scholarly journals Structural Analyses of Vanillin Derivative Compounds and their Molecular Docking with MPro and RdRp Enzymes of COVID-19

2021 ◽  
Vol 12 (2) ◽  
pp. 1660-1669
Keyword(s):  
Molecular Docking ◽  
Density Functional ◽  
Md Simulations ◽  
Aldehyde Group ◽  
Coupling Constants ◽  
Atomic Scale ◽  
Main Protease ◽  
Quadrupole Coupling ◽  
New Compounds ◽  
The Impact

In this work, structural analyses of vanillin (Vanl) and eleven of its derivatives based on the modification of the aldehyde group were investigated using density functional theory (DFT) calculations. In this regard, molecular orbital features and atomic-scale quadrupole coupling constants were evaluated for geometrically optimized structures to see the impact of structural modification on the whole structure. The results indicated that the main impact of such modification was significant only for the modification region, whereas the impact on the rest of the structure was almost negligible. However, electronic features indicated a different tendency for Vanl derivatives for involving in interaction with enzymatic targets. Because of the importance of innovating medication for COVID-19, main protease (MPro) and RNA-dependent RNA polymerase (RdRp) were chosen for the enzymatic target of Vanl ligands for the formation of ligand-target complexes through performing molecular docking (MD) simulations. The results indicated that among the complexes, Vanl 9 (–NHNH2) and 11 (–CH2Cl) could work as the best ligands for interacting with each of RdRp and MPro, respectively. Consequently, optimization of Vanl derivatives could help innovate new compounds for the possible medication of the COVID-19 pandemic.

Non-Covalent Functionalisation of C30 Fullerene by Pyrrole-n-Carboxylic Acid (n=2, 3): Density Functional Theory Studies

2017 ◽  
Vol 73 (1) ◽  
pp. 51-56
Author(s):  
Kun Harismah ◽  
Mahmoud Mirzaei ◽  
Nahid Ghasemi ◽  
Mohammad Nejati
Keyword(s):  
Density Functional Theory ◽  
Carboxylic Acid ◽  
Density Functional ◽  
Spherical Shape ◽  
Density Functional Theory Calculations ◽  
Coupling Constants ◽  
Atomic Scale ◽  
Functional Theory ◽  
Quadrupole Coupling ◽  
Non Covalent Interactions

AbstractFor functionalisation of a representative C30 fullerene nanostructure by pyrrole-n-carboxylic acid (PnCA; n=2, 3) their stabilities and properties were investigated based on density functional theory calculations. Parallel calculations were also done for C60 fullerene as evidence for comparing the results. Non-covalent interactions are considered to make the functionalised structures. In contrast with the spherical shape of C60, the shape of C30 fullerene is elliptical; therefore, the functionalisation processes were done for both axial and equatorial elliptical positions (AC30 and EC30). The results indicated that both the positions of C30 have almost equivalent chances to be functionalised by PnCA; but functionalisation by P2CA is slightly more favourable than P3CA, either for C60. The illustrated molecular orbitals’ distributions indicated that the direction of charge transfer could be considered from PnCA counterparts to fullerene counterparts. The molecular properties indicated more reactivity for C30 than for C60 fullerene. Finally, the atomic scale quadrupole coupling constants indicated different roles for N and O atoms of PnCA in the functionalised models.

Investigating Functionalization Impacts on Structural Features of Barbituric Acid Derivatives: DFT Approach

2021 ◽  
pp. 1-9
Author(s):  
Narjes Hajali ◽  
Afshin Taghva Manesh ◽  
Ahmad Seif
Keyword(s):  
Density Functional ◽  
Barbituric Acid ◽  
Minimum Energy ◽  
Structural Features ◽  
Coupling Constants ◽  
Atomic Scale ◽  
Functional Theory ◽  
Quadrupole Coupling ◽  
Homo And Lumo ◽  
Characteristic Features

Density functional theory (DFT) calculations were performed to investigate electronic and structural properties of barbituric acid (BA) and sixtheen of its derivatives to show impacts of structural functionalization on the features of parent BA. The models were optimized and the minimum energy structures were confirmed by frequency calculations. Molecular and atomic descriptors were evaluated for the optimized models, in which the results of formation binding strength and molecular orbital features indicated significance of such functionalization processes on the observed properties. The highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO) and their related parameters all indicated magnitudes of changes from one molecule to another one. Furthermore, atomic scale quadrupole coupling constants (Cq) were evaluated for the nitrogen and oxygen atoms of BA compounds showing significance of structural functionalization impacts on the atomic properties of parent BA. As a consequence, such structural analyses of BA compounds could show their characteristic features for further developments especially for their efficient pharmaceutical applications.

scholarly journals Barbituric Acid Tautomers: DFT Computations of Keto-Enol Conversions, Frontier Molecular Orbitals and Quadrupole Coupling Constants

2021 ◽  
Vol 12 (1) ◽  
pp. 244-252
Keyword(s):  
Density Functional ◽  
Barbituric Acid ◽  
Molecular Orbitals ◽  
Coupling Constants ◽  
Atomic Scale ◽  
Model Systems ◽  
Frontier Molecular Orbitals ◽  
Hydrogen Atoms ◽  
Dft Computations ◽  
Quadrupole Coupling

In this work, density functional theory (DFT) computations were performed to investigate tautomeric formation processes of barbituric acid (BA). Ten tautomers were totally investigated for the purpose based on the movement of hydrogen atoms among nitrogen and oxygen atoms providing one pure keto form (BA1) and nine other keto-enol forms. The structures were optimized, and BA1 was found to be the most stable one, and both BA3 and BA7 were found to be the most unstable ones. The point was that the ring structure was broken for both BA3 and BA7, but the structure's stability was still approved. Indeed, such serious tautomeric conversion with breaking the structure warns for using such BA bio-organic molecules for further applications, especially in pharmacy-related ones, in which side effects or byproduct synthesis might appear. Further analyses of frontier molecular orbitals features indicated the effects of such tautomerism processes on all model systems, in which more details were obtained by atomic-scale quadrupole coupling constant (Qcc). All obtained results approved significant changes of tautomers regarding molecular and atomic scale features with more or less significant effects regarding the original BA1 reference model.

scholarly journals Molecular Docking Senyawa Gingerol dan Zingiberol pada Tanaman Jahe sebagai Penanganan COVID-19

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Belinda D. P. M. Ratu ◽  
Widdhi Bodhi ◽  
Fona Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Main Protease ◽  
Docking Method ◽  
Pubmed Database ◽  
Almost All ◽  
The Impact

Abstract: COVID-19 is a new disease. Many people feel the impact of this disease. There is no definite cure for COVID-19, so many people use traditional medicine to ward off COVID-19, including ginger. This study aims to determine whether there is an interaction between compounds in ginger (gingerol and zingiberol) and the COVID-19’s main protease (6LU7). This study uses a molecular docking method using 4 main applications, namely Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, and Open Babel GUI. The samples used were gingerol and zingiberol compounds in ginger plants downloaded from Pubchem. The data used in this study used Mendeley, Clinical Key, and PubMed database. The study showed that almost all of the amino acid residues in the gingerol compound acted on the 6LU7 active site, whereas the zingiberol did not. The results of the binding affinity of ginger compounds, both gingerol and zingiberol, do not exceed the binding affinity of remdesivir, a drug that is widely researched as a COVID-19 handling drug. In conclusion, gingerol and zingiberol compounds in ginger can’t be considered as COVID-19’s treatment.Keywords: molecular docking, gingerol, zingiberol Abstrak: COVID-19 merupakan sebuah penyakit yang baru. Banyak masyarakat yang merasakan dampak dari penyakit ini. Belum ada pengobatan pasti untuk menyembuhkan COVID-19, sehingga banyak masyarakat yang menggunakan pengobatan tradisional untuk menangkal COVID-19, termasuk jahe. Penelitian ini bertujuan untuk mengetahui apakah ada interaksi antara senyawa pada jahe (gingerol dan zingiberol) dengan main protease COVID-19 (6LU7). Penelitian ini menggunakan metode molecular docking dengan menggunakan 4 aplikasi utama, yaitu Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, dan Open Babel GUI. Sampel yang digunakan yaitu senyawa gingerol dan zingiberol pada tanaman jahe yang diunduh di Pubchem. Data yang digunakan dalam penelitian ini menggunakan database Mendeley, Clinical Key, dan PubMed. Penelitian menunjukkan bahwa hampir semua residu asam amino pada senyawa gingerol bekerja pada sisi aktif 6LU7, sedangkan tidak demikian pada zingiberol. Hasil binding affinity senyawa jahe, baik gingerol maupun zingiberol tidak  melebihi binding affinity remdesivir, obat yang banyak diteliti sebagai obat penanganan COVID-19. Sebagai simpulan, senyawa gingerol dan zingiberol pada tanaman jahe tidak dapat dipertimbangkan sebagai penanganan COVID-19Kata Kunci: molecular docking, gingerol, zingiberol

scholarly journals Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations

2020 ◽  
Vol 21 (11) ◽  
pp. 3922 ◽  
Author(s):  
Mohamed Hagar ◽  
Hoda A. Ahmed ◽  
Ghadah Aljohani ◽  
Omaima A. Alhaddad
Keyword(s):  
Dipole Moment ◽  
Molecular Docking ◽  
Dft Calculations ◽  
Binding Affinity ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Hydrophobic Interactions ◽  
Chemical Reactivity ◽  
Main Protease

The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease Mpro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2′-Fluoro-2′-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (−7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity −6.06 and −4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.

Density Functional Theory Studies of Bonding in Complexes H3N···XY of Ammonia and Dihalogen Molecules: A Comparison with Experimental Results from Rotational Spectroscopy

2002 ◽  
Vol 57 (6-7) ◽  
pp. 537-543 ◽  
Author(s):  
O. Kh. Poleshchuk ◽  
A. C. Legona
Keyword(s):  
Density Functional ◽  
Natural Bond Orbital ◽  
Coupling Constants ◽  
Rotational Spectroscopy ◽  
Charge Redistribution ◽  
Functional Theory ◽  
Quadrupole Coupling ◽  
Nuclear Quadrupole ◽  
Experimental Values

The electron density and nuclear quadrupole coupling constants (NQCC) of the H3N...XY (n a type in Mulliken notation) complexes, (X, Y = F, Cl, Br and I), are analyzed with the aid of density functional calculations. To demonstrate the quality of the calculations, various bond lengths and NQCCs obtained by using the hybrid Becke-Lee-Perdew-Yang functional are compared with the corresponding experimental values determined from rotational spectroscopy. An analysis of the NQCC values and various quantities derived fromthe natural bond orbital approach reveals that the molecular interaction is mainly electrostatic, with probably only a small extent of intermolecular electric charge redistribution on complex formation

A boroxol ring doped zigzag boron nitride nanotube: a computational DFT study of the quadrupole coupling constant

2009 ◽  
Vol 87 (6) ◽  
pp. 647-652 ◽  
Author(s):  
Asadollah Boshra ◽  
Ahmad Seif
Keyword(s):  
Density Functional Theory ◽  
Boron Nitride ◽  
Density Functional ◽  
Quadrupole Coupling Constant ◽  
Coupling Constants ◽  
Boron Nitride Nanotube ◽  
Coupling Constant ◽  
Functional Theory ◽  
Quadrupole Coupling ◽  
Dopant Atoms

Based upon density functional theory, we investigate the influence of oxygen dopant atoms that make a boroxol ring on the electrostatic properties of a zigzag (10, 0) boron nitride nanotube in which three of the nitrogen atoms are replaced by oxygen dopant atoms. The electric field gradient (EFG) tensors at the sites of 11B and 14N nuclei were calculated and converted to quadrupole coupling constants (CQ) in the two models of a perfect and a boroxol ring O-doped (10, 0) single-walled boron nitride nanotube (BNNT). Our calculations showed that the CQ values of the boron and nitrogen nuclei along the length of a perfect BNNT are divided into layers. Among the layers the mouth layers have the largest CQ magnitudes. In the doped model, in addition to the mouth layers, the CQ values of those nitrogen nuclei which directly bond to the boroxol ring are increased. However, the CQ values of the boron nuclei that make the boroxol ring and directly bond to the boroxol ring are decreased.

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