Characteristic vibration patterns of odor compounds from bread-baking volatiles upon protein binding: density functional and ONIOM study and principal component analysis

Abstract

As the mechanism underlying the sense of smell is unclear, different models have been used to rationalize structure-odor relationships. To gain insight into odorant molecules from bread baking, binding energies and vibration spectra in the gas phase and in the protein environment [7-transmembrane helices (7TMHs) of rhodopsin] were calculated using density functional theory [B3LYP/6-311++G(d,p)] and ONIOM [B3LYP/6-311++G(d,p):PM3] methods. It was found that acetaldehyde ("acid" category) binds strongly in the large cavity inside the receptor, whereas 2-ethyl-3-methylpyrazine ("roasted") binds weakly. Lys296, Tyr268, Thr118 and Ala117 were identified as key residues in the binding site. More emphasis was placed on how vibrational frequencies are shifted and intensities modified in the receptor protein environment. Principal component analysis (PCA) suggested that the frequency shifts of C-C stretching, CH(3) umbrella, C = O stretching and CH(3) stretching modes have a significant effect on odor quality. In fact, the frequency shifts of the C-C stretching and C = O stretching modes, as well as CH(3) umbrella and CH(3) symmetric stretching modes, exhibit different behaviors in the PCA loadings plot. A large frequency shift in the CH(3) symmetric stretching mode is associated with the sweet-roasted odor category and separates this from the acid odor category. A large frequency shift of the C-C stretching mode describes the roasted and oily-popcorn odor categories, and separates these from the buttery and acid odor categories.

Analytical Harmonic Vibrational Frequencies for the Green Fluorescent Protein Computed with ONIOM: Chromophore Mode Character and Its Response to Environment

“…Normal mode analysis of flexible proteins gives a large number of modes that are delocalized over the entire system, resulting in difficulties in interpretation . Comparison with measured experimental parameters, however, requires a global picture of vibrational motion.…”

“…Normal mode analysis of flexible proteins gives a large number of modes that are delocalized over the entire system, resulting in difficulties in interpretation. 29 Comparison with measured experimental parameters, however, requires a global picture of vibrational motion. Here, we present harmonic frequency calculations of the entire Green Fluorescent Protein using the ONIOM scheme and compare calculated frequency, intensity, and vibrational transition mode angle (VTMA) with experiment as follows:…”

Fate of pyrazines in the flavored liquids of e-cigarettes

“…These dicarbonyls are usually produced by the degradation of carbohydrates present in the tobacco leaves (Leffingwell 1976, Ishiguro and Sugawara 1977, Weeks et al 1995). Interestingly, similar transformations are usually detected in roasted foods, such as coffee and cocoa products, beans, baked potatoes, popcorn, and others (Heinzler and Eichner 1992, Huang and Barringer 2011, Treesuwan et al 2012, Pickard et al 2013, Yang et al 2013). …”

The ONIOM Method and Its Applications

“…ONIOM Hessian can be used to compute vibrational normal modes and accurate infrared (IR) spectra of large molecular systems . ONIOM infrared ( I IR ) and Raman ( I Raman ) intensity of the whole system can be expressed as where F is an electric field.…”