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
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......
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......
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......
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
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......
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
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......
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
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......
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
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......
Antifungal effect of 4-arylthiosemicarbazides against Candida species. Search for molecular basis of antifungal activity of thiosemicarbazide derivatives
Journal of Molecular Modeling - Tập 18 - Trang 4159-4170 - 2012
The in vitro antifungal potency of six series of 4-arylthiosemicarbazides was evaluated. Two isoquinoline derivatives with an ortho-methoxy or ortho-methyl group at the phenyl ring were the most potent antifungal agents. Molecular modeling studies and docking of all 4-arylthiosemicarbazides into the active sites of sterol 14α-demethylase (CYP51), topoisomerase II (topo II), l-glutamine: d-fructose......
Electrostatic interactions play an essential role in DNA repair and cold-adaptation of Uracil DNA glycosylase
Journal of Molecular Modeling - Tập 14 - Trang 201-213 - 2008
Life has adapted to most environments on earth, including low and high temperature niches. The increased catalytic efficiency and thermoliability observed for enzymes from organisms living in constantly cold regions when compared to their mesophilic and thermophilic cousins are poorly understood at the molecular level. Uracil DNA glycosylase (UNG) from cod (cUNG) catalyzes removal of uracil from D......
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