Browse
Submit Data
Databases
API
Help

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Machine-Learning Prediction of Metal-Organic Framework Guest Accessibility from Linker and Metal Chemistry.

ABSTRACT: The choice of metal and linker together define the structure and therefore the guest accessibility of a metal-organic framework (MOF), but the large number of possible metal-linker combinations makes the selection of components for synthesis challenging. We predict the guest accessibility of a MOF with 80.5 % certainty based solely on the identity of these two components as chosen by the experimentalist, by decomposing reported experimental three-dimensional MOF structures in the Cambridge Structural Database into metal and linker and then learning the connection between the components' chemistry and the MOF porosity. Pore dimensions of the guest-accessible space are classified into four ranges with three sequential models. Both the dataset and the predictive models are available to download and offer simple guidance in prioritization of the choice of the components for exploratory MOF synthesis for separation and catalysis based on guest accessibility considerations.

SUBMITTER: Petuya R

PROVIDER: S-EPMC9303542 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Infrared crystallography for framework and linker orientation in metal-organic framework films.

Project description:Pore alignment and linker orientation influence diffusion and guest molecule interactions in metal-organic frameworks (MOFs) and play a pivotal role for successful utilization of MOFs. The crystallographic orientation and the degree of orientation of MOF films are generally determined using X-ray diffraction. However, diffraction methods reach their limit when it comes to very thin films, identification of chemical connectivity or the orientation of organic functional groups in MOFs. Cu-based 2D MOF and 3D MOF films prepared via layer-by-layer method and from aligned Cu(OH)2 substrates were studied with polarization-dependent Fourier-transform infrared (FTIR) spectroscopy in transmission and attenuated total reflection configuration. Thereby, the degrees for in-plane and out-of-plane orientation, the aromatic linker orientation and the initial alignment during layer-by-layer MOF growth, which is impossible to investigate by laboratory XRD equipment, was determined. Experimental IR spectra correlate with theoretical explanations, paving the way to expand the principle of IR crystallography to oriented, organic-inorganic hybrid films beyond MOFs.

| S-EPMC8278957 | biostudies-literature

Guest-Controlled Incommensurate Modulation in a Meta-Rigid Metal-Organic Framework Material.

Project description:Structural transitions of host systems in response to guest binding dominate many chemical processes. We report an unprecedented type of structural flexibility within a meta-rigid material, MFM-520, which exhibits a reversible periodic-to-aperiodic structural transition resulting from a drastic distortion of a [ZnO4N] node controlled by the specific host-guest interactions. The aperiodic crystal structure of MFM-520 has no three-dimensional (3D) lattice periodicity but shows translational symmetry in higher-dimensional (3 + 2)D space. We have directly visualized the aperiodic state which is induced by incommensurate modulation of the periodic framework of MFM-520·H2O upon dehydration to give MFM-520. Filling MFM-520 with CO2 and SO2 reveals that, while CO2 has a minimal structural influence, SO2 can further modulate the structure incommensurately. MFM-520 shows exceptional selectivity for SO2 under flue-gas desulfurization conditions, and the facile release of captured SO2 from MFM-520 enabled the conversion to valuable sulfonamide products. MFM-520 can thus be used as a highly efficient capture and delivery system for SO2.

| S-EPMC7668537 | biostudies-literature

Host-Guest Interactions of Zirconium-Based Metal-Organic Framework with Ionic Liquid.

Project description:A metal-organic framework (MOF) is a three-dimensional crystalline compound made from organic ligands and metals. The cross-linkage between organic ligands and metals creates a network of coordination polymers containing adjustable voids with a high total surface area. This special feature of MOF made it possible to form a host-guest interaction with small molecules, such as ionic liquid (IL), which can alter the phase behavior and improve the performance in battery applications. The molecular interactions of MOF and IL are, however, hard to understand due to the limited number of computational studies. In this study, the structural parameters of a zirconium-based metal-organic framework (UiO-66) and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [EMIM][TFSI] were investigated via a combined experimental and computational approach using the linker model approach. When IL was loaded, the bond length and bond angle of organic linkers were distorted due to the increased electron density surrounding the framework. The increase in molecular orbital energy after confining IL stabilized the structure of this hybrid system. The molecular interactions study revealed that the combination of UiO-66 and [EMIM][TFSI] could be a promising candidate as an electrolyte material in an energy storage system.

| S-EPMC10055841 | biostudies-literature

Multiple rotational rates in a guest-loaded, amphidynamic zirconia metal-organic framework.

Project description:Amphidynamic motion in metal-organic frameworks (MOFs) is an intriguing emergent property, characterized by high rotational motion of the phenylene rings that are embedded within an open, rigid framework. Here, we show how the phenylene rings in the organic linkers of the water stable MOF PEPEP-PIZOF-2 exhibit multiple rotational rates as a result of the electronic structure of the linker, with and without the presence of highly interacting molecular guests. By selective 2H enrichment, we prepared isotopologues PIZOF-2d4 and PIZOF-2d8 and utilized solid-state 13C and 2H NMR to differentiate the dynamic behavior of specific phenylenes in the linker at room temperature. A difference of at least one order of magnitude was observed between the rates of rotation of the central and outer rings at room temperature, with the central phenylene ring, surrounded by ethynyl groups, undergoing ultrafast 180° jumps with frequencies higher than 10 MHz. Moreover, loading tetracyanoquinodimethane (TCNQ) within the pores produced significant changes in the MOF's electronic structure, but very small changes were observed in the rotational rates, providing an unprecedented insight into the effects that internal dynamics have on guest diffusion. These findings would help elucidate the in-pore guest dynamics that affect transport phenomena in these highly used MOFs.

| S-EPMC8162477 | biostudies-literature

Nanopore-induced host-guest charge transfer phenomena in a metal-organic framework.

Project description:A spontaneous entrapment of electron-donating small guest molecules, including tetrathiafulvalene (TTF) and N,N,N',N'-tetramethyl-1,3-propanediamine (TMPDA), was realized in a structurally flexible metal-organic framework, {Mn7(2,7-AQDC)6(2,6-AQDC)(DMA)6}∞ (AQDC = anthraquinone dicarboxylates, DMA = N,N-dimethylacetamide), with electron-accepting anthraquinone groups, generating two MOF guest charge transfer complexes: {Mn7(2,7-AQDC)6(2,6-AQDC)(DMA)6(TTF)5} and {Mn7(2,7-AQDC)6(2,6-AQDC)(DMA)4(H2O)2(TMPDA)7}. Using a mild impregnation procedure, single crystals of the target complexes were obtained via a crystal-to-crystal conversion, and the crystals were suitable for structural analysis. Single crystal X-ray analysis demonstrated the different arrangements of these intercalated donor molecules: some donor molecules interacted with the anthraquinone groups and formed infinite D-A-A-D stacks, some appeared beside the anthraquinone groups but only formed donor-acceptor pairs, and the remainder of the molecules simply filled the space. The charge transfer between the guests and the framework was spectroscopically confirmed, and the radical densities on the organic species were estimated using magnetic susceptibility measurements. Compared with a solid-state mixture of anthraquinone and donor molecules, the evenly distributed donor molecules in the micropores of the MOF resulted in a "solid solution" state and significantly promoted the degree of charge transfer between donors and acceptors. Such an encapsulation process may be adopted as a new strategy for post-modification of the electronic and magnetic properties of MOFs, as well as for generating new semiconducting charge-transfer complexes.

| S-EPMC5916106 | biostudies-literature

Cryo-EM structures of atomic surfaces and host-guest chemistry in metal-organic frameworks.

Project description:Host-guest interactions govern the chemistry of a broad range of functional materials, but direct imaging using conventional transmission electron microscopy (TEM) has not been possible. This problem is exacerbated in metal-organic framework (MOF) materials, which are easily damaged by the electron beam. Here, we use cryogenic-electron microscopy (cryo-EM) to stabilize the host-guest structure and resolve the atomic surface of zeolitic imidazolate framework (ZIF-8) and its interaction with guest CO2 molecules. We image step-edge sites on the ZIF-8 surface that provides insight to its growth behavior. Furthermore, we observe two distinct binding sites for CO2 within the ZIF-8 pore, which are predicted by density functional theory (DFT) to be energetically favorable. This CO2 insertion induces an apparent ~3% lattice expansion along the <002> and <011> directions of the ZIF-8 unit cell. The ability to stabilize and preserve host-guest chemistry opens a rich materials space for scientific exploration and discovery using cryo-EM.

| S-EPMC8184120 | biostudies-literature

Atomistic Insight Into the Host-Guest Interaction of a Photoresponsive Metal-Organic Framework.

Project description:Photoresponsive functional materials have gained increasing attention due to their externally tunable properties. Molecular switches embedded in these materials enable the control of phenomena at the atomic level by light. Metal-organic frameworks (MOFs) provide a versatile platform to immobilize these photoresponsive units within defined molecular environments to optimize the intended functionality. For the application of these photoresponsive MOFs (pho-MOFs), it is crucial to understand the influence of the switching state on the host-guest interaction. Therefore, we present a detailed insight into the impact of molecular switching on the intermolecular interactions. By performing atomistic simulations, we revealed that due to different interactions of the guest molecules with the two isomeric states of an azobenzene-functionalized MOF, both the adsorption sites and the orientation of the molecules within the pores are modulated. By shedding light on the host-guest interaction, our study highlights the unique potential of pho-MOFs to tailor molecular interaction by light.

| S-EPMC7027908 | biostudies-literature

Unraveling the Guest-Induced Switchability in the Metal-Organic Framework DUT-13(Zn)*.

Project description:The switching mechanism of the flexible framework Zn4 O(benztb)1.5 (benztb=N,N,N',N'-benzidine tetrabenzoate), also known as DUT-13, was studied by advanced powder X-ray diffraction (PXRD) and gas physisorption techniques. In situ synchrotron PXRD experiments upon physisorption of nitrogen (77 K) and n-butane (273 K) shed light on the hitherto unnoticed guest-induced breathing in the MOF. The mechanism of contraction is based on the conformationally labile benztb ligand and accompanied by a reduction in specific pore volume from 2.03 cm3 g-1 in the open-pore phase to 0.91 cm3 g-1 in the contracted-pore phase. The high temperature limit for adsorption-induced contraction of 170 K, determined by systematic temperature variation of methane adsorption isotherms, indicates that the DUT-13 framework is softer than other mesoporous MOFs like DUT-49 and does not support the formation of overloaded metastable states required for negative gas-adsorption transitions.

| S-EPMC8362161 | biostudies-literature

Guest-dependent single-ion magnet behaviour in a cobalt(ii) metal-organic framework.

Project description:Single-ion magnets (SIMs) are the smallest possible magnetic devices for potential applications in quantum computing and high-density information storage. Both, their addressing in surfaces and their organization in metal-organic frameworks (MOFs) are thus current challenges in molecular chemistry. Here we report a two-dimensional 2D MOF with a square grid topology built from cobalt(ii) SIMs as nodes and long rod-like aromatic bipyridine ligands as linkers, and exhibiting large square channels capable to host a large number of different guest molecules. The organization of the cobalt(ii) nodes in the square layers improves the magnetic properties by minimizing the intermolecular interactions between the cobalt(ii) centres. Moreover, the SIM behaviour was found to be dependent on the nature of the aromatic guest molecules. The whole process could be followed by single-crystal X-ray diffraction, providing comprehensive evidence of the putative role of the solvent guest molecules that leave a "fingerprint" on the 2D structures and thus, on the cobalt environment.

| S-EPMC5977934 | biostudies-literature

Locating Guest Molecules inside Metal-Organic Framework Pores with a Multilevel Computational Approach.

Project description:Molecular docking has traditionally mostly been employed in the field of protein-ligand binding. Here, we extend this method, in combination with DFT-level geometry optimizations, to locate guest molecules inside the pores of metal-organic frameworks. The position and nature of the guest molecules tune the physicochemical properties of the host-guest systems. Therefore, it is essential to be able to reliably locate them to rationally enhance the performance of the known metal-organic frameworks and facilitate new material discovery. The results obtained with this approach are compared to experimental data. We show that the presented method can, in general, accurately locate adsorption sites and structures of the host-guest complexes. We therefore propose our approach as a computational alternative when no experimental structures of guest-loaded MOFs are available. Additional information on the adsorption strength in the studied host-guest systems emerges from the computed interaction energies. Our findings provide the basis for other computational studies on MOF-guest systems and contribute to a better understanding of the structure-interaction-property interplay associated with them.

| S-EPMC9841564 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data