Quantitative Determination of Ala-Ala Conformer Ratios in Solution by Decomposition of Raman Optical Activity Spectra

Abstract

Raman optical activity (ROA) spectroscopy combined with quantum-chemical simulations is a sensitive method to determine the absolute configuration and conformation of chiral molecules in solutions. However, the precision of this approach varies for different systems. In the present study, the reliability and numerical stability of decomposing experimental spectra into calculated subspectra is tested on the Ala-Ala dipeptide. Molecular dynamics (MD) snapshots of Ala-Ala/water clusters are averaged to account for solvent effects and molecular flexibility. Multiple experiments with protonated, zwitterionic, and deprotonated dipeptide forms and natural and d- and d-isotopically labeled dipeptides are used to verify the results and estimate the overall accuracy. Although the precision is still limited by experimental noise and computational error, a very close match between the observed and theoretical spectral shapes has been achieved. This enabled quantitative determination of conformer populations with a typical dispersion of 10%. The spectroscopy also demonstrated how the conformation depends on pH. The ROA results were more consistent than the Raman ones. Typically, the ROA analysis was more resistant to artifacts in the experiment, such as incomplete baseline subtraction. Conformer ratios predicted by MD agree fairly but not fully with the experimental ones. This indicates minor deficiencies in the Amber force field, particularly for the protonated dipeptide. Overall, the combination of ROA experiment and computational chemistry appears to be a robust tool providing deep insight into molecular structure.

Tracking Conformational Changes in Phosvitin throughout a Crowding‐Agent‐Based Titration

“…In one of those studies, Raman optical activity (ROA), a technique with a high sensitivity towards conformational changes in intrinsically disordered proteins, was used to explore the conformational effects of crowded environments on proteins. ROA is a chiroptical spectroscopic technique that exhibits unprecedented sensitivity towards distinguishing and identifying local structure in proteins by means of band patterns in the spectra …”

Understanding CH-Stretching Raman Optical Activity in Ala–Ala Dipeptides

“…Simulations at the harmonic level are based on those described in ref . Briefly, for the quantum chemistry, the Gaussian 16 program was used, and the B3PW91/COSMO − /6-311++G** level of approximation was chosen as a default.…”

“…As shown below, in spite of the limited accuracy, the approach allowed for assignment of the most important Raman and ROA bands and for evaluation of the flexibility and solvent effects. This gives us a hope that in the future, more quantitative analysis of the CH-stretching ROA pattern is possible, allowing to estimate the conformer ratios, for example, in the same way as usual in the region of lower wavenumbers …”

Paving the way to conformationally unravel complex glycopeptide antibiotics by means of Raman optical activity

“…[6][7][8] For small organic (bio)molecules (peptides, carbohydrates, natural products) the ROA spectra have proven to be substantially more difficult to interpret solely based on empirical data. From the implementation of ROA intensity calculations in density functional theory (DFT) level programs onwards many structural characterization studies of peptides [9][10][11][12][13][14][15][16][17][18][19] and carbohydrates [20][21][22][23][24][25][26] have been published. Consequently, we now have a clear understanding of the spectral response to the conformational variability in peptides and carbohydrates as well as how to best approach these types of systems.…”