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Journal of Molecular Modeling

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https://www.readbyqxmd.com/read/28321656/molecular-modeling-of-the-piezoelectric-properties-of-ferroelectric-composites-containing-polyvinylidene-fluoride-pvdf-and-either-graphene-or-graphene-oxide
#1
Vladimir S Bystrov, Igor K Bdikin, Maksim Silibin, Dmitry Karpinsky, Svitlana Kopyl, Ekaterina V Paramonova, Gil Goncalves
Molecular modeling of ferroelectric composites containing polyvinylidene fluoride (PVDF) and either graphene (G) or graphene oxide (GO) were performed using the semi-empirical quantum approximation PM3 in HyperChem. The piezo properties of the composites were analyzed and compared with experimental data obtained for P(VDF-TrFE)-GO films. Qualitative agreement was obtained between the results of the modeling and the experimental results in terms of the properties of the measured effective piezoelectric coefficient d 33eff and its decrease in the presence of G/GO in comparison with the average computed piezoelectric coefficient <d 33>...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28321655/quantum-chemical-nmr-ft-ir-and-esi-ms-studies-of-complexes-of-colchicine-with-zn-ii
#2
Wojciech Jankowski, Joanna Kurek, Piotr Barczyński, Marcin Hoffmann
Colchicine is a tropolone alkaloid from Colchicinum autumnale. It shows antifibrotic, antimitotic, and anti-inflammatory activities, and is used to treat gout and Mediterranean fever. In this work, complexes of colchicine with zinc(II) nitrate were synthesized and investigated using DFT, (1)H and (13)C NMR, FT IR, and ESI MS. The counterpoise-corrected and uncorrected interaction energies of these complexes were calculated. We also calculated their (1)H, (13)C NMR, and IR spectra and compared them with the corresponding experimentally obtained data...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28321654/theoretical-insight-into-the-bh3%C3%A2-hcn-adsorption-on-the-co-100-and-co-110-surfaces-as-hydrogen-storage
#3
He Zhao, Fu-de Ren, Yan-Hong Wang
Fifteen configurations and adsorption energies of the adsorption sites of BH3∙∙∙HCN on Co(100) and Co(110) surfaces were investigated using the density functional theory. The results show that after BH3∙∙∙HCN is adsorbed, although there is no general behavior for the H∙∙∙H distances, the adsorption energies of BH3∙∙∙HCN are always far stronger than those of H2 on Co surfaces, suggesting that the dihydrogen-bonded complex, one kind of prospective material for reversible hydrogen storage, can be tightly adsorbed on the surfaces of metals...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28316041/the-structure-of-cu-ii-and-hg-ii-complexes-of-bispyrenyl-azine-revisited
#4
Arturo Espinosa Ferao, Rafaela García
Azine ligands show preference for the antiperiplanar conformation, but their 2:2 ligand-metal complexes can exhibit a central N4M2 core in the most stable chair arrangement, as in the case of the model lithium complex, with the ligand displaying a synclinal conformation that is not stable in the free ligand. According to DFT calculations, complexation of Cu(2+) with bis(1-pyrenyl)azine (1) affords a C2-symmetric [1·Cu(2+)]2 species with a planar central N4Cu2 core exhibiting a weak cuprophilic interaction...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28316040/chlorine-gas-reaction-with-zno-wurtzoid-nanocrystals-as-a-function-of-temperature-a-dft-study
#5
Mudar Ahmed Abdulsattar
In the present work, we applied density functional theory and temperature-dependent Gibbs free energy calculations to wurtzoid structures to explain the sensitivity of ZnO nanocrystals towards chlorine molecules. In agreement with experimental findings, our results revealed that chlorine sensing under ambient conditions is feasible. Higher temperatures increased the sensitivity of ZnO nanocrystals towards chlorine gas molecules. Peak calculated sensitivities were in the temperature ranges (167-220 °C), (447-578 °C) and (952-1159 °C), which is in good agreement with experimentally determined temperatures...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28315081/effect-of-the-crystalline-environment-on-the-third-order-nonlinear-optical-properties-of-l-arginine-phosphate-monohydrate-a-theoretical-study
#6
Clodoaldo Valverde, Rosemberg F N Rodrigues, Daniel F S Machado, Basílio Baseia, Heibbe C B de Oliveira
A supermolecular approach combined with an iterative electrostatic scheme was employed to investigate the nonlinear optical properties of the hybrid L-arginine phosphate monohydrate crystal, the procedure being aided by DFT calculations. The supermolecular scheme basically treated the molecules surrounding the unit cell as point charges; this approximation results in rapid convergence, making it a feasible method. DFT functionals of different flavors were considered: B3LYP, B2PLYP, CAM-B3LYP, ωB97, and M06HF, utilizing the 6-311 + G(d) basis set...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28315080/unsaturated-trinuclear-iron-fluoroborylene-complexes
#7
Liancai Xu, Qian-Shu Li, R Bruce King
The unsaturated trinuclear iron fluoroborylene complexes Fe3(BF)3(CO) n (n = 7, 6) have been studied using density functional theory (DFT). Relatively complicated potential energy surfaces are found with nine and eight structures within 15 kcal mol(-1) of the lowest energy structures for the Fe3(BF)3(CO)7 and Fe3(BF)3(CO)6 systems, respectively. In each of these low-energy structures all three BF groups are either edge-bridging or face-bridging but never terminal groups. Some, but not all, of the low-energy structures also have edge-bridging and/or face-bridging CO groups leading to some structures with as many as five bridging groups...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28303437/molecular-dynamics-simulations-of-the-first-charge-of-a-li-ion-si-anode-nanobattery
#8
Diego E Galvez-Aranda, Victor Ponce, Jorge M Seminario
Rechargeable lithium-ion batteries are the most popular devices for energy storage but still a lot of research needs to be done to improve their cycling and storage capacity. Silicon has been proposed as an anode material because of its large theoretical capacity of ∼3600 mAh/g. Therefore, focus is needed on the lithiation process of silicon anodes where it is known that the anode increases its volume more than 300%, producing cracking and other damages. We performed molecular dynamics atomistic simulations to study the swelling, alloying, and amorphization of a silicon nanocrystal anode in a full nanobattery model during the first charging cycle...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28303436/mutations-in-catalase-peroxidase-katg-from-isoniazid-resistant-mycobacterium-tuberculosis-clinical-isolates-insights-from-molecular-dynamics-simulations
#9
Arethusa Lobo Pimentel, Regiane Bertin de Lima Scodro, Katiany Rizzieri Caleffi-Ferracioli, Vera Lúcia Dias Siqueira, Paula Aline Zanetti Campanerut-Sá, Luciana Dias Ghiraldi Lopes, Aryadne Larissa de Almeida, Rosilene Fressatti Cardoso, Flavio Augusto Vicente Seixas
The current multidrug therapy for tuberculosis (TB) is based on the use of isoniazid (INH) in combination with other antibiotics such as rifampin, ethambutol and pyrazinamide. Literature reports have shown that Mycobacterium tuberculosis, the causative agent of TB, has become resistant to this treatment by means of point mutations in the target enzymes of these drugs, such as catalase-peroxidase (KatG). By means of equilibrium molecular dynamics in the presence of the ligand, this work evaluated ten point mutations described in the enzyme KatG that are related to resistance to INH ...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28299480/stability-and-molecular-properties-of-the-boron-nitrogen-alternating-analogs-of-azulene-and-naphthalene-a-computational-study
#10
Anderson José Lopes Catão, Alejandro López-Castillo
In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investigated boron-nitrogen naphthalene (boroazanaphthalene) and two isomers of boron-nitrogen azulene, 1,3,4,6,8-pentaaza-2,3a,5,7,8a-pentaboraazulene (BN-azulene) and 2,3a,5,7,8a-pentaaza-1,3,4,6,8- pentaboraazulene (NB-azulene), are stable systems...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28293795/a-workflow-for-in-silico-design-of-hil-10-and-ebvil-10-inhibitors-using-well-known-miniprotein-scaffolds
#11
Salvador Dueñas, Sergio A Aguila, Genaro Pimienta
The over-expression of immune-suppressors such as IL-10 is a crucial landmark in both tumor progression, and latent viral and parasite infection. IL-10 is a multifunctional protein. Besides its immune-cell suppressive function, it also promotes B-cell tumorigenesis of lymphomas and melanoma. Human pathogens like unicellular parasites and viruses that remain latent inside B cells promote the over-expression of hIL-10 upon infection, which inhibits cell-mediated immune surveillance, and at the same time mediates B cell proliferation...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28289959/quantum-isotope-effects-on-the-h-li2-reaction
#12
Thiago Ferreira da Cunha, Henrique Vieira Rivera Vila, Wiliam Ferreira da Cunha, Luiz Guilherme M de Macedo, Ricardo Gargano
This work presents a detailed study concerning the quantum isotope effects on the H+Li[Formula: see text] reaction, when the hydrogen is replaced by muonium, deuterium, and tritium. To verify such effects on these isotope reactions, it was applied an accurate time-independent quantum scattering approach to determine the dynamic properties, such as state-to-state probabilities as a function of the total energy, the product energetic distribution, and the contribution of the ro-vibrational excitation on the reaction probabilities...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28289958/density-functional-study-of-the-structures-and-properties-of-holmium-doped-silicon-clusters-hosi-n-n%C3%A2-%C3%A2-3-9-and-their-anions
#13
Liyuan Hou, Jucai Yang, Yuming Liu
The structures and properties of Ho-doped Si clusters, including their adiabatic electron affinities (AEAs), simulated photoelectron spectra (PESs), stabilities, magnetic moments, and charge-transfer characteristics, were systematically investigated using four density-functional methods. The results show that the double-hybrid functional (which includes an MP2 correlation component) can accurately predict the ground-state structure and properties of Ho-doped Si clusters. The ground-state structures of HoSi n (n = 3-9) are sextuplet electronic states...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28289957/molecular-dynamics-simulation-of-effect-of-glycerol-monostearate-on-amorphous-polyethylene-in-the-presence-of-water
#14
Shinya Iwata
Polyethylene (PE) is used widely as an electrical insulating material. However, the deterioration of its insulating ability is accelerated by exposure to a humid environment. To prevent the influence of water molecules, mixing 2,3-dihydroxypropyl octadecanoate-known as glycerol monostearate (GMS)-into PE has been proposed. However, the physical mechanism underlying the effect of GMS remains unclear. In the present study, the behavior of water molecules in amorphous PE with and without GMS molecule(s) was investigated in terms of diffusion and clustering using molecular dynamics (MD) simulations...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28289956/investigation-of-the-morphological-transition-of-a-phospholipid-bilayer-membrane-in-an-external-electric-field-via-molecular-dynamics-simulation
#15
Zhe Kong, Hongbo Wang, Lijun Liang, Zhisen Zhang, Shibo Ying, Quan Hu, Jia-Wei Shen
Elucidating the mechanisms for morphological transitions of the phospholipid bilayer membrane during cellular activity should lead to greater understanding of these membrane transitions and allow us to optimize biotechnologies such as drug delivery systems in organisms. To investigate the mechanism for and the dynamics of morphological changes in the phospholipid membrane, we performed molecular dynamics simulation of a phospholipid membrane with and without membrane protein under the influence of electric fields with different strengths...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28289955/atomistic-simulation-study-of-tensile-deformation-in-nanocrystalline-and-single-crystal-au
#16
Cheng-Da Wu, Hsing-Wei Tsai
The effect of notch size (r) on nanocrystalline (NC) and single-crystal (SC) Au at a temperature of 300 K under tension testing is studied using molecular dynamics simulations based on the many-body embedded-atom potential. The effect is investigated in terms of atomic trajectories, common neighbor analysis, and the stress-strain curve. The simulation results show that for the NC samples, stacking faults nucleate at grain boundaries (GBs), propagate inside grains, and eventually are terminated by GBs or transect them...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28289954/characterizing-the-impact-of-surfactant-structure-on-interfacial-tension-a-molecular-dynamics-study
#17
Zi-Yu Liu, Ce Wang, He Zhou, Yanlei Wang, Lei Zhang, Lu Zhang, Sui Zhao
The effect of sodium branched-alkylbenzene sulfonates on the NaCl solution/oil interface was studied via classical molecular dynamics simulation. The interfacial properties were found to depend on the surfactant concentration and to change dramatically when the concentration exceeded a critical value, the simulated limit area (A c). When A c is not close to the theoretical saturated adsorption area (A min), the surfactant cannot produce ultralow interfacial tension (IFT). When A c is equal or almost equal to A min, the effect of the structure of the surfactant must be considered to determine if ultralow IFT is possible: if the sizes of the hydrophobic and hydrophilic groups in the surfactant are similar, the surfactant can produce ultralow interfacial tension (and vice versa)...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28285444/the-interaction-strengths-and-spectroscopy-parameters-of-the-c2h2%C3%A2-%C3%A2-%C3%A2-hx-and-hcn%C3%A2-%C3%A2-%C3%A2-hx-complexes-x-f-cl-cn-and-cch-and-related-ternary-systems-valued-by-fluxes-of-charge-densities-qtaim-ccfo-and-nbo-calculations
#18
Marco A A Viana, Regiane C M U Araújo, José A Maia Neto, Henrique C Chame, Arquimedes M Pereira, Boaz G Oliveira
This theoretical work exhibits a new systematic study of structural parameters, electronic properties, infrared vibration modes, and molecular topography of hydrogen complexes, namely linear-type HCN⋯HX and T-type C2H2⋯HX (X = F, Cl, CN, and CCH). Ideally, the knowledge of the ternary systems of C2H2⋯HCN⋯HF and HCN⋯HCN⋯HF whose subparts integrate the linear and T-shaped complexes were used to give support in this current research. By means of computational calculations carried out in both levels B3LYP and MP2, the variations of the HX bond lengths are clearly overestimated in the HCN⋯HX linear complexes...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28285443/docking-based-virtual-screening-of-brazilian-natural-compounds-using-the-oomt-as-the-pharmacological-target-database
#19
Ana Paula Carregal, Flávia V Maciel, Juliano B Carregal, Bianca Dos Reis Santos, Alisson Marques da Silva, Alex G Taranto
The demand for new therapies has encouraged the development of faster and cheaper methods of drug design. Considering the number of potential biological targets for new drugs, the docking-based virtual screening (DBVS) approach has occupied a prominent role among modern strategies for identifying new bioactive substances. Some tools have been developed to validate docking methodologies and identify false positives, such as the receiver operating characteristic (ROC) curve. In this context, a database with 31 molecular targets called the Our Own Molecular Targets Data Bank (OOMT) was validated using the root-mean-square deviation (RMSD) and the area under the ROC curve (AUC) with two different docking methodologies: AutoDock Vina and DOCK 6...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28285442/thymine-adsorption-on-two-dimensional-boron-nitride-structures-first-principles-studies
#20
J Castro-Medina, D García-Toral, M López-Fuentes, A Sánchez-Castillo, S Torres-Morales, L Morales de la Garza, Gregorio H Cocoletzi
First-principles total-energy calculations were performed to investigate the structural and electronic properties of thymine (T) adsorption on pristine and Al-doped two-dimensional hexagonal boron nitride (2D-hBN) surfaces. Periodic density functional theory, as developed in the PWscf code of the quantum espresso package, was applied. The pseudopotential theory was used to deal with electron-ion interactions. The generalized gradient approximation was applied to treat the exchange-correlation energies. Van der Waals interactions were incorporated in the calculations...
April 2017: Journal of Molecular Modeling
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