Conformational Preference and Chiroptical Response of Carbohydratesd-Ribose and 2-Deoxy-d-ribose in Aqueous and Solid Phases

Abstract

This work targets the structural preferences of D-ribose and 2-deoxy-D-ribose in water solution and solid phase. A theoretical DFT (B3LYP and M06-2X) and MP2 study has been undertaken considering the five possible configurations (open-chain, α-furanose, β-furanose, α-pyranose, and β-pyranose) of these two carbohydrates with a comparison of the solvent treatment using only a continuum solvation model (PCM) and the PCM plus one explicit water molecule. In addition, experimental vibrational studies using both nonchiroptical (IR-Raman) and chiroptical (VCD) techniques have been carried out. The theoretical and experimental results show that α- and β-pyranose forms are the dominant configurations for both compounds. Moreover, it has been found that 2-deoxy-D-ribose presents a non-negligible percentage of open-chain forms in aqueous solution, while in solid phase this configuration is absent.

Understanding the Aldo‐Enediolate Tautomerism of Glycolaldehyde in Basic Aqueous Solutions

“…Carbohydrates experiment many fundamentalp rocesses including pseudorotation, [2] mutarotation, [3] and glycosylation; [4] however,t he literaturer emains unclear concerning the isomerizationp rocess, which has its basis in the aldo-enediolt automerism. Fedoroň ko et al [5] studied,p olarographically,the kinetics of enolization of glycolaldehyde and methoxyacetaldehyde in acid (HCl at 30-60 8C) and alkaline (NaOH at 20-40 8C) media.…”

“…From the values obtained for the rate constants,t hey observedt hat the enolization of glycolaldehydei na cid medium is much slower than in basic medium. Furthermore, Kobayashi et al [6] analyzed the far-IR (FIR), IR andR amans pectra of glycolaldehyde in the solid phase, in melted form and in fresh saturated H 2 O, D 2 O, DMSO and DMSO-d 6 solutions, observing (in the DMSO spectrum) that several new bands appeared five days after preparation of the solution. These bands were attributed to the dissociation of dimeric molecules into monomeric ones.…”

“…The addition of hydrochloric acid to the aqueous solution did not result in any noticeable change in the carbonyl absorption band. In addition, Collinsa nd George [8] performed NMR studies on glycolaldehyde at room temperature in D 2 Os olution, demonstrating the presence of at least four different molecular species: 70 %h ydrated aldehyde, 4% aldehyde form, and 26 %d imers (9 %2 ,5-dihydroxy-1,4-dioxane and 17 %2 -hydroxymethyl-4-hydroxy-1,3-dioxolane). More recently,t hese results were supported by Yaylayan and co-workers [9] in as tudy of the mechanism of dissociation of glycolaldehyded imers in different solvents and at different pH values and temperatures by meanso f IR spectroscopy.T hey tentatively assigned ab and that appeared at 1703 cm À1 to the presence of enediol, which increased during the heating cycle and decreased during the cooling cycle.…”

Mass balance and metabolite profiling of 14C-guadecitabine in patients with advanced cancer

“…4, dashed lines). [13,17,18] The presence of α-decitabine in urine could be confirmed using a stable isotope-labeled internal standard of decitabine, containing a mixture of αand ßdecitabine ( Supplementary Fig. 1).…”

“…It is known that deoxyribose can be interconverted to multiple isoforms at physiological conditions, and it is therefore hypothesized that αand ß-decitabine are converted to these isoforms in-vivo as well. [17,22,23] Using radioactivity analysis, these structures could not be identified, as the proportional presence of ß-decitabine itself and its isomers were a negligible part of the excreted metabolites in urine and was below the limit of quantification. However, the identification of these structures using a more sensitive LC-MS/MS approach gave additional insight into the metabolic pathway of guadecitabine and ß-decitabine.…”