"What chemical bonds commonly found in minerals exhibit activity in the IR region ?"
Generally, all covalent bonds are IR active. As such, IR is preferentially used when it comes to identifying the commpound type, i.e. the dominant anions in a mineral. It also allows for speciation, i.e. it easily distinguishes the different oxo-anions of a given element (e.g. sulphate - sulphite - thiosulphate; phosphate - diphosphate ("pyrophosphate") - phosphite). For instance, it can easily distinguish zeunerite and torbernite and with a little extra work (if you have reference standards with precisely known phosphate and arsenate contents, that is), will quickly tell you the composition of a questionable member of that series.
"How can I use a standard FTIR to detect Raman scattering ?"
There is no way. Although the technical difference between IR (more, precisely, IR absorption spectroscopy) and Raman (= IR scattering spectroscopy) is only the mode of observation, and one could think of simply rearranging the components (sample holder and detector, relative to the light source), the construction of a spectrometer is in fact more sophisticated and quite specifically designed so as to meet the requirements of the measuring technique. For instance, IR typically uses a polychromatic light source (which would be detrimental for recording a Raman spectrum) and Raman uses a monochromatic source, which is not of much use in recording an absorption spectrum. Though, there also are significant differences in detector design.
"Finally, what is the best mode of sample preparation for analysis ?"
KBr pellets are fine to start with and when you have basic IR equipment (sample amount should be several milligrams per gram of KBr; if you need to evaluate a spectrum quantitatively, extinction at the wavelength of interest should not be higher than 10% of the intensity of incident light - why ?). There also are other matrices to consider, although they are rarely used (best ask an IR specialist). If you have access to IR microscopy and/or an ATR probe, you can record spectra in situ (although they are not always suited for quantitative evaluation - this will depend on several factors).
"If the latter suggested method was used, would crystallographic orientation influence spectra ?"
No. Wavelengths in the IR range are too long to be affected by subtle differences in the arrangement of individual ions in a lattice and therefore, most matrix effects that may pose serious problems e.g. in x-ray diffraction will go completely unnoticed in IR.
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