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Van der waal

Takashi Kumagai, Janina N Ladenthin, Yair Litman, Mariana Rossi, Leonhard Grill, Sylwester Gawinkowski, Jacek Waluk, Mats Persson
Tautomerization in single porphycene molecules is investigated on Cu(111), Ag(111), and Au(111) surfaces by a combination of low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. It is revealed that the trans configuration is the thermodynamically stable form of porphycene on Cu(111) and Ag(111), whereas the cis configuration occurs as a meta-stable form. The trans → cis or cis → trans conversion on Cu(111) can be induced in an unidirectional fashion by injecting tunneling electrons from the STM tip or heating the surface, respectively...
March 14, 2018: Journal of Chemical Physics
Zelig Chernia, Yoav Tsori
Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description...
March 14, 2018: Journal of Chemical Physics
Giovanni Rillo, Miguel A Morales, David M Ceperley, Carlo Pierleoni
We performed simulations for solid molecular hydrogen at high pressures (250 GPa ≤ P ≤ 500 GPa) along two isotherms at T = 200 K (phase III) and at T = 414 K (phase IV). At T = 200 K, we considered likely candidates for phase III, the C2c and Cmca12 structures, while at T = 414 K in phase IV, we studied the Pc48 structure. We employed both Coupled Electron-Ion Monte Carlo (CEIMC) and Path Integral Molecular Dynamics (PIMD). The latter is based on Density Functional Theory (DFT) with the van der Waals approximation (vdW-DF)...
March 14, 2018: Journal of Chemical Physics
Peter A Beckmann, Arnold L Rheingold, Jason Schmink
No abstract text is available yet for this article.
March 14, 2018: Journal of Chemical Physics
E Pafong Sanjon, B Drossel, M Vogel
Silica is a network-forming liquid that shares many properties with water due to its tetrahedral structure. It undergoes a transition from a fragile to a strong liquid as the temperature is decreased, which is accompanied by a structural change to lower density and higher tetrahedral order. In order to disentangle the effects of Coulomb and van der Waals interactions on the structure and dynamics of liquid silica, we modify the bond polarity by changing the partial charges assigned to each atom. Using molecular dynamics simulations, we show that density, tetrahedral order, and structural relaxation times decrease when reducing bond polarity...
March 14, 2018: Journal of Chemical Physics
Robert I Cukier
Intrinsically disordered proteins (IDPs) sample a diverse conformational space. They are important to signaling and regulatory pathways in cells. An entropy penalty must be payed when an IDP becomes ordered upon interaction with another protein or a ligand. Thus, the degree of conformational disorder of an IDP is of interest. We create a dichotomic Markov model that can explore entropic features of an IDP. The Markov condition introduces local (neighbor residues in a protein sequence) rotamer dependences that arise from van der Waals and other chemical constraints...
March 14, 2018: Journal of Chemical Physics
Yair Litman, Davide Donadio, Michele Ceriotti, Mariana Rossi
Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQEs) influence the structural stability and the dynamical properties of these systems. In this work, we explore the impact of NQEs on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states...
March 14, 2018: Journal of Chemical Physics
Jia Wen, Ying Fang, Guangming Zeng
The efficient removal of heavy metals (HMs) from the environment has become an important issue from both biological and environmental perspectives. Recently, porous metal-organic frameworks (MOFs), combining central metals and organic ligands, have been proposed as promising materials in the capture of various toxic substances, including HMs, due to their unique characteristics. Here we review recent progress in the field of water remediation from the perspective of primary HMs (including divalent metals and variable-valent metals) in water pollution and the corresponding MOFs (including virgin and modified MOFs, magnetic MOFs composites and so on) that can remove these metals from water...
March 6, 2018: Chemosphere
Irena Branyikova, Monika Filipenska, Katerina Urbanova, Marek C Ruzicka, Martin Pivokonsky, Tomas Branyik
Alkaline flocculation has been studied due to its potential as a low-cost harvesting method for microalgae. However, surface properties (zeta potential, contact angles) as inputs into physicochemical interaction models have not yet been applied systematically. In this work, forced alkaline flocculation of the freshwater microalgae Chlorella vulgaris induced by calcium phosphate precipitates was studied as a model system. Response surface methodology was used to quantify the effect of independent variables (concentration of Ca2+ (0...
March 6, 2018: Colloids and Surfaces. B, Biointerfaces
Ahmad Alsaad, Chris M Marin, Nabil Alaqtash, Hsien-Wen Chao, Tsun-Hsu Chang, Chin Li Cheung, A Ahmad, I A Qattan, Renat F Sabirianov
The Crystallographic data of the α-DIPAB sample was measured using powder X-ray diffraction (PXRD). The crystal structure was also optimized using density functional based method. The calculations were performed both including van der Waals (vdW) interactions and excluding them to quantify the effects of vdW interaction on the crystal formation. The vibrational modes of DIPAB crystal corresponding to the Bromine deficient samples are calculated and presented. These show the origin of drastic change in dielectric response in Br deficient samples as compared to the ideal stoichiometric DIPAB crystal (Alsaad et al...
February 2018: Data in Brief
Siavash Atashgahi, Bastian Hornung, Marcelle J van der Waals, Ulisses Nunes da Rocha, Floor Hugenholtz, Bart Nijsse, Douwe Molenaar, Rob van Spanning, Alfons J M Stams, Jan Gerritse, Hauke Smidt
In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation...
March 14, 2018: Scientific Reports
Zhao Xiaojuan, Leiming Tao, Hao Li, Wenchao Huang, Pengyu Sun, Jun Liu, Shuangshuang Liu, Qiang Sun, Zhifang Cui, Lijie Sun, Yan Shen, Yang Yang, Mingkui Wang
Organic-inorganic hybrid lead halide perovskites have been widely investigated in optoelectronics both experimentally and theoretically. The present work incorporates chemical modified graphene into nanocrystal SnO2 as electron transporting layer (ETL) for highly efficient planar perovskite solar cells. The modification of SnO2 with highly conductive two-dimensional naphthalene diimide-graphene can increase surface hydrophobicity and form van der Waals interaction between the surfactant and the organic-inorganic hybrid lead halide perovskite compounds...
March 14, 2018: Nano Letters
Shu Fen Tan, Sanoj Raj, Geeta Bisht, Harshini V Annadata, Christian A Nijhuis, Petr Král, Utkur Mirsaidov
Self-assembly of solvated nanoparticles (NPs) is governed by numerous competing interactions. However, relatively little is known about the time-dependent mechanisms through which these interactions enable and guide the nanoparticle self-assembly process. Here, using in situ transmission electron microscopy imaging combined with atomistic modeling, it is shown that the forces governing the self-assembly of hydrophobic nanoparticles change with the nanoparticle shapes. By comparing how gold nanospheres, nanocubes, nanorods, and nanobipyramids assemble, it is shown that the strength of the hydrophobic interactions depends on the overlap of the hydrophobic regions of the interacting nanoparticle surfaces determined by the nanoparticle shapes...
March 14, 2018: Advanced Materials
Thao P Nguyen, P Roy, Ji Hoon Shim
The relationship between structure and charge transport properties of phenacene organic semiconductors has been studied with focus on [6] → [10]phenacene. Upon inserting phenyl rings, the π-extended structure results in strong electronic coupling interactions and reduction of reorganization energy. Using the classical Marcus charge transport theory, we predict that hole mobility in the phenacene series increases gradually up to 8.0 cm2 V-1 s-1 at [10]phenacene. This is remarkably high among other discovered OSCs, surpassing that of pentacene...
March 14, 2018: Physical Chemistry Chemical Physics: PCCP
Yaowu Hu, Feng Zhang, Michael Titze, Biwei Deng, Hebin Li, Gary J Cheng
Strain-engineering of two-dimensional (2D) transition metal dichalcogenides (TMDs) has great potential to alter their electronic and optical properties. Thus far, experimental studies of the straining effects in 2D TMDs primarily focused on the static property measurements at room temperature. However, low-temperature and temperature-dependence studies are essential in understanding the underlying mechanisms of the unique properties of monolayer TMDs. Herein, the temperature-dependent dynamic properties of laser shock strain-engineered monolayer MoS2 were studied using temperature-dependent photoluminescence (PL) and pump-probe spectroscopy...
March 14, 2018: Nanoscale
Mehdi Yoosefian, Nazanin Etminan
We have designed a novel nanobiosensor for in silico detecting proteins based on leucine/Pd-loaded single-walled carbon nanotube matrix. Density functional theory at the B3LYP/6-31G (d) level of theory was realized to analyze the geometrical and electronic structure of the proposed nanobiosensor. The solvent effects were investigated using the Tomasi's polarized continuum model. Atoms-in-molecules theory was used to study the nature of interactions by calculating the electron density ρ(r) and Laplacian at the bond critical points...
March 14, 2018: Amino Acids
Shan Ping Liu, Ming Zhao, Guo En Sun, Wang Gao, Qing Jiang
The effects of water molecules (promotion/prohibition) on CO oxidation remain debated. Herein, using density functional theory calculations, we demonstrate that water molecules can facilitate the CO + O/O2 oxidation process, but prohibit the CO + OH oxidation process, which is consistent with the experimental finding that water molecules have two distinct effects on CO oxidation. For the CO + O/O2 oxidation mechanisms, we find that the reactants were pushed towards each other due to the steric effect of the water molecules, which decreases the reaction barriers and promotes the CO + O/O2 oxidation process...
March 13, 2018: Physical Chemistry Chemical Physics: PCCP
Adejoke N Kolawole, Valentine T Akinladejo, Olusola O Elekofehinti, Afolabi C Akinmoladun, Ayodele O Kolawole
Aldehyde dehydrogenases (ALDHs) are a diverse family of enzymes that catalyze the NAD(P)+ -dependent detoxification of toxic aldehyde compounds. ALDHs are also involved in non-enzymatic ligand binding to endobiotics and xenobiotics. Here, the enzyme crucial non-canonical and non-catalytic interaction with kolaflavanone, a component of kolaviron, and a major bioflavonoid isolated from Garcinia kola (Bitter kola) was characterized by various spectroscopic and in silico approaches under stimulated physiological condition...
February 27, 2018: Bioorganic Chemistry
Martin Dehnert, Robert Magerle
In the atomic force microscopy (AFM) investigation of soft polymers and liquids, the tip-sample interaction is dominated by long-range van der Waals forces, capillary forces and adhesion. Furthermore, the tip can indent several tens of nanometres into the surface, and it can pull off a polymer filament from the surface. Therefore, measuring the unperturbed shape of a polymeric fluid can be challenging. Here, we study the tip-sample interaction with polystyrene droplets swollen in chloroform vapour, where we can utilize the solvent vapour concentration to adjust the specimen's mechanical properties from a stiff solid to a fluid film...
March 13, 2018: Nanoscale
Jinkyoung Yoo, Towfiq Ahmed, Renjie Chen, Aiping Chen, Yeon Hoo Kim, Ki Chang Kwon, Chan Woong Park, Hee Seong Kang, Ho Won Jang, Young Joon Hong, Woo Seok Yang, Chul-Ho Lee
The preparation of crystalline materials on incommensurate substrates has been a key topic of epitaxy. van der Waals (vdW) epitaxy on two-dimensional (2D) materials opened novel opportunities of epitaxial growth overcoming the materials compatibility issue. Therefore, vdW epitaxy has been considered as a promising approach for the preparation of building blocks of flexible devices and thin film-based devices at the nano/microscale. However, an understanding of vdW epitaxy has not been thoroughly established...
March 13, 2018: Nanoscale
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