Conjugation in Organic Group 14 Element Compounds : Design, Synthesis and Experimental Evaluation

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

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

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

Conducting Redox Polymers for Renewable Energy Storage

Susbat

A Computational Investigation of the Substituent Effects on Geometric, Electronic, and Optical Properties of Siloles and 1,4-Disilacyclohexa-2,5-dienes

Thirty two differently substituted siloles 1aâ\u80\u931p and 1,4-disilacyclohexa-2,5-dienes 2aâ\u80\u932p were investigated by quantum chemical calculations using the PBE0 hybrid density functional theory (DFT) method. The substituents included Ï\u83-electron donating and withdrawing, as well as Ï\u80-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 Î\u94εHL, motivated by the fact that the first allowed transitions involve excitation between these orbitals. Even though Î\u94εHL 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 Î\u94εHL of the siloles vary within 4.57â\u80\u935.35 eV (Î\u94Î\u94εHL = 0.78 eV) while for the 1,4-disilacyclohexa-2,5-dienes the range is 5.49â\u80\u937.15 eV (Î\u94Î\u94εHL = 1.66 eV). The excitation energy of the first allowed transitions display a moderate variation for siloles (3.60â\u80\u934.41 eV) whereas the variation for 1,4-disilacyclohexa-2,5-dienes is nearly doubled (4.69â\u80\u936.21 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 (3.47â\u80\u934.77 eV, variation of 1.30 eV).Title of manuscript in list of papers in Julius Tibbelin´s thesis: A comparative computational investigation of the substituent effects on geometric, electronic, and optical properties of 1,4-disilacyclo-hexa-2,5- dienes and siloles</p

Tetraphenylporphyrin electrocatalysts for the hydrogen evolution reaction: applicability of molecular volcano plots to experimental operating conditions

Recent years have seen an increasing interest in molecular electrocatalysts for the hydrogen evolution reaction (HER). Efficient hydrogen evolution would play an important role in a sustainable fuel economy, and molecular systems could serve as highly specific and tunable alternatives to traditional noble metal surface catalysts. However, molecular catalysts are currently mostly used in homogeneous setups, where quantitative evaluation of catalytic activity is non-standardized and cumbersome, in particular for multistep, multielectron processes. The molecular design community would therefore be well served by a straightforward model for prediction and comparison of the efficiency of molecular catalysts. Recent developments in this area include attempts at applying the Sabatier principle and the volcano plot concept – popular tools for comparing metal surface catalysts – to molecular catalysis. In this work, we evaluate the predictive power of these tools in the context of experimental operating conditions, by applying them to a series of tetraphenylporphyrins employed as molecular electrocatalysts of the HER. We show that the binding energy of H and the redox chemistry of the porphyrins depend solely on the electron withdrawing ability of the central metal ion, and that the thermodynamics of the catalytic cycle follow a simple linear free energy relation. We also find that the catalytic efficiency of the porphyrins is almost exclusively determined by reaction kinetics and therefore cannot be explained by thermodynamics alone. We conclude that the Sabatier principle, linear free energy relations and molecular volcano plots are insufficient tools for predicting and comparing activity of molecular catalysts, and that experimentally useful information of catalytic performance can still only be obtained through detailed knowledge of the catalytic pathway for each individual system

SPECLUST: a web tool for clustering of mass spectra

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

Quinone based Conducting Redox Polymers for Renewable Energy Storage

To meet future energy needs and to minimize CO2-emissions, a higher share of produced electricity must come from renewable resources [1]. Unfortunately, the output of renewable energy sources varies and does not always correlate with the temporal demand for electricity. For this reason, high capacity electrical energy storage (EES) is needed to fully utilize renewable energy sources [2]. Today’s battery technologies primarily rely on metals extracted at large economic and environmental costs [3],and the benefits of converting to carbon based materials are several, e.g. lower weight, flexible materials, and better recycling possibilities. In addition, the total energy consumption in the production chain may be reduced if the high temperatures required for extracting and processing metals can be avoided. Conducting redox polymers (CRPs), i.e. conducting polymers with redox active side groups, are currently investigated as possible organic electrode materials [4]. In this work we focus on finding stable side groups with high charge storage capacity. Quinones, which occur in natural energy conversion systems, i.e. during photosynthesis and respiration, are an attractive side group for CRPs due to their high gravimetric capacity. Importantly, for a functioning battery application the redox group and the polymer backbone must be active in the same potential window and this can be tuned effectively over a wide potential range by substitution on the quinone ring; hence various quinone derivatives could match different polymer backbones. A high potential- and high charge capacity quinone derivative has been synthesized and electrochemically characterized with the aim of producing a novel CRP to function as an organic high charge capacity material, targeting renewable organic batteries for a future of sustainable EES.   References [1]  D. Larcher, J. M. Tarascon,, Nat. Chem. 7 (2015) 19-29. [2] Z. Yang, J. Zhang, M. C. W. Kintner-Meyer, X. Lu, D. Choi, J. P. Lemmon, J. Liu, Chem. Rev. 111 (2011) 3577–3613. [3] P. Poizot, F. Dolhem, Energy Environ. Sci. 4 (2011) 2003-2019. [4] (a) C. Karlsson, H. Huang, M. Stromme, A. Gogoll, M. Sjodin, RSC Adv. 5 (2015) 11309-11316; (b) C. Karlsson, H. Huang, M. Stromme, A. Gogoll, M. Sjodin, Electrochim. Acta 179 (2015) 336-342. [5] L. Åkerlund, R. Emanuelsson, A. Gogoll, M. Strömme, M. Sjödin, To be submitted.Susbat

Proteomic variation is as large within as between strawberry varieties

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

Characterization of a porphyrin-functionalized conducting polymer : A first step towards sustainable electrocatalysis

The climate crisis has created a demand for molecular catalysts that can drive redox reactions for production of sustainable fuels. To this end, we present the design, synthesis and characterization of a conducting polymer backbone functionalized with free base porphyrin pendant groups. Combining intrinsic charge transport with catalytic prospect, this system offers possibilities of molecular heterogeneous electrocatalysis with straightforward energy supply and product extraction. Using cyclic voltammetry and spectroelectrochemistry, we show that the polymerized system is stable, and that the properties of the polymer and the porphyrins are independently preserved. With in-situ conductance measurements, we demonstrate that polaronic charge transport through the polymer backbone is superimposed by redox conductivity through the porphyrin pendant groups. These results suggest that our system is a reliable fundamental structure suitable for tuning towards heterogeneous catalysis of redox reactions