| 1. |
- Alm, Rikard, et al.
(författare)
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Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra
- 2006
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 5:4, s. 785-792
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Tidskriftsartikel (refereegranskat)abstract
- We describe an approach to screen large sets of MALDI-MS mass spectra for protein isoforms separated on two-dimensional electrophoresis gels. Mass spectra are matched against each other by utilizing extracted peak mass lists and hierarchical clustering. The output is presented as dendrograms in which protein isoforms cluster together. Clustering could be applied to mass spectra from different sample sets, dates, and instruments, revealed similarities between mass spectra, and was a useful tool to highlight peptide peaks of interest for further investigation. Shared peak masses in a cluster could be identified and were used to create novel peak mass lists suitable for protein identification using peptide mass fingerprinting. Complex mass spectra consisting of more than one protein were deconvoluted using information from other mass spectra in the same cluster. The number of peptide peaks shared between mass spectra in a cluster was typically found to be larger than the number of peaks that matched to calculated peak masses in databases, thus modified peaks are probably among the shared peptides. Clustering increased the number of peaks associated with a given protein.
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| 2. |
- Alm, Rikard, et al.
(författare)
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Proteomic variation is as large within as between strawberry varieties
- 2007
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 6:8, s. 3011-3020
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Tidskriftsartikel (refereegranskat)abstract
- in search for a strawberry (Fragaria ananassa) with low allergen content, we determined the proteomic variation within and between different varieties. Proteomics data were generated by DIGE and proteins identified with MALDI-MS/MS. The amount of the strawberry allergen Fra a 1 varied between different strawberry varieties (CV = 39%). The variation was at the same level, or even slightly larger, due to different growth conditions (CV = 43%). For 153 other proteins, the biological variation was more affected by different growth conditions than by different varieties (mean CV = 52% and 43%, respectively) due to variation in a subset of proteins. Thus, the allergen variation due to growth conditions must be taken into consideration in attempts to obtain a low-allergen strawberry. However, the allergen content was always lower in colorless (white) strawberry varieties than in the red ones. Moreover, of the spots whose expression correlated with the allergen and the color (32 and 68, respectively), only 3 were the same. This implies that these two phenotypic traits are not inseparable, and it may be possible to breed a red strawberry with low amount of allergen.
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| 3. |
- Alvi, Muhammad Rouf, et al.
(författare)
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Scope and Limitations of an Acid Catalyzed Protocol for Hypersilyl Protection of Alcohols
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- A highly efficient and convenient triflic acid (TfOH) catalyzed protocol for the protection of various functionalized alcohols in CH2Cl2 at ambient temperature using tris(trimethylsilyl)silyl-N,N-dimethyl-methaneamide (hypersilylamide) 1 as the protecting reagent is developed. Herein, results on the scope and limitations of this protocol for a number of functionalized alcohols are presented. This method was found to be effective for the selective protection of less hindered OH groups in different classes of diols containing both pri/tert, sec/tert, or aromatic/aliphatic hydroxyl groups. In general, our protocol exhibited excellent functional group tolerance in the protection of alcohols containing alkoxy, keto, amino, as well as halo substituents in good to excellent yields.
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| 4. |
- Denisova, Aleksandra, et al.
(författare)
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Expanding the (Cross-)Hyperconjugation of 1,4-Disilacyclohexa-2,5-dienes to Larger Monomers and Oligomers : A Computational Investigation
- 2016
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Ingår i: RSC Advances. - 2046-2069. ; 6:43, s. 36961-36970
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Tidskriftsartikel (refereegranskat)abstract
- We used density functional theory calculations to examine molecules that can be regarded as expanded 1,4-disilacyclohexa-2,5-dienes as well as oligomers based on these or 1,4-disilacyclohexa-2,5-diene with the aim to identify systems with extended (cross-)hyperconjugation. Among the three "expanded 1,4-disilacyclohexa-2,5-dienes" considered cyclobutadisilole is the most interesting as it has a higher thermodynamic stability than the isomeric 1,6-disilacyclodeca-2,3,4,7,8,9-hexaene and significantly lower first electronic excitation energy than 1,6-disilacyclodeca-2,4,7,9-tetraene. Cyclobutadisilole with trimethylsilyl substituents at Si shows particularly low excitations with the first strong transition at 3.46 eV (358 nm), i.e., similar to 1.1 eV lower than in 1,4-disilacyclohexa-2,5-diene. The monomers were connected into oligomers via their Si atoms using bis(dimethylsilanediyl) linkers, and some extended hyperconjugation was revealed. The first allowed UV/Vis excitation in the cyclobutadisilole-based tetramers is calculated at 2.57 eV (482 nm), although the lowering in excitation energies when going from monomer to tetramer is merely similar to 0.5 eV and hyperconjugation has modest impact on geometries. Yet, the tetra(cyclobutadisilole) has a significantly lower first allowed excitation when compared to a previously studied tetra(1,4-disilacyclohexadiene) with first excitation at 3.9 eV (318 nm).
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| 5. |
- Denisova V, Aleksandra, et al.
(författare)
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A Computational Investigation of the Substituent Effects on Geometric, Electronic, and Optical Properties of Siloles and 1,4-Disilacyclohexa-2,5-dienes
- 2017
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Ingår i: Molecules. - : MDPI AG. - 1431-5157 .- 1420-3049. ; 22:3
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Tidskriftsartikel (refereegranskat)abstract
- Thirty two differently substituted siloles 1a–1p and 1,4-disilacyclohexa-2,5-dienes 2a–2p were investigated by quantum chemical calculations using the PBE0 hybrid density functional theory (DFT) method. The substituents included σ-electron donating and withdrawing, as well as π-electron donating and withdrawing groups, and their effects when placed at the Si atom(s) or at the C atoms were examined. Focus was placed on geometries, frontier orbital energies and the energies of the first allowed electronic excitations. We analyzed the variation in energies between the orbitals which correspond to HOMO and LUMO for the two parent species, here represented as ΔεHL, motivated by the fact that the first allowed transitions involve excitation between these orbitals. Even though ΔεHL and the excitation energies are lower for siloles than for 1,4-disilacyclohexa-2,5-dienes the latter display significantly larger variations with substitution. The ΔεHL of the siloles vary within 4.57–5.35 eV (ΔΔεHL = 0.78 eV) while for the 1,4-disilacyclohexa-2,5-dienes the range is 5.49–7.15 eV (ΔΔεHL = 1.66 eV). The excitation energy of the first allowed transitions display a moderate variation for siloles (3.60–4.41 eV) whereas the variation for 1,4-disilacyclohexa-2,5-dienes is nearly doubled (4.69–6.21 eV). Cyclobutadisiloles combine the characteristics of siloles and 1,4-disilacyclohexa-2,5-diene by having even lower excitation energies than siloles yet also extensive variation in excitation energies to substitution of 1,4-disilacyclohexa-2,5-dienes (3.47–4.77 eV, variation of 1.30 eV).
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| 6. |
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| 7. |
- Emanuelsson, Rikard, et al.
(författare)
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An All-Organic Proton Battery
- 2017
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 139:13, s. 4828-4834
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Tidskriftsartikel (refereegranskat)abstract
- Rechargeable batteries that use organic matter as. the capacity-carrying material have previously been considered a technology for the future. Earlier batteries in which both the anode and cathode consisted of organic material required significant amounts of conductive additives and were often based on metal-ion electrolytes containing Li+ or Na+. However, we have used conducting poly(3,4-ethylenedioxythiophene) (PEDOT), functionalized with anthraquinone (PEDQT-AQ) or, benzonquinone (PEDOT-BQ) pendant groups as the negative and positive electrode materials, respectively, to make an all-organic proton battery devoid of metals. The electrolyte consists of a proton donor and acceptor slurry containing substituted pyridinium triflates and the corresponding pyridine base. This slurry allows the 2e(-)/2H(+) quinone/hydroquinone redox reactions while suppressing proton reduction in the battery cell. By using strong (acidic) proton donors, the formal potential of the quinone redox reactions is tuned into the potential region in which the PEDOT backbone is conductive, thus eliminating the need for conducting additives. In this all-organic proton battery cell, PEDOT-AQ and PEDOT-BQ deliver 103 and 120 mAh g(-1), which correspond to 78% and 75%, respectively, of the theoretical specific capacity of the materials at an average cell potential of 0.5 V. We show that PEDOT-BQ determines the cycling stability of the device while PEDOT-AQ provides excellent reversibility for at least 1000 cycles. This proof-of-concept shows the feasibility of assembling all organic proton batteries which require no conductive additives and also reveals where the challenges and opportunities lie on the path to producing plastic batteries.
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| 8. |
- Emanuelsson, Rikard, et al.
(författare)
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Configuration- and Conformation-Dependent Electronic-Structure Variations in 1,4-Disubstituted Cyclohexanes Enabled by a Carbon-to-Silicon Exchange
- 2014
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 20:30, s. 9304-9311
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Tidskriftsartikel (refereegranskat)abstract
- Cyclohexane, with its well-defined conformers, could be an ideal force-controlled molecular switch if it were to display substantial differences in electronic and optical properties between its conformers. We utilize sigma conjugation in heavier analogues of cyclohexanes (i.e. cyclohexasilanes) and show that 1,4-disubstituted cyclohexasilanes display configuration-and conformation-dependent variations in these properties. Cis- and trans-1,4-bis(trimethylsilylethynyl)-cyclohexasilanes display a 0.11 V difference in their oxidation potentials (computed 0.11 V) and a 0.34 eV difference in their lowest UV absorption (computed difference between first excitations 0.07 eV). This is in stark contrast to differences in the corresponding properties of analogous all-carbon cyclohexanes (computed 0.02 V and 0.03 eV, respectively). Moreover, the two chair conformers of the cyclohexasilane trans isomer display large differences in electronic-structure-related properties. This enables computational design of a mechanically force-controlled conductance switch with a calculated single-molecule ON/OFF ratio of 213 at zero-bias voltage.
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| 9. |
- Emanuelsson, Rikard
(författare)
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Conjugation in Organic Group 14 Element Compounds : Design, Synthesis and Experimental Evaluation
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis focuses on the chemical concept of conjugation, i.e., electron delocalization, and the effect it has on electronic and optical properties of molecules. The emphasis is on electron delocalization across a saturated σ-bonded segment, and in our studies these segments are either inserted between π-conjugated moieties or joined together to form longer chains. The electronic and optical properties of these compounds are probed and compared to those of traditionally π-conjugated compounds. The investigations utilize a combination of qualitative chemical bonding theories, quantum chemical calculations, chemical syntheses and different spectroscopic methods.Herein, it is revealed that a saturated σ-bonded segment inserted between two π-systems can have optical and electronic properties similar to a cross-conjugated compound when substituents with heavy Group 14 elements (Si, Ge or Sn) are attached to the central atom. We coined the terminology cross-hyperconjugation for this interaction, and have shown it by both computational and spectroscopic means. This similarity is also found in cyclic compounds, for example in the 1,4-disilacyclohexa-2,5-dienes, as we reveal that there is a cyclic aspect of cross-hyperconjugation. Cross-hyperconjugation can further also be found in smaller rings such as siloles and cyclopentadienes, and we show on the similarities between these and their cross-π-conjugated analogues, the fulvenes. Here, this concept is combined with that of excited state aromaticity and the electronic properties of these systems are rationalized in terms of “aromatic chameleon” effects. We show that the optical properties of these systems can be rationally tuned and predicted through the choice of substituents and knowledge about the aromaticity rules in both ground and excited states.We computationally examine the relation between conjugation and conductance and reveal that oligomers of 1,4-disilacyclohexa-2,5-dienes and related analogues can display molecular cord properties. The conductance through several σ-conjugated silicon compounds were also examined and show that mixed silicon and carbon bicyclo[2.2.2]octane compounds do not provide significant benefits over the open-chain oligosilanes. However, cyclohexasilanes, a synthetic precursor to the bicyclic compounds, displayed conformer-dependent electronic structure variations that were not seen for cyclohexanes. This allowed for computational design of a mechanically activated conductance switch.
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| 10. |
- Emanuelsson, Rikard, et al.
(författare)
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Cross-hyperconjugation : An unexplored orbital interaction between pi-conjugated and saturated molecular segments
- 2013
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 52:3, s. 983-987
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Tidskriftsartikel (refereegranskat)abstract
- Crossing a barrier: Molecules with saturated ER2 units (E=C or Si, R=electron-releasing group) inserted between two π-conjugated segments have electronic and optical properties that resemble those of cross-conjugated molecules (see figure). This cross-hyperconjugation provides a deeper understanding of the conjugation phenomenon, and is an alternative to cross-conjugation in the design of molecules for nano and materials applications.
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| 11. |
- Emanuelsson, Rikard, et al.
(författare)
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Enthalpic versus Entropic Contribution to the Quinone Formal Potential in a Polypyrrole-Based Conducting Redox Polymer
- 2016
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 120:38, s. 21178-21183
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Tidskriftsartikel (refereegranskat)abstract
- A conducting redox polymer (CPR) based on pyrrole with a hydroquinone pendant group was synthesized through electropolymerization of the corresponding monomer. The formal potential (E-0') in aqueous solution at different pH as well as in MeCN containing equal amounts of pyridiniumtriflates and the corresponding free pyridine with different pK(a) was investigated. E-0' could be completely recovered in MeCN, and by utilizing pyridine bases with different donor acceptor strengths, a decrease of 61 meV/pK(a) was found that corresponded exactly to the pH dependence of E-0' in aqueous electrolyte. To separate the entropic and enthalpic contributions to E-0', temperature-dependent electrochemistry was performed. Two different modes of operation with changing pH/pK(a) between the two media were revealed. In MeCN, E-0' varies only because of the enthalpic contribution as the entropic contribution is unaffected by change in pKa. In water, there is primarily an entropic contribution to E-0' with changing pH due to solvation of the proton. The presented results are expected to open up for new design possibilities of CRPs based on ion coordinating redox groups for electrical energy storage.
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| 12. |
- Emanuelsson, Rikard, et al.
(författare)
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In Search of Flexible Molecular Wires with Near Conformer-Independent Conjugation and Conductance : A Computational Study
- 2014
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 118:11, s. 5637-5649
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Tidskriftsartikel (refereegranskat)abstract
- Oligomers of 1,4-disila/germa/stannacyclohexa-2,5-dienes as well as all-carbon 1,4-cyclohexadienes connected via E-E single bonds (E = C, Si, Ge, or Sn) were studied through quantum chemical calculations in an effort to identify conformationally flexible molecular wires that act as molecular "electrical cords" hang conformer-independent conjugative and conductive properties. Our oligomers display neutral hyperconjugative interactions (sigma/pi-conjugation) between adjacent sigma(E-E) and pi(C=C) bond orbitals, and these interactions do not change with conformation. The energies and spatial distributions of the highest occupied molecular orbitals of methyl-, silyl-, and trimethylsilyl (TMS)-substituted 1,4-disilacyclohexa-2,5-diene dimers, and stable conformers of trimers and tetramers, remain rather constant upon Si-Si bond rotation. Yet, steric congestion may be a concern in some of the oligomer types. The calculated conductances for the Si-containing tetramers are similar to that of a sigma-conjugated linear all-anti oligosilane (a hexadecasilane) with equally many bonds in the conjugated paths. Moreover, the Me-substituted 1,4-disilacyclohexadiene tetramer has modest conductance fluctuations with Si-Si bond rotations when the electrode-electrode distance is locked (variation by factor similar to 30), while the fluctuations under similar conditions are larger for the analogous TMS-substituted tetramer. When the electrode-electrode distance is changed several oligomers display small conductance variations within certain distance intervals, e.g., the mean conductance of TMS-substituted 1,4-disilacyclohexa-2,5-diene tetramer is almost unchanged over 9 A of electrode-electrode distances.
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| 13. |
- Emanuelsson, Rikard, et al.
(författare)
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Optimization of the Cyclic Cross-Hyperconjugation in 1,4-Ditetrelcyclohexa-2,5-dienes
- 2014
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Ingår i: Organometallics. - : American Chemical Society (ACS). - 0276-7333 .- 1520-6041. ; 33:12, s. 2997-3004
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Tidskriftsartikel (refereegranskat)abstract
- Cyclic cross-hyperconjugation can exist to variable extents in 1,4-ditetrelcyclohexa-2,5-dienes, i.e., all-carbon cyclohexa-1,4-dienes and 1,4-disila/digerma/distanna/diplumbacyclohexa-2,5-dienes. In this study we first use density functional theory (DFT) computations to optimize the conjugation strength by seeking the optimal atom E and substituent group E'Me-3 in the two saturated E(E'Me-3)(2) moieties (E and E' as the same or different tetrel (group 14) elements). We reveal that the all-carbon cyclohexadienes with gradually heavier E'Me-3 substituents at the two saturated carbon atoms display significant cross-hyperconjugation. The first electronic excitations in these compounds, which formally have two isolated C=C bonds, are calculated to reach wavelengths as long as 400 nm (excitation energies of 3.1 eV). These transitions are mostly forbidden, and the lowest allowed transitions are found at 387 nm (3.2 eV). The silicon analogues are also cross-hyperconjugated, while a decline is observed in the 1,4-digerma/distanna/diplumbacyclohexa-2,5-diene. Experiments on two substituted 1,4-disilacyclohexa-2,5-dienes confirm the effect of the E'Me3 substituents, with regard to both electronic excitations and geometries as determined by UV absorption spectroscopy and X-ray crystallography, respectively. At the end, we reveal through computations how electron-donating and electron-withdrawing substituents at the C=C double bonds influence the electronic properties of the all-carbon ring. We find that the first calculated excitation, which is forbidden, can be shifted to 440 nm (2.83 eV). This shows to what extent cyclic cross-hyperconjugation can affect the electronic and optical properties of a compound with two formally isolated C=C double bonds.
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| 14. |
- Emanuelsson, Rikard, et al.
(författare)
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Quinone based conducting redox polymers for electrical energy storage
- 2017
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Ingår i: Russian journal of electrochemistry. - : MAIK NAUKA/INTERPERIODICA/SPRINGER. - 1023-1935 .- 1608-3342. ; 53:1, s. 8-15
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Tidskriftsartikel (refereegranskat)abstract
- Conducting redox polymers (CRPs) constitute a promising class of materials for the development of organic matter based batteries with the potential to overcome the main limitations connected to this type of rechargeable battery systems including low conductivity and dissolution problems. In this report we show that the potential of quinones can be effectively tuned into the conducting region of polypyrrole (PPy), both in water based solutions and in acetonitrile, which is a prerequisite for profitable combination of the two units. We also present a device where both anode and cathode are made from PPy substituted with different quinone pendant groups and where good rate performance is achieved without any conductivity additives thus providing support for the hypothesized synergetic effect of a conducting polymer backbone and a covalently attached redox active pendant group. This device constitutes, to the best of our knowledge, the first all-CRP based battery reported to date.
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| 15. |
- Emanuelsson, Rikard, et al.
(författare)
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Quinone based conducting redox polymers for electrical energy storage
- 2017
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Ingår i: Elektrokhimiya. - : MAIK NAUKA/INTERPERIODICA. - 0424-8570. ; 53:1, s. 11-20
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Tidskriftsartikel (refereegranskat)abstract
- Conducting redox polymers (CRPs) constitute a promising class of materials for the development of organic matter based batteries with the potential to overcome the main limitations connected to this type of rechargeable battery systems including low conductivity and dissolution problems. In this report we show that the potential of quinones can be effectively tuned into the conducting region of polypyrrole (PPy), both in water based solutions and in acetonitrile, which is a prerequisite for profitable combination of the two units. We also present a device where both anode and cathode are made from PPy substituted with different quinone pendant groups and where good rate performance is achieved without any conductivity additives thus providing support for the hypothesized synergetic effect of a conducting polymer backbone and a covalently attached redox active pendant group. This device constitutes, to the best of our knowledge, the first all-CRP based battery reported to date.
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| 16. |
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| 17. |
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| 18. |
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| 19. |
- Granlund, Irene, et al.
(författare)
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Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS
- 2011
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 74:8, s. 1190-1200
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Tidskriftsartikel (refereegranskat)abstract
- It is an established fact that allelic variation and post-translational modifications create different variants of proteins, which are observed as isoelectric and size subspecies in two-dimensional gel based proteomics. Here we explore the stromal proteome of spinach and Arabidopsis chloroplast and show that clustering of mass spectra is a useful tool for investigating such variants and detecting modified peptides with amino acid substitutions or post-translational modifications. This study employs data mining by hierarchical clustering of MALDI-MS spectra, using the web version of the SPECLUST program (http://bioinfo.theplu.se/speclust.html). The tool can also be used to remove peaks of contaminating proteins and to improve protein identification, especially for species without a fully sequenced genome. Mutually exclusive peptide peaks within a cluster provide a good starting point for MS/MS investigation of modified peptides, here exemplified by the identification of an A to E substitution that accounts for the isoelectric heterogeneity in protein isoforms. (C) 2011 Elsevier B.V. All rights reserved.
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| 20. |
- Günther, Tyran, et al.
(författare)
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Redox-site accessibility of composites containing a 2D redox-active covalent organic framework : from optimization to application
- 2023
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Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry. - 2050-7488 .- 2050-7496. ; 11:26, s. 13923-13931
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Tidskriftsartikel (refereegranskat)abstract
- Redox-active covalent organic frameworks (RACOFs) can be employed in various functional materials and enesrgy applications. A crucial performance or efficiency indicator is the percentage of redox centres that can be utilised. Herein, the term redox-site accessibility (RSA) is defined and shown to be an effective metric for developing and optimising a 2D RACOF (viz., TpOMe-DAQ made from 2,4,6-trimethoxy-1,3,5-benzenetricarbaldehyde [TpOMe] and 2,6-diaminoanthraquinone [DAQ]) as an anode material for potential organic-battery applications. Pristine TpOMe-DAQ utilises only 0.76% of its redox sites, necessitating the use of conductivity-enhancement strategies such as blending it with different conductive carbons, or performing in situ polymerisation with EDOT (3,4-ethylenedioxythiophene) to form a conductive polymer. While conductive carbon-RACOF composites showed a modest RSA improvement of 4.0%, conductive polymer-RACOF composites boosted the redox-site usage (RSA) to 90% at low mass loadings. The material and electrochemical characteristics of the conductive polymer-RACOF composite containing more-than-necessary conductive polymer showed a reduced surface area but almost identical electrochemical behaviour, compared to the optimal ratio. The high RSA of the optimally loaded composite was replicated in a RACOF-air battery with over 90% active redox sites. We believe that the reported approach and methods, which can be employed on a milligram scale, could serve as a general guide for the electrification and characterisation of RACOFs, as well as for other redox-active porous polymers.
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| 21. |
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| 22. |
- Göransson, Erik, et al.
(författare)
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Charge transfer through cross-hyperconjugated versus cross-pi-conjugated bridges : an intervalence charge transfer study
- 2013
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 4:9, s. 3522-3532
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Tidskriftsartikel (refereegranskat)abstract
- Recently there has been much interest in electron transfer and transport through cross-conjugated molecules as interesting test cases for the interplay between molecular and electronic structure as well as potential motifs in the design of new compounds for molecular electronics. Herein we expand on this concept and present the synthesis and characterization of a series of four organic mixed-valence dyads to probe the effect of the bridge structure on the electronic coupling. The electronic coupling between two triarylamine units could be mediated either by cross-hyperconjugation through a saturated ER2 bridge (E = C or Si, R = alkyl or silyl group), or via a cross-conjugated pi-system. The aim of the study is to compare the electron transfer through the various saturated bridges to that of a cross-pi-conjugated bridge. The electronic coupling in these mixed-valence compounds was determined by analysis of intervalence charge transfer bands, and was found to be in the range of 100-400 cm(-1). A complementary DFT and TD-DFT study indicated that the electronic coupling in the dyads with saturated ER2 segments is highly conformer dependant. Furthermore, the calculations showed that two types of interactions contribute to the electronic coupling; a through-bond cross-(hyper)conjugation mechanism and a through-space mechanism. Taken together, these findings suggest the possibility for new architectures for molecular electronics applications utilizing cross-hyperconjugation through properly selected saturated segments which have comparable electron transfer characteristics as regular cross-pi-conjugated molecules.
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| 23. |
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| 24. |
- Hjernö, K, et al.
(författare)
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Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colorless strawberry mutant
- 2006
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 6:5, s. 1574-1587
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Tidskriftsartikel (refereegranskat)abstract
- Proteomic screening of strawberry (Fragaria ananassa) yielded a 58% success rate in protein identification in spite of the fact that no genomic sequence is available for this species. This was achieved by a combination of MALDI-MS/MS de novo sequencing of double-derivatized peptides and indel-tolerant searching against local protein databases built on both EST and full-length nucleotide sequences. The amino acid sequence of a strawberry allergen, homologous to the well-known major birch pollen allergen Bet v 1, was partially determined. This strawberry allergen, named Fra a 1 according to the nomenclature for allergen proteins, showed sequence identity of 54 and 77%, respectively, with corresponding allergens from birch and apple. Differential expression, as evaluated by 2-D DIGE, occurred in 10% of protein spots when red strawberries were compared to a colorless (white) strawberry mutant. White strawberries, known to be tolerated by individuals affected by allergy, were found to be virtually free from the strawberry allergen. Also several enzymes in the pathway for biosynthesis of flavonoids, to which the red color pelargonidin belongs, were down-regulated. This approach to assess differential protein expression without access to genomic sequence information can also be applied to other crop plants and phenotypic traits.
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| 25. |
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| 26. |
- Huang, Xiao, et al.
(författare)
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A versatile route to polythiophenes with functional pendant groups using alkyne chemistry
- 2016
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Ingår i: Beilstein Journal of Organic Chemistry. - : Beilstein Institut. - 2195-951X .- 1860-5397. ; 12, s. 2682-2688
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Tidskriftsartikel (refereegranskat)abstract
- A new versatile polythiophene building block, 3-(3,4-ethylenedioxythiophene)prop-1-yne (pyEDOT) (3), is prepared from glycidol in four steps in 28% overall yield. pyEDOT features an ethynyl group on its ethylenedioxy bridge, allowing further functionalization by alkyne chemistry. Its usefulness is demonstrated by a series of functionalized polythiophene derivatives that were obtained by pre- and post-electropolymerization transformations, provided by the synthetic ease of the Sonogashira coupling and click chemistry.
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| 27. |
- Ivanko, Iryna, et al.
(författare)
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Conjugated redox polymer with poly(3,4-ethylenedioxythiophene) backbone and hydroquinone pendant groups as the solid contact in potassium-selective electrodes
- 2021
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Ingår i: Sensors and actuators. B, Chemical. - : Elsevier. - 0925-4005 .- 1873-3077. ; 329
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Tidskriftsartikel (refereegranskat)abstract
- We have used for the first time a conjugated redox polymer with hydroquinone (HQ) pendant groups covalently attached to the poly(3,4-ethylenedioxythiophene) (PEDOT) backbone as the solid contact (SC) in plasticized poly(vinyl chloride) (PVC) based K+-selective electrodes (K-SCISE). Redox couples are one of the simplest ways to precisely adjust the standard potential (E°) of the SCISEs, but usually the initially high E° reproducibility is lost quite quickly due to leaching out of non-covalently bound redox molecules from the SCISE. In PEDOT-HQ, the covalently attached HQ groups prevent the leaching and simultaneously allow additional charge storage in PEDOT-HQ that is ca. 25–30 times higher than for unsubstituted PEDOT. Before the ion-selective membrane (ISM) deposition, we controlled the potential of the SC with high reproducibility (±0.4 mV, n = 5) by pre-polarization in a mixture of acetonitrile containing potassium tetrakis(pentafluorophenyl)borate and perchloric acid as proton source. Pre-polarization of the SC close to the formal potential where the redox buffer capacity is highest gave the best potential reproducibility. However, after the ISM deposition, the K-SCISEs showed in the best case an E° reproducibility of ±2.8 mV (n = 5). Chronopotentiometric measurements reveal that only a minor fraction of the very high redox capacitance of PEDOT-HQ can be utilized for the ion-to-electron transduction beneath the ISM. The influence of this shortcoming on the E° reproducibility of the SCISEs has been underestimated for most SC materials. Modification of the commonly used PVC-ISM formulations to allow faster ion transfer at the SC/ISM interface could be one way of overcoming the disadvantage.
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| 28. |
- Johansson, Peter, et al.
(författare)
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SPECLUST: a web tool for clustering of mass spectra
- 2007
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- SPECLUST is a web tool for hierarchical clustering of peptide mass spectra obtained from protease-digested proteins. Mass spectra are clustered according to the peptide masses they contain, such that mass spectra containing similar masses are clustered together. Hierarchical clustering of mass spectra with SPECLUST can in particular be useful for MS-screening of large proteomic data sets derived from 2D-gels. SPECLUST can also be used to identify masses shared by mass spectra. Masses present in the majority of the mass spectra in a data set are likely to be contaminants. With SPECLUST, MS/MS can be focused on non-contaminant shared masses in a cluster, facilitating investigations of protein isoforms. Within a cluster, shared and unique masses represent peptides from regions that are similar and different, respectively, between protein isoforms. Taken together, SPECLUST is a versatile tool for analysis of mass spectrometry data. Availability: SPECLUST is freely available at http://bioinfo.thep.lu.se/speclust.html.
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| 29. |
- Jorner, Kjell, et al.
(författare)
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Impact of Ground- and Excited-State Aromaticity on Cyclopentadiene and Silole Excitation Energies and Excited-State Polarities
- 2014
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 20:30, s. 9295-9303
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Tidskriftsartikel (refereegranskat)abstract
- A new qualitative model for estimating the properties of substituted cyclopentadienes and siloles in their lowest pi pi* excited states is introduced and confirmed through quantum chemical calculations, and then applied to explain earlier reported experimental excitation energies. According to our model, which is based on excited-state aromaticity and antiaromaticity, siloles and cyclopentadienes are cross-hyperconjugated "aromatic chameleons" that adapt their electronic structures to conform to the various aromaticity rules in different electronic states (Huckel's rule in the pi(2) electronic ground state (S-0) and Baird's rule in the lowest pi pi* excited singlet and triplet states (S-1 and T-1)). By using pen-and-paper arguments, one can explain polarity changes upon excitation of substituted cyclopentadienes and siloles, and one can tune their lowest excitation energies by combined considerations of ground-and excited-state aromaticity/antiaromaticity effects. Finally, the "aromatic chameleon" model can be extended to other monocyclic compound classes of potential use in organic electronics, thereby providing a unified view of the S-0, T-1, and S-1 states of a range of different cyclic cross-pi-conjugated and cross-hyperconjugated compound classes.
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| 30. |
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| 31. |
- Jorner, Kjell, et al.
(författare)
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Unraveling factors leading to efficient norbornadiene-quadricyclane molecular solar-thermal energy storage systems
- 2017
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Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry (RSC). - 2050-7488 .- 2050-7496. ; 5:24, s. 12369-12378
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Tidskriftsartikel (refereegranskat)abstract
- Developing norbornadiene-quadricyclane (NBD-QC) systems for molecular solar-thermal (MOST) energy storage is often a process of trial and error. By studying a series of norbornadienes (NBD-R-2) doubly substituted at the C7-position with R = H, Me, and iPr, we untangle the interrelated factors affecting MOST performance through a combination of experiment and theory. Increasing the steric bulk along the NBD-R-2 series gave higher quantum yields, slightly red-shifted absorptions, and longer thermal lifetimes of the energy-rich QC isomer. However, these advantages are counterbalanced by lower energy storage capacities, and overall R = Me appears most promising for short-term MOST applications. Computationally we find that it is the destabilization of the NBD isomer over the QC isomer with increasing steric bulk that is responsible for most of the observed trends and we can also predict the relative quantum yields by characterizing the S-1/S-0 conical intersections. The significantly increased thermal half-life of NBD-iPr(2) is caused by a higher activation entropy, highlighting a novel strategy to improve thermal half-lives of MOST compounds and other photo-switchable molecules without affecting their electronic properties. The potential of the NBD-R-2 compounds in devices is also explored, demonstrating a solar energy storage efficiency of up to 0.2%. Finally, we show how the insights gained in this study can be used to identify strategies to improve already existing NBD-QC systems.
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| 32. |
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| 33. |
- Karlsson, Anne-Li, et al.
(författare)
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Bet v 1 homologues in strawberry identified as IgE-binding proteins and presumptive allergens
- 2004
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Ingår i: Allergy. - : Wiley. - 1398-9995 .- 0105-4538. ; 59:12, s. 1277-1284
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Tidskriftsartikel (refereegranskat)abstract
- Background: No strawberry allergen has so far been identified and characterized. Methods: Serum samples were collected from patients with a suggestive case history of adverse reactions to strawberry and other fruits. Extracts from fresh and frozen strawberries were analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting and mass spectrometry. Patient blood samples were analysed for inhibition of IgE binding and basophil degranulation. Results: Several IgE-binding proteins could be detected. In more than half of the patient sera, a 20/18-kDa doublet band was observed in Western blotting. These two bands were excised and analysed by mass spectrometry showing the presence of proteins belonging to the Bet v 1 family of allergens. Inhibition of the IgE binding to the 20/18-kDa doublet was obtained by addition of two recombinantly expressed allergens belonging to the Bet v 1 family (Bet v 1 and Mal d 1) and strawberry protein extract. In a cell-based assay of patient blood samples, basophil degranulation could be induced by strawberry protein extract and by Bet v 1 and Mal d 1. Conclusions: We conclude that strawberry homologues to Bet v 1 may be allergens of importance for adverse reactions to strawberry.
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| 34. |
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| 35. |
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| 36. |
- Löfås, Henrik, 1983-, et al.
(författare)
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A computational study of potential molecular switches that exploit Baird's rule on excited-state aromaticity and antiaromaticity
- 2014
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Ingår i: Faraday discussions. - 1359-6640 .- 1364-5498. ; 174, s. 105-124
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Tidskriftsartikel (refereegranskat)abstract
- A series of tentative single-molecule conductance switches which could be triggered by light were examined by computational means using density functional theory (DFT) with non-equilibrium Green's functions (NEGF). The switches exploit the reversal in electron counting rules for aromaticity and antiaromaticity upon excitation from the electronic ground state (S0) to the lowest [small pi][small pi]* excited singlet and triplet states (S1 or T1), as described by Huckel's and Baird's rules, respectively. Four different switches and one antifuse were designed which rely on various photoreactions that either lead from the OFF to the ON states (switches 1, 2 and 4, and antifuse 5) or from the ON to the OFF state (switch 3). The highest and lowest ideal calculated switching ratios are 1175 and 5, respectively, observed for switches 1 and 4. Increased thermal stability of the 1-ON isomer is achieved by benzannulation (switch 1B-OFF/ON). The effects of constrained electrode-electrode distances on activation energies for thermal hydrogen back-transfer from 1-ON to 1-OFF and the relative energies of 1-ON and 1-OFF at constrained geometries were also studied. The switching ratio is strongly distance-dependent as revealed for 1B-ON/OFF where it equals 711 and 148 when the ON and OFF isomers are calculated in electrode gaps with distances confined to either that of the OFF isomer or to that of the ON isomer, respectively.
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| 37. |
- Löfås, Henrik, et al.
(författare)
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Conductance through Carbosilane Cage Compounds : A Computational Investigation
- 2013
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 117:42, s. 21692-21699
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Tidskriftsartikel (refereegranskat)abstract
- Silicon is still the dominating material in microelectronics, yet primarily conjugated hydrocarbons are investigated in the field of single-molecule electronics even though linear oligosilanes are a-conjugated. A drawback with the latter is their high conformational flexibility which strongly affects conductance. Here we report on a first principles density functional theory investigation of a series of rigid [2.2.2]bicyclic carbosilanes with 3, 2, 1, or 0 disilanylene bridges, providing all-silicon paths for charge transport. It is explored if these paths can be seen as independent and equivalent current paths acting as parallel resistors. For high conductance through the carbosilanes they need to be anchored to the gold electrodes via groups that are matched with the a-conjugated paths of the oligosilane cage segment, and we find that silyl (SiH3) groups are better matched than thiophenol groups. Even for the carbosilane with three disilanylene bridges we find that the most transmitting conductance channel is not equally distributed on the three parallel bridges. In addition, there is significant communication between the various pathways, which results in destructive interference lowering the conductance. Taken together, the different disilanylene bridges in the cage compounds do not act as parallel resistors.
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| 38. |
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| 39. |
- Musidlowska Persson, Anna, et al.
(författare)
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Cloning and sequencing of the Bet v 1-homologous allergen Fra a 1 in strawberry (Fragaria ananassa) shows the presence of an intron and little variability in amino acid sequence
- 2007
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Ingår i: Molecular Immunology. - : Elsevier BV. - 1872-9142 .- 0161-5890. ; 44:6, s. 1245-1252
-
Tidskriftsartikel (refereegranskat)abstract
- The Fra a I allergen in strawberry (Fragaria ananassa) is homologous to the major birch pollen allergen Bet v 1, which has numerous isoforms differing in terms of amino acid sequence and immunological impact. To map the extent of sequence differences in the Fra a I allergen, PCR cloning and sequencing was applied. Several genomic sequences of Fra a 1, with a length of either 584, 591 or 594 nucleotides, were obtained from three different strawberry varieties. All contained one intron, with the length of either 10 1 or 110 nucleotides. By sequencing 30 different clones, eight different DNA sequences were obtained, giving in total five potential Fra a I protein isoforms, with high sequence similarity (> 97% sequence identity) and only seven positions of amino acid variability, which were largely confirmed by mass spectrometry of expressed proteins. We conclude that the sequence variability in the strawberry allergen Fra a I is small, within and between strawberry varieties, and that multiple spots, previously detected in 2DE, are presumably due to differences in post-translational modification rather than differences in amino acid sequence. The most abundant Fra a I isoform sequence, recombinantly expressed in Escherichia coli after removal of the intron, was recognized by IgE from strawberry allergic patients. It cross-reacted with antibodies to Bet v I and the homologous apple allergen Mal d 1 (61 and 78% sequence identity, respectively), and will be used in further analyses of variation in Fra a 1-expression. (c) 2006 Elsevier Ltd. All rights reserved.
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| 40. |
- Oka, Kouki, et al.
(författare)
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Characterization of PEDOT-Quinone conducting redox polymers in water-in-salt electrolytes for safe and high-energy Li-ion batteries
- 2019
-
Ingår i: Electrochemistry communications. - : Elsevier. - 1388-2481 .- 1873-1902. ; 105
-
Tidskriftsartikel (refereegranskat)abstract
- Li-ion batteries (LIBs) raise safety and environmental concerns, which mostly arise from their toxic and flammable electrolytes and the extraction of limited material resources by mining. Recently, water-in-salt electrolytes (WiSEs), in which a large amount of lithium salt is dissolved in water, have been proposed to allow for assembling safe and high-voltage (>3.0 V) aqueous LIBs. In addition, organic materials derived from abundant building blocks and their tunable properties could provide safe and sustainable replacements for inorganic cathode materials. In the current work, the electrochemical properties of a conducting redox polymer based on poly(3,4-ethylenedioxythiophene) (PEDOT) with hydroquinone (HQ) pendant groups have been characterized in WiSEs. The quinone redox reaction occurs within the potential region where the polymer is conducting, and fast redox conversion that involves lithium cycling during pendant group redox conversion was observed. These properties make conducting redox polymers promising candidates as cathode-active materials for safe and high-energy aqueous LIBs. An organic-based aqueous LIB, with a HQ-PEDOT as a cathode, Li4Ti5O12 (LTO) as an anode, and ca. 15 m lithium bis(trifluoromethanesulfonyl)imide water/dimethyl carbonate (DMC) as electrolyte, yielded an output voltage of 1.35 V and high rate capabilities up to 500C.
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| 41. |
- Oka, Kouki, et al.
(författare)
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Conducting Redox Polymer as Organic Anode Material for Polymer-Manganese Secondary Batteries
- 2020
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Ingår i: ChemElectroChem. - : Wiley. - 2196-0216. ; 7:15, s. 3336-3340
-
Tidskriftsartikel (refereegranskat)abstract
- Manganese-based aqueous batteries have attracted significant attention due to their earth-abundant components and low environmental burden. However, state-of-the-art manganese-zinc batteries are poorly rechargeable, owing to dendrite formation on the zinc anode. Organic materials could provide a safe and sustainable replacement. In the present work, a conducting redox polymer (CRP) based on a trimer of EPE (E=3,4-ethylenedioxythiophene; P=3,4-propylenedioxythiophene) and a naphthoquinone (NQ) pendant group is used as anode in polymer-manganese secondary batteries. The polymer shows stable redox conversion around+0.05 V vs. Ag/AgCl, and fast kinetics that involves proton cycling during pendant group redox conversion. For the first time, a CRP-manganese secondary battery was fabricated with pEP(NQ)E as the anode, manganese oxide as the cathode, and manganese-containing acidic aqueous solution as the electrolyte. This battery yielded a discharge voltage of 1.0 V and a discharging capacity of 76 mAh/ganode over >50 cycles and high rate capabilities (up to 10C).
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| 42. |
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| 43. |
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| 44. |
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| 45. |
- Sjödin, Martin, 1974-, et al.
(författare)
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Conducting redox oligomers
- 2022
-
Patent (populärvet., debatt m.m.)abstract
- The present disclosure relates to compounds of formula IVa or IVb, or salts thereof, as intermediates in the manufacture of conducting redox polymers. L is a covalent linker moiety and R is a reversible redox group.The disclosure further relates to conducting redox polymers produced from such compounds, as well as substrates coated with such conducting redox polymers, and organic batteries comprising such conducting redox polymers.
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| 46. |
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| 47. |
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| 48. |
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| 49. |
- Sjödin, Martin, 1974-, et al.
(författare)
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Conducting Redox Polymers as Electrical Energy Storage Materials
- 2019
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Konferensbidrag (refereegranskat)abstract
- Conducting redox polymers (CRPs) is an attractive alternative as organic matter based electrical energy storage materials as they provide means of combining the favorable charge transport properties of conducting polymers with the high capacity and well defined redox chemistry of small redox active groups. In general CRPs are composed of a conducting polymer backbone where each or some of the monomers building up the polymer is bearing a redox active functional group. Although the working principle of CRPs is straightforward several key criteria need to be met in the CRP design in order to benefit from synergetic effects of the conducting polymer backbone and the pendent group in CRPs that will be outlined in this presentation: 1) As conducting polymers are only conducting in their charged state successful polymer-pendent group combinations rely on that the pendant group has a redox potential within the conducting region of the polymer backbone. This condition is referred to as redox matching and the requirement in the CRP design will be explicitly proven.[1] 2) The purpose of the polymer backbone is to provide efficient electron transport through the material. We have previously shown the polymer conductivity can be severely compromised by the pendant group.[2] This could be overcome by judicious choice of polymer backbone and results will be presented that show that non-activated (semi-metallic) electron transport can be achieved in CRPs.[3-4] 3) A final design principle that will be discussed is related to the polymerizability and how it is affected by the nature of the link between the polymer backbone and the pendent.[5] In addition a novel polymerization method for CRP monomers will be presented that allow bulk processing even for insoluble CRPmaterials.
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| 50. |
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