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# WaaL

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#1
Jingjie Hu, Sina Youssefian, John Obayemi, Karen Malatesta, Nima Rahbar, Winston Soboyejo
The understanding of adhesive interaction at the nanoscale between functionalized nanoparticles and biological cells is of great importance to develop effective theranostic nanocarriers for targeted cancer therapy. Here, we report a combination of experimental and computational approaches to evaluate the adhesion between Triptorelin (a Luteinizing Hormone-Releasing Hormone (LHRH) agonist)-conjugated poly-(ethylene glycol) (PEG)-coated magnetite nanoparticles (Triptorelin-MNPs) and breast cells. The adhesion forces between Triptorelin-MNPs and normal/cancerous breast cells are obtained using atomic force microscopy...
February 16, 2018: Acta Biomaterialia
#2
Lei Xiang, Tao Xiao, Ce-Hui Mo, Hai-Ming Zhao, Yan-Wen Li, Hui Li, Quan-Ying Cai, Dong-Mei Zhou, Ming-Hung Wong
Aniline aerofloat (AAF), a high-toxic organic flotation reagent, is widely used in mineral processing industry. However, little information on its environmental fate is available. AAF sorption to four types of agricultural soils at low concentrations (1-10 mg/L) was investigated using batch experiments. AAF sorption kinetics involved both boundary layer diffusion and intraparticle diffusion, following pseudo-second-order kinetics with equilibrium time within 120 min. Both Langmuir and Freundlich models fitted well the AAF sorption with the former better...
February 15, 2018: Ecotoxicology and Environmental Safety
#3
Hongyan Wang, Yi Han, Wei Yuan, Mengjiao Wu, Yulan Chen
A new class of rod-coil-rod molecules with an azobenzene core were synthesized. They were found to form robust organogels in several kinds of organic solvents. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), atomic force microscopy (AFM), FT-IR spectroscopy, UV-vis absorption spectroscopy, 1H NMR, and X-ray diffraction (XRD) revealed that in these organogels, the molecules self-assembled into nanofiber network with an H-type aggregation mode under the joint effect of Pi-Pi stacking, intermolecular hydrogen bonding, and van der Waals forces...
February 17, 2018: Chemistry, An Asian Journal
#4
Mohammad Khalid Jawed, Nicolas G Hadjiconstantinou, David Parks, Pedro M Reis
We develop and perform continuum mechanics simulations of carbon nanotube (CNT) deployment directed by a combination of surface topography and rarefied gas flow. We employ the Discrete Elastic Rods method to model the deposition of CNT as a slender elastic rod that evolves in time under two external forces, namely van der Waals (vdW) and aerodynamic drag. Our results confirm that this self-assembly process is analogous to a previously studied macroscopic system, the `elastic sewing machine', where an elastic rod deployed onto a moving substrate forms nonlinear patterns...
February 16, 2018: Nano Letters
#5
Emil Ter Veer, Aafke Creemers, Laura de Waal, Martijn G H van Oijen, Hanneke W M van Laarhoven
According to the ToGA study, trastuzumab plus cisplatin and capecitabine/5-fluorouracil (5-FU) is standard first-line treatment for HER2-positive advanced esophagogastric cancer. We examined the relative efficacy and safety of alternative trastuzumab-based cytotoxic backbone regimens compared to the standard ToGA regimen using meta-analysis. We searched Medline, EMBASE, CENTRAL and ASCO and ESMO up to March 2017 for studies investigating alternative first-line trastuzumab-based regimens for HER2-positive esophagogastric cancer, defined as high protein expression IHC3+ or IHC2+ and gene amplification by in-situ-hybridisation...
February 16, 2018: International Journal of Cancer. Journal International du Cancer
#6
Fuyuan Zhang, Bing Liu, Guozhen Liu, Yan Zhang, Junping Wang, Shuo Wang
Based on the structural features of fluometuron, an immunizing hapten was synthesized and conjugated to bovine serum albumin as an immunogen to prepare a polyclonal antibody. However, the resultant antibody indicated cross-reactivity with 6 structurally similar phenylurea herbicides, with binding activities (expressed by IC 50 values) ranging from 1.67 µg/L to 42.71 µg/L. All 6 phenylurea herbicides contain a common moiety and three different substitutes. To understand how these three different chemical groups affect the antibody-phenylurea recognition activity, quantum chemistry, using density function theory (DFT) at the B3LYP/6-311++ G(d,p) level of theory, was employed to optimize all phenylurea structures, followed by determination of the 3D conformations of these molecules, pharmacophore analysis, and molecular electrostatic potential (ESP) analysis...
February 15, 2018: Scientific Reports
#7
Julien Claudot, Won June Kim, Anant Dixit, Hyungjun Kim, Tim Gould, Dario Rocca, Sébastien Lebègue
Seven methods, including three van der Waals density functionals (vdW-DFs) and four different variants of the Tkatchenko-Scheffler (TS) methods, are tested on the A24, L7, and Taylor et al.'s "blind" test sets. It is found that for these systems, the vdW-DFs perform better that the TS methods. In particular, the vdW-DF-cx functional gives binding energies that are the closest to the reference values, while the many-body correction of TS does not always lead to an improvement in the description of molecular systems...
February 14, 2018: Journal of Chemical Physics
#8
Yongbin Yan, Sang-Ho Kim, Fu Zhang, Longhai Piao, Hu Zhou
Rapid macroscopic-scale assembly of Ag nanowires was demonstrated through facile self-assembly at the water/air interface. This self-assembly was induced by heating due to the surface tension effect and convection. Interestingly, a rippled hairstyle superstructure was observed when the aqueous dispersions of thinner Ag nanowires were heated. Applying the Euler buckling theory for a set of aligned Ag nanowires, it was found that the water surface tension was sufficient to bend or buckle these free Ag nanowires trapped between two nanowire stripes, which resulted in the formation of the rippled hairstyle superstructure...
March 1, 2018: Journal of Nanoscience and Nanotechnology
#9
Jin-Ping Zha, Meng-Ting Zhu, Li Qin, Xin-Hong Wang
The interactions between Orange G (OG) with three kinds of ionic liquid surfactants (C 10 mimBF 4 , C 12 mimBF 4 , C 16 mimBF 4 ) and CTAB were studied with UV-Vis spectra and conductivity measurements. The systematic changes in UV-Vis spectra with an increase of carbon-chain length may be observed in presence of OG. They correspond to CMC of every system, respectively, and the CMCs of four systems have exhibit the decrease of CMCs compared to pure surfactant. The binding constants are calculated from the results of conductivity measurements in the order of C 16 mimBF 4 >CTAB>C 12 mimBF 4 >C 10 mimBF 4 ...
February 6, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
#10
Jan Hermann, Alexandre Tkatchenko
Short-range correlations in motion of electrons in matter are captured well by semilocal exchange-correlation (XC) functionals in density functional theory (DFT), but long-range correlations are neglected in such models and must be treated by van der Waals (vdW) dispersion methods.Whereas the effective range of distances at which fluctuations are correlated is usually explicit in the vdW models, the complementary range of semilocal functionals can be observed only implicitly, requiring an introduction of empirical damping functions to couple the semilocal and nonlocal contributions to the XC energy...
February 15, 2018: Journal of Chemical Theory and Computation
#11
Hamid Tanzadehpanah, Hanie Mahaki, Neda Hosseinpour Moghadam, Sadegh Salehzadeh, Omid Rajabi, Rezvan Najafi, Razieh Amini, Massoud Saidijam
This study was carried out to evaluate the binding interaction of gefitinib (GEF) with human serum albumin (HSA) and calf thymus DNA (ct-DNA) using fluorescence, UV-visible, zeta potential measurements and molecular docking methods in order to understand its pharmacokinetic mechanism. By increasing the temperature, a steady decrease in Stern-Volmer quenching constants was observed for HSA binding properties; this indicates a static type of ﬂuorescence quenching. Negative values were calculated for Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) changes, indicating that the reaction is spontaneous and enthalpy-driven...
February 15, 2018: Journal of Biomolecular Structure & Dynamics
#12
Yuuya Nagata, Tsuyoshi Nishikawa, Michinori Suginome, Sota Sato, Masaaki Sugiyama, Lionel Porcar, Anne Martel, Rintaro Inoue, Nobuhiro Sato
Small-angle neutron scattering (SANS) was used to examine dilute solutions of a poly(quinoxaline-2,3-diyl) (PQX) with (R)-2-octyloxymethyl side chains in deuterated THF or a mixture of deuterated 1,1,2-TCE and THF (8/2, v/v), in which the PQX adopts pure P- and M-helical structures. The structures of the PQX that were obtained based on the SANS experiments in combination with theoretical calculations suggest that in THF, the chiral side chains of the P-helical PQX are extended, whereas in the 1,1,2-TCE/THF mixture, the side chains of the M-helical PQX are folded...
February 15, 2018: Journal of the American Chemical Society
#13
Papri Chakraborty, Abhijit Nag, Ganesan Paramasivam, Ganapati Natarajan, Thalappil Pradeep
We report the formation of supramolecular adducts between monolayer-protected noble metal nanoclusters and fullerenes, specifically focussing on a well-known silver cluster, [Ag29(BDT)12]3-, where BDT is 1,3-benzene dithiol. We demonstrate that C60 molecules link with the cluster at specific locations and protect the fragile cluster core, enhancing the stability of the cluster. A combination of studies including UV-vis, high-resolution electrospray ionization mass spectrometry (ESI MS), collision-induced dissociation (CID), and nuclear magnetic resonance (NMR) spectroscopy revealed structural details of the fullerene-functionalized clusters, [Ag29(BDT)12(C60)n]3- (n=1-9)...
February 14, 2018: ACS Nano
#14
Divya Nayar, Nico F A van der Vegt
Water-mediated hydrophobic interactions play an important role in self-assembly processes, aqueous polymer solubility, and protein folding, to name a few. Cosolvents affect these interactions however the implications for hydrophobic polymer collapse and protein folding equilibria are not well-understood. This study examines cosolvent effects on the hydrophobic collapse equilibrium of a generic 32-mer hydrophobic polymer in urea, trimethylamine-N-oxide (TMAO), and acetone aqueous solutions using molecular dynamics simulations...
February 14, 2018: Journal of Physical Chemistry. B
#15
REVIEW
Marco Gobbi, Emanuele Orgiu, Paolo Samorì
van der Waals heterostructures, composed of vertically stacked inorganic 2D materials, represent an ideal platform to demonstrate novel device architectures and to fabricate on-demand materials. The incorporation of organic molecules within these systems holds an immense potential, since, while nature offers a finite number of 2D materials, an almost unlimited variety of molecules can be designed and synthesized with predictable functionalities. The possibilities offered by systems in which continuous molecular layers are interfaced with inorganic 2D materials to form hybrid organic/inorganic van der Waals heterostructures are emphasized...
February 14, 2018: Advanced Materials
#16
Zhi Li, Alexandre Tkatchenko, Ignacio Franco
We propose a computationally efficient strategy to accurately model non-reactive molecule-surface interactions that adapts density-functional theory calculations with the Tkatchenko-Scheffler scheme for van der Waals interactions into a simple classical force field. The resulting force field requires just two adjustable parameters per atom type that are needed to capture short-range and polarization interactions. The developed strategy allows for classical molecular dynamics simulation of molecules on surfaces with the accuracy of high-level electronic structure methods but for system sizes (10$^3-10^7$ atoms) and timescales ($\sim \mu$s) that go well beyond what can be achieved with first-principles methods...
February 13, 2018: Journal of Physical Chemistry Letters
#17
Carles Curutchet, Lorenzo Cupellini, Jacob Kongsted, Stefano Corni, Luca Frediani, Arnfinn Hykkerud Steindal, Ciro Achille Guido, Giovanni Scalmani, Benedetta Mennucci
Mixed QM/MM models are widely used to explore the structure, reactivity and electronic properties of complex chemical systems. Whereas such models typically include electrostatics, and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, non-electrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdWTS) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework...
February 13, 2018: Journal of Chemical Theory and Computation
#18
Naru Tanaka, Yi-Yang Zhan, Yuka Ozawa, Tatsuo Kojima, Takuya Koide, Takako Mashiko, Umpei Nagashima, Masanori Tachikawa, Shuichi Hiraoka
A novel method for the semi-quantitative evaluation of molecular meshing in molecular complexes and assemblies (SAVPR: surface analysis with varying probe radii) is proposed. SAVPR revealed that the extremely high stability of hexameric assemblies (nanocubes) is due to tight molecular meshing between the components in the assemblies, indicating the importance of van der Waals interactions in hydrophobic molecular assemblies.
February 13, 2018: Chemical Communications: Chem Comm
#19
REVIEW
Mangesh I Chaudhari, Ajay Muralidharan, Lawrence R Pratt, Susan B Rempe
Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples...
February 12, 2018: Topics in Current Chemistry (Journal)
#20
M Castellà-Ventura, A Moissette, E Kassab
The confinement effects of a zeolite framework on the adsorption of a bidentate 4,4'-bipyridine (44BPY) ligand on the straight channel of H-ZSM-5 have been investigated by density functional theory calculations using B3LYP, B3LYP-D3, M06-2X, M06-2X-D3 functionals, and the MP2 method with two basis sets 6-31+G* and 6-31++G(2d,2p). The straight channel is simulated by a realistic cluster model of 32 tetrahedra (T), having two aluminum atoms located in the straight and intersection regions, respectively. The potential energy surface of the double proton transfer reaction from the Brønsted acid sites of H-ZSM-5 to 44BPY is characterized by three minima corresponding to two monodentate ion pair complexes 44BPYH+/32T- and one bidentate ion pair complex 44BPYH22+/32T2- formed consecutively via two distinct pathways...
February 13, 2018: Physical Chemistry Chemical Physics: PCCP
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