I am looking for a software (ideally free) which can simulate polarized ATR-FTIR spectra of a stretched macromolecule, that has a specific orientation with respect to the electric field vector of the incoming IR light.
So far I have only found softwares that can predict unpolarized FTIR spectra.
Thank you for your suggestions,
Edith Perret
Dear Edith Perret as far as I know there is no such software, probably because most of the ATR accessories are not even able to host a polarizer and because usually linear dichroism theory is used which is just a very rough approximation. The additional problem with a stretched polymer is that a polymer is a polydomain medium, which means that linear polarized light does not stay linearly polarized if you orient it either parallel or perpendicular to the stretching direction. Maybe it is possible to see a strongly stretched polymer approximately as a uniaxial single crystal - then there is a way. I could provide you with a mathematica file with which you can calculate the spectra of such a single crystal, also under ATR conditions. Have a look at pp. 160- of Preprint Wave optics in Infrared Spectroscopy
Dear Mr. Mayerhöfer,
Thank you very much for your answer. Indeed, it seems like a challenging task to simulate polarized IR spectra. In the mathematica file that you mention, can you simulate polarized ATR-FTIR spectra from a single crystal? Meaning that you can give the electric field vector as an input along a certain crystal axis? If yes, then I would be interested in having a look at the file.
My main goal is to be able to assign the IR bands in linearly polarized spectra to specific vibrations of functional groups in the macromolecule.
Do you know if the assignments from an unpolarized spectra are identical to the ones of the polarized spectra? I expect that the band positions in the unpolarized spectra are the same as in the polarized spectra, right? I guess, that only the absorption is strongly changing as a function of the incident electric field vector. If the el. field vector points along the dipole moment, then the absorption is enhanced. Therefore, I will also look into standard softwares like Gaussian, Castep etc. But I believe that these softwares can only simulate the unpolarized spectra.
Yes, the program can simulate the reflectance for an arbitrary angle of incidence, arbitrary incidence medium and arbitrary orientation, provided you have either the oscillator parameters or the two principal components of the dielectric tensor function. Less information will not do the trick, since the spectra depend on both, the orientation of a transition moment with regard to the polarization direction and with regard to the interface between surface of the sample and the ATR crystal.
If an "unpolarized" spectrum is the same as a spectrum that does consists of more than one principal component, then in addition to peak values, bands can be shifted and shapes can be changed. These alterations are the stronger the stronger the underlying oscillators are. AFAIK Gaussian and Castep are not suitable for this job...
- Badges
- Science topic
- Similar topics
- Vectorization