DFT study of alpha- and beta-D-mannopyranose at the B3LYP/6-311++G** level

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.

Synthesis, Molecular Modeling Study, and Quantum-Chemical-Based Investigations of Isoindoline-1,3-diones as Antimycobacterial Agents

The condensation of phthalic anhydride afforded structurally modified isoindoline-1,3-dione derivatives with selected amino-containing compounds. The title compounds (2-30) have been characterized by thin-layer chromatography (TLC), infrared spectroscopy, ¹H and ¹³C NMR spectroscopy, and mass spectroscopy. All of the compounds were assessed for their antimycobacterial activity toward the H37Rv strain by a dual read-out assay method. Among the synthesized compounds, compound 27 possessed a significant IC₅₀ of 18 μM, making it the most potent compound of the series. The InhA inhibitory (IC₅₀) activity of compound 27 was 8.65 μM in comparison to Triclosan (1.32 μM). Computational studies like density functional theory (DFT) study, molecular docking, and dynamic simulation studies illustrated the reactivity and stability of the synthesized compounds as InhA inhibitors. A quantum-mechanics-based DFT study was carried out to investigate the molecular and electronic properties, reactivities, and nature of bonding present in the synthesized compounds and theoretical vibrational (IR) and isotropic value (¹H and ¹³C NMR) calculations.

Evaluation of hydrogen bonds formation in the selected rare sugars based on 6-31G* and 6-311 + + G(d,p) basis sets

Rare sugars are monosaccharides with tremendous potential for applications in pharmaceutical, cosmetics, nutraceutical, and flavors industries. The four rare sugars, including gulose, allose, altrose, and talose, are stereoisomers that are different in the hydroxyl group orientation (axial or equatorial) on the C_2-4 atoms. The basis sets effect in evaluation of the possibility intramolecular hydrogen bonding (H-bonds) in the selected rare sugars was studied from 6-31G* to 6-311 ++ G(d,p) basis sets using DFT, AIM, and NBO methods. The results show that the selected rare sugars are more stable at 6-311 ++ G(d,p) basis sets compared to 6-31G* because their electronic energies were reduced between 158 and 164 (kcal.mol^-1). The overall effect of basis set enhancement is to decrease H-bond energies in the range of  1.25 to 2.51 (kcal.mol^-1) and stabilization energies between 2 and 5 (kcal.mol^-1) in the selected rare sugars at the DFT level of theory. The intramolecular H-bond distances, H-bond energies obtained from the AIM analysis, and also the second-order stabilization energies obtained from the NBO analysis were fluctuated largely depending on the basis set. In summary, it was found that the use of 6-311 ++ G(d,p) basis set to be more efficient results in rare sugars geometry than the 6-31G* basis set.

NMR Spectroscopic Characterization of the C-Mannose Conformation in a Thrombospondin Repeat Using a Selective Labeling Approach

Despite the great interest in glycoproteins, structural information reporting on conformation and dynamics of the sugar moieties are limited. We present a new biochemical method to express proteins with glycans that are selectively labeled with NMR-active nuclei. We report on the incorporation of 13 C-labeled mannose in the C-mannosylated UNC-5 thrombospondin repeat. The conformational landscape of the C-mannose sugar puckers attached to tryptophan residues of UNC-5 is characterized by interconversion between the canonical 1 C4 state and the B03 / 1 S3 state. This flexibility may be essential for protein folding and stabilization. We foresee that this versatile tool to produce proteins with selectively labeled C-mannose can be applied and adjusted to other systems and modifications and potentially paves a way to advance glycoprotein research by unravelling the dynamical and conformational properties of glycan structures and their interactions.

Yeast cell wall - Silver nanoparticles interaction: A synergistic approach between surface-enhanced Raman scattering and computational spectroscopy tools

Candida species are becoming one of the pathogens developing antifungal resistance due to inappropriate treatment and overuse of antimycotic drugs in building construction and agriculture. Further, fungal infections are often difficult to detect, also due to slow in vitro growth of the organisms from clinical specimens. Thus, fast detection and discrimination of yeast cells in direct patient materials is essential for an adequate treatment and success rate. In this work, we investigated Candida species isolated from patients, by using surface-enhanced Raman scattering (SERS) combined with computational spectroscopy tools, aiming to detect and discriminate between the three considered species, Candida albicans, Candida glabrata, and Candida parapsilosis. Density functional theory (DFT) was used to calculate Raman spectra of yeasts' main cell wall components for elucidating the origin of the observed bands. Accurate assignments of normal modes helped for a better understanding of the interaction between silver nanoparticles with yeasts' cell wall. Further, SERS spectra were used as samples in a database on which we performed multivariate analyses. By Principal component analysis (PCA), we obtained a maximum variation of 79% between the three samples. Linear discriminant analysis (LDA) was successfully used to discriminate between the three species.

Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution

Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowest-energy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span less than 10 kcal/mol. Both second- as well as third-order DFTB methods are exhibiting similar deviations from B3LYP. Even after the inclusion of empirical dispersion corrections in vacuum, these deviations remain for a large majority of isomer energies and geometries when compared to dispersion-corrected B3LYP.

Fragmentation Pathways of Lithiated Hexose Monosaccharides

We characterize the primary fragmentation reactions of three isomeric lithiated D-hexose sugars (glucose, galactose, and mannose) utilizing tandem mass spectrometry, regiospecific labeling, and theory. We provide evidence that these three isomers populate similar fragmentation pathways to produce the abundant cross-ring cleavage peaks (^0,2A₁ and ^0,3A₁). These pathways are highly consistent with the prior literature (Hofmeister et al. J. Am. Chem. Soc. 113, 5964-5970, 1991, Bythell et al. J. Am. Soc. Mass Spectrom. 28, 688-703, 2017, Rabus et al. Phys. Chem. Chem. Phys. 19, 25643-25652, 2017) and the present labeling data. However, the structure-specific energetics and rate-determining steps of these reactions differ as a function of precursor sugar and anomeric configuration. The lowest energy water loss pathways involve loss of the anomeric oxygen to furnish B₁ ions. For glucose and galactose, the lithiated α-anomers generate ketone structures at C2 in a concerted reaction involving a 1,2-migration of the C2-H to the anomeric carbon (C1). In contrast, the β-anomers are predicted to form 1,3-anhydroglucose/galactose B₁ ion structures. Initiation of the water loss reactions from each anomeric configuration requires distinct reactive conformers, resulting in different product ion structures. Inversion of the stereochemistry at C2 has marked consequences. Both lithiated mannose forms expel water to form 1,2-anhydromannose B₁ ions with the newly formed epoxide group above the ring. Additionally, provided water loss is not instantaneous, the α-anomer can also isomerize to generate a ketone structure at C2 in a concerted reaction involving a 1,2-migration of the C2-H to C1. This product is indistinguishable to that from α-glucose. The energetics and interplay of these pathways are discussed. Graphical Abstract ᅟ.

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.

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.

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.

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.

Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains

This article describes a revised version 56A6(CARBO_R) of the GROMOS 56A6(CARBO) force field for hexopyranose-based carbohydrates. The simulated properties of unfunctionalized hexopyranoses are unaltered with respect to 56A6CARBO . In the context of both O1 -alkylated hexopyranoses and oligosaccharides, the revision stabilizes the regular (4) C1 chair for α-anomers, with the opposite effect for β-anomers. As a result, spurious ring inversions observed in α(1→4)-linked chains when using the original 56A6(CARBO) force field are alleviated. The (4) C1 chair is now the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. The methylation of a d-hexopyranose leads to a systematic shift in the ring-inversion free energy ((4) C1 to (1) C4 ) by 7-8 kJ mol(-1), positive for the α-anomers and negative for the β-anomers, which is qualitatively compatible with the expected enhancement of the anomeric effect upon methylation at O1. The ring-inversion free energies for residues within chains are typically smaller in magnitude compared to those of the monomers, and correlate rather poorly with the latter. This suggests that the crowding of ring substituents upon chain formation alters the ring flexibility in a nonsystematic fashion. In general, the description of carbohydrate chains afforded by 56A6(CARBO_R) suggests a significant extent of ring flexibility, i.e., small but often non-negligible equilibrium populations of inverted chairs, and challenges the "textbook" picture of conformationally locked carbohydrate rings.

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.

Three-dimensional potential energy surface of selected carbohydrates' CH/π dispersion interactions calculated by high-level quantum mechanical methods

In this study we present the first systematic computational three-dimensional scan of carbohydrate hydrophobic patches for the ability to interact through CH/π dispersion interactions. The carbohydrates β-d-glucopyranose, β-d-mannopyranose and α-l-fucopyranose were studied in a complex with a benzene molecule, which served as a model of the CH/π interaction in carbohydrate/protein complexes. The 3D relaxed scans were performed at the SCC-DFTB-D level with 3 757 grid points for both carbohydrate hydrophobic sides. The interaction energy of all grid points was recalculated at the DFT-D BP/def2-TZVPP level. The results obtained clearly show highly delimited and separated areas around each CH group, with an interaction energy up to -5.40 kcal mol(-1) . The results also show that with increasing H⋅⋅⋅π distance these delimited areas merge and form one larger region, which covers all hydrogen atoms on that specific carbohydrate side. Simultaneously, the interaction becomes weaker with an energy of -2.5 kcal mol(-1) . All local energy minima were optimized at the DFT-D BP/def2-TZVPP level and the interaction energies of these complexes were refined by use of the high-level ab initio computation at the CCSD(T)/CBS level. Results obtained from the optimization suggest that the CH group hydrogen atoms are not equivalent and the interaction energy at the CCSD(T)/CBS level range from -3.54 to -5.40 kcal mol(-1) . These results also reveal that the optimal H⋅⋅⋅π distance for the CH/π dispersion interaction is approximately (2.310±0.030) Å, and the angle defined as carbon-hydrogen-benzene geometrical centre is (180±30)°. These results reveal that whereas the dispersion interactions with the lowest interaction energies are quite strictly located in space, the slightly higher interaction energy regions adopt a much larger space.

Conformational free energy surface of alpha-N-acetylneuraminic acid: an interplay between hydrogen bonding and solvation

The conformational free energy surface of alpha-N-acetylneuraminic acid (Neu5Ac, sialic acid) in the space of ring-puckering coordinates was calculated using the metadynamics method. Free energy surfaces in vacuum and with an explicit solvent were calculated in GLYCAM 06 force field. In vacuum three structures are almost equivalently populated, namely, the (2)C(5) chair and the B(3,6)/(2)S(6) and (O)S(3) boat/skew-boat conformations. The B(3,6)/(2)S(6) structure is stabilized by an ionic hydrogen bond between the amide N-H bond and the carboxylic group. However, this structure is unfavorable in a water environment in which the experimentally observed (2)C(5) chair conformation is predicted to be more stable than the other structures. These results indicate that environment significantly influences conformation of Neu5Ac and that Neu5Ac-processing enzymes might modify a conformation of their substrates solely by a changing polarity of the environment. The structure of Neu5Ac bound in influenza neuraminidase ((4)S(2)/B(2,5)) belongs to conformations preferred in a water environment. The free energy penalty of this conformational change was calculated (relative to (2)C(5)) as 10.2 +/- 2.0 and 17.3 +/- 2.0 kJ/mol for (4,O)B/(O)S(3) and (4)S(2), respectively. This result indicates that mimicking of the enzyme-bound conformation is likely to be a viable strategy for the design of neuraminidase inhibitors.

DFT conformation and energies of amylose fragments at atomic resolution. Part 1: Syn forms of alpha-maltotetraose

DFT optimization studies of 90 syn alpha-maltotetraose (DP-4) amylose fragments have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments studied include V-helix, tightly bent conformations, a boat, and a (1)C(4) conformer. The standard hydroxymethyl rotamers (gg, gt, tg) were examined at different locations in the residue sequence, and their influence on the bridge conformations phi/psi values and conformer energy is described. Hydroxyl groups were considered to be homodromic, that is, they are either in the all clockwise, 'c', or all counterclockwise, 'r'. Energy differences between conformations are examined in order to assess the stability of the different conformations and to identify the sources of energy that dictate amylose polymer formation. A small nearly cyclic compact structure is of low energy as one would expect when these flexible molecules are studied in vacuo. Many conformations in which the only differences are a single hydroxymethyl variation in the residue sequence show similar energies and bridge conformations, with trends being a result of the hydroxymethyl as well as hydroxyl orientation. In general the 'c' structures are of lower energy than the 'r' structures, although this is only true for the in vacuo state. The solvent dependence on conformational preference of several low-energy DP-4 structures was investigated via the continuum solvation method COSMO. These results suggest that the 'r' structures may be favored for fully solvated molecules.

DFT studies of the disaccharide, α-maltose: relaxed isopotential maps

The disaccharide, alpha-maltose, forms the molecular basis for the analysis of the structure of starch, and determining the conformational energy landscape as the molecule oscillates around the glycosidic bonds is of importance. Thus, it is of interest to determine, using density functionals and a medium size basis set, a relaxed isopotential contour map plotted as a function of the phi(H) and psi(H) dihedral angles. The technical aspects include the method of choosing the starting conformations, the choice of scanning step size, the method of constraining the specific dihedral angles, and the fitting of data to obtain well defined contour maps. Maps were calculated at the B3LYP/6-31+G( *) level of theory in 5 degrees intervals around the (phi(H),psi(H))=(0 degrees ,0 degrees ) position, out to approximately +/-30 degrees or greater, for gg-gg'-c, gg-gg'-r, gt-gt'-c, gt-gt'-r, tg-tg'-c, and tg-tg'-r conformers, as well as one-split gg(c)-gg'(r) conformer. The results show that the preferred conformation of alpha-maltose in vacuo depends strongly upon the hydroxyl group orientations ('c'/'r'), but the energy landscape moving away from the minimum-energy position is generally shallow and transitions between conformational positions can occur without the addition of significant energy. Mapped deviations of selected parameters such as the dipole moment; the C1-O1-C4', H1-C1-O1, and H4'-C4'-O1 bond angles; and deviations in hydroxymethyl rotamers, O5-C5-C6-O6, O5'-C5'-C6'-O6', C5-C6-O6-H, and C5'-C6'-O6'-H', are presented. These allow visualization of the structural and energetic changes that occur upon rotation about the glycosidic bonds. Interactions across the bridge are visualized by deviations in H(O2)...O3', H(O3')...O2, and H1...H4' distances and the H(O2)-O2-C2-C1 and H'(O3')-O3'-C3'-C4' hydroxyl dihedral angles.

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.

Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations

High level correlated quantum chemical calculations, using MP2 and local MP2 theory, have been performed for conformations of the disaccharide, beta-maltose, and the trisaccharide, 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose. For beta-maltose, MP2 and local MP2 calculations using the 6-311++G** basis set are in good agreement, predicting a global minimum gas-phase conformation with a counterclockwise hydrogen bond network and the experimentally-observed intersaccharide hydrogen bonding arrangement. For conformations of 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose, MP2/6-311++G**, and local MP2/6-311++G** calculations do not provide a consensus prediction of relative energetics, with the MP2 method finding large differences in stability between extended and folded trisaccharide conformations. Local MP2 calculations, less susceptible to intramolecular basis set superposition errors, predict a narrower range of trisaccharide energetics, in line with estimates from Hartree-Fock theory and B3LYP and BP86 density functionals. All levels of theory predict compact, highly hydrogen-bonded conformations as lowest in energy on the in vacuo potential energy surface of the trisaccharide. These high level, correlated local MP2/6-311++G** calculations of di- and trisaccharide energetics constitute potential reference data in the development and testing of improved empirical and semiempirical potentials for modeling of carbohydrates in the condensed phase.

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.

Computational Study of the Conformational Space of Methyl 2,4-Diacetyl-β-d-xylopyranoside: 4C1 and 1C4 Chairs, Skew-Boats (2SO, 1S3), and B3,O Boat Forms

Ring and substituent rotamer conformations of methyl 2,4-diacetyl-beta-D-xylopyranoside, for which experimental results are controversial, were studied in the gas phase and in solvents of different polarity (CCl4, CHCl3, DMSO, and H2O) by B3LYP density functional theory. The 1C4 chair is the most stable ring form in the gas phase, followed by 4C1 and 2S0. Solvents of increasing polarity shift the equilibrium toward the 4C1 chair. Homodesmotic reaction energies show that the 1C4 and 2SO forms are stabilized by hydrogen bonding and anomeric effects and that steric repulsion is smallest in the 4C1 chair and largest in skew-boats.

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

Forty-one conformations of alpha- and beta-d-galactopyranose were geometry optimized using the B3LYP density functional and 6-311++G** basis set. Full geometry optimization was performed on different ring geometries and different 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-gg-(4)C(1)-c chair conformation, which is of lower electronic and free energy than the lowest energy alpha-d-glucopyranose conformer because of favorable hydrogen-bonding interactions. The in vacuo calculations showed considerable ( approximately 2.2kcal/mol) energetic preference for the alpha over the beta anomer for galactopyranose in both the (4)C(1) and (1)C(4) chair conformations. Results are compared to glucopyranose and mannopyranose calculations in vacuo. Boat and skew-boat forms were found that remained stable upon gradient optimization, although many starting conformations moved to other boat forms upon optimization. As with glucopyranose and mannopyranose, the orientation and interaction of the hydroxyl groups make the most significant contributions to the conformation-energy relationship in vacuo.

Gas-Phase and Solution Conformations of the α-L-Iduronic Acid Structural Unit of Heparin

The IdoA2S structural unit of heparin (subunit G) may oscillate among the three conformations (4C1, 1C4, and 2So). Only the twisted boat conformation allowed the biologically active pentasaccharide unit of heparin (DEFGH) to bind to antithrombin. Our work reports, in detail, the results of systematic large-scale theoretical investigations of the three basic conformations (4C1, 1C4, and 2So) of the IdoA2S structural unit of heparin, its anionic forms, and its sodium salt using the B3LYP/6-311++G(d, p) and B3LYP/6-31+G(d) model chemistries. According to our calculations, the most stable structure of these molecules corresponds to the 2So skew-boat conformation. This form is also the most stable in a water solution. The 2So conformation of neutral molecules is not maintained in the anionic species. With anions, both 1C4 and 4C1 conformations are present. The relative stability of individual species of the substituted iduronic acid affects extra stabilization by means of intramolecular hydrogen bonds. The calculated macroscopic pKa of 1,4-DiOMe IdoA2S are as follows: pKa = 0.25 for the terminal C(2)-OSO3H group, pKa = 3.67 for the terminal C(5)-CO2H group, and pKa = 14.00 for the C(3)-OH hydroxyl group. The computed Gibbs interaction energies, DeltaGdegrees , for the reaction 1,4-DiOMe IdoA2S(2-) + 2Na+ <==> 1,4-DiOMe IdoA2SNa2 (4C1, 1C4, and 2So conformations) are negative and span a rather small energy interval (from -1244 to -1290 kJ mol(-1)).