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The design of catalytic proteins with functional sites capable of specific chemistry is gaining momentum and a number of artificial enzymes have recently been reported, including hydrolases, oxidoreductases, retro-aldolases, and others. Our goal is to develop a peptide ligase for robust catalysis of amide bond formation that possesses no stringent restrictions to the amino acid composition at the ligation junction. We report here the successful completion of the first step in this long-term project by building a completely de novo protein with predefined acyl transfer catalytic activity. We applied a minimalist approach to rationally design an oxyanion hole within a small cavity that contains an adjacent thiol nucleophile. The N-terminus of the α-helix with unpaired hydrogen-bond donors was exploited as a structural motif to stabilize negatively charged tetrahedral intermediates in nucleophilic addition–elimination reactions at the acyl group. Cysteine acting as a principal catalytic residue was introduced at the second residue position of the α-helix N-terminus in a designed three-α-helix protein based on structural informatics prediction. We showed that this minimal set of functional elements is sufficient for the emergence of catalytic activity in a de novo protein. Using peptide-(α)thioesters as acyl-donors, we demonstrated their catalyzed amidation concomitant with hydrolysis and proved that the environment at the catalytic site critically influences the reaction outcome. These results represent a promising starting point for the development of efficient catalysts for protein labeling, conjugation, and peptide ligation.

Conversion of macrocyclic imine entities into helical strands was achieved through three- and four-component exchange reactions within constitutionally dynamic libraries. The generation of sequences of the intrinsic helicity codon, based on the hydrazone-pyrimidine fragment obtained by condensation of pyrimidine dialdehyde A with pyrimidine bis-hydrazine B, shifted the equilibrium between all the possible macrocycles and strands towards the full expression (> 98%) of helical product [A/B]. Furthermore, it was shown that chain folding accelerated the dynamic exchange reactions among the library members. Lastly, in four-component experiments (involving A, B, E and either C or D), even though the macrocyclic entities ([A/C], [B/E]; [A/D], [B/E]) were the kinetically preferred products, over time dialdehyde A relinquished its initial diamine partners C or D to opt for bis-hydrazine B, which allowed the preferential formation of the helically folded strand. The present results indicate that self-organisation pressure was able to drive the dynamic system towards the selective generation of the strand undergoing helical folding.

Control over the folding of molecular strands may be achieved by appropriate choice of the constituting subunits, in particular for chains of specific heterocycles such as sequences of directly connected pyridine (py) and pyrimidine (pym) rings, which are known to fold into extended helical structures. Since the hydrazone (hyz) group represents an isomorphic analogue of a py site, the condensation of hydrazine and carboxaldehyde derivatives of pym offers a very efficient approach to strands incorporating hyz instead of py units and constituted by sequences of alternating hyz and pym groups. A series of such strands of different lengths, up to ten hyz units, i.e., 1–7, were synthesized. Their spectral properties indicate that they fold indeed into helical shapes. Extensive characterization was performed in solution by 1HNMR spectroscopy and in the solid state by determination of the crystal structures of eight such strands. They all display the expected helical geometry with up to 3 1/3 turns and direct stacking contacts. The efficiency and flexibility of the synthetic approach as well as its wide potential for generation of diversity through lateral decoration make the (hyzpym) subunit a particularly attractive helicity codon.

The acidity–basicity effect on the catalytic behavior of exchanged Pt-β zeolites in hexane reforming reactions has shown: (i) from X-ray photoelectron spectroscopy, that the platinum binding energy decreases when the basicity increases (therefore there is an electronic shift from zeolite to Pt particles which increases with basicity); (ii) at low hydrogen pressure ( P H 2=226 or 38 Torr), the apparent activation energy for the 2MP reaction increases when the basicity of the zeolite increases; (iii) the ring enlargement reaction of methylcyclopentane to cyclohexane and benzene is increased when Bronsted acidity is increased; (iv) with acyclic molecules as 2-methylpentane and 4-methyl 1-pentene and n -hexane, the isomerization selectivity is high when the acidity is high but decreases when the basicity increases; (v) from the use of 13 C-labeled molecules, no cyclic mechanism was detected but only bond shifts, for which the ethyl bond shift predominates on the acidic catalyst and the methyl bond shifts on the basic catalyst. The combination of these experimental points with kinetic data suggests that the hydrocarbon rearranges at the metal–support interface and that electron donor or electron acceptor effects due to the acidity–basicity of the zeolite lead to changes of the reaction mechanism pathway.

Reactions of methylcyclopentane hydrogenolysis were performed at 140°C-160°C on two ruthenium catalysts 10%Ru-Al2 O3 - 0.2% RU-Al2 O3 and on two Pt-Ru bimetallic catalysts in order to determine the mechanistic change in hydrogenolysis caused by the interaction between Pt and Ru. The results of this research are explained using the "in-situ" X-ray absorption spectroscopy analysis which pointed out (9) that a Pt-Ru bimetallic phase in the Ru rich phase is present in the catalyst. As in these experimental conditions platinum is inactive, an "activated Pt-Ru clusters ", can explain why the values of the selectivity ratio : 3-methylpentane over n-hexane increase when the number of small metal particles also increase. This result shows that a dilution effect does not occur solely if it occurs.

In this paper in situ X-ray absorption in the dispersive mode on Ir Cu/γ-alumina catalysts during several oxidation-reduction cycles is described. Moreover, catalytic reactions as hydrogenolysis of methylcyclopentane and isomerization of labelled hexanes were performed as tests of the final reduced forms of the catalysts. Only the raw EXAFS data are reported here. But, even at this stage of our investigations, it is clear that the time resolved technique we used gives a large enough signal-to-noise ratio and energy band pass to describe various catalytic processes in full detail. Such new possibilities of looking at structural and electronic evolutions will undoubtly provide interesting insights in the kinetic aspects of a catalytic reaction. With Irx Cuy catalysts it has been observed that (i) both Ir and Cu are fully reduced at 150°C under H2, flow, (ii) the Ir Cu catalyst reduced at 150°C keeps the intrinsic properties of iridium, and (iii) after reduction at 300°C the properties of iridium seem to be lost. From a carbon-13 experiment we can suggest an Ir Cu interaction.

Skeletal isomerization of 2-methylpentane (2-MP) and hydrogenolysis of methylcyclopentane (MCP) have been studied over a series of Pt/Al2O3 and “cluster derived” (CD) catalysts of high dispersions. 13C labeling allowed estimation of the relative contributions of cyclic mechanisms in isomerization. High resolution electron microscopy was used jointly to determine the metal particle size distributions. In the isomerization of 2-MP to 3-MP the relative amount of selective cyclic mechanisms increases with the percentage of surface or length particles (d ⩽ 10 A) whatever the catalyst used. In the isomerization of 2-MP to n-hexane for catalysts having the same mean size of particles, the CD catalysts show differences in selectivity compared to the classical Pt/Al2O3 catalysts. The observed particle size effect could be explained by changes in electronic or geometrical factors, especially it is proposed that the electronic rather than the geometrical one should be considered in the case of the “organometallic cluster derived” catalysts.