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Tuning the reactivity of nitriles using Cu(ii) catalysis - potentially prebiotic activation of nucleotides.

ABSTRACT: During the transition from prebiotic chemistry to biology, a period of solution-phase, non-enzymatic activation of (oligo)nucleotides must have occurred, and accordingly, a mechanism for phosphate activation must have existed. Herein, we detail results of an investigation into prebiotic phosphate activation chemistry using simple, prebiotically available nitriles whose reactivity is increased by Cu²⁺ ions. Furthermore, although Cu²⁺ ions are known to catalyse the hydrolysis of phosphodiester bonds, we found this deleterious activity to be almost completely suppressed by inclusion of amino acids or dipeptides, which may suggest a productive relationship between protein and RNA from the outset.

SUBMITTER: Liu Z

PROVIDER: S-EPMC6137443 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Tuning the reactivity of nitriles using Cu(ii) catalysis - potentially prebiotic activation of nucleotides.

Liu Ziwei Z Mariani Angelica A Wu Longfei L Ritson Dougal D Folli Andrea A Murphy Damien D Sutherland John J

Chemical science 20180725 35

During the transition from prebiotic chemistry to biology, a period of solution-phase, non-enzymatic activation of (oligo)nucleotides must have occurred, and accordingly, a mechanism for phosphate activation must have existed. Herein, we detail results of an investigation into prebiotic phosphate activation chemistry using simple, prebiotically available nitriles whose reactivity is increased by Cu<sup>2+</sup> ions. Furthermore, although Cu<sup>2+</sup> ions are known to catalyse the hydrolysis ...[more]

PMID: 30310625

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Project description:Two new monomeric Cu(II) alkoxide complexes were prepared and fully characterized as models for intermediates in copper/radical mediated alcohol oxidation catalysis: Tp(tBuR)Cu(II)OCH2CF3 with Tp(tBu) = hydro-tris(3-tert-butyl-pyrazol-1-yl)borate 1 or Tp(tBuMe) = hydro-tris(3-tert-butyl-5-methyl-pyrazol-1-yl)borate 2. These complexes were made as models for potential intermediates in enzymatic and synthetic catalytic cycles for alcohol oxidation. However, the alkoxide ligands are not readily oxidized by loss of H; instead, these complexes were found to be hydrogen atom acceptors. They oxidize the hydroxylamine TEMPOH, 2,4,6-tri-t-butylphenol, and 1,4-cyclohexadiene to the nitroxyl radical, phenoxyl radical, and benzene, with formation of HOCH2CF3 (TFE) and the Cu(I) complexes Tp(tBuR)Cu(I)-MeCN in dichloromethane/1% MeCN or 1/2 [Tp(tBuR)Cu(I)]2 in toluene. On the basis of thermodynamics and kinetics arguments, these reactions likely proceed through concerted proton-electron transfer mechanisms. Thermochemical analyses give lower limits for the "effective bond dissociation free energies (BDFE)" of the O-H bonds in 1/2[Tp(tBuR)Cu(I)]2 + TFE and upper limits for the free energies associated with alkoxide oxidations via hydrogen atom transfer (effective alkoxide ?-C-H BDFEs). These values are summations of the free energies of multiple chemical steps, which include the energetically favorable formation of 1/2[Tp(tBuR)Cu(I)]2. The effective alkoxide ?-C-H bonds are very weak, BDFE ? 38 ± 4 kcal mol(-1) for 1 and ?44 ± 5 kcal mol(-1) for 2 (gas-phase estimates), because C-H homolysis is thermodynamically coupled to one electron transfer to Cu(II) as well as the favorable formation of the 1/2[Tp(tBuR)Cu(I)]2 dimer. Treating 1 with the H atom acceptor (t)Bu3ArO(•) did not result in the expected alkoxide oxidation to an aldehyde, but rather net 2,2,2-trifluoroethoxyl radical transfer occurred to generate an unusual 2-substituted dienone-ether product. Treating 2 with (t)Bu3ArO(•) gives no reaction, despite evidence that overall ligand oxidation and formation of 1/2[Tp(tBuMe)Cu(I)]2 is significantly exoergic. The origin of this lack of reactivity may be due to insufficient weakening of the alcohol ?-C-H bond upon complexation to copper.

Project description:We report a complex with a rare Cu(II)-O-Cu(II) structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. Interest in such compounds is fueled by the recent discovery that a Cu(II)-O-Cu(II) species on the surface of Cu-ZSM-5 is capable of oxidizing methane to methanol, and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. For the synthesis of our Cu2O complex we have developed a novel, neutral ligand system, FurNeu, exhibiting two N-(N',N'-dimethylaminoethyl)(2-pyridylmethyl)amino binding pockets connected by a dibenzofuran spacer. The reaction of FurNeu with CuCl yielded [FurNeu](Cu2(μ-Cl))(CuCl2), 1, demonstrating the geometric potential of the ligand to stabilize Cu-X-Cu moieties. A Cu(I) precursor with weakly coordinating anions was chosen in the next step, namely [Cu(NCCH3)4]OTf, which led to the formation of [FurNeu](Cu(NCCH3))2(OTf)2, 3. Treatment of 3 with O2 or PhIO led to identical green solutions, whose UV-vis spectra were markedly different from the one displayed by [FurNeu](Cu)2(OTf)4, 4, prepared independently from FurNeu and Cu(OTf)2. Further investigations including PhIO consumption experiments, NMR and UV-vis spectroscopy, HR-ESI mass spectrometry, and protonation studies led to the identification of the green product as [FurNeu](Cu2(μ-O))(OTf)2, 5. DOSY NMR spectroscopy confirmed its monomeric character. Over longer periods of time 5 decomposes to give [Cu(picoloyl)2], formed through an oxidative N-dealkylation reaction followed by further oxidation of the ligand. Due to its slow decomposition reaction, all attempts to crystallize 5 failed. However, its structure in solution could be determined by EXAFS analysis in combination with DFT calculations, which revealed a Cu-O-Cu angle that amounts to 105.17°. Moreover, TDDFT calculations helped to rationalize the UV-vis absorptions of 5. The reactivity of complex 5 with 2,4-di-tert-butylphenol, DTBP, was also investigated; the initially formed biphenol product, TBBP, was found to further react in the presence of excessive O2 to yield 2,4,7,9-tetra-tert-butyloxepino[2,3-b]benzofuran, TBOBF, via an intermediate diphenoquinone. It turned out that 5, or its precursor 3, can even be employed as a catalyst for the oxidation of DTBP to TBBP or for the oxidation of TBBP to TBOBF.

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Tuning the reactivity of nitriles using Cu(ii) catalysis - potentially prebiotic activation of nucleotides.

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Tuning the reactivity of nitriles using Cu(ii) catalysis - potentially prebiotic activation of nucleotides.

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