Carbohydrates play a pivotal role in numerous functions in all organisms. However, contrary to other biomolecules, such as DNA or proteins, where techniques for their structural determination are abundant, saccharides are usually harder to study, because of their high conformational flexibility in solution. As a result, the adaptation of established structural biology methods to sugars is rarely straightforward. Raman and ROA (its chiral sensitive counterpart) spectroscopies are highly sensitive to any structural changes and hydration. Therefore, they are promising tools to study subtle conformational changes of saccharides in solution. Moreover, the structural-sensitive spectral region of sugars, 200-1800 cm-1, is not cluttered by the water signal.
A critical drawback of Raman and ROA techniques is that the interpretation of their spectra is challenging. Contrary to other spectroscopic methods, it is impossible to extract precise structural information by direct analysis of the obtained peaks and bands. Computer modeling techniques can help to interpret the experimentally recorded Raman and ROA spectra, providing a natural complementarity to these techniques. These modeling techniques usually aim to calculate the same spectra. When the calculated spectra successfully compare to the experimental ones, we can assume that the sugar structures used for the calculations are the relevant ones present in solution. Previous attempts to calculate Raman and ROA spectra for monosaccharides resulted in reduced or, at best, qualitative agreement between the spectra. Furthermore, the computational techniques used are demanding, which restricts the general adoption of the used protocols, for example, to study larger saccharides. In this work, we have designed a new protocol that calculates Raman and ROA spectra resulting in a nearly quantitative agreement with experiments. Our new protocol also reduces the computational demands drastically, making it suitable for small oligosaccharides. This protocol combines classical molecular mechanics simulations (MM) to obtain an ensemble of saccharide structures with the usage of the QM/MM onion method on each structure to calculate the Raman and ROA spectra. In the QM/MM calculations, the sugar is treated in a quantum mechanics level using density functional theory. Instead, waters in contact with the sugar are treated as MM charges, while the rest are modeled using a continuum approach (cosmos). The result is an efficient protocol which ends in a quantitative agreement between the computed and experimental spectra. The developed method allows us to study the conformations of monosaccharides in solution and their anomeric ratio. It can also provide the presence of aggregates in solution or even when considering disaccharides the populations around the glycosidic bonds. As a result, we have direct information about the structure of sugars in solution which is of great interest in biology.