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  • 1. Battistel, Marcos D.
    et al.
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Freedberg, Daron I.
    Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study2013Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 17, s. 4860-4869Artikel i tidskrift (Refereegranskat)
    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.

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  • 2. Bortolini, C.
    et al.
    Zhao, Jingjing
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Ciccone, L.
    Xu, Hongyi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Zou, Xiaodong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Dong, Mingdong
    Atomic Structure of Amyloid CrystalsManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

     

    A deep understanding of the self-assembly and crystallization of biomolecules as highly ordered biomaterials is crucial to enable the design and the generation of complex functional systems for cutting-edge applications in nanotechnology and biomedicine. In this work, we determined the atomic structure of Aβ16-20 crystals, a fragment of amyloid-β which aberrant folding is linked to the etiology of Alzheimer’s disease, the most common cause of dementia. We detailed the hierarchical aggregation mechanism of Aβ16-20 into highly ordered crystals and revealed that the self-assembly is reversible, leading to the formation of oligomers as an intermediate. Our structural investigation combined with molecular dynamics simulations highlights how a combination of favorable non-covalent interactions drives the efficient fast self-assembly and enhanced stability. We studied the chemical and surface properties of amyloid crystals, including their mechanical properties and their capability to transmit light; the long-rang order of Aβ16-20 crystals enables them to be used as optical waveguide materials for biologically based modulation and sensing. Our results shed new light on pathogenic amyloid assembly at the atomic level and reveal the potential of amyloid crystals for applications in nanotechnology.

  • 3. Harper, James K.
    et al.
    Tishler, Derek
    Richardson, David
    Lokvam, John
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Solid-State NMR Characterization of the Molecular Conformation in Disordered Methyl alpha-L-Rhamnofuranoside2013Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, nr 26, s. 5534-5541Artikel i tidskrift (Refereegranskat)
    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.

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  • 4. Kotsyubynskyy, Dmytro
    et al.
    Zerbetto, Mirco
    Šoltésová, Mária
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Charles University Prague .
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kowalewski, Josef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Polimeno, Antonin
    Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: 2. Interpretation of Complex Dynamics in Linear Oligosaccharides2012Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 50, s. 14541-14555Artikel i tidskrift (Refereegranskat)
    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.

  • 5.
    Lightowler, Molly
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Investigating polymorphism in small molecules using three-dimensional electron diffraction2022Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    For scientific, regulatory and intellectual property reasons, the discovery and characterisation of polymorphic systems is an integral aspect of the development process of any solid-formulated drug product. Yet, these studies are often hindered by crystal quality and size, poor yields and the generation of mixtures of phases. Three-dimensional electron diffraction (3D ED) is a technique capable of structure determination from individually selected, nanometre-sized crystals. In this thesis, 3D ED is applied to investigate polymorphism in small molecules. The unique advantages of the method are highlighted across numerous studies to demonstrate how 3D ED can broaden the scope of polymorphism discovery and characterisation in the screening and selection of pharmaceutical crystal forms. 

    3D ED is first applied to reveal that two crystallisation methods believed for 47 years to produce Form δ of the pharmaceutical compound indomethacin result in two different polymorphs, highlighting the power of the method for polymorphism discovery. The polymorphic crystal structures of a small molecule are then determined directly from melt-grown compact spherulites for the first time to show how 3D ED can widen the application of melt crystallisation in polymorph screening, where polycrystalline spherulites are common products. Furthermore, 3D ED is combined with on-the-grid crystallisation and plunge freezing to follow the polymorph evolution of glycine during crystallisation from an aqueous solution to demonstrate the ability of the method to monitor crystallisation processes in situ. The final part of the thesis explores how a high-throughput method combining 3D ED data collection in batch mode with semi-automated data processing can be applied for the phase analysis of complex melt crystallisation products to improve the efficiency and accuracy of polymorph screening.

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    Investigating polymorphism in small molecules using three-dimensional electron diffraction
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  • 6.
    Nozière, Barbara
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Meteorologiska institutionen (MISU).
    Córdova, Armando
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    A Kinetic and Mechanistic Study of the Amino Acid Catalyzed Aldol Condensation of Acetaldehyde in Aqueous and Salt Solutions2008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 13, s. 2827-2837Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The amino acid-catalyzed aldol condensation is of great interest in organic synthesis and natural environments such as atmospheric particles. But kinetic and mechanistic information on these reactions is limited. In this work, the kinetics of the aldol condensation of acetaldehyde in water and aqueous salt solutions (NaCl, CaCl2, Na2SO4, MgSO4), catalyzed by five amino acids (glycine, alanine, serine, arginine, and proline) at room temperature (295 ± 2K) has been studied. Monitoring the formation of three products, crotonaldehyde, 2,4-hexadienal, and 2,4,6-octatrienal by UV-Visible absorption over 200 – 1100 nm revealed two distinct kinetic regimes: at low amino acid concentrations (in all cases, below 0.1 M) the overall reaction was first order with respect to acetaldehyde and kinetically limited by the formation of the enamine intermediate. At larger amino acid concentrations (at least 0.3 M) the kinetics was second order and controlled by the C-C bond-forming step. The first-order rate constants increased linearly with amino acid concentration, consistent with the enamine formation. Inorganic salts further accelerated the enamine formation according to their pKb plausibly by facilitating the iminium and/or enamine formation. The rate constant of the C-C bond-forming step varied with the square of amino acid concentration, suggesting the involvement of two amino acid molecules. Thus, the reaction proceeded via a Mannich pathway. However, the contribution of an aldol pathway, first-order in amino acid, could not be excluded. Our results show that the rate constant for the self-condensation of acetaldehyde in aqueous atmospheric aerosols (up to 10 of mM of amino acids) is identical as in sulfuric acid 10 - 15 M (kI ~ 10-7 - 10-6 s-1), clearly illustrating the potential importance of amino acid catalysis in natural environments. This work also demonstrates that under usual laboratory conditions and in natural environments aldol condensation is likely to be kinetically controlled by the enamine formation. Notably, kinetic investigations of the C-C bond-forming addition step would only be possible with high concentrations of amino acids.

  • 7.
    Pendrill, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sørensen, Ole W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Suppressing one-bond homonuclear 13C,13C scalar couplings in the J-HMBC NMR experiment: application to 13C site-specifically labeled oligosaccharides2014Ingår i: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 52, nr 3, s. 82-86Artikel i tidskrift (Refereegranskat)
    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.

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  • 8.
    Pu, Maoping
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Privalov, Timofei
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ab initio dynamics trajectory study of the heterolytic cleavage of H2 by a Lewis acid [B(C6F5)3] and a Lewis base [P(tBu)3]2013Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, nr 15, artikel-id 154305Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Activation of H-2 by a frustrated Lewis pair (FLP) composed of B(C6F5)(3) and P(tBu)(3) species has been explored with high level direct ab initio molecular dynamics (AIMD) simulations at finite temperature (T = 300 K) in gas phase. The initial geometrical conditions for the AIMD trajectory calculations, i.e., the near attack conformations of FLP + H-2, were devised using the host-guest model in which suitable FLP conformations were obtained from the dynamics of the B(C6F5)(3)/P(tBu)(3) pair in gas phase. AIMD trajectory calculations yielded microscopic insight into effects which originate from nuclear motion in the reacting complex, e. g., the alternating compression/elongation of the boron-phosphorous distance and the change of the pyramidality of boron in B(C6F5)(3). The ensemble averaged trajectory analysis has been compared with the minimum energy path (MEP) description of the reaction. Similar to MEP, AIMD shows that an attack of the acid/base pair on the H-H bond gives rise to the polarization of the H-2 molecule and as a consequence generates a large dipole moment of the reacting complex. The MEP and AIMD portrayals of the reaction are fundamentally different in terms of the magnitude of the motion of nuclei in B(C6F5)(3) and P(tBu)(3) during the H-2 cleavage. In the AIMD trajectory simulations, geometries of B(C6F5)(3) and P(tBu)(3) appear as nearly frozen on the short time scale of the H-2 cleavage. This is contrary to the MEP picture. Several of the concepts which arise from this work, e. g., separation of time scales of nuclear motion and the time-dependence of the donor-acceptor interactions in the reacting complex, are important for the understanding of chemical reactivity and catalysis.

  • 9.
    Ramstadius, Clinton
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Boklund, Mikael
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Conversion of fructose into a building block for the synthesis of carbocyclic mannose mimics2011Ingår i: Tetrahedron: asymmetry, ISSN 0957-4166, E-ISSN 1362-511X, Vol. 22, nr 4, s. 399-405Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fructose was converted into C-1 diastereomeric carbocyclic building blocks resembling mannose using ruthenium-catalysed ring-closing metathesis as a key step. The potential use of the compounds in the synthesis of valienamine pseudodisaccharides is demonstrated using Mitsunobu coupling chemistry directly between a carbohydrate sulfonamide and the carbasugar C-1 alcohols.

  • 10.
    Säwén, Elin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Östervall, Jennie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Molecular conformations in the pentasaccharide LNF-1 derived from NMR spectroscopy and molecular dynamics simulations2011Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, nr 21, s. 7109-7121Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The conformational dynamics of the human milk oligosaccharide lacto-N-fucopentaose (LNF-1), α-l-Fucp-(1 → 2)-β-d-Galp-(1 → 3)-β-d-GlcpNAc-(1 → 3)-β-d-Galp-(1 → 4)-d-Glcp, has been analyzed using NMR spectroscopy and molecular dynamics (MD) computer simulations. Employing the Hadamard 13C-excitation technique and the J-HMBC experiment, 1H,13C trans-glycosidic J coupling constants were obtained, and from one- and two-dimensional 1H,1H T-ROESY experiments, proton–proton cross-relaxation rates were determined in isotropic D2O solution. In the lyotropic liquid-crystalline medium consisting of ditetradecylphosphatidylcholine, dihexylphosphatidylcholine, N-cetyl-N,N,N-trimethylammonium bromide, and D2O, 1H, 1H and one-bond 1H, 13C residual dipolar couplings (RDCs), as well as relative sign information on homonuclear RDCs, were determined for the pentasaccharide. Molecular dynamics simulations with explicit water were carried out from which the internal isomerization relaxation time constant, τN, was calculated for transitions at the ψ torsion angle of the β-(1 → 3) linkage to the lactosyl group in LNF-1. Compared to the global reorientation time, τM, of 0.6 ns determined experimentally in D2O solution, the time constant for the isomerization relaxation process, τN(scaled), is about one-third as large. The NMR parameters derived from the isotropic solution show very good agreement with those calculated from the MD simulations. The only notable difference occurs at the reducing end, which should be more flexible than observed by the molecular simulation, a conclusion in complete agreement with previous 13C NMR relaxation data. A hydrogen-bond analysis of the MD simulation revealed that inter-residue hydrogen bonds on the order of 30% were present across the glycosidic linkages to sugar ring oxygens. This finding highlights that intramolecular hydrogen bonds might be important in preserving well-defined structures in otherwise flexible molecules. An analysis including generalized order parameters obtained from nuclear spin relaxation experiments was performed and successfully shown to limit the conformational space accessible to the molecule when the number of experimental data are too scarce for a complete conformational analysis.

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