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Journal of Molecular Modeling

L LoftiKatooli, A Shahsavand
Conventional molecular simulation techniques such as grand canonical Monte Carlo (GCMC) strictly rely on purely random search inside the simulation box for predicting the adsorption isotherms. This blind search is usually extremely time demanding for providing a faithful approximation of the real isotherm and in some cases may lead to non-optimal solutions. A novel approach is presented in this article which does not use any of the classical steps of the standard GCMC method, such as displacement, insertation, and removal...
January 2017: Journal of Molecular Modeling
Chunyu Chen, Ni Bai, Yan Zhang, Lina Jiao, Mingzhu Xia, Gang Chen
In this work, the molecular modeling method was performed to study adsorption interaction between PAMAM molecules of different generations and silicic acid molecules, and the inhibition effect on silica scale were discussed. The results show that adsorption energies of PAMAM molecule of generation 1.0 with amine-terminated groups are stronger than those of generation 1.5 with terminated carboxyl group. The composition of adsorption interactions are the dominating electrostatic interactions and van de Waals interactions as well as H-bond interactions...
January 2017: Journal of Molecular Modeling
Gui-Yun Hang, Wen-Li Yu, Tao Wang, Jin-Tao Wang, Zhen Li
To research and estimate the effects of molar ratios on structures, stabilities, mechanical properties, and detonation properties of CL-20/HMX cocrystal explosive, the CL-20/HMX cocrystal explosive models with different molar ratios were established in Materials Studio (MS). The crystal parameters, structures, stabilities, mechanical properties, and some detonation parameters of different cocrystal explosives were obtained and compared. The molecular dynamics (MD) simulation results illustrate that the molar ratios of CL-20/HMX have a direct influence on the comprehensive performance of cocrystal explosive...
January 2017: Journal of Molecular Modeling
Rachida Fodil, Majda Sekkal-Rahal, Adlane Sayede
Interaction of water molecules with κ-carrabiose disaccharide, within three H-bonding complexes, was investigated. Particular interest was focused on the way with which the BSSE correction has to be performed. Two strategies were used, either performing BSSE correction during or after optimization. For this aim, several DFT-functionals (hybrid GGA and hybrid meta-GGA) and 6-31 + G* basis set were considered. The results demonstrated the uselessness of including of BSSE-CP correction during optimization for all complexes...
January 2017: Journal of Molecular Modeling
Karl Sohlberg, Gloria Bazargan, Joseph P Angelo, Choongkeun Lee
Herein we report a study of the switchable [3]rotaxane reported by Huang et al. (Appl Phys Lett 85(22):5391-5393, 1) that can be mounted to a surface to form a nanomechanical, linear, molecular motor. We demonstrate the application of semiempirical electronic structure theory to predict the average and instantaneous force generated by redox-induced ring shuttling. Detailed analysis of the geometric and electronic structure of the system reveals technical considerations essential to success of the approach. The force is found to be in the 100-200 pN range, consistent with published experimental estimates...
January 2017: Journal of Molecular Modeling
Mingyue Sui, Shuangbao Li, Qingqing Pan, Guangyan Sun, Yun Geng
The upper efficiency of heterojunction organic photovoltaics depends on the increased open-circuit voltage (V oc) and short-circuit current (J sc). So, a higher lowest unoccupied molecular orbital (LUMO) level is necessary for organic acceptor material to possess higher V oc and more photons absorbsorption in the solar spectrum is needed for larger J sc. In this article, we theoretically designed some small molecule acceptors (2∼5) based on fluorene (F), benzothiadiazole, and cyano group (CN) referring to the reported acceptor material 2-[{7-(9,9-di-n-propyl-9H-fluoren-2-yl)benzo[c][1,2,5]thiadiazol-4-yl}methylene]malononitrile (1), the crucial parameters affecting photoelectrical properties of compounds 2∼5 were evaluated by the density functional theory (DFT) and time dependent density functional theory (TDDFT) methods...
January 2017: Journal of Molecular Modeling
Zhengyang Gao, Yi Ding, Weijie Yang, Wentao Han
High moisture content is a main characteristic of low-rank coal, such as lignite. Numerous oxygen containing functional groups in lignite make it represent some special properties, and these functional groups affect the adsorption mechanisms of water molecules on lignite surface. This study reports some typical water · · · lignite conformations, along with a detailed analysis of the geometry, electrostatic potential distribution, reduced density gradient of interaction, and interaction energy decomposition...
January 2017: Journal of Molecular Modeling
Eduardo Habib Bechelane Maia, Vinícius Alves Campos, Bianca Dos Reis Santos, Marina Santos Costa, Iann Gabriel Lima, Sandro J Greco, Rosy I M A Ribeiro, Felipe M Munayer, Alisson Marques da Silva, Alex Gutterres Taranto
Octopus is an automated workflow management tool that is scalable for virtual high-throughput screening (vHTS). It integrates MOPAC2016, MGLTools, PyMOL, and AutoDock Vina. In contrast to other platforms, Octopus can perform docking simulations of an unlimited number of compounds into a set of molecular targets. After generating the ligands in a drawing package in the Protein Data Bank (PDB) format, Octopus can carry out geometry refinement using the semi-empirical method PM7 implemented in MOPAC2016. Docking simulations can be performed using AutoDock Vina and can utilize the Our Own Molecular Targets (OOMT) databank...
January 2017: Journal of Molecular Modeling
Xuyun Yang, Junrui Lu, Ming Ying, Jiangbei Mu, Peichun Li, Yue Liu
FabI, enoyl-ACP reductase (ENR), is the rate-limiting enzyme in the last step for fatty acids biosynthesis in many bacteria. Triclosan (TCL) is a commercial bactericide, and as a FabI inhibitor, it can depress the substrate (trans-2-enoyl-ACP) binding with FabI to hinder the fatty acid synthesis. The structure-activity relationship between TCL derivatives and FabI protein has already been acknowledged, however, their combination at the molecular level has never been investigated. This paper uses the computer-aided approaches, such as molecular docking, molecular dynamics simulation, and binding free energy calculation based on the molecular mechanics/Poisson-Bolzmann surface area (MM/PBSA) method to illustrate the interaction rules of TCL derivatives with FabI and guide the development of new derivatives...
January 2017: Journal of Molecular Modeling
Aurélien Moncomble, Jean-Paul Cornard, Michel Meyer
The stereochemical activity of the lone pair on Pb(II) complexes is assessed using several theoretical methods, including structural analyses, computations of Fukui functions, natural bond orbitals, electron localization function, investigation of the electron density and of its laplacian. The attention is focused on four octadentate N-carbamoylmethyl-substituted tetraazamacrocycles of various ring sizes ranging from 8 to 14 atoms associated with the Pb(II) cation. The theoretical study illustrates the geometrical constraints imposed by the ring structure which limits the spatial development of the lone pair but without fully preventing it...
January 2017: Journal of Molecular Modeling
Julien Racine, Mohamed Abdelhak Touadjine, Ali Rahmouni, Stéphane Humbel
The (1)A1 ground and the first (1)B2 excited states of the methylenecyclopropene (triafulvene) are described by localized wave functions, based on 20 structures valence bond structures. The results are compared to CASSCF(4,4) calculations for both the energetics and the dipole moment. Additional calculations with partial electronic delocalization are presented, and it is shown that the dipole moment modification does not correspond to a situation where the antiaromatic situation prevails (with 4n electrons in the cycle)...
January 2017: Journal of Molecular Modeling
Fang Wang, Yuehan Cao, Shiqian Wei, Ying Zhou
We have provided a straightforward route to screen a series of metal-free doped bulk h-BN as potential visible-light photocatalysts via the first-principle computations. Various nonmetal dopants are considered including Si, P, C, S, Cl, O, and F atoms according to increasing electronegativity. The results show that the introduction of nonmetals leads to small lattice distortions but significant modifications of band structures, electron transition paths and chemical bonding interactions. Generally, all doped h-BN except Si doping have an active response to the visible-light, and dopants with higher electronegativity can significantly narrow the band gaps, which could induce easier optical transition under visible-light excitation...
January 2017: Journal of Molecular Modeling
Yamei Cheng, Xueye Wang, Weiwei Li, Dan Chang
The reaction of p-nitrophenyl acetate and α-alanine can be improved apparently with β-cyclodextrin (β-CD) according to previous research, the interaction mechanism between β-cyclodextrin and p-nitrophenyl acetate is described in this paper. Density functional theory (DFT) method is used throughout the study. According to the energy (the binding energy, the deformation energy) and structural deformation, entry models and reaction process can be pinpointed, viz p-nitrophenyl acetate embed β-CD from the wide rim...
January 2017: Journal of Molecular Modeling
Justyna Rogacka, Lucyna Firlej, Bogdan Kuchta
We simulated the low temperature (T = 77 K) hydrogen adsorption in carbon slit-shaped nanopores using consecutively united atom (UA) and all atom (AA) representation of hydrogen molecule. We showed that both approximations give comparable estimation of the amount stored, for the wide range of pore width (0.6-2.5 nm). We also showed that at very high pressure (P = 400 bar, corresponding to the fugacity f used in grand canonical Monte Carlo simulations of f = 800 bar) the density of the adsorbed hydrogen structures is larger than the density of bulk liquid at critical temperature (∼76 kg/m(3))...
January 2017: Journal of Molecular Modeling
Alexander M Andrianov, Ivan A Kashyn, Alexander V Tuzikov
Virtual screening of novel entry inhibitor scaffolds mimicking primary receptor CD4 of HIV-1 gp120 was carried out in conjunction with evaluation of their potential inhibitory activity by molecular modeling. To do this, pharmacophore models presenting different sets of the hotspots of cellular receptor CD4 for its interaction with gp120 were generated. These models were used as the templates for identification of CD4-mimetic candidates by the pepMMsMIMIC screening platform. Complexes of these candidates with gp120 were built by high-throughput ligand docking and their stability was estimated by molecular dynamics simulations and binding free energy calculations...
January 2017: Journal of Molecular Modeling
Yiliang Liu, Yawen Hua, Anying Yan, Shuang Wu, Fanjie Kong
One-dimensional (1D) gold nanostructures have been extensively studied due to their potential applications in nanoelectronic devices. Using first-principles calculations, composites consisting of a well-defined linear Au n (n = 2-4) chain encapsulated in a (9,0) single-walled carbon nanotube (SWCNT) were studied. The translational energy barrier of a single Au atom in a (9,0) SWCNT was found to be 0.03 eV. This low barrier guaranteed the formation of Au n @ (9,0) SWCNT (n = 1-4) composites. Bond lengths, differential charge densities, and electronic band structures of the composites were studied...
January 2017: Journal of Molecular Modeling
Nursel Acar, Cenk Selçuki, Emine Coşkun
Schiff bases have many chemical and biological applications in medicine and pharmaceuticals due to the presence of an imine group (-C=N-). These bases are used in many different fields of technology, and in photochemistry because of their photochromic properties. Here, the structural and electronic properties of the Schiff base formed by tacrine and saccharin (TacSac) were explored using density functional theory with the B3LYP, M06-2X, M06L, and ωB97XD functionals in combination with the 6-311++G(d,p) basis set...
January 2017: Journal of Molecular Modeling
B Vijaya Pandiyan, P Deepa, P Kolandaivel
Thirteen X-ray crystal structures containing various non-covalent interactions such as halogen bonds, halogen-halogen contacts and hydrogen bonds (I⋯N, I⋯F, I⋯I, F⋯F, I⋯H and F⋯H) were considered and investigated using the DFT-D3 method (B97D/def2-QZVP). The interaction energies were calculated at MO62X/def2-QZVP and MP2/aug-cc-pvDZ level of theories. The higher interaction and dispersion energies (2nd crystal) of -9.58 kcal mol(-1) and -7.10 kcal mol(-1) observed for 1,4-di-iodotetrafluorobenzene bis [bis (2-phenylethyl) sulfoxide] structure indicates the most stable geometrical arrangement in the crystal packing...
January 2017: Journal of Molecular Modeling
Alejandro Valderrama, Radamés Reynoso, Raúl W Gómez, Vivianne Marquina, Martín Romero
We report first-principles calculations carried out to analyze the adsorption of calcium on the outer surface of the fullerene C60, yielding [C60 + mCa]. Geometric optimization (GO) and molecular dynamics (MD) simulation were performed using the plane-wave pseudopotential method within the framework of density functional theory (DFT) and time-dependent DFT (TD-DFT) to investigate the configurations, the associated energies in the ground state, and the stabilities of fullerenes and endofullerenes doped with radioactive sodium iodide when they interact with calcium atoms on the outer fullerene surface (i...
January 2017: Journal of Molecular Modeling
Felipe de S Vilhena, José Walkimar de M Carneiro
The structures and energies for the Huisgen 1,3-dipolar cycloaddition reactions of methyl and ethyl azides with some cyclooctynes and dibenzocyclooctynes were computed at the B3LYP/6-311++G(d,p) level. The activation strain model (ASM) and quantitative molecular orbital (MO) theory were used to investigate the reactivity and regiochemistry in these reactions. The energy decomposition analysis (EDA) was used to identify the intrinsic electronic factor that lead to the preferential formation of 1,7-regiochemistry products...
January 2017: Journal of Molecular Modeling
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