A theoretical study of α- and β-d-glucopyranose conformations by the density functional theory

Cooperativity in alkane-1,2- and 1,3-polyols: NMR, QTAIM, and IQA study of O─H… OH and C─H… OH bonding interactions

Proton nuclear magnetic resonance chemical shifts and atom-atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─H^… OH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─H^… OH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─H^… OH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─H^… OH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.

UV-visible spectral analysis for the characterization of the titanium(iv)-4-(2-pyridylazo)resorcinol complex as a reagent for determining hydrogen peroxide

Titanium(iv)-4-(2-pyridylazo)resorcinol (Ti-PAR) has been effectively used for the determination of hydrogen peroxide. In 1985, Takamura et al. proposed its molecular structure showing the absorption peak at 508 nm. However the results obtained from computational calculations showed the absorption peak at 472 nm. Based on the UV-visible spectral simulations and crystal structures of metal-PAR registered in the Cambridge Structural Database (CSD), the structure of Ti-PAR-H2O2 showing the absorption peak at 508 nm was determined. Then the reaction profiles and the reaction mechanism were clarified.

Intramolecular O-H⋯O and C-H⋯O hydrogen bond cooperativity in D-glucopyranose and D-galactopyranose-A DFT/GIAO, QTAIM/IQA, and NCI approach

Density functional theory calculations are used to compute proton nuclear magnetic resonance (NMR) chemical shifts, interatomic distances, atom-atom interaction energies, and atomic charges for partial structures and conformers of α-D-glucopyranose, β-D-glucopyranose, and α-D-galactopyranose built up by introducing OH groups into 2-methyltetrahydropyran stepwisely. For the counterclockwise conformers, the most marked effects on the NMR shift and the charge on the OH1 proton are produced by OH2, those of OH3 and OH4 being somewhat smaller. This argues for a diminishing cooperative effect. The effect of OH6 depends on the configuration of the hydroxymethyl group and the position, axial or equatorial, of OH4, which controls hydrogen bonding in the 1,3-diol motif. Variations in the interaction energies reveal that a "new" hydrogen bond is sometimes formed at the expense of a preexisting one, probably due to geometrical constraints. Whereas previous work showed that complexing a conformer with pyridine affects only the nearest neighbour, successive OH groups increase the interaction energy of the N⋯H1 hydrogen bond and reduce its length. Analogous results are obtained for the clockwise conformers. The interaction energies for C-H⋯OH hydrogen bonding between axial CH protons and OH groups in certain conformers are much smaller than for O-H⋯OH bonds but they are largely covalent, whereas those of the latter are predominantly coulombic. These interactions are modified by complexation with pyridine in the same way as O-H⋯OH interactions: the computed NMR shifts of the CH protons increase, the atom-atom distances are shorter, and interaction energies are enhanced.

On the importance of intramolecular hydrogen bond cooperativity in d-glucose - an NMR and QTAIM approach

The idea that hydrogen bond cooperativity is responsible for the structure and reactivity of carbohydrates is examined. Density functional theory and gauge-including atomic orbital calculations on the known conformers of the α and β anomers of d-glucopyranose in the gas phase are used to compute proton NMR chemical shifts and interatomic distances, which are taken as criteria for probing intramolecular interactions. Atom-atom interaction energies are calculated by the interacting quantum atoms approach in the framework of the quantum theory of atoms in molecules. Association of OH1 in the counterclockwise conformers with a strong acceptor, pyridine, is accompanied by cooperative participation from OH2, but there is no significant change in the bonding of the two following 1,2-diol motifs. The OH6^... O5 (G-g+/cc/t and G+g-/cc/t conformers) or OH6^... O4 (Tg+/cc/t conformer) distance is reduced, and the OH6 proton is slightly deshielded. In the latter case, this shortening and the associated increase in the OH6-O4 interaction energy may be interpreted as a small cooperative effect, but intermolecular interaction energies are practically the same for all three conformers. In most of the pyridine complexes, one ortho proton interacts with the endocyclic oxygen O5. Analogous results are obtained when the clockwise conformer, G-g+/cl/g-, detected for the α anomer, and a hypothetical conformer, Tt/cl/g-, are complexed with pyridine through OH6. Generally, the cooperative effect does not go beyond the first two OH groups of a chain. Copyright © 2017 John Wiley & Sons, Ltd.

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.

Hydrogen bonding to carbonyl oxygen of nitrogen-pyramidalized amide – detection of pyramidalization direction preference by vibrational circular dichroism spectroscopy

Hydrogen-bonding to carbonyl of nitrogen-pyramidalized bicyclic β-proline amides can switch the preferred nitrogen-pyramidalization direction, as detected by VCD spectroscopy.

Recent advances in the use of vibrational chiroptical spectroscopic methods for stereochemical characterization of natural products

A comprehensive look into application of vibrational optical activity methods for conformational and configurational assignments in natural product molecules over the last 15 years is provided.

Ultraviolet-visible spectral analysis for the reaction of hydrogen peroxide with a titanium(IV)-porphyrin reagent

A Ti-TPyP reagent, i.e., an acidic aqueous solution of oxo[5,10,15,20-tetra(4-pyridyl)porphyrinato]titanium(IV) complex, TiO(tpyp), was developed as a highly sensitive and selective spectrophotometric reagent for the determination of traces of hydrogen peroxide. The reagent exhibited a single absorption peak at 432 nm, and the addition of hydrogen peroxide to the reagent gave rise to a new peak at 450 nm, with height being proportional to the added hydrogen peroxide concentration. Recently we succeeded in clarifying the reaction specificity of the TiO(tpyp) complex to hydrogen peroxide from the viewpoint of the reaction mechanisms and molecular orbitals based on ab initio calculations. In the present study, we performed ultraviolet-visible (UV-Vis) spectral simulations for individual species in the proposed reaction mechanisms based on the theoretical calculations carried out using the Zerner's intermediate neglect of differential overlap (ZINDO) method, since the assignment of the observed absorption peaks to the respective reaction species is important to confirm the reliability of the analysis of hydrogen peroxide using the Ti-TPyP reagent. The absorption peaks at 432 nm and 450 nm were assigned to a H(2)O-adduct structure of the protonated TiO(tpyp) complex and the important structure corresponding to the monoperoxo TiO(tpyp) complex, respectively, under acidic conditions. Particularly, it should be noted that the addition of water molecules to the protonated TiO(tpyp) complex affects the maximum absorption wavelength appreciably. Taking the addition of water molecules to the complex into consideration, the reaction mechanism proposed previously was revised in this study. The results should contribute to providing a new way to evaluate analytical reagents.

Stereochemical studies of sialic acid derivatives by vibrational circular dichroism

Systematic VCD studies of N-acetylneuraminic acid (Neu5Ac), a recognition-related unique carbohydrate, were performed for the first time. Two pairs of anomeric isomers regarding a quaternary C2 asymmetric carbon of Neu5Ac derivatives were synthesized. VCD spectral patterns around the ester carbonyl region, as well as other Mid-IR regions, would be practical markers to distinguish the C2 stereochemistry.

Spectrum–Structure Relationship in Carbohydrate Vibrational Circular Dichroism and Its Application to Glycoconjugates

Preliminary reports of the nature of the vibrational circular dichroism (VCD) peak at around 1145 cm(-1), which is characteristic of axial glycosidic sugars and is called the glycoside band (J. Am. Chem. Soc. 2004, 126, 9496), have been thoroughly examined. Through systematic carbohydrate measurements, it was found that the sign of the glycoside band reflects not only the anomeric configuration but also the pyranose conformation. Isotope and theoretical studies characterized its vibrational mode as C1-H1 deformation coupled with C1-O1 stretching, which indicates its applicability to more-complicated glycoconjugates. In this study, for the first time, carbohydrate VCD spectra were reliably predicted by means of density functional theory (DFT) calculations. The VCD technique was applied to glycopeptides, and simultaneous analysis of both the carbohydrate and aglycan parts was carried out.

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.

Vibrational circular dichroism (VCD) studies on disaccharides in the CH region: toward discrimination of the glycosidic linkage position

The structural features of carbohydrates are a combination of 1) sequence and types of mono-sugars, 2) stereochemistry of their glycosidic linkages, and 3) their glycosidic linkage sites. We performed the first systematic VCD study on glycoside linking site discrimination. VCD spectra, in the CH stretching region from 2000 to 4000 cm(-1), of eleven glucobioses (trehalose (alpha1-alpha1), neotrehalose (alpha1-beta1), isotrehalose (beta1-beta1), kojibiose (alpha1-2), nigerose (alpha1-3), maltose (alpha1-4), isomaltose (alpha1-6), sophorose (beta1-2), laminaribiose (beta1-3), cellobiose (beta1-4), gentiobiose (beta1-6)) suggested a possible new discrimination method for glyco analysis, while VCD spectra in the mid-IR region distinguished the stereochemistry (alpha or beta) of the glycosidic linkage. Both reducing and nonreducing glucobioses showed different VCD spectral features compared to their constituent D-glucose and the anomer-fixed model compounds. Interresidue interaction such as hydrogen bonding was suggested to cause these spectral differences. Interplay between residues is a common phenomenon and thus VCD analysis could be applicable to other di-, oligo- or poly-saccharides. Several isotropic labeled compounds were also measured to support spectral assignment and interpretation.