Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions.

Coevolution at the gene level, as reflected by correlated events of gene loss or gain, can be revealed by phylogenetic profile analysis. The optimal method and metric for comparing phylogenetic profiles, especially in eukaryotic genomes, are not yet established. Here, we describe a procedure suitable for large-scale analysis, which can reveal coevolution based on the assessment of the statistical significance of correlated presence/absence transitions between gene pairs. This metric can identify coevolution in profiles with low overall similarities and is not affected by similarities lacking coevolutionary information. We applied the procedure to a large collection of 60,912 orthologous gene groups (orthogroups) in 1,264 eukaryotic genomes extracted from OrthoDB. We found significant cotransition scores for 7,825 orthogroups associated in 2,401 coevolving modules linking known and unknown genes in protein complexes and biological pathways. To demonstrate the ability of the method to predict hidden gene associations, we validated through experiments the involvement of vertebrate malate synthase-like genes in the conversion of (S)-ureidoglycolate into glyoxylate and urea, the last step of purine catabolism. This identification explains the presence of glyoxylate cycle genes in metazoa and suggests an anaplerotic role of purine degradation in early eukaryotes.

Thiolated Cyanines Appended to Partially Pegylated Gold Nanoparticles for Fluorescence Quenching of Two-Channel Photothermal Inks.

Following a new approach, we prepared a nanoink with two separate photothermally responsive absorption bands. One is the localized surface plasmon resonance (LSPR) absorption of gold nanoparticles (AuNP, d =17 nm), the second is the absorption band of two cyanine (Cy) dyes, Cy7-C6 or Cy7-C11, grafted to the AuNP surface through thiolated bridges of different lengths: the close proximity to the Au surface induces full quenching of the Cy fluorescence, resulting in thermal relaxation on irradiation. Attempts to full coat AuNP with the lipophilic Cy7-C6 and Cy7-C11 lead to precipitation from aqueous solutions. We thus prepared AuNP with partial pegylation (30, 50, or 70%), using a long chain thiol-terminated PEG bearing a -COOH function. Addition until saturation of either Cy7-C6 or Cy7-C11 to the partially pegylated AuNP gave the AuNP@Cy/PEGX% hybrids (X = 30, 50, 70) that are stable in water and in the water/alcohol mixtures used to prepare the nanoinks. Further overcoating of AuNP@Cy7-C6/PEG50% with PAH (polyallylamine hydrochloride) avoids LSPR hybridization in the dry nanoink printouts, that present two separate bands. When irradiated with laser sources near their absorption maxima, the printouts of the AuNP@Cy7-C6/PEG50%@PAH nanoink respond on two channels, giving different temperature increases depending on the irradiation wavelength.

Iridium-Catalyzed C-H Borylations: Regioselective Functionalizations of Calix[4]arene Macrocycles.

We report iridium-catalyzed C-H borylations for the regioselective synthesis of distally disubstituted calix[4]arene macrocycles. The atom- and step-economical method led to a broad family of calix[4]arenes in good yields and functional group tolerance. The synthetic utility of the C-H borylation protocol was finally illustrated with several late-stage modifications for the synthesis of elaborate calix[4]arenes frameworks, otherwise challenging to achieve with commonly employed procedures.

A Multiresponsive Calix[6]arene Pseudorotaxane Empowered by Fluorophoric Dansyl Groups.

We report the synthesis and characterization, by means of NMR and UV-visible spectroscopy and electrochemical techniques, of a dansyl calix[6]arene derivative and of its pseudorotaxane complex with a bipyridinium-based axle. This novel macrocycle shows remarkable complexation ability, in analogy with parent compounds, while the dansyl moieties impart valuable features to the system. Indeed, these units: i) signal the state of the system by fluorescence; ii) can be reversibly protonated, enabling the modulation of the complexation abilities of the macrocycle; iii) participate in photoinduced electron transfer processes, which may be exploited to tune the stability of the supramolecular complex. Therefore, in this multiresponsive pseudorotaxane, the threading and de-threading motions of the molecular components can be modulated either by protonation of the calixarene host or by reduction of the bipyridinium guest, which can be accomplished both by electrochemical reduction and via photoinduced electron transfer. Overall, three orthogonal and reversible stimuli can be used to induce molecular movements of the pseudorotaxane components.

Triazole-enabled, iron-catalysed linear/branched selective C-H alkylations with alkenes.

Iron-catalysed C-H alkylations with alkenes were achieved on benzamides by N-triazole assistance. A notable switch of the regioselectivity from linear to branched was observed depending on the nature of the olefin employed. The approach allowed for the synthesis of a family of decorated benzamides with ample scope and high levels of chemo-, regio- and site-selectivity.

Gold(I)-catalysed hydroarylations of alkynes for the synthesis of inherently chiral calix[4]arenes.

We describe the first gold(I)-catalysed intramolecular hydroarylation of alkynes for the straightforward synthesis of inherently chiral calix[4]arenes. This step- and atom-economical approach, which exploits a formal meta-functionalisation of the calix[4]arene macrocycle, is able to deliver an ample family of N-heterocyclic, chiral compounds in high yields and functional group tolerance.

Calix[6]arene-Based [3]Rotaxanes as Prototypes for the Template Synthesis of Molecular Capsules.

In this work, the ability of several bis-viologen axles to thread a series of heteroditopic tris(N-phenylureido)calix[6]arene wheels to give interwoven supramolecular complexes to the [3]pseudorotaxane type was studied. The unidirectionality of the threading process inside these nonsymmetric wheels allows the formation of highly preorganised [3]pseudorotaxane and [3]rotaxane species in which the macrocycles phenylureido moieties, functionalised with either ester, carboxylic, or hydroxymethyl groups, are facing each other. As verified by NMR and semiempirical computational studies, these latter compounds possess the correct spatial arrangement of their subcomponents, which could lead, in principle, upon proper bridging reaction, to the realisation of upper-to-upper molecular capsules that are based on calix[6]arene derivatives.

Autonomous Non-Equilibrium Self-Assembly and Molecular Movements Powered by Electrical Energy.

The ability to exploit energy autonomously is one of the hallmarks of life. Mastering such processes in artificial nanosystems can open technological opportunities. In the last decades, light- and chemically driven autonomous systems have been developed in relation to conformational motion and self-assembly, mostly in relation to molecular motors. In contrast, despite electrical energy being an attractive energy source to power nanosystems, its autonomous harnessing has received little attention. Herein we consider an operation mode that allows the autonomous exploitation of electrical energy by a self-assembling system. Threading and dethreading motions of a pseudorotaxane take place autonomously in solution, powered by the current flowing between the electrodes of a scanning electrochemical microscope. The underlying autonomous energy ratchet mechanism drives the self-assembly steps away from equilibrium with a higher energy efficiency compared to other autonomous systems. The strategy is general and might be extended to other redox-driven systems.

Diametric calix[6]arene gold(I) catalysts for intramolecular cyclopropanations of 1,6-dienynes.

We report a solid-state structural investigation of diametric calix[6]arene-based phosphine gold(I) cavitands which are characterised by two specific, different 1,2,3-alternate conformations in solution and in the solid state. The effect of the specific orientation of phosphines, with respect to macrocycles, was studied in intramolecular cyclopropanation of 1,6-dienynes. The general applicability of these catalysts was disclosed, delivering a family of polycycles with high yields and functional group tolerance.

Multi-Dimensional Quantum Capacitance of the Two-Site Hubbard Model: The Role of Tunable Interdot Tunneling.

Few-electron states confined in quantum-dot arrays are key objects in quantum computing. The discrimination between these states is essential for the readout of a (multi-)qubit state, and can be achieved through a measurement of the quantum capacitance within the gate-reflectometry approach. For a system controlled by several gates, the dependence of the measured capacitance on the direction of the oscillations in the voltage space is captured by the quantum capacitance matrix. Herein, we apply this tool to study a double quantum dot coupled to three gates, which enable the tuning of both the bias and the tunneling between the two dots. Analytical solutions for the two-electron case are derived within a Hubbard model, showing the overall dependence of the quantum capacitance matrix on the applied gate voltages. In particular, we investigate the role of the tunneling gate and reveal the possibility of exploiting interdot coherences in addition to charge displacements between the dots. Our results can be directly applied to double-dot experimental setups, and pave the way for further applications to larger arrays of quantum dots.

Diametric calix[6]arene-based phosphine gold(I) cavitands.

We report the synthesis and characterization, in low polarity solvents, of a novel class of diametric phosphine gold(I) cavitands characterized by a 1,2,3-alternate geometry. Preliminary catalytic studies were performed on a model cycloisomerization of 1,6-enynes as a function of the relative orientation of the bonded gold(I) nuclei with respect to the macrocyclic cavity.

Merging Molecular Recognition and Gold(I) Catalysis with Triphoscalix[6]arene Ligands.

We report the synthesis and characterization of novel triphosphine calix[6]arene ligands. These supramolecular wheels, with recognition features governed by the hydrogen-bonding domain, were employed to synthesize multitasking trinuclear gold(I) complexes as a new platform for the synthesis of interwoven (pseudo)rotaxane species. In parallel, the multivalent, metal-bonded upper rim displayed catalytic features promoting highly selective gold-catalyzed cycloisomerization reactions of 1,6-enynes.

Heteroditopic Calix[6]arene Based Intervowen and Interlocked Molecular Devices.

Since the dawn of supramolecular chemistry, calixarenes have been employed as platforms onto which functional groups and binding sites can be loaded in a regio- and stereocontrolled manner for the recognition of charged and neutral species. Despite their wider annulus, potentially suitable to bind larger guests, the larger members of the calixarene series have been relatively less employed, mainly because of the synthetic difficulties to control their conformational flexibility and their regioselective functionalization. In this account, we will present the achievements gained during the last two decades on the use of the calix[6]arene as a platform to build-up structures in which the macrocycle acts as a wheel for the synthesis of oriented (pseudo)rotaxanes. We also account on how these calix[6]arene hosts affect the reactivity or spectroscopic properties of their bound guests.

Calix[6]arene-based Brønsted acids for molecular recognition and catalysis.

We report the synthesis of a versatile trifluoromethylsulfonamide calix[6]arene derivative with Brønsted acid features which can influence both molecular recognition and catalytic application. Indeed, in low polarity media, the trifluoromethyl-containing supramolecular wheel is able to respond to the complexation with charged species as a function of its selective ion-pair recognition. In parallel, the enhanced acidity is the key to promote Michael additions of indoles to nitroalkenes under pseudo-physiological reaction conditions (H2O, 37 °C).

Tuning the Fluorescence Through Reorientation of the Axle in Calix[6]arene-Based Pseudorotaxanes.

This work describes a calix[6]arene-based wheel that binds, in non-polar media, a stilbazolium salt to yield a mixture of pseudorotaxane orientational isomers. The isomer's abundance ratio evolves with time and can be reversibly tuned by adjusting the temperature. The spectroscopic properties, and notably the emission spectrum, of the bound guest depend on its orientation inside the non-palindromic wheel, suggesting such a system as a switch with spectroscopic readout.

Trisulfonamide calix[6]arene-catalysed Michael addition to nitroalkenes.

We describe the application of a novel family of trisulfonamide (TSA) calix[6]arenes in general acid catalysis. Hydrogen-bonding interactions between acidic TSA and methanol boosted the reactivity of the Michael addition of indoles to nitroalkene derivatives. The transformation occurs at a low catalyst loading of 5 mol%, allowing for the synthesis of nitroalkanes with good yields and functional group tolerance.

Redox-Switchable Calix[6]arene-Based Isomeric Rotaxanes.

Operating molecular machines are based on switchable systems whose components can be set in motion in a controllable fashion. The presence of nonsymmetrical elements is a mandatory requirement to obtain and demonstrate the unidirectionality of motion. Calixarene-based macrocycles have proved to be very efficient hosts in the design of oriented rotaxanes and of pseudorotaxanes with strict control over the direction of complexation. A series of two-station rotaxanes based on bipyridinium-ammonium axles was synthesized and characterized. A recently reported supramolecularly assisted strategy for the synthesis of different orientational isomers was exploited, and the ammonium unit was identified as a proper secondary station for the calixarene. Displacement of the macrocycle was triggered by electrochemical reduction of the bipyridinium primary station, and it was shown that the shuttling is influenced both by the length of the chain of the axle component and by the position of the secondary station with respect to the calixarene rims.

Electrochemically Triggered Co-Conformational Switching in a [2]catenane Comprising a Non-Symmetric Calix[6]arene Wheel and a Two-Station Oriented Macrocycle.

Catenanes with desymmetrized ring components can undergo co-conformational rearrangements upon external stimulation and can form the basis for the development of molecular rotary motors. We describe the design, synthesis and properties of a [2]catenane consisting of a macrocycle-the 'track' ring-endowed with two distinct recognition sites (a bipyridinium and an ammonium) for a calix[6]arene-the 'shuttle' ring. By exploiting the ability of the calixarene to thread appropriate non-symmetric axles with directional selectivity, we assembled an oriented pseudorotaxane and converted it into the corresponding oriented catenane by intramolecular ring closing metathesis. Cyclic voltammetric experiments indicate that the calixarene wheel initially surrounds the bipyridinium site, moves away from it when it is reduced, and returns in the original position upon reoxidation. A comparison with appropriate model compounds shows that the presence of the ammonium station is necessary for the calixarene to leave the reduced bipyridinium site.

Efficient active-template synthesis of calix[6]arene-based oriented pseudorotaxanes and rotaxanes.

A substrate can modify its chemical features, including a change of its reactivity, as a consequence of non-covalent interactions upon inclusion within a molecular host. Since the rise of supramolecular chemistry, this phenomenon has stimulated the ingenuity of scientists to emulate the function of enzymes by designing supramolecular systems in which the energetics and selectivity of reactions can be manipulated through programmed host-guest interactions and/or steric confinement. In this paper we investigate how the engulfment of a positively charged pyridinium-based guest inside the π-rich cavity of a tris-(N-phenylureido)calix[6]arene host affects its reactivity towards a SN2 reaction. We found that the alkylation of complexed substrates leads to the formation of pseudorotaxanes and rotaxanes with faster kinetics and higher yields with respect to the standard procedures exploited so far. More importantly, the strategy described here expands the range of efficient synthetic routes for the formation of mechanically interlocked species with a strict control of the mutual orientation of their non-symmetric molecular components.

The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism.

The S enantiomer of allantoin is an intermediate of purine degradation in several organisms and the final product of uricolysis in nonhominoid mammals. Bioinformatics indicated that proteins of the Asp/Glu racemase superfamily could be responsible for the allantoin racemase (AllR) activity originally described in Pseudomonas species. In these proteins, a cysteine of the catalytic dyad is substituted with glycine, yet the recombinant enzyme displayed racemization activity with a similar efficiency (kcat/KM ≈ 5 × 104 M-1 s-1) for the R and S enantiomers of allantoin. The protein crystal structure identified a glutamate residue located three residues downstream (E78) that can functionally replace the missing cysteine; the catalytic role of E78 was confirmed by site-directed mutagenesis. Allantoin can undergo racemization through formation of a bicyclic intermediate (faster) or proton exchange at the chiral center (slower). By monitoring the two alternative mechanisms by 13C and 1H nuclear magnetic resonance, we found that the velocity of the faster reaction is unaffected by the enzyme, whereas the velocity of the slower reaction is increased by 7 orders of magnitude. Protein phylogenies trace the origin of the racemization mechanism in enzymes acting on glutamate, a substrate for which proton exchange is the only viable reaction mechanism. This mechanism was inherited by allantoin racemase through divergent evolution and conserved in spite of the substitution of catalytic residues.