NMR calculation of Si(CH3)4 not converged

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hjaaj
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Re: NMR calculation of Si(CH3)4 not converged

Post by hjaaj » 01 Jul 2020, 14:50

Once more, please attach your dalton output instead of asking someone to repeat. You must change from "Quick Reply" to "Full Editor & Preview" in order to attach files.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 11 Jul 2020, 08:56

Deleted.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 16 Jul 2020, 10:50

The shielding constants of six hydrogen atoms in C2H6 in CCl4 are the same, thus what is wrong for the NMR calculation of Si(CH3)4? I will repeat it.

Very Best Regard!
Attachments
ethanenmr.log
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taylor
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Re: NMR calculation of Si(CH3)4 not converged

Post by taylor » 16 Jul 2020, 12:12

I do not understand why you post the output file of a calculation you say has worked, but you do not post the output file of the calculation (TMS) you have a question about? If the problem is with a TMS calculation, and you want some assistance with this problem, surely the best thing to do is to post the TMS output? As I have remarked many times on this forum, the Dalton developers share many skills, but telepathy is not one of them...

Best regards
Pete

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 17 Jul 2020, 09:54

Dear Profs. Jensen and Remigio
With the following PCMCAV
.INA
1
2
3
4
5
.RIN
1.8
2.1
2.1
2.1
2.1

The following can be got
@2 H 33.8213
@2 H 33.7630
@2 H 33.7506
@2 H 35.0592
@2 H 34.1591
@2 H 35.1911
@2 H 34.6104
@2 H 35.9867
@2 H 34.6842
@2 H 35.7429
@2 H 35.1618
@2 H 35.3002

I will optimize it with symmetry and retry.

Very Best Regards!
Last edited by xiongyan21 on 17 Jul 2020, 15:01, edited 1 time in total.

taylor
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Re: NMR calculation of Si(CH3)4 not converged

Post by taylor » 17 Jul 2020, 13:02

For TMS, B3LYP/pcS-1 in CCl4 (geometry optimized using B3LYP/pc-1, I think) I obtain
+--------------------------------+
! Summary of chemical shieldings !
+--------------------------------+

@1 Definitions from J. Mason, Solid state Nuc. Magn. Res. 2 (1993), 285

@1 London orbitals (GIAOs) has been used.

@1 atom shielding dia para skew span (aniso asym)
@1 ----------------------------------------------------------------------------
@1 C _1 179.4531 360.1113 -180.6582 0.9967 25.3710 25.3501 0.0025
@1 C _2 179.4531 360.1113 -180.6582 0.9967 25.3710 25.3501 0.0025
@1 C _3 179.4531 360.1113 -180.6582 0.9967 25.3710 25.3501 0.0025
@1 C _4 179.4531 360.1113 -180.6582 0.9967 25.3710 25.3501 0.0025
@1 SI 377.8445 995.1032 -617.2587 -0.8761 0.1417 0.0753 2.6501
@1 H1 _1 30.9626 17.2291 13.7334 0.5009 10.2081 8.9345 0.4277
@1 H1 _2 30.9626 17.2291 13.7334 0.5009 10.2081 8.9345 0.4277
@1 H1 _3 30.9626 17.2291 13.7334 0.5009 10.2081 8.9345 0.4277
@1 H1 _4 30.9626 17.2291 13.7334 0.5009 10.2081 8.9345 0.4277
@1 H2 _1 30.9622 17.2291 13.7331 0.4975 10.2116 8.9286 0.4311
@1 H2 _2 30.9622 17.2291 13.7331 0.4975 10.2116 8.9286 0.4311
@1 H2 _3 30.9622 17.2291 13.7331 0.4975 10.2116 8.9286 0.4311
@1 H2 _4 30.9622 17.2291 13.7331 0.4975 10.2116 8.9286 0.4311
@1 H3 _1 30.9621 17.2291 13.7329 0.4977 10.2114 8.9290 0.4309
@1 H3 _2 30.9621 17.2291 13.7329 0.4977 10.2114 8.9290 0.4309
@1 H3 _3 30.9621 17.2291 13.7329 0.4977 10.2114 8.9290 0.4309
@1 H3 _4 30.9621 17.2291 13.7329 0.4977 10.2114 8.9290 0.4309

I would regard discrepancies of less than 2 parts in a million as very satisfactory, especially since this is a DFT calculation and thus inolves numerical integration. I suspect an SCF calculation would lead to even smaller discrepancies.

Best regards
Pete

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 18 Jul 2020, 03:11

I think perhaps it is not the basis set that makes a difference. Could you please post you input and output file here because even almost identical, your shielding constants are a little low?

Very Best regards!

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 18 Jul 2020, 06:03

I am now using mp2, aug-cc-pVDZ and generator=1 xy to optimize Si(CH3)4.

Very Best Regards!

taylor
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Re: NMR calculation of Si(CH3)4 not converged

Post by taylor » 18 Jul 2020, 06:30

The values are irrelevant to your original question, which was that you apparently did not obtain 12 equal hydrogen shieldings. This must reflect some problem with your input, because as you see I do obtain 12 equal shieldings. Since you are unwilling to post your output file, despite multiple requests to do so, there is nothing more I can do. The same applies to your query about the MP2 optimization.

Best regards
Pete

taylor
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Re: NMR calculation of Si(CH3)4 not converged

Post by taylor » 18 Jul 2020, 06:54

I did not see your additional message that came in while I was writing mine, sorry. I myself used
Generators=2 XY XZ
to specify D2 symmetry. Exact Td symmetry is then trivially achieved for the SiC4 part by putting the single distinct carbon at a point with the same x, y, and z coordinates (and the Si at the origin, of course). The H atoms are trickier because there are three distinct atoms to specify: if we imagine a C atom to be at the vertex of a cube in which the other carbons occupy alternate vertices, then the CH bonds can either project onto the cube edges, or project onto the bisectors of the cube faces (achieved by rotating the CH3 groups by 30 degrees from the previous orientation). The latter geometry is the global minimum if I recall. Needless to say, care must be taken to ensure that the CH bond lengths are equal and the HCH bond angles are all equal in the distinct methyl group.

Best regards
Pete

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 18 Jul 2020, 07:51

Dear Dr. Taylor
Thanks a lot for your help.
MP2 and aug-cc-pVDZ for this molecule is very time-demanding, thus I am now using b3lyp and aug-cc-pVDZ, and the generators identical to yours.
The initial geometry is drawn by Avagodro without a template which cannot guarantee a successful optimization. It seems it gets stuck at
...

Nuclear contribution to dipole moments
--------------------------------------

All dipole components are zero by symmetry
...

indicating perhaps the symmetry is not suitable for the molecule drawn, thus I first use no symmetry again.


Very Best Regards!
Last edited by xiongyan21 on 19 Jul 2020, 01:43, edited 3 times in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 18 Jul 2020, 08:46

Using nosymmetry, geometry optimization moves on
...
.--------------------------------------------.
| Starting in Wave Function Section (SIRIUS) |
`--------------------------------------------'

* Read MO coefficients from SIRIUS.RST with label "NEWORB " and header info: 18Jul20 FOCKDIIS

**********************************************************************
*SIRIUS* a direct, restricted step, second order MCSCF program *
**********************************************************************

(Wave function specification suppressed here, see output above for initial geometry.)

...
Very Best Regards!
Last edited by xiongyan21 on 19 Jul 2020, 01:44, edited 2 times in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 18 Jul 2020, 12:21

It seems that neither the basis set nor the symmetry which makes a obvious difference, because with aug-cc-pVDZ and b3lyp nosymmetry optimized geometry obtained by Dalton2018, 3-21G(just for trying) and b3lyp in CCl4 gives insignificant differences of the shielding constants among all 12 hydrogen atoms around 32.898ppm, meaning for this kind of calculation with Dalton2018, the best way is using a geometry optimized by DALTON2018.

Very Best Regard!
Last edited by xiongyan21 on 03 Sep 2020, 05:17, edited 3 times in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 03 Sep 2020, 03:40

I forgot to give shielding constants previously got by NWCHEM7.0.0 of Si(CH3)4 in CCl4 using B3lyp and 6-311G
e.g.,

Atom: 15 H
Diamagnetic
...
Paramagnetic
...
Total Shielding Tensor
...

isotropic = 33.0510
...
Today, NWCHEM7.0.0 B3lyp and 6-311+G(d,p) gives that of isotropic = 32.1737

Those of all the other hydrogen atoms have negligible differences from this.


Very Best Regards!
Last edited by xiongyan21 on 01 Nov 2020, 14:43, edited 1 time in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 01 Nov 2020, 10:20

There is something unusual. When I use the geometry optimized by B3LYP and aug-cc-pvdz with DALTON2018 to calculate the chemical shifts of gaseous hymexazole of DFT and 6-311G. Hessians will be calculated to verify whether they are stationary points.
The inputs are
**DALTON INPUT
.OPTIMIZE
**WAVE FUNCTIONS
.DFT
B3LYP
**END OF DALTON INPUT



**DALTON INPUT
.RUN PROPERTIES
**WAVE FUNCTIONS
.DFT
B3LYP
*SCF INPUT
.MAX DIIS
100
**PROPERTIES
.SHIELD
.SPIN-SPIN
**END OF DALTON INPUT

The obtained chemical shifts of hydrogen atoms of the enol form based on that of gaseous Si(CH3)4 with the same functional and same basis
set are within 2.8 ppms deviances when compared with the data in an article published in China, with the largest of that of the atom connected with the N atom. The chemical shifts of the hydrogen atoms of the methyl have around 0.05 to 0.45 ppms differences deviating from the experimental data within 0.3 ppms.

Aug-CC-pVDZ makes the discrepency larger than 3 ppms. and makes the chemical shift of hydrogen atom of Si(CH3)4 become between 31 and 32 ppms, all identical.

Perhaps relativsitc effects should be included, and the change of functionals will make them agree.

Very Best Regards!
Last edited by xiongyan21 on 04 Nov 2020, 15:37, edited 2 times in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 04 Nov 2020, 12:28

I am now using ZORA to calculate it with NWCHEM7.0.0. Can Dalton2018 and DIRAC do it?

The chemical shifts of the enol form calculated using the same functional and basis set with ZORA in vacuum and in water have a very small difference, but the deviances of H of OH are close to 5 ppms compared with experimental data, based on that of Si(CH3)4 calculated in vacuum.

If it is calculated without ZORA, the deviance becomes close to 5.5 ppms.

All the above uses B3LYP and 6-311+G**.

That experimental signal(10.99 ppm), the author said DMSO-d6 was used as internal standard and solvent in that article.



Perhaps a functional devoting to condense phase calculation is suitable.


Very Best Regards!
Last edited by xiongyan21 on 07 Nov 2020, 04:23, edited 1 time in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 06 Nov 2020, 13:20

The NMR shielding tensor has been calculated in DMSO, because I haven't found the dielectric constants of DMSO-D6.
The samllest one is not obviously different from that in water, but the others are.

NWCHEM 7.0.0 with ZORA(cutoff 1d-30) in DMSO (dielectric constant=47.24) (6-311+G(d,p) and B3LYP), geometry optimized with GAMESS using mp2 and 6-311++G(2d,2p)
26.0269
26.5719
29.6874
29.5387
29.5387

in vacuum
26.6947
28.3846
29.6773
29.8147
29.8147

in water(dielectric constant=78)
26.0188
26.5530
29.6884
29.5350
29.5350

without ZORA in vacuum
26.7016
28.3888
29.6866
29.8245
29.8245

Dalton2018 aug-cc-pVDZ and B3LYP, geometry optimized by Dalton2018
@1 H 24.4194
@1 H 27.4387
@1 H 30.4214
@1 H 29.9694
@1 H 30.3864

Dalton2018 6-311G and B3LYP, geometry optimized by Dalton2018
@2 H 24.3217
@2 H 28.7198
@2 H 31.5485
@2 H 31.1391
@2 H 31.5062

NWCHEM7.0.0 calculation with B3lyp and 6-311G of the keto form without ZORA in water previously gave all the chemical shifts referring to Si(CH3)4 in vacuum with the same functional and basis set deviating within 2 ppms from those in the experimental article.

The warning in the geometry optimization of hymexazole using GAMESS only metions if convegence difficulties are eoncountered, some factors should be loosen, but actually, the optimization can converge with the default settings. There is not any warning during the keto form optimization.

Perhaps C13 NMR should be applied to this compound, but there is no published experimental data now.

Very Best Regards!

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