B3LYP/6-311++G** study of alpha- and beta-D-glucopyranose and 1,5-anhydro-D-glucitol: 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations

A True Reverse Anomeric Effect Does Exist After All: A Hydrogen Bonding Stereocontrolling Effect in 2-Iminoaldoses

The reverse anomeric effect is usually associated with the equatorial preference of nitrogen substituents at the anomeric center. Once postulated as another anomeric effect with explanations ranging from electrostatic interactions to delocalization effects, it is now firmly considered to be essentially steric in nature. Through an extensive research on aryl imines from 2-amino-2-deoxyaldoses, spanning nearly two decades, we realized that such substances often show an anomalous anomeric behavior that cannot easily be rationalized on the basis of purely steric grounds. The apparent preference, or stabilization, of the β-anomer takes place to an extent that not only neutralizes but also overcomes the normal anomeric effect. Calculations indicate that there is no stereoelectronic effect opposing the anomeric effect, resulting from the repulsion between electron lone pairs on the imine nitrogen and the endocyclic oxygen. Such data and compelling structural evidence unravel why the exoanomeric effect is largely inhibited. We are now confident, as witnessed by 2-iminoaldoses, that elimination of the exo-anomeric effect in the α-anomer is due to the formation of an intramolecular hydrogen bond between the anomeric hydroxyl and the iminic nitrogen, thereby accounting for a true electronic effect. In addition, discrete solvation may help justify the observed preference for the β-anomer.

A first-principles exploration of the conformational space of sodiated pyranose assisted by neural network potentials

Sampling the conformational space of monosaccharides using the first-principles methods is important and as a database of local minima provides a solid base for interpreting experimental measurements such as infrared photo-dissociation (IRPD) spectroscopy or collision-induced dissociation (CID). IRPD emphasizes low-energy conformers and CID can distinguish conformers with distinct reaction pathways. A typical computational approach is to engage empirical or semi-empirical methods to sample the conformational space first, and only selected minima are reoptimized at first-principles levels. In this work, we propose a computational scheme to explore the configurational space of 12 types of sodiated pyranoses with the assistance of a neural network potential (NNP). We demonstrated that it is possible to train an NNP based on the density functional calculations extracted from a previous study on sodiated glucose (Glc), galactose (Gal), and mannose (Man). This NNP yields a better description of the other five types of aldohexoses than the four types of ketohexoses. We further show that such a discrepancy in the accuracy of NNP can be resolved by an active learning scheme where the NNP model is engaged in generating the data and has itself updated. Through this iterative process, we can locate more than 17 000 distinct local minima at the B3LYP/6-311+G(d,p) level and an NNP with an accuracy of 1 kJ mol^-1 was created, which can be used for further studies.

Between Two Chairs: Combination of Theory and Experiment for the Determination of the Conformational Dynamics of Xylosides

The conformational properties of monosaccharides constitute fundamental features of oligosaccharides. While the energy landscape of monosaccharides can be altered by a specific biochemical environment or by chemical modifications, the analysis of resulting dynamic conformational equilibria is not feasible by experimental means alone. In this work, a series of β-d-xylopyranosides is used to outline how a combination of experimental NMR parameters and computed molecular properties can be used to determine conformers and quantify the composition of conformational equilibria. We demonstrate that identifying the most stable conformers using energy calculations is challenging and computing of NMR shieldings is typically not sensitive enough. On the other hand, computed spin-spin coupling constants for the xyloside ring can be used to unambiguously assign experimental NMR data of dynamic conformational equilibria and quantify the ratio of different conformers in the mixture. As a proof of principle, this procedure allowed to analyze a hitherto unknown dynamic equilibrium of a diamino-xyloside as a precursor of a molecular switch.

Origins of covalent linkages within the lignin-carbohydrate network of biomass

Covalent linkages between lignin and the surrounding carbohydrate network, often referred to as lignin-carbohydrate complexes (LCCs), have been proposed to affect the organization of the biomass microstructure and directly correlate with the recalcitrant nature of biomass. However, the existence and frequency of these LCC linkages remain controversial and largely unknown, primarily due to the harsh experimental techniques available to characterize them. During the predominant lignin polymerization pathway a reactive intermediate is formed. Though this intermediate can covalently bind to the surrounding cellulose/hemicellulose matrix, it has been traditionally assumed to react exclusively with water, leading to purely physical interactions between lignin and cellulose/hemicellulose in the cell wall. This work, for the first time, provides direct evidence of the molecular mechanism of the formation of benzyl ether and benzyl ester LCC linkages via the speculated lignin polymerization pathway. The formation of these LCC linkages showed thermodynamic favorability, while remaining kinetically facile, compared to the previously assumed mechanism of the lignin intermediate reacting with water. The present work suggests that the surrounding carbohydrate matrix could play a role in the organization of lignin deposition and these covalent linkages could be a key factor in biomass recalcitrance.

On the Physical and Evolutionary Limits to the Rates of Enzyme-Catalyzed Reactions

An existing model for the rate coefficients of enzyme-catalyzed processes involves the regularized gamma function of Euler replacing the exponential dependence of the rate coefficient from the reaction barrier. The application of this model to experimental data, on one hand, validates the model by correctly describing the negative curvature of Eyring plots. On the other hand, this analysis evidences that enzymes never reach the maximum theoretical efficiency, a counterintuitive fact that requires an explanation. This work interprets this evolutionary limit in terms of the necessity of living systems to achieve and maintain homeostasis. Further validation of the expression for the rate coefficients comes from the analysis of the discrepancy between the theoretically predicted energy difference between reactants and products in a chemical equilibrium and the corresponding value obtained by regression to the classical expression for the equilibrium constant. The discrepancy is resolved by making use of the proposed model.

Mechanism and theory of d-glucopyranose homogeneous acid catalysis in the aqueous solution phase

A detailed systematic theoretical study of the mechanism of the homogeneous Brønsted-acid catalysis of d-glucose in aqueous solution phase ("acid hydrolysis") is reported. G4MP2 with the SMD solvation model at B3LYP/6-31G(2df,p) are employed to compute the free energies of the molecular and ionic species pertaining to the isomerization, protonation, hydrogen cation transfer and decomposition processes of d-glucopyranose in aqueous solution phase. This information is used to hypothesise a reaction mechanism that is of improved accuracy and completeness from the existing art. It is found that rotation of the d-glucose alkyl carbon-carbon bond is a facile process and is very important to the subsequent catalytic mechanism. This rotation produces two rotameric isomers which are of notably different thermodynamic stability and reactivity, even with regard to the products of this acid catalysis. As a low energy process (ΔG‡ = ∼3.8-6.7 kcal mol-1), the alkyl carbon-carbon bond may rotate toward the hydroxyl group at the adjacent "4" position reducing the energy required to protonate that position by 3.0-7.2 kcal mol-1 (or 15-30%). The combination of two rotomeric isomers with the six structural isomers owing to the oxygen atoms, means that protonated d-glucose cations embark on a complex competition of interconversion and decomposition that is both thermodynamically and kinetically influenced. The calculations support the hypothesis that the acid-catalysed hydrolysis of d-glucose may yield a number of platform chemicals that have not previously been suggested. These include the prospect of three isomers of 5-hydroxymethylfurfural (HMF); 5-(hydroxymethyl)furan-2-carbaldehyde, 5-(hydroxymethyl)furan-3-carbaldehyde and 5-(hydroxymethyl)furan-4-carbaldehyde. Vibrational spectra of these HMF isomers are also computed and compared to experimentally determined infrared spectra of "humins". On this basis, it is cautiously speculated that the alternative HMF isomers, may be monomeric constituent of the polymeric "humins".

Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions

Molecular modelling provides a major impact in the field of glycosciences, helping in the characterisation of the molecular basis of the recognition between lectins from pathogens and human glycoconjugates, and in the design of glycocompounds with anti-infectious properties. The conformational properties of oligosaccharides are complex, and therefore, the simulation of these properties is a challenging task. Indeed, the development of suitable force fields is required for the proper simulation of important problems in glycobiology, such as the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics, including O-linkages in oligo- and polysaccharides, and N- and O-linkages in glycoproteins. The computational description of representative examples is discussed, herein, related to biologically active oligosaccharides and their interaction with lectins and other proteins, and the new routes open for the design of glycocompounds with promising biological activities.

Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution

Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.

Effects of varying the 6-position oxidation state of hexopyranoses: a systematic comparative computational analysis of 48 monosaccharide stereoisomers

Knowledge of multi-dimensional carbohydrate structure is essential when delineating structure-function relationships in the development of analytical techniques such as ion mobility-mass spectrometry and of carbohydrate-based therapeutics, as well as in rationally modifying the chemical and physical properties of drugs and materials based on sugars. Although monosaccharides are conventionally presumed to adopt the canonical ⁴C₁ chair conformation, it is not well known how altering the substituent identity around the pyranose ring affects the favored conformational state. This work provides a comprehensive and systematic computational comparison of all eight aldohexose isomers in the gas phase with reduction and oxidation at the C-6 position using density functional theory (M05-2X/cc-pVTZ(-f)//B3LYP/6-31G**) to determine the conformational and anomeric preference for each sugar in the gas phase. All 6-deoxyhexose and aldohexose isomers favored the ⁴C₁ chair conformation, while oxidation at C-6 showed a shift in equilibrium to favor the ¹C₄ chair for β-alluronic acid, β-guluronic acid, and β-iduronic acid. The anomeric preference was found to be significantly affected by a remote change in oxidation state, with the alternate anomer favored for several isomers. These findings provide a fundamental platform to empirically test steric and electronic effects of pyranose substituents, with the goal of formulating straightforward rules that govern carbohydrate reactivity and drive quicker, more efficient syntheses. Graphical abstract A systematic comparative conformational analysis of all eight aldohexose isomers using DFT methods (M05-2X/cc-pVTZ(-f)) reveals changes in anomeric and ring conformational preference upon reduction or oxidation at the C-6 position for several sugars.

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.

DFT/PCM theoretical study of the conversion of methyl 4-O-methyl-α-d-galactopyranoside 6-sulfate and its 2-sulfated derivative into their 3,6-anhydro counterparts

Modeling of the conversion of methyl 4-O-methyl-α-d-galactopyranoside 6-sulfate (2) and 2,6-disulfate (1) into methyl 3,6-anhydro-4-O-methyl-α-d-galactopyranoside (4) and its 2-sulfate (3), respectively (Scheme 1) has been carried out using DFT at the M06-2X/6-311 + G(d,p)//M06-2X/6-31 + G(d,p) level with the polarizable continuum model (PCM) in water. The three steps necessary for the alkaline transformation of 6-sulfated (and 2,6-disulfated) galactose units into 3,6-anhydro derivatives were evaluated. The final substitution step appears to be the rate limiting, involving an activation energy of ca. 23 kcal/mol. The other two steps (deprotonation and chair inversion) combined involve lower activation energies (9-12 kcal/mol). Comparison of the thermodynamics and kinetics of the reactions suggest that if the deprotonation step precedes the chair inversion, the reaction should be faster for both compounds. No major differences in reaction rate can be theoretically predicted to be caused by the presence of sulfate on O-2, although one experimental result suggested that O-2 sulfation should increase the reaction rate. The conformational pathways are complex, given the large number of rotamers available for each compound, and the way that some of these rotamers combine into some of the pathways. In any case, the conformation (O)S2 appears as a common intermediate for the chair inversion processes.

Simulation of Raman optical activity of multi-component monosaccharide samples

Determination of the saccharide structure in solution is a laborious process that can be significantly enhanced by chiral optical spectroscopies.

Multi-conformer molecules in solutions: an NMR-based DFT/MP2 conformational study of two glucopyranosides of a vitamin E model compound

Overall geometries of both glucosyl derivatives of PMC were found on the basis of their NMR spectra in CDCl₃and relatedδ_H,C/ⁿJ_HHIEF-PCM(UFF,CHCl₃)/DFT calculational results.

Carbohydrate-protein interactions: molecular modeling insights

The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.

Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water

We examined the conformational preferences of the 2-O-sulfated-3,6-α-D-anhydrogalactose (compound I) and two 1,3 linked disaccharides constituting-κ or ι-carrageenans using density functional and ab initio methods in gas phase and aqueous solution. Systematic modifications of two torsion angles leading to 324 and 144 starting geometries for the compound I and each disaccharide were used to generate adiabatic maps using B3LYP/6-31G(d). The lower energy conformers were then fully optimized using B3LYP, B3PW91 and MP2 with several basis sets. Overall, we discuss the impact of full relaxation on the energy and structure of the dominant conformations, present the performance comparison with previous molecular mechanics calculations if available, and determine whether our results are impacted, when polarization and diffuse functions are added to the 6-31G(d) basis set, or when the MP2 level of theory is used.

Vacuum-ultraviolet electronic circular dichroism study of methyl α-D-glucopyranoside in aqueous solution by time-dependent density functional theory

The vacuum-ultraviolet (VUV) electronic circular dichroism (ECD) spectrum of methyl α-D-glucopyranoside (methyl α-D-Glc) was measured down to 163 nm in aqueous solution using a synchrotron-radiation VUV-ECD spectrophotometer. The spectrum exhibited two characteristic ECD peaks around 170 nm, which depend on the trans (T) and gauche (G) configurations of the hydroxymethyl group at C-5. To elucidate the influences of the T and G configurations on the spectrum, the ECD spectra of three rotamers (α-GT, α-GG, and α-TG) of methyl α-D-Glc were calculated using time-dependent density functional theory (TDDFT) combined with molecular dynamics simulation. A linear combination of the ECD spectra of these three rotamers, which differ markedly from each other, produced a methyl α-D-Glc spectrum similar to that observed experimentally. The spectrum was assignable to the n-σ* transitions of the ring oxygen and methoxy oxygen with minor contributions from the hydroxyl oxygen. The differences in α-GT, α-GG, and α-TG spectra were attributed to fluctuations of the configurations of the hydroxymethyl group at C-5 and the hydroxyl group at C-4, which strongly affected the orientations of intramolecular hydrogen bonds around the ring oxygen. These findings demonstrate that combining VUV-ECD and TDDFT is useful for structural characterization of saccharides in aqueous solution.

Can an α-anomer of the trinitro form of D-glucopyranose be more easily hydrolyzed in alkaline environment than the β-anomer? A detailed theoretical analysis

Comprehensive computational investigations of detailed alkaline hydrolysis reaction pathways of the α-anomeric form of nitrocellulose monomer (2,3,6-trinitro-α-D-glucopyranose) in the (4)C(1) chair conformation within the S(N)2 framework in the gas phase and in bulk water solution are reported. Geometries of reactant complexes, transition states, intermediates, and completely denitrated product were optimized at the density functional theory (DFT) level using the B3LYP functional and the 6-311G(d,p) basis set both in the gas phase and in the bulk water solution. The effect of bulk water was modeled using the polarizable continuum model (PCM) approach. The nature of the potential energy surface of the local minima and transition states was ascertained through vibrational frequency analysis. Intrinsic reaction coordinate (IRC) calculations were also performed to validate the computed transition state structures. Effect of electron correlation on computed energies was considered through a single point energy calculation at the MP2 level using the cc-pVTZ basis set. It was revealed that the presence of hydrogen bonds between the attacking OH(-) ion and various hydrogen bond donating sites (including CH sites) of monomer was necessary for stabilization of the transition state. It was revealed that the α-anomer will be more reactive than the β-anomer with regard to the denitration reaction. The role of entropy and the denitration ability of various sites are also discussed.

Specific rotation as a property to validate monosaccharide conformations

Specific rotation ([α](D)) values were calculated for the 15 conformations of xylopyranose that are the most stable in the gas phase and in aqueous solution. The effects of different theoretical descriptions and the medium on the geometry of the conformers and the [α](D) values are evaluated. Differences in [α](D) values found for the same conformer in all descriptions used were smaller than those found between any two different conformers in the same description. The difference between [α](D) values is prominent, even for two conformations that are distinguished from each other only by the orientation of one secondary hydroxyl group. This finding suggests that [α](D) values may potentially be used in the validation of monosaccharide conformations that are theoretically sampled.

Is N-acetyl-D-glucosamine a rigid 4C1 chair?

Understanding microsecond-timescale dynamics is crucial to establish three-dimensional (3D) structure-activity relationships in sugars but has been intractable to experiments and simulations. As a consequence, whether arguably the most important chemical scaffold in glycobiology, N-acetyl-d-glucosamine (GlcNAc), deviates from a rigid (4)C(1) chair is unknown. Here, conformer populations and exchange kinetics were quantified from the longest aqueous carbohydrate simulations to date (0.2 ms total) of GlcNAc, four derivatives from heparan sulfate and their methylglycosides. Unmodified GlcNAc took 3-5 μs to reach a conformational equilibrium, which comprised a metastable (4)C(1) chair that underwent (4)C(1) ↔ (1)C(4) transitions at a predicted forward rate of 0.8 μs(-1) with an average (1)C(4)-chair lifetime of 3 ns. These predictions agree with high-resolution crystallography and nuclear magnetic resonance but not with the hypothesis that GlcNAc is a rigid (4)C(1) chair, concluded from previous experimental analyses and non-aqueous modeling. The methylglycoside was calculated to have a slower forward rate (0.3 μs(-1)) and a more stable (4)C(1) conformer (0.2 kcal mol(-1)), suggesting that pivotal 3D intermediates (particularly (2)S(O), (1)S(5) and B(2,5)) increased in energy, and water was implicated as a major cause. Sulfonation (N-, 3-O and 6-O) significantly augmented this effect by blocking pseudorotation, but did not alter the rotational preferences of hydroyxl or hydroxymethyl groups. We therefore propose that GlcNAc undergoes puckering exchange that is dependent on polymerization and sulfo substituents. Our analyses, and 3D model of the equilibrium GlcNAc conformer in water, can be used as dictionary data and present new opportunities to rationally modify puckering and carbohydrate bioactivity, with diverse applications from improving crop yields to disease amelioration.