Institut de Science et d'Ingénierie Supramoléculaires

Part 1 From molecular to supramolecular chemistry: concepts and language of supramolecular chemistry. Part 2 Molecular recognition: recognition, information, complementarity molecular receptors - design principles spherical recognition - cryptates of metal cations tetrahedral recognition by macrotricyclic cryptands recognition of ammonium ions and related substrates binding and recognition of neutral moelcules. Part 3 Anion co-ordination chemistry and the recognition of anionic substrates. Part 4 Coreceptor molecules and multiple recognition: dinuclear and polynuclear metal ion cryptates linear recognition of molecular length by ditopic coreceptors heterotopic coreceptors - cyclophane receptors, amphiphilic receptors, large molecular cage multiple recognition in metalloreceptors supramolecular dynamics. Part 5 Supramolecular reactivity and catalysis: catalysis by reactive macrocyclic cation receptor molecules catalysis by reactive anion receptor molecules catalysis with cyclophane type receptors supramolecular metallo-catalysis cocatalysis - catalysis of synthetic reactions biomolecular and abiotic catalysis. Part 6 Transport processes and carrier design: carrier-mediated transport cation-transport processes - cation carriers anion transport processes - anion carriers coupled transport processes electron-coupled transpoort in a redox gradient proton-coupled transport in a pH gradient light-coupled transport processes transfer via transmembrane channels. Part 7 From supermolecules to polymolecular assemblies: heterogeneous molecular recognition - supramolecular solid materials from endoreceptors to exoreceptors - molecular recognition at surfaces molecular and supramolecular morphogenesis supramolecular heterogeneous catalysis. Part 8 Molecular and supramolecular devices: molecular recognition, information and signals - semiochemistry supramolecular photochemistry - molecular and supramolecular photonic devices light conversion and energy transfer devices photosensitive molecular receptors photoinduced electron transfer in photoactive devices photoinduced reactions in supramolecular species non-linear optical properties of supramolecular species supramolecular effects in photochemical hole burning molecular and supramolecular electronic devices supramolecular electrochemistry electron conducting devices - molecular wires polarized molecular wires - rectifying devices modified and switchable molecular wires molecular magnetic devices molecular and supramolecular ionic devices tubular mesophases. (Part contents).

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.

Recent advances in supramolecular coordination chemistry allow access to transition-metal complexes of grid-type architecture comprising two-dimensional arrays of metal ions connecting a set of organic ligands in a perpendicular arrangement to generate a multiple wiring network. General design principles for these structures involve the thermodynamically driven synthesis of complex discrete objects from numerous molecular components in a single overall operation. Such supramolecular metal ion arrays combine the properties of their constituent metal ions and ligands, showing unique optical, electrochemical, and magnetic behavior. These features present potential relevance for nanotechnology, particularly in the area of supramolecular devices for information storage and processing. Thus, a dense organization of addressable units is represented by an extended "grid-of-grids" arrangement, formed by interaction of grid-type arrays with solid surfaces.

Supramolecular chemistry has developed over the last forty years as chemistry beyond the molecule. Starting with the investigation of the basis of molecular recognition, it has explored the implementation of molecular information in the programming of chemical systems towards self-organisation processes, that may occur either on the basis of design or with selection of their components. Supramolecular entities are by nature constitutionally dynamic by virtue of the lability of non-covalent interactions. Importing such features into molecular chemistry, through the introduction of reversible bonds into molecules, leads to the emergence of a constitutional dynamic chemistry, covering both the molecular and supramolecular levels. It considers chemical objects and systems capable of responding to external solicitations by modification of their constitution through component exchange or reorganisation. It thus opens the way towards an adaptive and evolutive chemistry, a further step towards the chemistry of complex matter.

Light usually diffracts in all directions when it emerges from a subwavelength aperture, which puts a lower limit on the size of features that can be used in photonics. This limitation can be overcome by creating a periodic texture on the exit side of a single aperture in a metal film. The transmitted light emerges from the aperture as a beam with a small angular divergence (approximately +/-3 degrees ) whose directionality can be controlled. This finding is especially surprising, considering that the radiating region is mainly confined to an area with lateral dimensions comparable to the wavelength of the light. The device occupies no more than one cubic micrometer and, when combined with enhanced transmission, suggests that a wide range of photonic applications is possible.

We estimate the stiffness of single-walled carbon nanotubes by observing their freestanding room-temperature vibrations in a transmission electron microscope. The nanotube dimensions and vibration amplitude are measured from electron micrographs, and it is assumed that the vibration modes are driven stochastically and are those of a clamped cantilever. Micrographs of 27 nanotubes in the diameter range 1.0--1.5 nm were measured to yield an average Young's modulus of $〈Y〉=1.25 \mathrm{TPa}.$ This value is consistent with previous measurements for multiwalled nanotubes, and is higher than the currently accepted value of the in-plane modulus of graphite.

We present a fully three-dimensional theoretical study of the extraordinary transmission of light through subwavelength hole arrays in optically thick metal films. Good agreement is obtained with experimental data. An analytical minimal model is also developed, which conclusively shows that the enhancement of transmission is due to tunneling through surface plasmons formed on each metal-dielectric interface. Different regimes of tunneling (resonant through a "surface plasmon molecule," or sequential through two isolated surface plasmons) are found depending on the geometrical parameters defining the system.

Optically thick metal films perforated with a periodic array of subwavelength holes show exceptional transmission properties. The zero-order transmission spectra exhibit well-defined maxima and minima of which the positions are determined by the geometry of the hole array. We show that the minima are the collection of loci for Wood's anomaly, which occurs when a diffracted beam becomes tangent to the film, and that the maxima are the result of a resonant excitation of surface plasmons (SP's). SP's from both surfaces of the metal film are apparent in the dispersion diagram, independent of which side of the film is illuminated, indicating an anomalously strong coupling between the two sides. This leads to wavelength-selective transmission with efficiencies that are about 1000 times higher than that expected for subwavelength holes.

As the wind of time blows into the sails of space, the unfolding of the universe nurtures the evolution of matter under the pressure of information. From divided to condensed and on to organized, living, and thinking matter, the path is toward an increase in complexity through self-organization.

A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems.

The explosive growth in our knowledge of genomes, proteomes, and metabolomes is driving ever-increasing fundamental understanding of the biochemistry of life, enabling qualitatively new studies of complex biological systems and their evolution. This knowledge also drives modern biotechnologies, such as molecular engineering and synthetic biology, which have enormous potential to address urgent problems, including developing potent new drugs and providing environmentally friendly energy. Many of these studies, however, are ultimately limited by their need for even-higher-throughput measurements of biochemical reactions. We present a general ultrahigh-throughput screening platform using drop-based microfluidics that overcomes these limitations and revolutionizes both the scale and speed of screening. We use aqueous drops dispersed in oil as picoliter-volume reaction vessels and screen them at rates of thousands per second. To demonstrate its power, we apply the system to directed evolution, identifying new mutants of the enzyme horseradish peroxidase exhibiting catalytic rates more than 10 times faster than their parent, which is already a very efficient enzyme. We exploit the ultrahigh throughput to use an initial purifying selection that removes inactive mutants; we identify approximately 100 variants comparable in activity to the parent from an initial population of approximately 10(7). After a second generation of mutagenesis and high-stringency screening, we identify several significantly improved mutants, some approaching diffusion-limited efficiency. In total, we screen approximately 10(8) individual enzyme reactions in only 10 h, using < 150 microL of total reagent volume; compared to state-of-the-art robotic screening systems, we perform the entire assay with a 1,000-fold increase in speed and a 1-million-fold reduction in cost.

We describe a highly efficient microfluidic fluorescence-activated droplet sorter (FADS) combining many of the advantages of microtitre-plate screening and traditional fluorescence-activated cell sorting (FACS). Single cells are compartmentalized in emulsion droplets, which can be sorted using dielectrophoresis in a fluorescence-activated manner (as in FACS) at rates up to 2000 droplets s(-1). To validate the system, mixtures of E. coli cells, expressing either the reporter enzyme beta-galactosidase or an inactive variant, were compartmentalized with a fluorogenic substrate and sorted at rates of approximately 300 droplets s(-1). The false positive error rate of the sorter at this throughput was <1 in 10(4) droplets. Analysis of the sorted cells revealed that the primary limit to enrichment was the co-encapsulation of E. coli cells, not sorting errors: a theoretical model based on the Poisson distribution accurately predicted the observed enrichment values using the starting cell density (cells per droplet) and the ratio of active to inactive cells. When the cells were encapsulated at low density ( approximately 1 cell for every 50 droplets), sorting was very efficient and all of the recovered cells were the active strain. In addition, single active droplets were sorted and cells were successfully recovered.

The reversible connection between sets of basic components allows the generation of a large collection of compounds constituted by all possible combinations that are potentially available. It makes virtual combinatorial libraries of substances accessible through a dynamic approach to combinatorial chemistry. The thermodynamically-driven evolution of the system leads to the actual expression of the constituent(s) that present(s) the best binding to/molecular recognition with the target site (see diagram). The general concept of this methodology has wide applications in a variety of areas of science and technology.

To a large extent, the field of "molecular machines" started after several groups were able to prepare, reasonably easily, interlocking ring compounds (named catenanes for compounds consisting of interlocking rings and rotaxanes for rings threaded by molecular filaments or axes). Important families of molecular machines not belonging to the interlocking world were also designed, prepared, and studied but, for most of them, their elaboration was more recent than that of catenanes or rotaxanes. Since the creation of interlocking ring molecules is so important in relation to the molecular machinery area, we will start with this aspect of our work. The second part will naturally be devoted to the dynamic properties of such systems and to the compounds for which motions can be directed in a controlled manner from the outside, that is, molecular machines. We will restrict our discussion to a very limited number of examples which we consider as particularly representative of the field.

Many chemical methods have been developed to favor a particular product in transformations of compounds that have two or more reactive sites. We explored a different approach to site selectivity using vibrational strong coupling (VSC) between a reactant and the vacuum field of a microfluidic optical cavity. Specifically, we studied the reactivity of a compound bearing two possible silyl bond cleavage sites-Si-C and Si-O, respectively-as a function of VSC of three distinct vibrational modes in the dark. The results show that VSC can indeed tilt the reactivity landscape to favor one product over the other. Thermodynamic parameters reveal the presence of a large activation barrier and substantial changes to the activation entropy, confirming the modified chemical landscape under strong coupling.

Images of the assembly of surfactants and synthetic lipids on the surface of carbon nanotubes were obtained by transmission electron microscopy. Above the critical micellar concentration, sodium dodecyl sulfate (SDS) forms supramolecular structures made of rolled-up half-cylinders on the nanotube surface. Depending on the symmetry and the diameter of the carbon nanotube, we observed rings, helices, or double helices. Similar self-assemblies were also obtained with several synthetic single-chain lipids designed for the immobilization of histidine-tagged proteins. At the nanotube-water interface, permanent assemblies were produced from mixed micelles of SDS and different water-insoluble double-chain lipids after dialysis of the surfactant. Such arrangements could be further exploited for the development of new biosensors and bioelectronic nanomaterials.

We present results of the transmitted, reflected, and absorbed power associated with the enhanced transmittance of light through a silver film pierced by a periodic array of subwavelength holes. Comparing experimentally acquired dispersion curves under different polarization conditions shows that the transmission features of the array are consistent with p-polarized resonant modes of the structure. By exploring the regime in which no propagating diffracted orders are allowed, we further show that the transmittance maxima are associated with both reflectance minima and absorption maxima. These new results provide strong experimental evidence for transmission based on diffraction, assisted by the enhanced fields associated with surface plasmon polaritons.

We demonstrate that photochromic molecules enable switching from the weak- to ultrastrong-coupling regime reversibly, by using all-optical control. This switch is achieved by photochemically inducing conformational changes in the molecule. Remarkably, a Rabi splitting of 700 meV is measured at room temperature, corresponding to 32% of the molecular transition energy. A similar coupling strength is demonstrated in a plasmonic structure. Such systems present a unique combination of coupling strength and functional capacities.

We report on realization of channel plasmon-polariton (CPP) propagation along a subwavelength metal groove. Using imaging with a near-field microscope and end-fire coupling with a tapered fiber connected to a tunable laser at telecommunication wavelengths (1425--1620 nm), we demonstrate low-loss (propagation length $\ensuremath{\sim}100\text{ }\text{ }\ensuremath{\mu}\mathrm{m}$) and well-confined (mode width $\ensuremath{\cong}1.1\text{ }\text{ }\ensuremath{\mu}\mathrm{m}$) CPP guiding along a triangular $0.6\text{ }\text{ }\text{ }\ensuremath{\mu}\mathrm{m}$-wide and $1\text{ }\text{ }\ensuremath{\mu}\mathrm{m}$-deep groove in gold. We develop a simple model based on the effective-index method that accounts for the main features of CPP guiding and provides a clear physical picture of this phenomenon.

The simple reaction of a tris-bpy ligand strand with FeCl2 leads to the self-assembly of the unique cation 1, which consists of a torus formed by five ligands wrapped around five FeII ions in a double-helical fashion and closed around a central chloride ion. This structure, a fivefold circular helicate, is a helicate analogue of circular DNA.