From simple surface models to lipid membranes: Universal aspects of the hydration interaction from solvent-explicit simulations

A review of atomistic simulation approaches including explicit water for the study of hydration forces between polar surfaces is presented. In particular, we discuss different methods for keeping the chemical potential of water constant and compare advantages and limitations of each method. It turns out that modifications of hydration forces due to surface softness can be accounted for by a convolution over the surface shape profile. Universal aspects of the hydration interaction observed in simulations of different surface chemistries are highlighted, while special attention is given to hydration forces between self-assembled phospholipid membranes.     

First order melting transitions of highly ordered dipalmitoyl phosphatidylcholine gel phase membranes in molecular dynamics simulations with atomistic detail

Molecular dynamics simulations with atomistic detail of the gel phase and melting transitions of dipalmitoyl phosphatidylcholine bilayers in water reveal the dependency of many thermodynamic and structural parameters on the initial system ordering. We quantitatively compare different methods to create a gel phase system and we observe that a very high ordering of the gel phase starting system is necessary to observe behavior which reproduces experimental data. We performed heating scans with speeds down to 0.5 K/ns and could observe sharp first order phase transitions. Also, we investigated the transition enthalpy as the natural intrinsic parameter of first order phase transitions, and obtained a quantitative match with experimental values. Furthermore, we performed systematic investigations of the statistical distribution and heating rate dependency of the microscopic phase transition temperature.     

Mechanistic studies of ethylene hydrophenylation catalyzed by bipyridyl Pt(II) complexes

Cationic platinum(II) complexes [((t)bpy)Pt(Ph)(L)](+) [(t)bpy =4,4'-di-tert-butyl-2,2'-bipyridyl; L = THF, NC(5)F(5), or NCMe] catalyze the hydrophenylation of ethylene to generate ethylbenzene and isomers of diethylbenzene. Using ethylene as the limiting reagent, an 89% yield of alkyl arene products is achieved after 4 h at 120 °C. Catalyst efficiency for ethylene hydrophenylation is diminished only slightly under aerobic conditions. Mechanistic studies support a reaction pathway that involves ethylene coordination to Pt(II), insertion of ethylene into the Pt-phenyl bond, and subsequent metal-mediated benzene C-H activation. Studies of stoichiometric benzene (C(6)H(6) or C(6)D(6)) C-H/C-D activation by [((t)bpy)Pt(Ph-d(n))(THF)](+) (n = 0 or 5) indicate a k(H)/k(D) = 1.4(1), while comparative rates of ethylene hydrophenylation using C(6)H(6) and C(6)D(6) reveal k(H)/k(D) = 1.8(4) for the overall catalytic reaction. DFT calculations suggest that the transition state for benzene C-H activation is the highest energy species along the catalytic cycle. In CD(2)Cl(2), [((t)bpy)Pt(Ph)(THF)][BAr'(4)] [Ar' = 3,5-bis(trifluoromethyl)phenyl] reacts with ethylene to generate [((t)bpy)Pt(CH(2)CH(2)Ph)(η(2)-C(2)H(4))][BAr'(4)] with k(obs) = 1.05(4) × 10(-3) s(-1) (23 °C, [C(2)H(4)] = 0.10(1) M). In the catalytic hydrophenylation of ethylene, substantial amounts of diethylbenzenes are produced, and experimental studies suggest that the selectivity for the monoalkylated arene is diminished due to a second aromatic C-H activation competing with ethylbenzene dissociation.     

Experimental and theoretical study of the complexation of the thallium cation with a hexaarylbenzene-based receptor

Abstract  

From extraction experiments in the two-phase water/nitrobenzene system and γ-activity measurements, the stability constant of a hexaarylbenzene-based receptor. Tl⁺ complex species dissolved in nitrobenzene saturated with water was determined. By using the quantum-mechanical density functional level of theory calculations, the most probable structure of this complex was derived.     

Effect of carbonate incorporation on the structural and superconducting properties of the double chain compound Y2Ba4Cu7O15−x

Structural investigations on powder samples of Y₂Ba₄Cu₇O_15–x with different carbonate content have been performed. Powder x-ray Rietveld refinements showed the remarkable influence of carbonate incorporation on the lattice parameters. Most important is the decrease of T_c with increasing carbonate content. We assign these effects to an incorporation of the carbonate ion into the crystal lattice, copper vacancies at the Cu(1) position and a possible misorientation of the copper oxygen single chains. No change of the structure (e. g. superstructure) could be found.     

Characterization of a putative Xylella fastidiosa diffusible signal factor by HRGC-EI-MS

Xylella fastidiosa (X.f.) is a plant pathogen with high levels of genomic similarity to Xanthomonas campestris pv. campestris (X.c.c.). It has been shown that X. fastidiosa synthesizes a putative diffusible signal factor (X.f.-DSF) that activates regulation of pathogenicity factor (rpf) genes in a X.c.c. reporter system, which might be involved in the regulation of pathogenesis associated genes as in X.c.c., as well as in quorum-sensing. The nature of the X.f.-DSF is not known, whereas the X.c.c.-DSF has been identified as cis-11-methyl-2-dodecenoic acid. In this work, the chemical nature of a putative X.f.-DSF molecule, able to restore endoglucanase activity in a X.c.c. rpfF mutant, was investigated as if it was a fatty acid derivative. Bioassays with X.c.c. reporter bacterium and X.f. culture extracts, based on endoglucanase restoration activity, were also carried out in order to confirm the DSFs molecules similarities. For this reason, a gas chromatography-mass spectrometry method was developed with standard fatty acids methyl esters mixtures. The retention time, as well as the fragmentation patterns, of each standard was used to identify the DSF molecule synthesized by X.f. in the culture medium. Typical ester fragmentation patterns (the derivatized analyte) were observed, such as: McLafferty rearrangement and migration of the Hdelta followed by 1,4-hydrogen shift and cleavage of the bond Cbeta-Cgamma, confirming the nature of this molecule. This confirmation was corroborated by the common peaks in both spectra. Besides, the observed retention time reinforces our conclusion since it corresponds to a methyl ester with 15 carbons. Since the X.f.-DSF molecule was tentatively identified as 12-methyl-tetradecanoic acid (by mass spectra library comparison), this standard compound was also analyzed, strongly suggesting that this is the identification of such a molecule. To our knowledge, this is the first time a DSF produced by X.f. has been characterized.     

Electrical Conductance Studies in Aqueous Solutions of Glutaric Acid,Disodium Glutarate and Sodium Hydrogen Glutarate

Conductivity measurements of glutaric acid and disodium glutarate in dilute aqueous solutions were performed in the 288.15 to 323.15 K temperature range. The limiting equivalent conductances of glutarate anions, λ ^o(HGlut⁻,T) and λ ^o(1/2Glut²⁻,T), and the dissociation constants of glutaric acid, K ₁(T) and K ₂(T), were derived by the use of the Onsager and the Quint and Viallard conductivity equations. The applied molecular model was successfully confirmed by analyzing the conductivities of sodium hydrogen glutarate at 298.15 K.     

Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples

Proteomic platforms that enable researchers to profile a high number of proteins across large sets of complex samples hold a great potential for biomarker discovery. LC-MS/MS-based methods can be used to analyse many samples without the need for protein labelling. As the analysis is a sequential process, the performance of the system has to be consistent throughout the entire experiment. In this study we used a set of spiked serum samples as well as a set of 55 clinical serum samples from schizophrenia patients and healthy volunteers to show that the label-free proteomic approach yields reproducible results across a large number of samples and can be used to accurately measure the relative protein abundance. Using this approach, we identified 1709 serum proteins covering a dynamic range of over three orders of magnitude. We believe that label-free quantitative proteomics is especially suited for biomarker discovery in large sample sets.