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Van der Waals

Suman Kumar Nandy, Alpana Seal
Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics...
2016: PloS One
David Gau, Raphael Nougué, Nathalie Saffon-Merceron, Antoine Baceiredo, Abel De Cózar, Fernando P Cossío, Daisuke Hashizume, Tsuyoshi Kato
A donor-stabilized 1,3-disila-2,4-diazacyclobutadiene presents an exceptionally short nonbonded Si⋅⋅⋅Si distance (2.23 Å), which is as short as that of Si=Si bonds (2.15-2.23 Å). Theoretical investigations indicate that there is no bond between the two silicon atoms, and that the unusual geometry can be related to a significant coulomb repulsion between the two ring nitrogen atoms. This chemical pressure phenomenon could provide an alternative and superior way of squeezing out van der Waals space in highly strained structures, as compared to the classical physical methods...
October 20, 2016: Angewandte Chemie
Gonzalo Abellán, Vicent Lloret, Udo Mundloch, Mario Marcia, Christian Neiss, Andreas Görling, Maria Varela, Frank Hauke, Andreas Hirsch
Black phosphorus (BP) was functionalized with organic moieties on the basis of liquid exfoliation. The treatment of BP with electron-withdrawing 7,7,8,8-tetracyano-p-quinodimethane (TCNQ) led to electron transfer from BP to the organic dopant. On the other hand, the noncovalent interaction of BP with a perylene diimide was mainly due to van der Waals interactions but also led to considerable stabilization of the BP flakes against oxygen degradation.
October 20, 2016: Angewandte Chemie
Xuexia He, WaiLeong Chow, Fucai Liu, BengKang Tay, Zheng Liu
2D transition metal dichalcogenides are promising channel materials for the next-generation electronic device. Here, vertically 2D heterostructures, so called van der Waals solids, are constructed using inorganic molybdenum sulfide (MoS2 ) few layers and organic crystal - 5,6,11,12-tetraphenylnaphthacene (rubrene). In this work, ambipolar field-effect transistors are successfully achieved based on MoS2 and rubrene crystals with the well balanced electron and hole mobilities of 1.27 and 0.36 cm(2) V(-1) s(-1) , respectively...
October 20, 2016: Small
Xiang Lin, Qing Wang, Xilin Peng, Hui Li
Metandienone (MET) is an exogenous anabolic androgenic steroid. The interaction between MET and human serum albumin (HSA) was investigated by molecular modeling and different optical techniques. There was no possibility of energy transfer, and the fluorescence quenching of HSA induced by MET was mainly due to the complex formation. The differences of binding ability between MET and compounds 1-5 were significantly caused by space steric hindrance. The single crystallographic data of two steroids (compounds 4 and 5) were obtained in the methanol at the first time...
October 20, 2016: Journal of Biochemical and Molecular Toxicology
Matthew Yankowitz, K Watanabe, T Taniguchi, Pablo San-Jose, Brian J LeRoy
Combining atomically-thin van der Waals materials into heterostructures provides a powerful path towards the creation of designer electronic devices. The interaction strength between neighbouring layers, most easily controlled through their interlayer separation, can have significant influence on the electronic properties of these composite materials. Here, we demonstrate unprecedented control over interlayer interactions by locally modifying the interlayer separation between graphene and boron nitride, which we achieve by applying pressure with a scanning tunnelling microscopy tip...
October 20, 2016: Nature Communications
Y Liu, L Huang, H Ye, X Lv
Interferon regulatory factor-7 (IRF-7) is involved in pulmonary infection and pneumonia. Here, a synthetic strategy that combined quantitative structure-activity relationship (QSAR)-based virtual screening and in vitro binding assay was described to identify new and potent mediator ligands of IRF-7 from natural products. In the procedure, a QSAR scoring function was developed and validated using Gaussian process (GP) regression and a structure-based set of protein-ligand affinity data. By integrating hotspot pocket prediction, pharmacokinetics profile analysis and molecular docking calculations, the scoring function was successfully applied to virtual screening against a large library of structurally diverse, drug-like natural products...
October 20, 2016: SAR and QSAR in Environmental Research
Yumiko Mizukoshi, Koh Takeuchi, Misa Arutaki, Yuji Tokunaga, Takeshi Takizawa, Hiroyuki Hanzawa, Ichio Shimada
The thermodynamic properties of a ligand in the bound state affect its binding specificity. Strict binding specificity can be achieved by introducing multiple spatially defined interactions, such as hydrogen bonds and van der Waals interactions, into the ligand-receptor interface. These introduced interactions are characterized by restricted local dynamics and improved surface complementarity in the bound state. In this study, we experimentally evaluated the local dynamics and the surface complementarity of weak-affinity ligands in the receptor-bound state by forbidden coherence transfer analysis in free-bound exchange systems (Ex-FCT), using the interaction between a ligand, a myocyte-enhancer factor 2A (MEF2A) docking peptide, and a receptor, p38α, as a model system...
October 20, 2016: Angewandte Chemie
Jingyu Chen, Bing Yuan, Zhenyu Li, Bin Tang, Akhil Gupta, Sheshanath-Vishwanath Bhosale, Jingliang Li
Co-assembly of molecules can produce materials with improved properties and functionalities. To this end, achieving a molecular level understanding of the interactions governing the co-assembly is essential. In this work, two molecular gelators with significantly different structures and main intermolecular forces for assembly were co-assembled. The elastic moduli of the hybrid gels are more than one order of magnitude higher than those of the gels formed by the individual gelators, showing an obvious synergistic effect...
October 19, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Agnieszka Jedrzejowska, Kia L Ngai, Marian Paluch
By systematic modifications of the canonical propylene carbonate, a family of van der Waals glass-formers with similar chemical structures are generated for dielectric studies of the dynamics of the structural α-relaxation with the purpose of critically testing the correlation of dynamic properties with the dipole-dipole interaction contribution to the intermolecular potential. With the dielectric strengths at Tg varying over a vast range from 4.2 to 182, the modified propylene carbonates provide strong support of the correlation by themselves and in conjunction with eighty eight van der Waals glassformers previously considered [M...
October 19, 2016: Journal of Physical Chemistry. A
Janne Kalikka, Xilin Zhou, Jitendra Behera, Giacomo Nannicini, Robert E Simpson
We use an evolutionary algorithm to explore the design space of hexagonal Ge2Sb2Te5; a van der Waals layered two dimensional crystal heterostructure. The Ge2Sb2Te5 structure is more complicated than previously thought. Predominant features include layers of Ge3Sb2Te6 and Ge1Sb2Te4 two dimensional crystals that interact through Te-Te van der Waals bonds. Interestingly, (Ge/Sb)-Te-(Ge/Sb)-Te alternation is a common feature for the most stable structures of each generation's evolution. This emergent rule provides an important structural motif that must be included in the design of high performance Sb2Te3-GeTe van der Waals heterostructure superlattices with interfacial atomic switching capability...
October 19, 2016: Nanoscale
Jasjeet Bhullar, Veena M Bhopale, Ming Yang, Kinjal Sethuraman, Stephen R Thom
This investigation explored the mechanism for microparticles (MPs) production by human and murine platelets exposed to high pressures of inert gases. Results demonstrate that MPs production occurs via an oxidative stress response in a dose-dependent manner and follows the potency series N2 > Ar > He. Gases with higher van der Waals volumes or polarizability such as SF6 and N2O, or hydrostatic pressure, do not cause MPs production. Singlet O2 is generated by N2, Ar and He, which is linked to NADPH oxidase (NOX) activity...
October 14, 2016: Free Radical Biology & Medicine
Yves Claude Guillaume, Lydie Lethier, Claire André
TRAIL is a member of the TNF family of cytokines which induces apoptosis of cancer cells via its binding to its cognate receptors, DR5 a high affinity site and DR4 a site of low affinity. Our working group has recently demonstrated that nanovectorization of TRAIL with single wall carbon nanotubes (abbreviated NPT) enhanced TRAIL affinity to the high affinity site DR5 and increased pro apoptotic potential in different human tumor cell lines. In this paper, the DR4 low affinity site was immobilized on a chromatographic support and the effect of temperature on a wide temperature range 1°C-50°C was studied to calculate the thermodynamic parameters of the binding of TRAIL and NPT to DR4 and DR5 receptors...
October 12, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Mingzhan Wang, Jinxiong Wu, Li Lin, Yujing Liu, Bing Deng, Yunfan Guo, Yuanwei Lin, Tian Xie, Wenhui Dang, Yubing Zhou, Hailin Peng
The key challenge of direct integration of two-dimensional (2D) chalcogenide crystals into functional modules lies on precise control of the nucleation sites of the building blocks. Herein, we exploit the chemical activities and surface engineering of the substrates to manipulate the nucleation energy barrier of 2D crystals, and thereby realize the patternable growth of 2D crystals. The selective-region chemical modifications of the substrates are achieved via micro-contact printing combined with the elegant self-assembly of octadecyltrichlorosilane (OTS) molecules on the substrates...
October 17, 2016: ACS Nano
Jiong Zhao, Honggi Nam, Thuc Hue Ly, Seok Joon Yun, Sera Kim, Suyeon Cho, Heejun Yang, Young Hee Lee
Defects in bulk crystals can be classified into vacancies, interstitials, grain boundaries, stacking faults, dislocations, and so forth. In particular, the vacancy in semiconductors is a primary defect that governs electrical transport. Concentration of vacancies depends mainly on the growth conditions. Individual vacancies instead of aggregated vacancies are usually energetically more favorable at room temperature because of the entropy contribution. This phenomenon is not guaranteed in van der Waals 2D materials due to the reduced dimensionality (reduced entropy)...
October 17, 2016: Small
Roshanak Farhoodi, Bahar Akbal-Delibas, Nurit Haspel
Discriminating native-like structures from false positives with high accuracy is one of the biggest challenges in protein-protein docking. While there is an agreement on the existence of a relationship between various favorable intermolecular interactions (e.g., Van der Waals, electrostatic, and desolvation forces) and the similarity of a conformation to its native structure, the precise nature of this relationship is not known. Existing protein-protein docking methods typically formulate this relationship as a weighted sum of selected terms and calibrate their weights by using a training set to evaluate and rank candidate complexes...
October 17, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Ross T Howie, Robin Turnbull, Jack Binns, Mungo Frost, Philip Dalladay-Simpson, Eugene Gregoryanz
Molecular nitrogen exhibits one of the strongest known interatomic bonds, while xenon possesses a closed-shell electronic structure: a direct consequence of which renders both chemically unreactive. Through a series of optical spectroscopy and x-ray diffraction experiments, we demonstrate the formation of a novel van der Waals compound formed from binary Xe-N2 mixtures at pressures as low as 5 GPa. At 300 K and 5 GPa Xe(N2)2-I is synthesised, and if further compressed, undergoes a transition to a tetragonal Xe(N2)2-II phase at 14 GPa; this phase appears to be unexpectedly stable at least up to 180 GPa even after heating to above 2000 K...
October 17, 2016: Scientific Reports
Rafael L H Freire, Adam Kiejna, Juarez L F Da Silva
We report the results of extensive computational investigation of the adsorption properties of water and ethanol on several Cu-, Pt-, and Au-based substrates, including the close-packed unreconstructed Cu(111), Pt(111), and Au(111) surfaces, defected metal substrates with on-surface low-coordinated sites generated by the intermixing of Pt-Cu and Pt-Au in the topmost surface layers and strained on-surface and sub-surface Pt-layers at Cu(111) and Au(111) substrates. The calculations are based on the density functional theory (DFT) within the van der Waals (vdW) correction...
October 17, 2016: Physical Chemistry Chemical Physics: PCCP
Darcie L Stack, Jason D Masuda
The title compound, C27H38ClN2(+)·C32H12BF24(-), was synthesized by reacting the product formed from a previous reaction between 1,3-bis-(2,6-diiso-propyl-phen-yl)imidazolinium-2-carboxyl-ate (SIPrCO2), and SOCl2, with sodium tetra-kis-[3,5-bis-(tri-fluoro-meth-yl)phen-yl]borate (NaBARF). In the cation, the imidazole ring is in a half-chair conformation and the formerly carbene carbon atom is bonded in a distorted trigonal-planar geometry with N-C-Cl angles of 122.96 (16) and 122.21 (16)° and an N-C-N angle of 114...
October 1, 2016: Acta Crystallographica. Section E, Crystallographic Communications
Martin van Megen, Guido J Reiss, Walter Frank
The asymmetric unit of the title mol-ecular salt, [C5H7N2(+)][(HO)2OP(CH2)9PO2(OH)(-)], consists of one 4-amino-pyridinium cation and one hydrogen (9-phos-phono-non-yl)phospho-nate anion, both in general positions. As expected, the 4-amino-pyridinium moieties are protonated exclusively at their endocyclic nitro-gen atom due to a mesomeric stabilization by the imine form which would not be given in the corresponding double-protonated dicationic species. In the crystal, the phosphonyl (-PO3H2) and hydrogen phospho-nate (-PO3H) groups of the anions form two-dimensional O-H⋯O hydrogen-bonded networks in the ab plane built from 24-membered hydrogen-bonded ring motifs with the graph-set descriptor R(6)6(24)...
October 1, 2016: Acta Crystallographica. Section E, Crystallographic Communications
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