Firefly and PC GAMESS-related discussion club

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Alex Granovsky
gran@classic.chem.msu.su

Note, with Firefly and GAMESS(US) FREQUENCIES are in CM**-1 and IR INTENSITIES are in DEBYE**2/AMU-ANGSTROM**2

IR intensities are printed in Debye**2/amu-Angstrom**2.
These can be converted into intensities as defined by
Wilson, Decius, and Cross's equation 7.9.25, in km/mole,
by multiplying by 42.255.  If you prefer 1/atm-cm**2, use
a conversion factor of 171.65 instead.  A good reference
for deciphering these units is A.Komornicki, R.L.Jaffe
J.Chem.Phys. 1979, 71, 2150-2155.

See also:

http://akira.ruc.dk/~spanget/IR_intensity_.pdf

Regards,
Alex Granovsky

On Tue Jul 26 '11 7:59pm, Thomas H. wrote
-----------------------------------------
>Hello,

>I want to scale the y-axis (IR activity) for a better direct comparison with experimental values (e. g. absorbance or absorption coefficient in 1/cm).

>I guess the unit for the Firefly IR intensities of the output file is km/mol (in comparison to Gaussian etc.). This is more or less the integrated absorptivity. I know the definition (integral of the molar absorption coefficient under a absorbing band), but it’s difficult to get the values in units like 1/cm or 1/(mol*cm).

>But how can I get from the frequencies and the IR activities a spectrum like experimental absorption spectra? E. g. in Gabedit (or Avogadro, Molekel) I can choose a peak width for Gaussian or Lorentz fits. But in no of these pre-processing programs the y-scale is defined/named.

>If I chose a special peak width for fitting (e. g. in Gabedit) and then I chose a second peak width (e. g. the half width or ten times widen etc.) I get more or less the same maximum peak intensity of the fit, which disagrees with the definition of the integrated absorptivity (wider peak -> higher max. value; smaller peak -> higher max. value in case of the same peak area/integral).

>I searched for relevant papers, but I did not found anything useful. I know, that the IR activity values are not literally, however it would be very useful to get a feeling for the magnitude. So I have the following questions:

>a) How can I transform the Firefly output values to a spectra like experimental results (and transform the scale from km/mol to 1/cm or 1/(cm*mol), respectively)?
>b) Are there standard/useful guidelines, how the value for the width (Gaussian or Lorentz fit) have to be chosen?

>Thanks for any remarks,

>Thomas
>