Regime Switch in the Dual-Catalyzed Coupling of Alkyl Silicates with Aryl Bromides.

Metallaphotoredox catalyzed cross-coupling of an arylbromide (Ar-Br) with an alkyl bis(catecholato)silicate (R-Si⊖ ) has been analyzed in depth using a continuum of analytical techniques (EPR, fluorine NMR, electrochemistry, photophysics) and modeling (micro-kinetics and DFT calculations). These studies converged on the impact of four control parameters consisting in the initial concentrations of the iridium photocatalyst ([Ir]0 ), nickel precatalyst ([Ni]0 ) and silicate ([R-Si⊖ ]0 ) as well as light intensity I0 for an efficient reaction between Ar-Br and R-Si⊖ . More precisely, two regimes were found to be possibly at play. The first one relies on an equimolar consumption of Ar-Br with R-Si⊖ smoothly leading to Ar-R, with no side-product from R-Si⊖ and a second one in which R-Si⊖ is simultaneously coupled to Ar-Br and degraded to R-H. This integrative approach could serve as a case study for the investigation of other metallaphotoredox catalysis manifolds of synthetic significance.

Encapsulation of phenolic acids into cyclodextrins: A global statistical analysis of the effects of pH, temperature and concentrations on binding constants measured by ACE methods.

Affinity capillary electrophoresis was used for the simultaneous measurement of the pKa values and of the binding constants relative to the encapsulation of naturally occurring phenolic acids (rosmarinic and caffeic acids) with cyclodextrins. A thorough study as a function of pH and temperature was coupled to a detailed statistical analysis of the resulting experimental data. A step-by-step curve fitting process was sufficient for obtaining individual binding constant for each experimental condition, but the influence of temperature remained unclear. A quantitative and qualitative gain was then obtained by supplementing this initial analysis with global multiparameter optimization. This leads to the estimation of both entropy and enthalpy of reaction and to the full description of the binding reactions as a function of pH and temperature. The encapsulation was shown to be very sensitive to pH and temperature, with optimal complexation occurring at low pH and low temperature, gaining up to a factor of 3 by cooling from 36 to 15°C, and up to a factor of 10 by lowering the pH from 7 to 2.

A chemically encoded timer for dual molecular delivery at tailored ranges and concentrations.

Spatiotemporal control of molecular distribution is much in demand in many fields of chemistry. To address this goal, we exploit a low molecular weight branched self-immolative architecture, which acts as a triggerable chemically encoded timer for autonomous sequential release of two chemicals. Using a light-activated model liberating two distinct fluorophores, we generated a tunable spatially contrasted molecular distribution.

The inclusion complex of rosmarinic acid into beta-cyclodextrin: A thermodynamic and structural analysis by NMR and capillary electrophoresis.

This work focuses on the characterization of the rosmarinic acid (RA)-ß-cyclodextrin (CD) complex in aqueous solution by (1)H NMR (1D- and 2D-ROESY), completed with studies by capillary electrophoresis (CE). From the (1)H NMR data, the stoichiometry of the complex was determined by a Job's plot and the binding constant was estimated from a linear regression (Scott's method). At pH 2.9, the results showed that RA binds CD with a 1:1 stoichiometry and a binding constant Kb of 445 (±53) M(-1) or 465 (±81) M(-1) depending on the CD protons (H-5 or H-3) selected for the evaluation. The Kb value was also calculated from the CD-induced chemical shifts of each RA proton in order to collect information on the structure of the complex. The pH dependence of Kb revealed that the RA carboxylic form displays the highest affinity for CD. An investigation by capillary electrophoresis fully confirmed these results. 2D ROESY analysis provided detailed structural information on the complex and showed a strong correlation between H-3 and H-5 of CD and most RA protons. In conclusion, RA, an efficient phenolic antioxidant from rosemary with a marketing authorization, spontaneously forms a relatively stable inclusion complex with CD in water.

Energy propagation throughout chemical networks.

In order to maintain their metabolism from an energy source, living cells rely on chains of energy transfer involving functionally identified components and organizations. However, propagation of a sustained energy flux through a cascade of reaction cycles has only been recently reproduced at a steady state in simple chemical systems. As observed in living cells, the spontaneous onset of energy-transfer chains notably drives local generation of singular dissipative chemical structures: continuous matter fluxes are dynamically maintained at boundaries between spatially and chemically segregated zones but in the absence of any membrane or predetermined material structure.

5(4H)-oxazolones as intermediates in the carbodiimide- and cyanamide-promoted peptide activations in aqueous solution.

The early days: although considered a species to be avoided in peptide chemistry, the intermediacy of 5(4H)-oxazolones is demonstrated to be essential for the formation of peptides through cyanamide and carbodiimide activation in aqueous solution.

Energy propagation through a protometabolism leading to the local emergence of singular stationary concentration profiles.

Living systems rely on chains of energy transfer from an energy source to maintain their metabolism. This task requires functionally identified components and organizations. However, propagation of a sustained energy flux through a cascade of reaction cycles has never been reproduced at a steady state in a simple chemical system. By using energy patterning and a diffusing hub reactant, we achieved the transfer of energy through an abiotic protometabolism. Patterned illumination was applied to a liquid solution of a reversible photoacid. It resulted in the local onset of a proton pump, which subsequently drove an extended reaction-diffusion cycle that involved pH-sensitive reactants. Thus, light has been used for locally setting out of chemical equilibrium a reaction involving "blind" reactants. The spontaneous onset of an energy-transfer chain notably drives the local generation of singular dissipative chemical structures; continuous matter fluxes are dynamically maintained at boundaries between spatially and chemically segregated zones, in the absence of any membrane or predetermined material structure.

Pathways for the formation and evolution of peptides in prebiotic environments.

α-Amino acids are easily accessible through abiotic processes and were likely present before the emergence of life. However, the role they could have played in the process remains uncertain. Chemical pathways that could have brought about features of self-organization in a peptide world are considered in this review and discussed in relation with their possible contribution to the origin of life. An overall scheme is proposed with an emphasis on possibilities that may have led to dynamically stable far from equilibrium states. This analysis defines new lines of investigation towards a better understanding of the contribution of the systems chemistry of amino acids and peptides to the emergence of life.

Autocatalyses.

Autocatalysis is a fundamental concept, used in a wide range of domains. From the most general definition of autocatalysis, that is, a process in which a chemical compound is able to catalyze its own formation, several different systems can be described. We detail the different categories of autocatalyses and compare them on the basis of their mechanistic, kinetic, and dynamic properties. It is shown how autocatalytic patterns can be generated by different systems of chemical reactions. With the notion of autocatalysis covering a large variety of mechanistic realizations with very similar behaviors, it is proposed that the key signature of autocatalysis is its kinetic pattern expressed in a mathematical form.

Reactivity of alanylalanine diastereoisomers in neutral and acid aqueous solutions: a versatile stereoselectivity.

A good comprehension of the reactivity of peptides in aqueous solution is fundamental in prebiotic chemistry, namely for understanding their stability and behavior in primitive oceans. Relying on the stereoselectivity of the involved reactions, there is a huge interest in amino acid derivatives for explaining the spontaneous emergence of homochirality on primitive Earth. The corresponding kinetic and thermodynamic parameters are however still poorly known in the literature. We studied the reactivity of alanylalanine in acidic to neutral conditions as a model system. The hydrolysis into amino acids, the epimerization of the N-terminal residue, and the cyclization into diketopiperazine could be successfully identified and studied. This kinetic investigation highlighted interesting behaviors. Complex mechanisms were observed in very acidic conditions. The relative kinetic stability of the diastereoisomers of the dipeptide is highly dependent of the pH, with the possibility to dynamically destabilize the thermodynamically more stable diastereoisomers. The existence of the cyclization of dipeptides adds complexity to the system. On one hand it brings additional stereoselectivities; on the other hand fast racemization of heterochiral dipeptides is obtained.

Autocatalysis: at the root of self-replication.

Autocatalysis is a fundamental concept, used in a wide range of domains. From its most general definition, that is, a process in which a chemical compound is able to catalyze its own formation, several different systems can be described. We detail the different categories of autocatalyses, and compare them on the basis of their mechanistic, kinetic, and dynamic properties. It is shown how autocatalytic patterns can be generated by different systems of chemical reactions. The notion of autocatalysis covers a large variety of mechanistic realizations with very similar behaviors; it is proposed that its key signature is its kinetic pattern expressed in a mathematical form. This notion, while describing dynamic behaviors at the most fundamental level, is at the basis for developing higher-level concepts towards life: autocatalytic sets, and autopoietic systems.

Programming an in vitro DNA oscillator using a molecular networking strategy.

Living organisms perform and control complex behaviours by using webs of chemical reactions organized in precise networks. This powerful system concept, which is at the very core of biology, has recently become a new foundation for bioengineering. Remarkably, however, it is still extremely difficult to rationally create such network architectures in artificial, non-living and well-controlled settings. We introduce here a method for such a purpose, on the basis of standard DNA biochemistry. This approach is demonstrated by assembling de novo an efficient chemical oscillator: we encode the wiring of the corresponding network in the sequence of small DNA templates and obtain the predicted dynamics. Our results show that the rational cascading of standard elements opens the possibility to implement complex behaviours in vitro. Because of the simple and well-controlled environment, the corresponding chemical network is easily amenable to quantitative mathematical analysis. These synthetic systems may thus accelerate our understanding of the underlying principles of biological dynamic modules.

An experimental investigation of the evolution of chirality in a potential dynamic peptide system: N-terminal epimerization and degradation into diketopiperazine.

The APED model (activation-polymerization-epimerization-depolymerization) is a unique example of a chemical system that allows symmetry breaking through a dynamic process involving indirect network autocatalysis. In its simplest version, the autocatalytic behavior of this model partly relies on the reproduction of local chiral centers in dipeptides through an epimerization process, with a thermodynamic preference for homochiral chains. We studied the reactivity of di- and tripeptides, containing a N-terminal phenylglycine (Phg) residue, as model compounds for the experimental determination of the kinetic and thermodynamic parameters related to the N-terminal epimerization process. Although the N-terminal residue is prone to spontaneous epimerization, catalysis was required for the epimerization to reach the equilibrium state in reasonable time. Unexpectedly, the observed equilibrium diastereoisomeric excesses have shown a general tendency for more stable heterochiral peptides, especially strong in the case of dipeptides. In parallel to this process, a stereoselective peptide cleavage through diketopiperazine formation was observed. Contrary to the N-terminal epimerization of peptides, the diketopiperazine formation did not need any catalyst, and heterochiral peptides were shown to be dynamically unstabilized, as they were cleaved faster than homochiral peptides. The validity of the extrapolation of these results to other residues and longer peptide chains is discussed, and some directions for future developments of the theoretical model are given.

2-Hydroxyazobenzenes to tailor pH pulses and oscillations with light.

This paper evaluates the 2-hydroxyazobenzene platform for tailoring proton concentration pulses and oscillations with monochromatic light. The easily prepared 2-hydroxyazobenzenes exhibit large absorptions in the near-UV range. Photoisomerization was investigated by UV/Vis absorption, (1)H NMR spectroscopy, and steady-state fluorescence emission. In the whole investigated series, the trans stereoisomer of the 2-hydroxyazobenzene motif provides the corresponding cis derivative with an action cross section in the 10(3) M(-1) cm(-1) range. At the same time, photoisomerization is accompanied by a significant pK drop of the phenol group. According to the phenyl-substituent pattern, cis-to-trans thermal back-isomerization can be tuned in the 10 ms-100 s range. Up to 2 units of reversible pH drops or pH oscillations on the 10 s timescale have been obtained by appropriately tailoring single-wavelength illumination of 2-hydroxyazobenzene solutions.

Homochirality and the need for energy.

The mechanisms for explaining how a stable asymmetric chemical system can be formed from a symmetric chemical system, in the absence of any asymmetric influence other than statistical fluctuations, have been developed during the last decades, focusing on the non-linear kinetic aspects. Besides the absolute necessity of self-amplification processes, the importance of energetic aspects is often underestimated. Going down to the most fundamental aspects, the distinction between a single object-that can be intrinsically asymmetric-and a collection of objects-whose racemic state is the more stable one-must be emphasized. A system of strongly interacting objects can be described as one single object retaining its individuality and a single asymmetry; weakly or non-interacting objects keep their own individuality, and are prone to racemize towards the equilibrium state. In the presence of energy fluxes, systems can be maintained in an asymmetric non-equilibrium steady-state. Such dynamical systems can retain their asymmetry for times longer than their racemization time.

Energetic and entropic analysis of mirror symmetry breaking processes in a recycled microreversible chemical system.

Understanding how biological homochirality emerged remains a challenge for the researchers interested in the origin of life. During the last decades, stable nonracemic steady states of nonequilibrium chemical systems have been discussed as a possible response to this problem. In line with this framework, a description of recycled systems was provided in which stable products can be activated back to reactive compounds. The dynamical behavior of such systems relies on the presence of a source of energy, leading to the continuous maintaining of unidirectional reaction loops. A full thermodynamic study of recycled systems, composed of microreversible reactions only, is presented here, showing how the energy is transferred and distributed through the system, leading to cycle competitions and the stabilization of asymmetric states.

Determination of synthetic polypeptide conformations and molecular geometrical parameters by nonaqueous CE.

The aim of this work was to study changes in homopolypeptide chain conformation as a function of the number of residues by the modeling of the electrophoretic mobility. For this purpose, the frictional coefficients of poly(N(epsilon)-trifluoroacetyl-L-lysine) with different number of residues (up to 11) were determined from the absolute ionic mobilities and modeled by the hydrodynamic frictional coefficient of an equivalent cylinder. This approach allowed determination of geometrical parameters of the polypeptide chain in a liquid phase (nonaqueous solution of the BGE). The fact that the BGE and analyte are dissolved in mixed (methanol-ACN) organic solvent implied to take into account different effects and corrections that are generally not considered in aqueous solvent: namely, the effect of ion-pairs between constituents of the BGE for the calculation of the ionic strength, the effect of ion-pairs between the solutes and the electrolyte counterions and the correction due to the dielectric friction (Hubbard-Onsager equations). In addition, the influence of the ionic strength on the electrophoretic mobility was corrected using the Pitts equation, and the effect of lateral charges due to a slight deprotonation of the -NH- group in the lateral chain was also considered. From this modeling, molecular geometrical parameters relative to the linear and helicoïdal conformations were obtained with very good correlation coefficients. Interestingly, this work also points out that the use of ionic mobility modeling for extracting molecular geometrical parameters can also be applied to end-charged polypeptides with slightly charged lateral chains (3% of elementary charge per residue).

Emergence of homochirality in far-from-equilibrium systems: mechanisms and role in prebiotic chemistry.

Since the model proposed by Frank (Frank FC, Biochem Biophys Acta 1953;11:459-463), several alternative models have been developed to explain how an asymmetric non-racemic steady state can be reached by a chirally symmetric chemical reactive system. This paper explains how a stable non-racemic regime can be obtained as a symmetry breaking occurring in a far-from-equilibrium reactive system initiated with an initial imbalance. Departing from the variations around the original Frank's model that are commonly described in the literature, i.e. open-flow systems of direct autocatalytic reactions, we discuss recent developments emphasizing both an active recycling of components and an autocatalytic network of simple reactions. We will present our APED model as the most natural realization of such thermodynamic openness and non-equilibrium, of recycling and of network autocatalysis, each of these in prebiotic conditions. The different experimental and theoretical models in the literature will be classified according to mechanism. The place and role of such self-structured networks responsible for the presence of homochirality in the primitive Earth will be detailed.

Experimental evidence and theoretical analysis for the chiral symmetry breaking in the growth front of conglomerate crystal phase of 1,1'-binaphthyl.

Chirally asymmetric states, chemical oscillations, propagating chemical waves, and spatial patterns, are examples of far-from-equilibrium self-organization. We have found that the crystal growth front of 1,1(')-binaphthyl shows many of the characteristics of an open system in which chiral symmetry breaking has occurred. From its supercooled molten phase, 1,1(')-binaphthyl crystallizes as a conglomerate of R and S crystals when the temperature is above 145 degrees C. In addition, 1,1(')-binaphthyl in its molten phase is always racemic due to its high racemization rate. Under appropriate conditions, bimodal probability distribution of enantiomeric excess (ee) with maxima around 60% was observed. The ee was mass independent, indicating that the growth front maintains a constant ee. A kinetic model that theoretically analyzes the chiral symmetry breaking transition in the growth front of a conglomerate crystal phase was formulated. Computer simulation of the model reproduced not only the average but also the large variation of the ee observed in crystallization experiments.