scholarly journals Computational Mechanistic Insights on the NO Oxidation Reaction Catalyzed by Non-Heme Biomimetic Cr-N-Tetramethylated Cyclam Complexes

2019 ◽  
Vol 20 (16) ◽  
pp. 3955 ◽  
Author(s):  
Tiziana Marino ◽  
Maria Grazia Fortino ◽  
Nino Russo ◽  
Marirosa Toscano ◽  
Marta Erminia Alberto
Keyword(s):  
Oxidation Reaction ◽  
Density Functional ◽  
Low Energy ◽  
No Oxidation ◽  
Bond Breaking ◽  
Functional Theory ◽  
Rate Determining Step ◽  
Energy Profiles ◽  
Cyclam Complexes ◽  
Catalytic Power

The conversion reaction of NO to NO3− ion catalyzed by the end-on [Cr(III)(n-TMC)(O2)(Cl)]+ superoxo and side-on [Cr(IV)(n-TMC)(O2)(Cl)]+ peroxo non-heme complexes (n = 12, 13, 14 and 15), which are biomimetic systems of nitric oxide dioxygenases (NODs), has been explored using a computational protocol in the framework of density functional theory. Results show that the potential energy profiles for the studied reactions lie above the reagent energies, regardless of the used catalyst. Both the O-O bond breaking in the biomimetics and the NO3− ion formation require low energy barriers suggesting an efficient catalytic power of the studied systems. The rate-determining step depends on ligand size.

scholarly journals Complex magnetism of the two-dimensional antiferromagnetic Ge2F: from a Néel spin-texture to a potential antiferromagnetic skyrmion

RSC Advances ◽  
2021 ◽  
Vol 11 (15) ◽  
pp. 8654-8663
Author(s):  
Fatima Zahra Ramadan ◽  
Flaviano José dos Santos ◽  
Lalla Btissam Drissi ◽  
Samir Lounis
Keyword(s):  
Density Functional Theory ◽  
Magnetic Properties ◽  
Density Functional ◽  
Low Energy ◽  
Two Dimensional ◽  
Functional Theory ◽  
2D Material ◽  
Energy Models ◽  
Spin Texture

Based on density functional theory combined with low-energy models, we explore the magnetic properties of a hybrid atomic-thick two-dimensional (2D) material made of germanene doped with fluorine atoms in a half-fluorinated configuration (Ge2F).

scholarly journals Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

2021 ◽  
Vol 22 (6) ◽  
pp. 3244
Author(s):  
Charuvaka Muvva ◽  
Natarajan Arul Murugan ◽  
Venkatesan Subramanian
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Amyloid Β ◽  
Density Functional Theory Calculations ◽  
Tau Proteins ◽  
Functional Theory ◽  
Energy Profiles ◽  
Α Helix ◽  
Semi Empirical ◽  
Β Sheet

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

scholarly journals A Computational Study of Direct CO2 Hydrogenation to Methanol on Pd Catalysts

2021 ◽  
Author(s):  
Igor Kowalec ◽  
Lara Kabalan ◽  
Richard Catlow ◽  
Andrew Logsdail
Keyword(s):  
Density Functional ◽  
Negative Charge ◽  
Computational Study ◽  
Adsorbed Species ◽  
Pd Catalysts ◽  
Functional Theory ◽  
Activation Barriers ◽  
Rate Determining Step ◽  
Adsorption Energies ◽  
Insight Into

<p>We investigate the mechanism of direct CO<sub>2</sub> hydrogenation to methanol on Pd (111), (100) and (110) surfaces using density functional theory (DFT), providing insight into the reactivity of CO<sub>2</sub> on Pd-based catalysts. The initial chemisorption of CO<sub>2</sub>, forming a partially charged CO<sub>2</sub><sup>δ-</sup>, is weakly endothermic on a Pd (111) surface, with an adsorption energy of 0.06 eV, and slightly exothermic on Pd (100) and (110) surfaces, with adsorption energies of -0.13 and -0.23 eV, respectively. Based on Mulliken analysis, we attribute the low stability of CO<sub>2</sub><sup>δ-</sup><sub> </sub>on the Pd (111) surface to a negative charge that accumulates on the surface Pd atoms interacting directly with the CO<sub>2</sub><sup>δ-</sup><sub> </sub>adsorbate. For the reaction of the adsorbed species on the Pd surface, HCOOH hydrogenation to H<sub>2</sub>COOH is predicted to be the rate determining step of the conversion to methanol in all cases, with activation barriers of 1.35, 1.26, and 0.92 eV on Pd (111), (100) and (110) surfaces, respectively.<br></p>

The Interaction between Graphene and the SiC Substrate: Ab Initio Calculations for Polar and Nonpolar Surfaces

2016 ◽  
Vol 858 ◽  
pp. 1125-1128
Author(s):  
Ioannis Deretzis ◽  
Filippo Giannazzo ◽  
Antonino La Magna
Keyword(s):  
Density Functional Theory ◽  
Energy Spectrum ◽  
Density Functional ◽  
Low Energy ◽  
Electrical Characteristics ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Structural And Electronic Properties ◽  
Exclusive Property

Notwithstanding the graphitization of SiC under high thermal treatment can take place for all SiC surfaces, the quality of the resulting graphene as well as its structural and electrical characteristics strongly depend on the SiC face where growth has taken place. In this paper we use the density functional theory to analyze the structural and electronic properties of epitaxial graphene grown on three different SiC planes. Calculations are presented for the (6√3×6√3)R30°-reconstructed SiC(0001) surface (Si face) as well as the nonpolar SiC(11-20) and SiC(1-100) planes. We argue that the formation of a strongly-bound interface buffer layer is an exclusive property of the SiC(0001) surface. Moreover, our results indicate that nonpolar planes give rise to graphene with a nearly ideal low-energy spectrum.

A Density Functional Theory Study of the Isomerization of Substituted 2and#39;-hydroxychalcones to the Corresponding Flavanones

2021 ◽  
Vol 43 (1) ◽  
pp. 25-25
Author(s):  
Said Abdelqadar Said Said Abdelqadar Said ◽  
Omar A Shareef and Abdulkhalik S Alkazzaz Omar A Shareef and Abdulkhalik S Alkazzaz
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Ring Closure ◽  
Basis Set ◽  
Functional Theory ◽  
Rate Determining Step ◽  
The Density Functional Theory ◽  
Electronic And Structural Properties ◽  
Maximum Hardness Principle

The transformation of 2and#39;-hydroxychalcones to their corresponding flavanones was studied theoretically by the use of the density functional theory (DFT) with B3-LYP/ 6-311G basis set to get important information about the role of both of electronic and structural properties in this process. The obtained energies were found to be in agreement with our previous results that obtained from HPLC studies. The estimated hardness, polarizability, and electrophilicity profiles were found to obey the maximum hardness principle (MHP), minimum polarizability principle (MPP), and the minimum electrophilicity principle (MEP) respectively. Flavanone ring closure was found to be the rate-determining step.

A reaction density functional theory study of the solvent effect in prototype SN2 reactions in aqueous solution

2019 ◽  
Vol 21 (45) ◽  
pp. 24876-24883 ◽  
Author(s):  
Cheng Cai ◽  
Weiqiang Tang ◽  
Chongzhi Qiao ◽  
Peng Jiang ◽  
Changjie Lu ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Density Functional Theory ◽  
Free Energy ◽  
Solvent Effect ◽  
Density Functional ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Sn2 Reactions ◽  
Energy Profiles ◽  
Free Energy Profiles

Reaction density functional theory (RxDFT), combining quantum DFT with classical DFT, has been employed to investigate the solvent effect and free energy profiles of SN2 reactions in aqueous solution.

scholarly journals CO oxidation catalysed by Pd-based bimetallic nanoalloys

2015 ◽  
Vol 17 (42) ◽  
pp. 28010-28021 ◽  
Author(s):  
Dennis Palagin ◽  
Jonathan P. K. Doye
Keyword(s):  
Density Functional Theory ◽  
Co Oxidation ◽  
Oxidation Reaction ◽  
Density Functional ◽  
Geometry Optimization ◽  
Energy Barriers ◽  
Functional Theory ◽  
Global Geometry ◽  
Co Oxidation Reaction

Density functional theory based global geometry optimization has been used to demonstrate the crucial influence of the geometry of the catalytic cluster on the energy barriers for the CO oxidation reaction over Pd-based bimetallic nanoalloys.

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