Geometry optimization of periodic systems using internal coordinates

An algorithm is proposed for the structural optimization of periodic systems in internal (chemical) coordinates. Internal coordinates may include in addition to the usual bond lengths, bond angles, out-of-plane and dihedral angles, various "lattice internal coordinates" such as cell edge lengths, cell angles, cell volume, etc. The coordinate transformations between Cartesian (or fractional) and internal coordinates are performed by a generalized Wilson B-matrix, which in contrast to the previous formulation by Kudin et al. [J. Chem. Phys. 114, 2919 (2001)] includes the explicit dependence of the lattice parameters on the positions of all unit cell atoms. The performance of the method, including constrained optimizations, is demonstrated on several examples, such as layered and microporous materials (gibbsite and chabazite) as well as the urea molecular crystal. The calculations used energies and forces from the ab initio density functional theory plane wave method in the projector-augmented wave formalism.     

1,4-thiazepines, 1,4-benzothiazepin-5-ones,and 1,4-benzothioxepin orthoamides via multicomponent reactions of isocyanides

The intramolecular Ugi four-component condensation between 6-oxo-4-thiacarboxylic acids, benzylamines, and cyclohexyl isocyanide gave hexahydro-1,4-thiazepin-5-ones and 1,4-benzothiazepin-5-ones, in some cases with high stereoselectivity, and the intramolecular Passerini three-component reaction, in the presence of catalytic amine, gave tetracyclic 1,4-benzothioxepin orthoamides.     

Viscoelastic properties of single polysaccharide molecules determined by analysis of thermally driven oscillations of an atomic force microscope cantilever

We report on single molecule measurements of the viscoelastic properties of the polysaccharide dextran using a new approach which involves acquiring the power spectral density of the thermal noise of an atomic force microscope cantilever while holding the single molecule of interest under force-clamp conditions. The attractiveness of this approach when compared with techniques which use forced oscillations under constant loading rate conditions is that it is a near-equilibrium measure of mechanical response which provides a more relevant probe of thermally driven biomolecular dynamics. Using a simple harmonic oscillator model of the cantilever-molecule system and by subtracting the response of the free cantilever taking into account hydrodynamic effects, the effective damping zetamol and elastic constant kmol of a single molecule are obtained. The molecular elasticity measured by this new technique shows a dependence on applied force that reflects the chair-boat conformational transition of the pyranose rings of the dextran molecule which is in good agreement with values obtained directly from the gradient of a conventional constant loading rate force-extension curve. The molecular damping is also seen to follow a nontrivial dependence on loading which we suggest indicates that it is internal friction and not work done on the solvent that is the dominant dissipative process.     

Photo-Oxidation of phenosafranine and neutral red in the presence of iron(III): Determination of trace amounts of iron and phosphate

Summary Phenosafranine (Ph) and Neutral Red (NR) in the presence of iron(III) are decolorized by illumination with light of wavelength shorter than 360 nm. The decolorization mechanism involves ·OH radicals, formed during the photo-excitation of hydrolysed iron(III) species. In the presence of oxygen, iron(III) acts as a catalyst in the photochemical process. The photo-oxidation of Ph and NR is followed by measuring the decrease in absorbance of the dyes, and linear calibration graphs in the range 1–11 ppm of iron are obtained. The decrease in the fluorescence of phenosafranine has also been used to measure the photo-oxidation of this dye, and is linearly related to iron concentration in the range 0.1–1.1 ppm. Phosphate strongly inhibits the iron(III)-catalysed photodecolorization and this can be made the basis of a method for its determination (concentration limit 1×10^–5 M).

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Photooxydation von Phenosafranin und Neutralrot in Gegenwart von Eisen(III): Bestimmung von Spuren Eisen und Phosphat

Zusammenfassung Phenosafranin (Ph) und Neutralrot (NR) werden in Gegenwart von Fe(III) durch Belichtung unter 360 nm entfärbt. Der Mechanismus dieses Vorgangs erfordert die Gegenwart von OH-Radikalen, die sich bei Belichtung von hydrolysierten Fe(III)-Verbindungen bilden. In Gegenwart von Sauerstoff wirkt Fe(III) als Katalysator der photochemischen Reaktion. Die Photooxydation von Ph und NR läßt sich durch Abnahme der Absorbanz der beiden Farbstoffe verfolgen. Dabei ergeben sich lineare Eichkurven für 1–11 ppm Fe. Die Abnahme der Fluoreszenz von Ph dient ebenfalls zur Messung der Photooxydation dieses Farbstoffes und verläuft für 0,1–1,1 ppm Fe linear. Phosphat hindert die Fe(III)-katalysierte Photoentfärbung, was als Grundlage für die Phosphatbestimmung bis zu 1×10^–5 M dienen kann.

     

Light-driven tyrosine radical formation in a ruthenium-tyrosine complex attached to nanoparticle TiO2

We demonstrate a possibility of multistep electron transfer in a supramolecular complex adsorbed on the surface of nanocrystalline TiO(2). The complex mimics the function of the tyrosine(Z)() and chlorophyll unit P(680) in natural photosystem II (PSII). A ruthenium(II) tris(bipyridyl) complex covalently linked to a L-tyrosine ethyl ester through an amide bond was attached to the surface of nanocrystalline TiO(2) via carboxylic acid groups linked to the bpy ligands. Synthesis and characterization of this complex are described. Excitation (450 nm) of the complex promotes an electron to a metal-to-ligand charge-transfer (MLCT) excited state, from which the electron is injected into TiO(2). The photogeneration of Ru(III) is followed by an intramolecular electron transfer from tyrosine to Ru(III), regenerating the photosensitizer Ru(II) and forming the tyrosyl radical. The tyrosyl radical is formed in less than 5 micros with a yield of 15%. This rather low yield is a result of a fast back electron transfer reaction from the nanocrystalline TiO(2) to the photogenerated Ru(III).     

Voltammetric analysis of iron oxide pigments

Eighteen earthy and four pure synthetic pigments containing alpha-Fe2O3 (hematite), alpha-FeOOH (goethite) and poorly crystalline Fe and Mn oxide species were analyzed by voltammetry of microparticles. Three natural samples were subjected to an interlaboratory test to evaluate the reproducibility of the voltammetric peak potentials and peak shapes. The results confirmed that linear-sweep voltammetry is able to distinguish between poorly crystalline, ferrihydrite-like oxides and well-crystalline hematite and goethite and to detect XRD-amorphous Mn(III,IV) oxides via the peak occurrence. Voltammetry is further able to distinguish between pigments containing well-crystalline goethite (according to its structural features) and hematite (according to its particle size). The microsamples of primers from two baroque paintings were also analyzed by XRD and voltammetry and shown to be analogous to common clayey ochres.     

Ni(0)L]-catalyzed cyclodimerization of 1,3-butadiene: a comprehensive density functional investigation based on the generic [(C(4)H(6))(2)Ni(0)PH(3)] catalyst

We present a comprehensive theoretical investigation of the mechanism for cyclodimerization of butadiene by the generic [bis(butadiene)Ni(0)PH(3)] catalyst employing a gradient-corrected DFT method. We have explored all critical elementary steps of the whole catalytic cycle, namely, oxidative coupling of two butadienes, reductive elimination under ring closure, and allylic isomerization. Oxidative coupling of two butadienes in the [bis(butadiene)Ni(0)L] complex and reductive elimination in the [(bis(eta(3))-octadienediyl)Ni(II)L] species take place under different stereocontrol, which makes isomerization indispensable. Commencing from a preestablished equilibrium between several configurations of the [(octadienediyl)Ni(II)L] complex, the major cyclodimer products, namely, VCH, cis-1,2-DVCB, and cis,cis-COD, are formed along competing reaction paths via reductive elimination, which is found to be the overall rate-determining step. Careful exploration of different possible conceivable routes revealed that bis(eta(1)) species are not involved as critical intermediates either in reductive elimination or in isomerization along the most feasible pathway. The regulation of the selectivity of the cyclodimer formation based on both thermodynamic and kinetic considerations is outlined.     

Generation and intermolecular reactions of 3-indolylacyl radicals

The generation of 3-indolylacyl radicals from the corresponding phenyl selenoesters and the scope of their participation in intermolecular addition reactions to carbon-carbon double bonds under both reductive and nonreductive conditions have been studied.     

Hydrophosphination of boron–boron multiple bonds

Five compounds containing boron–boron multiple bonds are shown to undergo hydrophosphination reactions with diphenylphosphine in the absence of a catalyst. With diborenes, the products obtained are highly dependent on the substitution pattern at the boron atoms, with both 1,1- and 1,2-hydrophosphinations observed. With a symmetrical diboryne, 1,2-hydrophosphination yields a hydro(phosphino)diborene. The different mechanistic pathways for the hydrophosphination of diborenes are rationalised with the aid of density functional theory calculations.

Compounds containing boron–boron double and triple bonds are shown to undergo uncatalysed hydrophosphination reactions with diphenylphosphine.