Rapid Three-Step Cleavage of RNA and DNA Model Systems Promoted by a Dinuclear Cu(II) Complex in Methanol. Energetic Origins of the Catalytic Efficacy

Chromium complexes bearing disubstituted organophosphate ligands and their use in ethylene polymerization

The crystal structures of three unusual chromium organophosphate complexes have been determined, namely, bis(μ-butyl 2,6-di-tert-butyl-4-methylphenyl hydrogen phosphato-κO:κO′)di-μ-hydroxido-bis[(butyl 2,6-di-tert-butyl-4-methylphenyl hydrogen phosphato-κO)(butyl 2,6-di-tert-butyl-4-methylphenyl phosphato-κO)chromium](Cr—Cr) heptane disolvate or {Cr2(μ2-OH)2[μ2-PO2(OBu)(O-2,6- t Bu2-4-MeC6H2)-κO:κO′]2[PO2(OBu)(O-2,6- t Bu2-4-MeC6H2)-κO]2[HOPO(OBu)(O-2,6- t Bu2-4-MeC6H2)-κO]2}·2C7H16, [Cr2(C19H32O4P)4(C19H33O4P)2(OH)2]·2C7H16, denoted (1)·2(heptane), [μ-bis(2,6-diisopropylphenyl) phosphato-1κO:2κO′]bis[bis(2,6-diisopropylphenyl) phosphato]-1κO,2κO-chlorido-2κCl-triethanol-1κ2 O,2κO-di-μ-ethanolato-1κ2 O:2κ2 O-dichromium(Cr—Cr) ethanol monosolvate or {Cr2(μ2-OEt)2[μ2-PO2(O-2,6-iPr2-C6H3)2-κO:κO′][PO2(O-2,6-iPr2-C6H3)2-κO]2Cl(EtOH)3}·EtOH, [Cr2(C2H5O)2(C24H34O4P)3Cl(C2H6O)3]·C2H6O, denoted (2)·EtOH, and di-μ-ethanolato-1κ2 O:2κ2 O-bis{[bis(2,6-diisopropylphenyl) hydrogen phosphato-κO][bis(2,6-diisopropylphenyl) phosphato-κO]chlorido(ethanol-κO)chromium}(Cr—Cr) benzene disolvate or {Cr2(μ2-OEt)2[PO2(O-2,6-iPr2-C6H3)2-κO]2[HOPO(O-2,6-iPr2-C6H3)2-κO]2Cl2(EtOH)2}·2C6H6, [Cr2(C2H5O)2(C24H34O4P)2(C24H35O4P)2Cl2(C2H6O)2]·2C6H6, denoted (3)·2C6H6. Complexes (1)–(3) have been synthesized by an exchange reaction between the in-situ-generated corresponding lithium or potassium disubstituted phosphates with CrCl3(H2O)6 in ethanol. The subsequent crystallization of (1) from heptane, (2) from ethanol and (3) from an ethanol/benzene mixture allowed us to obtain crystals of (1)·2(heptane), (2)·EtOH and (3)·2C6H6, whose structures have the monoclinic P21, orthorhombic P212121 and triclinic P\overline 1 space groups, respectively. All three complexes have binuclear cores with a single Cr—Cr bond, i.e. Cr2O6P2 in (1), Cr2PO4 in (2) and Cr2O2 in (3), where the Cr atoms are in distorted octahedral environments, formally having 16 ē per Cr atom. The complexes have bridging ligands μ2-OH in (1) or μ2-OEt in (2) and (3). The organophosphate ligands demonstrate terminal κO coordination modes in (1)–(3) and bridging μ2-κO:κO′ coordination modes in (1) and (2). All the complexes exhibit hydrogen bonding: two intramolecular Ophos...H—Ophos interactions in (1) and (3) form two {H[PO2(OR)2]2} associates; two intramolecular Cl...H—OEt hydrogen bonds additionally stabilize the Cr2O2 core in (3); two intramolecular Ophos...H—OEt interactions and two O...H—O intermolecular hydrogen bonds with a noncoordinating ethanol molecule are observed in (2)·EtOH. The presence of both basic ligands (OH− or OEt−) and acidic [H(phosphate)2]− associates at the same metal centres in (1) and (3) is rather unusual. Complexes may serve as precatalysts for ethylene polymerization under mild conditions, providing polyethylene with a small amount of short-chain branching. The formation of a small amount of α-olefins has been detected in this reaction.

Phosphodiester models for cleavage of nucleic acids

Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.

Design, RNA cleavage and antiviral activity of new artificial ribonucleases derived from mono-, di- and tripeptides connected by linkers of different hydrophobicity

A novel series of metal-free artificial ribonucleases (aRNases) was designed, synthesized and assessed in terms of ribonuclease activity and ability to inactivate influenza virus WSN/A33/H1N1 in vitro. The compounds were built of two short peptide fragments, which include Lys, Ser, Arg, Glu and imidazole residues in various combinations, connected by linkers of different hydrophobicity (1,12-diaminododecane or 4,9-dioxa-1,12-diaminododecane). These compounds efficiently cleaved different RNA substrates under physiological conditions at rates three to five times higher than that of artificial ribonucleases described earlier and displayed RNase A-like cleavage specificity. aRNases with the hydrophobic 1,12-diaminododecane linker displayed ribonuclease activity 3-40 times higher than aRNases with the 4,9-dioxa-1,12-diaminododecane linker. The assumed mechanism of RNA cleavage was typical for natural ribonucleases, that is, general acid-base catalysis via the formation of acid/base pairs by functional groups of amino acids present in the aRNases; the pH profile of cleavage confirmed this mechanism. The most active aRNases under study exhibited high antiviral activity and entirely inactivated influenza virus A/WSN/33/(H1N1) after a short incubation period of viral suspension under physiological conditions.

Mono- and dinuclear metal complexes containing the 1,5,9-triazacyclododecane ([12]aneN3) unit and their interaction with DNA

It takes two to tango: Only the dinuclear but not the mononuclear metal complexes of triazacyclododecane ([12]aneN₃) were able to induce the Z-DNA of poly d(GC).

Ligand effect and cooperative role of metal ions on the DNA cleavage efficiency of mono and binuclear Cu(II) macrocyclic ligands complexes

Two binuclear Cu(II) complexes of N-functionalized macrocycle ligands, namely 1,3-bis(1,4,7-triaza-1-cyclonomyl)propane and 1-(3-(1,4,7-triazonan-1-yl)propyl)-1,4,7,10-tetraazacyclo-dodecane, were synthesized and their ability to hydrolyze the cleavage of supercoiled plasmid DNA (pBR322) was compared with that of structurally related non-functionalized mononuclear Cu(II) complexes. The former, binuclear Cu(II) complex with the symmetrical ligand exhibited enhanced double-strand cleavage activity compared to the other three complexes at the same [Cu(2+)] concentration. In contrast, the latter binuclear complex with unsymmetrical macrocylic ligand did not give rise to double-strand DNA cleavage. The linear DNA formation induced by the mononuclear Cu(II) 1,4,7,10-tetraazacyclo-dodecane complex was realized via a non-random double-stranded scission process. The differential cleavage activity is discussed in relation to dimer formation, effective cooperation and coordination environment of the metal center. The hydrolytic cleavage by the copper complexes without H2O2 is supported by evidence from an anaerobic reaction, free radical quenching, and nitro blue tetrazolium assay. In contrast, both the binuclear complexes cleaved supercoiled DNA efficiently to Form III (linearized DNA) in the presence of H2O2, indicating that nuclearity is a crucial parameter in oxidative cleavage. The radical scavenger inhibition study and nitro blue tetrazolium assay suggested the involvement of H2O2 and superoxide ions in the oxidative cleavage of DNA by the binuclear complexes.

Efficient hydrolytic cleavage of plasmid DNA by chloro-cobalt(II) complexes based on sterically hindered pyridyl tripod tetraamine ligands: synthesis, crystal structure and DNA cleavage

Four new cobalt(ii) complexes [Co(6-MeTPA)Cl]ClO4/PF6 (2/2a), [Co(6-Me2TPA)Cl]ClO4/PF6 (3/3a), [Co(BPQA)Cl]ClO4/PF6 (4/4a) and [Co(BQPA)Cl]ClO4/PF6 (5/5a) as well as [Co(TPA)Cl]ClO4 (1) where TPA = tris(2-pyridylmethyl)amine, 6-MeTPA = ((6-methyl-2-pyridyl)methyl)bis(2-pyridylmethyl)amine, 6-Me2TPA = bis(6-methyl-2-pyridyl)methyl)-(2-pyridylmethyl)amine, BPQA = bis(2-pyridylmethyl)-(2-quinolylmethyl)-amine and BQPA = bis(2-quinolylmethyl)-(2-pyridylmethyl)amine were synthesized and structurally characterized. Single crystal X-ray crystallography confirmed the distorted trigonal bipyramidal geometries of complexes 2a-5a. Spectrophotometric titrations and conductivity measurements of the complexes in the CH3CN-H2O mixture showed that the chloro complexes exist in equilibrium with the corresponding hydrolyzed aqua species, [Co(L)(H2O)](2+). The pKa values of the coordinated H2O in aqua complexes vary from 8.4 to 8.7 (37 °C). The interactions of the complexes (1-5) with DNA have been investigated at pH = 7.0 and 9.0 (10 mM Tris-HCl buffer) and 37 °C where very high catalytic cleavage was observed. Under pseudo Michaelis-Menten kinetic conditions, the catalytic rate constants, kcat, decrease in the order 4>2>5>1>3. At pH 7.0 (10 mM Tris-HCl buffer) and 37 °C, the kcat value for complex 4 (6.02 h(-1)), where [Co(BPQA)(H2O)](2+) is the major species, corresponds to 170 million rate enhancement over the non-catalyzed DNA. Electrophoretic experiments conducted in the presence and absence of radical scavengers (DMSO, KI, NaN3) ruled out the oxidative mechanistic pathway of the reaction and suggested that the hydrolytic mechanism is the preferred one. This finding was in agreement with the observed increase in the kcat values at pH 9.0 compared to the corresponding values at pH 7.0 as a result of the increased concentration of the reactive hydroxo species, [Co(L)(OH)](+). The reactivity of the synthesized complexes in catalyzing the DNA cleavage is discussed in relation to the steric effect imposed by the coordinated pyridyl ligand around the central cobalt(ii) center.

Steric effects on the catalytic activities of zinc(II) complexes containing [12]aneN3 ligating units in the cleavage of the RNA and DNA model phosphates

A series of N-methylated mono- and di-[12]aneN(3) ligands () have been synthesized and characterized. The steric effects on the catalytic activities of their mononuclear and dinuclear zinc(ii) complexes in the cleavage of a RNA model 2-hydroxypropyl 4-nitrophenyl phosphate (HPNPP, ) and a DNA model methyl 4-nitrophenyl phosphates (MPNPP, 4) in methanol have been investigated at 25 °C. In the cleavage of phosphate catalyzed by the mononuclear complexes, derived from the N-methylation in the [12]aneN(3) backbone, the plots of k(obs)versus [Zn(II)] changed from an upward curvature to linearity with increasing level of methylation, indicating that N-methylations led to a reduction of dinuclear association that was responsible for the synergetic effect. Compared to the activities of the complex with non-methylated di-[12]aneN(3) ligand, those of the dinuclear zinc(ii) complex (Zn(2)-8), which has the two N-methyl groups, were reduced by two orders of magnitude as measured by the second-order rate constants and synergetic effect in the cleavage of both model compounds. For reactions catalyzed by the fully N-methylated dinuclear complex (Zn(2)-9), no synergetic effect was observed. Nevertheless, complex Zn(2)-8 still showed the remarkable catalytic efficiency, with rate accelerations of 10(9-10)-fold in the cleavage of each of the two phosphates relative to the background reactions, and the synergetic effects of up to 561 folds. pH jump experiments confirmed that the rate-limiting step in the cleavage of by Zn(2)-8 involved the binding process, while that in the reaction with 4 was the chemical cleavage of the P-O bond. Steric effects in the cleavage reactions were analyzed in detail and were compared with the electronic effect caused by oxy anion bridging group in the di-[12]aneN(3) ligand and also with the hydrophobic effect observed in other systems. The work has further confirmed that the combination of the cooperativity between two metal ions and a medium effect could result in excellent catalytic activities for the cleavage of phosphate diesters.

Density functional calculations on the effect of sulfur substitution for 2'-hydroxypropyl-p-nitrophenyl phosphate: C-O vs. P-O bond cleavage

Density functional theory calculations have been used to investigate the intra-molecular attack of 2'-hydroxypropyl-p-nitrophenyl phosphate (HPpNP) and its analogous compound 2-thiouridyl-p-nitrophenyl phosphate (s-2'pNP). Bulk solvent effect has been tested at the geometry optimization level with the polarized continuum model. It is found that the P-path involving the intra-molecular attack at the phosphorus atom and C-path involving the attack at the beta carbon atom proceed through the S(N)2-type mechanism for HPpNP and s-2'pNP. The calculated results indicate that the P-path with the free energy barrier of about 11 kcal/mol is more accessible than the C-path for the intra-molecular attack of HPpNP, which favors the formation of the five-membered phosphate diester. While for s-2'pNP, the C-path with the free energy barrier of about 21 kcal/mol proceeds more favorably than the P-path. The calculated energy barriers of the favorable pathways for HPpNP and s-2'pNP are both in agreement with the experimental results.

Multicomponent synthesis of artificial nucleases and their RNase and DNase activity

The synthesis of new, artificial ribonucleases containing two amino acid residues connected by an aliphatic linker has been developed. Target molecules were synthesized via a catalytic three-component Ugi reaction from aliphatic diisocyanides. Preliminary investigations proved unspecific nuclease activity of the new compounds towards single-stranded RNA and double-stranded circular DNA.

Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight

RNA molecules participate in many fundamental cellular processes either as a carrier of genetic information or as a catalyst, and hence, RNA has received increasing interest both as a chemotherapeutic agent and as a target of chemotherapy. In addition the dual nature of RNA has led to the RNA-world concept, i.e. an assumption that the evolution at an early stage of life was based on RNA-like oligomers that were responsible for the storage and transfer of information and as catalysts maintained primitive metabolism. Accordingly, the kinetics and mechanisms of the cleavage of RNA phosphodiester bonds have received interest and it is hoped they will shed light on the mechanisms of enzyme action and on the development of artificial enzymes. The major mechanistic findings concerning the cleavage by small molecules and ions and their significance for the development of efficient and biologically applicable artificial catalysts for RNA hydrolysis are surveyed in the present perspective.

Structural and catalytic performance of a polyoxometalate-based metal-organic framework having a lanthanide nanocage as a secondary building block

A polyoxometalate-based lanthanide-organic framework was achieved using the {[Ho(4)(dpdo)(8)(H(2)O)(16)BW(12)O(40)] (H(2)O)(2)}(7+) nanocage as a secondary building block for the heterogeneous catalysis of phosphodiester cleavage in an aqueous solution.

Synthesis of binuclear complexes bound in an enlarged tetraphosphamacrocycle: two diphosphine metal units linked in front-to-front style

A large-hole tetraphosphamacrocycle 2, with four phosphorus centers separated at the corners of a 3.7 A wide and 9.7 A long rectangle, was synthesized by a stepwise cyclization reaction between PCl-bridged [1.1]ferrocenophane and bisphenol A in a 2:2 ratio. The macrocycle 2 could incorporate two Ag(+) or Pt(0) fragments in the hole to provide binuclear complexes, which were identified as mu-2-[Ag(NCMe)(2)](2)(BF(4))(2) (3) and mu-2-[Pt(PhCCPh)](2) (5), respectively, using X-ray and spectroscopic analysis. The X-ray structure of 3 demonstrates that the macrocycle 2 serves as a framework in which two diphosphine silver units are aligned in a front-to-front style, while that of 5 indicates that 2 can also bind two bulky Pt(PhCCPh) fragments by the flexible change of its conformation.