Controlling the liberation rate of the in situ release of a chemical fuel for the operationally autonomous motions of molecular machines.

Second-order rate constants of the aminolysis of 2-cyano-2-phenylpropanoic anhydride 3 by a series of N-methylanilines differently substituted in the aromatic moiety (4a-d) were measured in dichloromethane. The common reaction product of aminolysis is 2-cyano-2-phenylpropanoic acid 1, which is known to be an effective fuel for acid-base driven molecular machines, but cannot be used in molar excess with respect to the machine. The motivation behind the kinetic study has been the prospect of using the aminolysis of 3 to supply the machine with fuel at a rate that is never so high as to overfeed the system, thus avoiding the malfunction of the machine with concomitant waste of fuel.

The Hydrolysis of the Anhydride of 2-Cyano-2-phenylpropanoic Acid Triggers the Repeated Back and Forth Motions of an Acid-Base Operated Molecular Switch.

This work aimed to render phenomenologically autonomous the otherwise stepwise operation of a catenane-based molecular switch, which is chemically triggered by the decarboxylation of 2-cyano-2-phenylpropanoic acid (2). Given that any amount of 2 in stoichiometric excess with respect to the catenane is consumed in a side reaction, the authors resorted to the corresponding anhydride 5, the slow hydrolysis of which, due to adventitious water in dichloromethane, continuously produces in situ the actual fuel 2. As a consequence, the machine does not require a reloading after each cycle, but switches back and forth as long as fuel is present.

The canonical behavior of the entropic component of thermodynamic effective molarity. An attempt at unifying covalent and noncovalent cyclizations.

This review article is concerned with the measurement, significance and applications of the concept of effective molarity (EM) in a large variety of cyclization reactions ranging from the formation of giant macromolecules in polymeric equilibrates to the self-assembly of cyclic supermolecules and supramolecular aggregates. Based on a dissection of EM into enthalpic and entropic components (EM = EM× EM), a careful examination of a large number of often overlooked quantitative studies of reversible cyclizations led to the definition of a set of "canonical" values of the entropic component EM, expressed in graphical form by the plot of EM* vs. n, where the asterisk denotes statistically corrected quantities, and n is the number of single bonds in the ring product.

Photoinduced Release of a Chemical Fuel for Acid-Base-Operated Molecular Machines.

Back and forth motions of the acid-base-operated molecular switch 1 are photo-controlled by irradiation of a solution, which also contains the photolabile pre-fuel 4. The photo-stimulated deprotection of the pre-fuel produces controlled amounts of acid 2, the base-promoted decarboxylation of which fuels the back and forth motions of the Sauvage-type [2]-catenane-based molecular switch. Because switch 1 and pre-fuel 4 do not interact in the absence of irradiation, an excess of the latter with respect to 1 can be added to the solution from the beginning.

Variations in the fuel structure control the rate of the back and forth motions of a chemically fuelled molecular switch.

This work deals with the use of 2-cyano-2-arylpropanoic acids as chemical fuels for an acid-base operated molecular switch that consists of a Sauvage-type catenand composed of two identical macrocycles incorporating a phenanthroline unit. When used as a base promoter of the decarboxylation of propanoic acid derivatives, the switch undergoes large amplitude motion from the neutral catenand to a protonated catenate and back again to the neutral state. The rate of back proton transfer, which determines the rate of the overall process, was markedly affected by -substituents in the order Cl > H > CH > OCH ( = +5.

Formation of Imidazo[1,5-a]pyridine Derivatives Due to the Action of Fe on Dynamic Libraries of Imines.

An imidazo[1,5-a]pyridine derivative was unexpectedly obtained through the action of Fe on a dynamic library of imines generated in situ via condensation of benzaldehyde and 2-picolylamine. The reaction product was easily isolated as the only nitrogen-containing product eluted from the chromatographic column. A reaction mechanism is proposed, in which combined kinetic and thermodynamic effects exerted by Fe on the various steps of the complex reaction sequence are discussed.

Phosphoryl Transfer Processes Promoted by a Trifunctional Calix[4]arene Inspired by DNA Topoisomerase I.

The cone-calix[4]arene derivative (1H), decorated at the upper rim with two guanidinium units and a phenolic hydroxyl in an ABAH functionalization pattern, effectively promotes the cleavage of the DNA model compound bis(p-nitrophenyl) phosphate (BNPP) in 80% DMSO solution at pH values in the range 8.5-12.0.

Coupling of the Decarboxylation of 2-Cyano-2-phenylpropanoic Acid to Large-Amplitude Motions: A Convenient Fuel for an Acid-Base-Operated Molecular Switch.

The decarboxylation of 2-cyano-2-phenylpropanoic acid is fast and quantitative when carried out in the presence of 1 molar equivalent of a [2]catenane composed of two identical macrocycles incorporating a 1,10-phenanthroline unit in their backbone. When decarboxylation is over, all of the catenane molecules have experienced large-amplitude motions from neutral to protonated catenane, and back again to the neutral form, so that they are ready to perform another cycle. This study provides the first example of the cyclic operation of a molecular switch at the sole expenses of the energy supplied by the substrate undergoing chemical transformation, without recourse to additional stimuli.

Upper Rim Bifunctional cone-Calix[4]arenes Based on a Ligated Metal Ion and a Guanidinium Unit as DNAase and RNAase Mimics.

The catalytic activity of an artificial phosphodiesterase that combines a ligated metal ion (Cu(II), Zn(II)) with a guanidinium unit connected by a 1,2-vicinal calix[4]arene spacer was investigated in the transesterification of RNA models HPNP and four diribonucleoside 3',5'-monophosphates. Comparison with previous data related to the 1,3-distal regioisomeric metal complexes confirms the superiority of the Cu(II) complexes over the Zn(II) analogs and shows that in the reactions of HPNP, GpU, and UpU, the catalytic efficiency depends very little on whether the substitution pattern is 1,2-vicinal or 1,3-distal. On the other hand, CpA turned out to be a good substrate for the Cu(II) complex of the 1,2-vicinal catalyst and a bad substrate for the corresponding 1,3-distal regioisomer, whereas the opposite holds for GpA.

Ribonuclease Activity of an Artificial Catalyst That Combines a Ligated Cu(II) Ion and a Guanidinium Group at the Upper Rim of a cone-Calix[4]arene Platform.

A cone-calix[4]arene derivative, featuring a guanidinium group and a Cu(II) ion ligated to a 1,4,7-triazacyclononane (TACN) ligand at the 1,3-distal positions of the upper rim, effectively catalyzes the cleavage of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) and a number of diribonucleoside 3',5'-monophosphates (NpN'). Kinetic and potentiometric measurements support the operation of a general-base/general-acid mechanism and demonstrate that the hydroxo form of the ligated Cu(II) ion is the sole catalytically active species. Rate enhancements relative to the background hydrolysis reaction at 1 mM catalyst concentration are 6 × 10(5)-fold for HPNP and cluster around 10(7)-fold with the most favorable catalyst-NpN' combinations.

Applications of dynamic combinatorial chemistry for the determination of effective molarity.

A new strategy for determining thermodynamic effective molarities (EM) for macrocylisation reactions using dynamic combinatorial chemistry under dilute conditions is presented. At low concentrations, below the critical value, Dynamic Libraries (DLs) of bifunctional building blocks contain only cyclic species, so it is not possible to quantify the equilibria between linear and cyclic species. However, addition of a monofunctional chain stopper can be used to promote the formation of linear oligomers allowing measurement of EM for all cyclic species present in the DL.

Copper(I)-induced amplification of a [2]catenane in a virtual dynamic library of macrocyclic alkenes.

Olefin cross-metathesis of diluted dichloromethane solutions (≤0.15 M) of the 28-membered macrocyclic alkene C1, featuring a 1,10-phenanthroline moiety in the backbone, as well as of catenand 1, composed of two identical interlocked C1 units, generates families of noninterlocked oligomers Ci. The composition of the libraries is strongly dependent on the monomer concentration, but independent of whether C1 or 1 is used as feedstock, as expected for truly equilibrated systems.

Effective catalysis of imine metathesis by means of fast transiminations between aromatic-aromatic or aromatic-aliphatic amines.

This paper reports on a quantitative investigation of rates of amine-imine exchange reactions of primary amines with their benzylidene derivatives in organic solvents at room temperature. Exchange reactions involving aromatic-aromatic or aromatic-aliphatic amines were in all cases fast enough to allow their use in the effective catalysis of imine metathesis in the absence of acid and metal catalysis. Transiminations based on exchange between aromatic and aliphatic amines were retarded both by electron-donating and electron-withdrawing substituents in the para-position of the benzylidene moiety.

Substituent effects on the catalytic activity of bipyrrolidine-based iron complexes.

The catalytic activity and the selectivity of the new bipyrrolidine-based Fe(II) complexes 2·Fe(OTf)2 and 3·Fe(OTf)2 in the oxidation of a series of alkyl and alkenyl hydrocarbons as well as of an aromatic sulfide with H2O2 were tested and compared with the catalytic efficiency of White's parent complex 1·Fe(OTf)2 in order to evaluate the sensitivity of the reaction to electronic effects.

Guanidine-guanidinium cooperation in bifunctional artificial phosphodiesterases based on diphenylmethane spacers; gem-dialkyl effect on catalytic efficiency.

Diphenylmethane derivatives 1-3, decorated with two guanidine units, are effective catalysts of HPNP transesterification. Substitution of the methylene group of the parent diphenylmethane spacer with cyclohexylidene and adamantylidene moieties enhances catalytic efficency, with gem-dialkyl effect accelerations of 4.5 and 9.

ATP cleavage by cone tetraguanidinocalix[4]arene.

The upper rim cone tetraguanidinocalix[4]arene 1 is a highly effective catalyst of ATP hydrolysis. The catalytically most active species is the triprotonated form of the catalyst. The three protonated guanidinium groups provide the electrostatic driving force for substrate binding and activation, while the neutral guanidine most likely acts as a nucleophilic catalyst.

Highly efficient intramolecular Cannizzaro reaction between 1,3-distal formyl groups at the upper rim of a cone-calix[4]arene.

The 1,3-distal cone-calix[4]arene dialdehyde 1 undergoes Cannizzaro disproportionation in the presence of strong base, but its 1,2-vicinal regioisomer 3 and the analogous monoaldehyde 2 are unreactive under the same conditions. The high intramolecular reactivity of the 1,3-distal regioisomer 1 is measured and discussed in terms of Effective Molarity (EM).

Upper rim guanidinocalix[4]arenes as artificial phosphodiesterases.

Calix[4]arene derivatives, blocked in the cone conformation and functionalized with two to four guanidinium units at the upper rim were synthesized and investigated as catalysts in the cleavage of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate. When compared with the behavior of a monofunctional model compound, the catalytic superiority of the calix[4]arene derivatives points to a high level of cooperation between catalytic groups. Combination of acidity measurements with the pH dependence of catalytic rates unequivocally shows that a necessary requisite for effective catalysis is the simultaneous presence, on the same molecular framework, of a neutral guanidine acting as a general base and a protonated guanidine acting as an electrophilic activator.

General base-guanidinium cooperation in bifunctional artificial phosphodiesterases.

Artificial phosphodiesterases that combine a guanidinium unit with a general base connected by a m-xylylene linker catalyze the transesterification of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate (HPNP). The bifunctional catalysts presented in this work show varying extents of cooperation between catalytic units and a rate enhancement of 4 × 10(4) in the most favorable case.

Photoinversion of sulfoxides as a source of diversity in dynamic combinatorial chemistry.

Photochemical interconversion of the two diastereoisomers cis- and trans-thianthrene dioxide (1) can be considered an example of photodynamic combinatorial chemistry (PDCC) in which the interconversion among diastereomeric equilibrating species is brought about by electromagnetic irradiation. Photoequilibrium can be shifted by irradiation at different wavelengths or by addition of SnCl(2) that binds cis-1 more efficiently than trans-1.

The role of attractive van der Waals forces in the catalysis of Michael addition by a phenyl decorated uranyl-salophen complex.

The Et(3)N-assisted addition of beta-ketoester 3 to MVK in chloroform is catalyzed with high turnover efficiency by the phenyl-substituted uranyl-salophen compound 2b but not by the parent compound 1b. A plausible mechanism is suggested, involving concomitant nucleophilic attack at the beta-carbon and hydrogen bonding between the Et(3)NH(+) countercation and the carbonyl oxygen of the s-cis conformation of the enone reactant. The role of the van der Waals interactions with the aromatic side arm of 2b as a crucial driving force for catalysis is discussed.

Enantiomerization of chiral uranyl-salophen complexes via unprecedented ligand hemilability: toward configurationally stable derivatives.

In the search for configurationally stable inherently chiral uranyl-salophen complexes, the newly synthesized compound 3 featuring a dodecamethylene chain was expected to be a promising candidate. Unexpectedly, dynamic HPLC on a enantioselective column showed that it still undergoes enantiomerization at high temperature. By comparison with the dynamic behavior of compounds 4 and 5, it was found that the enantiomerization rate is independent of the size of the ligand.

Fluoride-responsive organogelator based on oxalamide-derived anthraquinone.

Anthraquinone derived oxalamide gelator 1 forms with aromatic solvents and alcohols very stable gels which selectively respond to the presence of fluoride anion by colour change and/or gel-to-sol transition.

Efficient and selective cleavage of RNA oligonucleotides by calix[4]arene-based synthetic metallonucleases.

Di- and trinuclear copper(II) complexes of [12]aneN3 macrocycles anchored at the upper rim of cone calix[4]arenes in 1,2-, 1,3-, and 1,2,3-positions were investigated as cleaving agents of 6-, 7-, and 17-meric oligoribonucleotides. A kinetic investigation of the cleavage reactions was carried out using gel electrophoresis to separate and analyze reactants and products having a radioactive phosphate label in the terminal 5'-position. The degree of cooperation was assessed on the basis of a comparison with rates of cleavage by mononuclear controls.

Specific sensing of poly G by the aluminum-salophen complex.

The Al(III)-salophen complex 1 exhibited strong spectroscopic changes specifically upon addition of polyG and GpG, while double stranded DNA and RNA, and single stranded polyA, polyU and polyC induced negligible spectral changes of 1. Titrations with mono-nucleotides yielded no spectroscopic changes, revealing that there must be at least two consecutive guanines in single stranded oligonucleotide structure for a measurable spectroscopic change of 1. Preliminary results show that 1 has moderate antiproliferative effect on a number of human tumour cell lines.