A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements

Petersson, George A.; Bennett, Andrew F.; Tensfeldt, Thomas G.; Al‐Laham, Mohammad A.; Shirley, William A.; Mantzaris, J.

doi:10.1063/1.455064

Cited by 2,727 publications

(1,511 citation statements)

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“…The basis set 6-311G(d,p) augmented by "d" polarization function on heavy atom and "p" polarization function on hydrogen atoms were used for better description of polar bonds of molecules [14,15]. The UV-vis spectrum, electronic transitions, vertical excitation energies and oscillator strength were computed with time dependent DFT (TD-DFT) method [16,17].…”

Section: Computational Detailsmentioning

confidence: 99%

Conformational Stability, TGA, and Molecular Docking Investigations of p-Coumaric Acid with Special Relevance to Anti-Cancer and Antibacterial Activity

et al. 2017

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In this work an attempt is made to analysis of the possible different conformers of p-coumaric acid (PCA) by using density functional method. The total energy of four possible conformers were calculated by using B3LYP/6-311G(d,p) method. Computational result identifies that the most stable conformer of PCA is C2. The formation of inter-and intra-molecular hydrogen bonding between -OH and -COOH group gave the evidence for dimer formation for PCA molecule. The highest occupied-lowest unoccupied molecular orbital analysis shows that the negative electrostatic region situated over the -COOH group and positive electrostatic potential region are localized on ring system and all hydrogen. The PCA has been screened to anti-microbial activity and found to exhibit antibacterial effects. Molecular docking results suggest that PCA may exhibit inhibitory activity against lung cancer protein and may act as potential against lung cancer.

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Section: Computational Detailsmentioning

confidence: 99%

Conformational Stability, TGA, and Molecular Docking Investigations of p-Coumaric Acid with Special Relevance to Anti-Cancer and Antibacterial Activity

et al. 2017

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“…The widely employed hybrid method denoted by (B3LYP), which includes a mixture of Hartree-Fock (HF) and DFT exchange terms and the gradient-corrected correlation functional of Lee et al, [23,24] as proposed and parameterized by Becke, [25,26] was used, along with the double-zeta split valence basis set 6-31G * * . [27] Molecular geometries were fully optimized by the Berny algorithm, using redundant internal coordinates. [28] The bond lengths are accurate to within ca 0.1 pm and the bond angles to within ca 0.1 • .…”

Section: Dft Calculationsmentioning

confidence: 99%

Antioxidant phenolic esters with potential anticancer activity: solution equilibria studied by Raman spectroscopy

Machado

Calheiros

Gaspar

et al. 2008

J Raman Spectroscopy

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The solution Raman pattern of a series of structurally related hydroxycinnamic and hydroxybenzoicesters (caffeates and gallates) with potential antioxidant/anticancer activity was studied, for different biologically significant concentrations. The spectra were assigned with the help of theoretical calculations in the light of previously reported experimental data for these compounds in the solid state. Evidence of the formation of dimeric entities in solution, via (C) O· · ·H(O) and/or (C) O· · ·H(C) intermolecular hydrogen bonds, was obtained. The dimer-to-monomer equilibrium, which influences the antioxidant activity of this kind of systems, was monitored through Raman titration experiments.

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“…The Hartree-Fock method with the 6-31G* level used in the Gaussian 98 program were used to determine electrostatic potentials. 45 The RESP fitting technique in AMBER was applied to determine the partial charges. 46 2.4.…”

Section: Force Fieldmentioning

confidence: 99%

Predictions of Binding of a Diverse Set of Ligands to Gelatinase-A by a Combination of Molecular Dynamics and Continuum Solvent Models

Hou

Guo

2002

J. Phys. Chem. B

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The free energies of binding, ∆G bind , between a diverse set of eight hydroxamate inhibitors with gelatinase-A (MMP-2) were computed by using the recently developed MM/PBSA approach. In this paper, a nonbonded model was used to represent the potentials of the catalytic zinc center. Molecular dynamics (MD) simulations were used to generate the thermally averaged ensemble of conformations of the ligand-protein complexes. On the basis of the trajectories from MD simulations, the free energies of binding were calculated using molecular mechanics, the continuum solvent model, surface area estimation, and normal-mode analysis. The results show that MM/PBSA not only can rank the studied ligands effectively but also can reproduce the experimental binding free energies successfully. The predicted binding free energies correlate well with the experimental values (r ) 0.84, q ) 0.78). As a comparison, the free energies of binding were also computed by using the linear interaction energy approximation (LIE). The overall agreement between the calculated and experimental values for the diverse set of ligands means that the MM/PBSA approach is a useful tool for the general evaluation of protein-ligand interactions. The analysis of the separate energy terms contributing to MM/PBSA free energy indicates that the association between hydroxamate and MMP-2 is mainly driven by more favorable van der Waals/nonpolar interactions in the complex than in solution.

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A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements

Abstract: Articles you may be interested inExtension of complete basis set model chemistries to molecules containing third row atoms Ga-Kr

Cited by 2,727 publications

References 53 publications

Conformational Stability, TGA, and Molecular Docking Investigations of p-Coumaric Acid with Special Relevance to Anti-Cancer and Antibacterial Activity

Conformational Stability, TGA, and Molecular Docking Investigations of p-Coumaric Acid with Special Relevance to Anti-Cancer and Antibacterial Activity

Antioxidant phenolic esters with potential anticancer activity: solution equilibria studied by Raman spectroscopy

Predictions of Binding of a Diverse Set of Ligands to Gelatinase-A by a Combination of Molecular Dynamics and Continuum Solvent Models

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