Difference between revisions of "Birdjo"
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===Discussion=== | ===Discussion=== | ||
The calculated geometries and association energies indicate significant differences in the stability and hydrogen-bonding behaviour of structures A, B, and C. The most stable associated structure was A, with an association energy of −461 kJ mol⁻¹. While structures B and C were less stabilised upon association, with association energies of −404 and −429 kJ mol⁻¹ respectively. The more negative association energy for A indicates that its formation is more energetically favourable than formation of the other structures. | The calculated geometries and association energies indicate significant differences in the stability and hydrogen-bonding behaviour of structures A, B, and C. The most stable associated structure was A, with an association energy of −461 kJ mol⁻¹. While structures B and C were less stabilised upon association, with association energies of −404 and −429 kJ mol⁻¹ respectively. The more negative association energy for A indicates that its formation is more energetically favourable than formation of the other structures. | ||
| − | + | ||
| − | The greater stability of | + | The van der Waals radii are approximately 1.20 Å for H and 1.75 Å for Cl, giving a combined distance of approximately 2.95 Å. All calculated H···Cl distances (1.719–2.135 Å) are substantially shorter than this value, indicating attractive hydrogen bond interactions. Structure A showed the shortest H···Cl distance (1.719 Å), suggesting the strongest hydrogen bonding interaction. Structures B and C showed longer H···Cl separations (2.135 Å and 2.030 Å respectively), meaning their interactions are weaker. |
| + | |||
| + | The greater stability of structure A can be makes sense due to the location of the proton. In A, deprotonation occurs at nitrogen, producing an N–H···Cl interaction. Nitrogen is more electronegative than carbon and therefore polarises the N–H bond more strongly, increasing the partial positive charge on hydrogen and strengthening its interaction with chloride. This is supported by both the shorter H···Cl distance and the more favourable association energy observed for A. While, structures B and C involve C–H···Cl interactions, which will be weaker because the C–H bonds are less polar and therefore worse hydrogen bond donors. The relative energy between A and B of 57 kJ mol⁻¹, shows greater stabilisation of A relative to B and further supports this idea. | ||
| + | |||
Structure C is more strongly stabilised upon association than B despite both involving C-deprotonated structures. The association energy of C (−429 kJ mol⁻¹) is approximately 25 kJ mol⁻¹ more favourable than B (−404 kJ mol⁻¹), which correlates with the shorter H···Cl distance in C (2.030 Å compared with 2.135 Å in B). Structure C has the C-H being deprotonated adjacent to two N atoms in the structure. Leading to a greater dipole overall than C which only has one N atom adjacent to the C-H, and therefore leading to a greater interaction with the chloride. | Structure C is more strongly stabilised upon association than B despite both involving C-deprotonated structures. The association energy of C (−429 kJ mol⁻¹) is approximately 25 kJ mol⁻¹ more favourable than B (−404 kJ mol⁻¹), which correlates with the shorter H···Cl distance in C (2.030 Å compared with 2.135 Å in B). Structure C has the C-H being deprotonated adjacent to two N atoms in the structure. Leading to a greater dipole overall than C which only has one N atom adjacent to the C-H, and therefore leading to a greater interaction with the chloride. | ||
| − | |||
| + | Overall, the results demonstrate that association involving the N-deprotonated structure is energetically preferred over association involving the C-deprotonated structures. | ||
==Calculation and Convergence Proof for Each Molecule== | ==Calculation and Convergence Proof for Each Molecule== | ||
Revision as of 08:51, 28 May 2026
Contents
- 1 Analysis of 1-Methyl-Imidazolium Chloride and 1,3-Dimethyl-Imiazolium Chloride
- 2 Calculation and Convergence Proof for Each Molecule
- 3 Trimethylammonium Chloride
- 4 BH3 Molecule
- 5 NH3BH3 Molecule
- 6 Lab marking
- 7 NH3 molecule
- 8 Cis N2F2 molecule
Analysis of 1-Methyl-Imidazolium Chloride and 1,3-Dimethyl-Imiazolium Chloride
Tabulated Data
| Ion | H-Cl distance (Å) | C-H distance (Å) | N-H distance (Å) | Total Energy (AU) | Ion Energy (AU) | Cl- Energy (AU) | ΔE (AU) | ΔE (kj/mol) |
| A | 1.719 | 1.178 | -722.687898 | -264.455119 | -458.057087 | -0.175692 | -461 | |
| B | 2.135 | 1.104 | -722.666200 | -264.455119 | -458.057087 | -0.153994 | -404 | |
| C | 2.030 | 1.118 | -761.779525 | -303.559223 | -458.057087 | -0.163215 | -429 |
Diagrams
Raw Unedited Scan Graphs
Refined Scan Graphs
Discussion
The calculated geometries and association energies indicate significant differences in the stability and hydrogen-bonding behaviour of structures A, B, and C. The most stable associated structure was A, with an association energy of −461 kJ mol⁻¹. While structures B and C were less stabilised upon association, with association energies of −404 and −429 kJ mol⁻¹ respectively. The more negative association energy for A indicates that its formation is more energetically favourable than formation of the other structures.
The van der Waals radii are approximately 1.20 Å for H and 1.75 Å for Cl, giving a combined distance of approximately 2.95 Å. All calculated H···Cl distances (1.719–2.135 Å) are substantially shorter than this value, indicating attractive hydrogen bond interactions. Structure A showed the shortest H···Cl distance (1.719 Å), suggesting the strongest hydrogen bonding interaction. Structures B and C showed longer H···Cl separations (2.135 Å and 2.030 Å respectively), meaning their interactions are weaker.
The greater stability of structure A can be makes sense due to the location of the proton. In A, deprotonation occurs at nitrogen, producing an N–H···Cl interaction. Nitrogen is more electronegative than carbon and therefore polarises the N–H bond more strongly, increasing the partial positive charge on hydrogen and strengthening its interaction with chloride. This is supported by both the shorter H···Cl distance and the more favourable association energy observed for A. While, structures B and C involve C–H···Cl interactions, which will be weaker because the C–H bonds are less polar and therefore worse hydrogen bond donors. The relative energy between A and B of 57 kJ mol⁻¹, shows greater stabilisation of A relative to B and further supports this idea.
Structure C is more strongly stabilised upon association than B despite both involving C-deprotonated structures. The association energy of C (−429 kJ mol⁻¹) is approximately 25 kJ mol⁻¹ more favourable than B (−404 kJ mol⁻¹), which correlates with the shorter H···Cl distance in C (2.030 Å compared with 2.135 Å in B). Structure C has the C-H being deprotonated adjacent to two N atoms in the structure. Leading to a greater dipole overall than C which only has one N atom adjacent to the C-H, and therefore leading to a greater interaction with the chloride.
Overall, the results demonstrate that association involving the N-deprotonated structure is energetically preferred over association involving the C-deprotonated structures.
Calculation and Convergence Proof for Each Molecule
1-Methyl-Imidazolium A
Calculation Data
| name of submitted log file | JSDB_1-METHYL-IMIDAZOLIUM_A_OPT_CHARGED.LOG |
| molecule | 1-methyl-imidazolium A |
| method | RB3LYP |
| basis set | 3-21G |
| final energy | -264.455119 |
| RMS gradient | 8.695e-06 |
| point group | C1 |
Convergence Data
Item Value Threshold Converged? Maximum Force 0.000019 0.000450 YES RMS Force 0.000006 0.000300 YES Maximum Displacement 0.000444 0.001800 YES RMS Displacement 0.000123 0.001200 YES
Low frequencies --- -0.0008 -0.0005 -0.0004 1.4143 2.7351 5.5935 Low frequencies --- 80.6776 248.1401 352.9172
Log File
File:JSDB 1-METHYL-IMIDAZOLIUM A OPT CHARGED.LOG
Chloride Ion
Calculation Data
| name of submitted log file | JSDB_CHLORINE_OPT.LOG |
| molecule | Cl- |
| method | RB3LYP |
| basis set | 3-21G |
| final energy | -458.057087 |
| RMS gradient | 0 |
| point group | Oh |
Convergence Data
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
Low frequencies --- -0.0066 -0.0066 -0.0066
Log File
1-Methyl-Imidazolium Chloride A
Calculation Data
| name of submitted log file | JSDB_1-METHYL-IMIDAZOLIUM_CHLORIDE_A_OPT.LOG |
| molecule | 1-methyl-imidazolium chloride A |
| method | RB3LYP |
| basis set | 3-21G |
| final energy | -722.687898 |
| RMS gradient | 1.6519e-05 |
| point group | C1 |
Convergence Data
Item Value Threshold Converged? Maximum Force 0.000030 0.000450 YES RMS Force 0.000009 0.000300 YES Maximum Displacement 0.000713 0.001800 YES RMS Displacement 0.000190 0.001200 YES
Low frequencies --- -5.1515 -2.5544 -0.0030 -0.0030 -0.0020 3.3027 Low frequencies --- 36.1863 63.7820 80.3632
Log File
File:JSDB 1-METHYL-IMIDAZOLIUM CHLORIDE A OPT.LOG
1-Methyl-Imidazolium Chloride B
Calculation Data
| name of submitted log file | 1-METHYL-IMIDAZOLIUM_CHLORIDE_B_OPT2.LOG |
| molecule | 1-methyl-imidazolium chloride B |
| method | RB3LYP |
| basis set | 3-21G |
| final energy | -722.666200 |
| RMS gradient | 1.3228e-05 |
| point group | C1 |
Convergence Data
Item Value Threshold Converged? Maximum Force 0.000031 0.000450 YES RMS Force 0.000009 0.000300 YES Maximum Displacement 0.003701 0.001800 NO RMS Displacement 0.000761 0.001200 YES
Low frequencies --- -5.7636 -2.4971 -0.0015 0.0018 0.0032 2.4184 Low frequencies --- 45.4467 162.1595 198.7225
Log File
File:1-METHYL-IMIDAZOLIUM CHLORIDE B OPT2.LOG
1,3-Dimethyl-Imidazolium
Calculation Data
| name of submitted log file | JSDB_1,3-DIMETHYL-IMIDAZOLIUM_C_OPTIMISATION2.LOG |
| molecule | 1,3-Dimethyl-Imidazolium |
| method | RB3LYP |
| basis set | 3-21G |
| final energy | -303.559223 |
| RMS gradient | 9.197e-06 |
| point group | C1 |
Convergence Data
Item Value Threshold Converged? Maximum Force 0.000034 0.000450 YES RMS Force 0.000005 0.000300 YES Maximum Displacement 0.009909 0.001800 NO RMS Displacement 0.002322 0.001200 NO
Low frequencies --- -0.0005 -0.0001 0.0003 0.4283 2.6233 4.4264 Low frequencies --- 71.9601 73.9046 193.3269
Log File
File:JSDB 1,3-DIMETHYL-IMIDAZOLIUM C OPTIMISATION2.LOG
1,3-Dimethyl-Imidazolium Chloride
Calculation Data
| name of submitted log file | JSDB_1-METHYL-IMIDAZOLIUM_CHLORIDE_C_OPT.LOG |
| molecule | 1,3-Dimethyl-Imidazolium |
| method | RB3LYP |
| basis set | 3-21G |
| final energy | -761.779525 |
| RMS gradient | 2.2055e-05 |
| point group | C1 |
Convergence Data
Item Value Threshold Converged? Maximum Force 0.000046 0.000450 YES RMS Force 0.000013 0.000300 YES Maximum Displacement 0.001828 0.001800 NO RMS Displacement 0.000422 0.001200 YES
Low frequencies --- -3.6667 -2.4799 -0.0026 -0.0024 0.0003 3.4255 Low frequencies --- 52.1960 102.5543 107.1904
Log File
File:JSDB 1-METHYL-IMIDAZOLIUM CHLORIDE C OPT.LOG
Trimethylammonium Chloride
Calculation Data
| name of submitted log file | BH3 Opt.log |
| molecule | C3H10NCl |
| method | RB3LYP |
| basis set | 3-21G |
| final energy | -632.16208 |
| RMS gradient | 6.133e-06 |
| point group | C1 |
Convergence Data
Item Table
Item Value Threshold Converged? Maximum Force 0.000017 0.000450 YES RMS Force 0.000007 0.000300 YES Maximum Displacement 0.002004 0.001800 NO RMS Displacement 0.000651 0.001200 YES
Low Frequencies
Low frequencies --- -5.4821 -2.3017 -0.0033 -0.0020 0.0020 7.2673 Low frequencies --- 55.7661 56.4186 189.8351
Optimised C3H10NCl LOG file
File:TRIMETHYLAMMONIUM CHLORIDE OPT.LOG
Optimised C3H10NCl Molecule
Jmol Rotatable Molecule
Optimised CHNCl Molecule |
Scan Graph
BH3 Molecule
Calculation Data
| name of submitted log file | BH3 Opt.log |
| molecule | BH3 |
| method | RB3LYP |
| basis set | 6-31G(d,p) |
| final energy | -26.615324 |
| RMS gradient | 2.114e-06 |
| point group | D3H |
Convergence Data
Item Table
Item Value Threshold Converged? Maximum Force 0.000004 0.000015 YES RMS Force 0.000003 0.000010 YES Maximum Displacement 0.000017 0.000060 YES RMS Displacement 0.000011 0.000040 YES
Low Frequencies
Low frequencies --- -11.6940 -11.6861 -6.5543 0.0007 0.0280 0.4289 Low frequencies --- 1162.9745 1213.1390 1213.1392
Optimised BH3 Log File
Important Geometric Parameters
r(B-H)=1.19Â
θ (H-B-H)= 120°
Optimised BH3 Molecule
Jmol Rotatable Molecule
Optimised BH Molecule |
Infrared Info
| Mode | 1 | 2 | 3 | 4 | 5 | 6 |
| Wavenumber(cm-1) | 1163 | 1213 | 1213 | 2583 | 2716 | 2716 |
| Symmetry | A2 | E | E | A1 | E | E |
| Intensity (arbitrary units) | 93 | 14 | 14 | 0 | 126 | 126 |
Infrared Spectrum
NH3BH3 Molecule
| name of submitted log file | NH3BH3 opt2.log |
| molecule | NH3BH3 |
| method | RB3LYP |
| basis set | 6-31G(d,p) |
| final energy | -83.224689 |
| RMS gradient | 1.162e-06 |
| point group | C3V |
Convergence Data
Item Value Threshold Converged? Maximum Force 0.000002 0.000015 YES RMS Force 0.000001 0.000010 YES Maximum Displacement 0.000017 0.000060 YES RMS Displacement 0.000008 0.000040 YES
Low Frequencies
Low frequencies --- -5.4185 -0.3223 -0.0475 0.0010 1.1367 1.2199 Low frequencies --- 263.2927 632.9711 638.4651
Important Geometric Parameters
r(B-N)=1.67Â
r(B-H)=1.21Â
r(N-H)=1.02Â
θ (H-B-H)= 114°
θ (H-N-H)= 108°
Optimised NH3BH3
Jmol Rotatable Molecule
Optimised NHBH Molecule |
NH3BH3 Log File
Energies
E(NH3)= -26.615324 au E(BH3)= -56.557769 au E(NH3BH3)= -83.224689 au
Association Energy of NH3BH3
E= -0.051596 au E= -136 kJ/mol
Lab marking
You have a good working wiki. It would be good if you present your work more neatly and clearly. Overall, a good attempt. If you have any specific question, do email Prof. Hunt
NH3 molecule
Calculation Data
| name of submitted log file | JSDB_NH3OPT-POP.log |
| molecule | NH3 |
| method | RB3LYP |
| basis set | 6-31G(d,p) |
| final energy | -56.557769 |
| RMS gradient | 1.53e-07 |
| point group | C3v |
Convergence Data
Item Table
Item Value Threshold Converged? Maximum Force 0.000000 0.000015 YES RMS Force 0.000000 0.000010 YES Maximum Displacement 0.000003 0.000060 YES RMS Displacement 0.000001 0.000040 YES
Low Frequencies
Low frequencies --- -5.6864 -3.6131 -3.6124 0.0017 0.0048 0.0162 Low frequencies --- 1089.3674 1693.9284 1693.9284
Optimised NH3 Log File
Optimised NH3 Molecule
Optimised NH3 Molecule Rotatable Jmol
Important Geometric Parameters
r(N-H)=1.02Â
θ (H-N-H)= 106°
Infrared Information
| Mode | 1 | 2 | 3 | 4 | 5 | 6 |
| Wavenumber(cm-1) | 1089 | 1694 | 1694 | 3461 | 3590 | 3590 |
| Symmetry | A1 | E | E | A1 | E | E |
| Intensity (arbitrary units) | 145 | 14 | 14 | 1 | 0 | 0 |
Charge Distribution Data
| Atom | N | H |
| Charge | -1.13 | 0.38 |
Cis N2F2 molecule
Calculation Data
| name of submitted log file | birdjo_n2f2opt_pop.log |
| molecule | N2F2 |
| method | RB3LYP |
| basis set | 6-31G(d,p) |
| final energy | -309.01241 |
| RMS gradient | 3.17e-07 |
| point group | C2V |
Convergence Data
Item Table
Item Value Threshold Converged? Maximum Force 0.000001 0.000015 YES RMS Force 0.000000 0.000010 YES Maximum Displacement 0.000001 0.000060 YES RMS Displacement 0.000001 0.000040 YES
Low Frequencies
Low frequencies --- 0.0016 0.0018 0.0018 3.2233 4.3533 5.0998 Low frequencies --- 347.8772 561.2472 771.6105
Optimised N2F2 Log File
Optimised N2F2 Molecule
Why are there no bonds?
The reason there appears to be no bonds present is because Gaussview only represents bonds within a certain distance parameter. So the N-F bonds are in fact present; they are just not represented on the programme as they are outside this parameter.
Optimised N2F2 Molecule
Important Geometric Parameters
r(N-F)=1.22Â
r(N-F)=1.39Â
θ (F-N-N)=114°
θ (F-N-N-F)=0°
Infrared Information
Low frequencies --- 0.0016 0.0018 0.0018 3.2233 4.3533 5.0998 Low frequencies --- 347.8772 561.2472 771.6105
| Mode | 1 | 2 | 3 | 4 | 5 | 6 |
| Wavenumber(cm-1) | 348 | 561 | 772 | 949 | 987 | 1637 |
| Symmetry | A1 | A2 | B2 | A1 | B2 | A1 |
| Intensity (arbitrary units) | 1 | 0 | 75 | 75 | 81 | 21 |
Based on the 3N-6 rule we would expect to see 6 vibrational modes, so why do we only see 4 on the IR spectrum? Because mode 1 at 348cm-1 and mode 2 at 561cm-1 have essentially no absorption value so they are not present on the spectrum.
Which vibration is the asymmetric N-F stretch? The asymmetric N-F stretch is at 949cm-1.
What is the nature of the highest energy vibration? It is a symmetric stretch between the two N atoms.
Charge Distribution Data
| Atom | N | F |
| Charge | 0.22 | -0.22 |
Molecular Orbital Data
Which MOs are the core MOs?
MOs 1 and 2 are the core S orbitals for the Fluorine atoms MOs 3 and 4 are the core S orbitals for the Nitrogen atoms
MO9 Image:
LCAO Diagram of MO9
