Objectives: To characterize protein molecular structure using Fourier Transform Infrared Spectroscopy (FTIR) with univariate and multivariate molecular spectral analysis and identify the structure differences among barley cultivars. Place and Duration of Study: Six barley cultivars: (1) cv. Yousef, (2) cv. Nosrat, (3) cv. CB.79.10, (4) cv. Makooie, (5) cv. Abidar, and (6) cv. Sararood were provided from Crop Development Center Karaj, Iran. FTIR spectroscopy was carried out at the University of Saskatchewan (Saskatoon, Canada), between May 2012 to November 2012. Methodology: The spectral data were collected from feeds using JASCO FTIR-ATR-4200. The molecular structure spectral analyses involved protein amide I, amide II, α-helix, β- sheet, total carbohydrate, the ratio of amide I to amide II, α-helix to β-sheet, and starch to amide I. Results: Molecular spectral techniques were able to identify spectral differences associated with the molecular structural differences among barley cultivars. It was found that protein molecular structure in terms of amide II, the ratio of amides I to II and the ratioof α- helix to β-sheet significantly differed among cultivars. Makooie had the greatest peak area and height amide II and the ratio of α-helix to β-sheet. It had the lowest ratio of amide I to amide II and the ratio of starch to amide I. Carbohydrate molecular spectral intensities were also varied among barley cultivars, but it was not statistically significant. CB.79.10 had the greatest peak area CHO. The infrared absorbance intensity ratio of starch to amide I was different among barley cultivars. It was higher for CB.79.10 indicating that CB.79.10 is more heterogeneous than those of other barley cultivars. Conclusion: The biological function differences between barley cultivars may be related to molecular structure difference and biopolymer conformation between the cultivars of barley. Further study is needed to quantify protein and carbohydrate related molecular spectral features of barley in relation to nutrient supply and availability of protein and carbohydrate.

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