Acyclic forms of aldohexoses and ketohexoses in aqueous and DMSO solutions: conformational features studied using molecular dynamics simulations

Abstract

The molecular properties of aldohexoses and ketohexoses are usually studied in the context of their cyclic, furanose or pyranose structures which is due to the abundance of related tautomeric forms in aqueous solution. We studied the conformational features of a complete series of D-aldohexoses (D-allose, D-altrose, D-glucose, D-mannose, D-gulose, d-idose, D-galactose and D-talose) and D-ketohexoses (D-psicose, D-fructose, D-sorbose and D-tagatose) as well as of L-psicose by using microsecond-timescale molecular dynamics in explicit water and DMSO with the use of enhanced sampling methods. In each of the studied cases the preferred conformation corresponded to an extended chain structure; the less populated conformers included the quasi-cyclic structures, close to furanose rings and common for both aldo- and ketohexoses. The orientational preferences of the aldehyde or ketone groups are correlated with the relative populations of anomers characteristic of cyclic aldo- and ketohexoses, respectively, thus indicating that basic features of anomeric equilibria are preserved even if hexose molecules are not in their cyclic forms. No analogous relationship is observed in the case of other structural characteristics, such as the preferences of acyclic molecules to form either the furanose-or pyranose-like structures or maintaining the chair-like geometry of pseudo-pyranose rings.

Mechanistic Insights into the Brønsted Acid-Catalyzed Dehydration of β-d-Glucose to 5-Hydroxymethylfurfural under Ambient and Subcritical Conditions

“…The reverse reaction R1 → G was simulated by performing two independent simulations ( R1 → G1 and G1 → G ), as the direct conversion of R1 to G could not be achieved in our simulations. The presence of metastable conformations such as G1 is consistent with previous computational studies . It should be noted that step G1 → G is already part of pathway Cy2 .…”

“…The presence of metastable conformations such as G1 is consistent with previous computational studies. 135 It should be noted that step G1 → G is already part of pathway Cy2. The reverse reaction F2 → F1b was not simulated here because the relative free energy of F2 is known from the cyclic pathways.…”

A GROMOS Force Field for Furanose-Based Carbohydrates

“…The magnitude of discrepancy observed in the case of the present study is in line with those observed previously for aldohexopyranoses, 15,70 ketohexopyranoses, aldopentofuranoses, and deoxy-and dideoxyaldopentopyranoses 59 as well as for the indirect results concerning acyclic forms of aldo-and ketohexoses. 84 In conclusion, the present force field can be used to study the anomeric equilibrium of furanoses; however, some additional refinements (of character and magnitude dependent on the compound of interest) may be necessary to increase the accuracy of calculations.…”

Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: a molecular dynamics simulation study

“…† The ATB generated parameters were found to be reliable and have been widely used in several current studies. [48][49][50][51][52][53] However, the effectiveness of ATB parameters was also justied by calculating the transport properties (i.e. self-diffusion coefficient), structural properties (RDF and number of hydrogen bonds) and thermodynamic properties (density) of the TMAO box, and the results were compared with the Shea force eld 54 and the united atom force eld (generated from ATB) of TMAO as a benchmark test; 55 these are reported in the ESI.…”