How to specify a different isotope in the ORCA quantum chemistry program? 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?
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.