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  • 1. 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.

  • 2. Kaderavek, Pavel
    et al.
    Zapletal, Vojtech
    Fiala, Radovan
    Srb, Pavel
    Padrta, Petr
    Precechtelova, Jana Pavlikova
    Soltesova, Maria
    Kowalewski, Jozef
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chmelik, Josef
    Sklenar, Vladimir
    Zidek, Lukas
    Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies2016In: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 266, p. 23-40Article in journal (Refereed)
    Abstract [en]

    Standard spectral density mapping protocols, well suited for the analysis of N-15 relaxation rates, introduce significant systematic errors when applied to C-13 relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and C-13 frequencies can be obtained from data acquired at three magnetic fields for uniformly C-13-labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.

  • 3. Mensch, Carl
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johannessen, Christian
    Studying the Glycan Moiety of RNase B by Means of Raman and Raman Optical Activity2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 11, p. 2252-2254Article in journal (Refereed)
    Abstract [en]

    Raman and Raman optical activity (ROA) spectroscopy are used to study the solution-phase structure of the glycan moiety of the protein ribonuclease B (RNase B). Spectral data of the intact glycan moiety of RNase B is obtained by subtracting high-quality spectral data of RNase A, the non-glycosylated form of the RNase, from the spectra of the glycoprotein. The remaining difference spectra are compared to spectra generated from Raman and ROA data of the constituent disaccharides of the RNase glycan, achieving convincing spectral overlap. The results show that ROA spectroscopy is able to extract detailed spectral data of the glycan moieties of proteins, provided that the non-glycosylated isoform is available. Furthermore, good comparison between the full glycan spectrum and the regenerated spectra based on the disaccharide data lends great promise to ROA as a tool for the solution-phase structural analysis of this structurally elusive class of biomolecules.

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