A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge

As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies of 22 host–guest complexes employing a novel approach based on the BEDAM single-decoupling alchemical free energy protocol with parallel replica exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit solvation. Initial predictions were affected by the lack of treatment of ionic charge screening, which is very significant for these highly charged hosts, and resulted in poor relative ranking of negatively versus positively charged guests. Binding free energies obtained with Debye–Hückel treatment of salt effects were in good agreement with experimental measurements. Water displacement effects contributed favorably and very significantly to the observed binding affinities; without it, the modeling predictions would have grossly underestimated binding. The work validates the implicit/explicit solvation approach employed here and it shows that comprehensive physical models can be effective at predicting binding affinities of molecular complexes requiring accurate treatment of conformational dynamics and hydration.     

Structure and cytotoxicity of phidianidines A and B: first finding of 1,2,4-oxadiazole system in a marine natural product

Two indole alkaloids, phidianidines A (1) and B (2), exhibiting an uncommon 1,2,4-oxadiazole ring linked to the indole system, have been isolated from the marine opisthobranch mollusk Phidiana militaris. The structures of the two metabolites have been elucidated by spectroscopic techniques. Phidianidines exhibit high cytotoxicity against tumor and nontumor mammalian cell lines in in vitro assays.     

Steady-state photoinduced absorption of CdSe/CdS octapod shaped nanocrystals

Colloidal branched nanocrystals have been attracting increasing attention due to evidence of an interesting relationship between their complex shape and charge carrier dynamics. Herein, continuous wave photoinduced absorption (CW PIA) measurements of CdSe/CdS octapod-shaped nanocrystals are reported. CW PIA spectra show strong bleaching due to the one-dimensional (1D) CdS pod states (480 nm) and the zero-dimensional (0D) CdSe core states (690 nm). The agreement with previously reported ultrafast pump-probe experiments indicates that this strong bleaching signal may be assigned to state filling. Additional bleaching features at 520 and 560 nm are characterized by a longer lifetime and are thus ascribed to defect states, localized at the pod-core interface of the octapod, showing that some of the initially photogenerated carriers get quickly trapped into these long-lived defect states. However, we remark that a relevant part of electrons remain untrapped: this opens up the opportunity to exploit octapod shaped nanocrystals in photovoltaics applications, as electron acceptor materials, considering that several efficient hole extracting materials are already available for the realization of a composite bulk heterojunction.     

The effect of selective contact electrodes on the interfacial charge recombination kinetics and device efficiency of organic polymer solar cells

Organic polymer solar cells (OPSCs) have been prepared using TiO(x) metal oxides as selective electrodes for electron collection. The interfacial charge transfer reactions, under working conditions, that limit the energy conversion efficiency of these devices have been measured and compared to the standard OPSC geometry which collects the electrons through a low work function metal contact.     

Segments and Hilbert schemes of points

Using results obtained from a study of homogeneous ideals sharing the same initial ideal with respect to some term order, we prove the singularity of the point corresponding to a segment ideal with respect to a degreverse term order (as, for example, the degrevlex order) in the Hilbert scheme of points in Pⁿ. In this context, we look into the properties of several types of “segment” ideals that we define and compare. This study also leads us to focus on the connections between the shape of generators of Borel ideals and the related Hilbert polynomial, thus providing an algorithm for computing all saturated Borel ideals with a given Hilbert polynomial.     

Numerical detection of instability regions for delay models with delay-dependent parameters

In this paper we are interested in gaining local stability insights about the interior equilibria of delay models arising in biomathematics. The models share the property that the corresponding characteristic equations involve delay-dependent coefficients. The presence of such dependence requires the use of suitable criteria which usually makes the analytical work harder so that numerical techniques must be used. Most existing methods for studying stability switching of equilibria fail when applied to such a class of delay models. To this aim, an efficient criterion for stability switches was recently introduced in [E. Beretta, Y. Kuang, Geometric stability switch criteria in delay differential systems with delay dependent parameters, SIAM J. Math. Anal. 33 (2002) 1144–1165] and extended [E. Beretta, Y. Tang, Extension of a geometric stability switch criterion, Funkcial Ekvac 46(3) (2003) 337–361]. We describe how to numerically detect the instability regions of positive equilibria by using such a criterion, considering both discrete and distributed delay models.     

Set-theoretic complete intersections in characteristic

We describe a class of toric varieties which are set-theoretic complete intersections only over fields of one positive characteristic .