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  • 1.
    Bartholomeyzik, Teresa
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Jiang, Tuo
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Complex Kinetics in a Palladium(II)-Catalyzed Oxidative Carbocyclization: Untangling of Competing Pathways, Pre-Catalyst Activation, and Product MixturesManuscript (preprint) (Other academic)
  • 2. Battistel, Marcos D.
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Freedberg, Daron I.
    Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 17, p. 4860-4869Article in journal (Refereed)
    Abstract [en]

    We introduce the abundant hydroxyl groups of glycans as NMR handle's and structural probes to expand the repertoire of tools for structure function studies on glycans in solution. To this end, we present the facile detection and assignment of hydroxyl groups in a Wide range of sample concentrations (0.5-1700 mM) and temperatures, ranging from -5 to 25 degrees C.,We then exploit this information to directly detect hydrogen bonds, well-known for their importance in molecular structural determination through NMR. Via HSQC-TOCSY, we were able to determine the directionality; of these hydrogen bonds in sucrose Furthermore, by means Of molecular dynamics simulations in conjunction with NMR, we establish that one Out of the three detected hydrogen bonds arises from intermolecular interactions. This finding may shed light on glycan glycan interactions and glycan recognition by proteins.

  • 3. Chen, Mo
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Brady, John W.
    Wohlert, Jakob
    Molecular Dynamics Simulations of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Chloride and Its Binary Mixtures with Ethanol2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 10, p. 4465-4479Article in journal (Refereed)
    Abstract [en]

    Room temperature ionic liquids (ILs) of the imidazolium family have attracted much attention during the past decade for their capability to dissolve biomass. Besides experimental work, numerous compuational studies have been concerned with the physical properties of both neat ILs and their interactions with different solutes, in particular, carbohydrates. Many classical force fields designed specifically for ILs have been found to yield viscosities that are too high for the liquid state, which has been attributed to the fact that the effective charge densities are too high due to the lack of electronic polarizability. One solution to this problem has been uniform scaling of the partial charges by a scale factor in the range 0.6-0.9, depending on model. This procedure has been shown to improve the viscosity of the models, and also to positively affect other properties, such as diffusion constants and ionic conductivity. However, less attention has been paid to how this affects the overall thermodynamics of the system, and the problems it might create when the IL models are combined with other force fields (e.g., for solutes). In the present work, we employ three widely used IL force fields to simulate 1-n-buty1-3-methyl-imidazolium chloride in both the crystal and the liquid state, as well as its binary mixture with ethanol. Two approaches are used: one in which the ionic charge is retained at its full integer value and one in which the partial charges are uniformly reduced to 85%. We investigate and calculate crystal and liquid structures, molar heat capacities, heats of fusion, self-diffusion constants, ionic conductivity, and viscosity for the neat IL, and ethanol activity as a function of ethanol concentration for the binary mixture. We show that properties of the crystal are less affected by charge scaling compared to the liquid. In the liquid state, transport properties of the neat IL are generally improved by scaling, whereas values for the heat of fusion are unaffected, and results for the heat capacity are ambiguous. Neither full nor reduced charges could reproduce experimental ethanol activities for the whole range of compositions.

  • 4. Harper, James K.
    et al.
    Tishler, Derek
    Richardson, David
    Lokvam, John
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Solid-State NMR Characterization of the Molecular Conformation in Disordered Methyl alpha-L-Rhamnofuranoside2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 26, p. 5534-5541Article in journal (Refereed)
    Abstract [en]

    A combination of solid-state C-13 NMR tensor data and DFT computational methods is utilized to predict the conformation in disordered methyl alpha-L-rhamnofuranoside. This previously uncharacterized solid is found to be crystalline and consists of at least six distinct conformations that exchange on the kHz time scale. A total of 66 model structures were evaluated, and six were identified as being consistent with experimental C-13 NMR data. All feasible structures have very similar carbon and oxygen positions and differ most significantly in OH hydrogen orientations. A concerted rearrangement of OH hydrogens is proposed to account for the observed dynamic disorder. This rearrangement is accompanied by smaller changes in ring conformation and is slow enough to be observed on the NMR time scale due to severe steric crowding among ring substituents. The relatively minor differences in non-hydrogen atom positions in the final structures suggest that characterization of a complete crystal structure by X-ray powder diffraction may be feasible.

  • 5. Johannessen, Christian
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hecht, Lutz
    Barron, Laurence D.
    Glycan structure of a high-mannose glycoprotein from Raman optical activity2011In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, no 23, p. 5349-5351Article in journal (Refereed)
    Abstract [en]

    A revealing signature: The glycan structure of intact yeast external invertase, a high-mannose glycoprotein used as biocatalyst, was investigated by using Raman optical activity (ROA) spectroscopy. The conformational preferences present in mannose-containing di- and trisaccharides were found to be preserved in the glycan chains, with secondary polpeptide backbone structure suppressed.

  • 6.
    Jonsson, K. Hanna M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    NMR analysis of conformationally dependent nJC,H and nJC,C in the trisaccharide α-L-Rhap-(1→2)[α-L-Rhap-(1→3)]-α-L-Rhap-OMe and a site-specifically labeled isotopologue thereof2011In: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 49, no 3, p. 117-124Article in journal (Refereed)
    Abstract [en]

    An array of NMR spectroscopy experiments have been carried out to obtain conformationally dependent 1H,13C- and 13C,13C-spin–spin coupling constants in the trisaccharide α-L-Rhap-(1 → 2)[α-L-Rhap-(1 → 3)]-α-L-Rhap-OMe. The trisaccharide was synthesized with 13C site-specific labeling at C2′ and C2″, i.e. in the rhamnosyl groups in order to alleviate 1H spectral overlap. This facilitated the measurement of a key trans-glycosidic proton–proton cross-relaxation rate using 1D 1H,1H-T-ROESY experiments as well as a 3JC, H coupling employing 1D 1H,13C-long-range experiments, devoid of potential interference from additional J coupling. By means of both the natural abundance compound and the 13C-labeled sample 2D 1H,13C-J-HMBC and 1H,13C-HSQC-HECADE NMR experiments, total line-shape analysis of 1H NMR spectra and 1D 13C NMR experiments were employed to extract 3JC, H, 2JC, H, 3JC, C, and 1JC, C coupling constants. The 13C site-specific labeling facilitates straightforward determination of nJC, C as the splitting of the 13C natural abundance resonances. This study resulted in eight conformationally dependent coupling constants for the trisaccharide and illustrates the use of 13C site-specific labeling as a valuable approach that extends the 1D and 2D NMR methods in current use to attain both hetero- and homonuclear spin–spin coupling constants that subsequently can be utilized for conformational analysis.

  • 7. Kotsyubynskyy, Dmytro
    et al.
    Zerbetto, Mirco
    Šoltésová, Mária
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Charles University Prague .
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kowalewski, Josef
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Polimeno, Antonin
    Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: 2. Interpretation of Complex Dynamics in Linear Oligosaccharides2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 50, p. 14541-14555Article in journal (Refereed)
    Abstract [en]

    A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters.

  • 8. Patel, Dhilon S.
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mallajosyula, Sairam S.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    MacKerell, Alexander D., Jr.
    Conformational Properties of alpha- or beta-(1 -> 6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 11, p. 2851-2871Article in journal (Refereed)
    Abstract [en]

    Conformational sampling for a set of 10 alpha- or beta-(1 -> 6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton-proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated (3)J(H5,H6R) values from the experimental data, prompting optimization of the omega torsion angle parameters associated with (1 -> 6)-linkages. The resulting force field is in overall good agreement (i.e., within similar to 0.5 Hz deviation) from experimental (3)J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6 center dot center dot center dot HO2' hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the omega torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1 -> 6)-linkage as compared to the O6' atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of omega torsion angles in oligosaccharides is also explored.

  • 9.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Conformational studies of carbohydrates: MD simulation and NMR spectroscopy2011Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes various aspects of conformational studies of carbohydrates, from development of the methods by which experimental parameters are gathered to the application of NMR spectroscopy and MD simulation for the analysis of a disaccharide. Paper I describes the use of site-specific 13C labeling as a tool to resolve spectral overlap of 1H frequencies in a trisaccharide, allowing the measurement of important crossrelaxation rates and long-range couplings which were previously obscured. The newly acquired parameters are found to support the conformational equilibrium proposed in a previous study of the molecule. Paper II describes a problem in the J-HMBC experiment that occurs when there are large homonuclear 13C scalar couplings present, a situation typically occurring when studying labeled compounds. By introducing a constant-time element to the pulse-program, the interference by one-bond homonuclear 1JC,C couplings is shown to be suppressed when applied to site-specifically labeled disaccharides. The last project, paper III, concerns the conformation and dynamics of the disaccharide β-L-Fucp-(1→6)-α-D-Glcp-OMe, showing the difficulties associated with the flexible nature of (1→6) linkages. The molecule is found to have significant flexiblity in both the ω and ψ torsions. A three-state equilibrium is found for ω, while ψ has two states connected by a low barrier. The force field parm22/SU01 is able to reproduce and explain the experimental parameters reasonably well, but it is concluded that some of the states have slightly incorrect torsion angles and that the populations are not correctly represented.

  • 10.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Conformations of Flexible Oligosaccharides: Molecular Simulations and NMR spectroscopy2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The conformational preferences of several oligosaccharides are investigated herein using a combination of NMR spectroscopy and molecular dynamics (MD) simulations, focusing on the torsion angles associated with the glycosidic linkages.

    Strategies for obtaining usable J-HMBC spectra for carbons with an adjacent 13C label are described. By employing a selective pulse or a constant time modification, spectra free from interferences are obtained for site-specifically 13C labeled oligosaccharides.

    Intermolecular hydrogen bonding in sucrose is investigated using MD simulations performed at different concentrations. One of the most frequent intermolecular hydrogen bonds in the simulations, O3f∙∙∙HO3g, was detected using the HSQC-TOCSY NMR experiment.

    Based on MD simulations and NMR spectroscopy, the conformational ensemble for a trisaccharide segment of the LeaLex hexasaccharide is proposed to feature conformational exchange between conformations with positive and negative values for the ψ3 torsion angle in the β-D-GlcpNAc-(1→3)-β-D-Galp linkage.

    Using MD simulations, the conformation of the N-acetyl group is shown to influence the glycosidic conformation at a nearby linkage in two oligosaccharides.

    Short (1→6)-linked oligosaccharides are shown to exhibit conformational exchange at the ω and ψ torsion angles. Notably, the former torsion angle populates states with ψ ≈ ±90°. Conformationally sensitive homo- and heteronuclear coupling constants are determined using various NMR experiments. The experimental data, including effective distances from NOESY obtained for two of the compounds, is used to improve the representation of the ω torsion angle in the CHARMM36 force field.

  • 11.
    Pendrill, Robert
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Volpato, Andrea
    Zerbetto, Mirco
    Polimeno, Antonino
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and 13C NMR spin relaxation: conformational preferences of alpha-L-Rhap-alpha-(1 -> 2)-alpha-L-Rhap-OMe in water and dimethyl sulfoxide solutions2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 4, p. 3086-3096Article in journal (Refereed)
    Abstract [en]

    The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide alpha-L-Rhap-alpha-(1 -> 2)-alpha-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-C-13]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)J(CH) and (3)J(CC) coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the psi torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The C-13 NMR spin relaxation parameters T-1, T-2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d(6) at two magnetic field strengths, with standard deviations <= 1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed C-13 relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of C-13 relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.

  • 12.
    Pendrill, Robert
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Methyl 4-O-benzyl-alpha-l-rhamno-pyrano-side2014In: Acta Crystallographica Section E: Structure Reports Online, ISSN 1600-5368, E-ISSN 1600-5368, Vol. 70, p. o561-o562Article in journal (Refereed)
  • 13.
    Pendrill, Robert
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Jonsson, K. Hanna M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Glycan synthesis, structure, and dynamics: A selection2013In: Pure and Applied Chemistry, ISSN 0033-4545, E-ISSN 1365-3075, Vol. 85, no 9, p. 1759-1770Article in journal (Refereed)
    Abstract [en]

    Glycan structural information is a prerequisite for elucidation of carbohydrate function in biological systems. To this end we employ a tripod approach for investigation of carbo hydrate 3D structure and dynamics based on organic synthesis; different experimental spectroscopy techniques, NMR being of prime importance; and molecular simulations using, in particular, molecular dynamics (MD) simulations. The synthesis of oligosaccharides in the form of glucosyl fluorides is described, and their use as substrates for the Lam16A E115S glucosyl synthase is exemplified as well as a conformational analysis of a cyclic beta-(1 -> 3)-heptaglucan based on molecular simulations. The flexibility of the N-acetyl group of aminosugars is by MD simulations indicated to function as a gatekeeper for transitions of glycosidic torsion angles to other regions of conformational space. A novel approach to visualize glycoprotein (GP) structures is presented in which the protein is shown by, for example, ribbons, but instead of stick or space-filling models for the carbohydrate portion it is visualized by the colored geometrical figures known as CFG representation in a 3D way, which we denote 3D-CFG, thereby effectively highlighting the sugar residues of the glycan part of the GP and the position(s) on the protein.

  • 14.
    Pendrill, Robert
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mutter, Shaun T.
    Mensch, Carl
    Barron, Laurence D.
    Blanch, Ewan W.
    Popelier, Paul L. A.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johannessen, Christian
    Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity2019In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 20, no 5, p. 695-705Article in journal (Refereed)
    Abstract [en]

    Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.

  • 15.
    Pendrill, Robert
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Säwén, Elin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Conformation and Dynamics at a Flexible Glycosidic Linkage Revealed by NMR Spectroscopy and Molecular Dynamics Simulations: Analysis of β-ʟ-Fucp-(1→6)-α-ᴅ-Glcp-OMe in Water Solution2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 47, p. 14709-14722Article in journal (Refereed)
    Abstract [en]

    The intrinsic flexibility of carbohydrates facilitates different 3D structures in response to altered environments. At glycosidic (1 -> 46)-linkages, three torsion angles are variable, and herein the conformation and dynamics of beta-1.-Fucp-(1 -> 6)-alpha-D-Glcp-OMe are investigated using a combination of NMR spectroscopy and molecular dynamics (MD) simulations. The disaccharide shows evidence of conformational averaging for the psi and co torsion angles, best explained by a four-state conformational distribution. Notably, there is a significant population of conformations having psi = 85 degrees (clinal) in addition to those having psi = 180 degrees (anfiperiplanar). Moderate differences in C-13 R-1 relaxation rates are found to be best explained by axially symmetric tumbling in combination with minor differences in librational motion for the two residues, whereas the isomerization motions are occurring too slowly to significantly to the observed relaxation rates. The MD simulation was found to give a reasonably good agreement with experiment, especially with respect to diffusive properties, among which the rotational anisotropy, D parallel to/D parallel to, is found to be 2.35. The force field employed showed too narrow omega torsion angles in the gauche trans and gauche gauche states as well as overestimating the population of the gauche trans conformer. This information can subsequently be used in directing parameter developments and emphasizes the need for refinement of force fields for (1 -> 6)-linked carbohydrates.

  • 16.
    Pendrill, Robert
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sørensen, Ole W.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Suppressing one-bond homonuclear 13C,13C scalar couplings in the J-HMBC NMR experiment: application to 13C site-specifically labeled oligosaccharides2014In: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 52, no 3, p. 82-86Article in journal (Refereed)
    Abstract [en]

    Site-specific C-13 isotope labeling is a useful approach that allows for the measurement of homonuclear C-13,C-13 coupling constants. For three site-specifically labeled oligosaccharides, it is demonstrated that using the J-HMBC experiment for measuring heteronuclear long-range coupling constants is problematical for the carbons adjacent to the spin label. By incorporating either a selective inversion pulse or a constant-time element in the pulse sequence, the interference from one-bond C-13,C-13 scalar couplings is suppressed, allowing the coupling constants of interest to be measured without complications. Experimental spectra are compared with spectra of a nonlabeled compound as well as with simulated spectra. The work extends the use of the J-HMBC experiments to site-specifically labeled molecules, thereby increasing the number of coupling constants that can be obtained from a single preparation of a molecule.

  • 17.
    Rönnols, Jerk
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Fontana, Carolina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hamark, Christoffer
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Angles d'Ortoli, Thibault
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ståhle, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zaccheus, Mona V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Säwén, Elin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hahn, Liljan E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Iqbal, Shahzad
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Complete H-1 and C-13 NMR chemical shift assignments of mono- to tetrasaccharides as basis for NMR chemical shift predictions of oligosaccharides using the computer program CASPER2013In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 380, p. 156-166Article in journal (Refereed)
    Abstract [en]

    H-1 and C-13 NMR chemical shift data are used by the computer program CASPER to predict chemical shifts of oligo- and polysaccharides. Three types of data are used, namely, those from monosaccharides, disaccharides, and trisaccharides. To improve the accuracy of these predictions we have assigned the H-1 and C-13 NMR chemical shifts of eleven monosaccharides, eleven disaccharides, twenty trisaccharides, and one tetrasaccharide; in total 43 compounds. Five of the oligosaccharides gave two distinct sets of NMR resonances due to the alpha- and beta-anomeric forms resulting in 48 H-1 and C-13 NMR chemical shift data sets. In addition, the pyranose ring forms of Neu5Ac were assigned at two temperatures, due to chemical shift displacements as a function of temperature. The H-1 NMR chemical shifts were refined using total line-shape analysis with the PERCH NMR software. H-1 and C-13 NMR chemical shift predictions were subsequently carried out by the CASPER program (http://www.casper.organ.su.se/casper/) for three branched oligosaccharides having different functional groups at their reducing ends, namely, a mannose-containing pentasaccharide, and two fucose-containing heptasaccharides having N-acetyllactosamine residues in the backbone of their structures. Good to excellent agreement was observed between predicted and experimental H-1 and C-13 NMR chemical shifts showing the utility of the method for structural determination or confirmation of synthesized oligosaccharides.

  • 18.
    Zaccheus, Mona
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Jackson, Trudy A.
    Wang, An
    Auzanneau, France-Isabelle
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Conformational Dynamics of a Central Trisaccharide Fragment of the LeaLex Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations2012In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 25, p. 4705-4715Article in journal (Refereed)
    Abstract [en]

    Certain carbohydrate structures are recognized as cancer antigens, and identification of these and relevant epitopes are essential in fighting the disease. The trisaccharide beta-D-GlcpNAc-(1?3)-beta-D-Galp-(1?4)-beta-D-GlcpNAc-OMe represents a model for the central region of the LeaLex hexasaccharide and it has herein been investigated by 1D 1H,1H-NOESY experiments to obtain effective interresidue protonproton distances as well as by 2D J-HMBC experiments to determine transglycosidic 3JCH coupling constants. Molecular dynamics (MD) simulations using explicit water as solvent and three different carbohydrate force fields, namely, GLYCAM06, PARM22/SU01, and CHARMM2011, were employed for the interpretation of experimental data. Overall, the force field based MD simulations are able to reproduce the experimental data and the ? torsion angle at the beta-(1?3)-linkage is concluded to be flexible. In addition, different minor states were present for the three force fields with either anti-? or non-exo-anomeric conformations. Transitions between the exo-anomeric and the non-exo-anomeric conformations for the f torsion angle at the beta-(1?4)-linkage in one of the MD simulations were analyzed in detail. It was found that hydrogen-bonding water molecules, interresidue hydrogen bonds and the transitions between antiperiplanar and synperiplanar conformations for the tH torsion angle of an N-acetyl group were all essential in the description of the glycosidic transition process. In particular, the transition of tH may be a general way of regulating other transitions into less populated but biologically important conformational regions.

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