Difference between revisions of "Milmindani"

Revision as of 04:49, 15 May 2026

1 Observations
2 Question Answers and Tabulation
3 d.) Cl- Molecule Optimised Version
4 c.) HMim-Cl Molecule (Cl Attached to CH₃ Optimised Version
- 4.1 Bond Distances
- 4.2 Item Table
5 b.) HMim-Cl Molecule (Cl Attached to C-H and CH₃ Optimised Version
- 5.1 Bond Distances
- 5.2 Item Table
6 a.) HMim-Cl Molecule (Cl Attached to N-H-Cl Optimised Version
- 6.1 Bond Distances
- 6.2 Item Table
7 Me₃NH-Cl Molecule Optimised Version
8 Me₃NH-Cl Molecule Scanned Version
9 Bond Energy Calculations NH₃BH₃
- 9.1 Calculation Data
10 NH₃BH₃ Molecule
11 BH₃ Molecule
12 NH₃ Molecule
13 Project Molecule N₂F₂
14 Lab1 Marking

Observations

Friday 2:45pm: The computers failed to run jobs to optimize and check the frequency of the HMim-Cl Molecule many times. This probably occurred over 10-15 times. I have retried over and over again and it has been unsuccessful so far. Friday 3:00pm: Molecule B Optimised. Friday 3:30pm: Still trouble with optimising A and C. CHanged methyl groups angle on A. Made sure no spaces in names and saved in D Drive. Friday 3:45pm: Molecule A Optimised.

Question Answers and Tabulation

Tabulate and compare all the H---Cl distances for all ion-pairs.

Molecule A Bond Distance: r(H-Cl)=2.13353Â
Molecule B Bond Distance: r(H-Cl)=2.13353Â
Molecule C Bond Distance: r(H-Cl)=2.13353Â

how do the H-bonds of Me3NH and HMim compare? Optimised bond distance and angle for Me3NH-Cl Bond Distance: r(N-H)=1.16186Â Bond Distance: r(N-Cl)=2.90049Â

Compared to Molecule B Optimised bond distance and angle for HMim-Cl Bond Distance: r(N-H)=1.01395Â Bond Distance: r(N-CH3)=1.49638Â Bond Distance: r(N-Cl)=3.14742Â

The N-CL bond is longer in HMim-Cl compared to Me3NH-Cl by 0.24693Â. The N-H bond is shorter in HMim-Cl compared to Me3NH-Cl by 0.14791Â.

how do the H-bonds of the N-H and C-H H-bonds compare?

are these distances representative of a H-bond? Hint compare your distances to the sum of the van der waals radii of H and Cl.

will the ionic nature of the ions effect a distance based assessment of H-bonding?

d.) Cl- Molecule Optimised Version

name of submitted log file	DM CLMINUS.LOG
molecule	Cl-
method	B3LYP
Calculation Type	SP
calculation method	RB3LYP
basis set	3-21G
charge	-1
RMS gradient	0.000000
point group	OH
Confirmed it is Minima	Yes

Media:DM CLMINUS.LOG

rotateable 3D Jmol image BH

c.) HMim-Cl Molecule (Cl Attached to CH₃ Optimised Version

name of submitted log file	DM me3NHCL Optimisation.log
molecule	HMim-Cl (C₄H₇ClN₂)
method	B3LYP
Calculation Type	FREQ
calculation method	RB3LYP
basis set	3-21G
final energy
RMS gradient
point group	C1
Confirmed it is Minima	Yes

Media:DM me3NHCL Optimisation.log

rotateable 3D Jmol image BH

Bond Distances

Optimised bond distance and angle for Me₃NH-Cl
Bond Distance: r(N-H)=Â
Bond Distance: r(N-Cl)=Â

Item Table

 Item               Value     Threshold  Converged?

b.) HMim-Cl Molecule (Cl Attached to C-H and CH₃ Optimised Version

name of submitted log file	B-HMIM-CL-OPTIMISATION.LOG
molecule	HMim-Cl (C₄H₇ClN₂)
Calculation Type	FREQ
method	B3LYP
calculation method	RB3LYP
basis set	3-21G
final energy	-722.666200
RMS gradient	0.000014
point group	C1
Confirmed it is Minima	Yes

Media:B-HMIM-CL-OPTIMISATION.LOG

rotateable 3D Jmol image BH

Bond Distances

Optimised bond distance and angle for Me₃NH-Cl
Bond Distance: r(N-H)=1.01395Â
Bond Distance: r(N-CH₃)=1.49638Â
Bond Distance: r(N-Cl)=3.64990Â

Item Table

          Item               Value     Threshold  Converged?
 Maximum Force            0.000050     0.000450     YES
 RMS     Force            0.000008     0.000300     YES
 Maximum Displacement     0.004359     0.001800     NO 
 RMS     Displacement     0.001247     0.001200     NO

a.) HMim-Cl Molecule (Cl Attached to N-H-Cl Optimised Version

name of submitted log file	A HMIM CL OPTIMISATION.LOG
molecule	HMim-Cl (C₄H₇ClN₂)
Calculation Type	FREQ
method	B3LYP
calculation method	RB3LYP
basis set	3-21G
final energy	-722.687898
RMS gradient	0.000019
point group	C1
Confirmed it is Minima	Yes

Media:A HMIM CL OPTIMISATION.LOG

rotateable 3D Jmol image BH

Bond Distances

Optimised bond distance and angle for Me₃NH-Cl
Bond Distance: r(N-H)=1.17721Â
Bond Distance: r(N-CH₃)=1.47704Â
Bond Distance: r(N-Cl)=2.89156Â

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000052     0.000450     YES
 RMS     Force            0.000010     0.000300     YES
 Maximum Displacement     0.002398     0.001800     NO 
 RMS     Displacement     0.000450     0.001200     YES

Me₃NH-Cl Molecule Optimised Version

Calculation Data

name of submitted log file	DM me3NHCL Optimisation.log
molecule	Me₃NH-Cl
method	FOPT
calculation method
basis set	3-21G(d,p)
final energy	-632.162045
RMS gradient	0.000394
point group	C1
Confirmed it is Minima	Yes

Media:DM me3NHCL Optimisation.log

rotateable 3D Jmol image BH

Bond Distances

Optimised bond distance and angle for Me₃NH-Cl
Bond Distance: r(N-H)=1.16186Â
Bond Distance: r(N-Cl)=2.90049Â

Item Table

 Item               Value     Threshold  Converged?
 Maximum Force            0.000942     0.000015     NO 
 RMS     Force            0.000323     0.000010     NO 
 Maximum Displacement     0.087442     0.000060     NO 
 RMS     Displacement     0.014422     0.000040     NO

Me₃NH-Cl Molecule Scanned Version

Calculation Data

name of submitted log file	DM me3NHCL RIGID SCAN.log
molecule	Me₃NH-Cl
method	SCAN
calculation method	RB3LYP
basis set	3-21G
final energy	-632.066188
RMS gradient	Blank-No Gradient Listed
point group	C1
Confirmed it is Minima	Yes

Media:DM me3NHCL RIGID SCAN.log

rotateable 3D Jmol image BH

Bond Distances

Optimised bond distance and angle for Me₃NH-Cl
Bond Distance: r(N-H)=0.80000Â
Bond Distance: r(N-Cl)=3.20000Â

Scan of Total Energy

This is the total energy of the scanned molecule. It is a U-Shape. The Raw data is available below for your perusal.

File:Me3NHCl Scan of Total Energy Data.log

Bond Energy Calculations NH₃BH₃

Calculation Data

E(NH₃)	-56.557769 AU
E(BH₃)	-26.615324 AU
E(NH₃BH₃)	-83.224689 AU
ΔE AU)	E(NH3BH3)-[E(NH3)+E(BH3)] = -83.224689 - (-56.557769+-26.615324) = -0.051596AU
ΔE Kj/mol)	-0.051596AU * 2625.4999 kJ/mol = 1 a.u. = -135.46529284 kJ/mol

NH₃BH₃ Molecule

calculation data

name of submitted log file	NH3BH3_Optimisation_Log_File.log.log
molecule	NH₃BH₃
method	B3LYP
calculation method	RB3LYP
basis set	6-31G(d,p)
final energy	-83.224689
RMS gradient	0.000001
point group	C1
Confirmed it is Minima	Yes

Media:NH3BH3_Optimisation_Log_File.log.log

rotateable 3D Jmol image BH

Item Table

 Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000041     0.000060     YES
 RMS     Displacement     0.000020     0.000040     YES

Important geometric parameters

Optimised bond distance and angle for BH₃
Bond Distance: r(N-H)=1.01847Â
Bond Distance: r(B-H)=1.20977Â
Bond Distance: r(B-N)=1.66771Â

Bond Angle (N-H): 107.88°
Bond Angle (B-H): 113.88°

Low frequencies ---   -3.6199   -0.0014   -0.0010   -0.0009    2.3908    4.5604
Low frequencies ---  263.4365  632.9747  638.4332

Mode	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18
wavenumber (cm_-1)	263.4365	632.9747	638.4332	638.5054	1069.1617	1069.1617	1196.1866	1203.5225	1203.5771	1328.8170	1676.0434	1676.0577	2471.9811	2532.0716	2532.0950	3464.1021	3581.1459	3581.1541
Symmetry	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A
intensity (arbitrary units)	0.0000	14.0108	3.5475	3.5464	40.5051	40.5105	108.9677	3.4694	3.4694	113.6226	27.5645	27.5669	67.2027	231.2478	231.2478	2.5113	27.9556	27.9571

BH₃ Molecule

Calculation Data

name of submitted log file	BH3 Optimisation DM.log
molecule	BH₃
method	B3LYP
calculation method	RB3LYP
basis set	6-31G(d,p)
final energy	-26.615324
RMS gradient	0.000002
point group	D3H
Confirmed it is Minima	Yes

Media:BH3_Optimisation_Log_File.log.log

rotateable 3D Jmol image BH

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

Important geometric parameters

Optimised bond distance and angle for BH₃
Bond Distance: r(N-F)=1.19200Â
Bond Angle (N-F): 120°
Low frequencies --- -11.6940 -11.6861 -6.5543 -0.0002 0.0280 0.4289
Low frequencies --- 1162.9745 1213.1390 1213.1392

Mode	1	2	3	4	5	6
wavenumber (cm_-1)	1162.9745	1213.1390	1213.1392	2582.5813	2715.7180	2715.7189
Symmetry	A₂"	E'	E'	A₁'	E'	E'
intensity (arbitrary units)	92.5282	14.0550	14.0544	0.0000	126.3320	126.3260

NH₃ Molecule

calculation data

name of submitted log file	NH3 Optimisation DM.log
molecule	NH₃
method	RB3LYP
basis set	6-31G(d,p)
final energy	-56.557769
RMS gradient	0.000000
point group	C3V

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

Media:BH3_Optimisation_Log_File.log.log

rotateable 3D Jmol image NH

Important geometric parameters

Optimised bond distance and angle for NH₃
Bond Distance: r(N-H)=1.01797Â
Bond Angle: 37.12783°

Low frequencies --- -5.6864 -3.6131 -3.6124 0.0017 0.0048 0.0162
Low frequencies --- 1089.3674 1693.9284 1693.9284

Mode	1	2	3	4	5	6
wavenumber (cm_-1)	1089.3674	1693.9284	1693.9284	3461.3788	3589.9285	3589.9285
Symmetry	A₁	E	E	A₁	E	E
intensity (arbitrary units)	145.4277	13.5571	13.5572	1.0593	0.2699	0.2699

Charges	N-Atom	H-Atom	H-Atom	H-Atom
Charge	-1.125	0.375	0.375	0.375

Project Molecule N₂F₂

calculation data

name of submitted log file	N2F2 MOLECULE 1 DM.log
molecule	N₂F₂
method	RB3LYP
basis set	6-31G(d,p)
final energy	-309.012413
RMS gradient	0.000000
point group	C2V

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

Media:N2F2 MOLECULE 1 DM.LOG

rotateable 3D Jmol image Nf

Important geometric parameters

Optimised bond distance and angle for NH₃
Bond Distance: r(N-F)=1.28000Â
Bond Distance: r(N=N)=1.23200Â
Bond Angle (N-F): 120°

Low frequencies --- 0.0013 0.0015 0.0017 3.2233 4.3533 5.0998
Low frequencies --- 347.8772 561.2472 771.6105

Mode	1	2	3	4	5	6
wavenumber (cm_-1)	347.8772	561.2472	771.6105	949.4548	987.2543	1636.6075
Symmetry	A₁	A₂	B₂	A₁	B₂	A₁
intensity (arbitrary units)	0.6108	0.0000	74.7044	75.4125	81.1265	20.5391

Charges	N-Atom	F-Atom	N-Atom	F-Atom
Charge	0.191	-0.191	0.191	-0.191

Questions:

the molecule from the log file does not have bonds between the F and N atoms, what is going on here?
It does have bonds, you just need to change the number from 8 to 1 or 2 to see where the animation connects the bond together.

IR analysis

how many vibrations are expected from the 3N-6 rule?

The 3N-6 rule, calculates the number of vibrational modes in the molecule where N=the total number of atoms. As N₂F₂ has 4 atoms, N=4. So 3*(4)-6 = 6 vibrational modes are present in N₂F₂.

why are there only 4 peaks in the IR spectrum?
The molecule is symmetrical so although there are 6 vibrational modes, only 4 modes are visible because the symmetry of the molecule cancels dipole so they do not show up in an IR spectrum.

which vibration is the asymmetric N-F stretch?
The vibration at 775 cm_-1 is the asymmetric N-F stretch.

what is the nature of the highest energy vibration?
This is the N=N stretch located at 1640 cm_-1. The peak is small which is due to the tight N=N bond not moving that much.

MO analysis:

which MOs are core orbital MOs?
The 1S orbitals of both F atoms and the 1s orbitals of both N atoms. MO's 1-4.

provide a picture of MO 9 and beside it draw the LCAO diagram

Lab1 Marking

It's good that you have a working wiki. However, your reported image and charges of N2F2 do not correspond to an optimised structure. Don't forget to consider the accuracy to which you report your data the next time. If you have any queries, please contact Prof. Hunt.

@@ Line 164: / Line 164: @@
 Bond Distance: r(N-H)=1.01395&Acirc;<br>
 Bond Distance: r(N-CH<sub>3</sub>)=1.49638&Acirc;<br>
-Bond Distance: r(N-Cl)=3.14742&Acirc;<br>
+Bond Distance: r(N-Cl)=3.64990&Acirc;<br>
 ===Item Table===

Difference between revisions of "Milmindani"

Revision as of 04:49, 15 May 2026

Contents

Observations

Question Answers and Tabulation

d.) Cl- Molecule Optimised Version

c.) HMim-Cl Molecule (Cl Attached to CH3 Optimised Version

Bond Distances

Item Table

b.) HMim-Cl Molecule (Cl Attached to C-H and CH3 Optimised Version

Bond Distances

Item Table

a.) HMim-Cl Molecule (Cl Attached to N-H-Cl Optimised Version

Bond Distances

Item Table

Me3NH-Cl Molecule Optimised Version

Calculation Data

Bond Distances

Item Table

Me3NH-Cl Molecule Scanned Version

Calculation Data

Bond Distances

Scan of Total Energy

Bond Energy Calculations NH3BH3

Calculation Data

NH3BH3 Molecule

calculation data

Item Table

Important geometric parameters

BH3 Molecule

Calculation Data

Item Table

Important geometric parameters

NH3 Molecule

calculation data

Item Table

Important geometric parameters

Project Molecule N2F2

calculation data

Item Table

Important geometric parameters

Lab1 Marking

Navigation menu

Search

c.) HMim-Cl Molecule (Cl Attached to CH₃ Optimised Version

b.) HMim-Cl Molecule (Cl Attached to C-H and CH₃ Optimised Version

Me₃NH-Cl Molecule Optimised Version

Me₃NH-Cl Molecule Scanned Version

Bond Energy Calculations NH₃BH₃

NH₃BH₃ Molecule

BH₃ Molecule

NH₃ Molecule

Project Molecule N₂F₂