Theoretical Studies of the Potential Energy Surfaces and Compositions of thed-Aldo- andd-Ketohexoses

N-(1-Deoxy-α-d-tagatopyranos-1-yl)-N-methylaniline (“d-Tagatose-N-methylaniline”)

Tagatosamines form in thermally-processed dairy products and contribute to the foods’ organoleptic and nutritional value. d-Tagatose-N-methylaniline (N-(1-deoxy-d-tagatos-1-yl)-N-methylaniline, 1-deoxy-1-(N-methylphenylamino)-d-tagatose) was synthesized from d-galactose via the Amadori rearrangement. In aqueous solution, it established an anomeric equilibrium consisting of 62.8% α-pyranose, 21.3% β-pyranose, 1.5% α-furanose, 8.1% β-furanose, and 6.2% acyclic keto tautomer. The crystalline α-pyranose anomer of d-tagatose-N-methylaniline adopted the 5C2 chair conformation. All hydroxyl and ring oxygen atoms and the amino nitrogen are involved in an extensive H-bonding network dominated by infinite homodromic chains. The Hirshfeld surface analysis suggests a significant contribution of non-polar intermolecular contacts to the crystal structure.

Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy

Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations. The experimental results of lithiated GlcNAc and GalNAc show a good match to the theoretical spectra of low-energy structures adopting a ⁴ C ₁ chair conformation, consistent with this motif being the dominant conformation in condensed-phase monosaccharides. The epimerization effect upon going to lithiated ManNAc is significant, as in this case the ¹ C ₄ chair conformers give a more compelling match with the experimental results, consistent with their lower calculated energies. A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs (e.g., a ⁴ C ₁ versus ¹ C ₄ ) and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes. Graphical Abstract ᅟ.

Pyranose ring conformations in mono- and oligosaccharides: a combined MD and DFT approach

A two-step computational protocol is proposed to efficiently study the conformational properties of hexopyranoses with a special emphasis on their ring-inversion-properties. By applying it, the errors resulting from overestimating the contribution of the hydrogen bond-rich, low-energy structures that are not abundant in aqueous solutions are avoided.

Collision-induced dissociation of sodiated glucose and identification of anomeric configuration

Difference in dehydration barrier heights results in different branching ratio, a simple and fast method for anomeric configuration identification.

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.

Bimetallic ruthenium-copper nanoparticles embedded in mesoporous carbon as an effective hydrogenation catalyst

Bimetallic ruthenium-copper nanoparticles embedded in the pore walls of mesoporous carbon were prepared via a template route and evaluated in terms of catalytic properties in D-glucose hydrogenation. The existence of bimetallic entities was supported by Ru L3-edge and Cu K-edge X-ray absorption results. The hydrogen spillover effect of the bimetallic catalyst on the hydrogenation reaction was evidenced by the results of both hydrogen and carbon monoxide chemisorptions. The bimetallic catalyst displayed a higher catalytic activity than the single-metal catalysts prepared using the same approach, namely ruthenium or copper nanoparticles embedded in the pore walls of mesoporous carbon. This improvement was due to the changes in the geometric and electronic structures of the bimetallic catalyst because of the presence of the second metal.

Comparison between DFT- and NMR-based conformational analysis of methyl galactofuranosides

Galactofuranose (Galf) residues are found in a number of microbial polysaccharides, and knowledge of their conformation is key for developing a molecular-level understanding of their biological roles. To this end, we studied 180 conformations of methyl α- and β-Galf in aqueous solution (COSMO solvation model) using density functional theory (DFT). We compare the calculated low energy conformations to those determined from the program PSEUROT using (1)H NMR data. The lowest energy ring conformation for methyl α-Galf is (2)E, and this conformer is also the major solution conformation obtained by NMR spectroscopy. For methyl β-Galf, (4)E is the lowest energy ring conformation; however, DFT results do not agree with the solution NMR spectroscopic results. Additionally, we developed Galf-specific Karplus-like equations from these conformations.

On the stabilization of ribose by silicate minerals

The RNA-world theory hypothesizes that early Earth life was based on the RNA molecule. However, the notion that ribose, the sugar in RNA, is unstable still casts a serious doubt over this theory. Recently, it has been found that the silicate-mediated formose reaction facilitates the stabilization of ribose. Using accurate quantum chemical calculations, we determined the relative stability of the silicate complexes of arabinose, lyxose, ribose, and xylose with the intent to determine which would form predominantly from a formose-like reaction. Five stereoisomers were investigated for each complex. The stereoisomers of 2:1 ribose-silicate are the more stable ones, to the extent that the least stable of these is even more stable than the most stable stereoisomer of the other 2:1 sugar-silicate complexes. Thus, thermodynamically, a formose-like reaction in the presence of silicate minerals should preferentially form the silicate complex of ribose over the silicate complex of arabinose, lyxose, and xylose.

A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers

This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the force field to properties that had not been included previously into the parameterization procedure. The new 56A(CARBO) force field is characterized by: (i) the formulation of systematic build-up rules for the automatic generation of force-field topologies over a large class of compounds including (but not restricted to) unfunctionalized polyhexopyranoses with arbritrary connectivities; (ii) the systematic use of enhanced sampling methods for inclusion of experimental thermodynamic data concerning slow or unphysical processes into the parameterization procedure; and (iii) an extensive validation against available experimental data in solution and, to a limited extent, theoretical (quantum-mechanical) data in the gas phase. At present, the 56A(CARBO) force field is restricted to compounds of the elements C, O, and H presenting single bonds only, no oxygen functions other than alcohol, ether, hemiacetal, or acetal, and no cyclic segments other than six-membered rings (separated by at least one intermediate atom). After calibration, this force field is shown to reproduce well the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. As a result, the 56A(CARBO) force field should be suitable for: (i) the characterization of the dynamics of pyranose ring conformational transitions (in simulations on the microsecond timescale); (ii) the investigation of systems where alternative ring conformations become significantly populated; (iii) the investigation of anomerization or epimerization in terms of free-energy differences; and (iv) the design of simulation approaches accelerating the anomerization process along an unphysical pathway.

Permeation of membranes by ribose and its diastereomers

It was recently found that ribose permeates membranes an order of magnitude faster than its diastereomers arabinose and xylose (Sacerdote, M. G.; Szostak, J. W. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6004). On this basis it was hypothesized that differences in membrane permeability to aldopentoses provide a mechanism for preferential delivery of ribose to primitive cells for subsequent selective incorporation into nucleotides and their polymers. However, the origins of these unusually large differences have not been well understood. We address this issue in molecular dynamics simulations combined with free energy calculations. It is found that the free energy of transferring ribose from water to the bilayer is lower by 1.5-2 kcal/mol than the barrier for transferring the other two aldopentoses. The calculated and measured permeability coefficients are in excellent agreement. The sugar structures that permeate the membrane are beta-pyranoses, with a possible contribution of the alpha-anomer for arabinose. The furanoid form of ribose is not substantially involved in permeation, even though it is non-negligibly populated in aqueous solution. The differences in free energy of transfer between ribose and arabinose or xylose are attributed, at least in part, to stronger highly cooperative, intramolecular interactions between consecutive exocyclic hydroxyl groups, which are stable in nonpolar media but rare in water. Water/hexadecane partition coefficients of the sugars obtained from separate molecular dynamics simulations correlate with the calculated permeability coefficients, in qualitative agreement with the Overton rule. The relevance of our calculations to understanding the origins of life is discussed.

Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran

High level ab initio computations in vacuum and with the IEFPCM implicit solvent model are carried out on 5-(hydroxymethyl)tetrahydropyran to investigate the effects of water on the exocyclic torsional surface. Rotamer populations evaluated from the omega(C-C-C-O), theta(C-C-C-O) solvent surface agree almost quantitatively with experimental values for the closely related methyl 4-deoxy-alpha-D-xylohexopyranoside. Potentials of mean force obtained from the two surfaces show substantial solvent stabilization of the TG (omega = 180 +/- 60 degrees) rotamer and the barriers at omega= 120 and 240 degrees but solvent destabilization at the cis barrier (omega = 0 degrees). Natural bond orbital analyses indicate that energetics of these effects are largely explained by overstabilization of the vacuum GT (omega= 60 +/- 60 degrees) and GG (omega = 300 +/- 60 degrees) rotamers. Solvent stabilization of theta conformations provides entropic stabilization.

Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach

In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H...O interaction energies in sugar molecules using the recently developed molecular tailoring approach (MTA). The estimated H-bond energies are in the range of 1.2-4.1 kcal mol(-1). It is seen that the OH...O equatorial-equatorial interaction energies lie between 1.8 and 2.5 kcal mol(-1), with axial-equatorial ones being stronger (2.0-3.5 kcal mol(-1)). The strongest bonds are nonvicinal axial-axial H-bonds (3.0-4.1 kcal mol(-1)). This trend in H-bond energies is in agreement with the earlier reports based on the water-water H-bond angle, solvent-accessible surface area (SASA), and (1)H NMR analysis. The contribution to the H-bond energy from the cooperativity is also estimated using MTA. This contribution is seen to be typically between 0.1 and 0.6 kcal mol(-1) when H-bonds are a part of a relatively weak equatorial-equatorial H-bond network and is much higher (0.5-1.1 kcal mol(-1)) when H-bonds participate in an axial-axial H-bond network.

Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field

The present article reports long timescale (200 ns) simulations of four beta-D-hexopyranoses (beta-D-glucose, beta-D-mannose, beta-D-galactose and beta-D-talose) using explicit-solvent (water) molecular dynamics and vacuum stochastic dynamics simulations together with the GROMOS 45A4 force field. Free-energy and solvation free-energy differences between the four compounds are also calculated using thermodynamic integration. Along with previous experimental findings, the present results suggest that the formation of intramolecular hydrogen-bonds in water is an 'opportunistic' consequence of the close proximity of hydrogen-bonding groups, rather than a major conformational driving force promoting this proximity. In particular, the conformational preferences of the hydroxymethyl group in aqueous environment appear to be dominated by 1,3-syn-diaxial repulsion, with gauche and solvation effects being secondary, and intramolecular hydrogen-bonding essentially negligible. The rotational dynamics of the exocyclic hydroxyl groups, which cannot be probed experimentally, is found to be rapid (10-100 ps timescale) and correlated (flip-flop hydrogen-bonds interconverting preferentially through an asynchronous disrotatory pathway). Structured solvent environments are observed between the ring and lactol oxygen atoms, as well as between the 4-OH and hydroxymethyl groups. The calculated stability differences between the four compounds are dominated by intramolecular effects, while the corresponding differences in solvation free energies are small. An inversion of the stereochemistry at either C(2) or C(4) from equatorial to axial is associated with a raise in free energy. Finally, the particularly low hydrophilicity of beta-D-talose appears to be caused by the formation of a high-occurrence hydrogen-bonded bridge between the 1,3-syn-diaxial 2-OH and 4-OH groups. Overall, good agreement is found with available experimental and theoretical data on the structural, dynamical, solvation and energetic properties of these compounds. However, this detailed comparison also reveals some discrepancies, suggesting the need (and providing a solid basis) for further refinement.

Prediction of the 1H and 13C NMR Spectra of α-d-Glucose in Water by DFT Methods and MD Simulations

We have applied computational protocols based on DFT and molecular dynamics simulations to the prediction of the alkyl 1H and 13C chemical shifts of alpha-d-glucose in water. Computed data have been compared with accurate experimental chemical shifts obtained in our laboratory. 13C chemical shifts do not show a marked solvent effect. In contrast, the results for 1H chemical shifts provided by structures optimized in the gas phase are only fair and point out that it is necessary to take into account both the flexibility of the glucose structure and the strong effect exerted by solvent water thereupon. Thus, molecular dynamics simulations were carried out to model both the internal geometry as well as the influence of solvent molecules on the conformational distribution of the solute. Snapshots from the simulation were used as input to DFT NMR calculations with varying degrees of sophistication. The most important factor that affects the accuracy of computed 1H chemical shifts is the solute geometry; the effect of the solvent on the shielding constants can be reasonably accounted for by self-consistent reaction field models without the need of explicitly including solvent molecules in the NMR property calculation.

Energetics of xylose decomposition as determined using quantum mechanics modeling

The decomposition of xylose has been studied using quantum mechanical calculations supported by NMR data. Proposed mechanisms for the decomposition of xylose have been investigated by obtaining the structures and energies of transition states and products. The intent of this study was to understand the experimentally observed formation of furfural and formic acid that occurs during the decomposition of xylose in mildly hot acidic solutions. A mechanism of furfural formation involving the opening of the pyranose ring and subsequent dehydration of the aldose was compared to a direct intramolecular rearrangement of the protonated pyranose. Energies were determined using CBS-QB3, and it was shown that the barriers for dehydration of the aldose were high compared to intramolecular rearrangement. This result suggests that the latter mechanism is a more likely mechanism for furfural formation. The intramolecular rearrangement step results from protonation of xylose at the O2 hydroxyl group. In addition, it has been shown that formic acid formation is a likely result of the protonation of xylose at the O3 hydroxyl group. Finally, solvation of xylose decomposition was studied by calculating energy barriers for xylose in selected water clusters. The mechanisms proposed here were supported in part by 13C-labeling studies using NMR.

DFT study of α- and β-d-allopyranose at the B3LYP/6-311++G∗∗ level of theory

One hundred and two conformations of alpha- and beta-D-allopyranose, the C-3 substituted epimer of glucopyranose, were geometry optimized using the density functional, B3LYP, and the basis set, 6-311++G **. Full geometry optimization was performed on different ring geometries and on the hydroxymethyl rotamers (gg/gt/tg). Analytically derived Hessians were used to calculate zero point energy, enthalpy, and entropy. The lowest energy and free energy conformation found is the alpha-tg(g-)-4C1-c conformation, which is only slightly higher in electronic (approximately 0.2 kcal/mol) and free energy than the lowest energy alpha-D-glucopyranose. The in vacuo calculations showed a small (approximately 0.3 kcal/mol) energetic preference for the alpha- over the beta-anomer for allopyranose in the 4C1 conformation, whereas in the 1C4 conformation a considerable (approximately 1.6 kcal/mol) energetic preference for the beta- over the alpha-anomer for allopyranose was encountered. The results are compared to previous aldohexose calculations in vacuo. Boat and skew forms were found that remained stable upon gradient optimization although many starting boat conformations moved to other skew forms upon optimization. As found for glucose, mannose, and galactose the orientation and interaction of the hydroxyl groups make the most significant contributions to the conformation/energy relationship in vacuo. A comparison of different basis sets and density functionals is made in the Discussion section, confirming the appropriateness of the level of theory used here.

An investigation of the pyranose ring interconversion path of α-l-idose calculated using density functional theory

The interconversion pathways of the pyranose ring conformation of alpha-L-idose from a (4)C1 chair to other conformations were investigated using density functional calculations. From these calculations, four different ring interconversion paths and their transition state structures from the (4)C1 chair to other conformations, such as B(3,O), and (1)S3, were obtained. These four transition-state conformations cover four possible combinations of the network patterns of the hydroxyl group hydrogen bonds (clockwise and counterclockwise) and the conformations of the primary alcohol group (tg and gg). The optimized conformations, transition states, and their intrinsic reaction coordinates (IRC) were all calculated at the B3LYP/6-31G** level. The energy differences among the structures obtained were evaluated at the B3LYP/6-311++G** level. The optimized conformations indicate that the conformers of (4)C1, (2)S(O), and B(3,O) have similar energies, while (1)S3 has a higher energy than the others. The comparison of the four transition states and their ring interconversion paths, which were confirmed using the IRC calculation, suggests that the most plausible ring interconversion of the alpha-L-idopyranose ring occurs between (4)C1 and B(3,O) through the E3 envelope, which involves a 5.21 kcal/mol energy barrier.

Fluoro-substitution effects in deoxyfluoro-d-glucose derivatives: random conformational search and quantum chemical calculation

The effect of substitution by the fluorine atom at different positions of D-glucose was investigated by quantum chemical calculation of the low-energy conformers. These were obtained through the Random conformational search method. The geometries of conformers were optimized at the RHF/6-31(d) level, then reoptimization and vibrational analysis were performed at the B3LYP/6-31+G(d) level. Single-point energies were calculated at the B3LYP/6-311++G(2d,2p) level. The free energies of solvation in water were calculated utilizing the AM1-SM5.4 solvation model. For all substitution positions, the ring conformation does not change much, and the pyranoid 4C1 conformers are dominant, while variations in the substitution site result in different effects in the network of hydrogen bonds, anomeric effect, the solvation free energy, and the ratio of alpha- and beta-anomers.

Gas-phase structures, rotational barriers, and conformational properties of hydroxyl and mercapto derivatives of cyclohexa-2,5-dienone and cyclohexa-2,5-dienthione

The rotational barriers and conformational properties of the hydroxyl and mercapto groups attached to the alpha and beta positions of cyclohexa-2,5-dione and cyclohexa-2,5-dienthione have been studied at the B3LYP/ 6-311++G(d,p) level of theory. The results show that the conformational preferences of these studied systems are the result of a subtle interplay between different competing effects (conjugation, hyperconjugation, and steric repulsions). The applicability of the density functional theory reactivity indices and the maximum hardness principle for the present systems has been analyzed.

Infrared spectroscopy used to evaluate glycosylation of proteins

Infrared (IR) spectroscopy is used for studying the carbohydrate moieties of glycosylated proteins. IR spectra of mono- and disaccharides in the fingerprint region are specific to each sugar and to the environment of the sugar molecules (i.e., aqueous solution or anhydrous glass phase). The IR spectra of glycosylated proteins (mucin, soybean peroxidase, collagen IV, and avidin) were compared with those of the constituent sugars and cytochrome c (a protein with no glycosylation). Our results demonstrate that the IR absorption spectra of glycosylated proteins show distinct absorption bands for the sugar moiety, the protein amide group, and water. Therefore, IR can be used to detect glycosylation.