Modeling the DFT structural and reactivity studies of a pyrimidine -6-carboxylate derivative with reference to its wavefunction-dependent, MD simulations and evaluation for potential antimicrobial activity

Smitha, M.; Mary, Y. Sheena; Mary, Y. Shyma; Serdaroğlu, Goncagül; Chowdhury, Papia; Rana, Meenakshi; Umamahesvari, H.; Sarojini, B. K.; Mohan, B. J.; Pavithran, Rani

doi:10.1016/j.molstruc.2021.130397

Cited by 22 publications

(8 citation statements)

References 59 publications

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“…These shows the reactivity changes in the system [29]. The HOMO and LUMO are localized on IND with interchange in polarity while in all complexes, HOMO is over the DC and LUMO is over the IND [30,31]. This shows strong charge transfer from DC to IND (Fig.…”

Section: Structures and Energiesmentioning

confidence: 82%

Theoretical Investigation of the Modeling of Indole –dichlormethane Hydrogen Bonding in Different Solvents

Al‐Otaibi

Mary²,

Mary³

2021

Preprint

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Theoretical vibrational spectra of indole (IND) and its binary combination with dichloromethane (DC) in various solvents were computed to track the impact of molecular interactions on drug spectral characteristics. When transitioning from plain drug to complexes, 3561.26 cm− 1 mode of the IND displays a substantial shift in peak location. The 3561.26 band shows (~ 15.58) red shift upon dilution. The geometry of drug and IND-DC complex in various solvents was calculated using quantum chemical calculation utilizing DFT.

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Section: Structures and Energiesmentioning

confidence: 82%

Theoretical Investigation of the Modeling of Indole –dichlormethane Hydrogen Bonding in Different Solvents

Al‐Otaibi

Mary²,

Mary³

2021

Preprint

Self Cite

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“…[ 38 ] The RMSF values and Rg average from 0 to 100 ns for APO and DRG complexes are 29.5 Å and 2.85 Å (figure 9a and b). [ 39,40 ]…”

Section: Resultsmentioning

confidence: 99%

“…[38] The RMSF values and Rg average from 0 to 100 ns for APO and DRG complexes are 29.5 Å and 2.85 Å (figure 9a and b). [39,40] (a) (b) Figure 10: (a) The H-Bond result of the complex with LTB, (b) multiple contacts between the interacting residues and LTB…”

Section: Rdg Analysismentioning

confidence: 99%

Investigations into the electronic properties of lorlatinib, an anti‐cancerous drug using DFT, wavefunction analysis and MD simulations

Al‐Otaibi,

Mary,

Mary

et al. 2022

Vietnam Journal of Chemistry

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Lung cancer is a kind of cancer with high morbidity and mortality rate, making it one of the most dangerous tumors to humanity's health and existence. Wavefunction dependent reactivity analysis, atom in molecule (AIM) and molecular dynamics (MD) simulations of lorlatinib (LTB) are reported in the present work. Electrophilicity index predicts the biological activity. The bond ellipticity describes the anisotropy of the curvature of electron density and its maximum value is at C15‐H32. Chemical environments, N8 = C26‐N7, C18 = C30 ≡ N9, and C15 = C14‐C13 are found to be highest delocalization regions. The complexes were stable throughout the simulation and amino acids involved in bringing the overall structural deviation are explored.

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“…In recent work, υCÀ S functional of compound 3 was assigned at 657 and 621 cm À 1 . [79] Furthermore, the υCÀ H and υCC stretching modes were assigned in the range 3129-2884 cm À 1 and 1598-985 cm À 1 .…”

Section: Ft-ir Spectral Studymentioning

confidence: 99%

New Hybrid (E)‐4‐((pyren‐1‐ylmethylene)amino)‐N‐(thiazol‐2‐yl)benzenesulfonamide as a Potential Drug Candidate: Spectroscopy, TD‐DFT, NBO, FMO, and MEP Studies**

Erdoğan

Serdaroğlu

2021

ChemistrySelect

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A novel pyrene-sulfathiazole-based potential drug candidate 3 was designed, successfully synthesized by a condensation reaction of pyrenecarboxaldehyde (1) with sulfathiazole (2) in good yield, and fully characterized by NMR, IR, UV-Vis, and HRMS spectroscopic techniques. The TD-DFT/B3LYP calculations displayed that the recorded peaks at 396, 377, 280, and 236 nm were due to the mainly n-π* and partially π-π* transitions that occurred on pyrene, azomethine, and sulfathiazole moieties. The NBO results disclosed that the electron delocalizations happened onto sulfathiazole, aromatic rings (pyrene and Ph-), and azomethine groups had the main responsibility of the lowering stabilization energy of compound 3. The NMR shifts were calculated by using the GIAO approaches in the DMSO phase and compared with the relevant data recorded. The thermodynamic and quantum chemical quantities were used for elucidating the physicochemical properties and reactivity behavior, in THF, DMSO, and water simulation environments. Accordingly, the calculated DM (D) and α (au) order of compound 3 were calculated in the order of vacuum < THF < DMSO < water, which indicated that the stability and thus reactivity of the compound strongly depended on the solvent environment. The FMO studies implied that the electron-donating possibility of compound 3 was dominant to the electron-accepting potency. In this work, the SMD version of IEFPCM was used in solvent media simulations.

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Modeling the DFT structural and reactivity studies of a pyrimidine -6-carboxylate derivative with reference to its wavefunction-dependent, MD simulations and evaluation for potential antimicrobial activity

Cited by 22 publications

References 59 publications

Theoretical Investigation of the Modeling of Indole –dichlormethane Hydrogen Bonding in Different Solvents

Theoretical Investigation of the Modeling of Indole –dichlormethane Hydrogen Bonding in Different Solvents

Investigations into the electronic properties of lorlatinib, an anti‐cancerous drug using DFT, wavefunction analysis and MD simulations

New Hybrid (E)‐4‐((pyren‐1‐ylmethylene)amino)‐N‐(thiazol‐2‐yl)benzenesulfonamide as a Potential Drug Candidate: Spectroscopy, TD‐DFT, NBO, FMO, and MEP Studies**

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