Density functional theory predicts the barriers for radical fragmentation in solution

[reaction: see text] N-Methoxypyridyl radicals formed by one-electron reduction of the corresponding cationic heterocycles undergo N-O bond cleavage. Experimental activation free energies for a series of these bond fragmentations are compared to corresponding barriers determined from electronic structure calculations. The DFT barriers agree well with those from experiment, being smaller than the latter values by an average value of ca. 1 kcal/mol, for rate constants varying over almost 3 orders of magnitude, or within ca. 3 kcal/mol over 8 orders of magnitude of rate constant. For a model compound, the B3PW91/6-31+G hybrid density functional method is also found to be in good agreement with the MCSCF-MRMP2 method. One of the reactions is found by DFT to have no minimum for the reactant radical, consistent with a truly barrierless reaction.     

Synthesis, structure and spectroscopy of new thiopyrone and hydroxypyridinethione transition-metal complexes

The coordination chemistry of several O,S mixed donor ligands, namely thiopyrone and hydroxypyridinethione chelators, with a variety of middle and late first-row transition-metal ions is described. Complexes of 3-hydroxy-2-methyl-4-thiopyrone (thiomaltol) with cobalt(II), copper(II) and zinc(II); 3-hydroxy-1,2-dimethyl-4(1H)-pyridinethione (3,4-HOPTO) with iron(III), nickel(II), copper(II) and zinc(II); and 3-hydroxy-1-methyl-2(1H)-pyridinethione (3,2-HOPTO) with iron(III), nickel(II), copper(II) and zinc(II) have been synthesized and characterized. The structures, absorbance spectroscopy, cyclic voltammetry and superconducting quantum interferometer device (SQUID) measurements of selected metal complexes, as well as ligand protonation constants, are reported. Most of the metal complexes show coordination geometries indicative of a strong trans influence by the O,S chelators. The data presented herein provide the most detailed study of the transition-metal coordination chemistry of both thiopyrone and hydroxypyridinethione O,S donor ligands to date, and provide the basis for the investigation of these ligands in realm of biological inorganic chemistry.     

The 'hybrid cell': a new compensated infinity cell for larger radius ion excitation in Fourier transform ion cyclotron resonance mass spectrometry

A new 'hybrid' ion cyclotron resonance (ICR) trap is proposed and analyzed by computer simulations. The trap is basically a hybrid of a segmented end cap (Infinity) and capacitively coupled cylindrical cell, with additional electrodes placed at the center of each end cap. The new trap produces an on-axis electric field z-profile similar to that of the Infinity cell or capacitively coupled open cylindrical cell during ion excitation. Simion simulations demonstrate that, during detection, appropriate changes of the potentials applied to the two new sets of electrodes produce a radial electric field z-profile that more closely approaches that for an ideal axial three-dimensional quadrupolar potential at high post-excitation ICR orbital radius, for improved signal-to-noise ratio and resolving power, and minimal m/z-discrimination.     

A simple model for a two-stage chemical reaction with diffusion

We analyse the evolution of a two-stage chemical reaction betweentwo neighbouring plumes of reactants. Under the assumption thatthe plumes are approximately Gaussian we derive a system ofordinary differential equations for the total amount, the centroidand the variance of each reactant. We compare the solution ofthese equations with full numerical simulation of the reaction.Excellent agreement is obtained, with solution of the near-Gaussianmodel requiring considerably less computational effort thanthe full simulations. Of key importance is the yield of thereaction, and we discuss this feature in particular.     

Industrial scale-up of pH-controlled liquid hot water pretreatment of corn fiber for fuel ethanol production

The pretreatment of cellulose in corn fiber by liquid hot water at 160°C and a pH above 4.0 dissolved 50% of the fiber in 20 min. The pretreatment also enabled the subsequent complete enzymatic hydrolysis of the remaining polysaccharides to monosaccharides. The carbohydrates dissolved by the pretreatment were 80% soluble oligosaccharides and 20% monosaccharides with o1% of the carbohydrates lost to degradation products. Only a minimal amount of protein was dissolved, thus enriching the protein content of the un dissolved material. Replication of laboratory results in an industrial trial at 43 gallons per minute (163 L/min) of fiber slurry with a residence time of 20 min illustrates the utility and practicality of this approach for pretreating corn fiber. The added costs owing to pretreatment, fiber, and hydrolysis are equivalent to less than $0.84/gal of ethanol produced from the fiber. Minimizing monosaccharide formation during pretreatment minimized the formation of degradation products; hence, the resulting sugars were readily fermentable to ethanol by the recombinant hexose and by pentose-fermenting Saccharomyces cerevisiae 424A (LNH-ST) and ethanologenic Escherichia coli at yields >90% of theoretical based on the starting fiber. this cooperative effort and first successful trial opens the door for examining the robustness of the pretreatment system under extended run conditions as well as pretreatment of other cellulose-containing materials using water at controlled pH.     

Sorptive recovery of dilute ethanol from distillation column bottoms stream

Applied Biochemistry and Biotechnology - Modern ethanol distillation processes are designed to ensure removal of all ethanol from the column bottoms, i.e., to levels <100 ppm ethanol, and...     

Evaluation and optimization of electron capture dissociation efficiency in fourier transform ion cyclotron resonance mass spectrometry

Electron capture dissociation (ECD) efficiency has typically been lower than for other dissociation techniques. Here we characterize experimental factors that limit ECD and seek to improve its efficiency. Efficiency of precursor to product ion conversion was measured for a range of peptide (∼15% efficiency) and protein (∼33% efficiency) ions of differing sizes and charge states. Conversion of precursor ions to products depends on electron irradiation period and maximizes at ∼5–30 ms. The optimal irradiation period scales inversely with charge state. We demonstrate that reflection of electrons through the ICR cell is more efficient and robust than a single pass, because electrons can cool to the optimal energy for capture, which allows for a wide range of initial electron energy. Further, efficient ECD with reflected electrons requires only a short (∼500 μs) irradiation period followed by an appropriate delay for cooling and interaction. Reflection of the electron beam results in electrons trapped in or near the ICR cell and thus requires a brief (∼50 μs) purge for successful mass spectral acquisition. Further electron irradiation of refractory precursor ions did not result in further dissociation. Possibly the ion cloud and electron beam are misaligned radially, or the electron beam diameter may be smaller than that of the ion cloud such that remaining precursor ions do not overlap with the electron beam. Several ion manipulation techniques and use of a large, movable dispenser cathode reduce the possibility that misalignment of the ion and electron beams limits ECD efficiency.     

Construction of a hybrid quadrupole/fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa

Technological advancements including an open-cylindrical Penning trap with capacitively coupled ICR cell, selective ion accumulation with a resolving quadrupole, and a voltage gradient used during ion extraction from an octopole ion trap, have individually improved dynamic range and sensitivity in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS). Documented here is a new instrument utilizing these technologies toward the robust detection and fragmentation of biomolecules >10 kDa. Up to 55-fold enhancement in ion population by selective ion accumulation combined with 10- to 20- fold signal-to-noise improvement by application of a DC voltage gradient to an accumulation octopole during the ion transfer event offers improved signal-to-noise (or speed) of MS/MS experiments, for proteins from Methanococcus jannaschii and Saccharomyces cerevisiae whole cell lysates. After external quadrupole filtering with a 40 m/z window, three proteins were fragmented (and identified) in parallel from the database of Methanococcus jannaschii. Electron capture dissociation (ECD) of an intact yeast protein provides extensive sequence information resulting in a high degree of localization for an N-terminal acetylation. Hybrid fragmentation, infrared multiphoton dissociation (IRMPD) followed by low energy electrons (ECD), with the electron source located laterally off the z-axis and external to the magnet bore, presents a strategy for identification of proteins by means of the sequence tag approach. Automated implementation of diverse MS(n) approaches in a Q-FTMS instrument promises to help realize "top-down" proteomics in the future.     

Electron capture dissociation implementation progress in fourier transform ion cyclotron resonance mass spectrometry

Successful electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) applications to peptide and protein structural analysis have been enabled by constant progress in implementation of improved electron injection techniques. The rate of ECD product ion formation has been increased to match the liquid chromatography and capillary electrophoresis timescales, and ECD has been combined with infrared multiphoton dissociation in a single experimental configuration to provide simultaneous irradiation, fast switching between the two techniques, and good spatial overlap between ion, photon, and electron beams. Here we begin by describing advantages and disadvantages of the various existing electron injection techniques for ECD in FT-ICR MS. We next compare multiple-pass and single-pass ECD to provide better understanding of ECD efficiency at low and high negative cathode potentials. We introduce compressed hollow electron beam injection to optimize the overlap of ion, photon, and electron beams in the ICR ion trap. Finally, to overcome significant outgassing during operation of a powerful thermal cathode, we introduce nonthermal electron emitter-based electron injection. We describe the first results obtained with cold cathode ECD, and demonstrate a general way to obtain low-energy electrons in FT-ICR MS by use of multiple-pass ECD.