Factors controlling relative stability of anomers and hydroxymethyl conformers of glucopyranose

Barrows, Susan E.; Storer, Joey W.; Cramer, Christopher J.; French, Alfred D.; Truhlar, Donald G.

doi:10.1002/(sici)1096-987x(19980730)19:10<1111::aid-jcc1>3.0.co;2-p

Cited by 124 publications

(181 citation statements)

References 74 publications

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“…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. 70−76 At 298 K with M06-2X/6-311+G(2df,p) and implicit solvent, the α-glucose conformation is 0.32 kcal/mol lower in Gibbs free energy than the β conformation.…”

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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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: ■ 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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“…12 The HF/ 6-31G(d) and cc-pVDZ results provide quite good relative energies that are close to the results of the most expensive MP2 calculations. 14 Further increase of the basis set with the HF level of theory up to cc-pVTZ or cc-pV T QZ cause an opposite error. that is, destabilizing the 1 C 4 conformers (up to 6-10 kcal/mol).…”

Section: Introductionmentioning

confidence: 99%

Ab Initio Study of Lowest-Energy Conformers of Lewis X (Le^x) Trisaccharide

2000

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This paper presents the first ab initio conformational study of the Gal--1,4-[Fuc-R-1,3]-GlcNAc--OCH3 and Gal--1,4-[Fuc-R-1,3]-GlcNAc--OH trisaccharides (Lewis x) in the gas phase. Their lowest-energy conformers were selected first by the MM2*-SUMM conformational search technique. MM2* relative energies do not follow the same order for the two similar compounds. The molecular geometries and energies of the lowest-energy rotamers (7 of the acetal and 11 of the hemiacetal) were further analyzed at the HF/6-31G(d) level of theory. The ab initio method yields the same energetic order for the rotamers of the two molecules with considerably larger energetic differences for the first 7 rotamers: the MM2* method provides 0.3-0.5 kcal/mol, whereas the HF/6-31G(d) method provides 4.5 kcal/mol. In the most stable MM2* structures the hydrogen-bonded chains of galactose (in counterclockwise direction) and fucose (in clockwise direction) are not connected. The Gal(O6H) is a hydrogen bond donor (in clockwise direction) to the O3 glycosidic oxygen of GlcNAc. The Fuc(O2H)f(OdC)GlcNAc interaction connects the fucose and GlcNAc. In contrast, the most stable HF/6-31G(d) structure has a long chain of seven ordered hydrogen bonds including a Gal(O6H)f(O3)Fuc interaction (with clockwise hydrogen-bonded chain in galactose and fucose). The torsion angles for Fuc-R-1,3-GlcNAc and Gal--1,4-GlcNAc glycosidic bonds agree well in the solid, liquid, and gas phases. For example there is a rather good overlap between the GlcNAc moiety of one of the X-ray structures and the most similar HF/6-31G(d) structure. The stacking of the fucose and galactose moieties is similar. The orientations of the hydroxyl groups are usually different, as they are influenced by intramolecular hydrogen bonding in the gas-phase Hartree-Fock structure versus intermolecular hydrogen bonding in the solid-phase X-ray structure.

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“…[10][11][12][13] Earlier studies have found that the HF/6-31G(d) and cc-pVDZ results provide quite good relative energies for monosaccharides that are close to the results of the most expensive calculations. 14 This is discussed in our previous paper on Le x . 7 Barrows et al 14 summarized the performance of the best MM methods for energies of D-glucose rotamers and they have found that HF/ 6-31G(d) method is clearly superior compared to any MM parametrization.…”

Section: Introductionmentioning

confidence: 87%

“…[15][16][17][18] The earlier results showed that the HF/6-31G(d) equilibrium molecular geometries might differ noticeably from equilibrium molecular geometries calculated at correlated (mostly MP2 or GGA-DFT) levels of theory. 11,14 However, these geometry variations result in small changes in the relative energies. For example, when the optimized HF/6-31G(d) geometries of D-glucose rotamers are subsequently reoptimized using various correlation methods and basis sets, those initial and final energies differ by only 0.0-0.2 kcal/mol.…”

Section: Introductionmentioning

confidence: 99%

“…However, different methods and basis sets result in variations of 5-10 kcal/mol or more in the relative energies of different members of the set of conformers with or without geometry reoptimization. 11,14 In the present study, we compare the conformational space of the four molecules shown in Figure 1. The conformational space of III (1,2-cyclohexanediol derivative) is considerably simpler than that of the Le x (531 441 rotamers vs 28 697 814 possible rotamers).…”

Section: Introductionmentioning

confidence: 99%

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Ab Initio Conformational Study of Two Lewis X Analogues

Csonka

Sosa

2000

J. Phys. Chem. A

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This paper presents the first ab initio conformational study for analogues of a histo-blood group carbohydrate antigen, Le x (Gal--1,4-[Fuc-R-1,3]-GlcNAc). In these analogues, the GlcNAc group of Le x was replaced by a cyclohexanediol or an ethanediol group. The lowest energy conformers of these molecules were first found by the MM2*-SUMM conformational search technique. The molecular geometries and energies of lowest energy rotamers (within a 3 kcal/mol energy window) were further analyzed at the HF/6-31G(d) level of theory. This study provides a detailed description of the hydrogen-bonding properties of the low-energy conformers yielded by the MM2* and ab initio methods. The key torsion angles for Fuc-R-1,3-GlcNAc and Gal--1,4-GlcNAc glycosidic bonds in Le x mostly keep their value in the different environments (solid, liquid, and gas phase). The ab initio torsion angles agree considerably better with the experimental results than the MM2* results. Another essential difference between the MM2* and ab initio results is that the latter provide better differentiation of the rotamers. Complexes with selectins introduced varying levels of distortion of Le x , with the most tightly bound structure being most distorted. Nonstacked rotamers occur only once among the rotamers of 1,2-cyclohexanediol analogue, and that rotamer is not particularly stable (∆E ) 2.3 kcal/ mol). However, such kind of rotamers are more frequent among the rotamers of 1,2-ethanediol analogue. This clearly shows that while the conformational space of 1,2-cyclohexanediol analogue is rather similar to that of Le x , the conformational space of 1,2-ethanediol analogue is considerably less similar.

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Factors controlling relative stability of anomers and hydroxymethyl conformers of glucopyranose

Cited by 124 publications

References 74 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

Ab Initio Study of Lowest-Energy Conformers of Lewis X (Le^x) Trisaccharide

Ab Initio Conformational Study of Two Lewis X Analogues

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Factors controlling relative stability of anomers and hydroxymethyl conformers of glucopyranose

Cited by 124 publications

References 74 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

Ab Initio Study of Lowest-Energy Conformers of Lewis X (Lex) Trisaccharide

Ab Initio Conformational Study of Two Lewis X Analogues

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Product

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Ab Initio Study of Lowest-Energy Conformers of Lewis X (Le^x) Trisaccharide