Ion-Neutral complexes from protonated propyl phenyl ethers. Gas-phase solvolysis versus elimination-readdition

Ion-neutral complexes, well attested as intermediates in the expulsion of alkenes from M⁺? and MH⁺ ions from primary alkyl phenyl ethers, are shown to intervene in the decomposition of the MH⁺ ion of a secondary alkyl phenyl ether, (CD₃)₂CHOPh. Chemical ionization (CI) (methane reagent gas)-mass-analysed ion kinetic energy spectroscopy (MIKES) shows ions of both m/z 96 and 97, indicating that the proton deposited by the CI reagent exchanges with the methyl deuterium atoms. The ratio of daughter ion intensities, as well as the proportions of ions of m/z 95, 96 and 97 from the MH⁺ of CD₃CH₂CD₂OPh, agree with predictions based on the gas-phase solvolysis mechanism, in which [i-Pr⁺ PhOH] complexes form from the protonated parent via simple bond heterolysis. An alternative mechanism, elimination-readdition, would proceed via [propene PhOHD⁺] complexes. This latter mechanism predicts a ratio of daughter ion intensities that is very different from gas-phase solvolysis and which disagrees with experiment. The elimination-readdition pathway is effectively ruled out, while the gas-phase solvolysis mechanism is reinforced.     

Aggregation and protein binding of sodium maleate copolymers with varying hydrophobicities

Copolymers of sodium maleate with methyl methacrylate, styrene, or vinyl acetate have been synthesized and studied in aqueous NaCl solutions of various ionic strengths. The polymers are polyelectrolytes with varying hydrophobicities, and their solution properties have been studied using static and dynamic light scattering. Copolymers containing methyl methacrylate or styrene were shown to aggregate in water upon increasing salt concentration. Copolymers of sodium maleate and vinyl acetate do not associate with increasing ionic strength. The binding of bovine serum albumin and cytochrome C to the sodium maleate copolymers was also investigated by light scattering. It was observed that cytochrome C forms complexes with the copolymers containing methyl methacrylate or vinyl acetate whereas albumin does not bind to any of the copolymers studied. Copyright © 2004 John Wiley & Sons, Ltd.     

High-performance liquid chromatographic determination of oligomeric procyanidins from dimers up to the hexamer in hawthorn

An HPLC method using UV diode array detection was developed for analysing procyanidins qualitatively and quantitatively up to the hexameric level in hawthorn samples. The analysed compounds included procyanidin dimers B-2, B-4 and B-5, procyanidin trimers C-1, epicatechin-(4beta-->8)-epicatechin-(4beta-->6)-epicatechin and epicatechin-(4beta-->6)-epicatechin-(4beta-->8)-epicatechin, a tetramer D-1 and a pentamer E-1 both consisting of (-)-epicatechin units linked through C-4beta/C-8 bonds. The concentrations of two unknown tetramers and a hexamer F were also quantified. The oligomeric procyanidins (OPs) were specifically determined due to the development of a method for isolating them from hawthorn during sample preparation. The pattern of oligomeric procyanidins in the leaves, flowers and fruits was similar, but the concentrations varied depending on the part of the plant. The concentration in leaves was 1.6%, in flowers 1.2% and in fruits 0.2% of the dry mass. The method was validated with respect to repeatability, recovery, linearity, and sensitivity. The repeatability for the quantitative analytical method of all the OPs in leaves was 7.7%, in flowers 8.8%, and in fruits 12.3%. The recovery of the main OPs ranged from 91 to 97%. The correlation coefficients of calibration curves were between 0.997 and 1.000. The limits of quantitation for different procyanidin standards were 0.05-0.12 mg/ml, when 10 microl of each standard solution was injected into the HPLC.     

Continuous chromatographic protein refolding

Column-based protein refolding requires a continuous processing capability if reasonable quantities of protein are to be produced. A popular column-based method, size-exclusion chromatography (SEC) refolding, employs size-exclusion matrices to separate unfolded protein from denaturant, thus refolding the protein. In this work, we conduct a comparison of SEC refolding with refolding by batch dilution, using lysozyme as a model protein. Lysozyme refolding yield was found to be extremely sensitive to the chemical composition of the refolding buffer and particularly the concentration of dithiothreitol (DTT) introduced from the denatured protein mixture. SEC refolding was not adversely affected by DTT carry-over as small contaminants in the denatured solution are separated from protein during the refolding operation. We also find that, contrary to previous reports, size-exclusion refolding on batch columns leads to refolding yields slightly better than batch dilution refolding yields at low protein concentrations but this advantage disappears at higher protein concentrations. As batch-mode chromatography would be the limiting step in a column based refolding downstream process, the batch column refolding method was translated to a continuously operating chromatography system (preparative continuous annular chromatography, P-CAC). It was shown that the P-CAC elution profile is similar to that of a stationary column, making scale-up and translation to P-CAC relatively simple. Moreover, it was shown that high refolding yields (72%) at high protein concentration (>1 mg ml(-1)) could be obtained.     

Experimental and theoretical investigations of structural trends for selenium(IV) imides and oxides: X-ray structure of Se3(NAd)2

The thermal decomposition of Se(NAd)(2) (Ad = 1-adamantyl) in THF was monitored by (77)Se NMR and shown to give the novel cyclic selenium imide Se(3)(NAd)(2) as one of the products. An X-ray structural determination showed that Se(3)(NAd)(2) is a puckered five-membered ring with d(Se-Se) = 2.404(1) A and |d(Se-N)| = 1.873(4) A. On the basis of (77)Se NMR data, other decomposition products include the six-membered ring Se(3)(NAd)(3), and the four-membered rings AdNSe(micro-NAd)(2)SeO and OSe(micro-NAd)(2)SeO. The energies for the cyclodimerization of E(NR)(2) and RNEO (E = S, Se; R = H, Me, (t)Bu, SiMe(3)), and the cycloaddition reactions of RNSeO with E(NR)(2), RNSO(2) with Se(NR)(2), and S(NR)(2) with Se(NR)(2) have been calculated at MP2, CCSD, and CCSD(T) levels of theory using the cc-pVDZ basis sets and B3PW91/6-31G* optimized geometries. Sulfur(IV) and selenium(IV) diimide monomers are predicted to be stable, the sole exception being Se(NSiMe(3))(2) that shows a tendency toward cyclodimerization. The cyclodimerization energy for RNSeO and the cycloaddition reaction energies of RNSeO with Se(NR)(2) as well as that of RNSO(2) with Se(NR)(2) are negative, consistent with the observed formation of OSe(micro-N(t)Bu)(2)SeO, OSe(micro-N(t)Bu)(2)SeN(t)Bu, and O(2)S(micro-N(t)Bu)(2)SeN(t)Bu, respectively. Cycloaddition is unlikely when one of the reactants is a sulfur(IV) diimide.     

Overcharging of polyelectrolyte complexes by the guest polyelectrolyte studied by fluorescence spectroscopy

Polyion complexes (PICs) of anionic block copolymer poly(ethylene oxide)-block-poly(sodium methacrylate), PEO-block-(PMA)Na, and a cationic homopolymer, poly((methacryloyloxyethyl)trimethylammonium chloride), PMOTAC, have been studied by fluorescence spectroscopy. Pyrene and naphthalene singly labeled block copolymers were used with two different sodium methacrylate block lengths. The chain exchange between the stoichiometric PICs at the equilibrium state and the formation of the negatively charged PICs on addition of excess PEO-block-(PMA)Na to stoichiometric PIC solution were of interest. The chain exchange between the stoichiometric complexes was observed to occur via two mechanisms. The faster chain exchange occurs via insertion and expulsion of single chains, while merging and splitting of the PIC particles is behind the slower chain exchange event. Incorporation of an excess amount of the guest polyion into a stoichiometric PIC took place on further addition of the PEO-block-(PMA)Na. The same mechanisms were recognized in the overcharging process of the PICs as in the chain exchange between the stoichiometric PICs.     

Well-posedness for the continuity equation for vector fields with suitable modulus of continuity

We prove well-posedness of linear scalar conservation laws using only assumptions on the growth and the modulus of continuity of the velocity field, but not on its divergence. As an application, we obtain uniqueness of solutions in the atomic Hardy space, $H^1$, for the scalar conservation law induced by a class of vector fields whose divergence is an unbounded BMO function.     

Nickel as a Lewis Base in a T‐Shaped Nickel(0) Germylene Complex Incorporating a Flexible Bis(NHC) Ligand

Flexible, chelating bis(NHC) ligand 2 , able to accommodate both cis‐ and trans‐coordination modes, was used to synthesize ( 2 )Ni(η²‐cod), 3 . In reaction with GeCl₂, it produced ( 2 )NiGeCl₂, 4 , featuring a T‐shaped Ni⁰ and a pyramidal Ge center. Complex 4 could also be prepared from [( 2 )GeCl]Cl, 5 , and Ni(cod)₂, in a reaction that formally involved Ni–Ge transmetalation, followed by coordination of the extruded GeCl₂ moiety to Ni. A computational analysis showed that 4 possesses considerable multiconfigurational character and the Ni→Ge bond is formed through σ‐donation from the Ni 4s, 4p, and 3d orbitals to Ge. (NHC)₂Ni(cod) complexes 9 and 10 , as well as (NHC)₂GeCl₂ derivative 11 , incorporating ligands that cannot accommodate a wide bite angle, failed to produce isolable Ni–Ge complexes. The isolation of ( 2 )Ni(η²‐Py), 12 , provides further evidence for the reluctance of the ( 2 )Ni⁰ fragment to act as a σ‐Lewis acid.     

UV‐Vis Spectroscopy Reveals a Correlation Between Y263 and BV Protonation States in Bacteriophytochromes

Red‐light photosensory proteins, phytochromes, link light activation to biological functions by interconverting between two conformational states. For this, they undergo large‐scale secondary and tertiary changes which follow small‐scale Z to E bond photoisomerization of the covalently bound bilin chromophore. The complex network of amino acid interactions in the chromophore‐binding pocket plays a central role in this process. Highly conserved Y263 and H290 have been found to be important for the photoconversion yield, while H260 has been identified as important for bilin protonation and proton transfer steps. Here, we focus on the roles these amino acids are playing in preserving the chemical properties of bilin in the resting Pr state of the photosensory unit of a bacteriophytochrome from Deinococcus radiodurans. By using pH‐dependent UV‐Vis spectroscopy and spectral decomposition modeling, we confirm the importance of H260 for biliverdin protonation. Further, we demonstrate that in the canonical bacteriophytochromes, the pK_a value of the phenol group of the Y263 is uncommonly low. This directly influences the protonation of the bilin molecule and likely the functional properties of the protein. Our study expands the understanding of the tight interplay between the nearby amino acids and bilin in the phytochrome family.     

Parallel implementation of data assimilation

Kalman filter is a sequential estimation scheme that combines predicted and observed data to reduce the uncertainty of the next prediction. Because of its sequential nature, the algorithm cannot be efficiently implemented on modern parallel compute hardware nor can it be practically implemented on large‐scale dynamical systems because of memory issues. In this paper, we attempt to address pitfalls of the earlier low‐memory approach described in and extend it for parallel implementation. First, we describe a low‐memory method that enables one to pack covariance matrix data employed by the Kalman filter into a low‐memory form by means of certain quasi‐Newton approximation. Second, we derive parallel formulation of the filtering task, which allows to compute several filter iterations independently. Furthermore, this leads to an improvement of estimation quality as the method takes into account the cross‐correlations between consequent system states. We experimentally demonstrate this improvement by comparing the suggested algorithm with the other data assimilation methods that can benefit from parallel implementation. Copyright © 2016 John Wiley & Sons, Ltd.