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  • 1.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Topical chemical space in relation to biological space2010In: Comprehensive Natural Products II: Chemistry and Biology / Volume 3 / [ed] L. Mander & H.-W. Lui, Oxford: Elsevier, 2010, p. 47-79Chapter in book (Refereed)
    Abstract [en]

    In this chapter, the mapping of physical–chemical descriptor space of natural products and its relation to the biological space, with emphasis on evolutionary and topical biological space, is discussed. A brief presentation of methods for phylogenetic analysis and their different advantages is followed by discussions of evolutionary implications. Examples from both unpublished and previously published studies are presented.

  • 2.
    Bauer, Paul
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Barrozo, Alexandre
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Amrein, Beat Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Purg, Miha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Esguerra, Mauricio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Wilson, Philippe
    De Montfort University Leicester, School of Pharmacy .
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Major, Dan Thomas
    Department of Chemistry, The Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel.
    Kamerlin, Shina Caroline Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Q Version 6, a comprehensive toolkit for empirical valence bond and related free energy calculations.Manuscript (preprint) (Other academic)
  • 3.
    Belfrage, Anna Karin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Design and Synthesis of Hepatitis C Virus NS3 Protease Inhibitors: Targeting Different Genotypes and Drug-Resistant Variants2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Since the first approved hepatitis C virus (HCV) NS3 protease inhibitors in 2011, numerous direct acting antivirals (DAAs) have reached late stages of clinical trials. Today, several combination therapies, based on different DAAs, with or without the need of pegylated interferon-α injection, are available for chronic HCV infections. The chemical foundation of the approved and late-stage HCV NS3 protease inhibitors is markedly similar. This could partly explain the cross-resistance that have emerged under the pressure of NS3 protease inhibitors. The first-generation NS3 protease inhibitors were developed to efficiently inhibit genotype 1 of the virus and were less potent against other genotypes.

    The main focus in this thesis was to design and synthesize a new class of 2(1H)-pyrazinone based HCV NS3 protease inhibitors, structurally dissimilar to the inhibitors evaluated in clinical trials or approved, potentially with a unique resistance profile and with a broad genotypic coverage. Successive modifications were performed around the pyrazinone core structure to clarify the structure-activity relationship; a P3 urea capping group was found valuable for inhibitory potency, as were elongated R6 residues possibly directed towards the S2 pocket. Dissimilar to previously developed inhibitors, the P1’ aryl acyl sulfonamide was not essential for inhibition as shown by equally good inhibitory potency for P1’ truncated inhibitors. In vitro pharmacokinetic (PK) evaluations disclosed a marked influence from the R6 moiety on the overall drug-properties and biochemical evaluation of the inhibitors against drug resistant enzyme variants showed retained inhibitory potency as compared to the wild-type enzyme. Initial evaluation against genotype 3a displayed micro-molar potencies. Lead optimization, with respect to improved PK properties, were also performed on an advanced class of HCV NS3 protease inhibitors, containing a P2 quinazoline substituent in combination with a macro-cyclic proline urea scaffold with nano-molar cell based activities.

    Moreover, an efficient Pd-catalyzed C-N urea arylation protocol, enabling high yielding introductions of advanced urea substituents to the C3 position of the pyrazinone, and a Pd-catalyzed carbonylation procedure, to obtain acyl sulfinamides, were developed. These methods can be generally applicable in the synthesis of bioactive compounds containing peptidomimetic scaffolds and carboxylic acid bioisosteres.

    List of papers
    1. Synthesis and SAR of potent inhibitors of the Hepatitis C virus NS3/4A protease: Exploration of P2 quinazoline substituents
    Open this publication in new window or tab >>Synthesis and SAR of potent inhibitors of the Hepatitis C virus NS3/4A protease: Exploration of P2 quinazoline substituents
    Show others...
    2010 (English)In: Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, E-ISSN 1090-2120, Vol. 20, no 14, p. 4004-4011Article in journal (Refereed) Published
    Abstract [en]

    Novel NS3/4A protease inhibitors comprising quinazoline derivatives as P2 substituent were synthesized. High potency inhibitors displaying advantageous PK properties have been obtained through the optimization of quinazoline P2 substituents in three series exhibiting macrocyclic P2 cyclopentane dicarboxylic acid and P2 proline urea motifs. For the quinazoline moiety it was found that 8-methyl substitution in the P2 cyclopentane dicarboxylic acid series improved on the metabolic stability in human liver microsomes. By comparison, the proline urea series displayed advantageous Caco-2 permeability over the cyclopentane series. Pharmacokinetic properties in vivo were assessed in rat on selected compounds, where excellent exposure and liver-to-plasma ratios were demonstrated for a member of the 14-membered quinazoline substituted P2 proline urea series. (C) 2010 Elsevier Ltd. All rights reserved.

    Keywords
    HCV, NS3/4A protease, Inhibitors, P2 substituent, Quinazoline, Replicon assay, In vitro, DMPK, In vivo PK
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-136039 (URN)10.1016/j.bmcl.2010.05.029 (DOI)000279258800001 ()
    Available from: 2010-12-09 Created: 2010-12-09 Last updated: 2018-01-12Bibliographically approved
    2. Achiral Pyrazinone-Based Inhibitors of the Hepatitis C Virus NS3 Protease and Drug-Resistant Variants with Elongated Substituents Directed Toward the S2 Pocket
    Open this publication in new window or tab >>Achiral Pyrazinone-Based Inhibitors of the Hepatitis C Virus NS3 Protease and Drug-Resistant Variants with Elongated Substituents Directed Toward the S2 Pocket
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    2014 (English)In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 57, no 5, p. 1790-1801Article in journal (Refereed) Published
    Abstract [en]

    Herein we describe the design, synthesis, inhibitory potency, and pharmacokinetic properties of a novel class of achiral peptidomimetic HCV NS3 protease inhibitors. The compounds are based on a dipeptidomimetic pyrazinone glycine P3P2 building block in combination with an aromatic acyl sulfonamide in the P1P1′ position. Structure–activity relationship data and molecular modeling support occupancy of the S2 pocket from elongated R6 substituents on the 2(1H)-pyrazinone core and several inhibitors with improved inhibitory potency down to Ki = 0.11 μM were identified. A major goal with the design was to produce inhibitors structurally dissimilar to the di- and tripeptide-based HCV protease inhibitors in advanced stages of development for which cross-resistance might be an issue. Therefore, the retained and improved inhibitory potency against the drug-resistant variants A156T, D168V, and R155K further strengthen the potential of this class of inhibitors. A number of the inhibitors were tested in in vitro preclinical profiling assays to evaluate their apparent pharmacokinetic properties. The various R6 substituents were found to have a major influence on solubility, metabolic stability, and cell permeability.

    National Category
    Medicinal Chemistry
    Research subject
    Chemistry with specialization in Organic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-172003 (URN)10.1021/jm301887f (DOI)000333005800011 ()
    Available from: 2012-03-31 Created: 2012-03-31 Last updated: 2018-01-12Bibliographically approved
    3. Discovery of pyrazinone based compounds that potently inhibit the drug resistant enzyme variant R155K of the hepatitis C virus NS3 protease
    Open this publication in new window or tab >>Discovery of pyrazinone based compounds that potently inhibit the drug resistant enzyme variant R155K of the hepatitis C virus NS3 protease
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    2016 (English)In: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 24, no 12, p. 2603-2620Article in journal (Refereed) Published
    Abstract [en]

    Herein, we present the design and synthesis of 2(1H)-pyrazinone based HCV NS3 protease inhibitors with variations in the C-terminus. Biochemical evaluation was performed using genotype 1a, both the wildtype and the drug resistant enzyme variant, R155K. Surprisingly, compounds without an acidic sulfonamide retained good inhibition, challenging our previous molecular docking model. Moreover, selected compounds in this series showed nanomolar potency against R155K NS3 protease; which generally confer resistance to all HCV NS3 protease inhibitors approved or in clinical trials. These results further strengthen the potential of this novel substance class, being very different to the approved drugs and clinical candidates, in the development of inhibitors less sensitive to drug resistance.

    Keywords
    Hepatitis C virus; Drug resistance; Pyrazinone; NS3 protease inhibitors; R155K
    National Category
    Organic Chemistry
    Research subject
    Medicinal Chemistry
    Identifiers
    urn:nbn:se:uu:diva-243315 (URN)10.1016/j.bmc.2016.03.066 (DOI)000376727800002 ()27160057 (PubMedID)
    Funder
    Swedish Research Council, D0571301
    Available from: 2015-02-08 Created: 2015-02-08 Last updated: 2017-12-04Bibliographically approved
    4. Efficient and Selective Palladium-Catalysed C-3 Urea Couplings to 3,5-Dichloro-2(1H)-pyrazinones
    Open this publication in new window or tab >>Efficient and Selective Palladium-Catalysed C-3 Urea Couplings to 3,5-Dichloro-2(1H)-pyrazinones
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    2015 (English)In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 5, p. 978-986Article in journal (Refereed) Published
    Abstract [en]

    The development of a robust palladium-catalysed urea N-arylation protocol to install various ureas at the 3-position of the 2(1H)-pyrazinone scaffold is described. The method involves Pd(OAc)2 in combination with bidentate ligands, xantphos [4,5-bis(diphenylphosphino)-9,9-dimethylxanthene] in particular, and resulted in good to excellent coupling yields of aliphatic, aromatic, and sterically hindered ureas. Furthermore, the C-3 chlorine was shown to be selectively displaced in the presence of aryl halide ureas, and this finding was supported by density functional theory (DFT) calculations. This allows further diversification of the scaffold for the production of compound libraries. Overall, the protocol facilitates further exploitation of pyrazinones as beta-sheet-inducing scaffolds in the development of sophisticated peptidomimetics/protease inhibitors. This is exemplified here by the synthesis of a new pyrazinone-based hepatitis C virus (HCV) NS3 protease inhibitor.

    National Category
    Organic Chemistry
    Research subject
    Chemistry with specialization in Organic Chemistry; Medicinal Chemistry
    Identifiers
    urn:nbn:se:uu:diva-243254 (URN)10.1002/ejoc.201403405 (DOI)000349391700009 ()
    Available from: 2015-02-06 Created: 2015-02-06 Last updated: 2017-12-04Bibliographically approved
    5. Palladium-catalyzed carbonylation of aryl iodides with sulfinamides
    Open this publication in new window or tab >>Palladium-catalyzed carbonylation of aryl iodides with sulfinamides
    (English)Manuscript (preprint) (Other academic)
    Keywords
    palladium
    National Category
    Organic Chemistry
    Research subject
    Medicinal Chemistry; Chemistry with specialization in Organic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-243257 (URN)
    Available from: 2015-02-06 Created: 2015-02-06 Last updated: 2015-03-11
  • 4. Bickelhaupt, F Matthias
    et al.
    Nagle, Jeffrey K
    Klemm, William L
    Role of s-p orbital mixing in the bonding and properties of second-period diatomic molecules.2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 11, p. 2437-46Article in journal (Refereed)
    Abstract [en]

    Qualitative molecular orbital theory is widely used as a conceptual tool to understand chemical bonding. Symmetry-allowed orbital mixing between atomic or fragment orbitals of different energies can greatly complicate such qualitative interpretations of chemical bonding. We use high-level Amsterdam Density Functional calculations to examine the issue of whether orbital mixing for some familiar second-row homonuclear and heteronuclear diatomic molecules results in net bonding or antibonding character for a given molecular orbital. Our results support the use of slopes of molecular orbital energy versus bond distance plots (designated radial orbital-energy slope: ROS) as the most useful criterion for making this determination. Calculated atomic charges and frontier orbital properties of these molecules allow their acid-base chemistry, including their reactivities as ligands in coordination chemistry, to be better understood within the context of the Klopman interpretation of hard and soft acid-base theory. Such an approach can be extended to any molecular species.

  • 5.
    Björneholm, Olle
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Hansen, Martin H.
    Tech Univ Denmark, DK-2800 Lyngby, Denmark.;Univ Copenhagen, Dept Chem, Univ Pk 5, DK-2100 Copenhagen, Denmark..
    Hodgson, Andrew
    Univ Liverpool, Dept Chem, Liverpool L69 7ZD, Merseyside, England..
    Liu, Li-Min
    UCL, London Ctr Nanotechnol, Thomas Young Ctr, Dept Phys & Astron, London WC1E 6BT, England.;UCL, Dept Chem, London WC1E 6BT, England.;Beijing Computat Sci Res Ctr, Beijing 100193, Peoples R China..
    Limmer, David T.
    Princeton Univ, Princeton Ctr Theoret Sci, Princeton, NJ 08544 USA..
    Michaelides, Angelos
    UCL, London Ctr Nanotechnol, Thomas Young Ctr, Dept Phys & Astron, London WC1E 6BT, England.;UCL, Dept Chem, London WC1E 6BT, England..
    Pedevilla, Philipp
    UCL, London Ctr Nanotechnol, Thomas Young Ctr, Dept Phys & Astron, London WC1E 6BT, England.;UCL, Dept Chem, London WC1E 6BT, England..
    Rossmeisl, Jan
    Univ Copenhagen, Dept Chem, Univ Pk 5, DK-2100 Copenhagen, Denmark..
    Shen, Huaze
    Peking Univ, Int Ctr Quantum Mat, Beijing 100871, Peoples R China.;Peking Univ, Sch Phys, Beijing 100871, Peoples R China..
    Tocci, Gabriele
    UCL, London Ctr Nanotechnol, Thomas Young Ctr, Dept Phys & Astron, London WC1E 6BT, England.;UCL, Dept Chem, London WC1E 6BT, England.;Ecole Polytech Fed Lausanne, Sch Engn, Inst Bioengn & Mat Sci & Engn, Lab Fundamental BioPhoton,Lab Computat Sci & Mode, CH-1015 Lausanne, Switzerland.;Ecole Polytech Fed Lausanne, Lausanne Ctr Ultrafast Sci, CH-1015 Lausanne, Switzerland..
    Tyrode, Eric
    KTH Royal Inst Technol, Dept Chem, S-10044 Stockholm, Sweden..
    Walz, Marie-Madeleine
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Werner, Josephina
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. Swedish Univ Agr Sci, Dept Chem & Biotechnol, Box 7015, S-75007 Uppsala, Sweden..
    Bluhm, Hendrik
    Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 USA..
    Water at Interfaces2016In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 116, no 13, p. 7698-7726Article, review/survey (Refereed)
    Abstract [en]

    The interfaces of neat water and aqueous solutions play a prominent role in many technological processes and in the environment. Examples of aqueous interfaces are ultrathin water films that cover most hydrophilic surfaces under ambient relative humidities, the liquid/solid interface which drives many electrochemical reactions, and the liquid/vapor interface, which governs the uptake and release of trace gases by the oceans and cloud droplets. In this article we review some of the recent experimental and theoretical advances in our knowledge of the properties of aqueous interfaces and discuss open questions and gaps in our understanding.

  • 6.
    Blikstad, Cecilia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Dahlström, Käthe
    Salminen, Tiina
    Widersten, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Substrate scope and selectivity in offspring to an enzyme subjected to directed evolution2014In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 281, no 10, p. 2387-2398Article in journal (Refereed)
    Abstract [en]

    We have analyzed the effects of mutations inserted during directed evolution of a specialized enzyme, Escherichia coli S-1,2-propanediol oxidoreductase (FucO). The kinetic properties of evolved variants have been determined and the observed differences have been rationalized by modeling the tertiary structures of isolated variants and the wild-type enzyme. The native substrate, S-1,2-propanediol, as well as phenylacetaldehyde and 2S-3-phenylpropane-1,2-diol, which are new substrates accepted by isolated variants, were docked into the active sites. The study provides a comprehensive picture of how acquired catalytic properties have arisen via an intermediate generalist enzyme, which had acquired a single mutation (L259V) in the active site. Further mutagenesis of this generalist resulted in a new specialist catalyst. We have also been able to relate the native enzyme activities to the evolved ones and linked the differences to individual amino acid residues important for activity and selectivity. F254 plays a dual role in the enzyme function. First, mutation of F254 into an isoleucine weakens the interactions with the coenzyme thereby increasing its dissociation rate from the active site and resulting in a four-fold increase in turnover number with S-1,2-propanediol. Second, F254 is directly involved in binding of aryl-substituted substrates via π–π interactions. On the other hand, N151 is critical in determining the substrate scope since the side chain amide group stabilizes binding of 1,2-substituted diols and is apparently necessary for enzymatic activity with these substrates. Moreover, the side chain of N151 introduces steric hindrance, which prevents high activity with phenylacetaldehyde. Additionally, the hydroxyl group of T149 is required to maintain the catalytically important hydrogen bonding network.

  • 7. Boge, Lucas
    et al.
    Bysell, Helena
    Ringstad, Lovisa
    Wennman, David
    Umerska, Anita
    Cassisa, Viviane
    Eriksson, Jonny
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Joly-Guillou, Marie-Laure
    Edwards, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Andersson, Martin
    Lipid-Based Liquid Crystals As Carriers for Antimicrobial Peptides: Phase Behavior and Antimicrobial Effect2016In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 32, no 17, p. 4217-4228Article in journal (Refereed)
    Abstract [en]

    The number of antibiotic-resistant bacteria is increasing worldwide, and the demand for novel antimicrobials is constantly growing. Antimicrobial peptides (AMPs) could be an important part of future treatment strategies of various bacterial infection diseases. However, AMPs have relatively low stability, because of proteolytic and chemical degradation. As a consequence, carrier systems protecting the AMPs are greatly needed, to achieve efficient treatments. In addition, the carrier system also must administrate the peptide in a controlled manner to match the therapeutic dose window. In this work, lyotropic liquid crystalline (LC) structures consisting of cubic glycerol monooleate/water and hexagonal glycerol monooleate/oleic acid/water have been examined as carriers for AMPs. These LC structures have the capability of solubilizing both hydrophilic and hydrophobic substances, as well as being biocompatible and biodegradable. Both bulk gels and discrete dispersed structures (i.e., cubosomes and hexosomes) have been studied. Three AMPs have been investigated with respect to phase stability of the LC structures and antimicrobial effect: AP114, DPK-060, and LL-37. Characterization of the LC structures was performed using small-angle X-ray scattering (SAXS), dynamic light scattering, zeta-potential, and cryogenic transmission electron microscopy (Cryo-TEM) and peptide loading efficacy by ultra performance liquid chromatography. The antimicrobial effect of the LCNPs was investigated in vitro using minimum inhibitory concentration (MIC) and time-kill assay. The most hydrophobic peptide (AP114) was shown to induce an increase in negative curvature of the cubic LC system. The most polar peptide (DPK-060) induced a decrease in negative curvature while LL-37 did not change the LC phase at all. The hexagonal LC phase was not affected by any of the AMPs. Moreover, cubosomes loaded with peptides AP114 and DPK-060 showed preserved antimicrobial activity, whereas particles loaded with peptide LL-37 displayed a loss in its broad-spectrum bactericidal properties. AMP-loaded hexosomes showed a reduction in antimicrobial activity.

  • 8.
    Damas, Giane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ivashchenko, Dmitri
    Rivalta, Ivan
    Araujo, Carlos Moyses
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Carbon Dioxide  Reduction Mechanism on Ru-based Electrocatalysts: Insights from First-principles TheoryManuscript (preprint) (Other academic)
    Abstract [en]

    Solar fuel production through the so-called artificial photosynthesis has attracted a great deal of attention to the development of a new world energy matrix that is renewable and environmentally friendly. This process basically comprises the absorption of sunlight energy by an appropriate photocatalyst that is active for carbon dioxide conversion into organic fuels. Commonly, an electrocatalyst can be coupled to the system for later improvement of the photocatalytic efficiency and selectivity. In this work, we have undertaken a thorough investigation of the redox reaction mechanism of Ru-based electrocatalysts by means of density functional theory (DFT) methods under the experimental conditions that have been previously reported. More specifically, we have studied the electrochemistry and catalytic activity of the coordination complex [Ru(bpy)2(CO)2]2+. Our theoretical assessment support the following catalytic cycle: (i) [Ru(bpy)2(CO)2]2+ is transformed into [Ru(bpy)2(CO)]0 upon the two-electron reduction and CO release; (ii) [Ru(bpy)2(CO)]0 is protonated to form the hydride complex [Ru(bpy)2(CO)H]+; (iii) CO2 is activated by the hydride complex through an electrophilic addition to form the intermediate [Ru(bpy)2(CO)(OCHO)]+, with the formation of C-H bond; (iv) the resulting formate ligand ion is then released in solution; and, finally, (iv) CO ligand is reattached to the complex to recover the initial complex [Ru(bpy)2(CO)2]2+.  

  • 9.
    Damas, Giane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    von Kieseritzky, Fredrik
    Arubedo AB.
    Hellberg, Jonas
    Arubedo AB.
    Marchiori, Cleber
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Araujo, Carlos Moyses
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Symmetric Small-Molecules With Acceptor-Donor-Acceptor Architecture for Efficient Visible-Light Driven Hydrogen Production: Optical and Thermodynamic Aspects2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 51, p. 30799-30808Article in journal (Refereed)
    Abstract [en]

    Small-molecules (SM) have attracted a great deal of attention in the field of solar energy conversion due to their unique propertiescompared to polymers, such as well-defined molecular weight and lack of regio-isomeric impurities. Furthermore, these materials can be synthesized in a variety of configurational architectures, representing an opportunity for tailoring chemical and optical properties that could lead to a better photocatalytic efficiency for hydrogen generation. Here, we evaluate by means of density functional theory (DFT) and time-dependent DFT methods a set of small-molecules with A-D-A architecture (A-acceptor; D- donor) based on well-known building blocks like thiophene (T), cyclopentadithiophene (CPT) and benzothiadiazole (BT) as potential candidates for photocatalytic hydrogen evolution reaction (HER). We also propose i) the replacement of the thiophene unit by 3,4-ethylenedioxythiophene (EDOT) to form with CPT unit an extended donor core ii) an additional acceptor unit, the 1,3,4-thiadiazole (Tz), in the extremities and iii) insertion of the difluoromethoxy (DFM) as substituent in the BT unit. Our outcomes reveal that these materials have a broad absorption spectrum with λ= 318-719 nm, being the most intense absorption peak originated from an electronic transition with charge-transfer nature, as the spatial distribution of LUMO is concentrated on the acceptor units for all materials. Moreover, these small-molecules not only present catalytic power or thermodynamic driving force to carry out the chemical reactions involved in the process of hydrogen production, but can be coupled in cooperative photocatalytic systems to promote intramolecular charge transfer that is expected to boost the overall photocatalytic efficiency of these materials.

  • 10.
    Das, Biswanath
    et al.
    Univ New South Wales, Sch Chem, Sydney, NSW 2052, Australia.
    Thapper, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Ott, Sascha
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Colbran, Stephen B.
    Univ New South Wales, Sch Chem, Sydney, NSW 2052, Australia.
    Structural features of molecular electrocatalysts in multi-electron redox processes for renewable energy: recent advances2019In: SUSTAINABLE ENERGY & FUELS, ISSN 2398-4902, Vol. 3, no 9, p. 2159-2175Article, review/survey (Refereed)
    Abstract [en]

    Understanding the structural features of molecular electrocatalysts for carbon dioxide reduction and water oxidation is essential for manufacturing next generation catalysts for renewable energy. We will discuss the crucial structural motifs of those catalysts that have shown novel characteristics in recent years in terms of electrocatalytic efficacy (high TON, TOF and low overpotential), product selectivity and mechanisms. Both inorganic and organic homogeneous catalysts are scrutinized in this review. We will also highlight electrocatalysts with dual activity (i.e. they are able to catalyze both water oxidation and CO2 reduction) as an interesting prospect from the point of view of a single catalyst electrolyzer: a possible design for future easy-to-manufacture effective electrolyzers. This discussion will enrich the overall knowledge on the electrocatalyst design, an important step towards the development of efficient catalysts with cutting edge designs for a renewable energy future and practical applications.

  • 11.
    Dobrota, Ana S.
    et al.
    Univ Belgrade, Fac Phys Chem, Belgrade 11158, Serbia..
    Pasti, Igor A.
    Univ Belgrade, Fac Phys Chem, Belgrade 11158, Serbia..
    Skorodumova, Natalia V.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. KTH Royal Inst Technol, Sch Ind Engn & Management, Dept Mat Sci & Engn, Multiscale Mat Modelling Grp, S-10044 Stockholm, Sweden.;Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden..
    Oxidized graphene as an electrode material for rechargeable metal-ion batteries - a DFT point of view2015In: Electrochimica Acta, ISSN 0013-4686, E-ISSN 1873-3859, Vol. 176, p. 1092-1099Article in journal (Refereed)
    Abstract [en]

    In line with a growing interest in the use of graphene-based materials for energy storage applications and active research in the field of rechargeable metal-ion batteries we have performed a DFT based computational study of alkali metal atoms (Li, Na and K) interaction with an oxidized graphene. The presence of oxygen surface groups (epoxy and hydroxyl) alters the chemisorption properties of graphene. In particular, we observe that the epoxy groups are redox active and enhance the alkali metal adsorption energies by a factor of 2 or more. When an alkali metal atom interacts with hydroxyl-graphene the formation of metal-hydroxide is observed. In addition to a potential boost of metal ion storage capability, oxygen functional groups also prevent the precipitation of the metal phase. By simulating lithiation/de-lithiation process on epoxy-graphenes, it was concluded that the oxidized graphene can undergo structural changes during battery operation. Our results suggest that the content and the type of oxygen surface groups should be carefully tailored to maximize the performance of metal-ion batteries. This is mainly related to the control of the oxidation level in order to provide enough active centers for metal ion storage while preserving sufficient electrical conductivity.

  • 12. Duan, Sai
    et al.
    Xu, Xin
    Luo, Yi
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Tian, Zhong-Qun
    Thermal effects on electronic properties of CO/Pt(111) in water2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 32, p. 13619-13627Article in journal (Refereed)
    Abstract [en]

    Structure and adsorption energy of carbon monoxide molecules adsorbed on the Pt(111) surfaces with various CO coverages in water as well as work function of the whole systems at room temperature of 298 K were studied by means of a hybrid method that combines classical molecular dynamics and density functional theory. We found that when the coverage of CO is around half monolayer, i.e. 50%, there is no obvious peak of the oxygen density profile appearing in the first water layer. This result reveals that, in this case, the external force applied to water molecules from the CO/Pt(111) surface almost vanishes as a result of the competitive adsorption between CO and water molecules on the Pt(111) surface. This coverage is also the critical point of the wetting/non-wetting conditions for the CO/Pt(111) surface. Averaged work function and adsorption energy from current simulations are consistent with those of previous studies, which show that thermal average is required for direct comparisons between theoretical predictions and experimental measurements. Meanwhile, the statistical behaviors of work function and adsorption energy at room temperature have also been calculated. The standard errors of the calculated work function for the water-CO/Pt(111) interfaces are around 0.6 eV at all CO coverages, while the standard error decreases from 1.29 to 0.05 eV as the CO coverage increases from 4% to 100% for the calculated adsorption energy. Moreover, the critical points for these electronic properties are the same as those for the wetting/non-wetting conditions. These findings provide a better understanding about the interfacial structure under specific adsorption conditions, which can have important applications on the structure of electric double layers and therefore offer a useful perspective for the design of the electrochemical catalysts.

  • 13.
    Elmgren, Maja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Ho, Felix M.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Åkesson, Eva
    Uppsala University, University Administration.
    Schmid, Siegbert
    University of Sydney, School of Chemistry.
    Towns, Marcy
    Purdue University, Department of Chemistry.
    Comparison and Evaluation of Learning Outcomes from an International Perspective: Development of a Best-Practice Process2015In: Journal of Chemical Education, ISSN 0021-9584, E-ISSN 1938-1328, Vol. 92, no 3, p. 427-432Article in journal (Refereed)
    Abstract [en]

    Chemistry education focused on learning outcomes is increasingly practiced, providing new opportunities for international comparisons. The interest in intended learning outcomes and constructive alignment has grown in many parts of the world due to both research in higher education and political decisions. In an International Union of Pure and Applied Chemistry (IUPAC) project, we have developed a method of using critical evaluation of learning outcomes and descriptors at international, national, and institutional levels to enhance learner-centered chemistry education. This method is process-focused, aimed at learning by sharing and comparing practices around the world. Three overarching documents for the chemistry bachelor from the USA, Europe and Australia were compared. The differences were found to be more in style than in content. A tool for self-analysis was constructed to evaluate how learning outcomes for courses and modules are linked to each other and to learning outcomes for educational programs and how the expected learning outcomes can be aligned with learning activities and assessment. We conclude that the method can be used to elucidate the correspondence between learning outcomes at different levels, and the constructive alignment between learning outcomes, learning activities and assessment. The process gives new perspectives and shared knowledge. Chemistry education may need to be different depending on local considerations, and awareness of these differences is of value for further development.

  • 14.
    El-Shabasy, Rehan
    et al.
    KTH Royal Inst Technol, Dept Chem, Ecol Chem Grp, Sch Chem Sci & Engn, Stockholm, Sweden;Menoufia Univ, Fac Sci, Dept Chem, Shibin Al Kawm 32512, Egypt.
    Yosri, Nermeen
    Menoufia Univ, Fac Sci, Dept Chem, Shibin Al Kawm 32512, Egypt.
    El-Seedi, Hesham
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi. KTH Royal Inst Technol, Dept Chem, Ecol Chem Grp, Sch Chem Sci & Engn, Stockholm, Sweden;Menoufia Univ, Fac Sci, Dept Chem, Shibin Al Kawm 32512, Egypt.
    Shoueir, Kamel
    Kafrelsheikh Univ, Inst Nanosci & Nanotechnol, Kafrelsheikh 33516, Egypt.
    El-Kemary, Maged
    Kafrelsheikh Univ, Inst Nanosci & Nanotechnol, Kafrelsheikh 33516, Egypt.
    A green synthetic approach using chili plant supported Ag/Ag2O@P25 heterostructure with enhanced photocatalytic properties under solar irradiation2019In: Optik (Stuttgart), ISSN 0030-4026, E-ISSN 1618-1336, Vol. 192, article id 162943Article in journal (Refereed)
    Abstract [en]

    As the environmental pollution is a global, catastrophic occurrence, green synthesis of different catalysts has long been pursued. Herein, Capsicum annuum L (chili) extract-based catalysts were used for the fabrication of Ag/Ag2O nanoparticles (NPs) without harsh conditions. The prepared Ag/Ag2O NPs were uniform with an average size of 11.4 nm. The Ag/Ag2O was smoothly coupled with P25 to produce Ag/Ag2O@P25 photocatalyst which had effective electron-hole pair separation and active sites for high photocatalytic activity. The catalyst degraded 98.7% of the model pollutant methylene blue (MB) and catalytic conversion of 100% 2,4-dinitroaniline (2,4-DNA) within 60 s were realized under energy saving solar-light illumination, matching the rules of "green chemistry". In addition, the prepared photocatalyst exhibited superior stability and reusability, and the hot filtration test proved the heterogeneity of the catalyst.

  • 15.
    Falk, Adrian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Bengtsson, Emmy
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Juhlin, Stina
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Le, Dong
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Niklasson, Lovisa
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Svensson, Karolina
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Tesfamhret, Yonas
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Utveckling av flödesreaktor: Ett sammarbetesprojekt mellan fakulteten för teknik och naturvetenskap vid Uppsala Universitet och Fagrell produktutveckling AB2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

     This report deals with the

    collaborative project between Fagrell

    Produkt Utveckling AB and students

    from the Faculty of Science and

    Technology at Uppsala University. The

    overall objective of the project was

    in addition to developing students'

    abilities, to help Fagrell with

    verification and development of

    Fagrells prototype, Fundamental flow

    reactor, for flow chemistry. The

    uniqueness of Fagrells flow reactor is

    that it should be simple and

    affordable compared to competing flow

    reactors in the market.

    The verification was done by

    laboratory and simulation sessions.

    The verification shows that Fagrells

    idea on how to construct a flow

    reactor is very good.

    The development included both

    technology and business. The result of

    developments can be helpful for the

    commercialization of Fagrell flow

    reactor.

  • 16. Gadjieva, Rena
    et al.
    Mamedov, Fikret
    Albertsson, Per-Åke
    Styring, Stenbjörn
    Fractionation of the thylakoid membranes from tobacco. A tentative isolation of “end membrane” and purified “stroma lamellae” membranes1999In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1411, p. 92-100Article in journal (Refereed)
  • 17. Gadjieva, Rena
    et al.
    Mamedov, Fikret
    Renger, Gernot
    Styring, Stenbjörn
    Interconversion of low and high potential forms of cytochrome b559 in tris-washed photosystem II membranes under aerobic/anaerobic conditions1999In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Biochem, Vol. 38, p. 10578-10584Article in journal (Refereed)
  • 18.
    Gao, Jiajia
    et al.
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, SE-10044 Stockholm, Sweden.
    Yang, Wenxing
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    El-Zohry, Ahmed M.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Prajapati, Govind Kumar
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, SE-10044 Stockholm, Sweden.
    Fang, Yuan
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, SE-10044 Stockholm, Sweden.
    Dai, Jing
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, SE-10044 Stockholm, Sweden.
    Hao, Yan
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, SE-10044 Stockholm, Sweden.
    Leandri, Valentina
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, SE-10044 Stockholm, Sweden.
    Svensson, Per H.
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, SE-10044 Stockholm, Sweden;RISE Surface Proc Formulat, Forskargatan 20j, SE-15136 Sodertalje, Sweden.
    Furao, Istvan
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, SE-10044 Stockholm, Sweden.
    Boschloo, Gerrit
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Lund, Torben
    Roskilde Univ, Dept Sci & Environm, DK-4000 Roskilde, Denmark.
    Kloo, Lars
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, SE-10044 Stockholm, Sweden.
    Light-induced electrolyte improvement in cobalt tris(bipyridine)-mediated dye-sensitized solar cells2019In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 7, no 33, p. 19495-19505Article in journal (Refereed)
    Abstract [en]

    Lithium-ion-free tris(2,2 '-bipyridine) Co(ii/iii)-mediated electrolytes have previously been proposed for long-term stable dye-sensitized solar cells (DSSCs). Such redox systems also offer an impressive DSSC performance improvement under light soaking exposure, manifested by an increase in photocurrent and fill factor without the expense of decreasing photovoltage. Kinetic studies show that charge transfer and ion diffusion at the electrode/electrolyte interface are improved due to the light exposure. Control experiments reveal that the light effect is unambiguously associated with electrolyte components, [Co(bpy)(3)](3+) and the Lewis-base additive tert-butylpyridine (TBP). Electrochemical and spectroscopic investigation of the [Co(bpy)(3)](3+)/TBP mixtures points out that the presence of TBP, which retards the electrolyte diffusion, however causes an irreversible redox reaction of [Co(bpy)(3)](3+) upon light exposure that improves the overall conductivity. This discovery not only provides a new strategy to mitigate the typical J(sc)-V-oc trade-off in Co(ii/iii)-mediated DSSCs but also highlights the importance of investigating the photochemistry of a photoelectrochemical system.

  • 19. Haag, Sabrina
    et al.
    Tuncel, Jonatan
    Thordardottir, Soley
    Mason, Daniel E.
    Yau, Anthony C. Y.
    Dobritzsch, Doreen
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Backlund, Johan
    Peters, Eric C.
    Holmdahl, Rikard
    Positional Identification of RT1-B (HLA-DQ) as Susceptibility Locus for Autoimmune Arthritis2015In: Journal of Immunology, ISSN 0022-1767, E-ISSN 1550-6606, Vol. 194, no 6, p. 2539-2550Article in journal (Refereed)
    Abstract [en]

    Rheumatoid arthritis (RA) is associated with amino acid variants in multiple MHC molecules. The association to MHC class II (MHC-II) has been studied in several animal models of RA. In most cases these models depend on T cells restricted to a single immunodominant peptide of the immunizing Ag, which does not resemble the autoreactive T cells in RA. An exception is pristane-induced arthritis (PIA) in the rat where polyclonal T cells induce chronic arthritis after being primed against endogenous Ags. In this study, we used a mixed genetic and functional approach to show that RT1-Ba and RT1-Bb (RT1-B locus), the rat orthologs of HLA-DQA and HLA-DQB, determine the onset and severity of PIA. We isolated a 0.2-Mb interval within the MHC-II locus of three MHC-congenic strains, of which two were protected from severe PIA. Comparison of sequence and expression variation, as well as in vivo blocking of RT1-B and RT1-D (HLA-DR), showed that arthritis in these strains is regulated by coding polymorphisms in the RT1-B genes. Motif prediction based on MHC-II eluted peptides and structural homology modeling suggested that variants in the RT1-B P1 pocket, which likely affect the editing capacity by RT1-DM, are important for the development of PIA.

  • 20.
    Hamnevik, Emil
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Blikstad, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Norrehed, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Widersten, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Kinetic characterization of Rhodococcus ruber DSM 44541 alcohol dehydrogenase A2014In: Journal of Molecular Catalysis B: Enzymatic, ISSN 1381-1177, E-ISSN 1873-3158, Vol. 99, p. 68-78Article in journal (Refereed)
    Abstract [en]

    An increasing interest in biocatalysis and the use of stereoselective alcohol dehydrogenases in synthetic asymmetric catalysis motivates detailed studies of potentially useful enzymes such as alcohol dehydrogenase A (ADH-A) from Rhodococcus ruber. This enzyme is capable of catalyzing enantio-, and regioselective production of phenyl-substituted α-hydroxy ketones (acyloins) which are precursors for the synthesis of a range of biologically active compounds. In this study, we have determined the enzyme activity for a selection of phenyl-substituted vicinal diols and other aryl- or alkyl-substituted alcohols and ketones. In addition, the kinetic mechanism for the oxidation of (R)- and (S)-1-phenylethanol and the reduction of acetophenone has been identified as an Iso Theorell-Chance (hit and run) mechanism with conformational changes of the enzyme-coenzyme binary complexes as rate-determining for the oxidation of (S)-1-phenylethanol and the reduction of acetophenone. The underlying cause of the 270-fold enantiopreference for the (S)-enantiomer of 1-phenylethanol has been attributed to non-productive binding of the R-enantiomer. We have also shown that it is possible to tune the direction of the redox chemistry by adjusting pH with the oxidative reaction being favored at pH values above 7.

  • 21.
    Hellander, Stefan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Petzold, Linda
    University of California, Department of Computer Science.
    Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 147, no 23, article id 234101Article in journal (Refereed)
    Abstract [en]

    The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates. We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D.

  • 22.
    Henz Ryen, Astrid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Steinmetz, Julia
    Tahir, Ammar
    Jakobsson, Per-Johan
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Urban, Ernst
    Glasl, Sabine
    Bisabolane sesquiterpenes from the leaves of Lindera benzoin reduce prostaglandin E2 formation in A549 cellsIn: Phytochemistry Letters, ISSN 1874-3900, E-ISSN 1876-7486Article in journal (Other academic)
    Abstract [en]

    Phytochemical investigation of leaves from the American shrub Lindera benzoin (L.) Blume (Lauraceae) resulted in the isolation of one pure compound (1) and a diastereomeric mixture of (2 and 3). The structures of these new bisabolane sesquiterpenes were elucidated via MS and extensive NMR measurements and identified as 6-(2-hydroxy-6-methylhept-5-en-2-yl)-3-(hydroxymethyl)-4-oxocyclohex-2-en-1-yl acetate (1) and 3-(hydroxymethyl)-6-(5-(2-hydroxypropan-2-yl)-2-methyltetrahydrofuran-2-yl)-4-oxocyclohex-2-en-1-yl acetate (2 and 3). The compounds were evaluated in vitro for their anti-inflammatory activity. In cellular assays, 1-3 reduced pro-inflammatory prostaglandin E2 production in A549 cells in a dose-dependent manner.

  • 23.
    Henz Ryen, Astrid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Exploring evolutionary and chemical space using chemoinformatic tools and traditional methods in pharmacognosy2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The number of new drugs coming to the market is declining while interest in lead discovery from natural resources is seeing a revival. Although methods for isolation and identification of natural products have advanced tremendously, methods for selection of potential leads have fallen behind. As part of the Marie Curie ITN “MedPlant: Phylogenetic exploration of medicinal plant diversity” this thesis contributed to the exploration of chemical diversity in angiosperms and the development of new tools to analyze and define the chemical potential of a plant.

    In Paper I, it was demonstrated that physicochemical properties of selected specialized metabolites change in different plant groups. Changes in properties were assessed using ChemGPS-NP and diversity was quantified by calculating the volume occupied by the compounds in chemical space. By discussing the results against the background of possible underlying evolutionary mechanisms, it was concluded that evolutionary processes are reflected in chemical property space. These results hold great value for further studies on the evolution of chemical diversity and biochemical traits in plants. The methods developed can be used e.g. to define and predict the chemical diversity of related taxa, providing a strategy for a guided plant selection in search for new drug leads.

    In Paper II, the scaffold and molecular diversity of over 5,200 sesquiterpene lactones (STLs) was investigated, using different chemoinformatic tools. Quantity and distribution of skeleton classes was determined and it was shown that different plant families possess specific sets of molecular frameworks, with considerable variation in their frequency. Clustering analysis enabled qualitative division of STLs into smaller groups with similar structural features, pointing out the differentiation of various plant groups. Including the study results, the dataset offers a compelling resource for chemosystematics, natural product research and drug lead discovery focused on STLs. It provides the basis for phylogenetic implementations due to the detailed taxonomic annotation. Since STLs display a source for new drugs, it is of high value for a guided search for plant derived drug leads.

    In Paper III, Lindera benzoin was subjected to phytochemical and pharmacological investigations. Phytochemical investigations led to the isolation of three new sesquiterpenes. As Native American tribes used this shrub for various medicinal purposes, e.g. cold remedy or diaphoretic, the isolated compounds were evaluated in vitro for their anti-inflammatory activity. In cellular assays, they reduced pro-inflammatory prostaglandin E2 production in A549 cells in a dose-dependent manner, which may rationalize the traditional use of this plant.

    List of papers
    1. Charting Angiosperm Chemistry: Evolutionary Perspective on Specialized Metabolites Reflected in Chemical Property Space
    Open this publication in new window or tab >>Charting Angiosperm Chemistry: Evolutionary Perspective on Specialized Metabolites Reflected in Chemical Property Space
    2019 (English)In: Journal of Natural Products, ISSN 0163-3864, E-ISSN 1520-6025, Vol. 82, no 4, p. 798-812Article in journal (Refereed) Published
    Abstract [en]

    Plants possess an outstanding chemical diversity of specialized metabolites developed to adapt to environmental niches and increase fitness. The observed diversity is hypothesized to result from various evolutionary mechanisms, such as the continuous branching off and extension of existing biosynthetic pathways or enhanced levels of catalytic promiscuity in certain enzymes. In this study, ChemGPS-NP has been employed to chart the distribution and diversity of physicochemical properties for selected types of specialized metabolites from the angiosperms. Utilizing these charts, it is analyzed how different properties of various types of specialized metabolites change in different plant groups, and the chemical diversity from the volume they occupy in chemical property space is evaluated. In this context, possible underlying evolutionary mechanisms are discussed, which could explain the observed distribution and behavior in chemical property space. Based on these studies, it is demonstrated that evolutionary processes in plant specialized metabolism and the resultant metabolic diversification are reflected in chemical property space.

    National Category
    Bioinformatics and Systems Biology Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-383876 (URN)10.1021/acs.jnatprod.8b00767 (DOI)000466442100014 ()30912945 (PubMedID)
    Funder
    EU, FP7, Seventh Framework Programme, 606895-MedPlant
    Available from: 2019-06-12 Created: 2019-06-12 Last updated: 2020-01-04Bibliographically approved
    2. Structural classification and scaffold diversity of sesquiterpene lactones in the angiosperms
    Open this publication in new window or tab >>Structural classification and scaffold diversity of sesquiterpene lactones in the angiosperms
    (English)In: Phytochemistry, ISSN 0031-9422, E-ISSN 1873-3700Article in journal (Other academic) Submitted
    Abstract [en]

    Sesquiterpene lactones (STLs) present one of the largest groups of plant specialized metabolites with a wide range of biological activities. They are a valuable source for new plant derived drugs and drug leads since they contain several important chemical properties responsible for their versatile therapeutic potential.

    The aim of this study was to analyze and compare the chemical diversity of all types of STLs in different plant groups, both qualitatively and quantitatively. For this purpose, over 5,200 STLs have been compiled and their plant origin has been recorded, resulting in a comprehensive dataset comprising over 8,600 entries. An overview of skeleton classes and their distribution among plant families was given by assigning the STLs to their major classes. An extensive scaffold diversity analysis was performed based on the molecular framework of these compounds using established metrics. Furthermore, molecular diversity and similarity was assessed via 2D fingerprint and clustering analysis.

    The results highlighted significant differences in the degree of chemical diversity. It was demonstrated that the investigated plant families have tendencies to produce certain types of skeletons. The quantity and distribution of skeleton classes was determined per plant family and genus, as well as the proportions of skeleton classes to other STL producing families. Analyzing the scaffold diversity showed that they possessed specific sets of molecular frameworks with a considerable variation in their frequency of occurrence. Even if many plant families produce STLs belonging to the same skeleton class, their corresponding molecular frameworks differ. Clustering analysis confirmed the known large structural diversity and revealed similarities and differences of the compounds. The metrics employed enabled to qualitatively divide STLs into smaller groups with similar structural features, which reflected biologically and chemically different STLs and pointed out the differentiation of various plant groups, down to the taxonomic rank of the species.

    Taken together, these analyses provided a comprehensive insight into scaffold and molecular diversity of STLs. Due to the detailed taxonomic annotation, the distinct distribution of different types of STLs was captured. This dataset represents the latest detailed compilation of STLs in the angiosperms, which can be used as a basis for further chemoinformatic or chemosystematic analyses. To provide an example of potential implementations, the results were utilized in a phylogenetic exploration of these metabolites.

    Keywords
    angiosperm chemistry, sesquiterpene lactones, chemical diversity, dataset, scaffold diversity, molecular framework, clustering analysis, ECFP6
    National Category
    Natural Sciences Other Chemistry Topics
    Identifiers
    urn:nbn:se:uu:diva-399075 (URN)
    Available from: 2019-12-12 Created: 2019-12-12 Last updated: 2020-02-04Bibliographically approved
    3. Bisabolane sesquiterpenes from the leaves of Lindera benzoin reduce prostaglandin E2 formation in A549 cells
    Open this publication in new window or tab >>Bisabolane sesquiterpenes from the leaves of Lindera benzoin reduce prostaglandin E2 formation in A549 cells
    Show others...
    (English)In: Phytochemistry Letters, ISSN 1874-3900, E-ISSN 1876-7486Article in journal (Other academic) Submitted
    Abstract [en]

    Phytochemical investigation of leaves from the American shrub Lindera benzoin (L.) Blume (Lauraceae) resulted in the isolation of one pure compound (1) and a diastereomeric mixture of (2 and 3). The structures of these new bisabolane sesquiterpenes were elucidated via MS and extensive NMR measurements and identified as 6-(2-hydroxy-6-methylhept-5-en-2-yl)-3-(hydroxymethyl)-4-oxocyclohex-2-en-1-yl acetate (1) and 3-(hydroxymethyl)-6-(5-(2-hydroxypropan-2-yl)-2-methyltetrahydrofuran-2-yl)-4-oxocyclohex-2-en-1-yl acetate (2 and 3). The compounds were evaluated in vitro for their anti-inflammatory activity. In cellular assays, 1-3 reduced pro-inflammatory prostaglandin E2 production in A549 cells in a dose-dependent manner.

    Keywords
    Lindera benzoin, sesquiterpenes, structure elucidation, prostaglandin E2, anti-inflammatory
    National Category
    Natural Sciences Other Biological Topics Other Chemistry Topics
    Identifiers
    urn:nbn:se:uu:diva-399076 (URN)
    Available from: 2019-12-12 Created: 2019-12-12 Last updated: 2020-02-04Bibliographically approved
  • 24.
    Henz Ryen, Astrid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Kogej, Thierry
    Structural classification and scaffold diversity of sesquiterpene lactones in the angiospermsIn: Phytochemistry, ISSN 0031-9422, E-ISSN 1873-3700Article in journal (Other academic)
    Abstract [en]

    Sesquiterpene lactones (STLs) present one of the largest groups of plant specialized metabolites with a wide range of biological activities. They are a valuable source for new plant derived drugs and drug leads since they contain several important chemical properties responsible for their versatile therapeutic potential.

    The aim of this study was to analyze and compare the chemical diversity of all types of STLs in different plant groups, both qualitatively and quantitatively. For this purpose, over 5,200 STLs have been compiled and their plant origin has been recorded, resulting in a comprehensive dataset comprising over 8,600 entries. An overview of skeleton classes and their distribution among plant families was given by assigning the STLs to their major classes. An extensive scaffold diversity analysis was performed based on the molecular framework of these compounds using established metrics. Furthermore, molecular diversity and similarity was assessed via 2D fingerprint and clustering analysis.

    The results highlighted significant differences in the degree of chemical diversity. It was demonstrated that the investigated plant families have tendencies to produce certain types of skeletons. The quantity and distribution of skeleton classes was determined per plant family and genus, as well as the proportions of skeleton classes to other STL producing families. Analyzing the scaffold diversity showed that they possessed specific sets of molecular frameworks with a considerable variation in their frequency of occurrence. Even if many plant families produce STLs belonging to the same skeleton class, their corresponding molecular frameworks differ. Clustering analysis confirmed the known large structural diversity and revealed similarities and differences of the compounds. The metrics employed enabled to qualitatively divide STLs into smaller groups with similar structural features, which reflected biologically and chemically different STLs and pointed out the differentiation of various plant groups, down to the taxonomic rank of the species.

    Taken together, these analyses provided a comprehensive insight into scaffold and molecular diversity of STLs. Due to the detailed taxonomic annotation, the distinct distribution of different types of STLs was captured. This dataset represents the latest detailed compilation of STLs in the angiosperms, which can be used as a basis for further chemoinformatic or chemosystematic analyses. To provide an example of potential implementations, the results were utilized in a phylogenetic exploration of these metabolites.

  • 25.
    Holmboe, Michael
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Clay barrier properties studied with in silico techniques2014In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 248Article in journal (Other academic)
  • 26.
    Hussain, Afzal
    et al.
    King Saud Univ, Dept Pharmacognosy, Coll Pharm, Riyadh 11451, Saudi Arabia.
    Oves, Mohammad
    King Abdulaziz Univ, Ctr Excellence Environm Studies, Jeddah 21589, Saudi Arabia.
    Alajmi, Mohamed F.
    King Saud Univ, Dept Pharmacognosy, Coll Pharm, Riyadh 11451, Saudi Arabia.
    Hussain, Iqbal
    Jubail Ind Coll, Dept Gen Studies, Jubail Ind City 31961, Jubail, Saudi Arabia.
    Amir, Samira
    Alfaisal Univ, Dept Chem, Coll Sci & Gen Studies, Riyadh 11451, Saudi Arabia.
    Ahmed, Jahangeer
    King Saud Univ, Dept Chem, Coll Sci, Riyadh 11451, Saudi Arabia.
    Rehman, Md Tabish
    King Saud Univ, Dept Pharmacognosy, Coll Pharm, Riyadh 11451, Saudi Arabia.
    El-Seedi, Hesham
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Ali, Imran
    Taibah Univ, Dept Chem, Coll Sci, Al Medina Al Munawara 41477, Saudi Arabia;Jamia Millia Islamia, Dept Chem, New Delhi, India.
    Biogenesis of ZnO nanoparticles using Pandanus odorifer leaf extract: anticancer and antimicrobial activities2019In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 9, no 27, p. 15357-15369Article in journal (Refereed)
    Abstract [en]

    The continuously increasing incidence rates of cancer and infectious diseases are open threats to the sustainable survival of animals and humans. In the last two decades, the demands of nanomaterials as modern therapeutic agents have increased. In this study, biogenic zinc oxide nanoparticles (ZnO NPs) were developed from aqueous Pandanus odorifer leaf extract (POLE) and characterized using modern methods and tools, such as electron microscopy, X-ray diffraction, energy dispersive X-ray spectroscopy (EDX), Fourier transform infrared spectroscopy and UV-vis spectroscopy, which indicated the formation of very pure, spherical NPs approximately 90 nm in size. The anticancer activity of the ZnO NPs was evaluated by MTT and neutral red uptake (NRU) assays in MCF-7, HepG2 and A-549 cells at different doses (1, 2, 5, 10, 25, 50, 100 g ml(-1)). Moreover, the morphology of the treated cancer cells was examined by phase contrast microscopy. The results suggest that the synthesized ZnO NPs inhibited the growth of the cells when applied a concentration from 50-100 g ml(-1). Moreover, the biogenic ZnO NPs were analysed as an antimicrobial agent against pathogenic bacteria. The highest antibacterial activity was observed against Gram-positive Bacillus subtilis (26 nm) and Gram-negative Escherichia coli (24 mm) at 50 g per well. Complete bacterial growth (100%) vanished 100% upon treatment with ZnO NPs at 85 g ml(-1). Overall, POLE mediated derived biogenic ZnO NPs could serve as a significant anticancer and antimicrobial agent and be used in the development of novel drugs and skin care products.

  • 27.
    Hussain, Tanveer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Chakraborty, Sudip
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Kang, T. W.
    Johansson, Borje
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    BC3 Sheet Functionalized with Lithium-Rich Species Emerging as a Reversible Hydrogen Storage Material2015In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 16, no 3, p. 634-639Article in journal (Refereed)
    Abstract [en]

    The decoration of a BC3 monolayer with the polylithiated molecules CLi4 and OLi2 has been extensively investigated to study the hydrogen-storage efficiency of the materials by first principles electronic structure calculations. The binding energies of both lithiated species with the BC3 substrate are much higher than their respective cohesive energies, which confirms the stability of the doped systems. A significant positive charge on the Li atom in each of the dopants facilitates the adsorption of multiple H-2 molecules under the influence of electrostatic and van der Waals interactions. We observe a high H-2-storage capacity of 11.88 and 8.70 wt% for the BC3-CLi4 and BC3-OLi2 systems, respectively, making them promising candidates as efficient energy-storage systems.

  • 28.
    Israel, Liron L.
    et al.
    Bar Ilan Univ, Dept Chem, IL-5290002 Ramat Gan, Israel.;Bar Ilan Univ, Inst Nanotechnol & Adv Mat, IL-5290002 Ramat Gan, Israel..
    Karimi, Farhad
    Bencar AB, Uppsala, Sweden..
    Bianchessi, Silvia
    Fdn Filarete, I-20139 Milan, Italy..
    Scanziani, Eugenio
    Fdn Filarete, I-20139 Milan, Italy..
    Passoni, Lorena
    Fdn Filarete, I-20139 Milan, Italy..
    Matteoli, Michela
    Univ Milan, I-20129 Milan, Italy.;Univ Milan, Humanitas Clin & Res Ctr, Dipartimento Biotecnol Med & Med Traslaz, I-20129 Milan, Italy..
    Långström, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Bencar AB, Uppsala, Sweden..
    Lellouche, Jean-Paul
    Bar Ilan Univ, Dept Chem, IL-5290002 Ramat Gan, Israel.;Bar Ilan Univ, Inst Nanotechnol & Adv Mat, IL-5290002 Ramat Gan, Israel..
    Surface metal cation doping of maghemite nanoparticles: modulation of MRI relaxivity features and chelator-free Ga-68-radiolabelling for dual MRI-PET imaging2015In: MATERIALS RESEARCH EXPRESS, ISSN 2053-1591, Vol. 2, no 9, article id 095009Article in journal (Refereed)
    Abstract [en]

    Magnetically responsive maghemite (gamma-Fe2O3) nanoparticles (NPs) are the subject of current interest due to their potential use as contrast agents for in vivo magnetic resonance imaging (MRI). In addition, PET (positron emission tomography) is another non-invasive molecular imaging modality based on nuclear medicine and short-lived positron radionuclides incorporated in various bioprobes. In previous work (Haviv et al 2010 J. Am. Chem. Soc. 132 12519-12521), Massart magnetite (Fe3O4) oxidation using ceric ammonium nitrate (CAN) was explored. The resulting hydrophilic maghemite (gamma-Fe2O3) NPs formed a stable aqueous colloid/ferrofluid that disclosed a low level of NP surface doping by Ce3/4+ atoms/cations. In this work, magnetically responsive gallium(III) or various other lanthanide(III) cation-doped maghemite NPs were prepared in different ways which influenced their r(2)* MRI relaxivities, which were usually strengthened vs those of known FDA approved ferrofluids. In addition, this resulting NP surface chemistry enabled their direct labeling with PET-enabled Ga-68(III) cations (scheme 1) without using any attached chelating organic species/polymer, providing PET-enabled radioactive magnetic NPs towards a novel dual PET/MRI imaging nanoscale agent.

  • 29.
    Karlsson, Christoffer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Jämstorp, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Strømme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Sjödin, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Computational Electrochemistry Study of 16 Isoindole-4,7-diones as Candidates for Organic Cathode Materials2012In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 116, no 5, p. 3793-3801Article in journal (Refereed)
    Abstract [en]

    Prediction of the redox behavior of electroactive molecules enables screening of a variety of compounds and can serve as a guideline in the search for organic molecules for use as cathode materials in, for example, Li ion batteries. In this study, we present a computational strategy, based on density functional theory, to calculate redox potentials and acid dissociation constants for a series of 16 isoindole-4,7-dione (IID) derivatives. The calculations take all possible electron and proton transfers into account, and the results were found to correlate very well with electrochemical and spectroscopic measurements. The possibility of polymerizing the IID derivatives was also assessed computationally, as polymerization serves as a straightforward route to immobilize the active material. Three of the considered IIDs (5,6-dicyano-2-methyl-isoindole-4,7-dione, 5,6-dihydroxy-2-methyl-isoindole-4,7-dione, and 2-methyl-5-(trifluoromethyl)-isoindole-4,7-dione) are predicted to be particularly interesting for making polymers for organic cathodes because these are calculated to have high redox potentials and high specific capacities and to be readily polymerizable. The presented strategy is general and can be applied in the prediction of the electrochemical behavior of quinones as well as other systems involving proton and electron transfers.

  • 30.
    Karlsson, Christoffer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Jämstorp, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Strømme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Sjödin, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Isoindole-4,7-diones as Candidates for Organic Lithium Ion Battery Polymer Cathodes2012In: GRADuate School in Advanced Materials for the 21st century: Workshop 2012, February 8, 2012, Uppsala, 2012Conference paper (Refereed)
  • 31.
    Karlsson, Christoffer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Olsson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Maria, Strømme
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Sjödin, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Isoindole-4,7-dione Polymers As Candidates For Organic Lithium Ion Battery Cathodes2012In: 63rd Annual meeting of the International Society of Electrochemistry, August 19-24, 2012, Prague, Czech, 2012Conference paper (Refereed)
  • 32.
    Karo, Jaanus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    The Rôle of Side-Chains in Polymer Electrolytes for Batteries and Fuel Cells2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The subject of this thesis relates to the design of new polymer electrolytes for battery and fuel cell applications. Classical Molecular Dynamics (MD) modelling studies are reported of the nano-structure and the local structure and dynamics for two types of polymer electrolyte host: poly(ethylene oxide) (PEO) for lithium batteries and perfluorosulfonic acid (PFSA) for polymer-based fuel cells. Both polymers have been modified by side-chain substitution, and the effect of this on charge-carrier transport has been investigated. The PEO system contains a 89-343 EO-unit backbone with 3-15 EO-unit side-chains, separated by 5-50 EO backbone units, for LiPF6 salt concentrations corresponding to Li:EO ratios of 1:10 and 1:30; the PFSA systems correspond to commercial Nafion®, Hyflon® (Dow®) and Aciplex® fuel-cell membranes, where the major differences again lie in the side-chain lengths.

    The PEO mobility is clearly enhanced by the introduction of side-chains, but is decreased on insertion of Li salts; mobilities differ by a factor of 2-3. At the higher Li concentration, many short side-chains (3-5 EO-units) give the highest ion mobility, while the mobility was greatest for side-chain lengths of 7-9 EO units at the lower concentration. A picture emerges of optimal Li+-ion mobility correlating with an optimal number of Li+ ions in the vicinity of mobile polymer segments, yet not involved in significant cross-linkages within the polymer host.

    Mobility in the PFSA-systems is promoted by higher water content. The influence of different side-chain lengths on local structure was minor, with Hyflon® displaying a somewhat lower degree of phase separation than Nafion®. Furthermore, the velocities of the water molecules and hydronium ions increase steadily from the polymer backbone/water interface towards the centre of the proton-conducting water channels. Because of its shorter side-chain length, the number of hydronium ions in the water channels is ~50% higher in Hyflon® than in Nafion® beyond the sulphonate end-groups; their hydronium-ion velocities are also ~10% higher.

    MD simulation has thus been shown to be a valuable tool to achieve better understanding of how to promote charge-carrier transport in polymer electrolyte hosts. Side-chains are shown to play a fundamental rôle in promoting local dynamics and influencing the nano-structure of these materials.

    List of papers
    1. A molecular dynamics study of the effect of side-chains on mobility in a polymer host
    Open this publication in new window or tab >>A molecular dynamics study of the effect of side-chains on mobility in a polymer host
    2005 (English)In: Solid State Ionics, Vol. 176, no 39-40, p. 3041-3044Article in journal (Refereed) Published
    Abstract [en]

    The effect on polymer dynamics of adding methoxy-terminated poly(ethylene oxide) (PEO) side-chains with different lengths and separations to an amorphous long-chain PEO backbone has been studied by Molecular Dynamics (MD) simulation at 293 K and 330 K. The study is seen as having a direct general relevance to the optimal design of ion-conducting polymer hosts for both Li-ion battery and polymer fuel-cell applications. The MD box used contains a long-chain PEO backbone to which side-chains comprising 3, 6, 7, 8, 9 and 15 EO units are added. The chosen separations between the side-chains are 5, 10, 15, 20 and 50 EO units. All potentials used to describe these systems are taken from earlier work (J. Mater. Chem., 13 (2003) 214). The overall mobility of the polymer host system is found to have both minima and maxima at both temperatures for side-chain lengths in the range 6–9 EO units. This is almost totally independent of side-chain separation at 293 K, while the situation is more complex at 330 K.

    Keywords
    Molecular dynamics, Polymer side-chains, Chain separation, Ion conduction, Mobility, Polymer fuel cells
    National Category
    Inorganic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-75441 (URN)doi:10.1016/j.ssi.2005.10.003 (DOI)
    Available from: 2006-02-07 Created: 2006-02-07 Last updated: 2011-01-11
    2. A Molecular Dynamics study of the influence of side-chain length and spacing on lithium mobility in non-crystalline LiPF6·PEOx; x = 10 and 30
    Open this publication in new window or tab >>A Molecular Dynamics study of the influence of side-chain length and spacing on lithium mobility in non-crystalline LiPF6·PEOx; x = 10 and 30
    2009 (English)In: Solid State Ionics, ISSN 0167-2738, E-ISSN 1872-7689, Vol. 180, no 23-25, p. 1272-1284Article in journal (Refereed) Published
    Abstract [en]

    Molecular Dynamics (MD) simulation techniques have been used to investigate systematically how the length and spacing of poly(ethylene oxide) (PEO) side-chains along a PEO backbone influence ion mobility for two different salt concentrations. This is of fundamental relevance to the design of new polymer electrolytes for battery applications. The salt used has been LiPF6 in concentrations corresponding to Li:EO ratios of 1:30 and 1:10. The MD box contained PEO backbones of 89-343 EO units to which 3, 6, 7, 8, 9 and 15 EO unit side-chains were added. The selected spacings along the backbone between the PEO side-chains attachment points were 5, 10, 15, 20 and 50 EO units. The backbone and all side-chains were methoxy end-capped, and the simulations were all made at 293 K. Ion mobilities have been estimated from the variation of mean-square-displacement with time, and have been analysed in relation to chain dynamics, cross-linking and ion pairing. Comparisons are also made with the results of simulated PEO systems without side-chains and/or without salt. It is found that, at a higher concentration, many short side-chains give the highest ion mobility, while the mobility is highest for side-chain lengths of 7-9 EO units at the lower concentration.

    Keywords
    Molecular Dynamics; Ion conduction; Polymer electrolyte; Salt ions; Side-chain; Li-ion batteries
    National Category
    Inorganic Chemistry
    Research subject
    Inorganic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-101259 (URN)10.1016/j.ssi.2009.07.009 (DOI)000273493500008 ()
    Available from: 2009-04-21 Created: 2009-04-21 Last updated: 2017-12-13Bibliographically approved
    3. Molecular dynamics studies of the Nafion®, Dow® and Aciplex® fuel-cell polymer membrane systems
    Open this publication in new window or tab >>Molecular dynamics studies of the Nafion®, Dow® and Aciplex® fuel-cell polymer membrane systems
    2007 (English)In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 13, no 10, p. 1039-1046Article in journal (Refereed) Published
    Abstract [en]

    The Nafion, Dow and Aciplex systems – where the prime differences lies in the side-chain length – have been studied by molecular dynamics (MD) simulation under standard pressure and temperature conditions for two different levels of hydration: 5 and 15 water molecules per (H)SO3 end-group. Structural features such as water clustering, water-channel dimensions and topology, and the dynamics of the hydronium ions and water molecules have all been analysed in relation to the dynamical properties of the polymer backbone and side-chains. It is generally found that mobility is promoted by a high water content, with the side-chains participating actively in the H3O+/H2O transport mechanism. Nafion, whose side-chain length is intermediate of the three polymers studied, is found to have the most mobile polymer side-chains at the higher level of hydration, suggesting that there could be an optimal side-chain length in these systems. There are also some indications that the water-channel network connectivity is optimal for high water-content Nafion system, and that this could explain why Nafion appears to exhibit the most favourable overall hydronium/water mobility.

    Keywords
    Molecular dynamics, Nafion membrane, Proton exchange membrane fuel cell (PEMFC), Side-chain length
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-13970 (URN)10.1007/s00894-007-0230-7 (DOI)000248912300002 ()17665227 (PubMedID)
    Available from: 2008-01-28 Created: 2008-01-28 Last updated: 2018-01-03Bibliographically approved
    4. Molecular Dynamics Modelling of Proton Transport in Nafion® and Hyflon® Nano-Structures
    Open this publication in new window or tab >>Molecular Dynamics Modelling of Proton Transport in Nafion® and Hyflon® Nano-Structures
    (English)Manuscript (Other academic)
    Abstract
    Identifiers
    urn:nbn:se:uu:diva-101260 (URN)
    Available from: 2009-04-21 Created: 2009-04-21 Last updated: 2018-01-03
  • 33.
    Konda, Vivekananda R.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Veron, Jean-Baptiste
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Larhed, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preclinical PET Platform. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Continuous flow chemistry utilizing silicon carbide (SiC) reactors2014In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 247Article in journal (Other academic)
  • 34.
    Koptina, Anna
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Gunasekera, Sunithi
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Muhammad, Taj
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Bohlin, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Alsmark, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Göransson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Microwave-assisted solid phase peptide synthesis of Asteropine A2014In: Phytopharm 2014, Saint-Petersburg, Russia 3-5 July 2014 / [ed] Shabanov P.D., Saint-Petersburg, Russia, 2014, Vol. 12, p. 36-Conference paper (Refereed)
  • 35. Koroidov, Sergey
    et al.
    Anderlund, Magnus F.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Styring, Stenbjörn
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Thapper, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Messinger, Johannes
    First turnover analysis of water-oxidation catalyzed by Co-oxide nanoparticles2015In: Energy & Environmental Science, ISSN 1754-5692, E-ISSN 1754-5706, Vol. 8, no 8, p. 2492-2503Article in journal (Refereed)
    Abstract [en]

    Co-oxides are promising water oxidation catalysts for artificial photosynthesis devices. Presently, several different proposals exist for how they catalyze O2 formation from water. Knowledge about this process at molecular detail will be required for their further improvement. Here we present time-resolved 18O-labelling isotope-ratio membrane-inlet mass spectrometry (MIMS) experiments to study the mechanism of water oxidation in Co/methylenediphosphonate (Co/M2P) oxide nanoparticles using [Ru(bpy)3]3+ (bpy = 2,2'-bipyridine) as chemical oxidant. We show that 16O–Co/M2P-oxide nanoparticles produce 16O2 during their first turnover after simultaneous addition of H218O and [Ru(bpy)3]3+, while sequential addition with a delay of 3 s yields oxygen reflecting bulk water 18O-enrichment. This result is interpreted to show that the O–O bond formation in Co/M2P-oxide nanoparticles occurs via intramolecular oxygen coupling between two terminal Co–OHn ligands that are readily exchangeable with bulk water in the resting state of the catalyst. Importantly, our data allow the determination of the number of catalytic sites within this amorphous nanoparticular material, to calculate the TOF per catalytic site and to derive the number of holes needed for the production of the first O2 molecule per catalytic site. We propose that the mechanism of O–O bond formation during bulk catalysis in amorphous Co-oxides may differ from that taking place at the surface of crystalline materials.

  • 36.
    Kwong, Wai Ling
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Lee, Cheng Choo
    Umeå Core Facility for Electron Microscopy, Umeå University, 90187 Umeå, Sweden.
    Shchukarev, Andrey
    Department of Chemistry, Kemiskt Biologiskt Centrum (KBC), Umeå University, 90187 Umeå, Sweden.
    Björn, Erik
    Department of Chemistry, Kemiskt Biologiskt Centrum (KBC), Umeå University, 90187 Umeå, Sweden.
    Messinger, Johannes
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Department of Chemistry, Kemiskt Biologiskt Centrum (KBC), Umeå University, 90187 Umeå, Sweden.
    High-performance iron (III) oxide electrocatalyst for water oxidation in strongly acidic media2018In: Journal of Catalysis, ISSN 0021-9517, E-ISSN 1090-2694, Vol. 365, p. 29-35Article in journal (Refereed)
    Abstract [en]

    Stable and efficient oxygen evolution reaction (OER) catalysts for the oxidation of water to dioxygen in highly acidic media are currently limited to expensive noble metal (Ir and Ru) oxides since presentlyknown OER catalysts made of inexpensive earth-abundant materials generally suffer anodic corrosion at low pH. In this study, we report that a mixed-polymorph film comprising maghemite and hematite, prepared using spray pyrolysis deposition followed by low-temperature annealing, showed a sustained OER rate (>24 h) corresponding to a current density of 10 mA cm2 at an initial overpotential of 650mV, with a Tafel slope of only 56 mV dec1 and near-100% Faradaic efficiency in 0.5 M H2SO4 (pH 0.3). This performance is remarkable, since iron (III) oxide films comprising only maghemite were found toexhibit a comparable intrinsic activity, but considerably lower stability for OER, while films of pure hematite were OER-inactive. These results are explained by the differences in the polymorph crystal structures, which cause different electrical conductivity and surface interactions with water molecules and protons. Our findings not only reveal the potential of iron (III) oxide as acid-stable OER catalyst, but also highlight the important yet hitherto largely unexplored effect of crystal polymorphism on electrocatalytic OER performance.

  • 37.
    Lacey, Matthew
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Following internal resistance changes in batteries with a versatile intermittent current interruption technique2017Conference paper (Other academic)
  • 38.
    Lacey, Matthew J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Edström, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Brandell, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Visualising the problems with balancing lithium-sulfur batteries by "mapping'' internal resistance2015In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 51, no 92, p. 16502-16505Article in journal (Refereed)
    Abstract [en]

    Frequent and continuous determination of battery internal resistance by a simple current-interrupt method enables the visualisation of cell behaviour through the creation of resistance "maps'', showing changes in resistance as a function of both capacity and cycle number. This new approach is applied here for the investigation of cell failure in the lithium-sulfur system with Li electrode excesses optimised towards practically relevant specifications.

  • 39.
    Lacey, Matthew J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Jeschull, Fabian
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Edström, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Brandell, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Functional, water-soluble binders for improved capacity and stability of lithium-sulfur batteries2014In: Journal of Power Sources, ISSN 0378-7753, E-ISSN 1873-2755, Vol. 264, p. 8-14Article in journal (Refereed)
    Abstract [en]

    Binders based on mixtures of poly(ethylene oxide) (PEO) and poly(vinylpyrrolidone) (PVP) are here shown to significantly improve the reversible capacity and capacity retention of lithium- sulfur batteries compared to conventional binders. This mixed binder formulation combines the local improvement to the solvent system offered by PEO and the lithium (poly)sulfide-stabilising effect of PVP. Cells with cathodes made of simple mixtures of sulfur powder and carbon black with a binder of 4:1 PEO:PVP exhibited a reversible capacity of over 1000 mAh g(-1) at C/5 after 50 cycles and 800 mAh g(-1) at 1C after 200 cycles. Furthermore, these materials are water soluble, environmentally friendly and widely available, making them particularly interesting for large-scale production and applications in, for example, electric vehicles. 

  • 40. Leino, Hannu
    et al.
    Shunmugam, Sumathy
    Isojarvi, Janne
    Oliveira, Paulo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Mulo, Paula
    Saari, Lyudmila
    Battchikova, Natalia
    Sivonen, Kaarina
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Aro, Eva-Mari
    Allahverdiyeva, Yagut
    Characterization of ten H-2 producing cyanobacteria isolated from the Baltic Sea and Finnish lakes2014In: International journal of hydrogen energy, ISSN 0360-3199, E-ISSN 1879-3487, Vol. 39, no 17, p. 8983-8991Article in journal (Refereed)
    Abstract [en]

    The genetic background and activities of the enzymes involved in H-2 production were investigated from ten distinct H-2 producing cyanobacteria, revealed by a recent screening. All strains are N-2-fixing, filamentous and heterocystous. Southern hybridization revealed that the tested strains possess the genes encoding the conventional nitrogenase (nifHDK1), and lack the alternative nitrogenases. The high H-2 production rate of these strains was shown not to be dependent on the presence of highly active nitrogenase or bidirectional hydrogenase enzymes. Moreover, most of the strains possessed a highly active uptake hydrogenase enzyme. We also examined the structure of the nif and hup operons encoding nitrogenase and uptake hydrogenase enzymes in the Calothrix 336/3 strain, the best H-2 producer in the screening. We concluded that the ability of the cyanobacteria to produce high levels of H-2 is not directly linked to the maximum capacities of the enzymes involved in H-2 production.

  • 41.
    Lejonklo, Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Friction and wear study of lean powder metallurgy steel in a lubricated sliding contact2019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A fairly new technology used to produce metallic components is powder metallurgy (PM). Among the advantages with this technique are decreased cost of production for complex-shaped parts, new alloys are made possible, reduced end processing, less material loss, and vibrational damping effects. The downside is the number of pores created which can alter the tribological properties of the material.

    The focus of this report is to investigate how lean PM steel behaves under tribological contacts.  Friction and wear will be investigated using a pin-on-disc setup to mimic the sliding part of a gear tooth mesh.

    Previous studies show that the amount of wear, and if the wear increases or decreases with increased density is dependent on the degree of porosity and the pore size. This means that the wear might be minimized by optimizing the number of pores in the material and their shape and size.

    The result of this study shows that the friction coefficient decreases with increasing density. The wear coefficient show signs of the same correlations but further tests are needed. The main wear comes from adhesive wear, with signs of abrasive wear. The amount of abrasive wear seems to increase with an increase in density, supporting previous studies claiming that pores can trap wear debris and decrease the number of abrasive particles in the contact.

  • 42.
    Lindholm, Petra
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    El-Seedi, Hesham
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Göransson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Gullbo, Joachim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Larsson, Rolf
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Bioassay-guided isolation of a cytotoxic quinolizidine alkaloid from Nuphar luteumIn: Chemistry and Biodiversity, ISSN 1612-1872, E-ISSN 1612-1880Article in journal (Refereed)
  • 43.
    Liu, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Modelling Evolution: From non-life, to life, to a variety of life2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Life is able to replicate itself, e.g., a microorganism is able to divide into two identical ones, and a single plant is able to forest a whole island. But life is the only example of self-replication (note that a computer virus seems able to replicate itself, but it needs the assistance of a processor such as a CPU, and thus not a truly self-replicating entity). So before the appearance of life, nothing can self-replicate. How does life, a truly self-replicating entity, evolve from substances which is not able to self-replicate? Why can it ever happen? Is there a general underlying mechanism that governs how self-replicating entities can develop de novo on Earth, or even other plants?

    As long as the first life appears, it has the potential to cover the whole plant. But one single life form cannot do the job. Life has branched into a huge number of biological classes and species. Different species interact with each other, and with their environment, which, as a whole, is defined as an ecosystem. Distinct ecosystems are found at different scales and different places, e.g., microbes cross-feed and compete for resources within natural communities; and different types of cells interact by exchanging metabolite within an organism body. But, why sometimes we consider an ecosystem as an individual (such as the human body which is, in fact, an ecosystem inhabited by a huge number of microorganisms without which we cannot survive) while sometimes not? What really distinguishes an individual-level life from a system-level life? Are there general properties only a system-level life has, emerged from the interactions among its compositional individual-level life?

    This thesis is to investigate these two questions by mathematical models. For the evolution from non-life to life, namely the origin of life, we build an artificial chemistry model to investigate why an independent self-replicating entity can develop spontaneously from some chemical reaction system in which no reaction is self-replicating. For the evolution from life to a variety of life, we build an artificial ecosystem model to investigate general properties of ecosystems.

    List of papers
    1. Spontaneous emergence of self-replication in chemical reaction systems
    Open this publication in new window or tab >>Spontaneous emergence of self-replication in chemical reaction systems
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously proposed mathematical models either supply an explicit framework for a minimal living system or only consider catalyzed reactions, and thus fail to provide a comprehensive theory. We set up a general model for chemical reaction systems that properly accounts for energetics, kinetics and the conservation law. We find that (1) some systems are collectively-catalytic where reactants are transformed into end products with the assistance of intermediates (as in the citric acid cycle), while some others are self-replicating where different parts replicate each other and the system self-replicates as a whole (as in the formose reaction); (2) many alternative chemical universes often contain one or more such systems; (3) it is possible to construct a self-replicating system where the entropy of some parts spontaneously decreases, in a manner similar to that discussed by Schrodinger; (4) complex self-replicating molecules can emerge spontaneously and relatively easily from simple chemical reaction systems through a sequence of transitions. Together these results start to explain the origins of prebiotic evolution.

    Keywords
    Origin of life, Self-replication, Collectively-catalytic, Prebiotic evolution, Biological complexity
    National Category
    Other Mathematics Other Chemistry Topics Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-339615 (URN)
    Available from: 2018-01-22 Created: 2018-01-22 Last updated: 2018-01-23
    2. Is the golden ratio a universal constant for self-replication?
    Open this publication in new window or tab >>Is the golden ratio a universal constant for self-replication?
    2018 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 7, article id e0200601Article in journal (Other academic) Published
    Abstract [en]

    The golden ratio, ϕ = 1.61803..., has often been found in connection with biological phenomena, ranging from spirals in sunflowers to gene frequency. One example where the golden ratio often arises is in self-replication, having its mathematical origins in Fibonacci's sequence for "rabbit reproduction". Recently, it has been claimed that ϕ determines the ratio between the number of different nucleobases in human genome. Such empirical examples continue to give credence to the idea that the golden ratio is a universal constant, not only in mathematics but also for biology. In this paper, we employ a general framework for chemically realistic self-replicating reaction systems and investigate whether the ratio of chemical species population follows "universal constants". We find that many self-replicating systems can be characterised by an algebraic number, which, in some cases, is the golden ratio. However, many other algebraic numbers arise from these systems, and some of them—such as and 1.22074... which is also known as the 3rd lower golden ratio—arise more frequently in self-replicating systems than the golden ratio. The "universal constants" in these systems arise as roots of a limited number of distinct characteristic equations. In addition, these "universal constants" are transient behaviours of self-replicating systems, corresponding to the scenario that the resource inside the system is infinite, which is not always the case in practice. Therefore, we argue that the golden ratio should not be considered as a special universal constant in self-replicating systems, and that the ratios between different chemical species only go to certain numbers under some idealised scenarios.

    Keywords
    Golden ratio, Fibonacci sequence, Self-replication, Fibonacci rabbit, Universal constant
    National Category
    Other Mathematics
    Identifiers
    urn:nbn:se:uu:diva-339888 (URN)10.1371/journal.pone.0200601 (DOI)000438829800032 ()30011316 (PubMedID)
    Available from: 2018-01-23 Created: 2018-01-23 Last updated: 2018-09-27Bibliographically approved
    3. Insights into resource consumption, cross-feeding, system collapse, stability and biodiversity from an artificial ecosystem
    Open this publication in new window or tab >>Insights into resource consumption, cross-feeding, system collapse, stability and biodiversity from an artificial ecosystem
    2017 (English)In: Journal of the Royal Society Interface, ISSN 1742-5689, E-ISSN 1742-5662, Vol. 14, no 126, article id 20160816Article in journal (Refereed) Published
    Abstract [en]

    Community ecosystems at very different levels of biological organization often have similar properties. Coexistence of multiple species, cross-feeding, biodiversity and fluctuating population dynamics are just a few of the properties that arise in a range of ecological settings. Here we develop a bottom-up model of consumer-resource interactions, in the form of an artificial ecosystem ``number soup'', that reflects basic properties of many bacterial and other community ecologies. We demonstrate four key properties of the number soup model: (1) Communities self-organise so that all available resources are fully consumed; (2) Reciprocal cross-feeding is a common evolutionary outcome, which evolves in a number of stages, and many transitional species are involved; (3) The evolved ecosystems are often ``robust yet fragile'', with keystone species required to prevent the whole system from collapsing; (4) Non-equilibrium dynamics and chaotic patterns are general properties, readily generating rich biodiversity. These properties have been observed in empirical ecosystems, ranging from bacteria to rainforests. Establishing similar properties in an evolutionary model as simple as the number soup suggests that these four properties are ubiquitous features of all community ecosystems, and raises questions about how we interpret ecosystem structure in the context of natural selection.

    Keywords
    ecosystem evolution, consumer-resource interactions, emergence, community ecology, system-level property
    National Category
    Ecology Other Mathematics Other Biological Topics
    Identifiers
    urn:nbn:se:uu:diva-314360 (URN)10.1098/rsif.2016.0816 (DOI)000393380400009 ()
    Funder
    EU, European Research Council
    Available from: 2017-02-01 Created: 2017-02-01 Last updated: 2018-01-23Bibliographically approved
    4. The artificial ecosystem: number soup (part II)
    Open this publication in new window or tab >>The artificial ecosystem: number soup (part II)
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    This paper is a follow-up work about the artificial ecosystem model:number soup (Liu and Sumpter, J. Royal Soc. Interface, 2017). Itelaborates more details about this model and points out future directions.

    Keywords
    Artificial ecosystem, Species loop, Gillespie algorithm, Cooperators and cheaters, Artificial chemistry
    National Category
    Ecology Other Mathematics Other Biological Topics
    Identifiers
    urn:nbn:se:uu:diva-339595 (URN)
    Funder
    EU, European Research Council
    Available from: 2018-01-21 Created: 2018-01-21 Last updated: 2018-01-23
  • 44.
    Liu, Yu
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Sumpter, David J. T.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Spontaneous emergence of self-replication in chemical reaction systemsManuscript (preprint) (Other academic)
    Abstract [en]

    Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously proposed mathematical models either supply an explicit framework for a minimal living system or only consider catalyzed reactions, and thus fail to provide a comprehensive theory. We set up a general model for chemical reaction systems that properly accounts for energetics, kinetics and the conservation law. We find that (1) some systems are collectively-catalytic where reactants are transformed into end products with the assistance of intermediates (as in the citric acid cycle), while some others are self-replicating where different parts replicate each other and the system self-replicates as a whole (as in the formose reaction); (2) many alternative chemical universes often contain one or more such systems; (3) it is possible to construct a self-replicating system where the entropy of some parts spontaneously decreases, in a manner similar to that discussed by Schrodinger; (4) complex self-replicating molecules can emerge spontaneously and relatively easily from simple chemical reaction systems through a sequence of transitions. Together these results start to explain the origins of prebiotic evolution.

  • 45. Magnuson, Ann
    et al.
    Rova, Maria
    Mamedov, Fikret
    Fredriksson, Per-Olaf
    Styring, Stenbjörn
    The role of cytochrome b559 and tyrozineD in protection against photoinhibition during in vivo photoactivation of photosystem II1999In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1411, p. 180-191Article in journal (Refereed)
  • 46.
    Magnuson, Ann
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Styring, Stenbjörn
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Understanding Photosystem II Function by Artificial Photosynthesis2005In: Photosystem II: The Light-Driven Water:Plastoquinone Oxidoreductase / [ed] Wydrzynski, Thomas J.; Satoh, Kimiyuki; Freeman, Joel A., Springer Netherlands, 2005, p. 753-775Chapter in book (Other academic)
  • 47.
    Mamedov, Fikret
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Rintamäki, Eevi
    Aro, Eva-Mari
    Andersson, Bertil
    Styring, Stenbjörn
    Influence of protein phosphorylation on the electron transport properties of photosystem II2002In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 74, p. 61-72Article in journal (Refereed)
  • 48. Mamedov, Fikret
    et al.
    Stefansson, Hreinn
    Albertsson, Per-Åke
    Styring, Stenbjörn
    Photosystem II in different parts of the thylakoid membrane: a functional comparison between different domains2000In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 39, p. 10478-10486Article in journal (Refereed)
  • 49.
    Marchiori, Cleber F.N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Brandell, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Araujo, Carlos Moyses
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Predicting Structure and Electrochemistry of Dilithium Thiophene-2,5-Dicarboxylate Electrodes by Density Functional Theory and Evolutionary Algorithms2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 8, p. 4691-4700Article in journal (Refereed)
    Abstract [en]

    Organic electroactive materials are promising candidates to be TUC used as lithium insertion electrodes in the next generation of environmentally friendly battery technologies. In this work, evolutionary algorithms at interplay with density functional theory calculations have been employed to predict the crystal structure for both delithiated and lithiated phases of dilithium thiophene dicarboxylate (Li2TDC). On the basis of the resulting crystals, electronic structure modifications and voltage profiles for the lithiation process have been calculated. The obtained structure for the delithiated phase showed a well-defined salt layer intercalating the organic components, forming a so-called lithium organic framework (LOF). Upon lithiation, new structures appear which deviate from the LOF as a consequence of the reduction of the S atoms, which coordinate with the additional Li ions. The calculated average potential of similar to 1.00 V vs Li/Li+ is found to be in good agreement with experimental findings. An additional study at the molecular level has also been conducted aiming at gaining insight into the importance of the crystallographic environment on the structural and thermodynamics properties. This strategy is suitable for an initial assessment of the electrochemical process that underlies the lithiation mechanism of electrode materials. Moreover, the employed evolutionary algorithm emerges as a promising tool to predict crystal structures during lithiation, which are otherwise difficult to resolve experimentally.

  • 50.
    Meng, Qingnan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry. College of Construction Engineering, Jilin University, Changchun 130026, People's Republic of China.
    Malinovskis, Paulius
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Nedfors, Nils
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Mao, Fang
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Andersson, Matilda
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Sun, Youhong
    College of Construction Engineering, Jilin University, Changchun 130026, People's Republic of China.
    Jansson, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Characterization of amorphous Zr-Si-C thin films deposited by DC magnetron sputtering2015In: Surface & Coatings Technology, ISSN 0257-8972, E-ISSN 1879-3347, Vol. 261, p. 227-234Article in journal (Refereed)
    Abstract [en]

    Zr-x(SiyC1-y)(1-x) films with different Si/C atomic ratios and Zr contents were deposited using non-reactive dc-magnetron co-sputtering. All films exhibited an X-ray amorphous structure with a complex distribution of chemical bonds. The presence of Zr in the films reduced the amount of C-C and Si-C bonds but favored the formation of Zr-C and Zr-Si bonds. The mechanical and electrical properties were dependent on the bond distribution in the amorphous structure and a linear relationship between film hardness and the relative amount of Si-C bonds was observed. The addition of Zr in films also gave rise to an increase in metallic character resulting in a lower electrical resistivity. Analysis of the tribofilm showed that a low friction coefficient was favored by the formation of a lubricating a-C layer and that the formation of zirconium and silicon oxides in the more Zr-rich films has a detrimental effect on the tribological performance. (C) 2014 Elsevier B.V. All rights reserved.

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