Journal of Molecular Modeling

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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
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
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
Tomáš Zimmermann, Jiří Vaníček
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...... hiện toàn bộ
Interactions between Al12X (X = Al, C, N and P) nanoparticles and DNA nucleobases/base pairs: implications for nanotoxicity
Journal of Molecular Modeling - Tập 18 - Trang 559-568 - 2011
Peng Jin, Yongsheng Chen, Shengbai B. Zhang, Zhongfang Chen
The interactions between neutral Al12X(I h ) (X = Al, C, N and P) nanoparticles and DNA nucleobases, namely adenine (A), thymine (T), guanine (G) and cytosine (C), as well as the Watson−Crick base pairs (BPs) AT and GC, were investigated by means of density functional theory computations. The Al12X clusters can tightly bind to DNA bases and BPs to...... hiện toàn bộ
Dehydration of a polyether type extraction agent and of the corresponding K+ complex: insights into liquid-liquid extraction mechanisms by quantum chemical methods
Journal of Molecular Modeling - Tập 18 - Trang 4909-4915 - 2012
Mário Valente, Sérgio Filipe Sousa, Alexandre L. Magalhães, Cristina Freire
In this paper we report a quantum chemical study performed at the B3LYP/6-311G++(d,p) level of theory on structural and energetic aspects of the sequential dehydration of a tetra-hydrated polyethylene-glycol type podand (1,2-bis-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-benzene, hereafter b33) and its complex with the K+ cation. Thermodynamical parameters were determined by hessian quantum calculat...... hiện toàn bộ
Modeling zigzag CNT: dependence of structural and electronic properties on length, and application to encapsulation of HCN and C2H2
Journal of Molecular Modeling - Tập 23 - Trang 1-10 - 2017
Eduardo C. Aguiar, Ricardo L. Longo, João Bosco P. da Silva
Density functional theory (B3LYP, B3LYP-D2 and wB97XD functionals) was used in finite models of zigzag carbon nanotubes (CNT), (n,0)×k with n = 6–9 and k = 2–4, to systematically investigate the effects of size on their structural and electronic properties. We found that the ratio between the length (L t) and the diameter (d t) of the pristine CNT ha...... hiện toàn bộ
Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics
Journal of Molecular Modeling - Tập 28 - Trang 1-12 - 2022
José Cícero Alves Silva, Elton José Ferreira Chaves, Gabriel Aires Urquiza de Carvalho, Gerd Bruno Rocha
The role of knots in proteins remains elusive. Some studies suggest an impact on stability; the difficulty in comparing systems to assess this effect, however, has been a significant challenge. In this study, we produced and analyzed molecular dynamic trajectories considering three different temperatures of two variants of ornithine transcarbamylase (OTC), only one of which has a 31 knot, in order...... hiện toàn bộ
Half-metallicity of graphene nanoribbons and related systems: a new quantum mechanical El Dorado for nanotechnologies … or a hype for materials scientists?
Journal of Molecular Modeling - - 2013
Michaël S. Deleuze, Matija Huzak, Balázs Hajgató
Identification of CYP3A4 inhibitors as potential anti-cancer agents using pharmacoinformatics approach
Journal of Molecular Modeling - Tập 29 Số 5 - 2023
Pravin J. Wanjari, Asutosh Rath, Rohit Y. Sathe, Prasad V. Bharatam
A descriptor for the structural stability of organic–inorganic hybrid perovskites based on binding mechanism in electronic structure
Journal of Molecular Modeling - Tập 28 - Trang 1-11 - 2022
Xiaoshuo Liu, Yang Bai, Shengyi Chen, Chongchong Wu, Ian D. Gates, Tianfang Huang, Wei Li, Weijie Yang, Zhengyang Gao, Jianxi Yao, Xunlei Ding
The poor stability of organic–inorganic hybrid perovskites hinders its commercial application, which motivates a need for greater theoretical insight into its binding mechanism. To date, the binding mode of organic cation and anion inside organic–inorganic hybrid perovskites is still unclear and even contradictory. Therefore, in this work based on density functional theory (DFT), the binding mecha...... hiện toàn bộ
Study of the pyrolysis of coals of different rank using the ReaxFF reactive force field
Journal of Molecular Modeling - Tập 25 - Trang 1-17 - 2019
Longzhen Guo, Zhijun Zhou, Liping Chen, Shiquan Shan, Zhihua Wang
Based on the general coal model, the processes of pyrolysis of coals of different rank were studied by molecular dynamics simulations with the ReaxFF reactive force field. Simulations were performed over wide temperature ranges both for heating from 300 K to 3000 K and a constant temperature range from 2000 K to 3500 K. The pyrolysis of coals of different coal rank under different heating conditio...... hiện toàn bộ
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