Rep:Mod:01512921
MOD 1st year
Optimising the molecules
NH3 molecule
As the first exercise, a molecule of NH3 was built and optimised using GaussianView. The optimised bond length N-H and the bond angle H-N-H were found to be 1.01 ± 0.01Å and 105.7 ± 1°. The item from the optimisation file has been included to show that the optimisation has worked, since the threshold values for both the Maximum Force and the RMS are respectively of 0.00045 and 0.003.
File:SOFIA PATRI 744 OPT NH3 1ST POP.LOG
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) |
| E(RB3LYP) | -56.5577687 |
| RMS gradient | 0.00000485 |
| Point group | C3V |
NH3 Molecule |
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| Wavenumber cm-1 | 1089 | 1694 | 1694 | 3461 | 3590 | 3590 |
| Symmetry | A1 | E | E | A1 | E | E |
| Intensity arbitrary units | 145 | 13.5 | 13.5 | 1.06 | 0.27 | 0.27 |
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Since the molecule is not linear, from the 3N-6 rule, 6 modes would be expected to happen; this is confirmed from data obtained through GaussianView. There are two couples of modes that are degenerate: those with wavenumber of 1694 and 3590 cm-1. The bonding vibrations have wavenumber 1089 and 1694 cm-1 (there is two of the latter), while the stretching frequencies are 3461 and both 3590 cm-1. The mode with wavenumber 1890 is known as the "umbrella mode" and 3461 is the highly symmetric one (symmetry A1), although also there is also an other A1 symmetry, being the one with wavenumber 1890. If a sprectum of gaseous ammonia was acquired, four bands would be visible as there are two couples of the identical wavenumber. The bands with wavenumber 3461 and 3590, however, have such a small intensity that they could be not very evident from the spectrum.
The charges for the N and the H atoms obtained through GaussianView were respectively of -1.125 and 0.375, with a dipole moment of magnitude 1.8466. The molecule results to be neutral, as expected if calculation were done with their charge numbers (+1 for the H and -3 for the N). The nitrogen atom in the molecule has a lone pair with a slightly negative character, which is cancelled out by the hydrogen atoms forming a slightly positive area of the molecule.
N2 molecule
The analysis with Gaussianview was performed also on a N2 molecule. The item from the optimisation file has been included to show that the optimisation has worked, since the threshold for both the Maximum Force and the RMS are respectively of 0.00045 and 0.003. The bond length was found to be 1.10 ± 0.01Å. NBO charges: The molecule is neutral, since it is formed by two identical atoms which have the same electronegativity. Following the rule of 3N-5 modes for a linear molecule, this one, being diatomic, has only one stretching. This is confirmed by the vibration obtained through gaussianview.
File:SOFIA PATRI 744 N2 OPT 3.LOG
| Calculation Method | RB3LYP |
| basis set | 6-31G9(d,p) |
| E(UB3LYP) | -109.524129 |
| RMS Gradient norm | 0.00012532 |
| Point group | D∞h |
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Item Value Threshold Converged? Maximum Force 0.000217 0.000450 YES RMS Force 0.000217 0.000300 YES Maximum Displacement 0.000068 0.001800 YES RMS Displacement 0.000096 0.001200 YES
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NH3 Molecule |
| Wavenumber cm-1 | 2457 |
| Symmetry | SGG |
| Intensity arbitrary units | 0.0000 |
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N2* molecule
The analysis with Gaussianview was performed also on a N2 excited molecule with a triplet state to observe any difference in the values given in the summary. Altough the molecule is still neutral, the bond has been slightly lengthened, with a new value of 1.21 ± 0.01Å. Also, from the optimisation done with Gaussian, the final molecule results to have a double bond instead of a triple one. From the summary it is possible to observe that the excited molecule has higher values for the energy and the gradient norm. As a consequence of its excited state and popolation of a new orbital,also the stretching frequency had a lower value. The item from the optimisation file has been included to show that the optimisation has worked, since the threshold for both the Maximum Force and the RMS are respectively of 0.00045 and 0.003.
File:SOFIA PATRI 744 N2 OPT 1.LOG
| Calculation Method | UB3LYP |
| basis set | 6-31G9(d,p) |
| E(UB3LYP) | -109.26768806 |
| RMS Gradient norm | 0.00000144 |
| Point group | D∞h |
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Item Value Threshold Converged? Maximum Force 0.000002 0.000450 YES RMS Force 0.000002 0.000300 YES Maximum Displacement 0.000001 0.001800 YES RMS Displacement 0.000002 0.001200 YES
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NH3 Molecule |
| Wavenumber cm-1 | 1841 |
| Symmetry | SGG |
| Intensity arbitrary units | 0.0000 |
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H2 molecule
The same proceeding was done on a H2 molecule. The item from the optimisation file has been included to show that the optimisation has worked, since the threshold for both the Maximum Force and the RMS are respectively of 0.00045 and 0.003. The bond length was found to be 0.74 ± 0.01Å. NBO charges: The molecule is neutral, since it is formed by two identical atoms which have the same electronegativity. Following the rule of 3N-5 modes for a linear molecule, this one, being diatomic, has only one stretching. This is confirmed by the vibration obtained through gaussianview
File:SOFIA PATRI 744 H2 OPT 1.LOG
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=-1.164081D-13 Optimization completed.
| Calculation Method | RB3LYP |
| Basis set | 6-31G(d.p) |
| E(RB3LYP) | -1.17853936 a.u. |
| RMS gradient | 0.00000017 a.u. |
| Point group | D∞h |
H2 Molecule |
| Wavenumber cm-1 | 4465 |
| Symmetry | SGG |
| Intensity arbitrary units | 0.0000 |
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Comparing with CCDC
N2
The molecule searched has the name of bis(dinitrogen)-dihydrido-bis(tricyclohexylphosphine)-ruthenium and indentifies as YECMIF. In this molecule, the nitrogen bond distance 1.1 Å, the same as the one found in the the nitrogen molecule through gaussianview. Even though in YECMIF the nitrogen group belongs to a bigger complex, only one of the nitrogens is actually bonded to a ruthenium atom, which has lower electronegativity that the nitrogen. This means that the electrondendity is not pulled towards the ruthenium shortening the Ru-N bond, and the N_N as a consequence. Structure of YECMIF [1]
References
H2
The molecule found in Conquest is (η2-Dihydrogen)-chloro-(cyclohexane-1,2-diamino)-bis(triphenylphosphino)-ruthenium tetrafluoroborate tetrahydrofuran solvate , also known as DENQET. The bond distance for the hydrogen bond is 0.68 Å. The bond distance in a hydrogen molecule calculated through Gaussian view is of 0.74 ± 0.01Å . The difference is small, possible due to the hydrogen also bonding with a ruthenium atom: the Ru-H bond distance is of 1.67 ± 0.01Å for one hydrogen and 1.75 ± 0.01Å for the other. This means that the hydroges have a limited freedom on how they can be bondend, depending both on the distances from the ruthenium and from the phenyl complexes around them.
References
- ↑ Tianshu Li, A.J.Lough, C.Zuccaccia, A.Macchioni, R.H.Morris CCDC 274511: Experimental Crystal Structure Determination, 2006, DOI: 10.5517/cc96n6b
Calculation of energy wiht the Haber-Bosch reaction
The main source of production of ammonia in the world is the Haber-Bosch reaction:
N2 + 3H2 -> 2NH3
To calculate the energies:
E(NH3)= -56.557769 a.u.
2*E(NH3)= -113.115538 a.u.
E(N2)= -109.524129 a.u.
E(H2)=-1.178539 a.u.
3*E(H2)= -3.535614 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.055795 a.u = -146.4897837 kJ/mol
The reaction is exothermic, with the product having a more negative energy than the reagents. Because of this, we can consider the reaction spontaneous and therefore the side of ammonia is favoured, meaning ammonia is more stable.
Analysis of the chosen molecule
A molecule of SiH4 was built and optimised using GaussianView. The optimised bond length Si-H and the bond angle H-Si-H were found to be 1.48 ± 0.01Å and 109.4 ± 1°. The item from the optimisation file has been included to show that the optimisation has worked, since the threshold values for both the Maximum Force and the RMS are respectively below 0.0004 and 0.003. As for the charges, The Si atom was found to have -0.629, while the three hydrogen had 0.157. The overall molecule was found to be neutral. The Si atom has a lower electronegativity (1.9) than the hydrogen one (2.2); however, their electronegativity are similar, meaning that they form a neutral and unreactive compound.
File:SOFIA PATRI 744 OPT SiH4.LOG
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
| Calculation Method | RB3LYP |
| Basis set | 6-31G(d,p) |
| E(RB3LYP) | -291.888027 |
| RMS gradient | 0.00000002 |
| Point group | TD |
NH3 Molecule |
| Wavenumber cm-1 | 919 | 919 | 919 | 978 | 978 | 2244 | 2254 | 2254 | 2254 |
| Symmetry | T2 | T2 | T2 | E | E | A1 | T2 | T2 | T2 |
| Intensity arbitrary units | 136 | 136 | 136 | 0.000 | 0.000 | 0.000 | 143 | 143 | 143 |
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Through Gaussinview, nine vibrational mode were found. If the rule 3N-6 (for the non linear molecule) is applied, the number of the predicted modes confirms that the molecule has 9 modes. The vibrations with wavenumber 919 and 978 correspond to the bending movements, those with wavenumber 2244 and 2254 are the streching ones. Some on the modes are degenarate, meaning they have the same wavenumber and intensity, and therefore only one band will be visible on the IR spectrum. Arguibly, however, some of they insentiies are so small or non existent that no frequency will actually be visible. The vibration with wavenumber 2244 is a highly symmetric vibration since its symmetry is A1.
| Number Mos | 2 | 6 | 7 | 8 | 10 |
| Description | 2s2 Si | 1s1 of H and 3s2 of Li | 1s1 of H and 3p of Li | 1s1 of H and 3p of Li | LUMO |
| Energy | -5.28 | -0.54 | -0.35 | -0.35 | 0.05 |
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Five snapshot were taken of five different MOs which were chosen as examples to present in this wiki. The Mo carring number 2 is actually the 2s2 atomic orbital of the Silicium atom, whichis not involeved in the bonding as it is too deepenergy. The MOs number 6 is the σ bonding orbital which is obtained from mixing th e 3s2 orbital from the Li and the ligand orbitals 1s1 of the hydrogen atoms: this is the lowest bonding orbital in energy. Orbitals number 8 and 7 are the bonding orbital formed by mixing the 3p orbitals with the other 1s1 of the hydrogen atoms, froming two different π orbital which are degenerate in energy. One of their anti-boning orbital is the number 10, which is also the LUMO (lowest unoccupied molecular orbital) of the molecule. The HOMO of the molecule (highest occupied molecular orbital) is given by the obritals numbered 7-8-9 (the latter is not shown in the table).
Marking
Note: All grades and comments are provisional and subjecct 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 recieved your grade from blackboard.
Your wiki has been edited by you two times on the 04/03/2019. Your deadline of submission was 01/03/2019 18:00, therefore the last version before that time (last edit on 01/03/2019 12:34) has been marked.
Your wiki and the discussions are good! Unfortunately, a lot of typos accured as well as grammatical mistakes which are making it hard to understand your arguments. For the next submission pease check this before the deadline to make your discussions clear and easy to follow.
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, however your explanation regarding the atomic charges is not correct. The difference in electronegativity is the reason for the atomic charges rather than the lone pair of the nitrogen.
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?
NO -- but you included the unique identifiers instead.
Have you compared your optimised bond distance to the crystal structure bond distance?
YES
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?
NO - the energy in kJ/mol should only be reported to one decimal place!
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?
You have done a good job of presenting this information, well done! You missed to explicitly state how many bands you expect in an experimental spectrum but your arguments for the discussion are all there! 2 band are to be expected. You defined degenerate vibrations as such having the same frequency AND intensity. Please note that the intensity is not essential for degenerate modes! Your descriptions of the MOs are good! You managed to correctly state the contributing AOs, the bonding/anti-bonding/non-bonding nature and their energy. You only missed to explicitly state that MO2 is non-bonding. You missed to state which obrital is occupied/unoccupied. In this section there is a typo! You calculated SiH4 but you wrote several times Li instead of Si! This is an essential difference as both abbreviations are referring to two different 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
YES - well done!
Do some deeper analysis on your results so far