB3LYP): -199.49825218 a.u.

RMS gradient: 0.00007365 a.u.

Point group: D∞H

Geometric Information

Bond angle: 180°

Bond length: 1.40281 Å

"Item" table

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000128 0.000300 YES
Maximum Displacement 0.000156 0.001800 YES
RMS Displacement 0.000221 0.001200 YES

Predicted change in Energy= -1.995025D-08

Jmol and LOG file

Optimised fluorine molecule

LOG file

Analysis

Frequency analysis

Display vibrations window for the fluorine molecule. There is one bond stretch vibration (symmetric).
Bond stretching in the fluorine molecule

Charge

F2 is a homonuclear diatomic molecule so both atoms have the same electronegativity and the electron density is equally distributed between them. As a result, the atomic charge on either atom is zero.

Molecular Orbitals

  • First 12 MOs in the optimised fluorine molecule (hover over image for further information)
  • 1. energy=-24.7973016000, fully occupied.
    1. energy=-24.7973016000, fully occupied.
  • 2. energy=-24.7973016000, fully occupied.
    2. energy=-24.7973016000, fully occupied.
  • 3. energy=-1.3365938700, fully occupied.
    3. energy=-1.3365938700, fully occupied.
  • 4. energy=-1.0904729200, fully occupied.
    4. energy=-1.0904729200, fully occupied.
  • 5. energy=-0.5875332540, fully occupied.
    5. energy=-0.5875332540, fully occupied.
  • 6. energy=-0.5233218740, fully occupied.
    6. energy=-0.5233218740, fully occupied.
  • 7. energy=-0.5233218740, fully occupied.
    7. energy=-0.5233218740, fully occupied.
  • 8. energy=-0.3918998830, fully occupied.
    8. energy=-0.3918998830, fully occupied.
  • 9. energy=-0.3918998830, fully occupied.
    9. energy=-0.3918998830, fully occupied.
  • 10. energy=-0.1267921140, unoccupied.
    10. energy=-0.1267921140, unoccupied.
  • 11. energy=0.8392253090, unoccupied.
    11. energy=0.8392253090, unoccupied.
  • 12. energy=0.9647877580, unoccupied.
    12. energy=0.9647877580, unoccupied.

Five interesting orbitals

2: σ* orbital with ungerade symmetry formed from an out-of-phase combination of 1s atomic orbitals on both fluorine atoms. This is an antibonding orbital that is very deep in energy with an energy of -24.7973016000. It is doubly occupied. It will have no effect on bonding due to its low energy.

5: σ orbital with gerade symmetry formed from an in-phase combination of 2px atomic orbitals on both fluorine atoms. This is a bonding orbital that is slightly lower in energy than the HOMO/LUMO region with an energy of -0.5875332540. It is doubly occupied. It participates in bonding.

9: π* orbital with gerade symmetry formed from an out-of-phase combination of 2pz atomic orbitals on both fluorine atoms. This is an antibonding orbital that is in the HOMO/LUMO region with an energy of -0.3918998830. It is doubly occupied and is therefore the HOMO, along with MO 8, which is degenerate. It does not have an effect on bonding.

10: σ* orbital with ungerade symmetry formed from an out-of-phase combination of 2px atomic orbitals on both fluorine atoms. This is an antibonding orbital that is in the HOMO/LUMO region with an energy of -0.1267921140. It is unoccupied and is therefore the LUMO. It does not have an effect on bonding as it is completely unoccupied.

11: σ orbital with gerade symmetry formed from an in-phase combination of 3s atomic orbitals on both fluorine atoms. This is a bonding orbital that is high in energy with an energy of 0.8392253090. It is unoccupied and does not have an effect on bonding.

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