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Van der Waals

Claudia Ojeda-Aristizabal, Elton J G Santos, Seita Onishi, Aiming Yan, Haider Imad Rasool, Salman Kahn, Yinchuan Lv, Drew Latzke, Jairo Velasco, Michael F Crommie, Matthew Sorensen, Kenneth Gotlieb, Chiu-Yun Lin, Kenji Watanabe, Takashi Taniguchi, Alessandra Lanzara, Alex Zettl
Charge transfer at the interface between dissimilar materials is at the heart of electronics and photovoltaics. Here we study the molecular orientation, electronic structure, and local charge transfer at the interface region of C60 deposited on graphene, with and without supporting substrates such as hexagonal boron nitride. We employ ab initio density functional theory with van der Waals (vdW) interactions, and experimentally characterize interface devices using high-resolution transmission electron microscopy and electronic transport...
April 24, 2017: ACS Nano
Bess Vlaisavljevich, Johanna M Huck, Zeric Hulvey, Kyuho Lee, Jarad A Mason, Jeffrey B Neaton, Jeffrey R Long, Craig M Brown, Dario Alfè, Angelos Michaelides, Berend Smit
Small molecule binding in metal-organic frameworks (MOFs) can be accurately studied both experimentally and computationally, provided the proper tools are employed. Herein, we compare and contrast properties associated with guest binding by means of density functional theory (DFT) calculations using nine different functionals for the M2(dobdc) (dobdc4- = 2,5-dioxido,1,4-benzenedicarboxylate) series where M = Mg, Mn, Fe, Co, Ni, Cu, and Zn. Additionally, we perform Quantum Monte Carlo (QMC) calculations for one system to determine if this method can be used to assess the performance of DFT...
April 24, 2017: Journal of Physical Chemistry. A
Ran Tivony, Jacob Klein
Combining direct surface force measurements with in situ regulation of surface potential provides an exceptional opportunity for investigating and manipulating interfacial phenomena. Recently, we studied the interaction between gold and mica surfaces in water with no added salt, while controlling the metal potential, and found that the surface charge at the metal may vary, and possibly even change its sign, as it progressively approaches the (constant-charge) mica surface [Langmuir, 2015, 31(47), 12845-12849]...
April 24, 2017: Faraday Discussions
Morten N Gjerding, Mohnish Pandey, Kristian S Thygesen
Plasmonics currently faces the problem of seemingly inevitable optical losses occurring in the metallic components that challenges the implementation of essentially any application. In this work, we show that Ohmic losses are reduced in certain layered metals, such as the transition metal dichalcogenide TaS2, due to an extraordinarily small density of states for scattering in the near-IR originating from their special electronic band structure. On the basis of this observation, we propose a new class of band structure engineered van der Waals layered metals composed of hexagonal transition metal chalcogenide-halide layers with greatly suppressed intrinsic losses...
April 24, 2017: Nature Communications
Rosario C Sausa, Rose A Pesce-Rodriguez, Leah A Wingard, Pablo E Guzmán, Jesse J Sabatini
The mol-ecular structure of the title energetic compound, C8H6N4O8, is composed of two planar isoxazole rings and two near planar alkyl-nitrate groups (r.m.s deviation = 0.006 Å). In the crystal, the mol-ecule sits on an inversion center, thus Z' = 0.5. The dihedral angle between the isoxazole ring and the nitrate group is 69.58 (8)°. van der Waals contacts dominate the inter-molecular inter-actions. Inversion-related rings are in close slip-stacked proximity, with an inter-planar separation of 3.101 (3) Å [centroid-centroid distance = 3...
April 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
Shuling Xiong, Shusen Chen, Shaohua Jin
Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) is a newly synthesized energetic material with excellent comprehensive properties. Cyclotrimethylenetrinitramine (RDX) is currently one of the most widely used energetic materials in the world. TKX-50 and RDX supercell models and TKX-50/RDX cocrystal model were constructed based on their crystal cell parameters and the formation mechanism of cocrystal, respectively, then they were simulated by molecular dynamics (MD) simulations. The maximum trigger bond (NNO2) length(Lmax), binding energy (Ebind), radial distribution function (RDF), cohesive energy density(CED) and mechanical properties were simulated at different temperatures based on the simulated equilibrium structures of the models...
March 19, 2017: Journal of Molecular Graphics & Modelling
Fengcheng Wu, Timothy Lovorn, A H MacDonald
Moiré patterns are common in van der Waals heterostructures and can be used to apply periodic potentials to elementary excitations. We show that the optical absorption spectrum of transition metal dichalcogenide bilayers is profoundly altered by long period moiré patterns that introduce twist-angle dependent satellite excitonic peaks. Topological exciton bands with nonzero Chern numbers that support chiral excitonic edge states can be engineered by combining three ingredients: (i) the valley Berry phase induced by electron-hole exchange interactions, (ii) the moiré potential, and (iii) the valley Zeeman field...
April 7, 2017: Physical Review Letters
Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha
The encapsulation of nucleobases, inside CB7 has gained prominence due to its use as anticancer and antiviral drugs. With this respect, the nonconvalent interactions exists in the nucleobases encapsulated inside the CB7 cavity have been analyzed employing the dispersion corrected density functional theory. The CBn cavity has the ability to encapsulate two guest nucleobases molecules, when they are aligned in parallel configuration. The computed association energy using the two and three body correction method computed at B3LYP-D3 level is close to the experimental estimate...
April 21, 2017: Journal of Physical Chemistry. B
Yuezhi Mao, Yihan Shao, Jacek Dziedzic, Chris-Kriton Skylaris, Teresa Head-Gordon, Martin Head-Gordon
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4(+) , CN(-)) surrounded by increasing numbers of water molecules (up to 100)...
April 21, 2017: Journal of Chemical Theory and Computation
Maria Dayanne de A Dantas, Humberto de Araújo Tenório, Thiago Inácio B Lopes, Hugo Juarez V Pereira, Anita J Marsaioli, Isis M Figueiredo, Josué Carinhanha Caldas Santos
The interactions of tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC) with ovalbumin (OVA), the main allergen protein of egg white, were investigated by molecular spectroscopy and electrophoresis at three pH conditions (1.5, 4.6 and 7.4). Molecular and synchronous fluorescence, UV-vis spectroscopy, electrophoresis and (1)H NMR were used to study the interaction process. Tetracyclines interact with ovalbumin fluorescence by a static quenching mechanism with non-fluorescent complex formation changing the native protein structure...
April 17, 2017: International Journal of Biological Macromolecules
Margherita De Rosa, Carmen Talotta, Carmine Gaeta, Annunziata Soriente, Placido Neri, Sebastiano Pappalardo, Giuseppe Gattuso, Anna Notti, Melchiorre F Parisi, Ilenia Pisagatti
The through-the-annulus threading of calix[5]arene penta-O-ethers by dialkylammonium cations coupled to the loosely coordinating superweak TFPB- anion has been successfully accomplished. 1H NMR titration data show that the preorganization of the calix[5]arene scaffold leads to great thermodynamic stability of the pseudorotaxane complexes as well as to a favorable kinetic of threading. Accordingly, calix[5]arene 1c, bearing tert-butyl groups at the wide rim, was threaded by all the cations under study (with the exception of the dibenzylammonium 2b+) more tightly than the other derivatives under investigation (Kas up to 2...
April 20, 2017: Journal of Organic Chemistry
Ajay Shankar, Alexander P Safronov, Ekaterina A Mikhnevich, Igor V Beketov, Galina V Kurlyandskaya
A new kind of ferrogel with entrapped metallic iron nanoparticles causing unusual magnetodeformation is presented. Crosslinked polyacrylamide (PAAm) based ferrogels embedded with iron nanoparticles (MNPs) were synthesized by free radical polymerization in aqueous medium. Spherical iron MNPs with average diameter 66 nm were synthesized by the electrical explosion of wire and modified by interfacial adsorption of linear polyacrylamide (LPAAm). Extended Derjaguin-Landau-Verwey-Overbeek (xDLVO) calculations based on the superposing of van der Waals, electrostatic, steric, and magnetic contributions showed that polymeric encapsulation of nanoparticles by LPAAm is one of the most suitable pathways for preparing stable aqueous dispersions of iron nanoparticles...
April 20, 2017: Soft Matter
Yunjo Kim, Samuel S Cruz, Kyusang Lee, Babatunde O Alawode, Chanyeol Choi, Yi Song, Jared M Johnson, Christopher Heidelberger, Wei Kong, Shinhyun Choi, Kuan Qiao, Ibraheem Almansouri, Eugene A Fitzgerald, Jing Kong, Alexie M Kolpak, Jinwoo Hwang, Jeehwan Kim
Epitaxy-the growth of a crystalline material on a substrate-is crucial for the semiconductor industry, but is often limited by the need for lattice matching between the two material systems. This strict requirement is relaxed for van der Waals epitaxy, in which epitaxy on layered or two-dimensional (2D) materials is mediated by weak van der Waals interactions, and which also allows facile layer release from 2D surfaces. It has been thought that 2D materials are the only seed layers for van der Waals epitaxy...
April 19, 2017: Nature
Tanchanok Wisitponchai, Watshara Shoombuatong, Vannajan Sanghiran Lee, Kuntida Kitidee, Chatchai Tayapiwatana
BACKGROUND: Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in 10 top-rankings. The universal criteria for discriminating the near-native pose are not available since there are several classes of recognition protein. Currently, the explicit criteria for identifying the near-native pose of ankyrin-protein complexes (APKs) have not been reported yet...
April 19, 2017: BMC Bioinformatics
Hongseung Yeon, Chenxuan Wang, Reid Van Lehn, Nicholas L Abbott
We report an experimental investigation of the influence of molecular-level order (crystallinity) within non-polar monolayers on hydrophobic interactions. The measurements were performed using gold film-supported monolayers formed from alkanethiols (CH3(CH2)nSH, with n ranging from 3 to 17), which we confirmed by using polarization-modulation infrared reflection-adsorption spectroscopy to exhibit chain-length-dependent order (methylene peak moves from 2926 to 2919 cm-1, corresponding to a transition from liquid- to quasi-crystalline-like order) in the absence of substantial changes in chain-density (constant methyl peak intensity)...
April 18, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Tanveer A Wani, Ahmed H Bakheit, Seema Zargar, Mohammed A Hamidaddin, Ibrahim A Darwish
Linifanib (LNF) possess antitumor activity and acts by inhibiting receptor tyrosine kinase VEGF and PDGF. The interaction of BSA with the drug can provide valuable information regarding the pharmacokinetic and pharmacodynamics behavior of drug. In our study the spectrophotometric methods and molecular docking studies were executed to understand the interaction behavior of BSA and LNF. BSA has an intrinsic fluorescence and that fluorescence was quenched by LNF. This quenching process was studied at three different temperatures of 288, 300and 308 K...
2017: PloS One
Zigui Kan, Qiang Zhu, Lijiang Yang, Zhixiong Huang, Biaobing Jin, Jing Ma
Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C1mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid...
April 24, 2017: Journal of Physical Chemistry. B
Yuzhen Niu, Danfeng Shi, Lanlan Li, Jingyun Guo, Huanxiang Liu, Xiaojun Yao
SETD7 is associated with multiple diseases related signaling pathways. (R)-PFI-2 is the first SETD7 inhibitor with nanomolar inhibitory potency. The activity of (R)-PFI-2 is about 500 times over that of (S)-PFI-2. Understanding the mechanism behind this difference will be helpful to discovery and design of more potent SETD7 inhibitors. A computational study combining molecular dynamics simulation, binding free energy calculations, and residue interaction network (RIN) was performed on the (S)-PFI-2/SETD7 and (R)-PFI-2/SETD7 complexes to explore the molecular mechanism behind the different inhibition activity...
April 18, 2017: Scientific Reports
Yufeng Guo, Jiapeng Qiu, Wanlin Guo
Understanding the mechanical behaviors of van der Waals heterogeneous 2D materials is important for their actual applications. Our extensive first-principles calculations and continuum mechanical modeling on the wrinkling of MoSe2/WSe2 heterobilayers caused by compression reveal that the bending stiffness of MoSe2/WSe2 wrinkles strongly depend on the wrinkle structures, which first increase and then decrease with increasing the compressive strain. The bending stiffness of MoSe2/WSe2 wrinkles could be effectively mediated and tuned by adjusting the wrinkle geometry and size...
May 12, 2017: Nanotechnology
Andrey A Kuznetsov, Alexander F Pshenichnikov
Langevin dynamics simulation is used to study the suspension of interacting magnetic nanoparticles (dipolar spheres) in a zero applied magnetic field and in the presence of a gravitational (centrifugal) field. A particular emphasis is placed on the equilibrium vertical distribution of particles in the infinite horizontal slab. An increase in the dipolar coupling constant λ (the ratio of dipole-dipole interaction energy to thermal energy) from zero to seven units causes an increase in the particle segregation coefficient by several orders of magnitude...
March 2017: Physical Review. E
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