Neutron diffraction and simulation studies of the exocyclic hydroxymethyl conformation of glucose

Mason, Philip E.; Neilson, G. W.; Enderby, J. E.; Saboungi, Marie‐Louise; Cuello, G.J.; Brady, John W.

doi:10.1063/1.2393237

Cited by 35 publications

(42 citation statements)

References 45 publications

(32 reference statements)

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“…24 Mason and co-workers followed up that study with combined MD and neutron diffraction with isotopic substitution experiments, arguing that gg dominates. 25 Despite differences in absolute numbers, the studies agree that gg and gt both contribute significantly to the equilibrium populations, with tg accounting for 10% or less of the population. A host of molecular dynamics (MD) studies of glucose in water reveal increasing agreement between experiment and theoretical models.…”

Section: ■ Introductionmentioning

confidence: 84%

“…Both structures shown are in the gg conformation, in agreement with the most stable conformation reported in most experimental studies. 25 Other low-energy conformations of neat glucose have been enumerated in previous QM studies completed in gas, implicit water, and explicit water. 29,69 The ones shown here are the lowest-energy conformations from among a variety of conformations investigated at the M06-2X/6-311+G(2df,p) level of theory and implicit solvent, including conformations from previous computational and experimental studies.…”

Section: ■ Experimental Methodsmentioning

confidence: 99%

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Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment

Mayes

Tian

Nolte³

et al. 2013

J. Phys. Chem. B

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In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on B-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of Î±-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na + suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na + interacts similarly with a-and B-glucose. ABSTRACT: In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on β-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na + suggests that computational studies of g...

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Section: ■ Introductionmentioning

confidence: 84%

Section: ■ Experimental Methodsmentioning

confidence: 99%

Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment

Mayes

Tian

Nolte³

et al. 2013

J. Phys. Chem. B

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“…On the right is shown the expansion of the MD prediction for the first order difference, along with the contribution the hydrating water makes to this function (blue). 28 …”

Section: Figurementioning

confidence: 99%

Observation of Pyridine Aggregation in Aqueous Solution Using Neutron Scattering Experiments and MD Simulations

et al. 2010

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Neutron Diffraction with Isotopic Substitution (NDIS) experiments have been used to examine the structuring of aqueous solutions of pyridine. A new method is described for extracting the structure factors relating to intermolecular correlations from neutron scattering experiments on liquid solutions of complex molecular species. This approach performs experiments at different concentrations and exploits the intramolecular coordination number concentration invariance (ICNCI) to separate the internal and intermolecular contributions to the total intensities. The ability of this method to deconvolute molecular and intermolecular correlations is tested and demonstrated using simulated neutron scattering results predicted from molecular dynamics simulations of aqueous solutions of the polyatomic solute pyridine in which the inter- and intramolecular terms are known. The method is then implemented using neutron scattering measurements on solutions of pyridine. The results confirm that pyridine shows a significant propensity to aggregate in solution and demonstrate the prospects for the future application of the ICNCI approach to the study of large polyatomic solutes using next-generation neutron sources and detectors.

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“…This heuristic CANDIS approach has been used to successfully determine the conformations of several groups in aqueous solution, 56–58 including the exocyclic hydroxymethyl group D-glucose. 57 No previous neutron diffraction experiments have used such approaches to extract conformational information about a large solute molecule in aqueous solution, and these results serve to demonstrate and validate this newly developed technique.…”

Section: Resultsmentioning

confidence: 97%

“…57 No previous neutron diffraction studies of complex molecular solutes have achieved such specific resolution. The experimental structure factors contain information about both the intramolecular atomic distribution as well as about the distribution of solvent molecules.…”

Section: Resultsmentioning

confidence: 99%

Simulation and Neutron Diffraction Studies of Small Biomolecules in Water

et al. 2010

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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.

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Neutron diffraction and simulation studies of the exocyclic hydroxymethyl conformation of glucose

Cited by 35 publications

References 45 publications

Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment

Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment

Observation of Pyridine Aggregation in Aqueous Solution Using Neutron Scattering Experiments and MD Simulations

Simulation and Neutron Diffraction Studies of Small Biomolecules in Water

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