The use of 18-crown-6 (18-c-6) in place of 2.2.2-cryptand (crypt) in rare earth amide reduction reactions involving potassium has proven to be crucial in the synthesis of Ln( ii ) complexes and isolation of their CO reduction products. The faster speed of crystallization with 18-c-6 appears to be important. Previous studies have shown that reduction of the trivalent amide complexes Ln(NR 2 ) 3 (R = SiMe 3 ) with potassium in the presence of 2.2.2-cryptand (crypt) forms the divalent [K(crypt)][Ln II (NR 2 ) 3 ] complexes for Ln = Gd, Tb, Dy, and Tm. However, for Ho and Er, the [Ln(NR 2 ) 3 ] 1− anions were only isolable with [Rb(crypt)] 1+ counter-cations and isolation of the [Y II (NR 2 ) 3 ] 1− anion was not possible under any of these conditions. We now report that by changing the potassium chelator from crypt to 18-crown-6 (18-c-6), the [Ln(NR 2 ) 3 ] 1− anions can be isolated not only for Ln = Gd, Tb, Dy, and Tm, but also for Ho, Er, and Y. Specifically, these anions are isolated as salts of a 1 : 2 potassium : crown sandwich cation, [K(18-c-6) 2 ] 1+ , i.e. [K(18-c-6) 2 ][Ln(NR 2 ) 3 ]. The [K(18-c-6) 2 ] 1+ counter-cation was superior not only in the synthesis, but it also allowed the isolation of crystallographically-characterizable products from reactions of CO with the [Ln(NR 2 ) 3 ] 1− anions that were not obtainable from the [K(crypt)] 1+ analogs. Reaction of CO with [K(18-c-6) 2 ][Ln(NR 2 ) 3 ], generated in situ , yielded crystals of the ynediolate products, {[(R 2 N) 3 Ln] 2 (μ-OCCO)} 2− , which crystallized with counter-cations possessing 2 : 3 potassium : crown ratios, i.e. {[K 2 (18-c-6) 3 ]} 2+ , for Gd, Dy, Ho. In contrast, reaction of CO with a solution of isolated [K(18-c-6) 2 ][Gd(NR 2 ) 3 ], produced crystals of an enediolate complex isolated with a counter-cation with a 2 : 2 potassium : crown ratio namely [K(18-c-6)] 2 2+ in the complex [K(18-c-6)] 2 {[(R 2 N) 2 Gd 2 (μ-OCHCHO) 2 ]}.
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Computational predictions of metal–macrocycle stability constants require accurate treatments of local solvent and pH effects
Rational design of molecular chelating agents requires a detailed understanding of physicochemical ligand–metal interactions in solvent phase. Computational quantum chemistry methods should be able to provide this, but computational reports have shown poor accuracy when determining absolute binding constants for many chelating molecules. To understand why, we compare and benchmark static- and dynamics-based computational procedures for a range of monovalent and divalent cations binding to a conventional cryptand molecule: 2.2.2-cryptand ([2.2.2]). The benchmarking comparison shows that dynamics simulations using standard OPLS-AA classical potentials can reasonably predict binding constants for monovalent cations, but these procedures fail for divalent cations. We also consider computationally efficient static procedure using Kohn–Sham density functional theory (DFT) and cluster-continuum modeling that accounts for local microsolvation and pH effects. This approach accurately predicts binding energies for monovalent and divalent cations with an average error of 3.2 kcal mol −1 compared to experiment. This static procedure thus should be useful for future molecular screening efforts, and high absolute errors in the literature may be due to inadequate modeling of local solvent and pH effects.
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- Award ID(s):
- 1705592
- NSF-PAR ID:
- 10310191
- Date Published:
- Journal Name:
- Physical Chemistry Chemical Physics
- Volume:
- 23
- Issue:
- 15
- ISSN:
- 1463-9076
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Folding of ribozymes into well-defined tertiary structures usually requires divalent cations. How Mg2+ ions direct the folding kinetics has been a long-standing unsolved problem because experiments cannot detect the positions and dynamics of ions. To address this problem, we used molecular simulations to dissect the folding kinetics of the Azoarcus ribozyme by monitoring the path each molecule takes to reach the folded state. We quantitatively establish that Mg2+ binding to specific sites, coupled with counter-ion release of monovalent cations, stimulate the formation of secondary and tertiary structures, leading to diverse pathways that include direct rapid folding and trapping in misfolded structures. In some molecules, key tertiary structural elements form when Mg2+ ions bind to specific RNA sites at the earliest stages of the folding, leading to specific collapse and rapid folding. In others, the formation of non-native base pairs, whose rearrangement is needed to reach the folded state, is the rate-limiting step. Escape from energetic traps, driven by thermal fluctuations, occurs readily. In contrast, the transition to the native state from long-lived topologically trapped native-like metastable states is extremely slow. Specific collapse and formation of energetically or topologically frustrated states occur early in the assembly process.
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null (Ed.)Hydrostatic pressure can perturb biomolecular function by altering equilibrium structures and folding dynamics. Its influences are particularly important to deep sea organisms, as maximum pressures reach ≈1100 bar at the bottom of the ocean as a result of the rapid increase in hydraulic pressure (1 bar every 10 meters) under water. In this work, DNA hybridization kinetics has been studied at the single molecule level with external, tunable pressure control ( P max ≈ 1500 bar), realized by incorporating a mechanical hydraulic capillary sample cell into a confocal fluorescence microscope. We find that the DNA hairpin construct promotes unfolding (“denatures”) with increasing pressure by simultaneously decelerating and accelerating the unimolecular rate constants for folding and unfolding, respectively. The single molecule kinetics is then investigated via pressure dependent van’t Hoff analysis to infer changes in the thermodynamic molar volume, which unambiguously reveals that the effective DNA plus solvent volume increases (Δ V 0 > 0) along the folding coordinate. Cation effects on the pressure dependent kinetics are also explored as a function of monovalent [Na + ]. In addition to stabilizing the overall DNA secondary structure, sodium ions at low concentrations are also found to weaken any pressure dependence for the folding kinetics, but with these effects quickly saturating at physiologically relevant levels of [Na + ]. In particular, the magnitudes of the activation volumes for the DNA dehybridization (Δ V ‡unfold) are significantly reduced with increasing [Na + ], suggesting that sodium cations help DNA adopt a more fold-like transition state configuration.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/D1CP00611H
