Unveiling the Cleavage Mechanism of an RNA Model Compound on the whole pH Scale: Computations Meet Experiments in the Determination of Reaction Rates.

The knowledge of the mechanism of reactions occurring in solution is a primary research line both in the context of theoretical-computational chemistry and in the field of organic and bio-organic chemistry. Given the importance of the hydrolysis of nucleic acids in life-related phenomena, here we present a combined experimental and computational study on the cleavage of an RNA model compound. This phosphodiester features a cleavage rate strictly dependent on the pH with three different dependence domains. Such experimental evidence, highlighted by an in-depth kinetic investigation, unequivocally suggests a change in the reaction mechanism along the pH scale. In order to interpret the data and to explain the experimental behavior, we have applied a theoretical-computational procedure, involving a hybrid quantum/classical approach, able to model chemical reactions in complex environments, i. e. in solution. This study turns out to quantitatively reproduce the experimental data with accuracy and, in addition, provides useful mechanistic insight into the transesterification process of the investigated compound. The study indicates that the cleavage can occur through an A N D N ${A_N D_N }$ , an A N + D N ${A_N + D_N }$ , and a D N A N ${D_N A_N }$ mechanism depending on the pH values.

Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis.

(1) Background: the theoretical modelling of reactions occurring in liquid phase is a research line of primary importance both in theoretical-computational chemistry and in the context of organic and biological chemistry. Here we present the modelling of the kinetics of the hydroxide-promoted hydrolysis of phosphoric diesters. (2) Method: the theoretical-computational procedure involves a hybrid quantum/classical approach based on the perturbed matrix method (PMM) in conjunction with molecular mechanics. (3) Results: the presented study reproduces the experimental data both in the rate constants and in the mechanistic aspects (C-O bond vs. O-P bond reactivity). The study suggests that the basic hydrolysis of phosphodiesters occurs through a concerted ANDN mechanism, with no formation of penta-coordinated species as reaction intermediates. (4) Conclusions: the presented approach, despite the approximations, is potentially applicable to a large number of bimolecular transformations in solution and therefore leads the way to a fast and general method to predict the rate constants and reactivities/selectivities in complex environments.

Intra- and Intermolecular Cooperativity in the Catalytic Activity of Phosphodiester Cleavage by Self-Assembled Systems Based on Guanidinylated Calix[4]arenes.

The calix[4]arene scaffold, blocked in the cone conformation through alkylation with long alkyl chains, and decorated at the upper rim with four guanidine or arginine units, effectively catalyzes the cleavage of the phosphodiester bond of DNA and RNA model compounds in water. An exhaustive kinetic investigation unequivocally points to the existence of spontaneous aggregation phenomena, driven by hydrophobic effect, occurring at different critical concentrations that depend on the identity of the compound. A pronounced superiority of the assembled structures compared with the monomers in solution was observed. Moreover, the catalytically active units, clustered on the macrocyclic tetrafunctional scaffold, were proved to efficiently cooperate in the catalytic mechanism and result in improved reaction rates compared to those of the monofunctional model compounds. The kinetic analysis is also integrated and corroborated with further experiments based on fluorescence spectroscopy and light scattering. The advantage of the supramolecular assemblies based on tetrafunctional calixarenes leads to believe that the active units can cooperate not only intramolecularly but also intermolecularly. The molecules in the aggregates can probably mold, flex and rearrange but, at the same time, keep an ordered structure that favors phosphodiester bond cleavage. This dynamic preorganization can allow the catalytic units to reach a better fitting with the substrates and perform a superior catalytic activity.

Benzazetidines and Related Compounds: Synthesis and Potential.

Benzazetidines are a class of N-heterocycles potentially very interesting for a variety of purposes, including biological applications and drug design. In the past, their high ring strain has hampered the development of trustable, general, and efficient synthetic methodologies for their preparation. In this review article, the aim is to disclose all the literature contributions about the synthesis of these compounds and the study of their reactivity, from the early examples to the most recent synthetic approaches. Recently, there has been a growth of interest for this heterocycle, driven by the publication of novel synthetic methodologies based on palladium-catalyzed intramolecular C-H amination and organocatalyzed ring-closure of 2-(N-Boc-anilino)-α-ketoesters/amides.

A calix[4]arene with acylguanidine units as an efficient catalyst for phosphodiester bond cleavage in RNA and DNA model compounds.

A calix[4]arene scaffold, blocked in the cone conformation and decorated at the upper rim with two acylguanidine units, effectively catalyzes the cleavage of phosphodiester bonds of HPNP and BNPP under neutral pH conditions. The catalyst performance is discussed in terms of acceleration over background hydrolysis and effective molarity (EM). The combination of potentiometric acid-base titrations with pH-rate profiles for HPNP and BNPP cleavage in the presence of 2·2HCl additives points to a marked synergic action of an acylguanidine/acylguanidinium catalytic dyad in 2H+, via general base-electrophilic bifunctional catalysis. Acceleration factors over background larger than 3 orders of magnitude are obtained. The connection of the guanidine/guanidinium dyad to the calixarene scaffold by means of carbonyl joints has a double advantage: (i) the acidity of the guanidinium moiety is enhanced by the electron-withdrawing carbonyl group and maximum conversion into the catalytically active form 2H+ occurs at almost neutral pH, lower than the pH needed for the monoprotonated form 1H+ devoid of carbonyl groups; (ii) the EM value for HPNP cleavage with 2H+ is definitely higher than that with 1H+, suggesting a highly preorganized catalyst that perfectly fits in a strainless ring-shaped transition state in the catalyzed process. DFT calculations also provide useful insights into the reaction mechanisms and transition states.

Organocatalytic Synthesis of Benzazetidines by Trapping Hemiaminals with Protecting Groups.

Benzazetidines are highly strained and inherently unstable heterocycles. There are only few methodologies for assembling these compounds. Here, a protocol is presented to trap an elusive cyclic, four-membered hemiaminal structure. This method affords several benzazetidines in moderate to good yields (up to 81%), and it uses inexpensive materials and does not require catalysts based on transition metals. The high ring strain energy of these benzazetidine systems was estimated by density functional theory calculations to be about 32 kcal mol-1. This synthesis can be applied also on gram scale with reaction yield essentially unchanged.

Organocatalysis and catalyst aggregation: a study using the asymmetric synthesis of benzofuranones as a test reaction.

A common problem encountered in enantioselective organocatalysis is the aggregation of the catalyst, which can result in a relevant decrease of the efficiency and selectivity of the process. In the asymmetric synthesis of chiral benzofuranones, recently reported by us, we noted a remarkable increase of the reaction yield upon the addition of one of the reagents in a portionwise manner rather than in a single addition. We investigated this phenomenon by several experimental techniques such as 1D and 2D NMR experiments, UV-Vis spectroscopy, circular dichroism and dynamic light scattering. In addition, we studied the kinetic profile of this reaction using a simple numerical model and carried out in silico investigations. All these different approaches point to the conclusion that in the reaction medium a supramolecular polymerization/aggregation phenomenon, based on weak interactions, occurs and such a process is promoted by a quinone, which is one of the reagents of the benzofuranone synthesis. The portionwise mode of addition is a known strategy which can improve the performance of many synthetic procedures and this strategy is commonly adopted on account of empirical experience. However, our results provide an explanation, based on a chemical kinetic model, of the reason why the portionwise addition affects in such a dramatic way the yield of the benzofuranone synthesis catalyzed by Cinchona alkaloids.

Synthesis of Benzofuranones via Malonates Desymmetrization: Yield Increase by the Portion-wise Addition of Quinones.

The organocatalyzed addition of several malonates to 1,4-benzoquinones affords benzofuranones bearing a quaternary stereocenter with good enantioselectivity. This reaction is an intramolecular desymmetrization since it proceeds through the formation of an arylated achiral malonate that cyclizes to give the reaction product. The addition rate of the quinone dramatically affects the reaction yield which was originally low. The yield was considerably increased, in some cases, from less than 20 % to over 95 %, by adding the quinone in portions rather than at once, keeping similar enantioselectivity. A possible rationalization for the preferential formation of the indicated enantiomer has been investigated by DFT calculations.

An All-Glass Microfluidic Network with Integrated Amorphous Silicon Photosensors for on-Chip Monitoring of Enzymatic Biochemical Assay.

A lab-on-chip system, integrating an all-glass microfluidics and on-chip optical detection, was developed and tested. The microfluidic network is etched in a glass substrate, which is then sealed with a glass cover by direct bonding. Thin film amorphous silicon photosensors have been fabricated on the sealed microfluidic substrate preventing the contamination of the micro-channels. The microfluidic network is then made accessible by opening inlets and outlets just prior to the use, ensuring the sterility of the device. The entire fabrication process relies on conventional photolithographic microfabrication techniques and is suitable for low-cost mass production of the device. The lab-on-chip system has been tested by implementing a chemiluminescent biochemical reaction. The inner channel walls of the microfluidic network are chemically functionalized with a layer of polymer brushes and horseradish peroxidase is immobilized into the coated channel. The results demonstrate the successful on-chip detection of hydrogen peroxide down to 18 µM by using luminol and 4-iodophenol as enhancer agent.

Guanidinium Promoted Cleavage of Phosphoric Diesters: Kinetic Investigations and Calculations Provide Indications on the Operating Mechanism.

The catalytic activity of the guanidinium units toward the cleavage of phosphoric diesters is deeply investigated both with kinetic experiments and DFT calculations. The first part of the investigation aims to determine how the structure of the substrate (phenyl or alkyl esters) is able to influence the guanidinium-catalyzed hydrolysis changing the mechanism from ANDN to AN+DN. In the cleavage of the DNA model bis(4-nitrophenyl)phospate (BNPP), experimental kinetic data highlight the operation of a guanidine-guanidinium catalytic dyad that can act both intermolecularly and intramolecularly on different molecular scaffolds exhibiting notable values of effective molarity. 31P NMR spectra and DFT investigation provide indication that the deprotonated guanidine involved in such a catalysis acts as a general base in the deprotonation of a water molecule involved in the cleavage, and not as nucleophilic unit. Moreover, DFT calculations were carried out to determine the guanidinium promoted activation energy of pseudorotation. The results indicate a remarkable drop in the activation energy of this process for dialkylphosphate esters explaining, in part, the higher sensitivity of diribonucleoside to the presence of guanidinium-based catalysts compared to the more activated RNA model HPNP.

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

The cone-calix[4]arene derivative (1H3)2+, 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. The pH dependence of the kinetics was found to be fully consistent with the results of the potentiometric titration of the triprotic acid (1H3)2+. At pH 9.5, the rate enhancement of p-nitrophenol liberation from BNPP relative to background hydrolysis is 6.5 × 104-fold at 1 mM concentration of the calix[4]arene derivative. Experimental data clearly point to the effective cooperation of the three active units and to the involvement of the phenolate moiety as a nucleophile in the phosphoryl transfer step. Subsequent liberation of a second equivalent of p-nitrophenol from the phosphorylated calixarene intermediate is conceivably promoted by the "built-in" guanidine/guanidinium catalytic dyad.

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. Extension of the investigation to the cleavage of the DNA model BNPP showed that both Zn(II) and Cu(II) complexes exhibit good catalytic efficiency, with a superiority of the 1,2-vicinal catalyst in both cases. The data reported in this work show that rate accelerations over background for the best catalyst-substrate combinations at 0.5 mM catalyst concentration are 3.6 × 10(5)-fold for HPNP, 1.1 × 10(6)-fold for BNPP, and range from 1.3 × 10(6)- to 1.3 × 10(7)-fold for diribonucleoside monophosphates.

Quinine-Catalyzed Asymmetric Synthesis of 2,2'-Binaphthol-Type Biaryls under Mild Reaction Conditions.

Simple quinine as an organocatalyst mediates the addition of various naphthols to halogenated quinones to afford non-C2 -symmetrical, axially chiral biaryl products, which are promising compounds as chiral ligands and organocatalysts. The rotational barrier required to have two distinct atropisomers has been evaluated in the products generated from the addition of naphthols to various quinones by means of DFT calculations and HPLC. The use of halogenated quinones as reagents was necessary to have configurationally stable enantiomeric products which can be obtained in good yield and stereoselectivity. These compounds have also been prepared in gram quantities and recrystallized to near enantiopurity.

The guanidinium unit in the catalysis of phosphoryl transfer reactions: from molecular spacers to nanostructured supports.

Examples of guanidinium-based artificial phosphodiesterases are illustrated in this review article. A wide set of collected catalytic systems are presented, from the early examples to the most recent developments of the use of this unit in the design of supramolecular catalysts. Special attention is dedicated to illustrate the operating catalytic mechanism and the role of guanidine/ium units in the catalysis. One or more of these units can act by themselves or in conjunction with other active units. The analogy with the mechanism of enzymatic systems is presented and discussed. In the last part of this overview, recent examples of guanidinophosphodiesterases based on nanostructured supports are reported, namely gold-monolayer-protected clusters and polymer brushes grafted to silica nanoparticles. The issue of the dependence of the catalytic performance on the preorganization of the spacer is tackled and discussed in terms of effective molarity, a parameter that can be taken as a quantitative measurement of this preorganization for both conventional molecular linker and nanosized supports.

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.

Guanidine-based polymer brushes grafted onto silica nanoparticles as efficient artificial phosphodiesterases.

Polymer brushes grafted to the surface of silica nanoparticles were fabricated by atom-transfer radical polymerization (ATRP) and investigated as catalysts in the cleavage of phosphodiesters. The surfaces of silica nanoparticles were functionalized with an ATRP initiator. Surface-initiated ATRP reactions, in varying proportions, of a methacrylate moiety functionalized with a phenylguanidine moiety and an inert hydrophilic methacrylate species afforded hybrid nanoparticles that were characterized with potentiometric titrations, thermogravimetric analysis, and SEM. The activity of the hybrid nanoparticles was tested in the transesterification of the RNA model compound 2-hydroxypropyl para-nitrophenylphosphate (HPNP) and diribonucleoside monophosphates. A high catalytic efficiency and a remarkable effective molarity, thus overcoming the effective molarities previously observed for comparable systems, indicate the existence of an effective cooperation of the guanidine/guanidinium units and a high level of preorganization in the nanostructure. The investigated system also exhibits a marked and unprecedented selectivity for the diribonucleoside sequence CpA. The results presented open up the way for a novel and straightforward strategy for the preparation of supramolecular catalysts.

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 9.1, respectively. Activation parameters and DFT calculations of the rotational barriers around the C-Ar bonds indicate that a major contribution to the driving force for enhanced catalysis is entropic in nature.

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.

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. The additional guanidinium (guanidine) group in the diprotonated (monoprotonated) trifunctional calix[4]arene acts as a more or less innocent spectator. This is not the case with the tetrasubstituted calix[4]arene, whose mono-, di-, and triprotonated forms are slightly less effective than the corresponding di- and triguanidinocalix[4]arene derivatives, most likely on account of a steric interference with HPNP caused by overcrowding.

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.