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
Hockseng Nguan, Sara Ahmadi, Rauzah Hashim
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...... hiện toàn bộ
Docking-assisted 3D-QSAR studies on xanthones as α-glucosidase inhibitorsJournal of Molecular Modeling - Tập 23 - Trang 1-12 - 2017
Xuehua Zheng, Siyuan Zhou, Chen Zhang, Deyan Wu, Hai-Bin Luo, Yinuo Wu
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...... hiện toàn bộ
Formation enthalpies and dilute heats of HCP-HCP disordered binary alloys: modified ones of embedded atom method potentialsJournal of Molecular Modeling - Tập 27 - Trang 1-11 - 2021
Hak-Son Jin, Song-Nam Ho, Hyok-Chol Ri, He Yang
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...... hiện toàn bộ
Computational study of the NO, SO2, and NH3 adsorptions on fragments of 3N-graphene and Al/3N grapheneJournal of Molecular Modeling - Tập 24 - Trang 1-10 - 2018
Yao-Dong Song, Liang Wang, Qian-Ting Wang
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 ...... hiện toàn bộ
Reactivity of pyrazole derivatives with halomethanes: A DFT theoretical studyJournal of Molecular Modeling - Tập 24 - Trang 1-10 - 2018
Monia Chebbi, Youssef Arfaoui
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...... hiện toàn bộ
Inorganic benzenes as the noncovalent interaction donor: a study of the π-hole interactionsJournal of Molecular Modeling - Tập 23 Số 12 - Trang 1-9 - 2017
Chu, Runtian, Zhang, Xueying, Meng, Lingpeng, Zeng, Yanli
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 ...... hiện toàn bộ
Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approachesJournal of Molecular Modeling - Tập 15 - Trang 481-487 - 2008
Wei-Wei Han, Ying Wang, Yi-Han Zhou, Yuan Yao, Ze-Sheng Li, Yan Feng
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...... hiện toàn bộ
Chemical carcinogens in non-enzymatic cytosine deamination: 3-isocyanatoacrylonitrileJournal of Molecular Modeling - Tập 12 - Trang 731-737 - 2006
Rainer Glaser, Hong Wu, Francisca von Saint Paul
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...... hiện toàn bộ
Structure and electronic properties of (+)-catechin: aqueous solvent effectsJournal of Molecular Modeling - Tập 20 - Trang 1-13 - 2014
Erika N. Bentz, Alicia B. Pomilio, Rosana M. Lobayan
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...... hiện toàn bộ