Molecular modeling study of structures, Hirschfield surface, NBO, AIM, RDG, IGM and 1HNMR of thymoquinone/hydroxypropyl-β-cyclodextrin inclusion complex from QM calculations

Kadri, Rayene; Imane, Djellala; Bouhadiba, Abdelaziz; Leila, Nouar; Fatiha, Madi; Guendouzi, Abdelkrim; Gassoumi, Bouzid; Ismahan, Lafifi; Brahim, Houari; Oumeddour, Rabah

doi:10.1016/j.molstruc.2021.131565

Cited by 29 publications

(15 citation statements)

References 61 publications

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“…The nature of weak interactions is determined using the noncovalent interaction index, which is used to characterize intermolecular interactions. Based on a reduced density gradient (RDG), the noncovalent interaction method represents weak spatial interaction and gives information about the interactions between host and guest in a complex . The regions of the molecules that experience intermolecular and intramolecular noncovalent interactions are graphically visualized using the RDG analysis .…”

Section: Resultsmentioning

confidence: 99%

“…Based on a reduced density gradient (RDG), the noncovalent interaction method represents weak spatial interaction and gives information about the interactions between host and guest in a complex. 79 The regions of the molecules that experience intermolecular and intramolecular noncovalent interactions are graphically visualized using the RDG analysis. 80 It is a nondimensional quantity.…”

Section: Resultsmentioning

confidence: 99%

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Designing Thieno[3,4-c]pyrrole-4,6-dione Core-Based, A₂–D–A₁–D–A₂-Type Acceptor Molecules for Promising Photovoltaic Parameters in Organic Photovoltaic Cells

Noor,

Waqas,

Shaban

et al. 2024

ACS Omega

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Nonfullerene-based organic solar cells can be utilized as favorable photovoltaic and optoelectronic devices due to their enhanced life span and efficiency. In this research, seven new molecules were designed to improve the working efficiency of organic solar cells by utilizing a terminal acceptor modification approach. The perceived A 2 −D−A 1 −D−A 2 configuration-based molecules possess a lower band gap ranging from 1.95 to 2.21 eV compared to the pre-existing reference molecule (RW), which has a band gap of 2.23 eV. The modified molecules also exhibit higher λ max values ranging from 672 to 768 nm in the gaseous and 715− 839 nm in solvent phases, respectively, as compared to the (RW) molecule, which has λ max values at 673 and 719 nm in gas and chloroform medium, respectively. The ground state geometries, molecular planarity parameter, and span of deviation from the plane were analyzed to study the planarity of all of the molecules. The natural transition orbitals, the density of state, molecular electrostatic potential, noncovalent interactions, frontier molecular orbitals, and transition density matrix analysis of all studied molecules were executed to validate the optoelectronic properties of these molecules. Improved charge mobilities and dipole moments were observed, as newly designed molecules possessed lower internal reorganization energies. The open circuit voltage (V oc ) of W4, W5, W6, and W7 among newly designed molecules was improved as compared to the reference molecule. These results elaborate on the superiority of these novel-designed molecules over the pre-existing (RW) molecule as potential blocks for better organic solar cell applications.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Designing Thieno[3,4-c]pyrrole-4,6-dione Core-Based, A₂–D–A₁–D–A₂-Type Acceptor Molecules for Promising Photovoltaic Parameters in Organic Photovoltaic Cells

Noor,

Waqas,

Shaban

et al. 2024

ACS Omega

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“…Pauli repulsion is minimal [72]. The vivid maps of LOL and ELF of Allo-Ocimenol were produced using the Multiwfn software and are shown in particulars on contacts across filled and virtual orbital spaces, which can aid in the investigation of intermolecular and intramolecular contacts.…”

Section: Elf and Lol Analysismentioning

confidence: 99%

Quantum chemical calculation, topological analysis, biological evaluation and molecular docking of allo‐ocimenol against breast cancer

Chandran,

Zochedh,

Sukumaran

et al. 2023

Int J of Quantum Chemistry

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The main aim of this study is to identify the structural stability of allo‐ocimenol and its molecular reactivity against breast cancer‐associated proteins to confirm its anti‐cancer capability using density function theory and molecular docking analysis. The structural optimization was carried out via the DFT/B3LYP technique with a 6‐311++G (d,p) basis set. The molecular geometry and vibrational assignments of the Allo‐Ocimenol molecule were analyzed through density functional theory (DFT). Through optimized molecular structure, the vibrational frequencies (FT‐IR and FT‐Raman) were assigned and related with experimentally observed vibrational frequencies and the UV spectrum was computed and experimentally confirmed. The allo‐ocimenol's reactive activity was further analyzed through a computed molecular electrostatic potential surface. Utilizing the HOMO‐LUMO energies and molecular electrostatic potential energy gap, the reactivity and molecular stability of the allo‐ocimenol molecule was calculated. Mulliken and natural population analyses were used to determine the charge distribution across the allo‐ocimenol atoms. The natural bond orbitals were used to demonstrate the bioactivity of the titled molecule. RDG evaluation was used to examine the weak interactions of the allo‐ocimenol molecule. ELF and LOL analyses were utilized to investigate the topology of the allo‐ocimenol molecule. Thermodynamic evaluation has been utilized to acquire values and asses the thermodynamic parameters that reveal the thermal stability of the title molecule. Allo‐Ocimenol's anti‐microbial activity was assessed through an in‐vitro disc diffusion method, and its tumor inhibitory and pharmacokinetic properties were evaluated through an in‐silico approach using molecular docking and ADMET investigation. Zones of clearance were seen in anti‐microbial analyses at various concentrations, and the breast cancer target protein NAMPT established the greatest binding potential, with a docking value of −7.4 Kcal mol−1.

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“…NMR spectroscopy is a technique extremely sensitive to conformational effects as well as molecular structure effects, both of which can be directly affected by modifications in the chemical environment [106]. Interactions that are able to alter the electronic distribution or even the HOMO-LUMO boundary orbitals can be factors that modify the chemical shift of molecules [107]. By analysis of the figures, it is shown that the interactions of CPX with hTOPO-II caused a modification in the electronic density (figure 6) and the frontier orbitals of CPX (figure 7), which could explain the change in the fluorine chemical shift.…”

Section: Spectroscopic Parameters: 19 F-chemical Shifts (δ)mentioning

confidence: 99%

Structural parameters of the interaction between ciprofloxacin and human topoisomerase-II β enzyme: toward new 19F NMR Chemical Shift probes

Sales

Ramalho

Gonçalves

2022

Preprint

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New tools for cancer diagnosis are being studied day by day, since early diagnosis can be crucial for a successful treatment. In this context, the use of NMR probes constitutes an efficient way of diagnosis. In this work, we investigated the use of ciprofloxacin to indirectly label the overexpression of topoisomerase-II enzymes by changes in 19F NMR chemical shifts of ciprofloxacin. Increased topoisomerase-II expression has been associated with cancer occurrence, mainly with aggressive forms of breast cancer, thus constituting a promising molecular target for new tumor cell identifiers. Using DFT calculations, a spectroscopy analysis of ciprofloxacin in different chemical environments, evaluating the solvent and enzymatic effects was performed. Our results point that the ciprofloxacin forms a stable complex with the enzyme, and the main intermolecular interactions between ciprofloxacin and human topoisomerase-IIβ are hydrogen bonds, following by pi-pi stacking and electrostatic interactions. Also, a shift of 6.04 ppm occurs in the 19F NMR signal when ciprofloxacin is interacting with the human topoi-somerase-IIβ enzyme, and that this parameter may be a possible indirect marker to indicate the overexpression of these enzymes in the body.

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Molecular modeling study of structures, Hirschfield surface, NBO, AIM, RDG, IGM and 1HNMR of thymoquinone/hydroxypropyl-β-cyclodextrin inclusion complex from QM calculations

Cited by 29 publications

References 61 publications

Designing Thieno[3,4-c]pyrrole-4,6-dione Core-Based, A₂–D–A₁–D–A₂-Type Acceptor Molecules for Promising Photovoltaic Parameters in Organic Photovoltaic Cells

Designing Thieno[3,4-c]pyrrole-4,6-dione Core-Based, A₂–D–A₁–D–A₂-Type Acceptor Molecules for Promising Photovoltaic Parameters in Organic Photovoltaic Cells

Quantum chemical calculation, topological analysis, biological evaluation and molecular docking of allo‐ocimenol against breast cancer

Structural parameters of the interaction between ciprofloxacin and human topoisomerase-II β enzyme: toward new 19F NMR Chemical Shift probes

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Molecular modeling study of structures, Hirschfield surface, NBO, AIM, RDG, IGM and 1HNMR of thymoquinone/hydroxypropyl-β-cyclodextrin inclusion complex from QM calculations

Cited by 29 publications

References 61 publications

Designing Thieno[3,4-c]pyrrole-4,6-dione Core-Based, A2–D–A1–D–A2-Type Acceptor Molecules for Promising Photovoltaic Parameters in Organic Photovoltaic Cells

Designing Thieno[3,4-c]pyrrole-4,6-dione Core-Based, A2–D–A1–D–A2-Type Acceptor Molecules for Promising Photovoltaic Parameters in Organic Photovoltaic Cells

Quantum chemical calculation, topological analysis, biological evaluation and molecular docking of allo‐ocimenol against breast cancer

Structural parameters of the interaction between ciprofloxacin and human topoisomerase-II β enzyme: toward new 19F NMR Chemical Shift probes

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Designing Thieno[3,4-c]pyrrole-4,6-dione Core-Based, A₂–D–A₁–D–A₂-Type Acceptor Molecules for Promising Photovoltaic Parameters in Organic Photovoltaic Cells

Designing Thieno[3,4-c]pyrrole-4,6-dione Core-Based, A₂–D–A₁–D–A₂-Type Acceptor Molecules for Promising Photovoltaic Parameters in Organic Photovoltaic Cells