Mod:cbf5a234-49e7-4e4b-9d5d-85cf22add185

From ChemWiki
Revision as of 17:54, 21 November 2013 by Pk1811 (Talk | contribs) (→‎NBO charge distributions)

Jump to: navigation, search


Philip Kent: Inorganic Computational Lab


Ionic liquids: Designer solvents


Introduction

The aim of this project is to explore the physical nature of ionic liquids, which have application in designing solvents through customisation of the nature of the cation and anion[1]. In this work, a variety of cations have been investigated to identify what trends are present in the variation in central atom and its ligands.

Structures of methyl-ligand complexes

Optimisations

A number of cations have been optimised using Gaussian 09 D.01, namely [N(CH3)4]+, [P(CH3)4]+ and [F(CH3)3]+. All these complexes have been optimised to a DFT B3LYP 6-31G(d,p) level with the int=ultrafine scf=conver=9 keywords and tight convergence - this is as a consequence of behaviour seen in previous work[2] where low frequencies did not exist within a tight range unless these keywords were specified. All calculations were run on the supplied laptop due to a significant queue of jobs on the HPC (except for [S(CH3)3]+ as it took a very long time), and the log files are available here:

Once done, convergence was verified via inspection of the log file.

Summary outputs

[N(CH3)4]+ 

File Name		nch34_opt
File Type		.log
Calculation Type	FOPT
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-214.18128421	a.u.
RMS Gradient Norm	0.00000090	a.u.
Imaginary Freq
Dipole Moment		0.0000	 	Debye
Point Group		TD
Job cpu time:		0 days  0 hours  1 minutes 27.0 seconds.

[P(CH3)4]+ 

File Name		pch34_opt
File Type		.log
Calculation Type	FOPT
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-500.82701126	a.u.
RMS Gradient Norm	0.00000675	a.u.
Imaginary Freq
Dipole Moment		0.0001	 	Debye
Point Group		C1
Job cpu time:		0 days  0 hours 24 minutes 21.0 seconds.

[S(CH3)3]+ 

File Name		sch33_opt3
File Type		.log
Calculation Type	FOPT
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-517.68327460	 a.u.
RMS Gradient Norm	0.00000101	 a.u.
Imaginary Freq
Dipole Moment		0.9651	 	Debye
Point Group		C1
Job cpu time:		0 days  0 hours  2 minutes 52.2 seconds.

Convergence outputs

[N(CH3)4]+ 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000003     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000014     0.000060     YES
 RMS     Displacement     0.000005     0.000040     YES
 Predicted change in Energy=-1.010077D-10
 Optimization completed.
    -- Stationary point found.

[P(CH3)4]+ 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000014     0.000015     YES
 RMS     Force            0.000005     0.000010     YES
 Maximum Displacement     0.000026     0.000060     YES
 RMS     Displacement     0.000009     0.000040     YES
 Predicted change in Energy=-1.723206D-06
 Optimization completed.
    -- Stationary point found.

[S(CH3)3]+

Initial failed optimisation: 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000017     0.000015     NO 
 RMS     Force            0.000006     0.000010     YES
 Maximum Displacement     0.002915     0.000060     NO 
 RMS     Displacement     0.000869     0.000040     NO 
 Predicted change in Energy=-5.685776D-09
 Optimization stopped.
    -- Number of steps exceeded,  NStep=  61
    -- Flag reset to prevent archiving.

During this failed optimisation, it appears the molecule just spent a large amount of time rotating around the C3 axis through the sulphur.

The final optimisation yielded: 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000049     0.000060     YES
 RMS     Displacement     0.000018     0.000040     YES
 Predicted change in Energy=-6.520157D-11
 Optimization completed.
    -- Stationary point found.

Frequency analysis

Following this, frequency analysis was conducted with the same keywords and calculation level to ensure a minima has been found. This is ensured by checking there are no negative vibrations in the molecule. Calculations were again run on the laptop, and the log files, summaries, and frequencies are listed below. Actual animations of the modes have not been exported, however a Jmol of the log file is available and the modes can be seen by right clicking and choosing model -> the mode you want to see. This time, a range of -30 to +30 cm-1 has been accepted for the low frequencies as molecules investigated are quite complex, and a relatively simple basis set has been used. Optimising to 6-311G(d,p) would likely bring the frequencies within the range used previously however this would be at the expense of much longer computation times.

Summary outputs

[N(CH3)4]+ 

File Name		NCH34_FREQ
File Type		.log
Calculation Type	FREQ
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-214.18128421	a.u.
RMS Gradient Norm	0.00000085	a.u.
Imaginary Freq		0
Dipole Moment		0.0000	 	Debye
Point Group		TD
Job cpu time:		0 days  0 hours  3 minutes 17.0 seconds.

[P(CH3)4]+ 

File Name		PCH34_FREQ
File Type		.log
Calculation Type	FREQ
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-500.82701149	a.u.
RMS Gradient Norm	0.00000668	a.u.
Imaginary Freq		0
Dipole Moment		0.0001	 	Debye
Point Group		C1
Job cpu time:		0 days  0 hours 12 minutes 11.0 seconds.

[S(CH3)3]+ 

File Name		sch33_freq
File Type		.log
Calculation Type	FREQ
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-517.68327460	 a.u.
RMS Gradient Norm	0.00000104	 a.u.
Imaginary Freq		0
Dipole Moment		0.9651		 Debye
Point Group		C1
Job cpu time:		0 days  0 hours  9 minutes  6.7 seconds.

Vibration modes

[N(CH3)4]+ 

 Low frequencies ---    0.0007    0.0011    0.0013   21.5288   21.5288   21.5288
 Low frequencies ---  188.5488  292.6546  292.6546

Right click and use the Model menu to see the available modes

Vibration

[P(CH3)4]+ 

 Low frequencies ---  -15.1139   -0.0002    0.0012    0.0012    5.8940   14.7736
 Low frequencies ---  156.2222  191.5376  191.9513

Right click and use the Model menu to see the available modes

Vibration

[S(CH3)3]+ 

 Low frequencies ---   -8.5871    0.0029    0.0049    0.0051    5.7111    9.1755
 Low frequencies ---  162.4159  200.3446  200.5391

Right click and use the Model menu to see the available modes

Vibration

Conclusions on molecular structure

Investigation of structures is focused on the central atom as this is the only point at which variance should occur. The length of the M-C bonds and the angle between C-M-C on each complex is reported below:

Complex M-C Length (Å) Angle (°) M-C length (lit[3]) (Å)
[P(CH3)4]+ 1.82 109.5 1.84
[N(CH3)4]+ 1.51 109.5 1.46
[S(CH3)3]+ 1.82 102.7 1.79

Literature bond lengths are found by adding the covalent radii for the atoms.

Two key trends are:

  • As you go down a group, the bond length decreases
  • As you go across a group (so losing a ligand), the bond angle is reduced)

The first trend is straightforward to explain, as bond lengths increase down the group. This is in tandem with the increase in atomic radius down the group as orbitals in a greater shell begin to be filled. Thus, as you move from period 2 (N) to period 3 (P), the length of the bond increases and is in turn the overall size of each ion. There is slight variance in the length of a C-H bond in each complex, however no pattern is immediately discernible (it increases in the order S > P > N) - it is thought this is just some random error in the calculation.

Whilst there is an increase in bond length, there is no change in orientation of the bonds, thus the symmetry of TD is maintained in both the phosphorous and nitrogen molecules. As a result of this, the bond angle is the same for these two complexes. No other arrangement of the ligands is sterically possible, so ensuring that this symmetry label cannot be changed, and therefore the bond angle also cannot change. The bond angle is different for sulphur, as a result of the change of symmetry to C3v, it is not known if the change in metal centre contributes to this change - further investigation would be required.

Of note, the bond length does not appear to change going across the period. There is actually a small icnrease of 0.01Å if the bond length is reported accurate to 0.001Å, however it is not known if this is just an inherent error in the calculation or not. In any event, it is expected that there is a slight decrease in the bond length as you move towards the right of a period, as the increased nuclear charge better shields the electrons and thus shortens the bond length, but this is not observed here. This may be a result of this complex containing one less ligand, with the arrangement instead taken (along with the lone pair) resulting in some interactions (steric or electronic repulsion) which causes the carbon and metal atoms to move apart from each other. This theory is supported by the large deviation from bond length for the sulphur complex, indicating some feature about the arrangement it has taken is causing the bond length to be artificially lengthened.

Molecular orbitals and NBO charges of methyl-ligand complexes

All three complexes discussed previously have been subject to a full NBO and MO analysis via an energy calculation with the pop=(full,nbo) keyword, retaining any previously used keywords as appropriate. Calculations were performed on the laptop due to load on the HPC, except for the sulphur complex as the calculation took too long on the laptop.

Log files are available as follows:

Calculation output

[N(CH3)4]+ 

File Name		NCH34_EGY
File Type		.log
Calculation Type	SP
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-214.18128421	 a.u.
RMS Gradient Norm			 a.u.
Imaginary Freq
Dipole Moment		0.0000		Debye
Point Group		TD
Job cpu time:		0 days  0 hours  0 minutes 19.0 seconds.

[P(CH3)4]+ 

File Name		PCH34_EGY
File Type		.log
Calculation Type	SP
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-500.82701105	 a.u.
RMS Gradient Norm			 a.u.
Imaginary Freq
Dipole Moment		0.0001	 	Debye
Point Group		C1
Job cpu time:		0 days  0 hours  1 minutes 20.0 seconds.

[S(CH3)3]+ 

File Name		sch33_egy
File Type		.log
Calculation Type	SP
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-517.68327460	 a.u.
RMS Gradient Norm			 a.u.
Imaginary Freq
Dipole Moment		0.9651		 Debye
Point Group		C1
Job cpu time:		0 days  0 hours  0 minutes 57.7 seconds.

Sample MOs for [N(CH3)4]+

NBO charge distributions

NBO charge distributions were calculated from the checkpoint file for a range of -1.750 to 1.750 as this ensured the range of charges for all 3 complexes could be accommodated on the same scale. The charges are as follows:

Complex Metal charge (e) Carbon charge (e) Proton charge (e)
P 1.667 -1.060 0.298
N 0.917 -0.846 0.297
S -0.295 -0.483 0.269

  • Nitrogen complex

  • Phosphorous complex

  • Sulphur complex

Ligand influences on nitrogen metal centre complexes

To investigate how changes to the ligands affects the cation, two variants on the nitrogen complex analysed previously have been used. One has one of the protons on a methyl ligand replaced with CH2OH, the other has the proton replaced with CH2CN. Each complex is then optimised and subject to a frequency analysis so as to allow for investigation of its structure. A MO and NBO calculation is then subsequently run to analyse how the change in ligand affects the ions electronic behaviour.

Optimisations

Optimisations were conducted to the 6-31G(d,p) level directly with the same keywords as used previously (but no nosymm). The log files are available below on Dspace after being optimised on the HPC.

Summary output

[N(CH3)3(CH2OH)]+: 

File Name		nch33ch2oh_opt
File Type		.log
Calculation Type	FOPT
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-289.39470724	 a.u.
RMS Gradient Norm	0.00000102	 a.u.
Imaginary Freq
Dipole Moment		2.1358	 	Debye
Point Group		C1
Job cpu time:		0 days  1 hours 22 minutes 37.5 seconds.

[N(CH3)3(CH2CN)]+: 

File Name		nch33ch2cn_opt
File Type		.log
Calculation Type	FOPT
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-306.39376383	 a.u.
RMS Gradient Norm	0.00000045	 a.u.
Imaginary Freq
Dipole Moment		5.7642	 	Debye
Point Group		C1
Job cpu time:		0 days  0 hours 50 minutes 39.5 seconds.

Convergence output

[N(CH3)3(CH2OH)]+: 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000015     YES
 RMS     Force            0.000000     0.000010     YES
 Maximum Displacement     0.000034     0.000060     YES
 RMS     Displacement     0.000008     0.000040     YES
 Predicted change in Energy=-5.591936D-11
 Optimization completed.
    -- Stationary point found.

[N(CH3)3(CH2CN)]+: 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000001     0.000015     YES
 RMS     Force            0.000000     0.000010     YES
 Maximum Displacement     0.000036     0.000060     YES
 RMS     Displacement     0.000011     0.000040     YES
 Predicted change in Energy=-2.269581D-11
 Optimization completed.
    -- Stationary point found.

Frequency analysis

Optimisations were conducted to the 6-31G(d,p) level directly with the same keywords as used previously (but no nosymm). The log files are available below on Dspace after being optimised on the HPC.

Summary outputs

[N(CH3)3(CH2OH)]+ 

File Name		nch33ch2oh_freq
File Type		.log
Calculation Type	FREQ
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-289.39470724	 a.u.
RMS Gradient Norm	0.00000106	 a.u.
Imaginary Freq		0
Dipole Moment		2.1358	 	Debye
Point Group		C1
Job cpu time:		0 days  0 hours 26 minutes 10.7 seconds.

[N(CH3)3(CH2CN)]+ 

File Name		nch33ch2cn_freq
File Type		.log
Calculation Type	FREQ
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-306.39376383	 a.u.
RMS Gradient Norm	0.00000059	 a.u.
Imaginary Freq		0
Dipole Moment		5.7642	 Debye
Point Group		C1
Job cpu time:		0 days  0 hours 29 minutes 19.0 seconds.

Vibrational modes

[N(CH3)3(CH2OH)]+ 

 Low frequencies ---   -8.4158   -5.0201   -1.2272   -0.0010   -0.0008   -0.0007
 Low frequencies ---  131.1073  213.4620  255.7131

Right click and use the Model menu to see the available modes

Vibration

[N(CH3)3(CH2CN)]+ 

 Low frequencies ---   -8.4158   -5.0201   -1.2272   -0.0010   -0.0008   -0.0007
 Low frequencies ---  131.1073  213.4620  255.7131

Right click and use the Model menu to see the available modes

Vibration

MO and NBO calculations

pop=(nbo,full) energy calculations were then performed on the complexes to generate MOs and NBO charge diagrams, just as has been done previously. All calculations were performed on the HPC and log files are available as follows:

Summary outputs

[N(CH3)3(CH2OH)]+ 

File Name		nch33ch2oh_egy
File Type		.log
Calculation Type	SP
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-289.39470724	 a.u.
RMS Gradient Norm			 a.u.
Imaginary Freq
Dipole Moment		2.1358	 	Debye
Point Group		C1
Job cpu time:		0 days  0 hours  1 minutes 59.3 seconds.

[N(CH3)3(CH2CN)]+ 

File Name		nch33ch2cn_egy
File Type		.log
Calculation Type	SP
Calculation Method	RB3LYP
Basis Set		6-31G(d,p)
Charge			1
Spin			Singlet
E(RB3LYP)		-306.39376383	 a.u.
RMS Gradient Norm			 a.u.
Imaginary Freq
Dipole Moment		5.7642	 	Debye
Point Group		C1
Job cpu time:		0 days  0 hours  2 minutes 25.0 seconds.

Sample MOs

[N(CH3)3(CH2OH)]+

[N(CH3)3(CH2CN)]+

HOMO cell
LUMO cell
HOMO Energy
LUMO Energy

NBO energy distributions

Discussion

Ligand influence on structure

Ligand influence on charge distribution

Ligand influence on molecular orbitals

References

  1. ↑ M. Freemantle. Chem. Eng. News, 1998, 76, 32–37
  2. ↑ P. Kent, unpublished work (lab intro)
  3. ↑ CRC Handbook of Chemistry and Physics, ed. W. M. Haynes and D. R. Lide, CRC Press, Boca Raton, 93rd edn., 2012
Retrieved from "https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:cbf5a234-49e7-4e4b-9d5d-85cf22add185&oldid=378314"