scholarly journals Accelerated discovery of superoxide-dismutase nanozymes via high-throughput computational screening

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhenzhen Wang ◽  
Jiangjiexing Wu ◽  
Jia-Jia Zheng ◽  
Xiaomei Shen ◽  
Liang Yan ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Frontier Molecular Orbital ◽  
Side Reactions ◽  
The Novel ◽  
Energy Principle ◽  
Computational Screening ◽  
Metal Organic

AbstractThe activity of nanomaterials (NMs) in catalytically scavenging superoxide anions mimics that of superoxide dismutase (SOD). Although dozens of NMs have been demonstrated to possess such activity, the underlying principles are unclear, hindering the discovery of NMs as the novel SOD mimics. In this work, we use density functional theory calculations to study the thermodynamics and kinetics of the catalytic processes, and we develop two principles, namely, an energy level principle and an adsorption energy principle, for the activity. The first principle quantitatively describes the role of the intermediate frontier molecular orbital in transferring electrons for catalysis. The second one quantitatively describes the competition between the desired catalytic reaction and undesired side reactions. The ability of the principles to predict the SOD-like activities of metal-organic frameworks were verified by experiments. Both principles can be easily implemented in computer programs to computationally screen NMs with the intrinsic SOD-like activity.

scholarly journals Density-functional theory models of Fe(iv)O reactivity in metal–organic frameworks: self-interaction error, spin delocalisation and the role of hybrid exchange

2020 ◽  
Vol 22 (22) ◽  
pp. 12821-12830
Author(s):  
Fernan Saiz ◽  
Leonardo Bernasconi
Keyword(s):  
Density Functional Theory ◽  
Oxidation Reaction ◽  
Density Functional ◽  
Metal Organic Framework ◽  
Metal Organic Frameworks ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Metal Organic ◽  
Organic Framework

We study the reactivity of Fe(iv)O moieties supported by a metal–organic framework (MOF-74) in the oxidation reaction of methane to methanol using all-electron, periodic density-functional theory calculations.

scholarly journals Fluorescent Bis(guanidine) Copper Complexes as Precursors for Hydroxylation Catalysis

Inorganics ◽  
2018 ◽  
Vol 6 (4) ◽  
pp. 114 ◽  
Author(s):  
Florian Strassl ◽  
Alexander Hoffmann ◽  
Benjamin Grimm-Lebsanft ◽  
Dieter Rukser ◽  
Florian Biebl ◽  
...  
Keyword(s):  
Density Functional ◽  
Copper Complexes ◽  
Density Functional Theory Calculations ◽  
Special Role ◽  
The Novel ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Copper Dioxygen

Bis(guanidine) copper complexes are known for their ability to activate dioxygen. Unfortunately, until now, no bis(guanidine) copper-dioxygen adduct has been able to transfer oxygen to substrates. Using an aromatic backbone, fluorescence properties can be added to the copper(I) complex which renders them useful for later reaction monitoring. The novel bis(guanidine) ligand DMEG2tol stabilizes copper(I) and copper(II) complexes (characterized by single crystal X-ray diffraction, IR spectroscopy, and mass spectrometry) and, after oxygen activation, bis(µ-oxido) dicopper(III) complexes which have been characterized by low-temperature UV/Vis and Raman spectroscopy. These bis(guanidine) stabilized bis(µ-oxido) complexes are able to mediate tyrosinase-like hydroxylation activity as first examples of bis(guanidine) stabilized complexes. The experimental study is accompanied by density functional theory calculations which highlight the special role of the different guanidine donors.

Tuning the Redox Activity of Metal−Organic Frameworks for Enhanced, Selective O2 Binding

2019 ◽  
Author(s):  
Andrew Rosen ◽  
M. Rasel Mian ◽  
Timur Islamoglu ◽  
Haoyuan Chen ◽  
Omar Farha ◽  
...  
Keyword(s):  
Density Functional ◽  
Metal Organic Frameworks ◽  
Redox Activity ◽  
Screening Methods ◽  
Bridging Ligands ◽  
Metal Centers ◽  
Computational Screening ◽  
Open Metal Sites ◽  
Metal Organic ◽  
Unsaturated Metal Sites

<p>Metal−organic frameworks (MOFs) with coordinatively unsaturated metal sites are appealing as adsorbent materials due to their tunable functionality and ability to selectively bind small molecules. Through the use of computational screening methods based on periodic density functional theory, we investigate O<sub>2</sub> and N<sub>2</sub> adsorption at the coordinatively unsaturated metal sites of several MOF families. A variety of design handles are identified that can be used to modify the redox activity of the metal centers, including changing the functionalization of the linkers (replacing oxido donors with sulfido donors), anion exchange of bridging ligands (considering μ-Br<sup>-</sup>, μ-Cl<sup>-</sup>, μ-F<sup>-</sup>, μ-SH<sup>-</sup>, or μ-OH<sup>-</sup> groups), and altering the formal oxidation state of the metal. As a result, we show that it is possible to tune the O<sub>2</sub> affinity at the open metal sites of MOFs for applications involving the strong and/or selective binding of O<sub>2</sub>. In contrast with O<sub>2</sub> adsorption, N<sub>2</sub> adsorption at open metal sites is predicted to be relatively weak across the MOF dataset, with the exception of MOFs containing synthetically elusive V<sup>2+</sup> open metal sites. As one example from the screening study, we predict that exchanging the μ-Cl<sup>-</sup> ligands of M<sub>2</sub>Cl<sub>2</sub>(BBTA) (H<sub>2</sub>BBTA = 1<i>H</i>,5<i>H</i>-benzo(1,2-d:4,5-d′)bistriazole) with μ-OH<sup>-</sup> groups would significantly enhance the strength of O<sub>2</sub> adsorption at the open metal sites without a corresponding increase in the N<sub>2</sub> affinity. Experimental investigation of Co<sub>2</sub>Cl<sub>2</sub>(BBTA) and Co<sub>2</sub>(OH)<sub>2</sub>(BBTA) confirms that the former exhibits only weak physisorption, whereas the latter is capable of chemisorbing O<sub>2</sub> at room temperature. The chemisorption behavior is attributed to the greater electron-donating character of the μ-OH<sup>-</sup><sub> </sub>ligands and the presence of H-bonding interactions between the μ-OH<sup>-</sup> bridging ligands and the O<sub>2</sub> adsorbate.</p>

scholarly journals Role of Chemistry and Crystal Structure on the Electronic Defect States in Cs-Based Halide Perovskites

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 1032
Author(s):  
Anirban Naskar ◽  
Rabi Khanal ◽  
Samrat Choudhury
Keyword(s):  
Crystal Structure ◽  
Density Functional ◽  
Covalent Bond ◽  
Density Functional Theory Calculations ◽  
Antisite Defect ◽  
Defect States ◽  
Functional Theory ◽  
Electronic Defect ◽  
Constituent Elements

The electronic structure of a series perovskites ABX3 (A = Cs; B = Ca, Sr, and Ba; X = F, Cl, Br, and I) in the presence and absence of antisite defect XB were systematically investigated based on density-functional-theory calculations. Both cubic and orthorhombic perovskites were considered. It was observed that for certain perovskite compositions and crystal structure, presence of antisite point defect leads to the formation of electronic defect state(s) within the band gap. We showed that both the type of electronic defect states and their individual energy level location within the bandgap can be predicted based on easily available intrinsic properties of the constituent elements, such as the bond-dissociation energy of the B–X and X–X bond, the X–X covalent bond length, and the atomic size of halide (X) as well as structural characteristic such as B–X–B bond angle. Overall, this work provides a science-based generic principle to design the electronic states within the band structure in Cs-based perovskites in presence of point defects such as antisite defect.

scholarly journals Selective capture of carbon dioxide from hydrocarbons using a metal-organic framework

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Omid T. Qazvini ◽  
Ravichandar Babarao ◽  
Shane G. Telfer
Keyword(s):  
Carbon Dioxide ◽  
Density Functional ◽  
Metal Organic Framework ◽  
Density Functional Theory Calculations ◽  
Time Lags ◽  
X Ray Crystallography ◽  
Metal Organic ◽  
Adsorption Of Co ◽  
Short Time ◽  
Organic Framework

AbstractEfficient and sustainable methods for carbon dioxide capture are highly sought after. Mature technologies involve chemical reactions that absorb CO2, but they have many drawbacks. Energy-efficient alternatives may be realised by porous physisorbents with void spaces that are complementary in size and electrostatic potential to molecular CO2. Here, we present a robust, recyclable and inexpensive adsorbent termed MUF-16. This metal-organic framework captures CO2 with a high affinity in its one-dimensional channels, as determined by adsorption isotherms, X-ray crystallography and density-functional theory calculations. Its low affinity for other competing gases delivers high selectivity for the adsorption of CO2 over methane, acetylene, ethylene, ethane, propylene and propane. For equimolar mixtures of CO2/CH4 and CO2/C2H2, the selectivity is 6690 and 510, respectively. Breakthrough gas separations under dynamic conditions benefit from short time lags in the elution of the weakly-adsorbed component to deliver high-purity hydrocarbon products, including pure methane and acetylene.

A Density Functional Theory Study on the Ring-Opening Polymerization of D-Lactide Catalyzed by a Bifunctional-Thiourea Catalyst

2009 ◽  
Vol 62 (2) ◽  
pp. 157 ◽  
Author(s):  
Rong-Xiu Zhu ◽  
Ruo-Xi Wang ◽  
Dong-Ju Zhang ◽  
Cheng-Bu Liu
Keyword(s):  
Density Functional Theory ◽  
Ring Opening ◽  
Density Functional ◽  
Population Analysis ◽  
Density Functional Theory Calculations ◽  
Ring Opening Polymerization ◽  
Acyl Transfer ◽  
Frontier Molecular Orbital ◽  
Functional Theory ◽  
Elimination Pathway

The thiourea-catalyzed methanolysis of d-lactide, a model system for the initiation and propagation of the organocatalyzed ring-opening polymerization (ROP) of lactide, has been studied by performing density functional theory calculations. Both the catalyzed and uncatalyzed reactions are explored along two possible pathways: one involves the stepwise addition–elimination pathway and the other is related to the concerted pathway. It is found that the reaction without the presence of the catalyst is difficult because the barrier involved is as high as 176 kJ mol–1. With the aid of a thiourea catalyst, the barrier is reduced to 88 kJ mol–1 with a preference for the stepwise addition–elimination mechanism over the concerted one. The role of the catalyst has been rationalized by analyzing the frontier molecular orbital interactions between the catalyst and substrates and by performing natural population analysis. Finally, another mechanism involving acyl transfer is discussed for the thiourea-catalyzed ROP.

scholarly journals Exposing unsaturated Cu1-O2 sites in nanoscale Cu-MOF for efficient electrocatalytic hydrogen evolution

2021 ◽  
Vol 7 (18) ◽  
pp. eabg2580
Author(s):  
Weiren Cheng ◽  
Huabin Zhang ◽  
Deyan Luan ◽  
Xiong Wen (David) Lou
Keyword(s):  
Hydrogen Evolution ◽  
Density Functional ◽  
Metal Organic Framework ◽  
Density Functional Theory Calculations ◽  
Active Centers ◽  
Functional Theory ◽  
Hollow Nanostructure ◽  
Metal Organic ◽  
X Ray Absorption ◽  
A Current

Conductive metal-organic framework (MOF) materials have been recently considered as effective electrocatalysts. However, they usually suffer from two major drawbacks, poor electrochemical stability and low electrocatalytic activity in bulk form. Here, we have developed a rational strategy to fabricate a promising electrocatalyst composed of a nanoscale conductive copper-based MOF (Cu-MOF) layer fully supported over synergetic iron hydr(oxy)oxide [Fe(OH)x] nanoboxes. Owing to the highly exposed active centers, enhanced charge transfer, and robust hollow nanostructure, the obtained Fe(OH)x@Cu-MOF nanoboxes exhibit superior activity and stability for the electrocatalytic hydrogen evolution reaction (HER). Specifically, it needs an overpotential of 112 mV to reach a current density of 10 mA cm−2 with a small Tafel slope of 76 mV dec−1. X-ray absorption fine structure spectroscopy combined with density functional theory calculations unravels that the highly exposed coordinatively unsaturated Cu1-O2 centers could effectively accelerate the formation of key *H intermediates toward fast HER kinetics.

scholarly journals Elucidating the Drug Release from Metal-Organic Framework Nanocomposites via in Situ Synchrotron Microspectroscopy and Theoretical Modelling

2019 ◽  
Author(s):  
Barbara Souza ◽  
Lorenzo Dona ◽  
Kirill Titov ◽  
Paolo Bruzzese ◽  
Zhixin Zeng ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Density Functional ◽  
Metal Organic Framework ◽  
Density Functional Theory Calculations ◽  
Theoretical Modelling ◽  
Time Resolved ◽  
Drug Molecules ◽  
Metal Organic

Nanocomposites comprising metal-organic frameworks (MOFs) embedded in a polymeric matrix are promising carriers for drug delivery applications. While understanding the chemical and physical transformations of MOFs during the release of confined drug molecules is challenging, this is central to devising better ways for controlled release of therapeutic agents. Herein we demonstrate the efficacy of synchrotron microspectroscopy to track the in situ release of 5-fluorouracil (5-FU) anticancer drug molecules from a drug@MOF/polymer composite (5-FU@HKUST-1/polyurethane). Using experimental time-resolved infrared spectra jointly with newly developed density functional theory calculations, we reveal the detailed dynamics of vibrational motions underpinning the dissociation of 5-FU bound to the framework of HKUST-1 upon water exposure. We discover that HKUST-1 creates hydrophilic channels within the hydrophobic polyurethane matrix hence helping to tune drug release rate. The synergy between a hydrophilic MOF with a hydrophobic polymer can be harnessed to engineer a tunable nanocomposite that alleviates the unwanted burst effect commonly encountered in drug delivery.<br>

scholarly journals Mechanochemical Synthesis of a Mercury(II) Metal-Organic Framework Reveals a Two-Dimensional Polymorph Stabilized by Weak Interactions

2019 ◽  
Author(s):  
Isaiah R. Speight ◽  
Igor Huskić ◽  
Mihails Arhangelskis ◽  
Hatem M. Titi ◽  
Robin Stein ◽  
...  
Keyword(s):  
Density Functional ◽  
Weak Interactions ◽  
Metal Organic Framework ◽  
Three Dimensional ◽  
Density Functional Theory Calculations ◽  
Dimensional Structure ◽  
Reaction Monitoring ◽  
Two Dimensional ◽  
Functional Theory ◽  
Metal Organic

Solid-state mechanochemistry revealed a novel polymorph of the mercury(II) imidazolate framework, based on square-grid (sql) topology layers. Reaction monitoring and periodic density functional theory calculations show that the sql-structure is of higher stability than the previously reported three-dimensional structure, with the unexpected stabilization of a lower dimensionality structure explained by contributions of weak interactions, which include short C-H···Hg contacts.

scholarly journals Elucidating the Drug Release from Metal-Organic Framework Nanocomposites via in Situ Synchrotron Microspectroscopy and Theoretical Modelling

2019 ◽  
Author(s):  
Barbara Souza ◽  
Lorenzo Dona ◽  
Kirill Titov ◽  
Paolo Bruzzese ◽  
Zhixin Zeng ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Density Functional ◽  
Metal Organic Framework ◽  
Density Functional Theory Calculations ◽  
Theoretical Modelling ◽  
Time Resolved ◽  
Drug Molecules ◽  
Metal Organic

Nanocomposites comprising metal-organic frameworks (MOFs) embedded in a polymeric matrix are promising carriers for drug delivery applications. While understanding the chemical and physical transformations of MOFs during the release of confined drug molecules is challenging, this is central to devising better ways for controlled release of therapeutic agents. Herein we demonstrate the efficacy of synchrotron microspectroscopy to track the in situ release of 5-fluorouracil (5-FU) anticancer drug molecules from a drug@MOF/polymer composite (5-FU@HKUST-1/polyurethane). Using experimental time-resolved infrared spectra jointly with newly developed density functional theory calculations, we reveal the detailed dynamics of vibrational motions underpinning the dissociation of 5-FU bound to the framework of HKUST-1 upon water exposure. We discover that HKUST-1 creates hydrophilic channels within the hydrophobic polyurethane matrix hence helping to tune drug release rate. The synergy between a hydrophilic MOF with a hydrophobic polymer can be harnessed to engineer a tunable nanocomposite that alleviates the unwanted burst effect commonly encountered in drug delivery.<br>

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