scholarly journals Quantum processing of cytidine derivatives and evaluating their in silico interactions with the COVID-19 main protease

2021 ◽  
pp. 1-8
Author(s):  
Kun Harismah ◽  
Narjes Hajali ◽  
Mahmoud Mirzaei ◽  
Elham Salarrezaei
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
Density Functional ◽  
Md Simulations ◽  
Frontier Molecular Orbitals ◽  
Inhibitory Effects ◽  
Functional Theory ◽  
Main Protease ◽  
Promising Ligand ◽  
Better Than

This work was performed by the importance of exploring possible medications for COVID-19 pandemic. In this regard, cytidine (Cyd) derivatives were investigated to reach a point to see their benefit of employing for the purpose. Each of halogenated models of Cyd including CydF, CydCl, CydBr, and CydI were investigated in addition to the original CydH model. Density functional theory (DFT) based quantum processing were performed to obtain stabilized structures in addition to evaluation of frontier molecular orbitals features. Next, molecular docking (MD) simulations were performed to reach a point of formations of interacting ligand-target complexes. Among the investigated models CydH and CydI were working better than other model for reaching the purpose of this work, in which the derived CydI model was indeed the ligand with the highest suitability for formation of ligand-target complexes. As a consequence, such ligands of original and halogenated Cyd models might work for inhibition of main protease (MPro) enzyme of COVID-19 based on the obtained meaningful vales for complex strengths in addition interacting with the amino acids of active site. More precisely, the CydI model could be proposed as promising ligand for showing the inhibitory effects towards the MPro target of COVID-19.

Theoretical assessments on the interaction between amino acids and g‒Mg3N2 monolayer: dispersion corrected DFT and DFT-MD simulations

2021 ◽  
Author(s):  
Mahyar Rezvani ◽  
Mohammad Astaraki ◽  
Atyeh Rahmanzadeh ◽  
Masoud Darvish Ganji
Keyword(s):  
Amino Acids ◽  
Density Functional Theory ◽  
Density Functional ◽  
Md Simulations ◽  
Functional Theory ◽  
Monolayer Dispersion ◽  
Dft Simulations ◽  
Magnesium Nitride

The interaction of a few amino acids (AAs) with graphene-like magnesium nitride (g‒Mg3N2) monolayer has been investigated with density functional theory (DFT) simulations. The Mg site was found to cause...

scholarly journals Measuring the structure and equation of state of polyethylene terephthalate at megabar pressures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
J. Lütgert ◽  
J. Vorberger ◽  
N. J. Hartley ◽  
K. Voigt ◽  
M. Rödel ◽  
...  
Keyword(s):  
Equation Of State ◽  
Polyethylene Terephthalate ◽  
Density Functional ◽  
Equations Of State ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Shock Hugoniot ◽  
Highly Correlated

AbstractWe present structure and equation of state (EOS) measurements of biaxially orientated polyethylene terephthalate (PET, $$({\hbox {C}}_{10} {\hbox {H}}_8 {\hbox {O}}_4)_n$$ ( C 10 H 8 O 4 ) n , also called mylar) shock-compressed to ($$155 \pm 20$$ 155 ± 20 ) GPa and ($$6000 \pm 1000$$ 6000 ± 1000 ) K using in situ X-ray diffraction, Doppler velocimetry, and optical pyrometry. Comparing to density functional theory molecular dynamics (DFT-MD) simulations, we find a highly correlated liquid at conditions differing from predictions by some equations of state tables, which underlines the influence of complex chemical interactions in this regime. EOS calculations from ab initio DFT-MD simulations and shock Hugoniot measurements of density, pressure and temperature confirm the discrepancy to these tables and present an experimentally benchmarked correction to the description of PET as an exemplary material to represent the mixture of light elements at planetary interior conditions.

scholarly journals H2 Transformations on Graphene Supported Palladium Cluster: DFT-MD Simulations and NEB Calculations

Catalysts ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1306
Author(s):  
Francesco Ferrante ◽  
Antonio Prestianni ◽  
Marco Bertini ◽  
Dario Duca
Keyword(s):  
Atomic Hydrogen ◽  
Density Functional ◽  
Hydrogen Molecule ◽  
Md Simulations ◽  
Vacant Site ◽  
Functional Theory ◽  
H2 Adsorption ◽  
Palladium Cluster ◽  
Supported Palladium ◽  
Dynamics Simulations

Molecular dynamics simulations based on density functional theory were employed to investigate the fate of a hydrogen molecule shot with different kinetic energy toward a hydrogenated palladium cluster anchored on the vacant site of a defective graphene sheet. Hits resulting in H2 adsorption occur until the cluster is fully saturated. The influence of H content over Pd with respect to atomic hydrogen spillover onto graphene was investigated. Calculated energy barriers of ca. 1.6 eV for H-spillover suggest that the investigated Pd/graphene system is a good candidate for hydrogen storage.

scholarly journals Including dispersion in density functional theory for adsorption on flat oxide surfaces, in metal–organic frameworks and in acidic zeolites

2020 ◽  
Vol 22 (14) ◽  
pp. 7577-7585 ◽  
Author(s):  
Florian R. Rehak ◽  
GiovanniMaria Piccini ◽  
Maristella Alessio ◽  
Joachim Sauer
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Van Der Waals ◽  
Metal Organic Frameworks ◽  
Many Body ◽  
Functional Theory ◽  
Metal Organic ◽  
The Many ◽  
Acidic Zeolites ◽  
Better Than

Contrary to common believe, for eight adsorption cases, neither D3 or TS are an improvement compared to D2 nor van der Waals functionals or dDsC. Only the many body approaches are slightly better than D2(Ne) which uses Ne parameters for Mg2+ ions.

scholarly journals Computational Study of Methane C–H Activation by Main Group and Mixed Main Group–Transition Metal Complexes

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2794
Author(s):  
Carly C. Carter ◽  
Thomas R. Cundari
Keyword(s):  
Transition Metal Complexes ◽  
Active Site ◽  
Density Functional ◽  
Computational Study ◽  
Divalent Metal ◽  
Main Group ◽  
Free Energies ◽  
Functional Theory ◽  
Activation Barriers ◽  
Experimental Values

In the present density functional theory (DFT) research, nine different molecules, each with different combinations of A (triel) and E (divalent metal) elements, were reacted to effect methane C–H activation. The compounds modeled herein incorporated the triels A = B, Al, or Ga and the divalent metals E = Be, Mg, or Zn. The results show that changes in the divalent metal have a much bigger impact on the thermodynamics and methane activation barriers than changes in the triels. The activating molecules that contained beryllium were most likely to have the potential for activating methane, as their free energies of reaction and free energy barriers were close to reasonable experimental values (i.e., ΔG close to thermoneutral, ΔG‡ ~30 kcal/mol). In contrast, the molecules that contained larger elements such as Zn and Ga had much higher ΔG‡. The addition of various substituents to the A–E complexes did not seem to affect thermodynamics but had some effect on the kinetics when substituted closer to the active site.

Density Functional Theory Study on the Absorption of CO2 by the Ionic Liquid of 1-butyl-3-methylimidazolium Acetate

2013 ◽  
Vol 807-809 ◽  
pp. 543-548 ◽  
Author(s):  
Yan Fei Chen ◽  
Yan Hong Cui ◽  
Dong Shun Deng ◽  
Ning Ai
Keyword(s):  
Density Functional Theory ◽  
Ionic Liquid ◽  
Ionic Liquids ◽  
Density Functional ◽  
Ion Pairs ◽  
Ion Pair ◽  
Frontier Molecular Orbitals ◽  
Density Functional Theory Study ◽  
Electronic Density ◽  
Functional Theory

The absorptions of CO2on the 1-butyl-3-methylimidazolium acetate ([Bmi [Ac]) with different substituents are calculated systematically at GGA/PW91 level. Three hydrogen bonds are formed between [A and cations of 1-n-[Bmi [A ([NBmi+) and 1-tert-[Bmi [A ([TBmi+). The interaction between CO2and the [NBmi [A by a C-O bond is much weaker than that with the [TBmi [A by forming a O...O...C...C four member-ring. The chemisorption of CO2on the ion pairs of [NBmi [A is much weaker than that on the [TBmi [A, resulted from the absorption energies analysis. The frontier molecular orbitals shows the electronic density overlap between absorbed CO2and the [A in CO2-[NBmi [A is much weaker than that in [TBmi [A. Therefore, the chemisorption of CO2on the ion pair of [NBmi [A is much weaker than that on the [TBmi [A. The ionic liquids based [NBmi+can be used repetitively, and the adsorbed CO2would be easier desorbed.

scholarly journals Predicting Core Level Photoelectron Spectra of Amino Acids Using Density Functional Theory

2020 ◽  
Vol 11 (6) ◽  
pp. 2256-2262
Author(s):  
Jo M. Pi ◽  
Martina Stella ◽  
Nathalie K. Fernando ◽  
Aaron Y. Lam ◽  
Anna Regoutz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Density Functional Theory ◽  
Density Functional ◽  
Core Level ◽  
Photoelectron Spectra ◽  
Functional Theory

scholarly journals Polydopamine and eumelanin molecular structures investigated with ab initio calculations

2017 ◽  
Vol 8 (2) ◽  
pp. 1631-1641 ◽  
Author(s):  
Chun-Teh Chen ◽  
Francisco J. Martin-Martinez ◽  
Gang Seob Jung ◽  
Markus J. Buehler
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Dft Calculations ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Molecular Structures ◽  
Brute Force ◽  
Functional Theory

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin.

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