Journal of Molecular Modeling
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DFT study of glucose based glycolipid crown ethers and their complexes with alkali metal cations Na+ and K+
Journal of Molecular Modeling - Tập 18 - Trang 5041-5050 - 2012
A theoretical study of a series of five glucose based glycolipid crown ethers and their complexes with Na+ and K+ was performed using the density functional theory with B3LYP/6-31 G* to obtain the optimized geometrical structures and electronic properties. The local nucleophilicity of the five molecules was investigated using Fukui function, while the global nucleophilicity was calculated from the......
Docking-assisted 3D-QSAR studies on xanthones as α-glucosidase inhibitors
Journal of Molecular Modeling - Tập 23 - Trang 1-12 - 2017
Recently, a series of xanthone analogues has been identified as α-glucosidase inhibitors. To provide deeper insight into the three-dimensional (3D) structural requirements for the activities of these molecules, CoMFA and CoMSIA approaches were employed on 54 xanthones to construct 3D-QSAR models. Their bioactive conformations were first investigated by docking studies and optimized by subsequent m......
Formation enthalpies and dilute heats of HCP-HCP disordered binary alloys: modified ones of embedded atom method potentials
Journal of Molecular Modeling - Tập 27 - Trang 1-11 - 2021
The formation enthalpies and the dilute heats of HCP-HCP disordered binary alloys were evaluated by employing the improved ones of the modified analytic embedded atom method (EAM) potentials for HCP metals. We calculated the formation enthalpies according to the concentration of alloy elements for 36 kinds of HCP-HCP disordered binary alloys by using the modified ones of embedded atom method poten......
Computational study of the NO, SO2, and NH3 adsorptions on fragments of 3N-graphene and Al/3N graphene
Journal of Molecular Modeling - Tập 24 - Trang 1-10 - 2018
The adsorption properties of common gas molecules (NO, NH3, and SO2) on the surface of 3N-graphene and Al/3N graphene fragments are investigated using density functional theory. The adsorption energies have been calculated for the most stable configurations of the molecules on the surface of 3N-graphene and Al/3N graphene fragments. The adsorption energies of Al/3N graphene-gas systems are −220.5 ......
Reactivity of pyrazole derivatives with halomethanes: A DFT theoretical study
Journal of Molecular Modeling - Tập 24 - Trang 1-10 - 2018
The N-alkylation reaction of pyrazole derivatives with halomethanes was studied using density functional theory (DFT). The hybrid method B3LYP was employed, along with an ECP basis set such as LANL2DZ for halogen atoms (X = Cl, Br, I) and the 6–311 + G(d,p) basis set for all other atoms. In order to predict the specific site at which the pyrazole derivatives interact with halomethanes, local react......
Inorganic benzenes as the noncovalent interaction donor: a study of the π-hole interactions
Journal of Molecular Modeling - Tập 23 Số 12 - Trang 1-9 - 2017
For inorganic benzenes C3N3X3 and B3O3X3 (X = H, F, CN), the positive electrostatic potentials (π-hole) were discovered above and below the inorganic benzene ring center. Then, the π-hole interactions between the inorganic benzenes and NCH have been designed and investigated by MP2/aug-cc-pVDZ calculations. In this paper, the termolecular complexes B3O3X3···NCH···NCH, C3N3X3···NCH···NCH ......
Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approaches
Journal of Molecular Modeling - Tập 15 - Trang 481-487 - 2008
The 3D structure of the amidase from Rhodococcus erythropolis (EC 3.5.1.4) built by homology-based modeling is presented. Propionamide and acetamide are docked to the amidase. The reaction models were used to characterize the explicit enzymatic reaction. The calculated free energy barrier at B3LYP/6-31G* level of Model A (Ser194 + propionamide) is 19.72 kcal mol−1 in gas (6.47 kcal mol−1 in soluti......
Chemical carcinogens in non-enzymatic cytosine deamination: 3-isocyanatoacrylonitrile
Journal of Molecular Modeling - Tập 12 - Trang 731-737 - 2006
Uracil has long been known as the main product of nitrosative cytosine deamination in aqueous solution. Recent mechanistic studies of cytosinediazonium ion suggest that the cation formed by its dediazoniation can ring-open to N-protonated (Z,s-cis)-3-isocyanatoacrylonitrile 7. Stereochemical preferences are discussed of the 3-isocyanatoacrylonitriles (Z,s-cis)-10, (E,s-cis)-11, (Z,s-trans)-12, and......
Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene
Journal of Molecular Modeling - Tập 16 - Trang 1779-1787 - 2010
Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibrium and kinetic properties of molecules. Specifically, we explain how path integrals can be employed to evaluate the equilibrium (EIE) and kinet......
Structure and electronic properties of (+)-catechin: aqueous solvent effects
Journal of Molecular Modeling - Tập 20 - Trang 1-13 - 2014
We report a study of the structure of (+)-catechin, which belongs to the family of the flavan-3-ols—one of the five most widely distributed phenolic groups. The biological activities and pharmaceutical utility of these compounds are related to antioxidant activity due to their ability to scavenge free radicals. A breakthrough in the study of the conformational space of this compound, so far absent......
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