flexibility at a glycosidic linkage revealed by molecular dynamics stochastic modeling and 13c nmr spin relaxation conformational preferences of α l rhap α 1 2 α l rhap ome in water and dimethyl sulfoxide solutions

Coupling between global reorientation and local motion is essential for reproducing NMR relaxation parameters of a flexible molecule

Disentangling the numbers behind agriculture-driven tropical deforestation

Tropical deforestation continues at alarming rates with profound impacts on ecosystems, climate, and livelihoods, prompting renewed commitments to halt its continuation. Although it is well established that agriculture is a dominant driver of deforestation, rates and mechanisms remain disputed and often lack a clear evidence base. We synthesize the best available pantropical evidence to provide clarity on how agriculture drives deforestation. Although most (90 to 99%) deforestation across the tropics 2011 to 2015 was driven by agriculture, only 45 to 65% of deforested land became productive agriculture within a few years. Therefore, ending deforestation likely requires combining measures to create deforestation-free supply chains with landscape governance interventions. We highlight key remaining evidence gaps including deforestation trends, commodity-specific land-use dynamics, and data from tropical dry forests and forests across Africa

Conformations of Flexible Oligosaccharides : Molecular Simulations and NMR spectroscopy

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.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 5: Accepted. Paper 6: Manuscript.</p

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 Solution

The intrinsic flexibility of carbohydrates facilitates different 3D structures in response to altered environments. At glycosidic (1 -&gt; 46)-linkages, three torsion angles are variable, and herein the conformation and dynamics of beta-1.-Fucp-(1 -&gt; 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 -&gt; 6)-linked carbohydrates.AuthorCount:3;</p

Methyl 4-O-benzyl-α-l-rhamnopyranoside

In the title compound, C14H20O5, an intermediate in the synthesis of oligosaccharides, the glycosidic [H—C—O—C(H3)] torsion angle ϕH is 52.3° and the exo-cyclic [H—C—O—C(H2)] torsion angle θH is −11.7°. The hexapyranose ring has a chair conformation. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming chains propagating along [010]. Enclosed within the chains are R33(12) ring motifs involving three molecules. The chains are linked via C—H...π interactions, forming a three-dimensional network

Suppressing one-bond homonuclear 13C,13C scalar couplings in the J-HMBC NMR experiment : application to 13C site-specifically labeled oligosaccharides

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.AuthorCount:3;</p

Glycan synthesis, structure, and dynamics : A selection

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 -&gt; 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.AuthorCount:3;</p

Direct Evidence for Hydrogen Bonding in Glycans : A Combined NMR and Molecular Dynamics Study

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.AuthorCount:4;</p

Molecular Dynamics Simulations of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Chloride and Its Binary Mixtures with Ethanol

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.AuthorCount:5;</p