A convective replica‐exchange method for sampling new energy basins

Replica‐exchange is a powerful simulation method for sampling the basins of a rugged energy landscape. The replica‐exchange method's sampling is efficient because it allows replicas to perform round trips in temperature space, thereby visiting both low and high temperatures in the same simulation. However, replicas have a diffusive walk in temperature space, and the round trip rate decreases significantly with the system size. These drawbacks make convergence of the simulation even more difficult than it already is when bigger systems are tackled. Here, we present a simple modification of the exchange method. In this method, one of the replicas steadily raises or lowers its temperature. We tested the convective replica‐exchange method on three systems of varying complexity: the alanine dipeptide in implicit solvent, the GB1 β‐hairpin in explicit solvent and the Aβ_25–35 homotrimer in a coarse grained representation. For the highly frustrated Aβ_25–35 homotrimer, the proposed “convective” replica‐exchange method is twice as fast as the standard method. It discovered 24 out of 27 free‐energy basins in less than 500 ns. It also prevented the formation of groups of replicas that usually form on either side of an exchange bottleneck, leading to a more efficient sampling of new energy basins than in the standard method. © 2012 Wiley Periodicals, Inc.     

Pierre Turq,an inspirational scientist in charge and at interfaces

Pierre Turq has made decisive contributions to the theory and to the multiscale simulation of charged systems, such as molten salts, electrolyte solutions and colloidal suspensions, in the bulk, at interfaces and under confinement. His research line focussed on dynamical properties and was characterised by constant efforts to connect his theoretical work to both experiments and practical applications. In this article, his colleagues and former students pay a tribute to his past and current research interests by illustrating some recent developments accomplished in his laboratory.     

Electronic properties of 2D and 3D hybrid organic/inorganic perovskites for optoelectronic and photovoltaic applications

We herein investigate theoretically both 2D and 3D Hybrid Organic/inorganic perovskite crystal structures based on density functional theory (DFT) calculations and symmetry analyses. Our findings reveal the universal features of the electronic band structure for the class of lead-halide hybrids (R-NH \(_{3})_{n}\hbox {PbX}_{m}\) , where \((\mathrm{{n}}, \mathrm{{m}})=(2,4)\) and (1,3) respectively for 2D and 3D structures. Among those, the large spin-orbit coupling acting on the conduction band is shown to play a major role on the band gap of these materials. Moreover, this approach can easily be generalized to related layered and 3D hybrids, thus providing a clear-sighted inside in their electronic and optical properties.     

Ultrafast laser processing of drug particles in water for pharmaceutical discovery

The laser fragmentation technique has been extensively used to produce inorganic nanoparticles, but its practice on organic materials, especially on drugs, is less common. Here, we briefly review the recent advances in laser micro-/nanonization of organic materials and the rationale of using laser fragmentation for drug discovery. We present our case studies of two drug models: fenofibrate and naproxen. Both drugs were fragmented in water with femtosecond (fs) laser and characterized in terms of particle size distribution and physicochemical properties. Effects of fs laser fragmentation were also compared with nanosecond (ns) laser fragmentation and with conventional media milling technique. Fs laser was more suitable to produce sub-micron size drug particles than ns laser, but degradation of drugs after nanonization was also more pronounced than micronization. Physicochemical transformations such as oxidation, hydration and amorphisation might occur during the laser–material interactions. Laser nanonization showed improved dissolution kinetics, similar to media milling. Unlike the conventional milling techniques, laser fragmentation enabled the treatment of minute amount (as small as several milligrams) of drugs with high efficiency, thus is a useful tool for particle size reduction during the early phases of drug discovery.     

DNA Photosensitization by an “Insider”: Photophysics and Triplet Energy Transfer of 5‐Methyl‐2‐pyrimidone Deoxyribonucleoside

The main chromophore of (6‐4) photoproducts, namely, 5‐methyl‐2‐pyrimidone (Pyo), is an artificial noncanonical nucleobase. This chromophore has recently been reported as a potential photosensitizer that induces triplet damage in thymine DNA. In this study, we investigate the spectroscopic properties of the Pyo unit embedded in DNA by means of explicit solvent molecular‐dynamics simulations coupled to time‐dependent DFT and quantum‐mechanics/molecular‐mechanics techniques. Triplet‐state transfer from the Pyo to the thymine unit was monitored in B‐DNA by probing the propensity of this photoactive pyrimidine analogue to induce a Dexter‐type triplet photosensitization and subsequent DNA damage.     

Plate coating: influence of concentrated surfactants on the film thickness

We present a large range of experimental data concerning the influence of surfactants on the well-known Landau-Levich-Derjaguin experiment where a liquid film is generated by pulling a plate out of a bath. The thickness h of the film was measured as a function of the pulling velocity V for different kinds of surfactants (C(12)E(6), which is a nonionic surfactant, and DeTAB and DTAB, which are ionic) and at various concentrations near and above the critical micellar concentration (cmc). We report the thickening factor α = h/h(LLD), where h(LLD) is the film thickness obtained without a surfactant effect, i.e., as for a pure fluid but with the same viscosity and surface tension as the surfactant solution, over a wide range of capillary numbers (Ca = ηV/γ, with η being the surfactant solution viscosity and γ its surface tension) and identify three regimes: (i) at small Ca α is large due to confinement and surface elasticity (or Marangoni) effects, (ii) for increasing Ca there is an intermediate regime where α decreases as Ca increases, and (iii) at larger (but still small) Ca α is slightly higher than unity due to surface viscosity effects. In the case of nonionic surfactants, the second regime begins at a fixed Ca, independent of the surfactant concentration, while for ionic surfactants the transition depends on the concentration, which we suggest is probably due to the existence of an electrostatic barrier to surface adsorption. Control of the physical chemistry at the interface allowed us to elucidate the nature of the three regimes in terms of surface rheological properties.     

Analytical and Preparative Chiral Separation of β-Carboline Derivatives, LDL Oxidation Inhibitors, Using HPLC and CE Methodologies: Determination of Enantiomeric Purity

In the present study, baseline separation of the enantiomers of 16 β-carboline derivatives was successfully achieved using both capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC) techniques in short run times (<15?min) and thus permit the determination of enantiomeric excess. In HPLC methodology, cellulose chiral stationary phase (Chiralcel OD-H) was used with a binary mobile phase constituted of n-hexane/ethanol 85/15 leading to a resolution factor of 12.6 in 15?min. Preparative HPLC allowed to obtain pure enantiomers of two compounds. In CE, chiral selectivity was developed with an in-capillary stacking strategy using anionic (highly sulfated-γ) cyclodextrins 5% (w/v) as chiral selectors and a 60?mM phosphate buffer (pH 2.5) resulting in a resolution of 10.26 in 14?min of analysis. The analytical characteristics of the two developed methods were studied in terms of repeatability, limits of detection and limits of quantification showing their suitability to be extended to all the other molecules.     

Improving the Selectivity of the Phosphoric Acid β-Elimination on a Biotinylated Phosphopeptide

This study aims at improving the MALDI-TOF detection of a phosphorylated peptide containing a cysteine residue by ??-elimination of H₃PO₄ hardly enriched by classical methods. The experimental conditions were optimized on this phosphopeptide (biot-pAdd) and its nonphosphorylated counterpart (biot-Add). The major side-reactions were H₂S elimination on the cysteine residues and H₂O elimination on the non phosphorylated serine residue of biot-Add. The former dilutes the MALDI-TOF signal for the desired species. The latter gives a product similar to what is obtained by H₃PO₄ elimination and should prompt to caution when working with a mixture between phosphorylated and non phosphorylated peptides. Modifications on the solvent, the reaction temperature and time, the nature, and concentration of the base were made. Major improvement of the selectivity of the reaction was observed in 30?% ACN, at room temperature for 4?h. However, these optimizations are specific to these sequences and should be performed anew for different peptides. The selectivity of the reaction towards H₃PO₄ elimination is improved, but the persistence of side-reactions renders a previous sample fractionation necessary. In these optimized conditions, the ionization enhancement is 3-fold and the detection limits for biot-pAdd are similar to biot-Add (100?fmol).     

Asymmetric addition of a nitrogen nucleophile to an enoate in the presence of a chiral phase‐transfer catalyst: A novel approach toward enantiomerically enriched protected β‐amino acids

A proof of concept for the asymmetric organocatalytic aza‐Michael addition reaction of nitrogen nucleophiles with simple and readily available alkyl enoates as acceptor molecules in the presence of a chiral phase‐transfer catalyst has been demonstrated. The desired enantiomerically enriched β‐amino acid derivatives were obtained in up to 86% yield and with enantioselectivities of up to 37% ee. © 2012 Wiley Periodicals, Inc. Heteroatom Chem 23:202–209, 2012; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.21004