| 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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