Input file for mass labeled/13C molecules

[Ivan Titaley]

Dear all,

I am interested in predicting the thermodynamic of a gas phase reaction containing mass labeled molecules. However, I am not sure how to specify the different atomic mass in the input file to take into account the deuterium and/or carbon-13. Based on my search, NWChem can calculate deuterated molecules, but, if my understanding is correct, this can only be done if all hydrogen is replaced with deuterium (https://nwchemgit.github.io/Hessians-and-Vibrational-Frequencies.html). Is it possible to compute a molecule where there are only a few deuterium and/or carbon-13 in a molecule?

I have attached an example xyz coordinate of one of the compounds for reference. Note that it is formatted for ORCA.

Any suggestions?

Thank you!

Best,
Ivan

[Edoardo Aprà]

As described in https://nwchemgit.github.io/Hessians-and-Vibrational-Frequencies.html#redefining-masses-of-elements, you can redefine the mass of a specific center.

If I understand correctly the geometry file you sent, the following input should work in NWChem

geometry
   C       -2.70898        1.99060        0.27779
   F       -3.16606        2.97869       -0.52569
   C       -3.23498        2.12093        1.69329
   F       -3.06298        0.81536       -0.29048
   F       -2.82413        3.29787        2.24656
   F       -2.71991        1.13854        2.48523
   C       -4.74423        2.04989        1.68967
   F       -5.26315        3.03456        0.90697
   C       -5.29698        2.18260        3.09652
   F       -5.16442        0.87745        1.14438
   F       -4.90555        3.36226        3.65540
   F       -4.79766        1.20745        3.90216
   C       -6.81251        2.11551        3.10262
   F       -7.34724        3.10239        2.33045
   C       -7.36995        2.26521        4.51527
   F       -7.25791        0.94387        2.57689
   F       -7.01370        3.46184        5.08363
   F       -6.89310        1.31584        5.35774
   C       -8.89432        2.22163        4.58307 #19 M 13.003355
   H       -9.32070        2.99502        3.93347
   C       -9.38952        2.43460        6.01299 #21 M 13.003355
   H       -9.24934        1.24661        4.23091
   O       -9.10835        3.72018        6.51215
   F       -1.35585        2.05265        0.24867
   H       -8.94540        1.70319        6.69862 #25 M 2.00141
   H      -10.47181        2.28088        6.08727 #26 M 2.00141
   H       -8.17181        4.01214        6.32141
   H       -9.31049        3.79664        7.48103
end


freq
  mass 19 13.003355
  mass 21 13.003355
  mass 25 2.00141
  mass 26 2.00141
end
...

task scf freq

This results in the following mass output in the NWChem frequencies step.

---------------------------- Atom information ----------------------------
     atom    #        X              Y              Z            mass
 --------------------------------------------------------------------------
    C        1 -5.1192299D+00  3.7616886D+00  5.2494698D-01  1.2000000D+01
    F        2 -5.9829859D+00  5.6289079D+00 -9.9341005D-01  1.8998400D+01
    C        3 -6.1132258D+00  4.0079765D+00  3.1998541D+00  1.2000000D+01
    F        4 -5.7881929D+00  1.5408070D+00 -5.4892761D-01  1.8998400D+01
    F        5 -5.3368319D+00  6.2320706D+00  4.2453828D+00  1.8998400D+01
    F        6 -5.1398846D+00  2.1515286D+00  4.6964037D+00  1.8998400D+01
    C        7 -8.9652947D+00  3.8737304D+00  3.1930133D+00  1.2000000D+01
    F        8 -9.9459113D+00  5.7344869D+00  1.7139248D+00  1.8998400D+01
    C        9 -1.0009841D+01  4.1245159D+00  5.8515743D+00  1.2000000D+01
    F       10 -9.7593387D+00  1.6581401D+00  2.1625646D+00  1.8998400D+01
    F       11 -9.2701453D+00  6.3537501D+00  6.9077044D+00  1.8998400D+01
    F       12 -9.0662628D+00  2.2817496D+00  7.3740132D+00  1.8998400D+01
    C       13 -1.2873777D+01  3.9977342D+00  5.8631016D+00  1.2000000D+01
    F       14 -1.3884270D+01  5.8626670D+00  4.4039119D+00  1.8998400D+01
    C       15 -1.3927186D+01  4.2806262D+00  8.5326231D+00  1.2000000D+01
    F       16 -1.3715461D+01  1.7836557D+00  4.8696160D+00  1.8998400D+01
    F       17 -1.3253971D+01  6.5419290D+00  9.6066677D+00  1.8998400D+01
    F       18 -1.3026070D+01  2.4865770D+00  1.0124661D+01  1.8998400D+01
    C       19 -1.6807828D+01  4.1982719D+00  8.6607465D+00  1.3003355D+01
    H       20 -1.7613569D+01  5.6597671D+00  7.4331805D+00  1.0078250D+00
    C       21 -1.7743620D+01  4.6007269D+00  1.1362903D+01  1.3003355D+01
    H       22 -1.7478718D+01  2.3557513D+00  7.9952606D+00  1.0078250D+00
    O       23 -1.7212286D+01  7.0301208D+00  1.2306179D+01  1.5994910D+01
    F       24 -2.5621850D+00  3.8789461D+00  4.6991816D-01  1.8998400D+01
    H       25 -1.6904355D+01  3.2185624D+00  1.2658556D+01  2.0014100D+00
    H       26 -1.9788852D+01  4.3102382D+00  1.1503272D+01  2.0014100D+00
    H       27 -1.5442482D+01  7.5818452D+00  1.1945733D+01  1.0078250D+00
    H       28 -1.7594275D+01  7.1746093D+00  1.4137097D+01  1.0078250D+00
 --------------------------------------------------------------------------

[Ivan Titaley]

Aha! I suppose I the answer was already listed on the page that I myself posted :D Not sure how I missed that.

Thank you for pointing it out, Edoardo. I appreciate it a lot!