Jiri Mareda

Bio: Jiri Mareda is an academic researcher from University of Geneva. The author has contributed to research in topics: Steric effects & Synthetic ion channels. The author has an hindex of 37, co-authored 111 publications receiving 5667 citations. Previous affiliations of Jiri Mareda include Spanish National Research Council & University of Pittsburgh.

Experimental evidence for the functional relevance of anion– π interactions

Abstract: Attractive in theory and confirmed to exist, anion–π interactions have never really been seen at work. To catch them in action, we prepared a collection of monomeric, cyclic and rod-shaped naphthalenediimide transporters. Their ability to exert anion–π interactions was demonstrated by electrospray tandem mass spectrometry in combination with theoretical calculations. To relate this structural evidence to transport activity in bilayer membranes, affinity and selectivity sequences were recorded. π-acidification and active-site decrowding increased binding, transport and chloride > bromide > iodide selectivity, and supramolecular organization inverted acetate > nitrate to nitrate > acetate selectivity. We conclude that anion–π interactions on monomeric surfaces are ideal for chloride recognition, whereas their supramolecular enhancement by π,π-interactions appears perfect to target nitrate. Chloride transporters are relevant to treat channelopathies, and nitrate sensors to monitor cellular signaling and cardiovascular diseases. A big impact on organocatalysis can be expected from the stabilization of anionic transition states on chiral π-acidic surfaces.

Photoproduction of Proton Gradients with π-Stacked Fluorophore Scaffolds in Lipid Bilayers

Abstract: Rigid p-octiphenyl rods were used to create helical tetrameric pi-stacks of blue, red-fluorescent naphthalene diimides that can span lipid bilayer membranes. In lipid vesicles containing quinone as electron acceptors and surrounded by ethylenediaminetetraacetic acid as hole acceptors, transmembrane proton gradients arose through quinone reduction upon excitation with visible light. Quantitative ultrafast and relatively long-lived charge separation was confirmed as the origin of photosynthetic activity by femtosecond fluorescence and transient absorption spectroscopy. Supramolecular self-organization was essential in that photoactivity was lost upon rod shortening (from p-octiphenyl to biphenyl) and chromophore expansion (from naphthalene diimide to perylene diimide). Ligand intercalation transformed the photoactive scaffolds into ion channels.

Rigid oligonaphthalenediimide rods as transmembrane anion-π slides

Abstract: We report the design, synthesis, and evaluation of rigid oligonaphthalenediimide (O-NDI) rods that are expected to act as transmembrane anion-pi slides. Studies in fluorogenic large unilamellar egg yolk phosphatidylcholine vesicles reveal that rigid O-NDI rods mediate anion-selective transport with a rare halide VI selectivity sequence (Cl- > F- > Br- > I-). This and decreasing activity, selectivity, and halide sequence with increasing positive charge of the rod termini support the occurrence of anion-pi interactions. A strong anomalous mole fraction effect in Cl-/I- mixtures is in agreement with the existence of multiple active sites along the anion-pi slide and multi-anion hopping as a mechanism of transport. The strong inverted NDI quadruple moment found by DFT calculations is in excellent agreement with these results.

Synthetic Ion Transporters that Work with Anion−π Interactions, Halogen Bonds, and Anion–Macrodipole Interactions

Abstract: The transport of ions and molecules across lipid bilayer membranes connects cells and cellular compartments with their environment. This biological process is central to a host of functions including signal transduction in neurons and the olfactory and gustatory sensing systems, the translocation of biosynthetic intermediates and products, and the uptake of nutrients, drugs, and probes. Biological transport systems are highly regulated and selectively respond to a broad range of physical and chemical stimulation. A large percentage of today’s drugs and many antimicrobial or antifungal agents take advantage of these systems. Other biological transport systems are highly toxic, such as the anthrax toxin or melittin from bee venom.For more than three decades, organic and supramolecular chemists have been interested in developing new transport systems. Over time, curiosity about the basic design has evolved toward developing of responsive systems with applications in materials sciences and medicine. Our early...

Functional Supramolecular Polymers

Abstract: Supramolecular polymers can be random and entangled coils with the mechanical properties of plastics and elastomers, but with great capacity for processability, recycling, and self-healing due to their reversible monomer-to-polymer transitions. At the other extreme, supramolecular polymers can be formed by self-assembly among designed subunits to yield shape-persistent and highly ordered filaments. The use of strong and directional interactions among molecular subunits can achieve not only rich dynamic behavior but also high degrees of internal order that are not known in ordinary polymers. They can resemble, for example, the ordered and dynamic one-dimensional supramolecular assemblies of the cell cytoskeleton and possess useful biological and electronic functions.

The Halogen Bond

Abstract: The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

Synthetic molecular motors and mechanical machines.

Abstract: The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg