Submillimeter infrared absorption and chain conformations of poly(vinylidene fluoride) and copolymers. II. Phase transition analysis

Absorption spectra, and hence the dielectric properties, of poly(vinylidene fluoride-tri-fluoroethylene) copolymers have been obtained by far infrared spectroscopy in the frequency range 15–55 cm^?1. We have studied the evolutions of the absorption coefficient and imaginary part of the dielectric constant as a function of poling field and copolymer composition. During the phase transition from form II to form I, the whole absorption presents a strong increase. This behavior is explained by polarizability changes at phase transition.     

Cluster analysis of molecular simulation trajectories for systems where both conformation and orientation of the sampled states are important

Clustering methods have been widely used to group together similar conformational states from molecular simulations of biomolecules in solution. For applications such as the interaction of a protein with a surface, the orientation of the protein relative to the surface is also an important clustering parameter because of its potential effect on adsorbed‐state bioactivity. This study presents cluster analysis methods that are specifically designed for systems where both molecular orientation and conformation are important, and the methods are demonstrated using test cases of adsorbed proteins for validation. Additionally, because cluster analysis can be a very subjective process, an objective procedure for identifying both the optimal number of clusters and the best clustering algorithm to be applied to analyze a given dataset is presented. The method is demonstrated for several agglomerative hierarchical clustering algorithms used in conjunction with three cluster validation techniques. © 2016 Wiley Periodicals, Inc.     

Reversible (de)protonation-induced valence inversion in mixed-valent diiron(II,III) complexes

The coupling of electron and proton transfers is currently under intense scrutiny. This Communication reports a new kind of proton-coupled electron transfer within a homodinuclear first-row transition-metal complex. The triply-bridged complex [Fe(III)(μ-OPh)(μ(2)-mpdp)Fe(II)(NH(2)Bn)] (1; mpdp(2-) = m-phenylenedipropionate) bearing a terminal aminobenzyl ligand can be reversibly deprotonated to the anilinate complex 2 whose core [Fe(II)(μ-OPh)(μ(2)-mpdp)Fe(III)(NHBn)] features an inversion of the iron valences. This observation is supported by a combination of UV-visible, (1)H NMR, and M?ssbauer spectroscopic studies.     

The temperature intervals with global exchange of replicas empirical accelerated sampling method: parameter sensitivity and extension to a complex molecular system

The recently developed "temperature intervals with global exchange of replicas" (TIGER2) algorithm is an efficient replica-exchange sampling algorithm that provides the freedom to specify the number of replicas and temperature levels independently of the size of the system and temperature range to be spanned, thus making it particularly well suited for sampling molecular systems that are considered to be too large to be sampled using conventional replica exchange methods. Although the TIGER2 method is empirical in nature, when appropriately applied it is able to provide sampling that satisfies the balance condition and closely approximates a Boltzmann-weighted ensemble of states. In this work, we evaluated the influence of factors such as temperature range, temperature spacing, replica number, and sampling cycle design on the accuracy of a TIGER2 simulation based on molecular dynamics simulations of alanine dipeptide in implicit solvent. The influence of these factors is further examined by calculating the properties of a complex system composed of the B1 immunoglobulin-binding domain of streptococcal protein G (protein G) in aqueous solution. The accuracy of a TIGER2 simulation is particularly sensitive to the maximum temperature level selected for the simulation. A method to determine the appropriate maximum temperature level to be used in a TIGER2 simulation is presented.     

Cooperative Metal Binding and Helical Folding in Model Peptides of Treble‐Clef Zinc Fingers

Synergy in zinc fingers : The comparison between peptide folding and metal binding properties of two model peptides of treble‐clef zinc fingers presenting high affinities for zinc and cobalt reveals a cooperative effect: the metal folds the peptide into a α‐helix, which in turn strengthens the metal core.

     

Identification of iron(III) peroxo species in the active site of the superoxide reductase SOR from Desulfoarculus baarsii

The active site of superoxide reductase SOR consists of an Fe2+ center in an unusual [His4 Cys1] square-pyramidal geometry. It specifically reduces superoxide to produce H2O2. Here, we have reacted the SOR from Desulfoarculus baarsii directly with H2O2. We have found that its active site can transiently stabilize an Fe3+-peroxo species that we have spectroscopically characterized by resonance Raman. The mutation of the strictly conserved Glu47 into alanine results in a stabilization of this Fe3+-peroxo species, when compared to the wild-type form. These data support the hypothesis that the reaction of SOR proceeds through such a Fe3+-peroxo intermediate. This also suggests that Glu47 might serve to help H2O2 release during the reaction with superoxide.     

Low-temperature reaction of trialkoxysilanes on silica gel: a mild and controlled method for modifying silica surfaces

The room temperature reaction of 4-(triethoxysilyl)butyronitrile, 4-TBN ((C2H5O)3Si(CH2)3CN), on weakly hydrated silica samples pretreated at 393 K has been studied by desorption experiments and by diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy at different aging times under various water partial pressures. The reaction is demonstrated by the decrease of desorption of 4-TBN with time and the simultaneous disappearance of the 2980 and 1394 cm(-1) signals in the DRIFT spectra, assigned to the CH3 moiety of the ethoxy functions. Water partial pressure is shown to have a crucial effect on the rate and efficiency of the process as, after 6 days, for samples kept at room temperature under vacuum, ca. 50% of the silane has reacted, while for those kept in a water-saturated atmosphere the silane reaction reaches 96%. Although the silane appears to be irreversibly bonded to the surface, no definite conclusion may be drawn from these preliminary results as to the nature of the bonding (grafting or coating). These samples are compared to modified silicas prepared according to conventional methods. The same extent of silane reaction (50%) is achieved for preadsorbed samples kept under vacuum and either cured at 473 K for 30 h or kept at room temperature for 6 days. A mild and controlled modification of silica by triethoxysilanes can thus be achieved by first physisorbing known amounts of the modifying silanes from an organic solvent on pretreated silica and then letting the samples mature for a few days at room temperature in a water-saturated atmosphere.     

Binuclear manganese compounds of potential biological significance. Part 2. Mechanistic study of hydrogen peroxide disproportionation by dimanganese complexes: the two oxygen atoms of the peroxide end up in a dioxo intermediate

The dimanganese(II,II) complexes 1a [Mn(2)(L)(OAc)(2)(CH(3)OH)](ClO(4)) and 1b [Mn(2)(L)(OBz)(2)(H(2)O)](ClO(4)), where HL is the unsymmetrical phenol ligand 2-(bis-(2-pyridylmethyl)aminomethyl)-6-((2-pyridylmethyl)(benzyl)aminomethyl)-4-methylphenol, react with hydrogen peroxide in acetonitrile solution. The disproportionation reaction was monitored by electrospray ionization mass spectrometry (ESI-MS) and EPR and UV-visible spectroscopies. Extensive EPR studies have shown that a species (2) exhibiting a 16-line spectrum at g approximately 2 persists during catalysis. ESI-MS experiments conducted similarly during catalysis associate 2a with a peak at 729 (791 for 2b) corresponding to the formula [Mn(III)Mn(IV)(L)(O)(2)(OAc)](+) ([Mn(III)Mn(IV)(L)(O)(2)(OBz)](+) for 2b). At the end of the reaction, it is partly replaced by a species (3) possessing a broad unfeatured signal at g approximately 2. ESI-MS associates 3a with a peak at 713 (775 for 3b) corresponding to the formula [Mn(II)Mn(III)(L)(O)(OAc)](+) ([Mn(II)Mn(III)(L)(O)(OBz)](+) for 3b). In the presence of H(2)(18)O, these two peaks move to 733 and to 715 indicating the presence of two and one oxo ligands, respectively. When H(2)(18)O(2) is used, 2a and 3a are labeled showing that the oxo ligands come from H(2)O(2). Interestingly, when an equimolar mixture of H(2)O(2) and H(2)(18)O(2) is used, only unlabeled and doubly labeled 2a/b are formed, showing that its two oxo ligands come from the same H(2)O(2) molecule. All these experiments lead to attribute the formula [Mn(III)Mn(IV)(L)(O)(2)(OAc)](+) to 2a and to 3a the formula [Mn(II)Mn(III)(L)(O)(OAc)](+). Freeze-quench/EPR experiments revealed that 2a appears at 500 ms and that another species with a 6-line spectrum is formed transiently at ca. 100 ms. 2a was prepared by reaction of 1a with tert-butyl hydroperoxide as shown by EPR and UV-visible spectroscopies and ESI-MS experiments. Its structure was studied by X-ray absorption experiments which revealed the presence of two or three O atoms at 1.87 A and three or two N/O atoms at 2.14 A. In addition one N atom was found at a longer distance (2.3 A) and one Mn at 2.63 A. 2a can be one-electron oxidized at E(1/2) = 0.91 V(NHE) (DeltaE(1/2) = 0.08 V) leading to its Mn(IV)Mn(IV) analogue. The formation of 2a from 1a was monitored by UV-visible and X-ray absorption spectroscopies. Both concur to show that an intermediate Mn(II)Mn(III) species, resembling 4a [Mn(2)(L)(OAc)(2)(H(2)O)](ClO(4))(2), the one-electron-oxidized form of 1a, is formed initially and transforms into 2a. The structures of the active intermediates 2 and 3 are discussed in light of their spectroscopic properties, and potential mechanisms are considered and discussed in the context of the biological reaction.