Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality

The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.     

Artificial Water Channels: Towards Biomimetic Membranes for Desalination

Natural Aquaporin (AQP) channels are efficient water translocating proteins, rejecting ions. Inspired by this masterpiece of nature, Artificial Water Channels (AWCs) with controlled functional structures, can be potentially used to mimic the AQPs to a certain extent, offering flexible avenues toward biomimetic membranes for water purification. The objective of this paper is to trace the historical development and significant advancements of current reported AWCs. Meanwhile, we attempt to reveal important structural insights and supramolecular self-assembly principles governing the selective water transport mechanisms, toward innovative AWC-based biomimetic membranes for desalination.     

An Aggregating Amphiphilic Squaraine: A Light-up Probe That Discriminates Parallel G-Quadruplexes

G-quadruplexes (G4s) are peculiar DNA or RNA tertiary structures that are involved in the regulation of many biological events within mammalian cells, bacteria, and viruses. Although their role as versatile therapeutic targets has been emphasized for 35 years, G4 selectivity over ubiquitous double-stranded DNA/RNA, as well as G4 differentiation by small molecules, still remains challenging. Here, a new amphiphilic dicyanovinyl-substituted squaraine, SQgl , is reported to act as an NIR fluorescent light-up probe discriminating an extensive panel of parallel G4s while it is non-fluorescent in the aggregated state. The squaraine can form an unconventional sandwich π-complex binding two quadruplexes, which leads to a strongly fluorescent (Φ_F=0.61) supramolecular architecture. SQgl is highly selective against non-quadruplex and non-parallel G4 sequences without altering their topology, as desired for applications in selective in vivo high-resolution imaging and theranostics.     

Resolvent metric and the heat kernel estimate for random walks

In this paper we introduce the resolvent metric, the generalization of the resistance metric used for strongly recurrent walks. By using the properties of the resolvent metric we show heat kernel estimates for recurrent and transient random walks.     

Degrees of freedom effect on fragmentation in tandem mass spectrometry of singly charged supramolecular aggregates of sodium sulfonates

The characteristic collision energy (CCE) to obtain 50% fragmentation of positively and negatively single charged noncovalent clusters has been measured. CCE was found to increase linearly with the degrees of freedom (DoF) of the precursor ion, analogously to that observed for synthetic polymers. This suggests that fragmentation behavior (e.g. energy randomization) in covalent molecules and clusters are similar. Analysis of the slope of CCE with molecular size (DoF) indicates that activation energy of fragmentation of these clusters (loss of a monomer unit) is similar to that of the lowest energy fragmentation of protonated leucine–enkephalin. Positively and negatively charged aggregates behave similarly, but the slope of the CCE versus DoF plot is steeper for positive ions, suggesting that these are more stable than their negative counterparts. Copyright © 2013 John Wiley & Sons, Ltd.     

Simultaneous separation of different enantiomeric pairs in capillary electrophoresis by mixing different hemispherodextrins,a very versatile class of receptors

Six different racemates of the profen family were used as analytes in order to test the chiral selector properties of three members of a new class of cyclodextrin derivatives, hemispherodextrins (HMs), in capillary electrophoresis. In addition to experiments carried out to separate each enantiomeric pair one by one, other experiments were carried out on samples containing all six enantiomeric pairs. Electropherograms were obtained either by adding a single HM to the background electrolyte (BGE), or a binary mixture of HMs. The results obtained confirm the excellent chiral selector properties of the HMs, and furthermore show that these compounds can also be used for achiral selection. When mixing different HMs, a complementary effect in chiral selectivity is observed, which, in our opinion, deserves further study.     

The first kinetic evidence for acid catalysis in a monocyclic rearrangement of heterocycles: conversion of the Z-phenylhydrazone of 5-amino-3-benzoyl-1,2,4-oxadiazole into N,5-diphenyl-2H-1,2,3-triazol-4-ylurea

The title reaction has been studied in dioxane/water in a large (0.1-14.9) pS+ range, evidencing, together with an uncatalyzed process at intermediate (3.5-8.0) pS+ values, the occurrence of a catalyzed pathway both in the acidic (pS+ 0.1-3.5) and in the basic region (pS+ 8.0-14.9): specific-acid catalysis and general-base catalysis, respectively, have been found to take place by means of kinetic investigations at different buffer concentrations. Mechanisms for the three pathways have been advanced on the grounds of structural features. In a comparison with previous data particular attention has been paid to the acid-catalyzed pathway, herein observed for the first time in an azole-to-azole interconversion. The mechanistic hypotheses seem well supported by ab initio calculations.