scholarly journals In Silico Inhibitability of Copper Carbenes and Silylenes against Rhizoctonia solani and Magnaporthe oryzae

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Nguyen Thi Thanh Hai ◽  
Thanh Q. Bui ◽  
Tran Thi Ai My ◽  
Huynh Thi Phuong Loan ◽  
Tran Thai Hoa ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Magnaporthe Oryzae ◽  
Density Functional ◽  
Copper Complexes ◽  
Docking Simulation ◽  
Functional Theory ◽  
Quantum Analysis ◽  
The Density Functional Theory ◽  
Electronic Configurations ◽  
The Stability

Copper lighter tetrylenes are promising for inhibition towards Rhizoctonia solani-based protein PDB-4G9M and Magnaporthe oryzae-based PDB-6JBR in rice. Quantum properties of four hypothetic copper complexes of carbenes and silylenes (Cu-NHC1, Cu-NHC2, Cu-NHSi1, and Cu-NHSi2) were examined using the density functional theory. Their inhibitability towards the targeted proteins was evaluated using molecular docking simulation. Quantum analysis predicts the stability of the investigated complexes and thus their practical existability and practicable synthesisability. Their electronic configurations are justified as highly conducive to intermolecular interaction. Regarding ligand-protein as carbenes/silylenes-4G9M inhibitory structures, the stability is estimated in the order [Cu-NHC2]-4G9M (DS −12.9 kcal⋅mol−1) > [Cu-NHSi1]-4G9M (DS −11.8 kcal⋅mol−1) = [Cu-NHSi2]-4G9M (DS −11.7 kcal⋅mol−1) > [Cu-NHC1]-4G9M (DS –11.4 kcal⋅mol−1). In contrast, the corresponding order for the carbenes/silylenes-6JBR systems is [Cu-NHSi2]-6JBR (DS –13.4 kcal⋅mol−1) > [Cu-NHC2]-6JBR (DS −13.0 kcal⋅mol−1) = [Cu-NHSi1]-6JBR (DS −12.6 kcal⋅mol−1) > [Cu-NHC1]-6JBR (DS −12.3 kcal⋅mol−1). In theory, this study suggests a potentiality of copper lighter tetrylenes and their derivatives against the infection of fungi Rhizoctonia solani and Magnaporthe oryzae, thus encouraging attempts for experimental developments.

Study of the Stability and Chemical Reactivity of a Series of Tetrazole Pyrimidine Hybrids by the Density Functional Theory Method (DFT)

2021 ◽  
Vol 37 (4) ◽  
pp. 805-812
Author(s):  
Ahissandonatien Ehouman ◽  
Adjoumanirodrigue Kouakou ◽  
Fatogoma Diarrassouba ◽  
Hakim Abdel Aziz Ouattara ◽  
Paulin Marius Niamien
Keyword(s):  
Density Functional ◽  
Theoretical Study ◽  
Molecular Descriptors ◽  
Chemical Reactivity ◽  
Density Functional Theory Method ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
The Density Functional Theory ◽  
The Stability ◽  
Global Reactivity Descriptors

Our theoretical study of stability and reactivity was carried out on six (06) molecules of a series of pyrimidine tetrazole hybrids (PTH) substituted with H, F, Cl, Br, OCH3 and CH3 atoms and groups of atoms using the density function theory (DFT). Analysis of the thermodynamic formation quantities confirmed the formation and existence of the series of molecules studied. Quantum chemical calculations at the B3LYP / 6-311G (d, p) level of theory determined molecular descriptors. Global reactivity descriptors were also determined and analyzed. Thus, the results showed that the compound PTH_1 is the most stable, and PTH_5 is the most reactive and nucleophilic. Similarly, the compound PTH_4 is the most electrophilic. The analysis of the local descriptors and the boundary molecular orbitals allowed us to identify the preferred atoms for electrophilic and nucleophilic attacks.

CH2O Adsorption on M (M = Li, Mg and Al) Atom Deposited ZnO Nano-Cage: DFT Study

2018 ◽  
Vol 786 ◽  
pp. 384-392 ◽  
Author(s):  
Hussein Y. Ammar
Keyword(s):  
Density Functional Theory ◽  
Bond Length ◽  
Density Functional ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Structural And Electronic Properties ◽  
Formaldehyde Molecule ◽  
Electronic Configurations ◽  
Adsorption Energies ◽  
Homo Lumo

The structural and electronic properties of Li, Mg and Al deposited ZnO nanocages and their effects on the adsorption of formaldehyde molecule have been investigated using the density functional theory (DFT) computations. To understand the behavior of the adsorbed CH2O molecule on the ZnO nanocage, results of DFT calculations of the M-deposited nanocages (M=Li, Mg and Al), as well as complex systems consisting of the adsorbed CH2O molecule on M-deposited ZnO nanocage were reported. The results presented include adsorption energies, bond lengths, electronic configurations, density of states and molecular orbitals. It was found that, the most energetically stable adsorption configurations of CH2O molecule on the bare ZnO leads to 12% dilation in C=O bond length of CH2O and 14% decrease in HOMO-LUMO gap of ZnO cluster. The most energetically stable adsorption configurations of CH2O molecule on Li, Mg and Al-deposited ZnO lead to 4%, 4% and 11% dilation in C=O bond length of CH2O and-0.66, -45 and , +66% change in HOMO-LUMO gap of ZnO nanocages, respectively. The interaction between CH2O with bare ZnO and M-deposited ZnO nanocages is attributed to charge transfer mechanism. These results may be meaningful for CH2O degradation and detection.

scholarly journals Structural, elastic, electronic and thermal properties of InAs: A study of functional density

2017 ◽  
Vol 26 (46) ◽  
Author(s):  
Víctor Mendoza-Estrada ◽  
Melissa Romero-Baños ◽  
Viviana Dovale-Farelo ◽  
William López-Pérez ◽  
Álvaro González-García ◽  
...  
Keyword(s):  
Thermal Properties ◽  
Density Functional ◽  
Experimental Studies ◽  
Debye Model ◽  
Band Gap Energy ◽  
Functional Theory ◽  
Zinc Blende ◽  
The Density Functional Theory ◽  
The Stability ◽  
Experimental Values

In this research, first-principles calculations were carried out within the density functional theory (DFT) framework, using LDA and GGA, in order to study the structural, elastic, electronic and thermal properties of InAs in the zinc-blende structure. The results of the structural properties (a, B0, ) agree with the theoretical and experimental results reported by other authors. Additionally, the elastic properties, the elastic constants (C11, C12 and C44), the anisotropy coefficient (A) and the predicted speeds of the sound ( , , and ) are in agreement with the results reported by other authors. In contrast, the shear modulus (G), the Young's modulus (Y) and the Poisson's ratio (v) show some discrepancy with respect to the experimental values, although, the values obtained are reasonable. On the other hand, it is evident the tendency of the LDA and GGA approaches to underestimate the value of the band-gap energy in semiconductors. The thermal properties (V, , θD yCV) of InAs, calculated using the quasi-harmonic Debye model, are slightly sensitive as the temperature increases. According to the stability criteria and the negative value of the enthalpy of formation, InAs is mechanically and thermodynamically stable. Therefore, this work can be used as a future reference for theoretical and experimental studies based on InAs.

Density Functional Theory Calculations of Properties of the Grain Boundaries in Aluminum

2011 ◽  
Vol 1297 ◽  
Author(s):  
Marek Muzyk ◽  
Krzysztof J. Kurzydlowski
Keyword(s):  
Density Functional Theory ◽  
Grain Boundaries ◽  
Density Functional ◽  
Quantitative Description ◽  
Aluminum Matrix ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Nano Crystalline ◽  
The Density Functional Theory ◽  
The Stability

ABSTRACTThe Density Functional Theory has been used to analyze an inter-granular segregation of Cu and Mg. The stability of Cu and Mg atoms in the aluminum matrix, intermetallic phases and symmetric twist grain boundaries has been compared. The quantitative description of solubility of Cu and Mg atoms in the nano-crystalline aluminum has been proposed. The calculations have been carried out to investigate the properties of symmetric twist boundaries in aluminum with and without Cu/Mg atoms. The phenomena of are discussed and its effect on the stability of precipitates containing these elements.

Influences of Fe Doping on the Electronic Structure of Mg(0001) Surface and Hydrogenation Mechanism in Fe-Doped Mg(0001) Surface

2013 ◽  
Vol 873 ◽  
pp. 114-120 ◽  
Author(s):  
Zhi Wen Wang ◽  
Xin Jun Guo ◽  
Hong Xia Zhang ◽  
Li Li
Keyword(s):  
Density Functional ◽  
Hydrogen Molecule ◽  
Functional Theory ◽  
Practical Applications ◽  
Atom Diffusion ◽  
Charge Density Difference ◽  
The Density Functional Theory ◽  
Diffusion Paths ◽  
The Stability ◽  
Dissociation Path

First-principles calculations within the density functional theory (DFT) have been carried out to study the interaction of hydrogen molecule with Fe-doped Mg (0001) surfaces. First we have calculated the stability of the Fe atom on the Mg surface, On the basis of the energetic criteria, Fe atom prefer to substitute one of the Mg atoms from the second layer. In the second step, we have studied the interaction between hydrogen molecule and the Fe-doped Mg (0001) surface. The results show that for Fe atoms doped Mg (0001) surface in the second layer, enhances the chemisorption interaction between H2molecule and Fe atom, but also benefits H atom diffusion into Mg bulk with relatively more diffusion paths compared with that of clean Mg surface. Charge density difference plots provided some ideas about why certain alloying elements on the surface reduce the energy barrier of H2molecule dissociation on Fe-doped Mg (0001) surface. We can see that Fe as catalyst for the hydrogenation/dehydrogenation of Mg alloy samples and provide more dissociation path for H2molecule and diffusion paths for H atom, The present results not only beneficial for clarify the experimentally observed fast hydrogenation kinetics for Fe-capped Mg materials but also help to design new types of hydrogen storage materials for practical applications in the auto industry.

scholarly journals The difference in stability between 5′R and 5′S diastereomers of 5′,8-cyclopurine-2′-deoxynucleosides. DFT study in gaseous and aqueous phase

2010 ◽  
Vol 8 (1) ◽  
pp. 134-141 ◽  
Author(s):  
Boleslaw Karwowski
Keyword(s):  
Density Functional ◽  
Bond Cleavage ◽  
Basis Set ◽  
Small Range ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Formic Acid Hydrolysis ◽  
The Difference ◽  
The Stability ◽  
First Time

AbstractOxidatively generated damage to DNA frequently appears in the human genome as an effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents. Due to these facts it has been decided to calculate the stability of 5′,8-cyclo-2′-deoxyadenosine/guanosine (cdA, cdG) in their 5′R and 5′S diastereomeric forms. For all points of quantum mechanics studies presented, the density functional theory (DFT) with B3LYP parameters on 6-311++G** basis set level was used. The calculations showed a significant negative enthalpy for glycosidic bond cleavage reaction for cationic forms and slightly negative for neutral ones. The preliminary study of the discussed process has shown the nature of stepwise nucleophilic substitution DN*AD type mechanism. Surprisingly, the different values in free energy, between short-lived oxacarbenium ion intermediates, have been found to lie over a relatively small range, around 1 and 2.8 kcal mol−1. For anions, the decomposition enthalpies were found as positive in aqueous phases. These theoretical results are supported by the formic acid hydrolysis experiments of both diastereomers of cdA, for the first time. (5′S)cdA exhibited higher stability than (5′R)cdA.

First-principle study of the electronic structure and optical property of Nb-doped anatase TiO2

2014 ◽  
Vol 28 (17) ◽  
pp. 1450091
Author(s):  
Q. Y. Hou ◽  
Q. L. Liu ◽  
C. W. Zhao ◽  
Y. Zhang
Keyword(s):  
Electronic Structure ◽  
Optical Property ◽  
Band Gap ◽  
Absorption Edge ◽  
Short Wavelength ◽  
Density Functional ◽  
Functional Theory ◽  
Long Wavelength ◽  
The Density Functional Theory ◽  
The Stability

The absorption edge shifted to long wavelength direction and short wavelength direction of two opposite experimental conclusions have been reported, when the band-gap and absorption spectra of Nb -doped anatase TiO 2 were studied. In order to solve this contradiction, the electronic structure and the optical property of Nb heavy doped anatase TiO 2 have been studied by the first-principles plane-wave ultrasoft pseudopotential method based on the density functional theory with +U method modification. The calculated results indicate that the higher the Nb -doping is, the higher the total energy is, the worse the stability is, the higher the formation energy is, the more difficult the doping is, the wider the optical band-gap is, the more obvious the absorption edge shifting to short wavelength direction is, the lower the absorptivity and the reflectivity is, which is in agreement with the experimental results. The reasonable interpretation of the contradiction has been reported in this paper, too.

scholarly journals Numerical Investigation of the Stability and Spintronic Properties of Selected Quaternary Alloys

2021 ◽  
Vol 3 (4) ◽  
pp. 6-12
Author(s):  
Adewumi I. Popoola ◽  
S. Babatunde Akinpelu
Keyword(s):  
Data Storage ◽  
Density Functional ◽  
First Principles Calculation ◽  
Electronic Charge ◽  
Quaternary Alloys ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Ferromagnetic Character ◽  
The Stability ◽  
Full Heusler

The use of electronic charge and spins (spintronics) has been proposed for much better data storage. This class of material is believed to have excellent capability for data integrity, low dynamic power consumption and high-density storage that showcases excellent protection against data loss. The spintronic and related properties have been investigated on four newly proposed quaternary alloys (NbRhGeCo, NbRhGeCr, NbRhGeFe and NbRhGeNi) through the first-principles calculation method of the Density Functional Theory (DFT). Specifically, the phonon frequencies, elastic stabilities, and the electronic structure were systematically studied in the full Heusler structure. The results predict that NbRhGeFe and NbRhGeCr are elastically and structurally stable. Both NbRhGeFe and NbRhGeCo are half-metals with ferromagnetic character, but NbRhGeCo is unfortunately elastically unstable. NbRhGeCr and NbRhGeNi are non-magnetic metallic alloys in their spin channels.  All the results predict NbRhGeFe to be the only suitable among all the four alloys for spintronic application.

The Structure and Stability of C20 Dimer

2015 ◽  
Vol 1096 ◽  
pp. 228-231
Author(s):  
Ting Ting Dai ◽  
Pei Ying Huo ◽  
Ji Cai Yu ◽  
Huan Liu ◽  
Yan Xia Song ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Ground State ◽  
Electronic Structures ◽  
Density Functional ◽  
Ground State Structure ◽  
State Structure ◽  
Carbon Cage ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
The Stability

The possible geometrical and electronic structures of C20dimer are optimized by using the density functional theory at B3LYP/LANL2DZ level, stable structure of C20dimer are obtained. The stability of the ground state structure have been studied. The results showed that: there was a slight expansion in carbon cage of C20 dimer ; its chemical stability and thermal stability have been improved.

Stability and Physicochemical Principles for Icosahedral Ti12X (X = Li to Xe) Clusters: A DFT Study

2008 ◽  
Vol 8 (5) ◽  
pp. 2475-2478
Author(s):  
M. Salazar-Villanueva ◽  
P. H. Hernandez Tejeda ◽  
J. F. Rivas-Silva ◽  
J. A. Ascencio
Keyword(s):  
Density Functional ◽  
Chemical Affinity ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Generalized Gradient Approximation ◽  
Stable Clusters ◽  
The Density Functional Theory ◽  
The Stability ◽  
Chemical Selectivity ◽  
Homo Lumo

Results about stability, electronic structure and characteristic electronic properties are reported for cluster structures based on icosahedra structure with a composition of Ti12X (X = Li to Xe) within the generalized gradient approximation of the density functional theory. It is demonstrated that several elements allow an improvement on the stability of Ti13 by a doping process where the central atoms is substituted. C, Si, P, Co, Ge, Ru and Te lead to the largest gain in energy, while the HOMO-LUMO maximum gap distinguishes to just C, Si, P and Te as the most probable to be found in experimental samples. The analysis included physicochemical study of the most stable clusters to predict chemical affinity and new properties. Results reported here are in agreement with partial studies of Ti12X but because of the considered elements, a new scope is open of possible application mainly in the fields as sensors, catalysis and medicine, where the chemical selectivity is an important parameter.

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