Cleavage of an RNA Model Catalyzed by Dinuclear Zn(II) Complexes Containing Rate-Accelerating Pendants. Comparison of the Catalytic Benefits of H-Bonding and Hydrophobic Substituents

Abstract

The transesterification of a simple RNA model, 2-hydroxypropyl p-nitrophenyl phosphate (2, HpNPP) promoted by seven dinuclear Zn(II) catalysts (3,4,5,6,7,8,9:Zn(II)2:(-OCH3)) based on the bis[bis(2-substituted-pyridinyl-6-methyl)]amine ligand system was investigated in methanol under sspH-controlled conditions at 25.0 ± 0.1 °C. The two metal complexing ligands were joined together via the amino N connected to a m-xylyl linker (3, 4, 5, 6, 7) where the 2-pyridinyl substituent = H, CH3, (CH)4, NH2, and NH(C═O)CH3, respectively, and a propyl linker (8, 9) where the ring substituent = H and CH3. All of the dinuclear complexes except 8:Zn(II)2 exhibit saturation kinetics for the kobs versus [catalyst] plots from which one can determine catalyst:substrate binding constants (KM), the catalytic rate constants for their decomposition (kcat), and the second order catalytic rate constants (k2cat = kcat/KM). In the case of 8:Zn(II)2, the plots of kobs versus [catalyst] as a function of sspH are linear, and the catalytic rate constants (k2cat) are defined as the gradients of the plots. Analysis of all of the data at the sspH optimum for each reaction indicates that the presence of the amino and acetamido H-bonding groups and the CH3 group provides similar increases of the kcat terms of 25−50 times that exhibited by the parent complex 3:Zn(II)2. However, in terms of substrate catalyst binding (KM), there is no clear trend that H-bonding groups or the CH3 group provides stronger binding than the parent complex. In terms of the overall second order catalytic rate constant, the CH3, amino, and NH(C═O)CH3 groups provide 20, 10, and 68 times the k2cat observed for the parent complex. In the case of 9:Zn(II)2, the presence of the methyl groups provides a 1000-fold increase in activity (judged by k2cat) over the parent complex 8:Zn(II)2. The results are interpreted to indicate that H-bonding effects may be important for catalysis and less so for substrate binding, but the steric effect and impact on the local polarity provided by a methyl substituent is just as effective and in fact may form part of the acceleratory effect attributed to H-bonding in related systems.

Enantioselective hydrolysis of amino acid esters by non-chiral copper complexes equipped with bis (β-cyclodextrin)s

“…The value was among the largest ones which were gained by using CD-based [29][30][31] or other surfactants containing complex [49,50] as artificial mimics, and are close to those cases by using enzymes or modified enzymes [5,47,50,51], for the hydrolysis of amino acid esters or peptide esters. The hydrolysis of Boc-Lys(Boc)-ONp enantiomers promoted by CuL 1 resulted in more pronounced enantioselectivity than that of Boc-Ala-ONp, with an enantiomer selectivity of 8.8.…”

“…Fig. 2 shows the dependence of the rate constants on the CuL 1 concentration [28,29,[47][48][49]. By increasing the initial catalyst concentration from 5.0 to 100.0 M, deviation from linear increase was observed (Fig.…”

Osmium Complexes Coordinated with Poly(pyridylmethyl)diamine‐Based Hexadentate Ligands

“…On the other hand, TPPN [ N , N , N′ , N′ ‐tetrakis(2‐pyridylmethyl) propylenediamine], that is a propylenediamine analogue of TPEN, is also a hexadentate ligand, but has attracted less attention as compared to TPEN. This is probably due to the existence of an equilibrium between a monomer, [M(TPPN)] 2+ , and a dimer, [M 2 (TPPN) 2 ] 4+ or [M 2 (TPPN)] 4+ , in solution, where the dinuclear metal complexes have been isolated and structurally characterized in the cases of M = Cu 2+ and Zn 2+ , …”

The impact of the second coordination sphere in phosphatase model complexes

“…287 Moreover, an impaired BDNPP affinity was found for the dizinc(II) complex of a bulky ; KM = (9.48 ± 1.74) mM; kcat/KM = 0.26 s -1 M -1 ), which was proposed to be a steric effect attributed to the bulky vinylbenzyl group. 276 Therefore, the exact origin of the acceleration of the BDNPP hydrolysis with the dizinc(II)…”

“…In conclusion, the effect of the functionalization of the dizinc(II) catalyst with hydrophobic and sterically demanding CH3 groups seems comparable afforded by amino and acetamido substituents. 287 Therefore, other effects such as steric and local polarity seem to be as important in such systems as hydrogen-bond formation and should be considered in order to generate more active model complexes.…”