Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO–LUMO energy, Mulliken charge and thermodynamic analysis of N′-hydroxy-pyrimidine-2-carboximidamide by DFT approach

Jasmine, N. Jeeva; Muthiah, Packianathan Thomas; Arunagiri, C.; Subashini, A.

doi:10.1016/j.saa.2015.02.100

Cited by 34 publications

(6 citation statements)

References 45 publications

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“…The MPA and NPA are derived from the optimized geometry and NBO outcomes, respectively. The results indicate that all hydrogen atoms possess a net positive charge [60] . The NPA analysis reveals that the H46 atom exhibits a larger positive atomic charge (0.26952) compared to the remaining hydrogen atoms.…”

Section: Resultsmentioning

confidence: 91%

“…The results indicate that all hydrogen atoms possess a net positive charge. [60] The NPA analysis reveals that the H46 atom exhibits a larger positive atomic charge (0.26952) compared to the remaining hydrogen atoms. The observed phenomenon can be attributed to the existence of a robust intramolecular hydrogen bond between the (N-(pyrimidin-2-yl)-4-((1,7,7-trimethylbicyclo [2.2.1] heptan-2-ylidene) amino) benzenesulfonamide) atoms.…”

Section: Natural Population and Mulliken Analysismentioning

confidence: 99%

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Synthesis, vibrational analysis, absorption and emission spectral studies, topology and molecular docking studies on sulfadiazine derivative

Elangovan,

Sowrirajan,

Arumugam

et al. 2024

ChemistrySelect

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A new class of (N‐(pyrimidin‐2‐yl)‐4‐((1,7,7‐trimethylbicyclo [2.2.1] heptan‐2‐ylidene) amino) benzenesulfonamide (CDA) was synthesized from commercially available camphor and sulfadiazine. The synthesized Schiff‐base was characterized by FT‐IR, 1H and 13C NMR spectroscopic analyses. The HOMO, LUMO, MEP, chemical reactivity parameters, and NBO were calculated using the WB97XD/cc‐pVDZ basis set. For better understanding, the electronic absorption and emission of the compound were recorded using UV‐Vis and fluorescence spectra. Molecular docking simulations were investigated between ligand (compound) and target protein. The computational results correlate well with observed values. The frontier molecular orbital energy gap (3.78 eV) revealed that the studied molecule has higher polarizability and chemical reactivity with lower kinetic stability. In addition, compound showed the highest binding score −5.72 kcal/mol, which was confirmed by a molecular docking simulation.

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Section: Resultsmentioning

confidence: 91%

Section: Natural Population and Mulliken Analysismentioning

confidence: 99%

Synthesis, vibrational analysis, absorption and emission spectral studies, topology and molecular docking studies on sulfadiazine derivative

Elangovan,

Sowrirajan,

Arumugam

et al. 2024

ChemistrySelect

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show abstract

“…In Table 4 30 This index evaluates the system's energy stability when it receives an additional electronic charge from the environment by calculating the global electrophilic power of a ligand as being equal to = 2/2. A system is said to be electrophilic if it resists exchanging electrons with its surroundings and has the ability to store more electrons than a system that is not.…”

Section: Homo and Lumo Analysismentioning

confidence: 99%

HOMO–LUMO, NBO, NLO, MEP analysis and molecular docking using DFT calculations in DFPA molecule

BAĞLAN>

GÖREN>

Yıldıko

2023

International Journal of Chemistry and Technology

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Using the Gaussian09 software package, N-(6-(2-(dimethylamino)ethoxy)-5-fluoropyridin-3-yl)-2-(4-fluorophenyl)-5-(trifluoromethyl)pyrazolo[1,5 α]pyrimidine-7-amine(DFPA) the theoretically optimal molecular structure, vibration frequencies and related vibrational movements of the molecule were researched. The DFT(B3PW91 and B3LYP) techniques' 6-311G(d,p) basis set was used to perform quantum chemical computations. HOMO and LUMO analysis were performed for charge transfer in the molecule. NBO analysis was used to examine the stability of the molecule as a result of both charge delocalization and hyperconjugative interaction. DFT approach was used to perform MEP and expected infrared sensitivities and Raman activity are also presented. Geometric parameters of both calculated DFT methods are compatible. Binding affinity values and molecular coupling studies show that the title substance forms a stable complex with MtPanK and PanK. It is possible that the molecule has inhibitory activity against MtPanK and PanK, paving the way for new anti-tuberculosis drugs’ the development.

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“…Moreover, to further explain the dispersion interactions that the B3LYP function is unable to describe, B3LYP-D3 was employed [77]. Meanwhile, the basis set 6-311+G (d,p) was augmented by polarization functions on heavy atoms, polarization functions on hydrogen atoms, and diffuse functions for both hydrogen and heavy atoms [78]. Optimized geometries were used to calculate the HOMO and LUMO energy parameters in this study.…”

Section: Quantum Chemical Analysismentioning

confidence: 99%

De Novo Potent Peptide Nucleic Acid Antisense Oligomer Inhibitors Targeting SARS-CoV-2 RNA-Dependent RNA Polymerase via Structure-Guided Drug Design

Shehzadi,

Yu,

Liang

2023

IJMS

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Global reports of novel SARS-CoV-2 variants and recurrence cases continue despite substantial vaccination campaigns, raising severe concerns about COVID-19. While repurposed drugs offer some treatment options for COVID-19, notably, nucleoside inhibitors like Remdesivir stand out as curative therapies for COVID-19 that are approved by the US Food and Drug Administration (FDA). The emergence of highly contagious SARS-CoV-2 variants underscores the imperative for antiviral drugs adaptable to evolving viral mutations. RNA-dependent RNA polymerase (RdRp) plays a key role in viral genome replication. Currently, inhibiting viral RdRp function remains a pivotal strategy to tackle the notorious virus. Peptide nucleic acid (PNA) therapy shows promise by effectively targeting specific genome regions, reducing viral replication, and inhibiting infection. In our study, we designed PNA antisense oligomers conjugated with cell-penetrating peptides (CPP) aiming to evaluate their antiviral effects against RdRp target using structure-guided drug design, which involves molecular docking simulations, drug likeliness and pharmacokinetic evaluations, molecular dynamics simulations, and computing binding free energy. The in silico analysis predicts that chemically modified PNAs might act as antisense molecules in order to disrupt ribosome assembly at RdRp’s translation start site, and their chemically stable and neutral backbone might enhance sequence-specific RNA binding interaction. Notably, our findings demonstrate that PNA-peptide conjugates might be the most promising inhibitors of SARS-CoV-2 RdRp, with superior binding free energy compared to Remdesivir in the current COVID-19 medication. Specifically, PNA-CPP-1 could bind simultaneously to the active site residues of RdRp protein and sequence-specific RdRp-RNA target in order to control viral replication.

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Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO–LUMO energy, Mulliken charge and thermodynamic analysis of N′-hydroxy-pyrimidine-2-carboximidamide by DFT approach

Cited by 34 publications

References 45 publications

Synthesis, vibrational analysis, absorption and emission spectral studies, topology and molecular docking studies on sulfadiazine derivative

Synthesis, vibrational analysis, absorption and emission spectral studies, topology and molecular docking studies on sulfadiazine derivative

HOMO–LUMO, NBO, NLO, MEP analysis and molecular docking using DFT calculations in DFPA molecule

De Novo Potent Peptide Nucleic Acid Antisense Oligomer Inhibitors Targeting SARS-CoV-2 RNA-Dependent RNA Polymerase via Structure-Guided Drug Design

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