8
$\begingroup$

I would like to carry out a calculation using deuterium instead of hydrogen. I tried the following ORCA input file:

!cc-pVDZ B3LYP opt freq

*xyzfile 0 1 bi_guess.xyz

The contents of bi_guess.xyz:

34
Coordinates from ORCA-job kie_computation_bi_b3lyp
  N   -1.36522940768289      1.43090120637739     -1.29989163642319
  C   -0.44442228001060      0.38103756632797     -1.36699056491989
  S   1.11938175575132      0.89828742472636     -0.68162779041360
  C   0.39936643411072      2.45263744108356     -0.17598894082966
  C   -0.88737920921729      2.55508413237739     -0.58575891095156
  C   -1.81988687350823      3.70483170564282     -0.34149534660368
  H   -2.02914244079129      4.28099946722255     -1.25957521107675
  H   -1.38928363000205      4.40377070305222      0.38811759209947
  H   -2.78814652651823      3.35404865266229      0.05306751853438
  C   -2.42958273785510      1.55203191145485     -2.29150912214068
  H   -2.13103494174077      1.01505106288885     -3.20503185208371
  H   -2.58921987988251      2.60821448709764     -2.54320899415084
  H   -3.38528969660347      1.12099748064241     -1.94940612103283
  C   1.24350647485456      3.43182218478396      0.59010704636463
  C   2.34455035926304      4.09444738435286     -0.25628872453066
  H   1.70917002774078      2.91928017185310      1.45151071835754
  H   0.59149967441242      4.21059012151118      1.01775365078364
  H   3.02263338128754      3.34129107817330     -0.68945118759167
  H   2.94960251527178      4.78111271092864      0.35865283243980
  H   1.90986274364991      4.66846424028840     -1.09098042345273
  C   -0.58896270899179     -0.87335406540114     -1.89161187230330
  O   0.62483817548640     -1.53234971307262     -2.12144915093809
  C   -1.81093059712914     -1.61627205233074     -2.20313985412716
  C   -1.78295926336086     -2.62665829989993     -3.19412484968867
  C   -2.91185414985907     -3.39920051566432     -3.46720312726732
  C   -4.10190122740441     -3.19660857990940     -2.75883040599387
  C   -4.14025228929028     -2.21734676116007     -1.75913366985694
  C   -3.01353021224531     -1.44485219171837     -1.47688481122363
  H   -3.04567986529299     -0.72442989166239     -0.65687581329096
  H   -0.86205885646938     -2.78256837851931     -3.75966518262305
  H   -4.98552287920138     -3.80160445008789     -2.97478885669734
  H   -5.05406866849322     -2.06721957203355     -1.17765661592474
  H   -2.86371065052297     -4.16497387835216     -4.24648540168365
  H   0.55630745024474     -2.41808278363585     -1.72738492075924 M = 2

However, the output shows me that there are only normal protons, no deuterium atoms. What am I doing wrong here?

Improve this question
$\endgroup$
2
  • 1
    $\begingroup$ Important correction: It seems that at least with the Orca installation I am using (seems to be ORCA 3.0.1) you have to specify the mass without the equals sign, e.g. "H 0.556307 -2.4180827 -1.72738492 M 2". $\endgroup$
    – logical x 2
    Dec 1, 2016 at 17:59
  • $\begingroup$ Indeed, sometimes ORCA wants an equals sign, sometimes it insists it not be there ... and sometimes it just doesn't care. $\endgroup$
    – hBy2Py
    Dec 2, 2016 at 12:01

1 Answer 1

Reset to default
11
$\begingroup$

ORCA cannot read isotope information from XYZ files -- the OpenBabel specification does not include it and so ORCA doesn't look for it in the geometry file.

You need to copy-paste the geometry into your input file:

* xyz 0 1
  ...
  H   0.55630745024474     -2.41808278363585     -1.72738492075924 M 2
*

Alternatively, if you are only interested in the frequencies, normal modes, and/or IR spectrum, you can edit the atomic masses in the .hess file after the run is completed and use the orca_vib utility program to re-run the analysis with the substituted isotopes. See pp. 201-202 of the ORCA v3.0.3 manual for more details.

Improve this answer
$\endgroup$
2
  • $\begingroup$ Editing the .hess file is mentioned in the ORCA manual, as you pointed out. I intend to compare the gibbs free enthalpy G of the deuterated compound with the protio isotopomer (to compute the kinetic isotope effect by comparison with the transition state). I was unsure if the free enthalpy G will also be available via orca_vib. $\endgroup$
    – logical x 2
    Dec 1, 2016 at 15:29
  • $\begingroup$ @ketbra Ah, yeah, I think you have to include the isotope mass in the input file in order to get the correct thermochemical values. $\endgroup$
    – hBy2Py
    Dec 1, 2016 at 15:45

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.