Hydrogen-bond geometry around sugar molecules: comparison of crystal statistics with simulated aqueous solutions

Crystallization Behavior and Crystallographic Properties of dl-Arabinose and dl-Xylose Diastereomer Sugars

Natural sugar molecules such as xylose and arabinose exhibit sweetness profiles similar to sucrose, which makes them a valuable alternative in low-calorie foods as well as excipients or cocrystallization agents in pharmaceutical formulations. Xylose and arabinose are also chiral diastereomers that can exhibit specific crystallization behavior. In this work, the solid-state landscapes of the chiral pairs of both xylose and arabinose have been investigated to determine whether racemic compounds or conglomerates are formed. Furthermore, single crystals of xylose and arabinose have been grown and characterized by X-ray diffraction and optical microscopy to study their crystallographic properties and relate them to the crystallization behavior. Differential scanning calorimetry (DSC) measurements were used to determine the phase diagrams of the two analyzed chiral systems. The solubilities of the different solid forms of xylose and arabinose were measured in different solvent mixtures by a thermogravimetric method. An analysis was conducted to assess the main thermodynamic parameters and the activity coefficients of the compounds in solution. Finally, slurry experiments in a 50:50 w/w ethanol/water solvent have also been performed to determine the relative stability of each solid form and the kinetics of transformation in this solvent mixture. It was found that dl-arabinose crystallizes as a stable racemic compound, which transforms quickly from its constituent enantiomers when in solution; whereas d- and l-xylose molecules crystallize separately as a conglomerate.

Glycan OH Exchange Rate Determination in Aqueous Solution: Seeking Evidence for Transient Hydrogen Bonds

Hydrogen bonds (Hbonds) are important stabilizing forces in biomolecules. However, for glycans in aqueous solution, direct NMR detection of Hbonds is elusive because of their transient nature. Here, we present Isotope-based Natural-abundance TOtal correlation eXchange SpectroscopY (INTOXSY), a new ¹H-¹³C heteronuclear single quantum coherence-total correlation spectroscopy based method, to extract OH groups' exchange rate constants (k_ex) for molecules in natural ¹³C abundance and show that OH Hbonds can be inferred from "slower" H/D k_ex. We evaluate k_ex measured with INTOXSY in light of those extracted with line-shape analysis. Subsequently, we use a set of common glycans to establish a k_ex reference basis set and to infer the existence of transient Hbonds involving OH donor groups. Then, we report k_ex values for a series of mono- and disaccharides, as well as for oligosaccharides sialyl Lewis X and β-cyclodextrin, and compare the results with those from the reference set to extract Hbond information. Finally, we utilize NMR experimental data in conjunction with molecular dynamics simulations to establish donor and acceptor Hbond pairs. Our exchange rate measurements indicate that OH/OD exchange rates, k_HD, values <10 s^-1 are consistent with transient Hbond OH groups and potential acceptor groups can be uncovered through MD simulations.

Stability of conformationally locked free fructose: theoretical and computational insights

Total stabilization is governed by three predominant factors viz. the sum of energy of all H-bonds, ring strain and anomeric stabilization.

Simulation and Neutron Diffraction Studies of Small Biomolecules in Water

Modern biophysics has benefited greatly from the use of X-ray and neutron diffraction from ordered single crystals of proteins and other macromolecules to give highly detailed pictures of these molecules in the solid state. However, the most biologically relevant environments for these molecules are liquid solutions, and their liquid state properties are sensitive to details of the liquid structuring. The best experimental method for studying such structuring is also neutron diffraction, but of course, the inherent disorder of the liquid state means that these experiments cannot hope to achieve the level of informational detail available from single crystal diffraction. Nonetheless, recent advances in neutron beam intensity, beam stability, and detector sensitivity mean that it should be possible, at least in principle, to use such measurements to extract information about structuring in much more complex systems than have previously been studied. We describe a series of neutron diffraction studies of isotopically labeled molecules in aqueous solution which, when combined with results from computer simulations, can be used to extract conformational information of the hydration of the molecules themselves, essentially opening up new avenues of investigation in structural biology.

Structure of aqueous glucose solutions as determined by neutron diffraction with isotopic substitution experiments and molecular dynamics calculations

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to examine the structuring of solvent around d-glucose in aqueous solution. As expected, no significant tendency for glucose molecules to aggregate was found in either the experiments or the simulation. To the extent that solute pairing does occur as the result of the high concentration, it was found to take place through hydroxyl-hydroxyl hydrogen bonds, in competition with water molecules for the same hydrogen-bonding sites. A detailed analysis of the hydrogen-bonding patterns occurring in the simulations found that the sugar hydroxyl groups are more efficient hydrogen bond donors than acceptors. From the comparison of the MD and NDIS data, it was found that while the modeling generally does a satisfactory job in reproducing the experimental data the force fields may produce sugar rings that are too rigid and thus may require future revisions.

QM/MM study of d-fructose in aqueous solution

The QM/MM molecular dynamics methodology was applied to the study of the two main D-fructose tautomers present in aqueous solution, beta-D-fructofuranose and beta-D-fructopyranose. The solute was treated at the AM1 semi-empirical level, and for the solvent water molecules we used the TIP3P potential. We analyzed the structure of the water molecules around the hydroxyl groups to explain the differences in sweet taste between the two tautomers.

Circular Hydrogen Bond Networks on the Surface of β-Ribofuranose in Aqueous Solution

This paper examines the hydration structure on the surface of beta-ribofuranose in aqueous solution, using the ab initio molecular dynamics method. In particular, we focus on circular hydrogen bond networks involving two ribofuranose oxygens and three water molecules. In our simulations, the circular hydrogen bond networks near the ring oxygen of beta-ribofuranose are found to be significantly influenced by the orientation of the hydroxymethyl group. The arrangements of hydrogen bonds observed in the circular hydrogen bond networks are both homodromic and antidromic. To explain these observations, we analyze the electronic properties of the first-hydration-shell water molecules and the OH groups of beta-ribofuranose, using the centers of their maximally localized Wannier functions. The dipole moments of the proton-accepting first-hydration-shell water molecules in our well-defined circular hydrogen bond networks are found to increase by about 0.3 D compared with that of liquid water, indicating the relatively strong polarization effects created by the interactions between the OH groups of the solute and the surrounding water molecules. Our analysis also implies that circular H-bond networks cannot be fully explained from a simple geometrical point of view.

Studies of Disaccharide Solvation—Molecular Dynamics versus HPLC Retention

Molecular dynamics simulations have been used to assess the conformational behaviour of seven disaccharides in aqueous solution. Solvation decreased the overall conformational fluctuations of the sugars, compared to in vacuo simulations using a high dielectric constant. The most significant finding was a linear correlation between the experimental chromatographic retention parameter K´ and a molecular modelling parameter based on the next-nearest oxygen–oxygen distances in the disaccharides. The results support previous proposals for a stereospecific hydration model for carbohydrates and demonstrate the utility of a combined experimental/molecular modelling approach to its study.

Theoretical Study of the Relative Stability of Rotational Conformers of α and β-d-Glucopyranose in Gas Phase and Aqueous Solution

The alpha-beta anomer energy difference and the stability of 10 rotamers of counterclockwise D-glucopyranose were studied in vacuo and in aqueous solution at the B3LYP/6-31+G(d,p) level. To obtain the solute charge distribution and the solvent structure around it, we used the averaged solvent electrostatic potential from molecular dynamics method, ASEP/MD, which alternates molecular dynamics and quantum mechanics calculations in an iterative procedure. The main characteristics of the anomeric equilibrium, both in vacuo and in solution, are well reproduced. The relative stability of the different anomers is related to the availability of the free pairs of electrons in the anomeric oxygen to interact with the water molecules. The influence of solvation in the conformer equilibrium is also analyzed.

Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs

Free energies for stacking of unpaired nucleotides (dangling ends) at the termini of oligoribonucleotide Watson-Crick helixes (DeltaG(0)37,stack) depend on sequence for 3' ends but are always small for 5' ends. Here, these free energies are correlated with stacking at helix termini in a database of 34 RNA structures determined by X-ray crystallography and NMR spectroscopy. Stacking involving GA pairs is considered separately. A base is categorized as stacked by its distance from (</=4.0 A), angle with (</=30 degrees), and overlap with the terminal helix base-pair. A base is unstacked if it does not satisfy one or more of these criteria. Of the 36 unpaired bases in sequences with DeltaG(0)37,stackmore favorable than -0.7 kcal/mol, 30 (83 %) are stacked on the adjacent base-pair, indicating a propensity for such sequences to stack in the 3D structure. Structures containing the strongly stacked sequence [sequence: see text] show that the amino group of C closely overlaps the carbonyl-4 of U. Thermodynamic measurement of U stacking on a 2-pyrimidinone-guanine base-pair, where the amino group of C is replaced by hydrogen, suggests that interactions with the cytosine amino group contribute approximately 0.5 kcal/mol to DeltaG(0)37,stack. For GA mismatches at helix termini, the nucleotide at the 3' helix end is always stacked, and the nucleotide at the 5' end is stacked in almost 90 % of occurrences. In available structures, non-Watson-Crick paired bases 3' to an imino-hydrogen bonded GA are also always stacked; the GA provides a large platform for favorable stacking. For the 56 sequences associated with DeltaG(0)37,stackless favorable than -0.4 kcal/mol, 19 (34 %) are stacked; these sequences have a propensity for not stacking on adjacent base-pairs. Phylogenetic conservation of weakly stacking sequences at 3' ends may be a predictor of a backbone turn.

A 1H-NMR and MD study of intramolecular hydrogen bonds in methyl beta-cellobioside

The existence of an HO-3...O-5' intramolecular hydrogen bond in methyl beta-cellobioside in solution in Me2SO-d6 and H2O-CD3OD (4:1 w/w) was studied by 500-MHz 1H-NMR spectroscopy and MD simulations. Temperature coefficients for the chemical shift of the hydroxyl resonances in these solvents were determined and the rates of proton exchange in the latter solvent were obtained from NOE data. With H2O-CD3OD as the solvent, the HO-3...O-5' hydrogen bond was insignificant, but its presence in Me2SO-d6 was confirmed.