A growing string method for determining transition states: comparison to the nudged elastic band and string methods

Interpolation methods such as the nudged elastic band and string methods are widely used for calculating minimum energy pathways and transition states for chemical reactions. Both methods require an initial guess for the reaction pathway. A poorly chosen initial guess can cause slow convergence, convergence to an incorrect pathway, or even failed electronic structure force calculations along the guessed pathway. This paper presents a growing string method that can find minimum energy pathways and transition states without the requirement of an initial guess for the pathway. The growing string begins as two string fragments, one associated with the reactants and the other with the products. Each string fragment is grown separately until the fragments converge. Once the two fragments join, the full string moves toward the minimum energy pathway according to the algorithm for the string method. This paper compares the growing string method to the string method and to the nudged elastic band method using the alanine dipeptide rearrangement as an example. In this example, for which the linearly interpolated guess is far from the minimum energy pathway, the growing string method finds the saddle point with significantly fewer electronic structure force calculations than the string method or the nudged elastic band method.     

Oxidative additions of alkynyl/vinyl iodides to gold and gold-catalyzed vinylation reactions triggered by the MeDalphos ligand

The hemilabile Ad₂P(o-C₆H₄)NMe₂ ligand promotes fast, quantitative and irreversible oxidative addition of alkynyl and vinyl iodides to gold. The reaction is general. It works with a broad range of substrates of various electronic bias and steric demand, and proceeds with complete retention of stereochemistry from Z and E vinyl iodides. Both alkynyl and vinyl iodides react faster than aryl iodides. The elementary step is amenable to catalysis. Oxidative addition of vinyl iodides to gold and π-activation of alkenols (and N-alkenyl amines) at gold have been combined to achieve hetero-vinylation reactions. A number of functionalized heterocycles, i.e. tetrahydrofuranes, tetrahydropyranes, oxepanes and pyrrolidines were obtained thereby (24 examples, 87% average yield). Taking advantage of the chemoselectivity for vinyl iodides over aryl iodides, sequential transformations involving first a hetero-vinylation step and then a C–N coupling, a C–C coupling or an heteroarylation were achieved from a vinyl/aryl bis-iodide substrate.

The hemilabile Ad₂P(o-C₆H₄)NMe₂ ligand promotes fast, quantitative and irreversible oxidative addition of alkynyl and vinyl iodides to gold.     

Visible light-induced water oxidation on mesoscopic alpha-Fe2O3 films made by ultrasonic spray pyrolysis

Alpha-Fe(2)O(3) films having a mesoscopic leaflet type structure were produced for the first time by ultrasonic spray pyrolysis (USP) to explore their potential as oxygen-evolving photoanodes. The target of these studies is to use translucent hematite films deposited on conducting fluorine doped tin oxide (FTO) glass as top electrodes in a tandem cell that accomplishes the cleavage of water into hydrogen and oxygen by sunlight. The properties of layers made by USP were compared to those deposited by conventional spray pyrolysis (SP). Although both types of films show similar XRD and UV-visible and Raman spectra, they differ greatly in their morphology. The mesoscopic alpha-Fe(2)O(3) layers produced by USP consist mainly of 100 nm-sized platelets with a thickness of 5-10 nm. These nanosheets are oriented mainly perpendicularly to the FTO support, their flat surface exposing (001) facets. The mesoscopic leaflet structure has the advantage that it allows for efficient harvesting of visible light, while offering at the same time the very short distance required for the photogenerated holes to reach the electrolyte interface before recombining with conduction band electrons. This allows for water oxidation by the valence band holes even though their diffusion length is only a few nanometers. Distances are longer in the particles produced by SP favoring recombination of photoinduced charge carriers. Open-circuit photovoltage measurements indicate a lower surface state density for the nanoplatelets as compared to the round particles. These factors explain the much higher photoactivity of the USP compared to the SP deposited alpha-Fe(2)O(3) layers. Addition of hydrogen peroxide to the alkaline electrolyte further improves the photocurrent-voltage characteristics of films generated by USP indicating the hole transfer from the valence band of the semiconductor oxide to the adsorbed water to be the rate-limiting kinetic step in the oxygen generation reaction.     

Ketendithioacetal-S-imide

Starting from 2-isopropylidene-1,3-dithiane, various ketene-dithioacetal-S-imides have been prepared and characterized by¹H- and¹³C-NMR spectra.

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Ketendithioacetal-S-imideKurze Mitteilung

     

Xylanase production by Trichoderma reesei rut C-30 on rice straw

Xylanase production of Trichoderma reesei Rut C-30 was examined at different initial pH values (4.8, 5.9, and 7.0) on rice straw in shake flasks, and in a fermentor, for the best pH condition. Enzyme performance was tested on ammonia-treated dwarf elephant grass. The maximum xylanase activities, 92 and 122 IU/mL, were obtained at pH 4.8 in the shake flasks and fermentor, respectively, in which good growth of the fungus was observed during the first 24 h and consumption of proteins dissolved from the rice straw caused the pH to rise later to values between 6.4 and 6.7 (optimal for xylanase production). The xylanases from T. reesei were as effective as Multifect XL, a commercial enzyme preparation, in hydrolyzing ammonia-treated elephant grass.     

Synthesis of mixed acid anhydrides from methane and carbon dioxide in acid solvents

[reaction: see text] The reaction of CH(4) with CO(2) has been performed in anhydrous acids using VO(acac)(2) and K(2)S(2)O(8) as promoters. NMR analysis establishes that the primary product is a mixed anhydride of acetic acid and the acid solvent. In sulfuric acid, the overall reaction is CH(4) + CO(2) + SO(3) --> CH(3)C(O)-O-SO(3)H. Hydrolysis of the mixed anhydride produces acetic acid and the solvent acid. When trifluoroacetic acid is the solvent, acetic acid is primarily formed via the reaction CH(4) + CF(3)COOH --> CH(3)COOH + CHF(3).     

Relevance of electrokinetic theory for "soft" particles to bacterial cells: implications for bacterial adhesion

Bacterial cells and other biological particles carry charged macromolecules on their surface that form a "soft" ion-permeable layer. In this paper, we test the applicability of an electrokinetic theory for soft particles to characterize the electrophoretic mobility (EPM) and adhesion kinetics of bacterial cells. The theory allows the calculation of two parameters--the electrophoretic softness and the fixed charged density--that define the characteristics of the polyelectrolyte layer at the soft particle surface. The theory also allows the calculation of an outer-surface potential that may better predict the electrostatic interaction of soft particles with solid surfaces. To verify its relevance for bacterial cells, the theory was applied to EPM measurements of two well-characterized Escherichia coli K12 mutants having lipopolysaccharide (LPS) layers of different lengths and molecular compositions. Results showed that the obtained softness and fixed charge density were not directly related to the known characteristics of the LPS of the selected strains. Interaction energy profiles calculated from Derjaguin-Landau-Verwey-Overbeek (DLVO) theory were used to interpret bacterial deposition (adhesion) rates on a pure quartz surface. The outer surface potential failed to predict the low attachment efficiencies of the two bacterial strains. The lack of success in the application of the theory for soft particles to bacterial cells is attributed to chemical and physical heterogeneities of the polyelectrolyte layer at the cell surface.     

Siloxyaluminate and Siloxygallate Complexes as Models for Framework and Partially Hydrolyzed Framework Sites in Zeolites and Zeotypes

Anionic molecular models for nonhydrolyzed and partially hydrolyzed aluminum and gallium framework sites on silica, M[OSi(OtBu)₃]₄⁻ and HOM[OSi(OtBu)₃]₃⁻ (where M=Al or Ga), were synthesized from anionic chlorides Li{M[OSi(OtBu)₃]₃Cl} in salt metathesis reactions. Sequestration of lithium cations with [12]crown-4 afforded charge-separated ion pairs composed of monomeric anions M[OSi(OtBu)₃]₄⁻ with outer-sphere [([12]crown-4)₂Li]⁺ cations, and hydroxides {HOM[OSi(OtBu)₃]₃} with pendant [([12]crown-4)Li]⁺ cations. These molecular models were characterized by single-crystal X-ray diffraction, vibrational spectroscopy, mass spectrometry and NMR spectroscopy. Upon treatment of monomeric [([12]crown-4)Li]{HOM[OSi(OtBu)₃]₃} complexes with benzyl alcohol, benzyloxide complexes were formed, modeling a possible pathway for the formation of active sites for Meerwin–Ponndorf–Verley (MPV) transfer hydrogenations with Al/Ga-doped silica catalysts.