scholarly journals Unique intramolecular oxidative rearrangement N-nitrosation mechanism of non-heam iron-containing enzyme SznF

2020 ◽  
Author(s):  
Junkai Wang ◽  
Xixi Wang ◽  
Qingwen Ouyang ◽  
Wei Liu ◽  
Hongwei Tan ◽  
...  
Keyword(s):  
Density Functional ◽  
Catalytic Mechanism ◽  
Functional Theory ◽  
Oxidative Rearrangement ◽  
Rearrangement Process ◽  
Bond Homolysis ◽  
Nitrosation Reactions ◽  
Catalytic Mechanisms ◽  
High Valent ◽  
Shed Light

ABSTRACTNon-heam iron-dependent enzyme SznF catalyzes a critical step of the L-arginine derived guanidine group rearrangement to produce the N-nitrosourea pharmacophore in the process of SZN biosynthesis. The intramolecular oxidative rearrangement process is accomplished in the Fe(II)-containing active site located at the cupin domain of SznF, with which the catalytic mechanism remains elusive. In this work, density functional theory methods have been employed to investigate possible catalytic mechanisms of SznF. The N-nitrosation reaction in SznF was found to follow an energetically favorable pathway which includes six consecutive steps: (1) formation of FeII-superoxo species with dioxgen binding on the iron center; (2) superoxo group attacking on the Cε of substrate to form the peroxo-bridge complex; (3) Cε-Nω bond homolysis to release NωO; (4) peroxo bridge heterolytic cleavage; (5) deprotonation of by Fe-O group; (6) the couples with the NωO group and generates the N-nitroso product. The reaction proceeds in an unexpected way during which the electrons shuttle among two NO groups of the substrate and the peroxo moiety to promote Cε-Nω bond homolysis and O-O bond heterolysis sequentially without generating high-valent Fe-O species, which is distinct from any known reactions catalyzed by the iron-containing enzyme. The unusual mechanism of SznF shed light on the area of enzymatic N-nitrosation reactions.

scholarly journals Prediction of high-valent iron K-edge absorption spectra by time-dependent Density Functional Theory

2011 ◽  
Vol 40 (42) ◽  
pp. 11070 ◽  
Author(s):  
P. Chandrasekaran ◽  
S. Chantal E. Stieber ◽  
Terrence J. Collins ◽  
Lawrence Que, Jr. ◽  
Frank Neese ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Absorption Spectra ◽  
Density Functional ◽  
Time Dependent ◽  
Functional Theory ◽  
Edge Absorption ◽  
High Valent ◽  
Dependent Density

scholarly journals Mechanism and Chemoselectivity of Mn-Catalyzed Intramolecular Nitrene Transfer Reaction: C–H Amination vs. C=C Aziridination

Catalysts ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 292
Author(s):  
Juping Wang ◽  
Kangcheng Zheng ◽  
Ting Li ◽  
Xiaojing Zhan
Keyword(s):  
Density Functional ◽  
Structural Features ◽  
High Reactivity ◽  
Strong Electron ◽  
Functional Theory ◽  
Design Elements ◽  
Nitrene Transfer ◽  
Electrophilic Reactivity ◽  
High Valent ◽  
Orbital Character

The reactivity, mechanism and chemoselectivity of the Mn-catalyzed intramolecular C–H amination versus C=C aziridination of allylic substrate cis-4-hexenylsulfamate are investigated by BP86 density functional theory computations. Emphasis is placed on the origins of high reactivity and high chemoselectivity of Mn catalysis. The N p orbital character of frontier orbitals, a strong electron-withdrawing porphyrazine ligand and a poor π backbonding of high-valent MnIII metal to N atom lead to high electrophilic reactivity of Mn-nitrene. The calculated energy barrier of C–H amination is 9.9 kcal/mol lower than that of C=C aziridination, which indicates that Mn-based catalysis has an excellent level of chemoselectivity towards C–H amination, well consistent with the experimental the product ratio of amintion-to-aziridination I:A (i.e., (Insertion):(Aziridination)) >20:1. This extraordinary chemoselectivity towards C–H amination originates from the structural features of porphyrazine: a rigid ligand with the big π-conjugated bond. Electron-donating substituents can further increase Mn-catalyzed C–H amination reactivity. The controlling factors found in this work may be considered as design elements for an economical and environmentally friendly C–H amination system with high reactivity and high chemoselectivity.

The catalytic mechanism of the Au@TiO2−x/ZnO catalyst towards a low-temperature water-gas shift reaction

2020 ◽  
Vol 10 (3) ◽  
pp. 768-775
Author(s):  
Ning Liu ◽  
Pan Yin ◽  
Ming Xu ◽  
Yusen Yang ◽  
Shaomin Zhang ◽  
...  
Keyword(s):  
Density Functional ◽  
Catalytic Mechanism ◽  
Density Functional Theory Calculation ◽  
Water Gas Shift ◽  
Water Gas Shift Reaction ◽  
Functional Theory ◽  
Shift Reaction ◽  
Water Gas ◽  
Theory Calculation

A redox mechanism towards the water-gas shift reaction was certified based on in situ/operando experiments and density functional theory calculation studies.

scholarly journals Strain-dependent structure and Raman behaviours in the heavy-ion irradiated manganite at extreme low dose

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nam Nhat Hoang ◽  
Duc Huyen Yen Pham ◽  
The Nghia Nguyen
Keyword(s):  
Density Functional ◽  
Structural Changes ◽  
Low Dose ◽  
Blue Shift ◽  
Heavy Ion ◽  
Dynamic Calculation ◽  
Functional Theory ◽  
Lattice Dynamic Calculation ◽  
Strain Dependent ◽  
Shed Light

AbstractThe microstrains in heavy-ion irradiated manganite LaMnO3 can be managed in linear response of irradiation dose, and the corresponding internal pressure up to 8 GPa can be induced by varying doses. The response of structure under stress is studied by means of Density Functional Theory and Lattice Dynamic Calculation. All obtained Raman scattering lines are discussed in details to shed light onto structural changes during ion implantation. There appears new resonance peak at around 550 cm−1, which splits from broad features in the spectra, and attributes to the anti-symmetric vibrations of O6 cages. The blue shift of this peak scales to ~2.4 cm−1 per 1 GPa of stress. Another strong feature showing considerable blue shift is seen in the vicinity of 640 cm−1 and corresponds to one of rhombohedral distortion related soft modes. A weak mode, not frequently reported, is seen at around 420 cm−1 and corresponds to translation-like motions of fixed O6 cages.

Does a multiply bonded oxo ligand directly participate in B–H bond activation by a high-valent di-oxo-molybdenum(vi) complex? A density functional theory study

2015 ◽  
Vol 5 (6) ◽  
pp. 3259-3269 ◽  
Author(s):  
Liangfang Huang ◽  
Jiandi Wang ◽  
Xiaoqin Wei ◽  
Haiyan Wei
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Bond Activation ◽  
Organic Substrates ◽  
Density Functional Theory Study ◽  
Molybdenum Complex ◽  
Functional Theory ◽  
Multiply Bonded ◽  
High Valent ◽  
Oxo Ligand

The multiply bonded oxo ligand does not participate in the activation of the B–H bond with organic substrates of amides, amines, and nitriles by the high-valent oxo-molybdenum complex MoO2Cl2.

scholarly journals The dynamics of benzene on Cu(111): a combined helium spin echo and dispersion-corrected DFT study into the diffusion of physisorbed aromatics on metal surfaces

2017 ◽  
Vol 204 ◽  
pp. 471-485 ◽  
Author(s):  
M. Sacchi ◽  
P. Singh ◽  
D. M. Chisnall ◽  
D. J. Ward ◽  
A. P. Jardine ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Density Functional ◽  
Spin Echo ◽  
Metallic Surface ◽  
Bravais Lattice ◽  
Binding Interaction ◽  
Functional Theory ◽  
Adsorption Sites ◽  
Lattice Density ◽  
Shed Light

We use helium spin-echo spectroscopy (HeSE) to investigate the dynamics of the diffusion of benzene adsorbed on Cu(111). The results of these measurements show that benzene moves on the surface through an activated jump-diffusion process between the adsorption sites on a Bravais lattice. Density Functional Theory (DFT) calculations with van der Waals (vdW) corrections help us understand that the molecule diffuses by jumping through non-degenerate hollow sites. The results of the calculations shed light on the nature of the binding interaction between this prototypical aromatic molecule and the metallic surface. The highly accurate HeSE experimental data provide a quantitatively stringent benchmark for the vdW correction schemes applied to the DFT calculations and we compare the performances of several dispersion interaction schemes.

scholarly journals Assessing the stability of Pd-exchanged sites in zeolites with the aid of a high throughput quantum chemistry workflow

2021 ◽  
Author(s):  
Hassan Aljama ◽  
Martin Head-Gordon ◽  
Alexis Bell
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Active Sites ◽  
Density Functional ◽  
Functional Materials ◽  
No Adsorption ◽  
Functional Theory ◽  
Wide Range ◽  
The Stability ◽  
Shed Light

Abstract Cation exchanged-zeolites are functional materials with a wide range of applications from catalysis to sorbents. They present a challenge for computational studies using density functional theory due to the numerous possible active sites. From Al configuration, to placement of extra framework cation(s), to potentially different oxidation states of the cation, accounting for all these possibilities is not trivial. To make the number of calculations more tractable, most studies focus on a few active sites. We attempt to go beyond these limitations by implementing a workflow for a high throughput screening, designed to systematize the problem and exhaustively search for feasible active sites. We use Pd-exchanged CHA and BEA to illustrate the approach. After conducting thousands of individual calculations, we identify the sites most favorable for the Pd cation and discuss the results in detail. The high throughput screening identifies many energetically favorable sites that are non-trivial. Lastly, we employ these results to examine NO adsorption in Pd-exchanged CHA, which is a promising passive NOx adsorbent (PNA) during the cold start of automobiles. The results shed light on critical active sites for NOx capture that were not previously studied.

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