Low-temperature neutron diffraction structures of N-glycoprotein linkage models and analogues: structure refinement and trifurcated hydrogen bonds

The biological addition of oligosaccharide moieties to asparagine residues of N-glycoproteins influences the properties and bioactivities of these macromolecules. The low-temperature neutron crystal structures of three N-glycoprotein linkage models and analogues provide accurate characterization of the three-dimensional structure of the conserved GlcNAc-Asn linkage. These first crystal structures of N-acetylated carbohydrates obtained by neutron diffraction provide high-resolution geometrical parameters that can be used for force-field parametrization and subsequent molecular dynamics simulation of N-glycoproteins. The correct localization of hydrogen atoms demonstrates the occurrence of trifurcated hydrogen bonds and hydrophobic contacts.     

X-Ray Crystallographic Investigation of Fully Acetylated N-(2-Deoxy-2-Acetamido-β-D-Glucopyranosyl)Alkanamides as N-Glycoprotein Linkage Region Analogs

To understand the structural significance of the linkage region of N-glycoproteins, three title sugar amides have been prepared as analogs and their molecular assembly and crystal structures have been solved to explore the effect of acetyl protection and aglycon variation on the conformation, particularly of the N-glycosidic linkage. Comparative analysis of these structures with those of free sugar amides reported earlier showed that conformation of the amido aglycon moiety is not altered significantly by the masking of hydroxyl groups in the form of acetate. The bifurcated antiparallel pattern involving N?H…O and C?H…O hydrogen bonds, a hallmark of the N-glycoprotein models GlcNAcβNHAc and GlcNAcβAsn, is absent in all of the fully protected title alkanamides. The asymmetric unit of the tri-O-acetylated GlcNAcβNHAc contains two different conformations, in one of which the double-pillared hydrogen bond network involving C1 and C2 acetamido groups is antiparallel, while it is parallel in the other. The co-occurrence of a molecular assembly motif—a double-pillared parallel and antiparallel hydrogen bonding pattern—is hitherto unknown in the crystal structures of N-glycoprotein linkage region models and analogs.     

Exploring the Effect of Bioisosteric Replacement of Carboxamide by a Sulfonamide Moiety on N‐Glycosidic Torsions and Molecular Assembly: Synthesis and X‐ray Crystallographic Investigation of N‐(β‐D‐Glycosyl)sulfonamides as N‐Glycoprotein Linkage Region Analogues

N‐Glycoprotein linkage region constituents, 2‐acetamido‐2‐deoxy‐β‐D ‐glucopyranose (GlcNAc) and asparagine (Asn) are conserved among all the eukaryotes. To gain a better understanding for nature’s choice of GlcNAcβAsn as linkage region constituents and inter‐ and intramolecular carbohydrate–protein interactions, a detailed systemic structural study of the linkage region conformation is essential. Earlier crystallographic studies of several N‐(β‐glycopyranosyl)alkanamides showed that N‐glycosidic torsion, ?_N, is influenced to a larger extent by structural variation in the sugar part than that of the aglycon moiety. To explore the effect of the bioisosteric replacement of a carboxamide group by a sulfonamide moiety on the N‐glycosidic torsions as well as on molecular assembly, several glycosyl methanesulfonamides and glycosyl chloromethanesulfonamides were synthesized as analogues of the N‐glycoprotein linkage region, and crystal structures of seven of these compounds have been solved. A comparative analysis of this series of crystal structures as well as with those of the corresponding alkanamido derivatives revealed that N‐glycosidic torsion, ?_N, does not alter significantly. Methanesulfonamido and chloromethanesulfonamido derivatives of GlcNAc display a different aglycon conformation compared to other sulfonamido analogues. This may be due to the cumulative effect of the direct hydrogen bonding between N1 and O1′ and C? H???O interactions of the aglycon chain, revealing the uniqueness of the GlcNAc as the linkage sugar.     

Semiquantitative analysis of isomeric oligosaccharides by negative-ion mode UV-MALDI TOF postsource decay mass spectrometry and their fragmentation mechanism study at N-acetyl hexosamine moiety

Postsource decay (PSD) spectra of isomeric neutral lactooligosaccharide mixtures were measured from the chlorinated molecules [M + Cl]- by negative-ion mode ultraviolet matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (UV-MALDI TOF MS) to estimate quantitatively the mixing ratios in their mixtures. The PSD ions specific to each isomeric structure were used to distinguish the linkage and branching isomers, and the molar ratios of the isomers were estimated from their ion abundances. The relative ion abundances changed linearly in the PSD spectra of the mixtures of the isomers as their molar ratio was varied in the analyte solutions. Therefore, the molar ratios of the isomers in the analyte mixtures could be estimated semiquantitatively. In addition, we studied their fragmentation mechanisms in N-acetyl hexosamines such as GlcNAc, which enabled us to quantitatively analyze the structures of the isomers of lactooligosaccharides. The conjugated systems elongate in the chemical species of the Z-type fragmentation on the 3-linked GlcNAc owing to the acetoamido groups at the C-2 positions, which made the chemical species of the Z-type ions stable. The glycosyl bonds of the front of GlcNAc cleaved easily as a C-type fragmentation because the negative charge at the anomeric position could be delocalized to the carbonyl oxygen atom at the acetoamido group of GlcNAc. These factors caused the stabilization of the chemical species of the C/Z fragment ions produced by the double cleavage around GlcNAc.     

Conformational studies of Zn-Ligand-Hexose diastereomers using ion mobility measurements and density functional theory calculations

Ion mobility studies and density functional theory calculations were used to study the structures of [Zn/diethylenetriamine/Hexose/Cl]+ complexes in an effort to probe differences in the three-dimensional conformations. This information allows us to gain insight into the structure of these complexes before collisional activation, which is the first step in understanding the stereoselective dissociations observed under collisionally activated conditions. The collision cross sections obtained from the ion mobility measurements showed that the mannose structure is more compact than the galactose and glucose complexes, respectively. Using density functional theory, candidate structures for each of the experimentally observed complexes were generated. Two criteria were used to determine the most likely structures of these complexes before activation: (1) The allowed relative energies of the molecules (between 0-90 kJ/mol) and (2) collision cross section agreement (within 2%) between the theoretically determined structures and the experimentally determined cross section. It was found that the identity of the monosaccharide made a difference in the overall conformation of the metal-ligand-monosaccharide complex. For glucose and galactose, metal coordination to O(6) was found to be favorable, with the monosaccharide occupying the 4C1 chair conformation, while for mannose, O(2) metal coordination was found with the monosaccharide in a B3,0 conformation. Coordination numbers varied between four and six for the Zn(II) metal centers. Given these results, it appears that the stereochemistry of the monosaccharide influences the conformation and metal coordination sites of the Zn(II)/monosaccharide/dien complex. These differences may influence the dissociation products observed under collisionally activated conditions.     

Expeditious chemoenzymatic synthesis of homogeneous N-glycoproteins carrying defined oligosaccharide ligands

An efficient chemoenzymatic method for the construction of homogeneous N-glycoproteins was described that explores the transglycosylation activity of the endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae (Endo-A) with synthetic sugar oxazolines as the donor substrates. First, an array of large oligosaccharide oxazolines were synthesized and evaluated as substrates for the Endo-A-catalyzed transglycosylation by use of ribonuclease B as a model system. The experimental results showed that Endo-A could tolerate modifications at the outer mannose residues of the Man3GlcNAc-oxazoline core, thus allowing introduction of large oligosaccharide ligands into a protein and meanwhile preserving the natural, core N-pentasaccharide (Man3GlcNAc2) structure in the resulting glycoprotein upon transglycosylation. In addition to ligands for galectins and mannose-binding lectins, azido functionality could be readily introduced at the N-pentasaccharide (Man3GlcNAc2) core by use of azido-containing Man3GlcNAc oxazoline as the donor substrate. The introduction of azido functionality permits further site-specific modifications of the resulting glycoproteins, as demonstrated by the successful attachment of two copies of alphaGal epitopes to ribonuclease B. This study reveals a broad substrate specificity of Endo-A for transglycosylation, and the chemoenzymatic method described here points to a new avenue for quick access to various homogeneous N-glycoproteins for structure-activity relationship studies and for biomedical applications.     

Conformational isomerism of chlorophenylthioureas and intramolecular N---H … Cl hydrogen bonds: IR spectra of N---H stretching vibrations

The vN---H regions of the IR spectra of thioureas with chlorophenyl (ClPh) groups and those with halophenyl groups were measured in dilute CCl₄ solution. The observed vN---H bands were classified into eight groups according to the wavenumbers and the two substituent groups. The suggested conformational states and the formation of intramolecular N---H … Cl hydrogen bonds in these compounds were discussed in comparison with those of the urea analogs. It was found that these thiourea derivatives are more stable in the cis form than the urea analogs and that thioureas with o-ClPh groups form fewer intramolecular N---H … Cl hydrogen bonds than do the urea analogs.     

Characterization of oligosaccharide moieties of glycopeptides by microwave-assisted partial acid hydrolysis and mass spectrometry

Microwave-assisted partial acid hydrolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were used to study oligosaccharide structures of glycopeptides. Tryptic N-glycosylated peptides of horseradish peroxidase, with MH+ ions at m/z 2533, 2612, 3355, 3673, and 5647, were used as test cases. Within a microwave exposure with trifluoroacetic acid of 2 min, partial cleavages of the oligosaccharides of these tryptic N-glycosylated peptides were observed. The data showed that the most labile group within the oligosaccharides is the fucose (Fuc) residue, and that a majority of the end cleavage products are peptides with one N-acetylglucosamine (GlcNAc) residue linked to asparagine (Asn). In addition, the glycopeptides with m/z 3355 and 3673 carry an oligosaccharide (Xyl)Man3(Fuc)GlcNAc2, the glycopeptide at m/z 5647 carries two oligosaccharides (Xyl)Man3(Fuc)GlcNAc2, and the glycopeptides at m/z 2612 and 2533 carry (Xyl)Man3GlcNAc2 and (Fuc)GlcNAc, respectively. However, the glycosylation site of the m/z 2612 peptide at Asn286 is partially occupied. This simple and rapid method is particularly useful in identifying glycopeptides and obtaining monosaccharide compositions of glycopeptides.     

Unclassical hydrogen bonds of C-H?O and C-H?Cl in the crystals of 1,4-diaryl Hantzsch esters

Three novel N1-substituted derivatives of Hantzsch ester were synthesized and the molecular structures were studied by using X-ray crystallography. Two types of unclassical hydrogen bonds C-H?O and C-H?Cl were presented in the crystals. The formation of such a hydrogen bond is dependent on the nature of the substituent at C23.     

Ionic-liquid-based MS probes for the chemo-enzymatic synthesis of oligosaccharides

A new N-benzenesulfonyl-based ionic-liquid mass spectroscopy label (I-Tag2) for covalent attachment to substrates has been prepared. I-Tag2 was used to monitor oligosaccharide elongation and serve as a purification handle. Starting from chemically synthesized I-Tag2-labelled N-acetyl glucosamine (GlcNAc) 1, I-Tag2-LacNAc (Galβ(1-4)GlcNAc) 2 and I-Tag2-Lewis(X) (Galβ(1-4)[Fucα(1-3)]GlcNAc) 3, which are oligosaccharides of biological relevance, were enzymatically prepared. The apparent kinetic parameters for the enzyme catalysed transformations with β-1,4-galactosyltransferase (β-1,4-GalT) and fucosyltransferase VI (FucT VI) were measured by LC-MS demonstrating the applicability and versatility of the new I-Tags in enzymatic transformations with glycosyltransferases.     

Regioselective Glycosylation Strategies for the Synthesis of Group Ia and Ib Streptococcus Related Glycans Enable Elucidating Unique Conformations of the Capsular Polysaccharides

Group B Streptococcus serotypes Ia and Ib capsular polysaccharides are key targets for vaccine development. In spite of their immunospecifity these polysaccharides share high structural similarity. Both are composed of the same monosaccharide residues and differ only in the connection of the Neu5Acα2-3Gal side chain to the GlcNAc unit, which is a β1-4 linkage in serotype Ia and a β1-3 linkage in serotype Ib. The development of efficient regioselective routes for GlcNAcβ1-3[Glcβ1-4]Gal synthons is described, which give access to different group B Streptococcus (GBS) Ia and Ib repeating unit frameshifts. These glycans were used to probe the conformation and molecular dynamics of the two polysaccharides, highlighting the different presentation of the protruding Neu5Acα2-3Gal moieties on the polysaccharide backbones and a higher flexibility of Ib polymer relative to Ia, which can impact epitope exposure.     

Calix

Chiral calix[4]arene derivatives with four O-(N-acetyl-PhgOMe), (1), (Phg denotes R-phenylglycine), or O-(N-acetyl-LeuOMe) (2) strands have been synthesised. Both compounds exist in chloroform in stable cone conformations with a noncovalently organised cavity at the lower rim that is formed by circular interstrand amidic hydrogen bonds. Such organisation affects both the selectivity and extraction/transport properties of 1 and 2 toward metal cations. Calix[4]arene derivatives with one OCH2COPhgOMe strand (3), two OCH2COPhgOMe strands (5) and with 1,3-OMe-2,4-(O-CH2COPhgOMe) substituents (4) at the lower rim have also been prepared. For 3, a conformation stabilised by a circular hydrogen-bond arrangement is found in chloroform, while 4 exists as a time-averaged C2 conformation with two intramolecular NH ...OCH3 hydrogen bonds. Compound 5 has a unique hydrogen-bonding motif in solution and in the solid state with two three-centred NH-.. O and two OH...O hydrogen bonds at the lower rim. This motif keeps 5 in the flattened cone conformation in chloroform. The X-ray structure analysis of 1 revealed a molecular structure with C2 symmetry; this structure is organised in infinite chains by intra- and intermolecular H bonds. The solid-state and solution structures of the [1-Na]ClO4 complex are identical, C4 symmetric cone conformations.     

Effect of Through‐Bond Interaction on Conformation and Structure in Rod‐Shaped Donor–Acceptor Systems. Part 1

The crystal structures of five N‐arylpiperidin‐4‐one derivatives 2P2, 3P2, 5P2, 1P3 , and 2P3 are presented (Fig. 2 and Tables 1–5) and discussed together with the derivatives 1P2 and 4P2 published previously. In all but one structure, 1P2 , the aryl group is in an equatorial position. The piperidine ring adopts a normal chair conformation. In 1P2 , the piperidine ring central C? C bonds are significantly elongated, which is consistent with the idea that through‐bond interaction is more pronounced in the axial conformation. Through‐bond interaction also influences the pyramidalization at the piperidine C(4)‐atom in such a way that a strong interaction is directing the ethylene C‐atom C(9) into the axial direction.     

Linear synthesis of the tumor-associated carbohydrate antigens Globo-H,SSEA-3, and Gb3

The tumor-associated carbohydrate antigens Globo-H, SSEA-3, and Gb3 were synthesized in a linear fashion using glycosyl phosphate monosaccharide building blocks. All of the building blocks were prepared from readily available common precursors. The difficult alpha-(1-->4-cis)-galactosidic linkage was installed using a galactosyl phosphate donor with high selectivity. Introduction of the beta-galactosamine unit required the screening a variety of amine protecting groups to ensure good donor reactivity and protecting group compatibility. An N-trichloroacetyl-protected galactosamine donor performed best for the installation of the beta-glycosidic linkage. Conversion of the trichloroacetyl group to the N-acetyl group was achieved under mild conditions, fully compatible with the presence of multiple glycosidic bonds. This synthetic strategy is expected to be amenable to the synthesis of the globo-series of tumor antigens on solid-support.     

Effect of benzannelation on the conformational flexibility of the rings in oxo, imino, and methylene derivatives of cyclohexa-1,4-diene

The effect of benzannelation on the equilibrium conformation and flexibility of the dihydrocycle in cyclohexa-1,4-dienone,para-quinone, and their imino and methylene analogs was studied by the semiempirical quantum-chemical AM1 method. The equilibrium conformations of the carbonyl derivatives are planar. In the imino- and methylene-substituted analogs, the dihydrocycle adopts a boat conformation due to repulsions between substituted analogs, the dihydrocycle adopts a boat conformation due to repulsions between the hydrogen atoms at the exocyclic double bond and in theperi positions of the benzene rings. Annelation of cyclohexa-2,5-dien-1-one andpara-quinone with benzene rings at the C=C double bonds causes an increase in the conformational flexibility of the partially hydrogenated ring owing to an increase in the bending strain in the first compound and a decrease in the conjugation between the carbonyl groups and the remaining part of the molecule in the second compound. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 388–390, March, 1998.     

Interplay of intramolecular hydrogen bonds,OH orientations,and symmetry factors in the stabilization of polyhydroxybenzenes

Polyhydroxybenzenes are the parent compounds of large classes of derivatives, many of which exhibit biological activities. The study of derivatives highlights the importance of the conformation stabilizing factors of the parent compounds. To identify these factors, a systematic comparative study of polyhydroxybenzenes was carried out through a computational study of all possible structures and conformers in vacuo and in three solvents differing by their polarities and by the types of interactions with the solute molecule (water, chloroform, and acetonitrile); the results in solution are complemented by the study of adducts with explicit water molecules and, for the simpler structures, also with explicit acetonitrile molecules. The greatest conformation stabilizing effect pertains to intramolecular hydrogen bonds, with preference for consecutive H‐bonds. Uniform orientation of the phenol OH is a stabilizing factor for structures with meta OH groups. Preference for structures with meta OH and with greater symmetry increases as the medium polarity increases. The coexistence of intramolecular H‐bonds and solute–solvent intermolecular H‐bonds in water and acetonitrile solution narrows the solvent‐effect difference between conformers with and without intramolecular H‐bonds. Comparison of results from different calculation methods (HF, MP2, and DFT/B3LYP, with 6‐31G(d,p) and 6‐31++G(d,p) basis sets) shows consistency of the identified trends. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Self‐inclusion structure of 5,11,17,23‐tetrakis(azidomethyl)‐25,26,27,28‐tetrahydroxycalix[4]arene,and 5,11,17,23‐tetra‐tert‐butyl‐25,27‐bis(chloroacetoxy)‐26,28‐bis(2‐pyridylmethoxy)calix[4]arene

In the structures of the two title calix[4]arene derivatives, C₃₂H₂₈N₁₂O₄, (I), and C₆₀H₆₈Cl₂N₂O₆, (II), compound (I) adopts an open‐cone conformation in which there are four intramolecular O—H...O hydrogen bonds, while compound (II) adopts a distorted chalice conformation where the two pendant pyridyl rings, one of which is disordered, are almost mutually perpendicular, with an interplanar angle of 79.2 (2) or 71.4 (2)°. The dihedral angles between the virtual plane defined by the four bridging methylene C atoms and the phenol rings are 120.27 (7), 124.03 (6), 120.14 (8) and 128.25 (7)° for (I), and 95.99 (8), 135.93 (7), 97.21 (8) and 126.10 (8)° for (II). In the supramolecular structure of (I), pairs of molecules associate by self‐inclusion, where one azide group of the molecule is inserted into the cavity of the inversion‐related molecule, and the association is stabilized by weak intermolecular C—H...N hydrogen bonds and π(N₃)–π(aromatic) interactions. The molecular pairs are linked into a two‐dimensional network by a combination of weak intermolecular C—H...N contacts. Each network is further connected to its neighbor to produce a three‐dimensional framework via intersheet C—H...N hydrogen bonds. In the crystal packing of (II), the molecular components are linked into an infinite chain by intermolecular C—H...O hydrogen bonds. This study demonstrates the ability of calix[4]arene derivatives to form self‐inclusion structures.     

STM study on 2D molecular assemblies of luminescent quinacridone derivatives: structure fine-tuned by introducing bulky substitutes and co-adsorption with monofunctional/bifunctional acid

We describe the 2D assemblies of a series of N,N'-dialkyl-substituted quinacridone derivatives on highly oriented pyrolytic graphite observed by scanning tunneling microscopy. Our experiments have demonstrated that pure quinacridone derivatives take contractive conformations, but quinacridone derivatives take extended conformations when co-adsorbed with dicarboxylic acid. Interestingly, by co-adsorption with monofunctional acid stearic acid, quinacridone derivative bearing two smaller substituted groups of trifluoromethyl takes an extended conformation, while quinacridone derivative bearing two larger substituted groups of tert-butyl still takes a contractive conformation. Therefore, the 2D structure of the quinacridone derivatives can be fine-tuned by co-adsorbing with monofunctional/bifunctional acid through hydrogen bonds.     

Structural, infrared, and density functional theory studies of N,N,N',N'-Tetramethylimidazolidinium dichloride: a model for cation-anion association of headgroups and counterions in the interfacial regions of gemini micelles

N,N,N',N'-Tetramethylimidazolidinium dichloride (1-Im-1 2Cl) has been studied as a model system for cation-anion interactions in the interfacial regions of gemini micelles by X-ray crystallography, density functional theory (DFT) calculations, and infrared spectroscopy. Single crystals of 1-Im-1 2Cl contain 1-Im-1 dications, whose five-membered rings adopt a distorted envelope conformation. Eight chloride anions surround each dication, two of which are cradled above and below the five-membered ring (apical) and six of which are dispersed about the periphery of the ring (equatorial). The cations and anions are linked in the solid state by an extensive network of weak C-H...Cl hydrogen bonds that involve all of the H atoms of the dication. The calculated (DFT at the 6-31+G(d) level) structure of the asymmetric unit, which consists of a dication and two apical chloride ions, closely resembles the equivalent unit in the crystal structure with respect to bond distances and angles, the conformation of the 1-Im-1 ring, and the nature and location of the C-H...Cl hydrogen bonds. The calculated IR spectrum predicts a number of absorptions in the 3000 cm(-1) region, assigned as C-H...Cl stretching modes, which are consistent with the presence of an intense band in the observed IR spectrum of the crystals. Over all, this study supports the notion that apical chloride ions interact more strongly with gemini surfactant headgroups by forming multiple hydrogen bonds in ion pairs of a type that cannot be present in the corresponding ion pairs of quaternary headgroups with counterions of single-chain surfactants.     

Synthesis and Crystal Structure of N-Benzyl-N＇-（2-pyridyl）urea and Its Mononuclear Cu（Ⅱ） Complex

A new ligand of N-benzyl-N＇-（2-pyridyl）urea L and its self-assembly product with CuCl2, [Cu（Ⅱ）LCl2]∞ 1, have been synthesized and structurally characterized by IR, 1H NMR and single-crystal X-ray diffraction analysis. In the structure of L, the urea groups adopt Z,E conformation to form dimers through intermolecular hydrogen bonds; while in complex 1, it assumes Z,Z conformation to fit for the coordination sphere of the Cu（Ⅱ） ions. The coordinated units are connected through intermolecular N-H...Cl hydrogen bonds to form an extended 2D framework. Finally, a 3D structure is obtained via π-π stacking interactions between pyridyl rings