Computational model for the acylation step of the β-lactam ring: Potential application for l,d-transpeptidase 2 in mycobacterium tuberculosis

Fakhar, Zeynab; Govender, Thavendran; Lamichhane, Gyanu; Maguire, Glenn E. M.; Kruger, Hendrik G.; Honarparvar, Bahareh

doi:10.1016/j.molstruc.2016.08.049

Cited by 44 publications

(37 citation statements)

References 56 publications

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“…NBO analysis represents the electronic wave functions defined based on the Lewis occupied and non‐Lewis unoccupied localized orbitals . The strength of delocalization related to the stabilization energy E 2 derived from the second‐order perturbation theory is associated with i , j Fock matrix . The higher the E 2 value the stronger the intermolecular charge transfer .…”

Section: Resultsmentioning

confidence: 99%

Synthesis, characterization, molecular docking, biological activity and density functional theory studies of novel 1,4‐naphthoquinone derivatives and Pd(II), Ni(II) and Co(II) complexes

Ekennia

Osowole

Onwudiwe

et al. 2018

Applied Organom Chemis

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Two novel heterocyclic ligands, 2-[(5-fluoro-1,3-benzothiazol-2-yl)amino]naphthalene-1,4-dione (HL 1 ) and 2-[(5-methyl-1,3-benzothiazol-2-yl)amino]naphthalene-1,4-dione (HL 2 ), and their Pd(II), Ni(II) and Co(II) complexes were prepared and characterized using 1 H NMR, 13 C NMR, infrared and UV-visible spectroscopic techniques, elemental analysis, magnetic susceptibility, thermogravimetry and molar conductance measurements. The infrared spectral data showed that the chelation behaviours of the ligands towards the transition metal ions were through one of the carbonyl oxygen and deprotonated nitrogen atom of the secondary amine group. Molar conductance results confirmed that the complexes are non-electrolytes in dimethylsulfoxide. The geometries of the complexes were deduced from magnetic susceptibility and UV-visible spectroscopic results. Second-order perturbation analysis using density functional theory calculation revealed a stronger intermolecular charge transfer between ligand and metal ion in [NiL 1 (H 2 O) 2 (CH 3 COO-)] and CoL 1 compared to the other complexes. The in vitro antibacterial activity of the compounds against some clinically isolated bacteria strains showed varied activities. [NiL 1 (H 2 O) 2 (CH 3 COO-)] exhibited the best antibacterial results with a minimum inhibitory concentration of 50 μg mL −1 . The molecular interactions of the compounds with various drug targets of some bacterial organisms were established in a bid to predict the possible mode of antibacterial action of the compounds. The ferrous ion chelating ability of the

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Section: Resultsmentioning

confidence: 99%

Synthesis, characterization, molecular docking, biological activity and density functional theory studies of novel 1,4‐naphthoquinone derivatives and Pd(II), Ni(II) and Co(II) complexes

Ekennia

Osowole

Onwudiwe

et al. 2018

Applied Organom Chemis

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“…The application of DFT‐based quantum chemical properties to shine more light on the preference of chemical reactions at the molecular level remained substantial . For many stable models, the gap between the energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) defines the electronic properties of such systems .…”

Section: Resultsmentioning

confidence: 99%

“…For many stable models, the gap between the energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) defines the electronic properties of such systems . The energies of HOMO and LUMO are often referred to as the energies of the FMOs and can be applied to TS molecules to provide a vital basis for estimating the chemical reactivity, selectivity and stability of the TS structures studied herein . The energies of the FMOs were calculated to study some quantum chemical parameters (Equations ) for the five TS structures.…”

Section: Resultsmentioning

confidence: 99%

DFT study of the acid‐catalyzed esterification reaction mechanism of methanol with carboxylic acid and its halide derivatives

Lawal

Govender

Maguire

et al. 2017

Int J of Quantum Chemistry

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Extensive experimental studies have been dedicated to the esterification mechanisms from carboxylic acids and acid halides. However, attention on the theoretical aspect of the mechanism has been scarcely addressed. Herein, the acid-catalyzed esterification mechanism of methanol with acetic acid and its halide derivatives is described using density functional theoretical method and solvation model based on density. The mechanistic investigation involved formation of cyclic prereaction and 6-membered ring transition structures, which favors the esterification process and product formation. A good comparison with experimental data from literature for the esterification reaction of acetic acid with methanol was achieved through this in silico approach. Density Functional Theory-based quantum descriptors were applied to provide a better understanding on the reactivity, selectivity, and stability of this reaction. This theoretical results provide a crucial guide to study classical acid-catalyzed reaction mechanisms and applying a reasonable theoretical model to study similar organic reactions. In addition, it can be applied to larger systems such as enzymatic mechanism. K E Y W O R D S acetic acid (HOAc), acetyl halides (XAc), Density Functional Theory (DFT), esterification reaction 1 | I N TR ODU C TI ON Esters remained important intermediates in the chemical industry due to their widespread pharmaceutical applications and biodiesel production.Dating back to the 1890s, the Fischer esterification [1] reaction has remained a crucial process through which esters are formed via dehydrative coupling of carboxylic acids (RCOOH) with alcohol (ROH) in the presence of inorganic liquid acids. [2][3][4] Among studies on kinetics and mechanism of acid-catalyzed RCOOH esterification, methyl acetate (MeOAc) formation from acetic acid (HOAc) and methanol (MeOH) using homogeneous and heterogeneous acid catalysts are abundant. [4][5][6] R€ onnback et al. [2] had earlier hypothesized the nature of the acid-catalyzed esterification of HOAc with MeOH as a stepwise model involving 7 transition structures and 3 intermediates in acidic solution. This experimental study [2] was novel and serves as a basis for subsequent investigations.The overall reaction process is presented as:The production of MeOAc from HOAc and MeOH has been kinetically mediated by homogeneous [2,[6][7][8][9][10][11] or heterogeneous catalysts, [5,6,[12][13][14][15] with more research being performed on the latter due to increased reusability, [16] high selectivity, [17] and less product contamination. [6,16,18] The synthesis and kinetics via microwave, membrane, batch, and microchannel reactors have also been addressed. [12,13,19,20] Most recent experimental investigations (from 2011) have reported free energy of activation for this process with values ranging from 7.7 to 15.1 kcal mol 21[4-6,15,21-26] in Int J Quantum Chem. 2018;118:e25497.

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“…The combination of B3LYP/6–31 + G(d,p)/LANL2DZ has been reported to be effective and suitable for calculations involving metal complexes . Frontier molecular orbital (FMO), referred to as the highest occupied molecular orbital (HOMO), and the lowest unoccupied molecular orbital (LUMO), were determined (reactivity index) . To obtain the fundamental thermodynamic properties, frequency calculation was performed.…”

Section: Computational Detailsmentioning

confidence: 99%

Novel 3‐Hydroxy‐2‐naphthoic hydrazone and Ni(II), Co(II) and Cu(II) Complexes: Synthesis, Spectroscopic Characterization, Antimicrobial, DNA Cleavage and Computational Studies

Ekennia

Ibezim

Okpareke

et al. 2019

Applied Organom Chemis

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A novel hydrazone ligand derived from condensation reaction of 3-hydroxy-2naphthoic hydrazide with dehydroacetic acid, and its Ni(II), Cu(II) and Co(II) complexes were synthesized, characterized by spectroscopic, elemental analyses, magnetic susceptibility and conductivity methods, and screened for antimicrobial, DNA binding and cleavage properties. Spectroscopic analysis and elemental analyses indicated the formula, [MLCl 2 ], for the complexes; square planar geometry for the nickel, and tetrahedral geometry for copper and cobalt complexes. The non-electrolytic natures of the complexes in Dimethyl Sulphoxide (DMSO) were confirmed by their molar conductance values in the range of 6.11-14.01 Ω −1 cm 2 mol −1 . The copper complex had the best antibacterial activity against Staphylococcus aureus (ATCC 29213). DNA cleavage activities of the compounds, evaluated on pBR322 DNA, by agarose gel electrophoresis, in the presence and absence of oxidant (H 2 O 2 ) and free radical scavenger (DMSO), indicated no activity for the ligand, and moderate activity for the complexes, with the copper complex cleaving pBR322 DNA more efficiently in the presence of H 2 O 2 . When the complexes were evaluated for antibacterial and A-DNA activity using Molecular docking technique, the copper complex was found to be most effective against Gram-positive (S. aureus) bacteria. [CuLCl 2 ] showed good hydrogen bonding interaction with the major-groove (C 2 . G 13 base pair) of A-DNA. Density functional theory (DFT) calculations of the structural and electronic properties of the complexes revealed that [CuLCl 2 ] had a smaller HOMO-LUMO gap, suggesting a higher tendency to donate electrons to electron-accepting species of biological targets.

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Computational model for the acylation step of the β-lactam ring: Potential application for l,d-transpeptidase 2 in mycobacterium tuberculosis

Cited by 44 publications

References 56 publications

Synthesis, characterization, molecular docking, biological activity and density functional theory studies of novel 1,4‐naphthoquinone derivatives and Pd(II), Ni(II) and Co(II) complexes

Synthesis, characterization, molecular docking, biological activity and density functional theory studies of novel 1,4‐naphthoquinone derivatives and Pd(II), Ni(II) and Co(II) complexes

DFT study of the acid‐catalyzed esterification reaction mechanism of methanol with carboxylic acid and its halide derivatives

Novel 3‐Hydroxy‐2‐naphthoic hydrazone and Ni(II), Co(II) and Cu(II) Complexes: Synthesis, Spectroscopic Characterization, Antimicrobial, DNA Cleavage and Computational Studies

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