Insights into sulfinate formation from tosyl hydrazides

Benzylation of 1,2-ditosylhydrazine in DMF under various basic conditions results in a benzyl sulfone via intermediary sulfinate formation, providing new insights and allowing practical conclusions to be drawn. The half-lives of 1,2-ditosylhydrazine and several monotosylated hydrazides with 1,1,3,3-tetramethylguanidine in DMSO have been determined by ¹H NMR spectroscopy and are found to vary from a few minutes to several months. In the course of this work a benzylated, partly detosylated compound has been identified and a 1,1,3,3-tetramethyl guanidine-containing side-product characterized. A contradictory report is also commented on.     

Molecular charge distributions, core-ionization energies, and the point-charge approximation. An addendum

In earlier papers the atoms-in-molecules concept of Bader was used to show the inadequacies of the point-charge model for calculating potentials at atoms in molecules and, hence, for accounting for shifts in core-ionization energies in terms of atomic charges. Because questions have been raised about the suitability of the basis set that was used, part of these calculations has been repeated with the 6-31G^** basis set. The conclusions of the earlier study are unchanged: the point-charge model does not accurately give the potentials at atoms in molecules. A multipole model gives better results, but needs to be carried at least to octupole terms.     

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.     

Theoretical characterization of four distinct isomer types in hydrated-electron clusters, and proposed assignments for photoelectron spectra of water cluster anions

Water cluster anions, (H(2)O)(N)(-), are examined using mixed quantum/classical molecular dynamics based on a one-electron pseudopotential model that incorporates many-body polarization and predicts vertical electron detachment energies (VDEs) with an accuracy of ~0.1 eV. By varying the initial conditions under which the clusters are formed, we are able to identify four distinct isomer types that exhibit different size-dependent VDEs. On the basis of a strong correlation between the electron's radius of gyration and its optical absorption maximum, and extrapolating to the bulk limit (N → ∞), our analysis supports the assignment of the "isomer Ib" data series, observed in photoelectron spectra of very cold clusters, as arising from cavity-bound (H(2)O)(N)(-) cluster isomers. The "isomer I" data reported in warmer experiments are assigned to surface-bound isomers in smaller clusters, transitioning to partially embedded isomers in larger clusters. The partially embedded isomers are characterized by a partially formed solvent cavity at the cluster surface, and they are spectroscopically quite similar to internalized cavity isomers. These assignments are consistent with various experimental data, and our theoretical characterization of these isomers sheds new light on a long-standing assignment problem.     

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.     

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.     

Stereo‐Inversion in the (4R)‐γ‐Decanolactone Synthesis by Saccharomyces cerevisiae: (2E,4S)‐4‐Hydroxydec‐2‐enoic Acid Acts as a Key Intermediate

Methyl (2E,4R)‐4‐hydroxydec‐2‐enoate, methyl (2E,4S)‐4‐hydroxydec‐2‐enoate, and ethyl (±)‐(2E)‐4‐hydroxy[4‐²H]dec‐2‐enoate were chemically synthesized and incubated in the yeast Saccharomyces cerevisiae. Initial C‐chain elongation of these substrates to C₁₂ and, to a lesser extent, C₁₄ fatty acids was observed, followed by γ‐decanolactone formation. Metabolic conversion of methyl (2E,4R)‐4‐hydroxydec‐2‐enoate and methyl (2E,4S)‐4‐hydroxydec‐2‐enoate both led to (4R)‐γ‐decanolactone with >99% ee and 80% ee, respectively. Biotransformation of ethyl (±)‐(2E)‐4‐hydroxy(4‐²H)dec‐2‐enoate yielded (4R)‐γ‐[²H]decanolactone with 61% of the ²H label maintained and in 90% ee indicating a stereoinversion pathway. Electron‐impact mass spectrometry analysis (Fig. 4) of 4‐hydroxydecanoic acid indicated a partial C(4)→C(2) ²H shift. The formation of erythro‐3,4‐dihydroxydecanoic acid and erythro‐3‐hydroxy‐γ‐decanolactone from methyl (2E,4S)‐4‐hydroxydec‐2‐enoate supports a net inversion to (4R)‐γ‐decanolactone via 4‐oxodecanoic acid. As postulated in a previous work, (2E,4S)‐4‐hydroxydec‐2‐enoic acid was shown to be a key intermediate during (4R)‐γ‐decanolactone formation via degradation of (3S,4S)‐dihydroxy fatty acids and precursors by Saccharomyces cerevisiae.