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  • 1. Ai, Yue-jie
    et al.
    Tian, Guangjun
    Liao, Rong-zhen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Zhang, Qiong
    Fang, Wei-hai
    Luo, Yi
    Intrinsic Property of Flavin Mononucleotide Controls its Optical Spectra in Three Redox States2011Inngår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, nr 16, s. 2899-2902Artikkel i tidsskrift (Fagfellevurdert)
  • 2. 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 Study2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 17, s. 4860-4869Artikkel i tidsskrift (Fagfellevurdert)
    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, Hong
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Deng, Youqian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Yu, Zhengbao
    Zhao, Huishuang
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Yao, Qingxia
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Zou, Xiaodong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sun, Junliang
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    3D Open-Framework Vanadoborate as a Highly Effective Heterogeneous Pre-catalyst for the Oxidation of Alkylbenzenes2013Inngår i: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 25, nr 24, s. 5031-5036Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Three three-dimensional (3D) open-framework vanadoborates, denoted as SUT-6-Zn, SUT-6-Mn, and SUT-6-Ni, were synthesized using diethylenetriamine as a template. SUT-6-Zn, SUT-6-Mn, and SUT-6-Ni are isostructural and built from (VO)(12)O-6 B18O36(OH)(6) clusters bridged by ZnO5, MnO6, and NiO6 polyhedra, respectively, to form the 3D frameworks. SUT-6 is the first vanadoborate with a 3D framework. The framework follows a semiregular hxg net topology with a 2-fold interpenetrated diamond-like channel system. The amount of template used in the synthesis played an important role in the dimensionality of the resulting vanadoborate structures. A small amount of diethylenetriamine led to the formation of this first 3D vanadoborate framework, while an increased amount of diethylenetriamine resulted in vanadoborates with zero-dimensional (0D) and one-dimensional (1D) structures. SUT-6-Zn was proved to be an efficient heterogeneous precatalyst for the oxidation of alkylbenzenes.

  • 4. Coll, Mercedes
    et al.
    Pamies, Oscar
    Adolfsson, Hans
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Dieguez, Montserrat
    Second-Generation Amino Acid Furanoside Based Ligands from D-Glucose for the Asymmetric Transfer Hydrogenation of Ketones2013Inngår i: ChemCatChem, ISSN 1867-3880, E-ISSN 1867-3899, Vol. 5, nr 12, s. 3821-3828Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A novel series of modular amino acid thioamide ligands functionalized with carbohydrates were introduced and employed in the rhodium-catalyzed asymmetric transfer hydrogenation (ATH) of aryl alkyl ketones, including the less-studied heteroaromatic ketones. The ligands are based on amino acid hydroxyamides (pseudodipeptides), which are the most successful ligands previously used in asymmetric hydrogen transfer reactions. High enantioselectivities [up to 99% enantiomeric excess (ee)] were achieved in the ATH of a wide range of aryl alkyl ketones by using catalysts generated insitu from [RhCl2Cp*](2) (Cp*=C5Me5) and thioamide ligands comprising a 3-benzyl glucofuranoside backbone and a bulky isopropyl group in the -amino acid moiety. Interestingly, both enantiomers of the alcohol products can readily be obtained with high enantioselectivity by simply changing the absolute configuration of the -amino acid. The good performance can be extended to a very challenging class of industrially interesting heteroaromatic ketones (up to 99%ee).

  • 5. Ghobril, Cynthia
    et al.
    Hammar, Peter
    Kodepelly, Sanjeevarao
    Spiess, Bernard
    Wagner, Alain
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Baati, Rachid
    Structure-Reactivity Relationship Studies for Guanidine-Organocatalyzed Direct Intramolecular Aldolization of Ketoaldehydes2010Inngår i: ChemCatChem, ISSN 1867-3880, E-ISSN 1867-3899, Vol. 2, nr 12, s. 1573-1581Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Structure-reactivity studies are performed to explore the reaction mechanism of the guanidine-catalyzed intramolecular aldol reaction of ketoaldehydes. A large number of guanidine and guanidine-like catalysts are synthesized and their properties studied. Kinetic profiles and pK(a) values of the catalysts are measured and correlated to reaction barriers calculated using density functional theory (DFT). The DFT calculations show that structural rigidity influences the pKa of the guanidines. Although the basicity is a very important factor in the catalysis, it is not sufficient to fully account for its catalytic efficiency. The availability of two aligned nitrogen reaction sites for proton shuttling in the transition state is an essential feature that helps to rationalize the reactivity pattern and the activation mode for this family of organocatalysts.

  • 6. 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-Rhamnofuranoside2013Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, nr 26, s. 5534-5541Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 7.
    Kamerlin, Shina C. L.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Warshel, Arieh
    Multiscale modeling of biological functions2011Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, nr 22, s. 10401-10411Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent years have witnessed a tremendous explosion in computational power, which in turn has resulted in great progress in the complexity of the biological and chemical problems that can be addressed by means of all-atom simulations. Despite this, however, our computational time is not infinite, and in fact many of the key problems of the field were resolved long before the existence of the current levels of computational power. This review will start by presenting a brief historical overview of the use of multiscale simulations in biology, and then present some key developments in the field, highlighting several cases where the use of a physically sound simplification is clearly superior to a brute-force approach. Finally, some potential future directions will be discussed.

  • 8.
    Kapla, Jon
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Wohlert, Jakob
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems2015Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 34, s. 22438-22447Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.

  • 9.
    Kapla, Jon
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Wohlert, Jakob
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Molecular Dynamics Simulations of Membrane-Sugar Interactions2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 22, s. 6667-6673Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH by means of molecular dynamics (MD) computer simulations. Ten different TRH concentrations were studied in the range W-TRH = 0-0.20 (w/w). The potential of mean force (PMF) for DMPC bilayer TRH interactions was determined using two different force fields, and was subsequently used in a simple analytical model for description of sugar binding at the membrane interface. The MD results were in good agreement with the predictions of the model. The net affinities of TRH for the DMPC bilayer derived from the model and MD simulations were compared with experimental results. The area per lipid increases and the membrane becomes thinner with increased TRH concentration, which is interpreted as an intercalation effect of the TRH molecules into the polar part of the lipids, resulting in conformational changes in the chains. These results are consistent with recent experimental observations. The compressibility modulus related to the fluctuations of the membrane increases dramatically with increased TRH concentration, which indicates higher order and rigidity of the bilayer. This is also reflected in a decrease (by a factor of 15) of the lateral diffusion of the lipids. We interpret these observations as a formation of a glassy state at the interface of the membrane, which has been suggested in the literature as a hypothesis for the membrane sugar interactions.

  • 10. 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 Oligosaccharides2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 50, s. 14541-14555Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 11.
    Landersjö, Clas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Eklund, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Östervall, Jennie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Söderman, Peter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Molecular conformations of a disaccharide investigated using NMR spectroscopy2006Inngår i: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 35, s. 89-101Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The molecular structure of -l-Rhap-(1→ 2)--l-Rhap-OMe has been investigated using conformation sensitive NMR parameters: cross-relaxation rates, scalar 3 J CH couplings and residual dipolar couplings obtained in a dilute liquid crystalline phase. The order matrices of the two sugar residues are different, which indicates that the molecule cannot exist in a single conformation. The conformational distribution function, , related to the two glycosidic linkage torsion angles and was constructed using the APME method, valid in the low orientational order limit. The APME approach is based on the additive potential (AP) and maximum entropy (ME) models. The analyses of the trajectories generated in molecular dynamics and Langevin dynamics (LD) computer simulations gave support to the distribution functions constructed from the experimental NMR parameters. It is shown that at least two conformational regions are populated on the Ramachandran map and that these regions exhibit very different molecular order. Electronic Supplementary Material  Supplementary material is available for this article at http://www.dx.doi.org/10.1007/s10858-006-9006-0 and is accessible for authorized users.

  • 12.
    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 Solutions2008Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 13, s. 2827-2837Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 13.
    Nozière, Barbara
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Dziedzic, Pawel
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Córdova, Armando
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Products and Kinetics of the Liquid-Phase Reaction of Glyoxal Catalyzed by Ammonium Ions (NH4+)2009Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, Vol. 113, nr 1, s. 231-237Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Glyoxal, a common atmospheric gas, has been reported to be depleted in some regions of the atmosphere. The corresponding sink could be accounted for by reactions in or at the surface of atmospheric particles, but these reactions were not identified. Recently, we showed that inorganic ammonium ions, NH4+, are efficient catalysts for reactions of carbonyl compounds, including glyoxal, in the liquid phase. To determine whether ammonium-catalyzed reactions can contribute to depletion of glyoxal in the atmosphere, the reactivity of this compound in aqueous solutions containing ammonium salts (ammonium sulfate, chloride, fluoride, and phosphate) at 298 K has been studied. The products identified by LC-HRMS and UV absorption revealed a mechanism involving two distinct pathways: a Bronsted acid pathway and an iminium pathway. The kinetics of the iminium pathway was studied by monitoring formation of a specific product. This pathway was second order in glyoxal in most of the solutions studied and should therefore be second order in most ammonium containing aerosols in the atmosphere. The corresponding rate constant, kII (M-1 s-1), increased strongly with ammonium ion activity, aNH4+, and pH:

    kII (M-1 s-1) ) (2 ( 1) × 10-10 exp(1.5 ( 0.8)aNH4+ exp(2.5 ( 0.2)pH.

    This iminium pathway is a lower limit for the ammonium-catalyzed consumption of glyoxal, but the contribution of the acid pathway is expected to be small in tropospheric aerosols. With these results the reactive uptake of glyoxal on ammonium-containing aerosols was estimated and shown to be a possible explanation for the depletion of this compound in Mexico City.

  • 14.
    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 oligosaccharides2014Inngår i: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 52, nr 3, s. 82-86Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 15.
    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]2013Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, nr 15, artikkel-id 154305Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 16.
    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 mimics2011Inngår i: Tetrahedron: asymmetry, ISSN 0957-4166, E-ISSN 1362-511X, Vol. 22, nr 4, s. 399-405Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 17.
    Rudbeck, Maria E.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Blomberg, Margareta R. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Barth, Andreas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Hydrolysis of the E2P Phosphoenzyme of the Ca2+-ATPase: A Theoretical Study2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 31, s. 9224-9232Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dephosphorylation of the E2P phosphoenzyme intermediate of the sarcoplasmic reticulum Ca2+-ATPase was studied using density functional theory. The hydrolysis reaction proceeds via a nucleophilic attack on the phosphorylated residue Asp351 by a water molecule, which is positioned by the nearby residue Glu183 acting as a base. The activation barrier was calculated to be 14.3 kcal/mol, which agrees well with values of 15-17 kcal/mol derived from experimentally observed rates. The optimized structure of the transition state reveals considerable bond breakage between phosphorus and the Asp351 oxygen (distance 2.19 angstrom) and little bond formation to the attacking water oxygen (distance 2.26 angstrom). Upon formation of the singly protonated phosphate product, Glu183 becomes protonated. The bridging aspartyl phosphate oxygen approaches Lys684 progressively when proceeding from the reactant state (distance 1.94 angstrom) via the transition state (1.78 angstrom) to the product state (1.58 angstrom). This stabilizes the negative charge that develops on the leaving group. The reaction was calculated to be slightly endergonic (+0.9 kcal/mol) and therefore reversible, in line with experimental findings. It is catalyzed by a preorganized active site with little movement of the nonreacting groups except for a rotation of Thr625 toward the phosphate group.

  • 18.
    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 simulations2011Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, nr 21, s. 7109-7121Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 19. Tavagnacco, Letizia
    et al.
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Schnupf, Udo
    Saboungi, Marie-Louise
    Himmel, Michael
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cesaro, Attilio
    Brady, John W.
    Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 38, s. 11701-11711Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 in solution of alpha-D-glucopyranose, at a caffeine concentration of 0.083 m, a single caffeine in a 3 in solution of beta-D-glucopyranose, and a single caffeine molecule in a 1.08 m solution of sucrose (table sugar). Parallel nuclear magnetic resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol.

  • 20.
    Thaning, Johan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Östervall, Jennie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Naidoo, Kevin J.
    University of Cape Town. , CSIR Campus Rosebank..
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    NMR Studies of Molecular Conformations in α-Cyclodextrin2008Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, nr 29, s. 8434-8436Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A new approach for analysis of NMR parameters is proposed. The experimental data set includes scalar couplings, NOEs, and residual dipolar couplings. The method, which aims at construction of the conformational distribution function, is applied to α-cyclodextrin in isotropic solution and dissolved in a dilute liquid crystal. An attempt to analyze the experimental data using an average molecular conformation resulted in unacceptable errors. Our approach rests on the maximum entropy method (ME), which gives the flattest possible distribution, consistent with the experimental data. Very good agreement between experimental and calculated NMR parameters was observed. In fact, two conformational states were required in order to obtain a satisfactory agreement between calculated and experimental data. In addition, good agreement with Langevin dynamics computer simulations was obtained.

  • 21. Zerbetto, Mirco
    et al.
    Kotsyubynskyy, Dmytro
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Widmalm, Goran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Polimeno, Antonino
    Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: I. Internal Dynamics of Cyclodextrins; y-Cyclodextrin as a Case Study2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 44, s. 13159-13171Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this work, we address the description of the dynamics of cyclodextrins in relation with nuclear magnetic resonance (NMR) relaxation data collected for hydroxymethyl groups. We define an integrated computational approach based on the definition and parametrization of a stochastic equation able to describe the relevant degrees of freedom affecting the NMR observables. The computational protocol merges molecular dynamics simulations and hydrodynamics approaches for the evaluation of most of the molecular parameters entering the stochastic description of the system. We apply the method to the interpretation of the C-13 NMR relaxation of the -CH2OH group of cyclodextrins. We use gamma-cyclodextrin as a case study. Results are in agreement with quantitative and qualitative analyses performed in the past with simpler models and molecular dynamics simulations. The element of novelty in our approach is in the treatment of the coupling of the relevant internal (glucopyranose ring twisting/tilting and hydroxymethyl group jumps) and global (molecular tumbling) degrees of freedom.

  • 22.
    Šoltésová, Mária
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Charles University in Prague.
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Dynamics of exocyclic groups in the Escherichia coli O91 O-antigen polysaccharide in solution studied by carbon-13 NMR relaxation2013Inngår i: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 57, nr 1, s. 37-45Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Carbon-13 relaxation data are reported for exocyclic groups of hexopyranosyl sugar residues in the repeating unit within the Escherichia coli O91 O-antigen polysaccharide in a dilute D2O solution. The measurements of T 1, T 2 and heteronuclear nuclear Overhauser enhancements were carried out at 310 K at two magnetic fields (16.4 T, 21.1 T). The data were analyzed using the standard and extended Lipari–Szabo models, as well as a conformational jump model. The extended version of the Lipari–Szabo and the two-site jump models were most successful for the hydroxymethyl groups of Gal and GlcNAc sugar residues. Different dynamics was found for the hydroxymethyl groups associated with different configurations (d-gluco, d-galacto) of the sugar residues, the latter being faster than the former.

1 - 22 of 22
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