DFT studies of the ionization of alpha and beta glycopyranosyl donors

Current attempts at mimicking the transition states (TSs) of glycosyl processing enzymes (GPEs) that proceed through TSs with a high degree of oxacarbenium ion formation suffer from a paucity of data about the conformations of such oxacarbenium ions. Because TSs are maxima, the current models based on minimized structures may need some refinement. As part of studies directed at optimizing chemical glycosylation the ionization of 3,4,6-tri-O-acetyl-alpha/beta-D-glucopyranosyl chlorides and triflates, 2,3,4,6-tetra-O-methyl-alpha/beta-D-glucopyranosyl fluorides, chlorides and triflates, 2,3,4,6-tetra-O-methyl-alpha/beta-D-mannopyranosyl fluorides, 2,3-di-O-methyl 4,6-O-benzylidene alpha/beta-D-mannopyranosyl triflates and 2,3-di-O-methyl 4,6-O-benzylidene alpha/beta-D-glucopyranosyl triflates was studied by a prototypic density functional theory (DFT) procedure. In all cases, the alpha-anomers ionized smoothly to 4H3 half chair conformations or adjacent envelopes. By contrast, all beta-anomers exhibited an abrupt conformational change before ionization was complete. The nature of the conformations sampled depends on both the leaving group and the protecting group. The methods presented can be readily adapted to the study of any GPE or chemical glycosylation and provide a method for initial evaluation of plausible TSs, which in turn can be used in mimetic design.     

Unexpected alpha-stereochemical outcomes of attempted beta-glycosylations

In an effort to prepare complex oligosaccharide derivatives, a series of unexpected alpha glycosides were predominantly formed in the presence of neighboring group participation using imidates or thioglycosides as glycosyl donors under standard glycosylation conditions. The observations are especially suitable in the case of alpha-(1-->3) glycosidic bond formation.     

Investigations into the role of oxacarbenium ions in glycosylation reactions by ab initio molecular dynamics

We present a constrained ab initio molecular dynamics method that allows the modeling of the conformational interconversions of glycopyranosyl oxacarbenium ions. The model was successfully tested by estimating the barriers to ring inversion for two 4-substituted tetrahydropyranosyl oxacarbenium ions. The model was further extended to predict the pathways that connect the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-glucopyranosyl cation to its inverted (5)S(1) conformation and the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-mannopyranosyl cation to its inverted (3)E conformation. The modeled interconversion pathways reconcile a large body of experimental work on the acid-catalyzed hydrolysis of glycosides and the mechanisms of a number of glucosidases and mannosidases.     

Remote control of alpha- or beta-stereoselectivity in (1-->3)-glucosylations in the presence of a C-2 ester capable of neighboring-group participation

In (1-->3)-glucosylation the glycosyl bond originally present in either donor or acceptor is shown to control the stereoselectivity of the forthcoming bond, i.e., the newly formed glycosidic linkage has the opposite anomeric configuration of that of either the donor or acceptor. Therefore, with alpha-(1-->3)-linked disaccharides with nonreducing ends that have the 3-OH free as the acceptor and an acetylated glucosyl trichloroacetimidate as the donor, or with an alpha-(1-->3)-linked acetylated disaccharide trichloroacetimidate as the donor and a glucoside with 3-OH free as the acceptor, beta-linked trisaccharides were obtained. Meanwhile, with beta-(1-->3)-linked disaccharides that have nonreducing ends with the 3-OH free as the acceptor and an acetylated glucosyl trichloroacetimidate as the donor, or with a beta-(1-->3)-linked acetylated disaccharide trichloroacetimidate as the donor and a glucoside with the 3-OH free as the acceptor, alpha-linked trisaccharides were obtained in spite of the C-2 neighboring group participation.     

Computational study of the influence of cyclic protecting groups in stereoselectivity of glycosylation reactions

Protecting groups often have profound influences on the stereoselectivity of glycosylation reactions. The effects of many protecting groups, especially cyclic protecting groups, are not well understood and difficult to explain and predict. Computational methods were used to study the effect of benzylidene acetal and cyclic carbonate protecting groups in glycosylation reactions, and the results provided a theoretical explanation for experimental observations.     

Benzene and heterocyclic rings formation in cycloaddition reactions catalyzed by RuCp derivatives: DFT studies

The mechanism of the RuCp(COD)Cl catalyzed cyclotrimerization of acetylene, as well as the cyclocotrimerization of two alkynes with one molecule of ethylene, R-CN (R = H, Me, Cl, COOMe), CX₂ (X = O, S, Se), and HNCX (X = O, S) investigated by means of high level DFT/B3LYP calculations, has been reviewed. The key reaction step is in all cases the oxidative coupling of two alkyne ligands to give a metallacyclopentatriene intermediate (or metallacyclopentadiene in other systems). This metallacycle adds unsaturated molecules, containing CC, CC and CX bonds, or RCN, CX₂, and HNCX, in a concerted fashion, directly to the RuC bond, forming bicyclic carbenes. The cycle is completed by a rearrangement followed by an exothermic displacement of the arene or pyridine, by two acetylene molecules regenerating the catalytically active species. Small differences are found depending on the molecules and bonds involved. These reactions are reviewed and the proposed mechanisms compared with other available studies.     

Theoretical studies of regioselectivity of Ni- and Rh-catalyzed C-C bond forming reactions with unsymmetrical alkynes

This review highlights our theoretical studies of regioselectivities of Rh-catalyzed (5 + 2) cycloadditions, Ni-catalyzed reductive alkyne-aldehyde couplings, and Rh-catalyzed hydrogenative couplings of diynes and carbonyl partners. Factors that control the regioselectivities in these reactions are analyzed; these include steric repulsions involving the substrate and ligands, electronic effects dictated by metal-substrate interactions, and directing effects of conjugated alkenyl and alkynyl groups involving coordination to the metal.     

DFT and MP2 studies on the C2C2α bond cleavage in thiamin catalysis

Thiamin diphosphate (ThDP), the biologically active derivative of vitamin B₁, is an important cofactor of several enzymes that catalyze the oxidative and non-oxidative conversion of α-keto acids. The final step of non-oxidative decarboxylation of pyruvate by pyruvate decarboxylase – the liberation of acetaldehyde – requires deprotonation of the α-hydroxyl group and cleavage of the C2–C2α bond of the transitory 2-(1-hydroxyethyl)-ThDP intermediate. It has been proposed that the cofactor 4′-amino/imino function is essentially involved in the deprotonation of the α-hydroxyl group. Proton transfer and C2–C2α cleavage may occur in a stepwise manner, or, alternatively in a concerted mechanism. Here, density functional theory (DFT) calculations as well as second order Møller–Plesset perturbation theory (MP2) studies were performed on a simple model for the enzyme using the program package Gaussian 03. Calculations favor a stepwise mechanism with initial formation of the C2α alkoxide, followed by C2–C2α bond cleavage.     

Neighboring group participation. Part 15. Stereoselective synthesis of some steroidal tetrahydrooxazin-2-ones, as novel presumed inhibitors of human 5alpha-reductase

During the alkaline methanolysis of 3beta-acetoxy-21-chloromethyl-pregn-5-ene-20beta-N-phenylurethane, and its p-substituted phenyl derivatives, cyclization occurs, in the course of which 17beta-[3-(N-phenyl)tetrahydrooxazin-2-on-6-yl]androst-5-en-3beta-ol and its p-substituted phenyl derivatives are formed. The cyclization takes place with (N(-)-6) neighboring group participation. Oppenauer oxidation of the 3beta-hydroxy-exo-heterocyclic steroids yielded the corresponding delta4-3-ketosteroids. The structures of the new compounds were proved by IR, 1H and 13C NMR spectroscopy, using up-to-date measuring techniques such as 2D-COSY, HMQC, and HMBC. The inhibitory effects (CI50) of the delta4-3-ketosteroids on 5alpha-reductase were studied.     

Recent advances in the glycosylation of sphingosines and ceramides

Glycosphingolipids (GSLs) are ubiquitous components of eukaryotic cell membranes. They are highly bioactive and are involved in many aspects of cell signalling like cell-cell interaction, cell-substratum interaction and cell-pathogen interaction. GSLs also are involved in the modulation of signal transduction, resulting in regulation of cell proliferation and differentiation. The biological importance and complexity of these compounds afford many opportunities to prepare synthetic analogues for studies of their metabolism in intra- and intercellular processes. This review focuses on recent contributions in the synthesis of GSLs, highlighting improvements in glycosylation reactions leading to alpha and beta glycosyl sphingosines and ceramides and related compounds. Literature from 2000 to the present is covered. The glycosylation reactions leading to the synthesis of GSLs are classified in function of the configuration of the created glycosidic bond (alpha or beta) and of the acceptor used, either azido-sphingosine or ceramide.     

Kinetics and DFT studies on the reaction of copper(II) complexes and H2O2

Copper(II) complexes supported by bulky tridentate ligands L1^H (N,N-bis(2-quinolylmethyl)-2-phenylethylamine) and L1^Ph (N,N-bis(2-quinolylmethyl)-2,2-diphenylethylamine) have been prepared and their crystal structures as well as some physicochemical properties have been explored. Each complex exhibits a square pyramidal structure containing a coordinated solvent molecule at an equatorial position and a weakly coordinated counter anion (or water) at an axial position. The copper(II) complexes reacted readily with H₂O₂ at a low temperature to give mononuclear hydroperoxo copper(II) complexes. Kinetics and DFT studies have suggested that, in the initial stage of the reaction, deprotonated hydrogen peroxide attacks the cupric ion, presumably at the axial position, to give a hydroperoxo copper(II) complex retaining the coordinated solvent molecule (H ^R ·S). H ^R ·S then loses the solvent to give a tetragonal copper(II)-hydroperoxo complex (H ^R ), in which the –OOH group may occupy an equatorial position. The copper(II)–hydroperoxo complex H ^R exhibits a relatively high O–O bond stretching vibration at 900 cm⁻¹ compared to other previously reported examples.Electronic Supplementary Material Supplementary material is available for this article at     

Advances in the biotechnological glycosylation of valuable flavonoids

The natural flavonoids, especially their glycosides, are the most abundant polyphenols in foods and have diverse bioactivities. The biotransformation of flavonoid aglycones into their glycosides is vital in flavonoid biosynthesis. The main biological strategies that have been used to achieve flavonoid glycosylation in the laboratory involve metabolic pathway engineering and microbial biotransformation. In this review, we summarize the existing knowledge on the production and biotransformation of flavonoid glycosides using biotechnology, as well as the impact of glycosylation on flavonoid bioactivity. Uridine diphosphate glycosyltransferases play key roles in decorating flavonoids with sugars. Modern metabolic engineering and proteomic tools have been used in an integrated fashion to generate numerous structurally diverse flavonoid glycosides. In vitro, enzymatic glycosylation tends to preferentially generate flavonoid 3- and 7-O-glucosides; microorganisms typically convert flavonoids into their 7-O-glycosides and will produce 3-O-glycosides if supplied with flavonoid substrates having a hydroxyl group at the C-3 position. In general, O-glycosylation reduces flavonoid bioactivity. However, C-glycosylation can enhance some of the benefits of flavonoids on human health, including their antioxidant and anti-diabetic potential.     

Studies on the role of goat heart galectin-1 as a tool for detecting post-malignant changes in glycosylation pattern

Galectins are mammalian lectins established to play a crucial role in the progression of various cancer types by the virtue of their differential expression in normal and cancerous cells. In the present study, goat heart galectin-1 (GHG-1) was purified and investigated for its potential role in the detection of post-malignant changes in glycosylation pattern. When exposed to superoxide radicals generated from a pyrogallol auto-oxidation system, GHG-1 treated erythrocyte suspension released higher amount of oxyhemoglobin than the unagglutinated erythrocytes. The extent of erythrocyte hemolysis was found to be directly proportional to concentrations of hypochlorous acid. GHG-1 was used to detect the change in the β-galactoside expression pattern in erythrocyte membrane from human donors suffering from prostate and breast cancer. No significant change was observed in the hemolysis of lectin agglutinated erythrocytes collected from pre-operated breast cancer patients, whereas significant increase was observed in normal healthy control and post-operated samples. Findings of this study proclaim GHG-1 as an important tool for the detection of post-malignant changes in glycosylation pattern.Abbreviations: Gal-1, galectin-1; GHG-1, goat heart galectin-1; HOCl, hypochlorous acid; OxyHb, oxyhemoglobin     

NMR evidence for the participation of triflated ionic liquids in glycosylation reaction mechanisms

A systematic low-temperature NMR study of a glycosylation reaction was performed in the presence of different ionic liquids and acidic catalysts. The influence of the triflate anion derived from [emim][OTf] on the stereochemistry of the glycosylation products was evaluated.     

Functional studies on three novel HCNH2 mutations in Taiwan: identification of distinct mechanisms of channel defect and dissociation between glycosylation defect and assembly defect

Mutations of the KCNH2 with decreased channel activity lead to congenital long QT syndrome (LQTS). We studied the electrophysiological, glycosylation, trafficking and assembly properties of three novel KCNH2 mutations identified in Taiwanese patients with LQTS (p.N633D, p.R744fs, and p.P923fs). When expressed in HEK293T cells, p.N633D and p.R744fs HERG channels displayed no HERG current while p.P923fs HERG channel showed HERG current with significantly lower (34%) current density and faster inactivation kinetics. In Western blot analysis, pR744fs was the only one with glycosylation defect, which was in consistence with the confocal microscopic findings showing that p.R744fs-GFP was the only one with trafficking defect. However, p.R744fs-GFP differed from pR744fs in being fully glycosylated while p.R744fs fusion with GFP at the N-terminus revealed glycosylation defect. To access the assembly capacity of each mutant, co-immunoprecipitation was conducted. Wild type (WT), p.N633D, and p.P923fs HERG protein showed assembly ability while p.R744fs failed to assemble with neither WT nor itself.In conclusion, we identified three novel LQTS-related KCNH2 mutations and each had a distinct mechanism of channel defect. For p.R744fs mutant, adding GFP to the C-terminus rescued the glycosylation defect but the channel was still assembly defective indicating a dissociation between glycosylation and assembly defects.     

The pH-induced glycosylation of secreted phosphatases is mediated in Aspergillus nidulans by the regulatory gene pacC-dependent pathway

In this communication, we show that the pacC(c)14 mutation drastically reduced the mannose and N-acetylglycosamine content of the pacA-encoded acid phosphatase secreted by the fungus Aspergillus nidulans when grown at 22 degrees C, pH 5.0, compared to a control strain. The staining after PAGE was not observed for the pacA-encoded acid phosphatase, while the palD-encoded Pi-repressible alkaline phosphatase had an altered electrophoretic mobility. In addition, the secreted acid phosphatase also had a reduced number of isoforms visualized by staining after IEF and glycosylation had a protective effect against its heat inactivation. We also show that a full-length version of gene pacC-1 cloned from Neurospora crassa complemented the pacC(c)14 mutation of A. nidulans, including the remediation of both the acid and alkaline Pi-repressible phosphatases secreted at pH 5.0, which indicates that glycosylation of secreted phosphatases is mediated in A. nidulans by the conserved PacC pathway that governs pH-responsive gene expression.     

The role of cyclopentadienyl versus indenyl in Mo(II) spirodiene complexes reactivity: A DFT mechanistic study

Spiro[2,4]hepta-4,6-diene and spiro[4,4]nona-1,3-diene react with [Mo(CO)₂Cp’(NCCH₃)₂][BF₄] (Cp’ = Cp, Ind; Ind = η⁵-C₉H₇) to afford the corresponding diene complex [Mo(diene)(CO)₂Cp′]⁺. When Cp’ = Ind, the reaction proceeded forward leading to ring opening in the case of the small spiro ring. Although this and another product resulting from migration of the side arm to the carbonyl were detected when Cp’ = Cp, they did not form from the diene complex. A DFT/PBE1PBE study was carried out and showed a kinetically controlled reaction pathway leading from the [Mo(diene)(CO)₂Ind]⁺ to the reaction product, with an activation barrier of 21.3 kcal mol⁻¹. The thermodynamic preferred species was the non-observed complex (insertion), and its formation required higher barriers. In the presence of Cp, all the barriers increased significantly, explaining the inertness of the initial diene complex. The interpretation of this behaviour is associated with the ease of the η⁵ → η³ haptotropic rearrangement of the indenyl, which helps to lower some relevant barriers. This route is not available for the Cp analogue.     

Synthetic studies on the trisaccharide intermediate of resin glycoside merremoside H2

A protected trisaccharide imidate, 2,3-di-O-acetyl-4,6-O-benzylidene-β-d-glucopyranosyl-(1→3)-2-O-chloroacetyl-3-O-benzyl-4-isobutyryl-α-l-rhamnopyranosyl-(1→4)-2-O-isobutyryl-α-l-rhamnopyranosyl trichloroacetimidate (1), has been synthesized by a block synthesis approach. Compound 1 can serve as a key intermediate in the total synthesis of resin glycoside merremoside H₂.     

Simple, automated, high resolution mass spectrometry method to determine the disulfide bond and glycosylation patterns of a complex protein: subgroup A avian sarcoma and leukosis virus envelope glycoprotein

Enveloped viruses must fuse the viral and cellular membranes to enter the cell. Understanding how viral fusion proteins mediate entry will provide valuable information for antiviral intervention to combat associated disease. The avian sarcoma and leukosis virus envelope glycoproteins, trimers composed of surface (SU) and transmembrane heterodimers, break the fusion process into several steps. First, interactions between SU and a cell surface receptor at neutral pH trigger an initial conformational change in the viral glycoprotein trimer followed by exposure to low pH enabling additional conformational changes to complete the fusion of the viral and cellular membranes. Here, we describe the structural characterization of the extracellular region of the subgroup A avian sarcoma and leukosis viruses envelope glycoproteins, SUATM129 produced in chicken DF-1 cells. We developed a simple, automated method for acquiring high resolution mass spectrometry data using electron capture dissociation conditions that preferentially cleave the disulfide bond more readily than the peptide backbone amide bonds that enabled the identification of disulfide-linked peptides. Seven of nine disulfide bonds were definitively assigned; the remaining two bonds were assigned to an adjacent pair of cysteine residues. The first cysteine of surface and the last cysteine of the transmembrane form a disulfide bond linking the heterodimer. The surface glycoprotein contains a free cysteine at residue 38 previously reported to be critical for virus entry. Eleven of 13 possible SUATM129 N-linked glycosylation sites were modified with carbohydrate. This study demonstrates the utility of this simple yet powerful method for assigning disulfide bonds in a complex glycoprotein.     

Spectro-electrochemical and DFT studies of a planar Cu(II)-phenolate complex active in the aerobic oxidation of primary alcohols

A square-planar compound [Cu(pyrimol)Cl] (pyrimol = 4-methyl-2-N-(2-pyridylmethylene)aminophenolate) abbreviated as CuL-Cl) is described as a biomimetic model of the enzyme galactose oxidase (GOase). This copper(II) compound is capable of stoichiometric aerobic oxidation of activated primary alcohols in acetonitrile/water to the corresponding aldehydes. It can be obtained either from Hpyrimol (HL) or its reduced/hydrogenated form Hpyramol (4-methyl-2-N-(2-pyridylmethyl)aminophenol; H₂L) readily converting to pyrimol (L⁻) on coordination to the copper(II) ion. Crystalline CuL-Cl and its bromide derivative exhibit a perfect square-planar geometry with Cu-O(phenolate) bond lengths of 1.944(2) and 1.938(2) Å. The cyclic voltammogram of CuL-Cl exhibits an irreversible anodic wave at +0.50 and +0.57 V versus ferrocene/ferrocenium (Fc/Fc⁺) in dry dichloromethane and acetonitrile, respectively, corresponding to oxidation of the phenolate ligand to the corresponding phenoxyl radical. In the strongly donating acetonitrile the oxidation path involves reversible solvent coordination at the Cu(II) centre. The presence of the dominant Cu^II-L chromophore in the electrochemically and chemically oxidised species is evident from a new fairly intense electronic absorption at 400-480 nm ascribed to a several electronic transitions having a mixed π → π^∗(L) intraligand and Cu-Cl → L charge transfer character. The EPR signal of CuL-Cl disappears on oxidation due to strong intramolecular antiferromagnetic exchange coupling between the phenoxyl radical ligand (L) and the copper(II) centre, giving rise to a singlet ground state (S = 0). The key step in the mechanism of the primary alcohol oxidation by CuL-Cl is probably the α-hydrogen abstraction from the equatorially bound alcoholate by the phenoxyl moiety in the oxidised pyrimol ligand, Cu-L, through a five-membered cyclic transition state.