Dataset Information

Free Energy of Ligand Removal in the Metal-Organic Framework UiO-66.

ABSTRACT: We report an investigation of the "missing-linker phenomenon" in the Zr-based metal-organic framework UiO-66 using atomistic force field and quantum chemical methods. For a vacant benzene dicarboxylate ligand, the lowest energy charge-capping mechanism involves acetic acid or Cl-/H2O. The calculated defect free energy of formation is remarkably low, consistent with the high defect concentrations reported experimentally. A dynamic structural instability is identified for certain higher defect concentrations. In addition to the changes in material properties upon defect formation, we assess the formation of molecular aggregates, which provide an additional driving force for ligand loss. These results are expected to be of relevance to a wide range of metal-organic frameworks.

SUBMITTER: Bristow JK

PROVIDER: S-EPMC5010357 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Free Energy of Ligand Removal in the Metal-Organic Framework UiO-66.

Bristow Jessica K JK Svane Katrine L KL Tiana Davide D Skelton Jonathan M JM Gale Julian D JD Walsh Aron A

The journal of physical chemistry. C, Nanomaterials and interfaces 20160412 17

We report an investigation of the "missing-linker phenomenon" in the Zr-based metal-organic framework UiO-66 using atomistic force field and quantum chemical methods. For a vacant benzene dicarboxylate ligand, the lowest energy charge-capping mechanism involves acetic acid or Cl<sup>-</sup>/H<sub>2</sub>O. The calculated defect free energy of formation is remarkably low, consistent with the high defect concentrations reported experimentally. A dynamic structural instability is identified for cer ...[more]

PMID: 27610208

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Project description:Dye-loaded UiO-66 metal-organic framework nanoparticles (NMOFs) modified with catalytic hemin/G-quadruplex DNAzyme labels act as functional hybrid modules for the chemiluminescence resonance energy transfer (CRET) analysis of miRNAs (miRNA-155 or miRNA-21) or genes (p53 or BRCA1). The dye-loaded NMOFs (dye = fluorescein (Fl) or rhodamine 6G (Rh 6G)) are modified with hairpin probes that are engineered to include in their loop domains recognition sequences for the miRNAs or genes, and in their stem regions caged G-quadruplex domains. In the presence of the analytes miRNAs or genes, the hairpin structures are opened, leading, in the presence of hemin, to the self-assembly of hemin/G-quadruplex DNAzyme labels linked to the dye-loaded NMOFs. In the presence of luminol and H2O2, the hemin/G-quadruplex DNAzyme labels catalyze the generation of chemiluminescence that provides radiative energy to stimulate the process of CRET to the dye loaded in the NMOFs, resulting in the luminescence of the loaded dye without external excitation. The resulting CRET signals relate to the concentrations of the miRNAs or the genes and allow the sensitive analysis of miRNAs and genes. In addition, the DNA hairpin-functionalized dye-loaded NMOF sensing modules were further applied to develop amplified miRNA or gene CRET-based sensing platforms. The dye-loaded NMOFs were modified with hairpin probes that include in their loop domain the recognition sequences for miRNA-155 or miRNA-21 or the recognition sequences for the p53 or BRCA1 genes. Subjecting the hairpin-modified NMOFs to the respective miRNAs or genes, in the presence of two hairpins H i and H j that include in their stem regions caged G-quadruplex subunit domains, results in the analyte-triggered opening of the probe hairpin linked to the NMOFs, and the opened hairpin tethers induce the cross-opening of the hairpins H i and H j by the hybridization chain reaction, HCR, resulting in the assembly of G-quadruplex wires tethered to the NMOFs. The binding of hemin to the HCR-generated chains yields hemin/G-quadruplex DNAzyme wires that enhance, in the presence of luminol/H2O2, the CRET processes in the hybrid nanostructures. These amplification platforms lead to the amplified sensing of miRNAs and genes. By mixing the Fl- and Rh 6G-loaded hairpin-functionalized UiO NMOFs, the multiplexed CRET detection of miRNA-155, miRNA-21 and the p53 and BRCA1 genes is demonstrated.

Dataset Information

Free Energy of Ligand Removal in the Metal-Organic Framework UiO-66.

Publications

Free Energy of Ligand Removal in the Metal-Organic Framework UiO-66.

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