Charged molecular films on brownian particles: structure, interactions, and relation to stability

The interfacial film of physically adsorbed ionic amphiphilic molecules on submicron particles dispersed in water was studied by a combination of surface tension measurements, laser light scattering (LLS) and high-shear experiments in a microchannel. General features in the structure and morphology of the molecular film are identified and understood in the framework of the two-step Langmuir adsorption model deduced from the adsorption isotherm. On the basis of this approach, the phase transitions and structural ordering of the film at the solid-liquid interface are analyzed in detail. A novel methodology based on high-shear aggregation experiments subsequently analyzed by means of LLS is proposed and turns out to be able to provide significant information on the phase transitions and structural arrangements of the adsorbed molecules (in substantial agreement with the adsorption isotherm model) as well as on the resulting interactions. Particularly important for applications is the result that, with no added salt, the films on two particles can adhere/fuse, leading to aggregation as long as an uncovered (hydrophobic) patch is present (unsaturated molecular layers). In the opposite case of fully developed layers, by analyzing the mechanism of shear aggregation of charged particles in the low-salt limit, we show that, when the hydrophobic attraction is absent, short-range hydration repulsive forces dominate over Derjaguin-Landau-Verwey-Overbeek (DLVO) forces and adhesion can never be achieved even upon application of very high collision energies. Consistently, a lower limiting boundary for the hydration interaction is calculated and found to be in agreement with data in the literature.     

G-Quadruplex Recognition by DARPIns through Epitope/Paratope Analogy**

We investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4 s specific sensors. To this end we carried out all-atom molecular dynamic simulations to unravel the interactions between specific nucleic acids, including human-telomeric (h-telo), Bcl-2, and c-Myc, with different peptides, forming a DARPin/G4 complex. By comparing the sequences of DARPin with that of a peptide known for its high affinity for c-Myc, we show that the recognition cannot be ascribed to sequence similarity but, instead, depends on the complementarity between the three-dimensional arrangement of the molecular fragments involved: the α-helix/loops domain of DARPin and the G4 backbone. Our results reveal that DARPins tertiary structure presents a charged hollow region in which G4 can be hosted, thus the more complementary the structural shapes, the more stable the interaction.     

Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.     

Driving Organic Nanocrystals Dissolution Through Electrochemistry

We have recently discussed how organic nanocrystal dissolution appears in different morphologies and the role of the solution pH in the crystal detriment process. We also highlighted the role of the local molecular chemistry in porphyrin nanocrystals having comparable structures: in water-based acid solutions, protonation of free-base porphyrin molecules is the driving force for crystal dissolution, whereas metal (Zn^II) porphyrin nanocrystals remain unperturbed. However, all porphyrin types, having an electron rich π-structure, can be electrochemically oxidized. In this scenario, a key question is: does electrochemistry represent a viable strategy to drive the dissolution of both free-base and metal porphyrin nanocrystals? In this work, by exploiting electrochemical atomic force microscopy (EC-AFM), we monitor in situ and in real time the dissolution of both free-base and metal porphyrin nanocrystals, as soon as molecules reach the oxidation potential, showing different regimes according to the applied EC potential.     

Forever Young: Structural Stability of Telomeric Guanine Quadruplexes in the Presence of Oxidative DNA Lesions**

Human telomeric DNA, in G-quadruplex (G4) conformation, is characterized by a remarkable structural stability that confers it the capacity to resist to oxidative stress producing one or even clustered 8-oxoguanine (8oxoG) lesions. We present a combined experimental/computational investigation, by using circular dichroism in aqueous solutions, cellular immunofluorescence assays and molecular dynamics simulations, that identifies the crucial role of the stability of G4s to oxidative lesions, related also to their biological role as inhibitors of telomerase, an enzyme overexpressed in most cancers associated to oxidative stress.     

Synthesis and Spectroscopic Characterization of Thienopyrazine-Based Fluorophores for Application in Luminescent Solar Concentrators (LSCs)

Organic fluorophores have found broad application as emitters in luminescent solar concentrators (LSCs) for silicon photovoltaics. In particular, the preparation of organic conjugated systems with intense light-harvesting ability, emissions in the deep-red and NIR regions, and large Stokes shift values represent a very challenging undertaking. Here, we report a simple and easy way to prepare three symmetrical donor–acceptor–donor (DAD) organic-emitting materials based on a thienopyrazine core. The central core in the three dyes was modified with the introduction of aromatic substituents, aiming to affect their optical properties. The fluorophores were characterized by spectroscopic studies. In all cases, visible-NIR emissions with large Stokes shifts were found, highlighting these molecules as promising materials for the application in LSCs.     

First total synthesis of A(2) isoprostane

A stereoselective Julia-Lythgoe olefination has allowed the first total synthesis of A(2) isoprostane (1), a recently discovered member of the growing isoprostane family. This elusive compound opens up numerous new avenues for the molecular biology of cyclopentenone prostaglandins, which are endowed of intriguing biological effects such as antitumor, antiinflammatory, and antiviral activities.     

Direct meta-C−H Perfluoroalkenylation of Arenes Enabled by a Cleavable Pyrimidine-Based Template

The development of efficient and mild methods for the synthesis of organofluorine compounds is of foremost interest in various fields of chemistry. A direct pyrimidine-based selective meta-C−H perfluoroalkenylation of arenes involving several commercially available perfluoroolefins is described. The synthetic versatility of the protocol is demonstrated by an extensive substrate scope including different benzylsulfonyl, alkylarene and phenylacetic acid scaffolds. The generality of this methodology including the meta-C−H perfluoroalkenylation of Ibuprofen, the facile cleavage of the directing group and gram-scale reactions are presented.     

Bifunctional Ligand Enables Efficient Gold‐Catalyzed Hydroalkenylation of Propargylic Alcohol

Using the previously designed biphenyl‐2‐ylphosphine ligand, featuring a remote tertiary amino group, the first gold‐catalyzed intermolecular hydroalkenylation of alkynes has been developed. Synthetically valuable conjugated dienyl alcohols are formed in moderate to good yields. A range of alkenyltrifluoroborates are allowed as the alkenyl donor, and no erosion of alkene geometry and/or the propargylic configuration are detected. DFT calculations confirm the critical role of the remote basic group in the ligand as a general‐base catalyst for promoting this novel gold catalysis with good efficiency.     

Understanding the role of carbamate reactivity in fatty acid amide hydrolase inhibition by QM/MM mechanistic modelling

QM/MM modelling of FAAH inactivation by O-biphenyl-3-yl carbamates identifies the deprotonation of Ser241 as the key reaction step, explaining why FAAH is insensitive to the electron-donor effect of conjugated substituents; this may aid design of new inhibitors with improved selectivity and in vivo potency.