NMR and chemical shifts in NWChem
Clicked A Few Times
5:01:16 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

Forum Regular
5:06:10 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

Forum Regular
5:06:26 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

Forum Regular
5:06:28 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

Clicked A Few Times
5:54:15 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 pentane-2-thione
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.

Forum Regular
12:01:02 PM 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 exchange-correlation 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

Clicked A Few Times
7:05:51 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:   0.10E-06
                                NWChem CPHF Module
                                ------------------


  scftype          =     RHF 
  nclosed          =       21
  nopen            =        0
  variables        =     1281
  # of vectors     =        3
  tolerance        = 0.10D-03
  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:   0.10E-06
 SCF residual:    1.4943092224402321E-004


Iterative solution of linear equations
  No. of variables     1281
  No. of equations        3
  Maximum subspace       30
        Iterations       50
       Convergence  1.0D-04
        Start time     40.0


   iter   nsub   residual    time
   ----  ------  --------  ---------
     1      3    4.48D-01      47.1
     2      6    2.25D-02      55.3
     3      9    9.19D-04      62.1
     4     12    1.91D-05      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 K-bytes		     30914	     22516
	maximum total M-bytes		        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?

Forum Regular
9:58:14 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.

Clicked A Few Times
4:12:51 AM PST - Tue, Jan 19th 2016
Thank you @Sean, that is exactly what I was looking for.


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