Calculation of the Absorption Spectrum from an ATR Infrared Experiment

Barbara Grobelnik and Jože Grdadolnik*

National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
* Corresponding author: E-mail: joze.grdadolnik@ki.si

Abstract
The most efficient and precise method for separation of absorption and reflection contributions in the ATR (attenuated total reflection) spectrum is the calculation of pure absorption spectrum from optical constants. However, the precision of calculated optical constants depends on the alignment of the optical component of an ATR attachment. The arrangement of the ATR attachment always produces imperfections in optical path alignment. Therefore, we calculated the expected error analytically. The calculated error of Rs and Rp is in the range between 3%–8% per deviation of the incidence angle of 1°. To reduce the error of calculated reflectivities, a new procedure for recording the ATR spectrum is proposed. It is based on the calibration of the number of reflection by probing the spectrum of pure liquid water. The proposed procedure significantly reduces the error (< 2%) due to a divergence of the incidence angle. This approach is included in the program for routine calculation of the optical constants and absorption spectra of anisotropic solutions. A structural analysis of three dipeptides in water solutions is shown as an example of the application of an ATR attachment and the calculation of the absorption spectrum. The calculated spectra of dipeptides and bulk water provide ideal conditions for reliable subtraction. The OH stretching region in the difference spectrum of the leucine dipeptide shows characteristic patterns of rearranged water molecules in the vicinity of solutes. From the positions of negative and positive bands we hypothesize that the presence of leucine molecules creates a denser structure of water molecules near the solutes. The modelling of the amide III band shape in the spectra of the methionine and asparagine dipeptide in water reveals the conformation of the dipeptide backbone. The methionine dipeptide possesses mainly the PPII conformation, while the asparagine dipeptide is mostly in the βconformation. The population of α_R is small in both dipeptides.

Keywords: Infrared spectroscopy, ATR experiment, calculation of optical constants, anisotropic solutions, preferential dipeptide conformations