Synthesis of a library of oligothiophenes and their utilization as fluorescent ligands for spectral assignment of protein aggregates

Molecular probes for selective identification of protein aggregates are important to advance our understanding of the molecular pathogenesis underlying protein aggregation diseases. Here we report the chemical design of a library of anionic luminescent conjugated oligothiophenes (LCOs), which can be utilized as ligands for detection of protein aggregates. Certain molecular requirements were shown to be necessary for detecting (i) early non-thioflavinophilic protein assemblies of Aβ1-42 and insulin preceding the formation of amyloid fibrils and (ii) for obtaining distinct spectral signatures of the two main pathological hallmarks observed in human Alzheimer's diease brain tissue (Aβ plaques and neurofibrillary tangles). Our findings suggest that a superior anionic LCO-based ligand should have a backbone consisting of five to seven thiophene units and carboxyl groups extending the conjugated thiophene backbone. Such LCOs will be highly useful for studying the underlying molecular events of protein aggregation diseases and could also be utilized for the development of novel diagnostic tools for these diseases.     

Proton-coupled electron transfer from tryptophan: a concerted mechanism with water as proton acceptor

The mechanism of proton-coupled electron transfer (PCET) from tyrosine in enzymes and synthetic model complexes is under intense discussion, in particular the pH dependence of the PCET rate with water as proton acceptor. Here we report on the intramolecular oxidation kinetics of tryptophan derivatives linked to [Ru(bpy)(3)](2+) units with water as proton acceptor, using laser flash-quench methods. It is shown that tryptophan oxidation can proceed not only via a stepwise electron-proton transfer (ETPT) mechanism that naturally shows a pH-independent rate, but also via another mechanism with a pH-dependent rate and higher kinetic isotope effect that is assigned to concerted electron-proton transfer (CEP). This is in contrast to current theoretical models, which predict that CEP from tryptophan with water as proton acceptor can never compete with ETPT because of the energetically unfavorable PT part (pK(a)(Trp(?)H(+)) = 4.7 ? pK(a)(H(3)O(+)) ≈ -1.5). The moderate pH dependence we observe for CEP cannot be explained by first-order reactions with OH(-) or the buffers and is similar to what has been demonstrated for intramolecular PCET in [Ru(bpy)(3)](3+)-tyrosine complexes (Sjo?din, M.; et al. J. Am. Chem. Soc.2000, 122, 3932. Irebo, T.; et al. J. Am. Chem. Soc.2007, 129, 15462). Our results suggest that CEP with water as the proton acceptor proves a general feature of amino acid oxidation, and provide further experimental support for understanding of the PCET process in detail.     

On the origins of core-electron chemical shifts of small biomolecules in aqueous solution: insights from photoemission and ab initio calculations of glycine(aq)

The local electronic structure of glycine in neutral, basic, and acidic aqueous solution is studied experimentally by X-ray photoelectron spectroscopy and theoretically by molecular dynamics simulations accompanied by first-principle electronic structure and spectrum calculations. Measured and computed nitrogen and carbon 1s binding energies are assigned to different local atomic environments, which are shown to be sensitive to the protonation/deprotonation of the amino and carboxyl functional groups at different pH values. We report the first accurate computation of core-level chemical shifts of an aqueous solute in various protonation states and explicitly show how the distributions of photoelectron binding energies (core-level peak widths) are related to the details of the hydrogen bond configurations, i.e. the geometries of the water solvation shell and the associated electronic screening. The comparison between the experiments and calculations further enables the separation of protonation-induced (covalent) and solvent-induced (electrostatic) screening contributions to the chemical shifts in the aqueous phase. The present core-level line shape analysis facilitates an accurate interpretation of photoelectron spectra from larger biomolecular solutes than glycine.     

Double photoionisation spectra of small molecules and a new empirical rule for double ionisation energies

Complete double photoelectron spectra are presented for 18 small molecules where the location of charges in the cations and dications is relatively clearly defined. The data demonstrate the importance of a coulombic repulsion contribution to the double ionisation energies. Examination of data for a wide range of molecules leads to a new empirical rule to calculate double ionisation energies from the molecules’ single ionisation energies and maximum dimensions. Where single and double ionisation energies are known the rule allows the deduction of plausible intercharge distances.     

Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Investigation of the Catalytic Activity of a 2‐Phenylidenepyridine Palladium(II) Complex Bearing 4,5‐Dicyano‐1,3‐bis(mesityl)imidazol‐2‐ylidene in the Mizoroki‐Heck Reaction

The phenylidenepyridine (ppy) palladacycles [PdCl(ppy)(IMes)] ( 4 ) [IMes = 1,3‐bis(mesityl)imidazol‐2‐ylidene] and [PdCl(ppy){(CN)₂IMes}] ( 6 ) [(CN)₂IMes = 4,5‐dicyano‐1,3‐bis(mesityl)imidazol‐2‐ylidene] were prepared by facile two step syntheses, starting with the reaction of palladium(II) chloride with 2‐phenylpyridine followed by subsequent addition of the NHC ligand to the precatalyst precursor [PdCl(ppy)]₂. Suitable crystals for the X‐ray analysis of the complexes 4 and 6 were obtained. It was shown that 6 has a shorter NHC‐palladium bond than the IMes complex 4 . The difference of the palladium carbene bond lengths based on the higher π‐acceptor strength of (CN)₂IMes in comparison to IMes. Thus, (CN)₂IMes should stabilize the catalytically active central palladium atom better than IMes. As a measure for the π‐acceptor strength of (CN)₂IMes compared to IMes, the selone (CN)₂IMes · Se ( 7 ) was prepared and characterized by ⁷⁷Se‐NMR spectroscopy. The π‐acceptor strength of 7 was illuminated by the shift of its ⁷⁷Se‐NMR signal. The ⁷⁷Se‐NMR signal of 7 was shifted to much higher frequencies than the ⁷⁷Se‐NMR signal of IMes · Se. Catalytic experiments using the Mizoroki‐Heck reaction of aryl chlorides with n‐butyl acrylate showed that 6 is the superior performer in comparison to 4 . Using complex 6 , an extensive substrate screening of 26 different aryl bromides with n‐butyl acrylate was performed. Complex 6 is a suitable precatalyst for para‐substituted aryl bromides. The catalytically active species was identified by mercury poisoning experiments to be palladium nanoparticles.     

Spektroskopische Untersuchungen zu Substituenteneffekten in Silylmethylsilanen

Spectroscopic Investigations on Substituent Effects in Silylmethylsilanes The silanes Me_3?n(Me₃SiCH₂)_nSiH (n = 1–3), (RMe₂SiCH₂)₃SiH (R = n-Bu, n-Pr, Et, PhCH₂, Ph) and Me₃ElCH₂SiMe₂H (El = Ge, Sn) were prepared. The frequencies of the Si? H stretching vibration, the ²⁹Si? ¹H coupling constants and the ²⁹Si n.m.r. chemical shifts were measured. The ?(SiH) and J(²⁹Si? ¹H) values in the silanes Me_3?n(Me₃SiCH₂)_nSiH depend on the number of trimethylsilymethyl groups. There is hardly an influence of the substituents R on these values in the silanes (RMe₂SiCH₂)₃SiH. The frequencies of the Si? H stretching vibrations in the silanes Me₃ElCH₂SiMe₂H (El = Si, Ge, Sn) show the order Si?Ge > Sn. The ₂₉Si n.m.r. chemical shifts of the Si(H) signals are approximately equal in the silanes Me_3?n(Me₃SiCH₂)_nSiH and (RMe₂SiCH₂)₃SiH.     

Structure-based engineering of strictosidine synthase: auxiliary for alkaloid libraries

The highly substrate-specific strictosidine synthase (EC 4.3.3.2) catalyzes the biological Pictet-Spengler condensation between tryptamine and secologanin, leading to the synthesis of about 2000 monoterpenoid indole alkaloids in higher plants. The crystal structure of Rauvolfia serpentina strictosidine synthase (STR1) in complex with strictosidine has been elucidated here, allowing the rational site-directed mutation of the active center of STR1 and resulting in modulation of its substrate acceptance. Here, we report on the rational redesign of STR1 by generation of a Val208Ala mutant, further describing the influence on substrate acceptance and the enzyme-catalyzed synthesis of 10-methyl- and 10-methoxystrictosidines. Based on the addition of strictosidine to a crude strictosidine glucosidase preparation from Catharanthus cells, a combined chemoenzymatic approach to generating large alkaloid libraries for future pharmacological screenings is presented.     

Optimal conditions for alkaline detoxification of dilute-acid lignocellulose hydrolysates

Alkaline detoxification strongly improves the fermentability of dilute-acid hydrolysates in the production of bioethanol from lignocellulose with Saccharomyces cerevisiae. New experiments were performed with NH₄OH and NaOH to define optimal conditions for detoxification and make a comparison with Ca(OH)₂ treatment feasible. As too harsh conditions lead to sugar degradation, the detoxification treatments were evaluated through the balanced ethanol yield, which takes both the ethanol production and the loss of fermentable sugars into account. The optimization treatments were performed as factorial experiments with 3-h duration and varying pH and temperature. Optimal conditions were found roughly in an area around pH 9.0/60°C for NH₄OH treatment and in a narrow area stretching from pH 9.0/80°C to pH 12.0/30°C for NaOH treatment. By optimizing treatment with NH₄OH, NaOH, and Ca(OH)₂, it was possible to find conditions that resulted in a fermentability that was equal or better than that of a reference fermentation of a synthetic sugar solution without inhibitors, regardless of the type of alkali used. The considerable difference in the amount of precipitate generated after treatment with different types of alkali appears critical for industrial implementation.