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Turkish Computational and Theoretical Chemistry
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This is an Open Access Journal

Open Access journal
ISSN (Print) 2587-1722 - ISSN (Online) 2602-3237
Published by DergiPark

[187 journals]

Structural Analysis of Some Pyrrolopyrimidine Derivatives and Examining
their Binding Affinity against Cyclooxygenase-2 Enzyme
- Authors: Kun HARİSMAH; Mahmoud MIRZAEI, Kimia GHAFARI
  Abstract: This work was performed to investigate structural features of ten models (L1-1L10) of pyrrolopyrimidine derivatives in addition to evaluating their activity against the cyclooxygenase-2 (COX-2) enzyme target. In this regard, celecoxib (CEL) was employed as a reference model for evaluating features of the investigated models. Frontier molecular orbitals features were evaluated for the models including the highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO) in addition to evaluating chemical hardness and softness (H and S) features. Afterwards, molecular docking (MD) simulations were performed for examining the contribution of each compound against the COX-2 enzyme for formation of ligand-target complexes. The models showed that the investigated structures could work as efficient ligands for building string complexes with the COX-2 target, in which some of them with CN, F, and OMe functional groups were also more efficient than the reference CEL drug. As a consequence, details of ligand-target complex formations including types of interactions and surrounding amino acids were all recognized for the models systems.
  PubDate: Wed, 15 Dec 2021 00:00:00 +030
DFT/TDDFT studies of the structural, electronic, NBO and non-linear
optical proper-ties of triphenylamine functionalized tetrathiafulvalene
- Authors: Mohammed BOUACHRINE; Ahmed AZAID, Tayeb ABRAM, Rchid KACİMİ, Marzouk RAFTANI, Abdelouahid SBAİ, Tahar LAKHLIFI
  Abstract: In this paper, we present a theoretical analysis of the molecular structure of a conjugated molecule TTPA-TTF at the DFT level using the B3LYP method and the 6-31G (d) basis set. The TTPA-TTF mole-cule presented a twisted configuration, which gave it good solubility in different organic solvents. The Partial atomic charge, molecular electrostatic potential (MEP) map, and global reactivity descriptors highlight the reactive sites of the molecule with the possible prediction of its reactivity. Moreover, a clear image of the intra- and intermolecular interactions illustrates hyperconjugative interactions based on the charge delocalization that emerges from the natural bond orbital analysis. The non-linear optical proper-ties of the TTPA-TTF molecule can also be calculated by determining their first hyperpolarizabilities. The time-dependent density theory method TD-DFT-B3LYP 6-31G (d) was used for the study of absorption. The obtained results show a broad spectrum in the visible range favorable to harvest solar light.
  PubDate: Wed, 15 Dec 2021 00:00:00 +030
Study of dipolar 1.3 cycloaddition reaction by DFT method, as well as
study of antibacterial activity of two isomers 1.4 and 1.5 on two
- Authors: Mohammed Aziz AJANA; Abdessadak OUMAYMA, Halima HAJJI, Yassıne KOUBI, Tahar LAKHLIFI, Mohammed BOUACHRINE
  Abstract: A study was carried out on the 1.3 dipolar cycloaddition reaction between Phenylethyne and Benzyl (diazyn-1-ium-1-yl) azanide, using the different theoretical approaches, to know precisely the reaction path, and the regioselectivity of reaction, as well as the transition state. We carried out this study by using the DFT method on the one hand, on the other hand we studied the antibacterial activity of two isomers 1.4 and 1.5 obtained from cycloaddition reaction on two therapeutic targets E. coli and Helicobacter pylori, using Molecular docking.
  PubDate: Wed, 15 Dec 2021 00:00:00 +030
The theoretical study of anticancer rhodium complexes and methyl groups
effect on ligands in chemical reactivity, global descriptors, ADMET by DFT
study
- Authors: Mohammad Jahidul ISLAM; Ajoy KUMER, Md Wahab KHAN
  Abstract: As there are a potential application of rhodium (0) complexes and rhodium (II) complexes in anticancer drug discovery, the key point of this study is to design new rhodium(0) complexes with amine ligand, and was estimated their properties. To predict the thermo-physical, chemical reactivity and biological activity of most expected rhodium (0) complexes with amine and alkyl amine were conducted by the computational method of density functional theory (DFT). The thermo-physical parameters, such as free energy, entropy, dipole moment, binding energy, nuclear energy, electronics energy and heat of formation were calculated, as well as chemical reactivity, for example, Highest Occupied Molecular Orbital (HOMO), Lowest Unoccupied Molecular Orbital (LUMO) and HOMO-LUMO gap. Some descriptors, such as ionization potential, electronegativity, hardness, softness and electron affinity were estimated of rhodium (0) complexes. To explain about biological indication, the charge density, surface area grid, volume, LogP, polarizability, refractivity and molecular mass had also calculated. The ADMET was illustrated through the online database AdmetSAR for the safe uses and toxicological evidence. Regarding the chemical reactivity study in view of softness and LUMO HOMO gap, the L03 is a more suitable drug than others, and stands for that secondary alkyl amine as ligand is more effective than primary and tertiary amine ligands.
  PubDate: Wed, 15 Dec 2021 00:00:00 +030
Methyl-mercaptane adsorption and sensing on Fe-/Co-graphene structures: A
DFT study
- Authors: Numan YUKSEL; Ahmet KOSE, Mehmet Ferdi FELLAH
  Abstract: In this research, the adsorption and detection abilities of Fe and Co doped graphene structures for methyl-mercaptan molecule were investigated by Density Functional Theory (DFT) method. B3LYP hybrid functional and LANL2DZ/6-31G(d,p) basis sets were used in the calculations. At the end of the adsorption processes, Fe and Co doped graphene structures were determined to be suitable adsorbents for the methyl-mercaptan molecule. In addition, charge transfer happened from the methyl-mercaptan molecule to the Fe and Co-doped graphene structures. The electronic sensor and the Φ-type sensor properties were also investigated and it was determined that Fe-graphene structure could be only used as an electronic sensor for methyl-mercaptan molecule at room temperature.
  PubDate: Wed, 15 Dec 2021 00:00:00 +030

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