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NMR and chemical shifts in NWChem
From NWChem
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4:01:16 AM PST  Sat, Jan 9th 2016 

Dear NWChem forum,
As a work for my Masters Degree I have to study NMR spectra (S, Pt, N and P) of different compounds and discuss the shifts. My question is? can I use NWChem to simulate shifts other than 1H and 13C? Can someone point me an example on how to do it and how to extract the shifts from my output?
Thanks in advance for any hint.


Henrique C. S. Junior
Inorganic Chemist  UFRRJ  Rio de Janeiro


Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


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Posts 194


4:06:10 PM PST  Sat, Jan 9th 2016 

Hi,
Definitely. The procedure is exactly the same as you have already done for 1H and 13C. With regard to Pt, are you interested in the Pt shift or the chemical shift of some of the atoms in the ligand attached to the transition metal center ?
If you are interested in the Pt chemical shift, you will need to add relativistic corrections as this is a third row element.
Send me your molecule that you are interested in and I can give you more help.
Best,
Niri
niri.govind@pnnl.gov




Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


Forum Regular
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Posts 194


4:06:26 PM PST  Sat, Jan 9th 2016 

Hi,
Definitely. The procedure is exactly the same as you have already done for 1H and 13C. With regard to Pt, are you interested in the Pt shift or the chemical shift of some of the atoms in the ligand attached to the transition metal center ?
If you are interested in the Pt chemical shift, you will need to add relativistic corrections as this is a third row element.
Send me your molecule that you are interested in and I can give you more help.
Best,
Niri
niri.govind@pnnl.gov




Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


Forum Regular
Threads 4
Posts 194


4:06:28 PM PST  Sat, Jan 9th 2016 

Hi,
Definitely. The procedure is exactly the same as you have already done for 1H and 13C. With regard to Pt, are you interested in the Pt shift or the chemical shift of some of the atoms in the ligand attached to the transition metal center ?
If you are interested in the Pt chemical shift, you will need to add relativistic corrections as this is a third row element.
Send me your molecule that you are interested in and I can give you more help.
Best,
Niri
niri.govind@pnnl.gov




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Posts 18


4:54:15 PM PST  Sat, Jan 9th 2016 

Hi, Niri, Thanks for your kind reply!
I'm interested in the shifts of the centers and the cases I'm looking for are as generic as possible: since I just have to discuss changes in the shifts as I change ligands.
For Pt, cisplatin is a nice example (NMR Pt):
Pt 0.0000000000 0.0000000000 0.5490000000
Cl 1.3380000000 0.0000000000 2.0390000000
Cl 1.3380000000 0.0000000000 2.0390000000
N 1.1670000000 0.0000000000 0.4210000000
N 1.1670000000 0.0000000000 0.4210000000
H 2.0610000000 0.0000000000 0.1470000000
H 1.1880000000 0.8320000000 1.0200000000
H 1.1880000000 0.8320000000 1.0200000000
H 1.1880000000 0.8320000000 1.0200000000
H 1.1880000000 0.8320000000 1.0200000000
H 2.0610000000 0.0000000000 0.1470000000
For NMR 33S something as simple as a pentane2thione
S 2.0126039971 0.7057568749 0.9892147752
C 1.4572870092 1.7692560622 0.1297002820
C 1.0355430215 0.3402259051 0.1099268498
C 0.3202179169 0.1077466416 0.4062306655
C 1.4529323559 0.5254982104 0.3996040888
C 2.8044481870 0.0524938220 0.0126816209
H 2.5179039586 1.9290059824 0.0849756732
H 0.8662779053 2.4329882351 0.5082904851
H 1.2728254229 2.0308776543 1.1758346198
H 0.3994008514 0.1872182798 1.4595774532
H 0.3982657278 1.2010021749 0.3739390036
H 1.2882085228 0.3716488078 1.4725891718
H 1.4660715631 1.6093750640 0.2354685558
H 3.6023295002 0.4373613819 0.5796126760
H 2.8464844765 1.1251976779 0.2271334020
H 3.0046506874 0.0937240909 1.0534492808
And I'm sorry if this is a very simple question (I'm reading as much as I can). I'm new to NWChem and this is the first time I have to deal with NMR shifts.




Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


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11:01:02 AM PST  Mon, Jan 11th 2016 

Hi,
For the second molecule you don't need relativistic effects. However, you need to assess the quality of the basis sets and exchangecorrelation functional. For starters, you could use a reasonably large Pople style basis sets and the B3LYP functional to see if the chemical shifts are in reasonable agreement with experiment. By default, we calculate all the shieldings. But if you are just interested in 33S, you just have to calculate the shielding for sulfur alone. Here's an example of the property block to just calculate shielding on S.
property
shielding 1 1
end
task dft property
If you are interested in the first and fourth atoms, then the input would like like
property
shielding 2 1 4
end
task dft property
For the Pt complex, you need to use relativistic effects for this. You can do this by turning on the zora option in the input file.
Best regards,
Niri




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Posts 18


6:05:51 PM PST  Tue, Jan 12th 2016 

Thanks, Niri, with your help it looks a lot less complicated.
Here is my try for P(Me)3

Chemical Shielding Tensors (GIAO, in ppm)

Grid integrated density: 42.000015081313
Requested integration accuracy: 0.10E06
NWChem CPHF Module

scftype = RHF
nclosed = 21
nopen = 0
variables = 1281
# of vectors = 3
tolerance = 0.10D03
level shift = 0.00D+00
max iterations = 50
max subspace = 30
Integral file = ./molecule.aoints.0
Record size in doubles = 65536 No. of integs per rec = 43688
Max. records in memory = 47 Max. records in file = 27313
No. of bits per label = 8 No. of bits per value = 64
#quartets = 4.513D+05 #integrals = 5.434D+06 #direct = 0.0% #cached =100.0%
File balance: exchanges= 2 moved= 11 time= 0.0
Grid integrated density: 42.000015081313
Requested integration accuracy: 0.10E06
SCF residual: 1.4943092224402321E004
Iterative solution of linear equations
No. of variables 1281
No. of equations 3
Maximum subspace 30
Iterations 50
Convergence 1.0D04
Start time 40.0
iter nsub residual time
   
1 3 4.48D01 47.1
2 6 2.25D02 55.3
3 9 9.19D04 62.1
4 12 1.91D05 68.9
Parallel integral file used 127 records with 0 large values
Wrote CPHF data to ./molecule.shieldcphf
Calc. par tensor> nonrel
Atom: 1 P
Diamagnetic
968.1936 0.0016 0.0002
0.0016 968.2032 0.0038
0.0002 0.0038 961.6820
Paramagnetic
529.1638 0.0271 0.2429
0.0271 529.0450 0.3423
0.2429 0.3423 549.2152
Total Shielding Tensor
439.0298 0.0287 0.2431
0.0287 439.1582 0.3460
0.2431 0.3460 412.4668
isotropic = 430.2183
anisotropy = 13.4277
Principal Components and Axis System
1 2 3
439.1701 439.0247 412.4601
1 0.2249 0.9743 0.0091
2 0.9743 0.2250 0.0129
3 0.0147 0.0060 0.9999
Task times cpu: 62.7s wall: 68.4s
NWChem Input Module

Summary of allocated global arrays

No active global arrays
GA Statistics for process 0

create destroy get put acc scatter gather read&inc
calls: 378 378 1.76e+06 3846 6.15e+05 100 0 569
number of processes/call 1.02e+00 1.67e+00 1.10e+00 1.94e+00 0.00e+00
bytes total: 1.69e+08 6.63e+06 1.38e+08 1.05e+06 0.00e+00 4.55e+03
bytes remote: 1.07e+08 2.13e+06 1.01e+08 3.86e+05 0.00e+00 0.00e+00
Max memory consumed for GA by this process: 744952 bytes
MA_summarize_allocated_blocks: starting scan ...
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
MA usage statistics:
allocation statistics:
heap stack
 
current number of blocks 0 0
maximum number of blocks 26 51
current total bytes 0 0
maximum total bytes 30913032 22515096
maximum total Kbytes 30914 22516
maximum total Mbytes 31 23
And I'm expecting a shift at about 62 ppm relative to 85% H3PO4. Is there any analysis tool to extract such values from my outputs? Can you show me how to do it?




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Posts 149


8:58:14 AM PST  Fri, Jan 15th 2016 

You need to calculate the chemical shielding tensor of your reference molecule as well (at the same level of theory), and then taking the difference of the values of the isotropic shielding will give you the relevant value with which to compare with experiment.




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3:12:51 AM PST  Tue, Jan 19th 2016 

Thank you @Sean, that is exactly what I was looking for.



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