scholarly journals A two-fold approach towards understanding properties of two self-assembled macrocycles: resorcin[4]arene and pyrogallol[4]arene

2015 ◽  
Author(s):  
◽  
Amanda M. Drachnik
Keyword(s):  
Functional Group ◽  
Electronic Structure Calculations ◽  
Industrial Applications ◽  
Molecular Magnetism ◽  
Metal Coordination ◽  
Metal Organic ◽  
Self Assembled ◽  
Synthetic Work ◽  
Structure Calculations

Self-assembled macrocycles, molecular entities that are connected together spontaneously in a cyclic manner, are studied herein. Pyrogallol[4]arene (PgC) and resorcin[4]arene (RsC), self-assembled macrocycles made from four units of pyrogallol and four units of resorcinol, respectively, are be the main focus of this work. The first two topics discussed are metal-coordination of PgC and RsC. PgC forms both dimeric and hexameric metal-organic nanocapsules (MONCs); however, these types of architectures have not yet been observed for RsC. In our attempt to create analogous MONCs involving RsC, manganese and cobalt complexes were encapsulated inside a hydrogen-bonded dimeric capsule of RsC. The investigation into metal-coordinated PgC MONCs led to additional metal-coordination on the exterior of the MONCs, thus creating metal-organic frameworks using MONCs. Both of these systems have potential in the applications of molecular magnetism, gas sorption/separation, and encapsulation of other molecules. PgC and RsC also may be used to encapsulate pharmaceuticals, e.g. Humalog and gabapentin. In this work, cocrystallization of RsC with pregabalin, a pharmaceutical similar to gabapentin in both structure (GABA functional group) and usage, was attempted. Unexpectantly, pregabalin underwent a cyclization to 4-isobutylpyrrolidone-2, a compound known in polymer synthesis. Both pregabalin and 4- isobutylpyrrolidone-2 are linked to important industrial applications. The final chapter discusses the study of the various stereoisomers of RsCs by means of electronic structure calculations, in both the gas and solution phase. Stereoisomers are structures of a molecule for which the atoms are orientated differently in space but the molecule retains its identity. It was found from these calculations that the cone conformer, where the hydroxyl-substituted side (top) of all four resorcinol subunits point up, is most stable when the tail group of the macrocycle is a hydrogen. The chair stereoisomer, where top of one subunit points up, the top of the opposite subunit points down, and tops of the remaining two subunits lie in the plane, is most stable when the tail group of the macrocycle is a phenyl. These studies are of importance to the synthetic work on this macrocycle, which affects all further studies on the macrocycle.

Message Passing Neural Networks for Partial Charge Assignment to Metal-Organic Frameworks

2020 ◽  
Author(s):  
Ali Raza ◽  
Arni Sturluson ◽  
Cory Simon ◽  
Xiaoli Fern
Keyword(s):  
Electronic Structure ◽  
Message Passing ◽  
Gas Adsorption ◽  
Metal Organic Frameworks ◽  
Computational Cost ◽  
Electronic Structure Calculations ◽  
High Fidelity ◽  
Partial Charges ◽  
Metal Organic ◽  
Structure Calculations

Virtual screenings can accelerate and reduce the cost of discovering metal-organic frameworks (MOFs) for their applications in gas storage, separation, and sensing. In molecular simulations of gas adsorption/diffusion in MOFs, the adsorbate-MOF electrostatic interaction is typically modeled by placing partial point charges on the atoms of the MOF. For the virtual screening of large libraries of MOFs, it is critical to develop computationally inexpensive methods to assign atomic partial charges to MOFs that accurately reproduce the electrostatic potential in their pores. Herein, we design and train a message passing neural network (MPNN) to predict the atomic partial charges on MOFs under a charge neutral constraint. A set of ca. 2,250 MOFs labeled with high-fidelity partial charges, derived from periodic electronic structure calculations, serves as training examples. In an end-to-end manner, from charge-labeled crystal graphs representing MOFs, our MPNN machine-learns features of the local bonding environments of the atoms and learns to predict partial atomic charges from these features. Our trained MPNN assigns high-fidelity partial point charges to MOFs with orders of magnitude lower computational cost than electronic structure calculations. To enhance the accuracy of virtual screenings of large libraries of MOFs for their adsorption-based applications, we make our trained MPNN model and MPNN-charge-assigned computation-ready, experimental MOF structures publicly available.<br>

scholarly journals Influence of size, shape, heteroatom content and dispersive contributions on guest binding in a coordination cage

2017 ◽  
Vol 53 (87) ◽  
pp. 11933-11936 ◽  
Author(s):  
Susanne Löffler ◽  
Axel Wuttke ◽  
Bo Zhang ◽  
Julian J. Holstein ◽  
Ricardo A. Mata ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Electronic Structure Calculations ◽  
Guest Molecules ◽  
Guest Binding ◽  
Self Assembled ◽  
Structure Calculations

Encapsulation of neutral guest molecules inside a self-assembled coordination cage was systematically studied using NMR and MS experiments. Electronic structure calculations reveal substantial contributions of dispersive interactions to binding.

Message Passing Neural Networks for Partial Charge Assignment to Metal-Organic Frameworks

2020 ◽  
Author(s):  
Ali Raza ◽  
Arni Sturluson ◽  
Cory Simon ◽  
Xiaoli Fern
Keyword(s):  
Electronic Structure ◽  
Message Passing ◽  
Gas Adsorption ◽  
Metal Organic Frameworks ◽  
Computational Cost ◽  
Electronic Structure Calculations ◽  
High Fidelity ◽  
Partial Charges ◽  
Metal Organic ◽  
Structure Calculations

Virtual screenings can accelerate and reduce the cost of discovering metal-organic frameworks (MOFs) for their applications in gas storage, separation, and sensing. In molecular simulations of gas adsorption/diffusion in MOFs, the adsorbate-MOF electrostatic interaction is typically modeled by placing partial point charges on the atoms of the MOF. For the virtual screening of large libraries of MOFs, it is critical to develop computationally inexpensive methods to assign atomic partial charges to MOFs that accurately reproduce the electrostatic potential in their pores. Herein, we design and train a message passing neural network (MPNN) to predict the atomic partial charges on MOFs under a charge neutral constraint. A set of ca. 2,250 MOFs labeled with high-fidelity partial charges, derived from periodic electronic structure calculations, serves as training examples. In an end-to-end manner, from charge-labeled crystal graphs representing MOFs, our MPNN machine-learns features of the local bonding environments of the atoms and learns to predict partial atomic charges from these features. Our trained MPNN assigns high-fidelity partial point charges to MOFs with orders of magnitude lower computational cost than electronic structure calculations. To enhance the accuracy of virtual screenings of large libraries of MOFs for their adsorption-based applications, we make our trained MPNN model and MPNN-charge-assigned computation-ready, experimental MOF structures publicly available.<br>

On the Electronic and Optical Properties of Metal-Organic Frameworks: Case Study of MIL-125 and MIL-125-NH2

2020 ◽  
Author(s):  
Gloria Capano ◽  
Francesco Ambrosio ◽  
Stavroula Kampouri ◽  
Kyriakos Stylianou ◽  
Alfredo Pasquarello ◽  
...  
Keyword(s):  
Metal Organic Frameworks ◽  
Electronic Structure Calculations ◽  
Charge Carriers ◽  
Order Of Magnitude ◽  
Novel Material ◽  
Active Nanoparticles ◽  
Metal Organic ◽  
Structure Calculations ◽  
Catalytic Performances

<div>The photoactive MIL-125 and MIL-125-NH$_{2}$ Metal-Organic Frameworks (MOFs), despite a very similar crystalline structure, exhibit different optically behaviour. Luminescence in MIL-125 decays in about 1 ns while for its amino counterpart the lifetime of the charge-carriers is at least one order of magnitude larger. The origin of this difference is the key element for understanding the photocatalytic behaviour of MIL-125-NH<sub>2</sub> when associated with active nanoparticles, behaviour that is completely absent in MIL-125. By performing advanced</div><div>ab-initio electronic structure calculations, we find that charge-carriers interact differently in the two MOFs with subsequent effects on the luminescence lifetimes and their catalytic performances. To confirm the predictions of our model we synthesized a novel material in the MIL-125 family, MIL-125-NH<sub>2</sub>-[10%](OH)<sub>2</sub>, and confirm that our theory correctly predicts a faster decay compared to MIL-125-NH<sub>2</sub>.</div>

On the Electronic and Optical Properties of Metal-Organic Frameworks: Case Study of MIL-125 and MIL-125-NH2

2020 ◽  
Author(s):  
Gloria Capano ◽  
Francesco Ambrosio ◽  
Stavroula Kampouri ◽  
Kyriakos Stylianou ◽  
Alfredo Pasquarello ◽  
...  
Keyword(s):  
Metal Organic Frameworks ◽  
Electronic Structure Calculations ◽  
Charge Carriers ◽  
Order Of Magnitude ◽  
Novel Material ◽  
Active Nanoparticles ◽  
Metal Organic ◽  
Structure Calculations ◽  
Catalytic Performances

<div>The photoactive MIL-125 and MIL-125-NH$_{2}$ Metal-Organic Frameworks (MOFs), despite a very similar crystalline structure, exhibit different optically behaviour. Luminescence in MIL-125 decays in about 1 ns while for its amino counterpart the lifetime of the charge-carriers is at least one order of magnitude larger. The origin of this difference is the key element for understanding the photocatalytic behaviour of MIL-125-NH<sub>2</sub> when associated with active nanoparticles, behaviour that is completely absent in MIL-125. By performing advanced</div><div>ab-initio electronic structure calculations, we find that charge-carriers interact differently in the two MOFs with subsequent effects on the luminescence lifetimes and their catalytic performances. To confirm the predictions of our model we synthesized a novel material in the MIL-125 family, MIL-125-NH<sub>2</sub>-[10%](OH)<sub>2</sub>, and confirm that our theory correctly predicts a faster decay compared to MIL-125-NH<sub>2</sub>.</div>

scholarly journals Flexible and Responsive Nature of 2D Layered Conductive Metal-Organic Frameworks Determine Their Catalytic Activity in Oxidative Dehydrogenation of Propane

2020 ◽  
Author(s):  
Mohammad R. Momeni ◽  
Zeyu Zhang ◽  
Farnaz A. Shakib
Keyword(s):  
Electronic Structure ◽  
Catalytic Activity ◽  
Active Sites ◽  
Metal Organic Framework ◽  
Electronic Structure Calculations ◽  
Electronic Structure Methods ◽  
Catalytically Active ◽  
Metal Organic ◽  
Dynamics Simulations ◽  
Structure Calculations

A multi-faceted approach is introduced for investigating the effects of intrinsic and guest(water)-induced structural transformations/deformations and heterogeneity on catalytic activity of the 2D π-stacked layered Co3(HTTP)2, HTTP = hexathiotriphenylene, metal-organic framework. Through comprehensive molecular dynamics simulations coupled with periodic and cluster electronic structure calculations, we uncover a complex array of catalytically active sites in 2D Co3(HTTP)2 MOF which would have been entirely missed if conventional static electronic structure methods were to be employed.

scholarly journals Flexible and Responsive Nature of 2D Layered Conductive Metal-Organic Frameworks Determine Their Catalytic Activity in Oxidative Dehydrogenation of Propane

2020 ◽  
Author(s):  
Mohammad R. Momeni ◽  
Zeyu Zhang ◽  
Farnaz A. Shakib
Keyword(s):  
Electronic Structure ◽  
Catalytic Activity ◽  
Active Sites ◽  
Metal Organic Framework ◽  
Electronic Structure Calculations ◽  
Electronic Structure Methods ◽  
Catalytically Active ◽  
Metal Organic ◽  
Dynamics Simulations ◽  
Structure Calculations

A multi-faceted approach is introduced for investigating the effects of intrinsic and guest(water)-induced structural transformations/deformations and heterogeneity on catalytic activity of the 2D π-stacked layered Co3(HTTP)2, HTTP = hexathiotriphenylene, metal-organic framework. Through comprehensive molecular dynamics simulations coupled with periodic and cluster electronic structure calculations, we uncover a complex array of catalytically active sites in 2D Co3(HTTP)2 MOF which would have been entirely missed if conventional static electronic structure methods were to be employed.

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