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  • 1. Ai, Yue-jie
    et al.
    Tian, Guangjun
    Liao, Rong-zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhang, Qiong
    Fang, Wei-hai
    Luo, Yi
    Intrinsic Property of Flavin Mononucleotide Controls its Optical Spectra in Three Redox States2011In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, no 16, 2899-2902 p.Article in journal (Refereed)
  • 2. Aidas, Kestutis
    et al.
    Agren, Hans
    Kongsted, Jacob
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. the case of na+ in aqueous solution2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 5, 1621-1631 p.Article in journal (Refereed)
    Abstract [en]

    The Na-23 quadrupolar coupling constant of the Na+ ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na+ ions in solution are found to differ significantly.

  • 3.
    Aldener, Mattias
    Stockholm University.
    Pulsed laser experiments in chemical physics2001Doctoral thesis, comprehensive summary (Other academic)
  • 4. Altomare, Angela
    et al.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Werner, Per-Erik
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Advances in powder pattern indexing: N-TREOR092009In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 42, 768-775 p.Article in journal (Refereed)
    Abstract [en]

    Powder pattern indexing can still be a challenge, despite the great recent advances in theoretical approaches, computer speed and experimental devices. More plausible unit cells, belonging to different crystal systems, are frequently found by the indexing programs, and recognition of the correct one may not be trivial. The task is, however, of extreme importance: in case of failure a lot of effort and computing time may be wasted. The classical figures of merit for estimating the unit-cell reliability {i.e.M20 [de Wolff (1968). J. Appl. Cryst.1, 108–113] and FN [Smith & Snyder (1979). J. Appl. Cryst.12, 60–65]} sometimes fail. For this reason, a new figure of merit has been introduced in N-TREOR09, the updated version of the indexing package N-TREOR [Altomare, Giacovazzo, Guagliardi, Moliterni, Rizzi & Werner (2000). J. Appl. Cryst. 33, 1180–1186], combining the information supplied by M20 with additional parameters such as the number of unindexed lines, the degree of overlap in the pattern (the so-called number of statistically independent observations), the symmetry deriving from the automatic evaluation of the extinction group, and the agreement between the calculated and observed profiles. The use of the new parameters requires a dramatic modification of the procedures used worldwide: in the approach presented here, extinction symbol and unit-cell determination are simultaneously estimated. N-TREOR09 benefits also from an improved indexing procedure in the triclinic system and has been integrated into EXPO2009, the updated version of EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst. 37, 1025–1028]. The application of the new procedure to a large set of test structures is described.

  • 5.
    Andersson, Klas
    Stockholm University, Faculty of Science, Department of Physics.
    Structure, Bonding and Chemistry of Water and Hydroxyl on Transition Metal Surfaces2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The structure, bonding and chemistry of water and hydroxyl on metal surfaces are presented. Synchrotron based x-ray photoelectron- and x-ray absorption spectroscopy along with density functional theory calculations mainly form the basis of the results. Conditions span the temperature range 35 - 520 K and pressures from ultra-high vacuum (~10 fAtm) to near ambient pressures (~1 mAtm). The results provide, e.g, new insights on the importance of hydrogen bonding for surface chemical kinetics.

    Water adsorbs intact on the Pt(111), Ru(001) and Cu(110) surfaces at low temperatures forming 2-dimensional wetting layers where bonding to the metal (M) mainly occurs via H2O-M and M-HOH bonds. Observed isotope differences in structure and kinetics for H2O and D2O adsorption on Ru(001) are due to qualitatively different surface chemistries. D2O desorbs intact but H2O dissociates in kinetic competition with desorption similar to the D2O/Cu(110) system. The intact water layers are very sensitive to x-ray and electron induced damage.

    The mixed H2O:OH phase on Ru(001) consists of stripe-like structures 4 to 6 Ru lattice parameters wide where OH decorates the edges of the stripes. On Pt(111), two different long-range ordered mixed H2O:OH structures are found to be inter-related by geometric distortions originating from the asymmetric H-bond donor-acceptor properties of OH towards H2O.

    Water adsorption on Cu(110) was studied at near ambient conditions and compared to Cu(111). Whereas Cu(111) remains clean, Cu(110) holds significant amounts of water in a mixed H2O:OH layer. The difference is explained by the differing activation barriers for water dissociation, leading to the presence of OH groups on Cu(110) which lowers the desorption kinetics of water by orders of magnitude due to the formation of strong H2O-OH bonds. By lowering the activation barrier for water dissociation on Cu(111) by pre-adsorbing atomic O, generating adsorbed OH, similar results to those on Cu(110) are obtained.

  • 6. Aristov, Maria
    et al.
    Eichhorn, Ralf
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Bechinger, Clemens
    Separation of chiral colloidal particles in a helical flow field2013In: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 9, no 8, 2525-2530 p.Article in journal (Refereed)
    Abstract [en]

    Stereoisomeric molecules with opposite chirality, so-called enantiomers, often vary regarding their sensory, pharmacological and toxicological properties. Such enantiomer specific effects play a central role in the development, testing and evaluation of drugs, pesticides and food related products. Accordingly, efficient techniques for separation of chiral mixtures into enantiopure compounds are of enormous practical relevance. Most current enantiomer separation methods are based on enantioselective interactions with an auxiliary substance which has to be developed and optimized for different chiral molecules in an elaborate and costly process. Here, we experimentally demonstrate the separation of micron-sized chiral particles in a helical fluid flow which is created inside a microfluidic device patterned with slanted grooves. We observe that the retention time of particles in a helical flow field strongly depends on their chirality which leads to an effective chiral separation within the channel. Our experimental results are confirmed by numerical calculations which demonstrate how the coupling of rotational and translational degrees of freedom leads to differences in the trajectories of particles with opposite chirality. Since our separation mechanism does not rely on material specific interactions, this offers considerable advantages over existing methods. We expect that our approach can be also applied at nanometre length scales by using channels with smaller diameters and with an optimized geometry.

  • 7.
    Aski, Sahar Nikkhou
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Takacs, Zoltan
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Kowalewski, Jozef
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Inclusion complexes of cryptophane–E with dichloromethane and chloroform: A thermodynamic and kinetic study using the 1D-EXSY NMR method2008In: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 46, no 12, 1135-1140 p.Article in journal (Refereed)
    Abstract [en]

    Complexation equilibria and kinetics of exchange of chloroform and dichloromethane molecules between the cavity of cryptophane-E and bulk solution were investigated using NMR methods. Using one dimensional magnetization transfer (1D-EXSY type sequence), chemical exchange rates were measured in different temperature ranges, limited by the equilibrium constant values of the complexes and the boiling points of the guest substances. From the kinetic data, activation energies were calculated using the Arrhenius equation. From the temperature dependence of the association constant data, the enthalpy and entropy of complexation were estimated and compared with values for similar complexes of other cryptophanes.

  • 8.
    Atluri, Rambabu
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Hedin, Niklas
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Garcia-Bennett, Alfonso E.
    Non-Surfactant Supramolecular Templating Synthesis of Ordered Mesoporous Silica2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 9, 3189-3191 p.Article in journal (Refereed)
    Abstract [en]

    Hoogsteen-bonded tetrads and pentamers are formed by a large variety of organic molecules through H-donor and acceptor groups capable of inducing self-organization to form columnar and hexagonal mesophases. The biological importance of such macromolecular structures is exemplified by the assembly of guanosine-rich groups of telomere units and their implication in chromosomal replication. Folic acid is composed of a pterin group, chemically and structurally similar to guanine, conjugated to an l-glutamate moiety via a p-amino benzoic acid. Our aim has been to develop a delivery vehicle for folic acid and at the same time provide a novel synthetic route for ordered mesoporous materials without the use of amphiphilic surfactants. We present a new nonsurfactant route for the synthesis of highly ordered mesoporous materials, based on the supramolecular templating of stacked arrays of the tetramer-forming pterin groups of folic acid under a variety of synthetic conditions. This method leads to hexagonally ordered mesoporous structures with gyroid, spherical, and chiral morphologies with pores on the order of 25−30 Å in diameter and surface areas above 1000 m2/g. More importantly circular dichroism studies reveal that the folate template possesses a chiral signature within the pores in the as-synthesized solid and that chirality is transferred from the folate template to the pore surface via the aminopropyl triethoxysilane costructure directing agent used in the supramolecular assembly. This novel templating approach for ordered mesoporous materials breaks the hegemony of surfactant micellar systems for the preparation of these exciting high surface area solids and opens new opportunities for structural control, design of pore geometry, and novel applications.

  • 9.
    Baldassarre, Maurizio
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Li, Chenge
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Eremina, Nadejda
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Goormaghtigh, Erik
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra2015In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 20, no 7, 12599-12622 p.Article in journal (Refereed)
    Abstract [en]

    Infrared spectroscopy is a powerful tool in protein science due to its sensitivity to changes in secondary structure or conformation. In order to take advantage of the full power of infrared spectroscopy in structural studies of proteins, complex band contours, such as the amide I band, have to be decomposed into their main component bands, a process referred to as curve fitting. In this paper, we report on an improved curve fitting approach in which absorption spectra and second derivative spectra are fitted simultaneously. Our approach, which we name co-fitting, leads to a more reliable modelling of the experimental data because it uses more spectral information than the standard approach of fitting only the absorption spectrum. It also avoids that the fitting routine becomes trapped in local minima. We have tested the proposed approach using infrared absorption spectra of three mixed α/β proteins with different degrees of spectral overlap in the amide I region: ribonuclease A, pyruvate kinase, and aconitase.

  • 10. 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, 4860-4869 p.Article 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.

  • 11. Berggren, Gustav
    et al.
    Huang, Ping
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Anderlund, Magnus F.
    Synthesis, Characterization and Reactivity Study of a New Penta-Coordinated Mn(II) Complex2009In: Applied Magnetic Resonance, ISSN 0937-9347, E-ISSN 1613-7507, Vol. 36, no 1, 9-24 p.Article in journal (Refereed)
    Abstract [en]

    A penta-coordinated Mn(II) compound [dqpMnCl2] (1) (dqp = 2,6-di-(8-quinoline-yl)-pyridine) has been synthesized and its X-ray crystallographic structure is reported here. Magnetic susceptibility measurements confirmed a high-spin Mn(II) (S = 5/2) center in 1. The X-band EPR spectrum of 1 in dimethylformamide solution exhibits widely distributed transitions in the spectral range from 0 to 700 mT with particularly well-resolved hyperfine lines due to the 55Mn (I = 5/2) nucleus. The abundance of highly resolved transition lines in the spectrum facilitated the electron paramagnetic resonance spectral simulation which revealed large zero-field splitting and g-anisotropies. When dissolved, 1 exists in equilibrium with a hexa-coordinated species, the latter probably resulting from disassociation of one chlorido-ligand allowing ligation of two solvent molecules. The redox behavior of 1 was studied and was compared to that of a structural analog for which water oxidation in the presence of a chemical oxidant has been shown. The results from water oxidation trials of 1 are discussed

  • 12. Berggren, Gustav
    et al.
    Thapper, Anders
    Anderlund, Magnus
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Two tetranuclear Mn-complexes as biomimetic models of the oxygen evolving complex in Photosystem II - A synthesis, characterisation and reactivity study2009In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 45, 10044-10054 p.Article in journal (Refereed)
    Abstract [en]

    In this work we report the preparation of two metallamacrocyclic tetranuclear manganese(II) complexes, [L1(4)Mn(4)](ClO4)(4) and [L2(4)Mn(4)](ClO4)(4) where L1 and L2 are the anions of the heptadentate ligands 2-((2-(bis(pyridin-2-ylmethyl) amino) ethyl)(methyl) amino) acetic acid and 2-(benzyl(2-(bis(pyridin-2-ylmethyl) amino) ethyl) amino) acetic acid), respectively. The complexes have been fully characterized by ESI-MS, elemental analysis, single-crystal X-ray diffraction, magnetic susceptibility, and EPR spectroscopy. Electrochemical reactions as well as reactions with different chemical redox reagents have been performed and a reversible two electron oxidation per manganese ion has been identified. The reaction of [L1(4)Mn(4)](ClO4)(4) with oxone or cerium(IV) results in the evolution of oxygen which makes this system interesting for future studies in the search for a functional mimic of the oxygen evolving complex in Photosystem II.

  • 13.
    Bergman, Dan
    Stockholm University.
    Computer simulation of topological and spatial structure in water and aqueous solutions1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The present thesis concerns molecular-dynamics and expanded-ensemble simulation of topological and spatial structure in water and aqueous solutions.

    First, methods for analysis of molecular pair configurations using angularly resolved density distributions were considered. It was shown that these distributions expose major features of liquid structure and that they can be used to define the hydrogen bond. Second, a method was developed for analysis of hydrogen-bond network topology. It characterizes networks in terms of the local bond patterns surrounding the water molecules and in terms of loops and chains of directed bonds.

    The methods developed have been applied to pure water, to water--acetonitrile mixtures and to charged Lennard-Jones spheres dissolved in water. Solvation structures in aqueous solutions of methylamine and tert-butyl alcohol have also been considered. The main results are: (a) In pure water, there is proton ordering around short loops, but not along chains. (b) The hydrogen-bond network in water--acetonitrile mixtures with acetonitrile mole fractions x=0.1, 0.5 and 0.9 have been characterized. As x increases from 0.1 to 0.9, the network is depleted of crosslinks, the proton ordering along chains increases and the most probable loop length decreases. For x=0.5 and 0.9 large water clusters form. (c) The hydration structures surrounding charged Lennard-Jones solutes corresponding to extrema in the solvation entropy have been characterized. Of the two solutes corresponding to the maxima, one acts as a double proton-donor and the other as a double proton-acceptor. The solute corresponding to the minimum enhances the water--water correlations. Further, the orientational and the radial parts of the two-body solute--water entropy have been calculated. The orientational part has a single maximum, whereas the radial part maintains the bimodal form of the full solvation entropy.

  • 14.
    Bergström, Lennart
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Laakssonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Self-assembled Materials2009In: Encyclopedia of Complexity and Systems Science / [ed] Robert A. Meyers, Berlin: Springer , 2009, 7931-7953 p.Chapter in book (Other academic)
  • 15. Bordoloi, Ankur
    et al.
    Sahoo, Suman
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Halligudi, S. B.
    Immobilized Molybdovanadophosphoric Acid for Selective Oxidations2013In: Catalysis surveys from Asia, ISSN 1571-1013, E-ISSN 1574-9266, Vol. 17, no 3-4, 132-146 p.Article in journal (Refereed)
    Abstract [en]

    In this review, we have summarized our work on the immobilization of molybdovanadophosphoric acids onto mesoporous silica and mesoporous carbon by different approaches such as amine functionalization and ionic liquid functionalization. All catalyst materials were well characterized by various ex-situ and in situ techniques for their structural integrity and physico-chemical properties. These materials were tested in different selective oxidation processes to develop environmentally benign protocols for the synthesis of fine chemicals and tried to study their mechanisms.

  • 16.
    Brinkmann, Andreas
    Stockholm University.
    Dipolar recoupling in magic-angle-spinning nuclear magnetic resonance2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis concerns the development of radio-frequency pulse sequences in magic-angle-spinning solid-state nuclear magnetic resonance.

    First, two classes of pulse sequences are presented which are synchronized with the sample rotation. Symmetry theorems are described which link the symmetry of the pulse sequences to selection rules for the recoupling and/or decoupling of certain spin interactions. Pulse sequences are demonstrated which recouple direct homonuclear dipolar interactions at high sample spinning frequencies. Several applications are shown, including the efficient excitation of double-quantum coherences, two-dimensional double-quantum spectroscopy, transfer of longitudinal magnetization and two-dimensional correlation spectroscopy. In addition, generalized Hartmann-Hahn sequences are demonstrated in which radio-frequency irradiation is applied simultaneously to two isotopic spin species. These sequences selectively recouple direct heteronuclear dipolar interactions and suppress all homonuclear interactions for both spin species. Experimental demonstrations are given of heteronuclear two-dimensional correlation spectroscopy, heteronuclear multiple-quantum spectroscopy and the estimation of heteronuclear dipolar couplings.

    Second, a magic-angle-spinning nuclear magnetic resonance method is developed which directly estimates the backbone torsional angle Psi. in peptides and proteins. The method exploits multiple-quantum 13C coherence evolving under heteronuclear 13C-15N dipolar interactions. Single torsional angles Psi are determined with an accuracy of 5-10 degrees in the tripeptides gly-gly-gly and ala-gly-gly by exploiting double-quantum and triple-quantum coherences respectively.

  • 17. Brinkmann, Andreas
    et al.
    Edén, Mattias
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Estimating internuclear distances between half-integer quadrupolar nuclei by central-transition double-quantum sideband NMR spectroscopy2011In: Canadian journal of chemistry (Print), ISSN 0008-4042, E-ISSN 1480-3291, Vol. 89, no 7, 892-899 p.Article in journal (Refereed)
    Abstract [en]

    We demonstrate the estimation of homonuclear dipolar couplings, and thereby internuclear distances, between half-integer spin quadrupolar nuclei by central-transition (CT) double-quantum (2Q) sideband nuclear magnetic resonance (NMR) spectroscopy. It is shown that the rotor-encoded sideband amplitudes from CT 2Q coherences in the indirect dimension of the two-dimensional NMR spectrum are sensitive probes of the magnitude of the homonuclear dipolar coupling, but are significantly less affected by other NMR parameters such as the magnitudes and orientations of the electric field gradient tensors. Experimental results of employing the R2(2)(1)R2(2)(-1) recoupling sequence to the (11)B spin pair of bis(catecholato)diboron resulted in an estimation of the internuclear B-B distance as (169.6 +/- 3) pm, i.e., with a relative uncertainty of +/- 2%, and in excellent agreement with the distance of 167.8 pm determined by single-crystal X-ray diffraction.

  • 18.
    Carravetta, Marina
    Stockholm University.
    Symmetry-based double quantum recoupling in solid state NMR2002Doctoral thesis, comprehensive summary (Other academic)
  • 19.
    Castro, Vasco
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Solid-State NMR Characterization of Lipid Membranes2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with the study of lipid bilayer systems by solid-state nuclear magnetic resonance. Two-dimensional 1H-13C separated local field experiments under magic-angle spinning were employed to investigate structural and dynamical modifications of cell membranes, resulting from the addition of compounds with some biological relevance. For further interpretation of the segmental order obtained from the 2D experiments other methods, such as 31P-NMR, 2H-NMR and molecular dynamics simulations, were also employed.

    The work presented in this thesis can be divided into two parts. The first part refers to the setup of experimental conditions. Heating and hydration effects were addressed in order to define both the temperature of the system as well as the number of water molecules per lipid necessary to fully hydrate the bilayer. Application of this experimental setup to lipid membrane systems with biological relevance constitutes the second part. The interaction of monogalactosyl- diacylglycerol, the most abundant lipid on earth, with dimyristoylphosphatidylcholine, was studied, which resulted in a frustrated bilayer. Furthermore, small molecules of local anesthetics, with focus on lidocaine, were inserted in the model membrane with the purpose of understanding the influence of local anesthetics on lipid bilayers.

  • 20.
    Castro, Vasco
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Stevensson, Baltzar
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Dvinskikh, Sergey V.
    Division of Physical Chemistry, Royal Institute of Technology, SE-10044 Stockholm, Sweden.
    Högberg, Carl-Johan
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Zimmermann, Herbert
    Department of Biophysics, Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany.
    Sandström, Dick
    Bruker BioSpin Scandinavia AB, Polygonvägen 79, SE-187 66 Täby, Sweden.
    Maliniak, Arnold
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    NMR investigations of interactions between anesthetics and lipid bilayers2008In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1178, no 11, 2604-2611 p.Article in journal (Refereed)
    Abstract [en]

    Interactions between anesthetics (lidocaine and short chain alcohols) and lipid membranes formed by dimyristoylphosphatidylcholine (DMPC) were studied using NMR spectroscopy. The orientational order of lidocaine was investigated using deuterium NMR on a selectively labelled compound whereas segmental ordering in the lipids was probed by two-dimensional 1H–13C separated local field experiments under magic-angle spinning conditions. In addition, trajectories generated in molecular dynamics (MD) computer simulations were used for interpretation of the experimental results. Separate simulations were carried out with charged and uncharged lidocaine molecules. Reasonable agreement between experimental dipolar interactions and the calculated counterparts was observed. Our results clearly show that charged lidocaine affects significantly the lipid headgroup. In particular the ordering of the lipids is increased accompanied by drastic changes in the orientation of the P–N vector in the choline group.

  • 21.
    Cavalleri, Matteo
    Stockholm University, Faculty of Science, Department of Physics.
    Local Structure of Hydrogen-Bonded Liquids2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Ordinary yet unique, water is the substance on which life is based. Water seems, at first sight, to be a very simple molecule, consisting of two hydrogen atoms attached to one oxygen. Its small size belies the complexity of its action and its numerous anomalies, central to a broad class of important phenomena, ranging from global current circulation, terrestrial water and CO2 cycles to corrosion and wetting. The explanation of this complex behavior comes from water's unique ability to form extensive three-dimensional networks of hydrogen-bonds, whose nature and structures, in spite of a great deal of efforts involving a plethora of experimental and theoretical techniques, still lacks a complete scientific understanding.

    This thesis is devoted to the study of the local structure of hydrogen-bonded liquids, with a particular emphasis on water, taking advantage of a combination of core-level spectroscopies and density functional theory spectra calculations. X-ray absorption, in particular, is found to be sensitive to the local hydrogen-bond environment, thus offering a very promising tool for spectroscopic identification of specific structural configurations in water, alcohols and aqueous solutions. More specifically, the characteristic spectroscopic signature of the broken hydrogen-bond at the hydrogen side is used to analyze the structure of bulk water, leading to the finding that most molecules are arranged in two hydrogen-bond configurations, in contrast to the picture provided by molecular dynamics simulations. At the liquid-vapor interface, an interplay of surface sensitive measurements and theoretical calculations enables us to distinguish a new interfacial species in equilibrium with the gas. In a similar approach the cluster form of the excess proton in highly concentrated acid solutions and the different coordination of methanol at the vacuum interface and in the bulk can also be clearly identified.

    Finally the ability of core-level spectroscopies, aided by sophisticated density functional theory calculations, to directly probe the valence electronic structure of a system is used to observe the nature of the interaction between water molecules and solvated ions in solution. Water around transition metal ions is found to interact with the solute via orbital mixing with the metal d-orbitals. The hydrogen-bond between water molecules is explained in terms of electrostatic interactions enhanced by charge rehybridization in which charge transfer between connecting molecules is shown to be fundamental.

  • 22. Chen, Chen
    et al.
    Huang, Congcong
    Waluyo, Iradwikanari
    Nordlund, Dennis
    Weng, Tsu-Chien
    Sokaras, Dimosthenis
    Weiss, Thomas
    Bergmann, Uwe
    Pettersson, Lars G.M.
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, Anders
    Solvation structures of protons and hydroxide ions in water2013In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, no 15, 154506- p.Article in journal (Refereed)
    Abstract [en]

    X-ray Raman spectroscopy (XRS) combined with small-angle x-ray scattering (SAXS) were used to study aqueous solutions of HCl and NaOH. Hydrated structures of H+ and OH- are not simple mirror images of each other. While both ions have been shown to strengthen local hydrogen bonds in the hydration shell as indicated by XRS, SAXS suggests that H+ and OH- have qualitatively different long-range effects. The SAXS structure factor of HCl (aq) closely resembles that of pure water, while NaOH (aq) behaves similar to NaF (aq). We propose that protons only locally enhance hydrogen bonds while hydroxide ions induce tetrahedrality in the overall hydrogen bond network of water.

  • 23. Chen, Chun Lin
    et al.
    Furusho, Hirotoshi
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Mori, Hirotaro
    In situ TEM observation of decomposition of high-purity sapphire2009In: Philosophical Magazine Letters, ISSN 0950-0839, E-ISSN 1362-3036, Vol. 89, no 2, 113-119 p.Article in journal (Refereed)
    Abstract [en]

    The decomposition of agr-Al2O3 under 200 keV electron irradiation has been investigated by in situ high-resolution electron microscopy (HREM). It was confirmed that aluminium precipitated from agr-Al2O3 under 200 keV electron irradiation for less than 1 min over the temperature range from 700 to 1273 K. The electron dose rate was of the order of 1023 e m-2 s-1 and the vacuum level of the microscope was better than 10-6 Pa. The mechanisms of agr-Al2O3 decomposition were discussed based on two possible decomposition models: the thermally activated atom movement and the forced atom displacement

  • 24.
    Chen, Hong
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Deng, Youqian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Yu, Zhengbao
    Zhao, Huishuang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Yao, Qingxia
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    3D Open-Framework Vanadoborate as a Highly Effective Heterogeneous Pre-catalyst for the Oxidation of Alkylbenzenes2013In: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 25, no 24, 5031-5036 p.Article in journal (Refereed)
    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.

  • 25. Cho, Hae Sung
    et al.
    Miyasaka, Keiichi
    Kim, Hyungjun
    Kubota, Yoshiki
    Takata, Masaki
    Kitagawa, Susumu
    Ryoo, Ryong
    Terasaki, Osamu
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Study of Argon Gas Adsorption in Ordered Mesoporous MFI Zeolite Framework2012In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 116, no 48, 25300-25308 p.Article in journal (Refereed)
    Abstract [en]

    An ordered mesoporous MFI zeolite material (Meso-MFI) was prepared by using CMK-type mesoporous carbons as a hard template. The Meso-MFI exhibits both structural and adsorption differences compared to the conventional bulk MFI zeolite. To study the argon (Ar) adsorption process in Meso-MFI, an in situ gas adsorption powder X-ray diffraction (XRD) analysis was performed using synchrotron X-ray source. Structural rearrangement of the mesoporous MFI zeolite upon Ar adsorption at low temperature (83 K) was intensively studied together with Ar adsorption process in Meso-MFI. We observed that a structural transition of the Meso-MFI zeolite framework from monoclinic (P2(1)/n) to orthorhombic (Pnma) occurred at around 126 Pa at 83 K. Positions of Ar atoms are determined as a function of the Ar gas pressure through Rietveld refinement of powder XRD data. Ar atoms are observed at straight channels, sinusoidal channels, and the intersection of these channels at low pressure. As gas pressure increases, Ar atoms in the pore intersection are pulled off from the intersection toward the straight and sinusoidal channels. The pore shape of the straight channel is changed accordingly with the amount of adsorbed Ar atoms within the pores from circular to oval. These results indicate that Ar adsorption induces not only continuous rearrangement of framework atoms but also symmetry change in the Meso-MFI. A molecular simulation study combined with Rietveld refinement of in situ XRD data provided a full understanding of the adsorption process of Ar in Meso-MFI.

  • 26. Coll, Mercedes
    et al.
    Pamies, Oscar
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dieguez, Montserrat
    Second-Generation Amino Acid Furanoside Based Ligands from D-Glucose for the Asymmetric Transfer Hydrogenation of Ketones2013In: ChemCatChem, ISSN 1867-3880, E-ISSN 1867-3899, Vol. 5, no 12, 3821-3828 p.Article in journal (Refereed)
    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).

  • 27. Cronholm, Pontus
    et al.
    Karlsson, Hanna L.
    Hedberg, Jonas
    Lowe, Troy A.
    Winnberg, Lina
    Elihn, Karine
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Wallinder, Inger Odnevall
    Möller, Lennart
    Intracellular Uptake and Toxicity of Ag and CuO Nanoparticles: A Comparison Between Nanoparticles and their Corresponding Metal Ions2013In: Small, ISSN 1613-6810, E-ISSN 1613-6829, Vol. 9, no 7, 970-982 p.Article in journal (Refereed)
    Abstract [en]

    An increased understanding of nanoparticle toxicity and its impact on human health is essential to enable a safe use of nanoparticles in our society. The aim of this study is to investigate the role of a Trojan horse type mechanism for the toxicity of Ag-nano and CuO-nano particles and their corresponding metal ionic species (using CuCl2 and AgNO3), i.e., the importance of the solid particle to mediate cellular uptake and subsequent release of toxic species inside the cell. The human lung cell lines A549 and BEAS-2B are used and cell death/membrane integrity and DNA damage are investigated by means of trypan blue staining and the comet assay, respectively. Chemical analysis of the cellular dose of copper and silver is performed using atomic absorption spectroscopy. Furthermore, transmission electron microscopy, laser scanning confocal microscopy, and confocal Raman microscopy are employed to study cellular uptake and particle-cell interactions. The results confirm a high uptake of CuO-nano and Ag-nano compared to no, or low, uptake of the soluble salts. CuO-nano induces both cell death and DNA damage whereas CuCl2 induces no toxicity. The opposite is observed for silver, where Ag-nano does not cause any toxicity, whereas AgNO3 induces a high level of cell death. In conclusion: CuO-nano toxicity is predominantly mediated by intracellular uptake and subsequent release of copper ions, whereas no toxicity is observed for Ag-nano due to low release of silver ions within short time periods.

  • 28.
    Dahlberg, Martin
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Molecular Modeling of Cardiolipin2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biological membranes are assembled from many different lipids. Our understanding of membrane function and morphology is dependent on linking the properties of the lipids to the properties of the membranes. In the inner mitochondrial membrane, one of the main lipids is cardiolipin, which is involved in the formation of high curvature tubular regions. In this thesis a series of molecular models of cardiolipin is presented, with the aim of providing a bottom-up understanding for its influence on model and biological membranes. The models allow detailed control over the headgroup charge and the chain volumes, which experimentally have shown to be important for the packing, mechanical, and electrostatic properties of membranes.To achieve these aims, three levels of detail were used: i) quantum chemical calculations for the cardiolipin headgroup, ii) atomistic united atom molecular dynamics simulations for cardiolipin and phosphatidylcholine lipid mixtures, and iii) coarse grained molecular dynamics simulations for larger lipid systems, including phase transitions between the micellar, lamellar, and inverse hexagonal phases, as well as mixtures of cardiolipin with zwitterionic lipids. These models are presented in the context of various experiments on cardiolipin systems done by others, and some basic theory of electrostatics and mechanics of membranes are discussed.The simple coarse grained model gave lipid phase preferences in agreement with experimental data. Relatively small amounts of partially neutralized cardiolipin molecules introduced mechanical instability in phosphatidylcholine bilayers, and showed some evidence of domain formation due to curvature frustration. The small effective headgroup volume of cardiolipin induced order in the hydrocarbon chains, partly due to strong sodium ion binding. Different types of intramolecular hydrogen bond networks in cardiolipin were described, and proton transfer between the phosphate groups within a cardiolipin molecule was estimated to have a 4-5 kcal/mol barrier. Such transfer might play a role in the surface conduction of protons at the inner mitochondrial membrane.

  • 29.
    Dahlberg, Martin
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Polymorphic phase behavior of cardiolipin derivatives studied by coarse-grained molecular dynamics2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 25, 7194-7200 p.Article in journal (Refereed)
    Abstract [en]

    Cardiolipin (CL) is a negatively charged four acyl chain lipid, associated with energy production in bacterial and mitochondrial membranes. Due to the shape of CL, negative curvatures of aggregates are favorable if the charges in the head group can be reduced. The phase polymorphism of CL, and of associated derivatives with 2, 3, 4, or 5 chains, has been determined previously and offers a model system in which micellar, lamellar, and inverse hexagonal phases can be observed. We present an extension to a previously established coarse-grained molecular dynamics model with the aim of reproducing the different CL phases with two adjustable parameters: the number of acyl chains and the effective head group charge. With molecular dynamics simulations of large lipid systems, we observed transitions between different phases on the nanosecond to microsecond time scale. Charge screening by high salt or low pH was successfully modeled by a reduction of phosphate charge, which led to the adoption of aggregates with more negative curvature. Although specific ion binding at the interface and other atomistic details are sacrificed in the coarse-grained model, we found that it captures general phase features over a large range of aggregate geometries.

  • 30.
    Dahlberg, Martin
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Arnold, Maliniak
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Mennucci, Benedetta
    Department of Chemistry, University of Pisa.
    Marini, Alberto
    Department of Chemistry, University of Pisa.
    Quantum Chemical Modeling of the Cardiolipin Headgroup2010In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 12, 4375-4387 p.Article in journal (Refereed)
    Abstract [en]

    Cardiolipin is a key lipid component in many biological membranes. Proton conduction and proton−lipid interactions on the membrane surface are thought to be central to mitochondrial energy production. However, details on the cardiolipin headgroup structure are lacking and the protonation state of this lipid at physiological pH is not fully established. Here we present ab initio DFT calculations of the cardiolipin (CL) headgroup and its 2′-deoxy derivative (dCL), with the aim of establishing a connection between structure and acid−base equilibrium in CL. Furthermore, we investigate the effects of solvation on the molecular conformations. In our model, both CL and dCL showed a significant gap between the two pKa values, with pKa2 above the physiological range, and intramolecular hydrogen bonds were found to play a central role in the conformations of both molecules. This behavior was also observed experimentally in CL. Structures derived from the DFT calculations were compared with those obtained experimentally, collected for CL in the Protein Data Bank, and conformations from previous as well as new molecular dynamics simulations of cardiolipin bilayers. Transition states for proton transfer in CL were investigated, and we estimate that protons can exchange between phosphate groups with an approximate 4−5 kcal/mol barrier. Computed NMR and IR spectral properties were found to be in reasonable agreement with experimental results available in the literature.

  • 31.
    Dahlberg, Martin
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Maliniak, Arnold
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Mechanical properties of coarse grained bilayers formed by cardiolipin and zwitterionic lipids2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 5, 1638-1649 p.Article in journal (Refereed)
    Abstract [en]

    Lipid shape and charge are connected with the physical properties and biological function of membranes. Cardiolipin, a double phospholipid with four chains and the potential of changing its charge with pH, is crucially connected with mitochondrial inner membrane shape, and recent experiments suggest that local pH changes allow highly curved local geometries. Here, we use a coarse grained molecular dynamics model to investigate the mechanical properties of cardiolipin bilayers, systematically varying the headgroup charge and composition in mixtures with zwitterionic DOPC or DOPE. Low cardiolipin charge, corresponding to low pH, was found to induce bending moduli on the order of kBT, and curved microdomains. On the length scale investigated, in contrast to continuum theoretical models, we found the area modulus and bending modulus to be inversely correlated for mixtures of cardiolipin and DOPC/DOPE, explainable by changes in the effective head group volume.

  • 32.
    Danielsson, Jonas
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Computational chemistry studies of UV induced processes in human skin2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents and uses the techniques of computational chemistry to explore two different processes induced in human skin by ultraviolet light. The first is the transformation of urocanic acid into a immunosuppressing agent, and the other is the enzymatic action of the 8-oxoguanine glycosylase enzyme.

    The photochemistry of urocanic acid is investigated by time-dependent density functional theory. Vertical absorption spectra of the molecule in different forms and environments is assigned and candidate states for the photochemistry at different wavelengths are identified.

    Molecular dynamics simulations of urocanic acid in gas phase and aqueous solution reveals considerable flexibility under experimental conditions, particularly for for the cis isomer where competition between intra- and inter-molecular interactions increases flexibility.

    A model to explain the observed gas phase photochemistry of urocanic acid is developed and it is shown that a reinterpretation in terms of a mixture between isomers significantly enhances the agreement between theory and experiment , and resolves several peculiarities in the spectrum.

    A model for the photochemistry in the aqueous phase of urocanic acid is then developed, in which two excited states governs the efficiency of photoisomerization. The point of entrance into a conical intersection seam is shown to explain the wavelength dependence of photoisomerization quantum yield.

    Finally some mechanistic aspects of the DNA repair enzyme 8-oxoguanine glycosylase is investigated with density functional theory. It is found that the critical amino acid of the active site can provide catalytic power in several different manners, and that a recent proposal involving a SN1 type of mechanism seems the most efficient one.

  • 33.
    Danielsson, Mathias
    Stockholm University, Faculty of Science, Department of Physics.
    Spectroscopic study of titanium monohydride and storage ring experiments2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes two projects, spectroscopy of the astrophysically relevant molecule TiH and its isotopologue TiD, and the dissociative recombination (DR) reaction of astrophysically and atmospherically relevant molecules. Emphasis in the thesis is on the first project.

    A series of laser aided spectroscopic studies of TiH/TiD has been carried out. A search for forbidden transitions in the (green) B-X band of TiH was performed. This was followed by a rather bitter fight for the analysis of the perturbed and congested B-X band of TiD, and this was finally rewarding. A substantial extension of a previously reported analysis of this band was performed. The new analysis includes transitions between higher vibrational levels never previously identified. This made it possible to report the first experimentally derived equilibrium constants for the TiH/TiD molecules. There is a need for such results for metal hydrides in the work of calculating the opacity of the atmospheres of cool M and L type stars.

    The DR storage ring experiments have been carried out at the ion storage ring CRYRING in Stockholm. Measurements of the branching fractions and DR rate constants of molecular ions have been done. These results find use in the modeling of the chemistry in interstellar clouds as well as of atmospheres, like the one of Titan, one of the moons of Saturn, which was recently visited by the spacecraft Cassini.

  • 34.
    de Marothy, Sven
    Stockholm University, Faculty of Science, Department of Physics.
    Autocatalytic decomposition of carbonic acid2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 20, 2306-2311 p.Article in journal (Refereed)
    Abstract [en]

    Long held to be unstable or metastable in the gas phase, carbonic acid has successfully been produced and identified in its gaseous form in recent decades. Theoretical studies have indicated that isolated carbonic acid in the gas phase may in fact be quite stable, its decomposition attributable to the catalytic effect of water molecules, either present or produced in a chain reaction by an initially slow decomposition. In this study, a previously unreported autocatalytic decomposition route is studied using high-accuracy ab initio quantum chemical methods. Results indicate that a carbonic acid dimer may react and decompose in a single-step, highly concerted reaction. The transition state of this reaction was characterized, and the reaction pathway was found to have significantly lower activation energy than the uncatalyzed decomposition, and comparable or lower energy than the water-catalyzed reaction. The results indicate that gaseous carbonic acid should be unstable even in the absence of water.

  • 35. Dekov, Vesselin M.
    et al.
    Hålenius, Ulf
    Stockholm University, Faculty of Science, Department of Geology and Geochemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Native Sn–Pb droplets in a zeolitic amygdale (Isle of Mull, Inner Hebrides)2009In: Geochimica et Cosmochimica Acta, ISSN 0016-7037, E-ISSN 1872-9533, Vol. 73, no 10, 2907-2919 p.Article in journal (Refereed)
    Abstract [en]

    Despite the particular scientific interest in the elements with high affinity to S and O2, but found in zero-valence state in nature, the origin of these native minerals has been little explored and remains obscure. Here we describe unique Sn–Pb droplets found in a closed analcime–calcite amygdale collected from a basaltic unit cropping out at Carsaig Bay (Isle of Mull, Inner Hebrides). The droplets consist of intimate intergrowths of nearly pure Sn0 and Pb0 domains in proportion 88:12 and are enveloped in a thin, brownish film of organic composition. The occurrence of the Sn–Pb droplets in a closed amygdale, their relationship with the host analcime + calcite and their Pb isotope composition (which does not match any known anthropogenic Pb source) rule out the possibility of anthropogenic contamination and support the natural origin of the Sn–Pb alloy.

    The variable isotope (Pb, Sr, Nd) compositions in different members of the host basaltic sequence suggest that a parent basaltic magma was modified by crustal assimilation and post-emplacement alteration processes. Considering all possible explanations, it appears that the most likely source of Pb for the Sn–Pb alloy is a discrete basaltic unit with an isotopic composition comparable to the Antrim basalts (Northern Ireland). The amygdale phases, on the other hand, show isotopic evidence for incorporation of elements from both local basaltic and sedimentary units. The apparent isotopic disequilibrium between Sn–Pb droplets and amygdale phases indicates a complex, multi-stage fluid evolution. The occurrence of Sn–Pb droplets in organic capsules suggests that the droplets and the enveloping organic substances are co-precipitates. This implies that the transportation and deposition of Sn and Pb might have occurred through organometallic compounds. We assume interaction of seawater fluids carrying metals leached from basaltic rocks with hydrocarbons from sedimentary units as a prerequisite for the formation of the organometallic complexes. The zeolites lining the basaltic vesicles might have destabilized the migrating organo-Sn and Pb compounds causing their breakdown and precipitation of Sn–Pb alloy.

  • 36. Donahue, Neil M.
    et al.
    Robinson, Allen L.
    Trump, Erica R.
    Riipinen, Ilona
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Kroll, Jesse H.
    Volatility and Aging of Atmospheric Organic Aerosol2014In: Atmospheric and aerosol chemistry, Springer, 2014, 97-143 p.Chapter in book (Refereed)
    Abstract [en]

    Organic-aerosol phase partitioning (volatility) and oxidative aging are inextricably linked in the atmosphere because partitioning largely controls the rates and mechanisms of aging reactions as well as the actual amount of organic aerosol. Here we discuss those linkages, describing the basic theory of partitioning thermodynamics as well as the dynamics that may limit the approach to equilibrium under some conditions. We then discuss oxidative aging in three forms: homogeneous gas-phase oxidation, heterogeneous oxidation via uptake of gas-phase oxidants, and aqueous-phase oxidation. We present general scaling arguments to constrain the relative importance of these processes in the atmosphere, compared to each other and compared to the characteristic residence time of particles in the atmosphere.

  • 37.
    Dong, Kun
    et al.
    Institute of Process Engineering, Chinese Academy of Sciences, 100190 Beijing, China.
    Zhou, Guohui
    Institute of Process Engineering, Chinese Academy of Sciences, 100190 Beijing, China.
    Liu, Xiaomin
    Institute of Process Engineering, Chinese Academy of Sciences, 100190 Beijing, China.
    Yao, Xiaoguian
    Institute of Process Engineering, Chinese Academy of Sciences, 100190 Beijing, China.
    Zhang, Suojiang
    Institute of Process Engineering, Chinese Academy of Sciences, 100190 Beijing, China.
    Lyubartsev, Alexander
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Structural Evidence for the Ordered Crystallites of Ionic Liquid in Confined Carbon Nanotubes2009In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 113, no 23, 10013-10020 p.Article in journal (Refereed)
    Abstract [en]

    Ionic liquids (ILs) are a class of new green materials that have attracted extensive attention in recent decades. Many novel properties not evident under normal conditions may appear when ionic liquids are confined to a nanometer scale. As was observed in the experiment, an anomalous phase behavior from liquid to high melting point perfect crystal occurred when 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) ionic liquid was confined in a carbon nanotube. In this work, we performed molecular dynamics (MD) simulations for [bmim][PF6] ionic liquid and provided direct structural evidence that the ionic crystallizes in a carbon nanotube. The ordered ionic arrangement in both the radial and the axial directions can be observed inside the channels of the CNTs to induce the form of crystallites. The ionic stacking and distributing can be determined by the sizes of the CNTs. Hydrogen bonds remain the dominant interactions between cations and anions when the ionic liquid enters into the CNT from the bulk phase. The free energies as the thermal driven forces were calculated, and it is found that it is very difficult for a single anion to enter into the channel of the CNT spontaneously. A more favorable way is through an ion-pair in which a cation “pulls” an anion to enter into the channel of the CNT together. It is predicted that other ionic liquids that possess similar structures, even including the pyridinium-based ionic liquids, can show higher melting points when confined in CNTs.

  • 38.
    Dvinskikh, Sergey V.
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Thaning, Johan
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Stevensson, Baltzar
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Jansson, Kjell
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Kumar, Sandeep
    Raman Research Institute, C. V. Raman Avenue, Bangalore 560 080, India.
    Zimmermann, Herbert
    Department of Biomedical Optics, Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany.
    Maliniak, Arnold
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Mesomorphism in columnar phases studied by solid-state nuclear magnetic resonance2006In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 74, no 2, 021703- p.Article in journal (Refereed)
    Abstract [en]

    In this paper, we present 13C and 1H NMR investigations of 2, 3, 6, 7, 10, 11-hexahexyl-thiotriphenylene (HHTT). The measurements were carried out under both static and magic-angle spinning conditions. The phase diagram of HHTT is K↔H↔Dhd↔I, where H is a helical phase and Dhd is a columnar liquid crystal. The motivation was to characterize the molecular order and dynamics and to investigate differences at the molecular level between the two mesophases: H and Dhd. It is shown that Dhd is a conventional columnar liquid crystal, where the molecular core undergoes fast rotation about the symmetry axis. The orientational order in this mesophase is lower and the temperature dependence of the order parameter is steeper than in other triphenylene-based compounds. On the other hand, in the helical phase the core, similarly to the solid phase, is essentially rigid. The difference between the solid and helical phases is mainly manifested in an increased mobility of the aliphatic chains observed in the latter phase. In addition, the sample exhibits thermal history effects, which are observed in the different behavior upon cooling and heating.

    © 2006 The American Physical Society

  • 39.
    Eden, Mattias
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Determination of absolute quadrupolar tensor orientations by double-quantum NMR on powders2009In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 470, no 4-6, 318-324 p.Article in journal (Refereed)
    Abstract [en]

    We introduce a new nuclear magnetic resonance (NMR) approach for determining electric field gradient (‘quadrupolar’) tensor orientations directly from polycrystalline powders. It involves a homonuclear 2D experiment that correlates (two-spin) double-quantum and single-quantum coherences of half-integer quadrupolar spin nuclei undergoing magic-angle-spinning. The 2D NMR spectrum is sensitive both to the relative orientations between the correlated quadrupolar tensors and to their orientations relative to the dipolar vector of the spin-pair. A novel strategy to calculate 2D spectra from multi-spin systems is used to extract the tensor orientations. We demonstrate the method by estimating the three 23Na quadrupolar tensor orientations in Na2SO3

  • 40.
    Eden, Mattias
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Homonuclear dipolar recoupling of half-integer spin quadrupolar nuclei: techniques and applications2009In: Solid State Nuclear Magnetic Resonance, ISSN 0926-2040, E-ISSN 1527-3326, Vol. 36, no 1, 1-10 p.Article in journal (Refereed)
    Abstract [en]

    We review recent advances in solid state NMR methodology for recovering homonuclear dipolar interactions among half-integer quadrupolar spins undergoing sample rotation. Existing dipolar recoupling techniques are contrasted, based on (i) the form of their associated dipolar Hamiltonian, (ii) the different experimental conditions necessitating their realization and (iii) their roles as components in multi-dimensional NMR correlation spectroscopy. Various types of structural information accessible from such solid state NMR experimentation is reviewed. Promises and limitations of methodologies targeting homonuclear dipolar couplings between half-integer spins under high-resolution conditions are discussed, with particular focus on the demands set for structural investigations of crystalline as well as structurally disordered (amorphous) inorganic network materials

  • 41.
    Edén, Mattias
    Stockholm University.
    Solid state NMR of multiple-spin systems1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many nuclear magnetic resonance (NMR) experiments subject the nuclear spins to time-periodic modulations, for example, mechanical sample rotation and irradiation by periodic radio-frequency pulse sequences. An efficient simulation algorithm (COMPUTE) has been proposed for calculating NMR spectra from such systems.

    Computation of NMR spectra of powders involves an average over all possible crystallite orientations. It is desirable that a reasonable numerical approximation to a full powder average is obtained, using a minimum number of orientational samples. This thesis discusses methods for selecting these. Furthermore, it has been demonstrated that averaging over one of the three orientational variables may be performed within the COMPUTE framework with minimum computational effort. In many cases, these advances combine to reduce the computational time by an order of magnitude compared to previous methods.

    This thesis also discusses excitation and exploitation of multiple-quantum coherences in the NMR of rotating solids. A method has been developed that determines the backbone torsion angle y in peptides and proteins, by using evolution of multiple-quantum coherence under heteronuclear 13C-15N dipolar interactions. It operates under magic-angle-spinning conditions, and has been implemented in double-quantum and triple-quantum versions. The technique has been demonstrated by determining y in fragments of the tripeptides gly-gly-gly and ala-gly-gly, with an accuracy of 5o-10o.

  • 42.
    Edén, Mattias
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    The split network analysis for exploring composition-structure correlations in multi-component glasses: I. Rationalizing bioactivity-composition trends of bioglasses2011In: Journal of Non-Crystalline Solids, ISSN 0022-3093, E-ISSN 1873-4812, Vol. 357, no 6, 1595-1602 p.Article in journal (Refereed)
    Abstract [en]

    We present a strategy, referred to as “split network” analysis, for assessing the average network polymerization (r(F)) and mean number of bridging oxygen (BO) atoms ( (N) over bar (F)(BO)) for each individual network former F in multi-component oxide-based glasses, primarily targeting those involving Al, B, P and Si. This requires a priori knowledge about the parameters (r(F), (N) over bar (F)(BO)) of all network builders, but one, whose values are deduced by the split network procedure. We illustrate split-network concepts for establishing composition/structure/bioactivity correlations in Na-Ca-Si-P-O glasses. The cooperating influences on the bioactivity from the average polymerization degree of the silicate network and the amounts of orthophosphate and sodium ions are discussed.

  • 43.
    Edén, Mattias
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Two-dimensional MAS NMR correlation protocols involving double-quantum filtering of quadrupolar spin-pairs2010In: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 204, no 1, 99-110 p.Article in journal (Refereed)
    Abstract [en]

    Three two-dimensional (2D) NMR homonuclear correlation techniques invoking double-quantum (2Q) filtration of the central transitions of half-integer spins are evaluated numerically and experimentally. They correlate directly detected single-quantum (1Q) coherences in the t(2) domain with either of 1Q, two-spin 2Q or single-spin multiple-quantum coherence-evolutions in the indirect (t(1)) dimension. We employ experimental Na-23 and Al-22 NMR on sodium sulfite and the natural mineral sillimanite (SiAl2O5), in conjunction with simulated 2D spectra from pairs of dipolar-recoupled spins-3/2 and 5/2 at different external magnetic fields, to compare the correlation strategies from the viewpoints of 2D spectral resolution, signal sensitivity, implementational aspects and their relative merits for establishing internuclear proximities and quadrupolar tensor orientations.

  • 44.
    Edén, Mattias
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Sundberg, Peter
    Stålhandske, Christina
    The split network analysis for exploring composition-structure correlations in multi-component glasses: II. Multinuclear NMR studies of alumino-borosilicates and glass-wool fibers2011In: Journal of Non-Crystalline Solids, ISSN 0022-3093, E-ISSN 1873-4812, Vol. 357, no 6-7, 1587-1594 p.Article in journal (Refereed)
    Abstract [en]

    The preceding part [M. Eden, J. Non.-Cryst. Solids, 357, (2011) 1595-1602] introduced the “split network” strategy for estimating the network polymerization degree (r(A)) and mean number of bridging oxygen (BO) atoms ((N) over bar (A)(BO)) for a network former A, given that these parameters are known for all other network builders in the multi-component oxide glass. However, as the detailed ordering of BO and non-bridging oxygen (NBO) species is often difficult to assess experimentally, we summarize some “rules of thumb” for predicting the coordination number and tendency to accept NBO ions for Al(3+), B(3+), Si(4+) and P(5+) cations: they are helpful in scenarios devoid of experimental data. Using the parameters r and (N) over bar (BO), we present expressions for the BO/NBO distributions among tetrahedrally coordinated cations, as predicted from the binary and random models. Multinuclear (11)B, (27)Al and (29)Si solid-state NMR is exploited to derive the split network representations of a set of Na-Ca-(Al)-(B)-Si-O glasses. These results are subsequently used to gain structural insight into two commercial glass-wool fibers that constitute alumino-borosilicate networks modified by Na(+), K(+), Ca(2+) and Mg(2+) ions.

  • 45.
    Eklöf, Daniel
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Fischer, A.
    Wu, Y.
    Scheidt, E. -W
    Scherer, W.
    Haussermann, Ulrich
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Transport properties of the ii v semiconductor znsb2013In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 1, no 4, 1407-1414 p.Article in journal (Refereed)
    Abstract [en]

    The intermetallic compound ZnSb is an electron poor (II-V) semiconductor with interesting thermoelectric properties. Electrical resistivity, thermopower and thermal conductivity were measured on single crystalline and various polycrystalline specimens. The work establishes the presence of impurity band conduction as an intrinsic phenomenon of ZnSb. The impurity band governs electrical transport properties at temperatures up to 300-400 K after which ZnSb becomes an intrinsic conductor. Furthermore this work establishes an inherently low lattice thermal conductivity of ZnSb, which is comparable to the state-of-the- art thermoelectric material PbTe. It is argued that the impurity band relates to the presence of Zn defects and the low thermal conductivity to the electron-poor bonding properties of ZnSb.

  • 46. Eland, J. H. D.
    et al.
    Linusson, Per
    Stockholm University, Faculty of Science, Department of Physics.
    Mucke, M.
    Feifel, R.
    Homonuclear site-specific photochemistry by an ion-electron multi-coincidence spectroscopy technique2012In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 548, 90-94 p.Article in journal (Refereed)
    Abstract [en]

    By combining multi-particle coincidence detection of electrons and ions with ionisation by soft X-ray synchrotron radiation we demonstrate an effective tool for atomic spectroscopy and site-specific photochemistry. Its most novel capability is application to molecular fragmentation after K-shell vacancy production in atoms distinguished only by their chemical environment.

  • 47.
    Eremina, Nadejda
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Use of Creatine Kinase To Induce Multistep Reactions in Infrared Spectroscopic Experiments2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 48, 14967-14972 p.Article in journal (Refereed)
    Abstract [en]

    An extension of current approaches to trigger enzymatic reactions in reaction-induced infrared difference spectroscopy experiments is described. A common procedure is to add a compound that induces a reaction in the protein of interest. To be able to induce multistep reactions, we explored here the use of creatine kinase (CK) for the study of phosphate transfer mechanisms. The enzymatic reaction of CK could be followed using bands at 1614 and 979 cm(-1) for creatine phosphate consumption, at 944 cm(-1) for ADP consumption, and at 1243, 992, and 917 cm(-1) for ATP formation. The potential of CK to induce multistep reactions in infrared spectroscopic experiments was demonstrated using the sarcoplasmic reticulum Ca2+-ATPase (SERCA1a) as the protein of interest. ADP binding to the ATPase was triggered by photolytic release of ADP from P-3-1-(2-nitro)phenylethyl ADP (caged ADP). CK added in small amounts converted the released ADP to ATP on the time scale of minutes. This phosphorylated the ATPase and led to the formation of the first phosphoenzyme intermediate Ca(2)E1P. Thus a difference spectrum could be obtained that reflected the reaction from the ADP ATPase complex to the first phosphoenzyme intermediate. Comparison with a phosphorylation spectrum obtained when the initial state was the ATP ATPase complex revealed the contribution of ATP's gamma-phosphate to the conformational change of the ATPase upon nucleotide binding: gamma-phosphate binding modifies the structure of a beta-sheet, likely in the phosphorylation domain, and shifts its spectral position from similar to 1640 to similar to 1630 cm(-1). Upon phosphorylation of the ATPase, the beta-sheet relaxes back to a structure that is intermediate between that adopted in the ADP bound state and that in the ATP bound state.

  • 48.
    Feng, Xiaolong
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Estimating molecular conformations by solid-state NMR spectroscopy1998Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Our understanding of structure-function relationships in biological systems demands new and more sophisticated methods for examining molecular structure. This thesis presents an effort of methodology development for molecular structure determination by solid-state NMR spectroscopy and applications to biological systems.

    Rotational Resonance NMR is established as a major tool for extracting molecular structural information in solids. Some further aspects of the technique are explored. The technique is applied to obtain the binding conformation of an inhibitor, TMPIP, bound to gastric H+/K+-ATPase, an ab heterodimer with a molecular weight of over 150 kDa.

    A novel solid-state NMR method for the determination of the torsional angle of a 13C-labeled H-C-C-H moiety is developed. A detailed theoretical introduction of the method is presented. The technique has been applied to determine the H-C10-C11-H torsional angle of the retinylidene chromophore in bovine rhodopsin, a 41 kDa integral membrane protein, and its photo-intermediate metarhodopsin-I.

    A new solid-state NMR method is developed. It may be used to estimate the Ramachandran ( angle in a protein backbone chain. A detailed theory is presented. It is demonstrated on an isotopically labeled tripeptide.

  • 49. Fischer, Christian E.
    et al.
    Mink, Janos
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Hajba, Laszlo
    Bacsik, Zoltan
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Materials Chemistry.
    Nemeth, Csaba
    Mihaly, Judith
    Raith, Alexander
    Cokoja, Mirza
    Kuehn, Fritz E.
    Vibrational spectroscopic study of SiO2-based nanotubes2013In: Vibrational Spectroscopy, ISSN 0924-2031, E-ISSN 1873-3697, Vol. 66, 104-118 p.Article in journal (Refereed)
    Abstract [en]

    Novel organic-inorganic hybrid nanotubes containing silica and ethane (EtSNT), ethylene (ESNT) and acetylene (ASNT) units, as well as brominated ESNT (Br-ESNT) and glycine-modified Br-ESNT (Gly-ESNT) have been studied by IR and Raman spectroscopy. The results are compared with the spectral features for conventional silica nanotubes (SNT) and amorphous silica. Bands peculiar to organic moieties have been detected and assigned. Assignment of the silicate backbone vibrations was based on the results of normal coordinate calculations. Furthermore, characteristic silicate, so-called 'nanotube' vibrations have been identified and their band positions have been summarized to serve as a future reference for such compounds. SiOSi antisymmetric stretchings were observed in the range 1000-1110 cm(-1), while the symmetric stretchings appeared between 760 and 960 cm(-1) for EtSNT, ESNT and Br-ESNT. Force constants have been refined for models of the repeating structure units: O3SiOSi(OSi)(3) for SNT and SiCHnCHnSi(OSi)(3) for organosilica nanotubes (n = 2, EtSNT: n = 1, ESNT and n = 0, ASNT). The calculated SiO stretching force constants were increased from 4.79 to 4.88 and 5.11 N cm(-1) for EtSNT, ESNT and ASNT, respectively. The force constants have been compared with those for several silicates and SiO bond length are predicted and discussed.

  • 50.
    Fossépré, Mathieu
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry. University of Namur (UNamur), Belgium.
    Leherte, Laurence
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry. Stellenbosch University, South Africa.
    Vercauteren, Daniel P.
    On the Modularity of the Intrinsic Flexibility of the mu Opioid Receptor: A Computational Study2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 12, e115856- p.Article in journal (Refereed)
    Abstract [en]

    The mu opioid receptor (mu OR), the principal target to control pain, belongs to the G protein-coupled receptors (GPCRs) family, one of the most highlighted protein families due to their importance as therapeutic targets. The conformational flexibility of GPCRs is one of their essential characteristics as they take part in ligand recognition and subsequent activation or inactivation mechanisms. It is assessed that the intrinsic mechanical properties of the mu OR, more specifically its particular flexibility behavior, would facilitate the accomplishment of specific biological functions, at least in their first steps, even in the absence of a ligand or any chemical species usually present in its biological environment. The study of the mechanical properties of the mu OR would thus bring some indications regarding the highly efficient ability of the mu OR to transduce cellular message. We therefore investigate the intrinsic flexibility of the mu OR in its apo-form using all-atom Molecular Dynamics simulations at the sub-microsecond time scale. We particularly consider the mu OR embedded in a simplified membrane model without specific ions, particular lipids, such as cholesterol moieties, or any other chemical species that could affect the flexibility of the mu OR. Our analyses highlighted an important local effect due to the various bendability of the helices resulting in a diversity of shape and volume sizes adopted by the mu OR binding site. Such property explains why the mu OR can interact with ligands presenting highly diverse structural geometry. By investigating the topology of the mu OR binding site, a conformational global effect is depicted: the correlation between the motional modes of the extra-and intracellular parts of mu OR on one hand, along with a clear rigidity of the central mu OR domain on the other hand. Our results show how the modularity of the mu OR flexibility is related to its preability to activate and to present a basal activity.

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