Non-covalent interactions of cadmium sulphide and gold nanoparticles with DNA

Energy Technology Data Exchange (ETDEWEB)

Atay, Z. [Bogazici University, Department of Chemistry (Turkey); Biver, T., E-mail: tarita@dcci.unipi.i [Universita di Pisa, Dipartimento di Chimica e Chimica Industriale (Italy); Corti, A. [Universita di Pisa, Dipartimento di Patologia Sperimentale BMIE (Italy); Eltugral, N. [Universita di Pisa, Dipartimento di Chimica e Chimica Industriale (Italy); Lorenzini, E.; Masini, M.; Paolicchi, A. [Universita di Pisa, Dipartimento di Patologia Sperimentale BMIE (Italy); Pucci, A.; Ruggeri, G.; Secco, F.; Venturini, M. [Universita di Pisa, Dipartimento di Chimica e Chimica Industriale (Italy)

2010-08-15

Mercaptoethanol-capped CdS nanoparticles (CdS{sub np}) and monohydroxy-(1-mercaptoundec-11-yl)tetraethylene-glycol-capped Au nanoparticles (Au{sub np}) were synthesised, characterised and their interactions with DNA were investigated. Au{sub np} are stable in different aqueous solvents, whereas CdS{sub np} do precipitate in 0.1 M NaCl and form two different cluster types in 0.1 M NaNO{sub 3}. As regards the CdS{sub np}/DNA interaction, absorbance and fluorescence titrations, ethidium bromide displacement assays and gel electrophoresis experiments indicate that a non-covalent interaction between DNA and the CdS{sub np} external surface does take place. The binding constant was evaluated to be equal to (2.2 {+-} 0.5) x 10{sup 5} M{sup -1}. On the contrary, concerning Au{sub np}, no direct interaction with DNA could be observed. Possible interaction with serum albumin was also checked, but no effects could be observed for either CdS{sub np} or Au{sub np}. Finally, short-time exposure of cultured cells to nanoparticles revealed the ability of CdS{sub np} to enter the cells and allocate both in cytosol and nucleus, thus promoting cell proliferation at low concentration (p < 0.005), while longer-time exposure resulted in a significant inhibition of cell growth, accompanied by apoptotic cell death. Au{sub np} neither enter the cells, nor do affect cell proliferation. In conclusion, our data indicate that CdS{sub np} can strongly interact with living cells and nucleic acid while no effects or interactions were observed for Au{sub np}.

Strategies to balance covalent and non-covalent biomolecule attachment within collagen-GAG biomaterials.

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Pence, Jacquelyn C; Gonnerman, Emily A; Bailey, Ryan C; Harley, Brendan A C

2014-09-01

Strategies to integrate instructive biomolecular signals into a biomaterial are becoming increasingly complex and bioinspired. While a large majority of reports still use repeated treatments with soluble factors, this approach can be prohibitively costly and difficult to translate in vivo for applications where spatial control over signal presentation is necessary. Recent efforts have explored the use of covalent immobilization of biomolecules to the biomaterial, via both bulk (ubiquitous) as well as spatially-selective light-based crosslinking, as a means to both enhance stability and bioactivity. However, little is known about how processing conditions during immobilization impact the degree of unintended non-covalent interactions, or fouling, that takes place between the biomaterial and the biomolecule of interest. Here we demonstrate the impact of processing conditions for bulk carbodiimide (EDC) and photolithography-based benzophenone (BP) crosslinking on specific attachment vs. fouling of a model protein (Concanavalin A, ConA) within collagen-glycosaminoglycan (CG) scaffolds. Collagen source significantly impacts the selectivity of biomolecule immobilization. EDC crosslinking intensity and ligand concentration significantly impacted selective immobilization. For benzophenone photoimmobilization we observed that increased UV exposure time leads to increased ConA immobilization. Immobilization efficiency for both EDC and BP strategies was maximal at physiological pH. Increasing ligand concentration during immobilization process led to enhanced immobilization for EDC chemistry, no impact on BP immobilization, but significant increases in non-specific fouling. Given recent efforts to covalently immobilize biomolecules to a biomaterial surface to enhance bioactivity, improved understanding of the impact of crosslinking conditions on selective attachment versus non-specific fouling will inform the design of instructive biomaterials for applications across tissue

Recognition of anions using urea and thiourea substituted calixarenes: A density functional theory study of non-covalent interactions

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Athar, Mohd; Lone, Mohsin Y.; Jha, Prakash C.

2018-02-01

Designing of new calixarene receptors for the selective binding of anions is an age-old concept; even though expected outcomes from this field are at premature stage. Herein, we have performed quantum chemical calculations to provide structural basis of anion binding with urea and thiourea substituted calixarenes (1, 2, and 3). In particular, spherical halides (F-, Cl-, Br-) and linear anions (CN-, N3-, SCN-) were modelled for calculating binding energies with receptor 1, 2 and 3 followed by their marked IR vibrations; taking the available experimental information into account. We found that the thiourea substitutions have better capability to stabilize the anions. Results have suggested that the structural behaviour of macrocyclic motifs were responsible for displaying the anion binding potentials. Moreover, second order "charge transfer" interactions of n-σ∗NH and n-σ∗OH type along the H-bond axis played critical role in developing hydrogen bonds. The present work also examines the role of non-covalent interactions (NCI) and their effects on thermodynamic and chemical-reactivity descriptors.

Atomic Ensemble Effects and Non-Covalent Interactions at the Electrode–Electrolyte Interface

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Angel Cuesta

2016-09-01

Full Text Available Cyanide-modified Pt(111 electrodes have been recently employed to study atomic ensemble effects in electrocatalysis. This work, which will be briefly reviewed, reveals that the smallest site required for methanol dehydrogenation and formic acid dehydration is composed of three contiguous Pt atoms. By blocking these trigonal sites, the specific adsorption of anions, such as sulfate and phosphate, can be inhibited, thus increasing the rate of oxygen reduction reaction by one order of magnitude or more. Moreover, alkali metal cations affect hydrogen adsorption on cyanide-modified Pt(111. This effect is attributed to the non-covalent interactions at the electrical double layer between specifically adsorbed anions or dipoles and the alkali metal cations. A systematic investigation is conducted on the effect of the concentration of alkali metal cations. Accordingly, a simple model that reproduces the experimental observations accurately and enables the understanding of the trends in the strength of the interaction between M+ and CNad when moving from Li+ to Cs+, as well as the deviations from the expected trends, is developed. This simple model can also explain the occurrence of super-Nernstian shifts of the equilibrium potential of interfacial proton-coupled electron transfers. Therefore, the model can be generally applied to explain quantitatively the effect of cations on the properties of the electrical double layer. The recently reported effects of alkali metal cations on several electrocatalytic reactions must be mediated by the interaction between these cations and chemisorbed species. As these interactions seem to be adequately and quantitatively described by our model, we expect the model to also be useful to describe, explain, and potentially exploit these effects.

ESI-MS study on non-covalent bond complex of rhFKBP12 and new neurogrowth promoter

Institute of Scientific and Technical Information of China (English)

WANG; Hongxia; (王红霞); ZHANG; Xuemin; (张学敏); YANG; Songcheng; (杨松成); XIAO; Junhai; (肖军海); NIE; Aihua; (聂爱华); ZHAO; Liqin; (赵丽琴); LI; Song; (李松)

2003-01-01

An ESI-MS method for studying the non-covalent bond complex of rhFKBP12 with its nonimmunosuppressive ligands was developed. The method was used to screen out three compounds capable of binding to rhFKBP12 non-covalently from 52 compounds. By competing binding experiment, the binding site and the relative binding strength of these three compounds 000107, 000308 and A2B12 with rhFKBP12 were measured. All of them have the same binding site as FK506 does. X-ray crystalline diffraction experiment of non-covalent bond complex of 000107, 000308 with rhFKBP12 by Tsinghua University showed the same results. Among them 000308 has good effect on stimulating neurite to grow in chicken sensory neuronal cultures.

Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls

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Hezekiel Mathambo Kumalo

2015-01-01

Full Text Available he present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages over non-covalent inhibitors such as covalent warheads can target rare, non-conserved residue of a particular target protein and thus led to development of highly selective inhibitors, covalent inhibitors can be effective in targeting proteins with shallow binding cleavage which will led to development of novel inhibitors with increased potency than non-covalent inhibitors. Several computational approaches have been developed to simulate covalent interactions; however, this is still a challenging area to explore. Covalent molecular docking has been recently implemented in the computer-aided drug design workflows to describe covalent interactions between inhibitors and biological targets. In this review we highlight: (i covalent interactions in biomolecular systems; (ii the mathematical framework of covalent molecular docking; (iii implementation of covalent docking protocol in drug design workflows; (iv applications covalent docking: case studies and (v shortcomings and future perspectives of covalent docking. To the best of our knowledge; this review is the first account that highlights different aspects of covalent docking with its merits and pitfalls. We believe that the method and applications highlighted in this study will help future efforts towards the design of irreversible inhibitors.

Preventing disulfide bond formation weakens non-covalent forces among lysozyme aggregates.

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Vijay Kumar Ravi

Full Text Available Nonnative disulfide bonds have been observed among protein aggregates in several diseases like amyotrophic lateral sclerosis, cataract and so on. The molecular mechanism by which formation of such bonds promotes protein aggregation is poorly understood. Here in this work we employ previously well characterized aggregation of hen eggwhite lysozyme (HEWL at alkaline pH to dissect the molecular role of nonnative disulfide bonds on growth of HEWL aggregates. We employed time-resolved fluorescence anisotropy, atomic force microscopy and single-molecule force spectroscopy to quantify the size, morphology and non-covalent interaction forces among the aggregates, respectively. These measurements were performed under conditions when disulfide bond formation was allowed (control and alternatively when it was prevented by alkylation of free thiols using iodoacetamide. Blocking disulfide bond formation affected growth but not growth kinetics of aggregates which were ∼50% reduced in volume, flatter in vertical dimension and non-fibrillar in comparison to control. Interestingly, single-molecule force spectroscopy data revealed that preventing disulfide bond formation weakened the non-covalent interaction forces among monomers in the aggregate by at least ten fold, thereby stalling their growth and yielding smaller aggregates in comparison to control. We conclude that while constrained protein chain dynamics in correctly disulfide bonded amyloidogenic proteins may protect them from venturing into partial folded conformations that can trigger entry into aggregation pathways, aberrant disulfide bonds in non-amyloidogenic proteins (like HEWL on the other hand, may strengthen non-covalent intermolecular forces among monomers and promote their aggregation.

Investigation of Non-Covalent Interactions of Aflatoxins (B1, B2, G1, G2, and M1 with Serum Albumin

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Miklós Poór

2017-10-01

Full Text Available Aflatoxins are widely spread mycotoxins produced mainly by Aspergillus species. Consumption of aflatoxin-contaminated foods and drinks causes serious health risks for people worldwide. It is well-known that the reactive epoxide metabolite of aflatoxin B1 (AFB1 forms covalent adducts with serum albumin. However, non-covalent interactions of aflatoxins with human serum albumin (HSA are poorly characterized. Thus, in this study the complex formation of aflatoxins was examined with HSA applying spectroscopic and molecular modelling studies. Our results demonstrate that aflatoxins form stable complexes with HSA as reflected by binding constants between 2.1 × 104 and 4.5 × 104 dm3/mol. A binding free energy value of −26.90 kJ mol−1 suggests a spontaneous binding process between AFB1 and HSA at room-temperature, while the positive entropy change of 55.1 JK−1 mol−1 indicates a partial decomposition of the solvation shells of the interacting molecules. Modeling studies and investigations with site markers suggest that Sudlow’s Site I of subdomain IIA is the high affinity binding site of aflatoxins on HSA. Interaction of AFB1 with bovine, porcine, and rat serum albumins was also investigated. Similar stabilities of the examined AFB1-albumin complexes were observed suggesting the low species differences of the albumin-binding of aflatoxins.

Network Formation via Anion Coordination: Crystal Structures Based on the Interplay of Non-Covalent Interactions

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Matteo Savastano

2018-03-01

Full Text Available We describe the synthesis and the structural characterization of new H2L(CF3CO22 (1 and H2L(Ph2PO42 (2 compounds containing the diprotonated form (H2L2+ of the tetrazine-based molecule 3,6-di(pyridin-4-yl-1,2,4,5-tetrazine. X-ray diffraction (XRD analysis of single crystals of these compounds showed that H2L2+ displays similar binding properties toward both anions when salt bridge interactions are taken into account. Nevertheless, the different shapes, sizes and functionalities of trifluoroacetate and diphenyl phosphate anions define quite different organization patterns leading to the peculiar crystal lattices of 1 and 2. These three-dimensional (3D architectures are self-assembled by a variety of non-covalent forces, among which prominent roles are played by fluorine–π (in 1 and anion–π (in 2 interactions.

Non-covalently functionalized carbon nanostructures for synthesizing carbon-based hybrid nanomaterials.

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Li, Haiqing; Song, Sing I; Song, Ga Young; Kim, Il

2014-02-01

Carbon nanostructures (CNSs) such as carbon nanotubes, graphene sheets, and nanodiamonds provide an important type of substrate for constructing a variety of hybrid nanomaterials. However, their intrinsic chemistry-inert surfaces make it indispensable to pre-functionalize them prior to immobilizing additional components onto their surfaces. Currently developed strategies for functionalizing CNSs include covalent and non-covalent approaches. Conventional covalent treatments often damage the structure integrity of carbon surfaces and adversely affect their physical properties. In contrast, the non-covalent approach offers a non-destructive way to modify CNSs with desired functional surfaces, while reserving their intrinsic properties. Thus far, a number of surface modifiers including aromatic compounds, small-molecular surfactants, amphiphilic polymers, and biomacromolecules have been developed to non-covalently functionalize CNS surfaces. Mediated by these surface modifiers, various functional components such as organic species and inorganic nanoparticles were further decorated onto their surfaces, resulting in versatile carbon-based hybrid nanomaterials with broad applications in chemical engineering and biomedical areas. In this review, the recent advances in the generation of such hybrid nanostructures based on non-covalently functionalized CNSs will be reviewed.

Combination of computational methods, adsorption isotherms and selectivity tests for the conception of a mixed non-covalent-semi-covalent molecularly imprinted polymer of vanillin.

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Puzio, Kinga; Delépée, Raphaël; Vidal, Richard; Agrofoglio, Luigi A

2013-08-06

A novel molecularly imprinted polymer (MIP) for vanillin was prepared by photo initiated polymerization in dichloromethane using a mixed semi-covalent and non-covalent imprinting strategy. Taking polymerisable syringaldehyde as "dummy" template, acrylamide was chosen as functional monomer on B3LYP/6-31+G(d,p) density functional theory computational method basis with counterpoise. The binding parameters for the recognition of vanillin on imprinted polymers were studied with three different isotherm models (Langmuir, bi-Langmuir and Langmuir-Freundlich) and compared. The results indicate an heterogeneity of binding sites. It was found and proved by DFT calculations that the specific binding of vanillin in the cavities is due to non-covalent interactions of the template with the hydroxyphenyl- and the amide-moieties. The binding geometry of vanillin in the MIP cavity was also modelled. The obtained MIP is highly specific for vanillin (with an imprinting factor of 7.4) and was successfully applied to the extraction of vanillin from vanilla pods, red wine spike with vanillin, natural and artificial vanilla sugar with a recovery of 80%. Copyright © 2013 Elsevier B.V. All rights reserved.

Non-bonding interactions and non-covalent delocalization effects play a critical role in the relative stability of group 12 complexes arising from interaction of diethanoldithiocarbamate with the cations of transition metals Zn(II), Cd(II), and Hg(II): a theoretical study.

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Bahrami, Homayoon; Farhadi, Saeed; Siadatnasab, Firouzeh

2016-07-01

The chelating properties of diethanoldithiocarbamate (DEDC) and π-electron flow from the nitrogen atom to the sulfur atom via a plane-delocalized π-orbital system (quasi ring) was studied using a density functional theory method. The molecular structure of DEDC and its complexes with Zn(II), Cd(II), and Hg(II) were also considered. First, the geometries of this ligand and DEDC-Zn(II), DEDC-Cd(II), and DEDC-Hg(II) were optimized, and the formation energies of these complexes were then calculated based on the electronic energy, or sum of electronic energies, with the zero point energy of each species. Formation energies indicated the DEDC-Zn(II) complex as the most stable complex, and DEDC-Cd(II) as the least stable. Structural data showed that the N1-C2 π-bond was localized in the complexes rather than the ligand, and a delocalized π-bond over S7-C2-S8 was also present. The stability of DEDC-Zn(II), DEDC-Cd(II), and DEDC-Hg(II) complexes increased in the presence of the non-specific effects of the solvent (PCM model), and their relative stability did not change. There was π-electron flow or resonance along N1-C2-S7 and along S7-C2-S8 in the ligand. The π-electron flow or resonance along N1-C2-S7 was abolished when the metal interacted with sulfur atoms. Energy belonging to van der Waals interactions and non-covalent delocalization effects between the metal and sulfur atoms of the ligand was calculated for each complex. The results of nucleus-independent chemical shift (NICS) indicated a decreasing trend as Zn(II) Hg(II) for the aromaticity of the quasi-rings. Finally, by ignoring van der Waals interactions and non-covalent delocalization effects between the metal and sulfur atoms of the ligand, the relative stability of the complexes was changed as follows:[Formula: see text] Graphical Abstract Huge electronic cloud localized on Hg(II) in the Hg(II)-DEDC complex.

Non-covalent associative structure of coal

Energy Technology Data Exchange (ETDEWEB)

Shui, H. [Anhui University of Technology, Maanshan (China). School of Chemistry and Chemical Engineering

2004-06-01

The recent progress of non-covalent associative structure of coal and the mechanisms of the carbon disulphide-N-methyl-2-pyrrolidone (CS{sub 2}/NMP) are mixed solvent and the additive addition enhancing the extraction yield of coals are reviewed, and the aggregation behaviour of coal in solid and solution states are presented, and the aggregation behavior of coal in solid and solution states are introduced in this paper. Coal extraction and swelling in organic solvents at room temperature were the most useful methods to understand the associative structure of coal. CS{sub 2}/NMP is a unique solvent to give high extraction yields for some bituminous coals. Some additives such as tetracyanoethylene (TCNE) can dissociate the stronger interactions among coal molecules and enhance the extraction yields of coal in the mixed solvent. 37 refs., 1 fig.

Hydrogels Based on Dynamic Covalent and Non Covalent Bonds: A Chemistry Perspective

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Francesco Picchioni

2018-03-01

Full Text Available Hydrogels based on reversible covalent bonds represent an attractive topic for research at both academic and industrial level. While the concept of reversible covalent bonds dates back a few decades, novel developments continue to appear in the general research area of gels and especially hydrogels. The reversible character of the bonds, when translated at the general level of the polymeric network, allows reversible interaction with substrates as well as responsiveness to variety of external stimuli (e.g., self-healing. These represent crucial characteristics in applications such as drug delivery and, more generally, in the biomedical world. Furthermore, the several possible choices that can be made in terms of reversible interactions generate an almost endless number of possibilities in terms of final product structure and properties. In the present work, we aim at reviewing the latest developments in this field (i.e., the last five years by focusing on the chemistry of the systems at hand. As such, this should allow molecular designers to develop a toolbox for the synthesis of new systems with tailored properties for a given application.

An NMR study of the covalent and noncovalent interactions of CC-1065 and DNA

International Nuclear Information System (INIS)

Scahill, T.A.; Jensen, R.M.; Swenson, D.H.; Hatzenbuhler, N.T.; Petzold, G.; Wierenga, W.; Brahme, N.D.

1990-01-01

The binding of the antitumor drug CC-1065 has been studied with nuclear magnetic resonance (NMR) spectroscopy. This study involves two parts, the elucidation of the covalent binding site of the drug to DNA and a detailed investigation of the noncovalent interactions of CC-1065 with a DNA fragment through analysis of 2D NOE (NOESY) experiments. A CC-1065-DNA adduct was prepared, and an adenine adduct was released upon heating. NMR ( 1 H and 13 C) analysis of the adduct shows that the drug binds to N3 of adenine by reaction of its cyclopropyl group. The reaction pathway and product formed were determined by analysis of the 13 C DEPT spectra. An octamer duplex, d(CGATTAGC·GCTAATCG), was synthesized and used in the interaction study of CC-1065 and the oligomer. The duplex and the drug-octamer complex were both analyzed by 2D spectroscopy (COSY, NOESY). The relative intensity of the NOEs observed between the drug (CC-1065) and the octamer duplex shows conclusively that the drug is located in the minor groove, covalently attached to N3 of adenine 6 and positioned from the 3' → 5' end in relation to strand A [d(CGATTA 6 GC)]. A mechanism for drug binding and stabilization can be inferred from the NOE data and model-building studies

Enzymatic Activity Enhancement of Non-Covalent Modified Superoxide Dismutase and Molecular Docking Analysis

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Fa-Jun Song

2012-03-01

Full Text Available The enzyme activity of superoxide dismutase was improved in the pyrogallol autoxidation system by about 27%, after interaction between hydroxypropyl-β-cyclo- dextrin and superoxide dismutase. Fluorescence spectrometry was used to study the interaction between hydroxypropyl-β-cyclodextrin and superoxide dismutase at different temperatures. By doing this, it can be found that these interactions increase fluorescence sensitivity. In the meantime, the synchronous fluorescence intensity revealed the interaction sites to be close to the tryptophan (Trp and tyrosine (Tyr residues of superoxide dismutase. Furthermore, molecular docking was applied to explore the binding mode between the ligands and the receptor. This suggested that HP-β-CD interacted with the B ring, G ring and the O ring and revealed that the lysine (Lys residues enter the nanocavity. It was concluded that the HP-β-CD caused specific conformational changes in SOD by non-covalent modification.

Non-covalent conjugation of cutinase from Fusarium sp. ICT SAC1 with pectin for enhanced stability: Process minutiae, kinetics, thermodynamics and structural study.

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Muley, Abhijeet B; Chaudhari, Sandeep A; Singhal, Rekha S

2017-09-01

Cutinase, a member of α/β-fold hydrolase family possess potentially diverse applications in several industrial processes and products. The present work aims towards thermo-stabilization of cutinase from novel source Fusarium sp. ICT SAC1 via non-covalent interaction with polysaccharides. Although all six polysaccharides chosen for study enhanced the thermal stability, pectin was found to be most promising. The interaction protocol for cutinase with pectin was optimized sequentially with respect to the ratio of enzyme to pectin, solution pH, and buffer strength. Cutinase-pectin conjugate under optimized conditions (1:12, pH-6.5, 50mM) showed enhanced thermal stability as evident from lower inactivation rate constant, higher half-life and D-value within the 40-55°C. A slender rise in K m and V max values and enhanced thermodynamic parameters of cutinase-pectin conjugate were observed after non-covalent interaction. Entropy values were 1.5-fold higher for cutinase-pectin conjugate at each temperature suggesting an upsurge in number of protein molecules in a transition activated state. Positive values of entropy for both forms of cutinase suggested a rise in disordered conformation. Noticeable conformational changes in cutinase after conjugation with pectin were confirmed by FTIR as well as fluorescence emission spectra. An increment in helix to turn conversion was observed in complexed cutinase vis-à-vis free cutinase. Copyright © 2017 Elsevier B.V. All rights reserved.

Covalent and non-covalent chemical engineering of actin for biotechnological applications.

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Kumar, Saroj; Mansson, Alf

2017-11-15

The cytoskeletal filaments are self-assembled protein polymers with 8-25nm diameters and up to several tens of micrometres length. They have a range of pivotal roles in eukaryotic cells, including transportation of intracellular cargoes (primarily microtubules with dynein and kinesin motors) and cell motility (primarily actin and myosin) where muscle contraction is one example. For two decades, the cytoskeletal filaments and their associated motor systems have been explored for nanotechnological applications including miniaturized sensor systems and lab-on-a-chip devices. Several developments have also revolved around possible exploitation of the filaments alone without their motor partners. Efforts to use the cytoskeletal filaments for applications often require chemical or genetic engineering of the filaments such as specific conjugation with fluorophores, antibodies, oligonucleotides or various macromolecular complexes e.g. nanoparticles. Similar conjugation methods are also instrumental for a range of fundamental biophysical studies. Here we review methods for non-covalent and covalent chemical modifications of actin filaments with focus on critical advantages and challenges of different methods as well as critical steps in the conjugation procedures. We also review potential uses of the engineered actin filaments in nanotechnological applications and in some key fundamental studies of actin and myosin function. Finally, we consider possible future lines of investigation that may be addressed by applying chemical conjugation of actin in new ways. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Photodissociative Cross-Linking of Non-covalent Peptide-Peptide Ion Complexes in the Gas Phase

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Nguyen, Huong T. H.; Andrikopoulos, Prokopis C.; Rulíšek, Lubomír; Shaffer, Christopher J.; Tureček, František

2018-05-01

We report a gas-phase UV photodissociation study investigating non-covalent interactions between neutral hydrophobic pentapeptides and peptide ions incorporating a diazirine-tagged photoleucine residue. Phenylalanine (Phe) and proline (Pro) were chosen as the conformation-affecting residues that were incorporated into a small library of neutral pentapeptides. Gas-phase ion-molecule complexes of these peptides with photo-labeled pentapeptides were subjected to photodissociation. Selective photocleavage of the diazirine ring at 355 nm formed short-lived carbene intermediates that underwent cross-linking by insertion into H-X bonds of the target peptide. The cross-link positions were established from collision-induced dissociation tandem mass spectra (CID-MS3) providing sequence information on the covalent adducts. Effects of the amino acid residue (Pro or Phe) and its position in the target peptide sequence were evaluated. For proline-containing peptides, interactions resulting in covalent cross-links in these complexes became more prominent as proline was moved towards the C-terminus of the target peptide sequence. The photocross-linking yields of phenylalanine-containing peptides depended on the position of both phenylalanine and photoleucine. Density functional theory calculations were used to assign structures of low-energy conformers of the (GLPMG + GLL*LK + H)+ complex. Born-Oppenheimer molecular dynamics trajectory calculations were used to capture the thermal motion in the complexes within 100 ps and determine close contacts between the incipient carbene and the H-X bonds in the target peptide. This provided atomic-level resolution of potential cross-links that aided spectra interpretation and was in agreement with experimental data. [Figure not available: see fulltext.

Spectroscopic and DFT Studies of Second Sphere Variants of the Type 1 Copper Site in Azurin: Covalent and Non-Local Electrostatic Contributions to Reduction Potentials

Science.gov (United States)

Hadt, Ryan G.; Sun, Ning; Marshall, Nicholas M.; Hodgson, Keith O.; Hedman, Britt; Lu, Yi; Solomon, Edward I.

2012-01-01

The reduction potentials (E0) of type 1 (T1) or blue copper (BC) sites in proteins and enzymes with identical first coordination spheres around the redox active copper ion can vary by ~400 mV. Here, we use a combination of low temperature electronic absorption and magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second sphere variants—F114P, N47S, and F114N in Pseudomonas aeruginosa azurin (Az)—which modulate hydrogen bonding to and protein derived dipoles nearby the Cu-S(Cys) bond. Density functional theory (DFT) calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E0 into covalent and non-local electrostatic components. These are found to be significant, comparable in magnitude, and additive for active H-bonds, while passive H-bonds are mostly non-local electrostatic in nature. For dipoles, these terms can be additive to or oppose one another. This study provides a methodology for uncoupling covalency from non-local electrostatics, which, when coupled to X-ray crystallographic data, distinguishes specific local interactions from more long range protein/active interactions, while affording further insight into the second sphere mechanisms available to the protein to tune the E0 of electron transfer sites in biology. PMID:22985400

Preparation of non-aggregated fluorescent nanodiamonds (FNDs) by non-covalent coating with a block copolymer and proteins for enhancement of intracellular uptake.

Science.gov (United States)

Lee, Jong Woo; Lee, Seonju; Jang, Sangmok; Han, Kyu Young; Kim, Younggyu; Hyun, Jaekyung; Kim, Seong Keun; Lee, Yan

2013-05-01

Fluorescent nanodiamonds (FNDs) are very promising fluorophores for use in biosystems due to their high biocompatibility and photostability. To overcome their tendency to aggregate in physiological solutions, which severely limits the biological applications of FNDs, we developed a new non-covalent coating method using a block copolymer, PEG-b-P(DMAEMA-co-BMA), or proteins such as BSA and HSA. By simple mixing of the block copolymer with FNDs, the cationic DMAEMA and hydrophobic BMA moieties can strongly interact with the anionic and hydrophobic moieties on the FND surface, while the PEG block can form a shell to prevent the direct contact between FNDs. The polymer-coated FNDs, along with BSA- and HSA-coated FNDs, showed non-aggregation characteristics and maintained their size at the physiological salt concentration. The well-dispersed, polymer- or protein-coated FNDs in physiological solutions showed enhanced intracellular uptake, which was confirmed by CLSM. In addition, the biocompatibility of the coated FNDs was expressly supported by a cytotoxicity assay. Our simple non-covalent coating with the block copolymer, which can be easily modified by various chemical methods, projects a very promising outlook for future biomedical applications, especially in comparison with covalent coating or protein-based coating.

Non-covalent and reversible functionalization of carbon nanotubes

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Antonello Di Crescenzo

2014-09-01

Full Text Available Carbon nanotubes (CNTs have been proposed and actively explored as multipurpose innovative nanoscaffolds for applications in fields such as material science, drug delivery and diagnostic applications. Their versatile physicochemical features are nonetheless limited by their scarce solubilization in both aqueous and organic solvents. In order to overcome this drawback CNTs can be easily non-covalently functionalized with different dispersants. In the present review we focus on the peculiar hydrophobic character of pristine CNTs that prevent them to easily disperse in organic solvents. We report some interesting examples of CNTs dispersants with the aim to highlight the essential features a molecule should possess in order to act as a good carbon nanotube dispersant both in water and in organic solvents. The review pinpoints also a few examples of dispersant design. The last section is devoted to the exploitation of the major quality of non-covalent functionalization that is its reversibility and the possibility to obtain stimuli-responsive precipitation or dispersion of CNTs.

Non-covalent interactions between {N,N′-bis[(2-pyridinyl)methylene]-1, 2-benzenediamine]-bis(nitrato)}Cu(II) with pyridoxine hydrochloride in methanol at T = (298.15, 308.15 and 318.15) K

International Nuclear Information System (INIS)

Brahman, Dhiraj; Sinha, Biswajit

2014-01-01

Highlights: • Methanolic solution of pyridoxine hydrochloride used as solvent. • {N,N′-bis[(2-pyridinyl)methylene]-1, 2-benzenediamine]-bis(nitrato)}Cu(II) used as solute. • Partial molar volumes and viscosity B-coefficients of the solute were determined. • Weak 1:1 association between the complex and pyridoxine hydrochloride found. • Non-covalent interactions and Cu(II) complex acts as a net structure maker in the ternary solutions. - Abstract: Non-covalent interactions between of {N,N′-bis[(2-pyridinyl)methylene]-1, 2-benzenediamine]-bis(nitrato)}Cu(II) with pyridoxine hydrochloride in methanol were investigated by a combination of physico-chemical and spectrophotometric methods at T = (298.15, 308.15 and 318.15) K under ambient pressure. From measured density and viscosity data the apparent molar volume (ϕ V ), the slope (S V ∗ ), standard partial molar volume (ϕ V 0 ), standard transfer volume (Δ t ϕ V 0 ), isobaric apparent molar expansibility (ϕ E ), standard isobaric partial molar expansibility (ϕ E 0 ), the viscosity B-coefficient, its temperature derivative (∂B/∂T), solvation number (S n ) were calculated and discussed on the basis of specific or non-specific (solute + cosolute) and (solute + solvent) interactions. Thermodynamics of viscous flow were discussed on the basis of the transition state theory. Spectrophotometric results indicated 1:1 (solute + cosolute) interaction between the complex and pyridoxine hydrochloride

Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH32BH3 and KN(CH32BH3

Directory of Open Access Journals (Sweden)

Filip Sagan

2016-03-01

Full Text Available In the present work, an in-depth, qualitative and quantitative description of non-covalent interactions in the hydrogen storage materials LiN(CH32BH3 and KN(CH32BH3 was performed by means of the charge and energy decomposition method (ETS-NOCV as well as the Interacting Quantum Atoms (IQA approach. It was determined that both crystals are stabilized by electrostatically dominated intra- and intermolecular M∙∙∙H–B interactions (M = Li, K. For LiN(CH32BH3 the intramolecular charge transfer appeared (B–H→Li to be more pronounced compared with the corresponding intermolecular contribution. We clarified for the first time, based on the ETS-NOCV and IQA methods, that homopolar BH∙∙∙HB interactions in LiN(CH32BH3 can be considered as destabilizing (due to the dominance of repulsion caused by negatively charged borane units, despite the fact that some charge delocalization within BH∙∙∙HB contacts is enforced (which explains H∙∙∙H bond critical points found from the QTAIM method. Interestingly, quite similar (to BH∙∙∙HB intermolecular homopolar dihydrogen bonds CH∙∙∙HC appared to significantly stabilize both crystals—the ETS-NOCV scheme allowed us to conclude that CH∙∙∙HC interactions are dispersion dominated, however, the electrostatic and σ/σ*(C–H charge transfer contributions are also important. These interactions appeared to be more pronounced in KN(CH32BH3 compared with LiN(CH32BH3.

Synthesis and non-covalent functionalization of carbon nanotubes rings: new nanomaterials with lectin affinity

International Nuclear Information System (INIS)

Assali, Mohyeddin; Leal, Manuel Pernía; Khiar, Noureddine; Fernández, Inmaculada

2013-01-01

We present a mild and practical carbon nanotubes rings (CNRs) synthesis from non-covalent functionalized and water-soluble linear single-wall carbon nanotubes. The hemi-micellar–supramolecular self-organization of lactose-based glycolipid 1 on the ring surface, followed by photo-polymerization of the diacetylenic function triggered by UV light afforded the first water-soluble and biocompatible CNRs. The obtained donut-like nanoconstructs expose a high density of lactose moieties on their surface, and are able to engage specific interactions with Arachis hypogea lectin similar to glycoconjugates on the cell membrane. (paper)

Non-covalent functionalization of single wall carbon nanotubes and graphene by a conjugated polymer

KAUST Repository

Jiwuer, Jilili

2014-07-07

We report first-principles calculations on the binding of poly[(9,9-bis-(6-bromohexylfluorene-2,7-diyl)-co-(benzene-1,4-diyl)] to a (8,0) single wall carbon nanotube (SWCNT) and to graphene. Considering different relative orientations of the subsystems, we find for the generalized gradient approximation a non-binding state, whereas the local density approximation predicts reasonable binding energies. The results coincide after inclusion of van der Waals corrections, which demonstrates a weak interaction between the polymer and SWCNT/graphene, mostly of van der Waals type. Accordingly, the density of states shows essentially no hybridization. The physisorption mechanism explains recent experimental observations and suggests that the conjugated polymer can be used for non-covalent functionalization.

Non-covalent functionalization of single wall carbon nanotubes and graphene by a conjugated polymer

KAUST Repository

Jiwuer, Jilili; Abdurahman, Ayjamal; Gü lseren, Oğuz; Schwingenschlö gl, Udo

2014-01-01

We report first-principles calculations on the binding of poly[(9,9-bis-(6-bromohexylfluorene-2,7-diyl)-co-(benzene-1,4-diyl)] to a (8,0) single wall carbon nanotube (SWCNT) and to graphene. Considering different relative orientations of the subsystems, we find for the generalized gradient approximation a non-binding state, whereas the local density approximation predicts reasonable binding energies. The results coincide after inclusion of van der Waals corrections, which demonstrates a weak interaction between the polymer and SWCNT/graphene, mostly of van der Waals type. Accordingly, the density of states shows essentially no hybridization. The physisorption mechanism explains recent experimental observations and suggests that the conjugated polymer can be used for non-covalent functionalization.

Catalyst recycling via specific non-covalent adsorption on modified silicas

NARCIS (Netherlands)

Kluwer, A.M.; Simons, C.; Knijnenburg, Q.; van der Vlugt, J.I.; de Bruin, B.; Reek, J.N.H.

2013-01-01

This article describes a new strategy for the recycling of a homogeneous hydroformylation catalyst, by selective adsorption of the catalyst to tailor-made supports after a batchwise reaction. The separation of the catalyst from the product mixture is based on selective non-covalent supramolecular

Theoretical Insights into Monometallofullerene Th@C76: Strong Covalent Interaction between Thorium and the Carbon Cage.

Science.gov (United States)

Zhao, Pei; Zhao, Xiang; Ehara, Masahiro

2018-03-19

Th@C 76 has been studied by density functional theory combined with statistical mechanics calculations. The results reveal that Th@ T d (19151)-C 76 satisfying the isolated pentagon rule possesses the lowest energy. Nevertheless, considering the enthalpy-entropy interplay, Th@ C 1 (17418)-C 76 with one pair of adjacent pentagons is thermodynamically favorable at elevated temperatures, which is reported for the first time. The bonding critical points in both isomers were analyzed to disclose covalent interactions between the inner Th and cages. In addition, the Wiberg bond orders of M-C bonding in different endohedral metallofullerenes (EMFs) were investigated to prove stronger covalent interactions of Th-C in Th-based EMFs.

Relationships between Cargo, Cell Penetrating Peptides and Cell Type for Uptake of Non-Covalent Complexes into Live Cells

Directory of Open Access Journals (Sweden)

Andrea-Anneliese Keller

2013-02-01

Full Text Available Modulating signaling pathways for research and therapy requires either suppression or expression of selected genes or internalization of proteins such as enzymes, antibodies, nucleotide binding proteins or substrates including nucleoside phosphates and enzyme inhibitors. Peptides, proteins and nucleotides are transported by fusing or conjugating them to cell penetrating peptides or by formation of non-covalent complexes. The latter is often preferred because of easy handling, uptake efficiency and auto-release of cargo into the live cell. In our studies complexes are formed with labeled or readily detectable cargoes for qualitative and quantitative estimation of their internalization. Properties and behavior of adhesion and suspension vertebrate cells as well as the protozoa Leishmania tarentolae are investigated with respect to proteolytic activity, uptake efficiency, intracellular localization and cytotoxicity. Our results show that peptide stability to membrane-bound, secreted or intracellular proteases varies between different CPPs and that the suitability of individual CPPs for a particular cargo in complex formation by non-covalent interactions requires detailed studies. Cells vary in their sensitivity to increasing concentrations of CPPs. Thus, most cells can be efficiently transduced with peptides, proteins and nucleotides with intracellular concentrations in the low micromole range. For each cargo, cell type and CPP the optimal conditions must be determined separately.

Covalent and non-covalent functionalization and solubilization of ...

Indian Academy of Sciences (India)

Wintec

photographs of the dispersions of amide-functio- nalized DWNTs in dichloromethane and tetrahydro- furan. In figure 3b, we show a TEM image of DWNTs after covalent functionalization. The images are not as sharp after functionalization as in the case of pris- tine nanotubes (figure 3a), and the bundles seem to be intact.

Dynamic covalent gels assembled from small molecules:from discrete gelators to dynamic covalent polymers

Institute of Scientific and Technical Information of China (English)

Jian-Yong Zhang; Li-Hua Zeng; Juan Feng

2017-01-01

Dynamic covalent chemistry has emerged recently to be a powerful tool to construct functional materials.This article reviews the progress in the research and development of dynamic covalent chemistry in gels assembled from small molecules.First dynamic covalent reactions used in gels are reviewed to understand the dynamic covalent bonding.Afterwards the catalogues of dynamic covalent gels are reviewed according to the nature of gelators and the interactions between gelators.Dynamic covalent bonding can be involved to form low molecular weight gelators.Low molecular weight molecules with multiple functional groups react to form dynamic covalent cross-linked polymers and act as gelators.Two catalogues of gels show different properties arising from their different structures.This review aims to illustrate the structure-property relationships of these dynamic covalent gels.

Non-covalent conjugates of single-walled carbon nanotubes and folic acid for interaction with cells overexpressing folate receptors

DEFF Research Database (Denmark)

Castillo, John J.; Rindzevicius, Tomas; Novoa, Leidy V.

2013-01-01

We here present amethod to form a noncovalent conjugate of single-walled carbon nanotubes and folic acid aimed to interact with cells over-expressing folate receptors. The bonding was obtained without covalent chemical functionalization using a simple, rapid “one pot” synthesis method. The zeta...... a low toxicity of the conjugates in the THP-1 cells. The low toxicity and the cellular uptake of single-walled carbon nanotube–folic acid by cancer cells suggest their potential use in carbon nanotube-based drug delivery systems and in the diagnosis of cancer or tropical diseases such as leishmaniasis....

Covalent bonding in heavy metal oxides

Energy Technology Data Exchange (ETDEWEB)

Bagus, Paul S.; Nelin, Connie J.; Hrovat, Dave A.; Ilton, Eugene S.

2017-04-07

Novel theoretical methods were used to quantify the magnitude and the energetic contributions of 4f/5f-O2p and 5d/6d-O2p interactions to covalent bonding in lanthanide and actinide oxides. Although many analyses have neglected the involvement of the frontier d orbitals, the present study shows that f and d covalency are of comparable importance. Two trends are identified. As is expected, the covalent mixing is larger when the nominal oxidation state is higher. More subtly, the importance of the nf covalent mixing decreases sharply relative to (n+1)d as the nf occupation increases. Atomic properties of the metal cations that drive these trends are identified.

Selective removal of 2,4-dichlorophenol from contaminated water using non-covalent imprinted microspheres

International Nuclear Information System (INIS)

Li Ying; Li Xin; Li Yuqi; Qi Jingyao; Bian Jiang; Yuan Yixing

2009-01-01

A molecularly imprinted polymer (MIP) for selective removal of 2,4-dichlorophenol (2,4-DCP) in water was prepared as microspheres by the reverse microemulsion polymerization method based on the non-covalent interactions between 2,4-DCP, oleic acid, and divinylbenzene in acetonitrile. Microspheres have been characterized by Fourier transform infrared spectrometer (FTIR) and energy dispersive X-ray spectrometer (EDS) studies with evidence of 2,4-DCP linkage in polymer particles and scanning electron microscopy (SEM) to study their morphological properties. The proper adsorption and selective recognition ability of the MIP were studied by an equilibrium-adsorption method. The MIP showed outstanding affinity towards 2,4-DCP in aqueous solution and the optimum pH value for binding has been found around the neutral range. The molecular recognition of 2,4-DCP was analyzed in detail by using molecular modeling software. In addition, by investigating the variation in the adsorption ability of the MIP, it clearly showed excellent reproducibility. - Molecular imprinting has potential as a remediation technology in water treatment.

Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding

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Finkelstein Alexei V

2007-07-01

Full Text Available Abstract Background The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation. Results A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease the interaction energy by about 20–40% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipole-dipole interactions at small distances, where Van der Waals interactions take place. Conclusion The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N in conventional pairwise Van der Waals interactions.

Covalent and non-covalent curcumin loading in acid-responsive polymeric micellar nanocarriers

International Nuclear Information System (INIS)

Gao, Min; Chen, Chao; Fan, Aiping; Wang, Zheng; Zhao, Yanjun; Zhang, Ju; Kong, Deling

2015-01-01

Poor aqueous solubility, potential degradation, rapid metabolism and elimination lead to low bioavailability of pleiotropic impotent curcumin. Herein, we report two types of acid-responsive polymeric micelles where curcumin was encapsulated via both covalent and non-covalent modes for enhanced loading capacity and on-demand release. Biodegradable methoxy poly(ethylene glycol)-poly(lactic acid) copolymer (mPEG-PLA) was conjugated with curcumin via a hydrazone linker, generating two conjugates differing in architecture (single-tail versus double-tail) and free curcumin was encapsulated therein. The two micelles exhibited similar hydrodynamic size at 95 ± 3 nm (single-tail) and 96 ± 3 nm (double-tail), but their loading capacities differed significantly at 15.0 ± 0.5% (w/w) (single-tail) and 4.8 ± 0.5% (w/w) (double-tail). Under acidic sink conditions (pH 5.0 and 6.0), curcumin displayed a faster release from the single-tail nanocarrier, which was correlated to a low IC_5_0 of 14.7 ± 1.6 (μg mL"−"1) compared to the value of double-tail micelle (24.9 ± 1.3 μg mL"−"1) in HeLa cells. The confocal imaging and flow cytometry analysis demonstrated a superior capability of single-tail micelle for intracellular curcumin delivery, which was a consequence of the higher loading capacity and lower degree of mPEG surface coverage. In conclusion, the dual loading mode is an effective means to increase the drug content in the micellar nanocarriers whose delivery efficiency is highly dependent on its polymer–drug conjugate architecture. This strategy offers an alternative nanoplatform for intracellularly delivering impotent hydrophobic agents (i.e. curcumin) in an efficient stimuli-triggered way, which is valuable for the enhancement of curcumin’s efficacy in managing a diverse range of disorders. (paper)

Covalent and non-covalent curcumin loading in acid-responsive polymeric micellar nanocarriers

Science.gov (United States)

Gao, Min; Chen, Chao; Fan, Aiping; Zhang, Ju; Kong, Deling; Wang, Zheng; Zhao, Yanjun

2015-07-01

Poor aqueous solubility, potential degradation, rapid metabolism and elimination lead to low bioavailability of pleiotropic impotent curcumin. Herein, we report two types of acid-responsive polymeric micelles where curcumin was encapsulated via both covalent and non-covalent modes for enhanced loading capacity and on-demand release. Biodegradable methoxy poly(ethylene glycol)-poly(lactic acid) copolymer (mPEG-PLA) was conjugated with curcumin via a hydrazone linker, generating two conjugates differing in architecture (single-tail versus double-tail) and free curcumin was encapsulated therein. The two micelles exhibited similar hydrodynamic size at 95 ± 3 nm (single-tail) and 96 ± 3 nm (double-tail), but their loading capacities differed significantly at 15.0 ± 0.5% (w/w) (single-tail) and 4.8 ± 0.5% (w/w) (double-tail). Under acidic sink conditions (pH 5.0 and 6.0), curcumin displayed a faster release from the single-tail nanocarrier, which was correlated to a low IC50 of 14.7 ± 1.6 (μg mL-1) compared to the value of double-tail micelle (24.9 ± 1.3 μg mL-1) in HeLa cells. The confocal imaging and flow cytometry analysis demonstrated a superior capability of single-tail micelle for intracellular curcumin delivery, which was a consequence of the higher loading capacity and lower degree of mPEG surface coverage. In conclusion, the dual loading mode is an effective means to increase the drug content in the micellar nanocarriers whose delivery efficiency is highly dependent on its polymer-drug conjugate architecture. This strategy offers an alternative nanoplatform for intracellularly delivering impotent hydrophobic agents (i.e. curcumin) in an efficient stimuli-triggered way, which is valuable for the enhancement of curcumin’s efficacy in managing a diverse range of disorders.

System in biology leading to cell pathology: stable protein-protein interactions after covalent modifications by small molecules or in transgenic cells.

Science.gov (United States)

Malina, Halina Z

2011-01-19

The physiological processes in the cell are regulated by reversible, electrostatic protein-protein interactions. Apoptosis is such a regulated process, which is critically important in tissue homeostasis and development and leads to complete disintegration of the cell. Pathological apoptosis, a process similar to apoptosis, is associated with aging and infection. The current study shows that pathological apoptosis is a process caused by the covalent interactions between the signaling proteins, and a characteristic of this pathological network is the covalent binding of calmodulin to regulatory sequences. Small molecules able to bind covalently to the amino group of lysine, histidine, arginine, or glutamine modify the regulatory sequences of the proteins. The present study analyzed the interaction of calmodulin with the BH3 sequence of Bax, and the calmodulin-binding sequence of myristoylated alanine-rich C-kinase substrate in the presence of xanthurenic acid in primary retinal epithelium cell cultures and murine epithelial fibroblast cell lines transformed with SV40 (wild type [WT], Bid knockout [Bid-/-], and Bax-/-/Bak-/- double knockout [DKO]). Cell death was observed to be associated with the covalent binding of calmodulin, in parallel, to the regulatory sequences of proteins. Xanthurenic acid is known to activate caspase-3 in primary cell cultures, and the results showed that this activation is also observed in WT and Bid-/- cells, but not in DKO cells. However, DKO cells were not protected against death, but high rates of cell death occurred by detachment. The results showed that small molecules modify the basic amino acids in the regulatory sequences of proteins leading to covalent interactions between the modified sequences (e.g., calmodulin to calmodulin-binding sites). The formation of these polymers (aggregates) leads to an unregulated and, consequently, pathological protein network. The results suggest a mechanism for the involvement of small molecules

Crystal structures of Mycobacterium tuberculosis GlgE and complexes with non-covalent inhibitors

Energy Technology Data Exchange (ETDEWEB)

Lindenberger, Jared J.; Veleti, Sri Kumar; Wilson, Brittney N.; Sucheck, Steven J.; Ronning, Donald R. (Toledo)

2015-08-06

GlgE is a bacterial maltosyltransferase that catalyzes the elongation of a cytosolic, branched α-glucan. In Mycobacterium tuberculosis (M. tb), inactivation of GlgE (Mtb GlgE) results in the rapid death of the organism due to a toxic accumulation of the maltosyl donor, maltose-1-phosphate (M1P), suggesting that GlgE is an intriguing target for inhibitor design. In this study, the crystal structures of the Mtb GlgE in a binary complex with maltose and a ternary complex with maltose and a maltosyl-acceptor molecule, maltohexaose, were solved to 3.3 Å and 4.0 Å, respectively. The maltohexaose structure reveals a dominant site for α-glucan binding. To obtain more detailed interactions between first generation, non-covalent inhibitors and GlgE, a variant Streptomyces coelicolor GlgEI (Sco GlgEI-V279S) was made to better emulate the Mtb GlgE M1P binding site. The structure of Sco GlgEI-V279S complexed with α-maltose-C-phosphonate (MCP), a non-hydrolyzable substrate analogue, was solved to 1.9 Å resolution, and the structure of Sco GlgEI-V279S complexed with 2,5-dideoxy-3-O-α-D-glucopyranosyl-2,5-imino-D-mannitol (DDGIM), an oxocarbenium mimic, was solved to 2.5 Å resolution. These structures detail important interactions that contribute to the inhibitory activity of these compounds, and provide information on future designs that may be exploited to improve upon these first generation GlgE inhibitors.

Assessing Covalency in Cerium and Uranium Hexachlorides: A Correlated Wavefunction and Density Functional Theory Study

Directory of Open Access Journals (Sweden)

Reece Beekmeyer

2015-11-01

Full Text Available The electronic structure of a series of uranium and cerium hexachlorides in a variety of oxidation states was evaluated at both the correlated wavefunction and density functional (DFT levels of theory. Following recent experimental observations of covalency in tetravalent cerium hexachlorides, bonding character was studied using topological and integrated analysis based on the quantum theory of atoms in molecules (QTAIM. This analysis revealed that M–Cl covalency was strongly dependent on oxidation state, with greater covalency found in higher oxidation state complexes. Comparison of M–Cl delocalisation indices revealed a discrepancy between correlated wavefunction and DFT-derived values. Decomposition of these delocalisation indices demonstrated that the origin of this discrepancy lay in ungerade contributions associated with the f-manifold which we suggest is due to self-interaction error inherent to DFT-based methods. By all measures used in this study, extremely similar levels of covalency between complexes of U and Ce in the same oxidation state was found.

Effects of Covalent Functionalization of MWCNTs on the Thermal Properties and Non-Isothermal Crystallization Behaviors of PPS Composites

Directory of Open Access Journals (Sweden)

Myounguk Kim

2017-09-01

Full Text Available In this study, a PPS/MWCNTs composite was prepared with poly(phenylene sulfide (PPS, as well as pristine and covalent functionalized multi-walled carbon nanotubes (MWCNTs via melt-blending techniques. Moreover, the dispersion of the MWCNTs on the PPS matrix was improved by covalent functionalization as can be seen from a Field-Emission Scanning Electron Microscope (FE-SEM images. The thermal properties of the PPS/MWCNTs composites were characterized using a thermal conductivity analyzer, and a differential scanning calorimeter (DSC. To analyze the crystallization behavior of polymers under conditions similar with those in industry, the non-isothermal crystallization behaviors of the PPS/MWCNTs composites were confirmed using various kinetic equations, such as the modified Avrami equation and Avrami-Ozawa combined equation. The crystallization rate of PPS/1 wt % pristine MWCNTs composite (PPSP1 was faster because of the intrinsic nucleation effect of the MWCNTs. However, the crystallization rates of the composites containing covalently-functionalized MWCNTs were slower than PPSP1 because of the destruction of the MWCNTs graphitic structure via covalent functionalization. Furthermore, the activation energies calculated by Kissinger’s method were consistently decreased by covalent functionalization.

Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta.

Science.gov (United States)

Combs, Steven A; Mueller, Benjamin K; Meiler, Jens

2018-05-29

Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identify and evaluate these PCIs through analyzing the geometry between participating atoms. However, we hypothesize that PCIs can be unified through a simplified electron orbital representation. To test this hypothesis, we have introduced orbital based chemical descriptors for PCIs into Rosetta, called the PCI score function. Optimal geometries for the PCIs are derived from a statistical analysis of high-quality protein structures obtained from the Protein Data Bank (PDB), and the relative orientation of electron deficient hydrogen atoms and electron-rich lone pair or π orbitals are evaluated. We demonstrate that nativelike geometries of hydrogen bonds, salt bridges, cation-π, and π-π interactions are recapitulated during minimization of protein conformation. The packing density of tested protein structures increased from the standard score function from 0.62 to 0.64, closer to the native value of 0.70. Overall, rotamer recovery improved when using the PCI score function (75%) as compared to the standard Rosetta score function (74%). The PCI score function represents an improvement over the standard Rosetta score function for protein model scoring; in addition, it provides a platform for future directions in the analysis of small molecule to protein interactions, which depend on partial covalent interactions.

Second-Generation Non-Covalent NAAA Inhibitors are Protective in a Model of Multiple Sclerosis.

Science.gov (United States)

Migliore, Marco; Pontis, Silvia; Fuentes de Arriba, Angel Luis; Realini, Natalia; Torrente, Esther; Armirotti, Andrea; Romeo, Elisa; Di Martino, Simona; Russo, Debora; Pizzirani, Daniela; Summa, Maria; Lanfranco, Massimiliano; Ottonello, Giuliana; Busquet, Perrine; Jung, Kwang-Mook; Garcia-Guzman, Miguel; Heim, Roger; Scarpelli, Rita; Piomelli, Daniele

2016-09-05

Palmitoylethanolamide (PEA) and oleoylethanolamide (OEA) are endogenous lipid mediators that suppress inflammation. Their actions are terminated by the intracellular cysteine amidase, N-acylethanolamine acid amidase (NAAA). Even though NAAA may offer a new target for anti-inflammatory therapy, the lipid-like structures and reactive warheads of current NAAA inhibitors limit the use of these agents as oral drugs. A series of novel benzothiazole-piperazine derivatives that inhibit NAAA in a potent and selective manner by a non-covalent mechanism are described. A prototype member of this class (8) displays high oral bioavailability, access to the central nervous system (CNS), and strong activity in a mouse model of multiple sclerosis (MS). This compound exemplifies a second generation of non-covalent NAAA inhibitors that may be useful in the treatment of MS and other chronic CNS disorders. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

Science.gov (United States)

Bereau, Tristan; DiStasio, Robert A.; Tkatchenko, Alexandre; von Lilienfeld, O. Anatole

2018-06-01

Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning (ML), coined IPML, which is transferable across small neutral organic and biologically relevant molecules. ML models provide on-the-fly predictions for environment-dependent local atomic properties: electrostatic multipole coefficients (significant error reduction compared to previously reported), the population and decay rate of valence atomic densities, and polarizabilities across conformations and chemical compositions of H, C, N, and O atoms. These parameters enable accurate calculations of intermolecular contributions—electrostatics, charge penetration, repulsion, induction/polarization, and many-body dispersion. Unlike other potentials, this model is transferable in its ability to handle new molecules and conformations without explicit prior parametrization: All local atomic properties are predicted from ML, leaving only eight global parameters—optimized once and for all across compounds. We validate IPML on various gas-phase dimers at and away from equilibrium separation, where we obtain mean absolute errors between 0.4 and 0.7 kcal/mol for several chemically and conformationally diverse datasets representative of non-covalent interactions in biologically relevant molecules. We further focus on hydrogen-bonded complexes—essential but challenging due to their directional nature—where datasets of DNA base pairs and amino acids yield an extremely encouraging 1.4 kcal/mol error. Finally, and as a first look, we consider IPML for denser systems: water clusters, supramolecular host-guest complexes, and the benzene crystal.

Identification of an estrogen receptor α non covalent ubiquitin-binding surface: role in 17β-estradiol-induced transcriptional activity.

Science.gov (United States)

Pesiri, Valeria; La Rosa, Piergiorgio; Stano, Pasquale; Acconcia, Filippo

2013-06-15

Ubiquitin (Ub)-binding domains (UBDs) located in Ub receptors decode the ubiquitination signal by non-covalently engaging the Ub modification on their binding partners and transduce the Ub signalling through Ub-based molecular interactions. In this way, inducible protein ubiquitination regulates diverse biological processes. The estrogen receptor alpha (ERα) is a ligand-activated transcription factor that mediates the pleiotropic effects of the sex hormone 17β-estradiol (E2). Fine regulation of E2 pleiotropic actions depends on E2-dependent ERα association with a plethora of binding partners and/or on the E2 modulation of receptor ubiquitination. Indeed, E2-induced ERα polyubiquitination triggers receptor degradation and transcriptional activity, and E2-dependent reduction in ERα monoubiquitination is crucial for E2 signalling. Monoubiquitinated proteins often contain UBDs, but whether non-covalent Ub-ERα binding could occur and play a role in E2-ERα signalling is unknown. Here, we report an Ub-binding surface within the ERα ligand binding domain that directs in vitro the receptor interaction with both ubiquitinated proteins and recombinant Ub chains. Mutational analysis reveals that ERα residues leucine 429 and alanine 430 are involved in Ub binding. Moreover, impairment of ERα association to ubiquitinated species strongly affects E2-induced ERα transcriptional activity. Considering the importance of UBDs in the Ub-based signalling network and the central role of different ERα binding partners in the modulation of E2-dependent effects, our discoveries provide novel insights into ERα activity that could also be relevant for ERα-dependent diseases.

Electromagnetic interference shielding and thermal properties of non-covalently functionalized reduced graphene oxide/epoxy composites

Directory of Open Access Journals (Sweden)

Suman Chhetri

2016-12-01

Full Text Available Graphene oxide (GO was non-covalently functionalized using sulfanilic acid azocromotrop (SAC followed by hydrazine reduction to achieve SAC functionalized reduced GO (SAC-rGO. Fourier transform infrared spectra analysis and electrical conductivity measurements confirmed the successful functionlization and reduction of GO. The electrical conductivity of ~515 S•m−1 for SAC-rGO was recorded. The non-covalently functionalized reduced GO was subsequently dispersed in epoxy matrix at the loading level of 0.3 to 0.5 wt% to investigate its electromagnetic interference (EMI shielding properties. The morphological and structural characterization of the SAC-rGO/epoxy composites was carried out using X-ray diffraction and Transmission electron microscopy analysis, which revealed the good dispersion of SAC-rGO in the epoxy. The SAC-rGO/epoxy composites showed the EMI shielding of −22.6 dB at the loading of 0.5 wt% SAC-rGO. Dynamical mechanical properties of the composites were studied to establish the reinforcing competency of the SAC-rGO. The storage modulus of the composites was found to increase within the studied temperature. Thermal stability of pure epoxy and its composites were compared by selecting the temperatures at 10 and 50% weight loss, respectively.

Stable non-covalent labeling of layered silicate nanoparticles for biological imaging.

Science.gov (United States)

Mortimer, Gysell M; Jack, Kevin S; Musumeci, Anthony W; Martin, Darren J; Minchin, Rodney F

2016-04-01

Layered silicate nanoparticles (LSN) are widely used in industrial applications and consumer products. They also have potential benefits in biomedical applications such as implantable devices and for drug delivery. To study how nanomaterials interact with cells and tissues, techniques to track and quantify their movement through different biological compartments are essential. While radiolabels can be very sensitive, particularly for in vivo studies, fluorescent labeling has been preferred in recent years because of the array of methods available to image and quantify fluorescent nanoparticles. However, labeling can be problematic, especially if it alters the physical properties of the nanomaterial. Herein is described a novel non-covalent labeling technique for LSN using readily available fluorescent dimeric cyanine dyes without the need to use excess amounts of dye to achieve labeling, or the need for removal of unbound dye. The approach utilizes the cationic binding properties of layered silicate clays and the multiple quaternary nitrogens associated with the dyes. Preparation of YOYO-1 labeled LSN with optimal dispersion in aqueous media is presented. The utilization of the labeled particles is then demonstrated in cell binding and uptake studies using flow cytometry and confocal microscopy. The labeled LSN are highly fluorescent, stable and exhibit identical physical properties with respect to the unlabeled nanoparticles. The general approach described here is applicable to other cyanine dyes and may be utilized more widely for labeling nanoparticles that comprise a crystalline plate structure with a high binding capacity. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies

Czech Academy of Sciences Publication Activity Database

Hobza, Pavel

2012-01-01

Roč. 45, č. 4 (2012), s. 663-672 ISSN 0001-4842 R&D Projects: GA ČR GBP208/12/G016 Grant - others:European Social Fund(XE) CZ.1.05/2.1.00/03.0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : non-covalent interactions * covalent interactions * quantum chemical approach Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 20.833, year: 2012

Non-Covalent Organocatalyzed Domino Reactions Involving Oxindoles: Recent Advances

Directory of Open Access Journals (Sweden)

Tecla Gasperi

2017-09-01

Full Text Available The ubiquitous presence of spirooxindole architectures with several functionalities and stereogenic centers in bioactive molecules has been appealing for the development of novel methodologies seeking their preparation in high yields and selectivities. Expansion and refinement in the field of asymmetric organocatalysis have made possible the development of straightforward strategies that address these two requisites. In this review, we illustrate the current state-of-the-art in the field of spirooxindole synthesis through the use of non-covalent organocatalysis. We aim to provide a concise overview of very recent methods that allow to the isolation of unique, densely and diversified spirocyclic oxindole derivatives with high structural diversity via the use of cascade, tandem and domino processes.

Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification.

Science.gov (United States)

van Rooden, Eva J; Florea, Bogdan I; Deng, Hui; Baggelaar, Marc P; van Esbroeck, Annelot C M; Zhou, Juan; Overkleeft, Herman S; van der Stelt, Mario

2018-04-01

Activity-based protein profiling (ABPP) has emerged as a valuable chemical proteomics method to guide the therapeutic development of covalent drugs by assessing their on-target engagement and off-target activity. We recently used ABPP to determine the serine hydrolase interaction landscape of the experimental drug BIA 10-2474, thereby providing a potential explanation for the adverse side effects observed with this compound. ABPP allows mapping of protein interaction landscapes of inhibitors in cells, tissues and animal models. Whereas our previous protocol described quantification of proteasome activity using stable-isotope labeling, this protocol describes the procedures for identifying the in vivo selectivity profile of covalent inhibitors with label-free quantitative proteomics. The optimization of our protocol for label-free quantification methods results in high proteome coverage and allows the comparison of multiple biological samples. We demonstrate our protocol by assessing the protein interaction landscape of the diacylglycerol lipase inhibitor DH376 in mouse brain, liver, kidney and testes. The stages of the protocol include tissue lysis, probe incubation, target enrichment, sample preparation, liquid chromatography-mass spectrometry (LC-MS) measurement, data processing and analysis. This approach can be used to study target engagement in a native proteome and to identify potential off targets for the inhibitor under investigation. The entire protocol takes at least 4 d, depending on the number of samples.

The effect of non-covalent functionalization on the thermal conductance of graphene/organic interfaces

International Nuclear Information System (INIS)

Lin Shangchao; Buehler, Markus J

2013-01-01

The intrinsic interfacial thermal resistance at graphene/organic interfaces, as a result of mismatches in the phonon vibrational spectra of the two materials, diminishes the overall heat transfer performance of graphene/organic nanocomposites. In this paper, we use molecular dynamics (MD) simulations to design alkyl-pyrene molecules that can non-covalently functionalize graphene surfaces in contact with a model organic phase composed of octane. The alkyl-pyrene molecules possess phonon-spectra features of both graphene and octane and, therefore, can serve as phonon-spectra linkers to bridge the vibrational mismatch at the graphene/octane interface. In support of this hypothesis, we find that the best linker candidate can enhance the out-of-plane graphene/organic interfacial thermal conductance by ∼22%, attributed to its capability to compensate the low-frequency phonon mode of graphene. We also find that the length of the alkyl chain indirectly affects the interfacial thermal conductance through different orientations of these chains because they dictate the contribution of the out-of-plane high-frequency carbon–hydrogen bond vibrations to the overall phonon transport. This study advances our understanding of the less destructive non-covalent functionalization method and design principles of suitable linker molecules to enhance the thermal performance of graphene/organic nanocomposites while retaining the intrinsic chemical, thermal, and mechanical properties of pristine graphene. (paper)

Combination of supramolecular cross-linking with covalent cross-linking through epoxide ring-opening including gel studies

NARCIS (Netherlands)

Hofmeier, H.; El-Ghayoury, A.; Schubert, U.S.

2003-01-01

Terpolymers based on poly(methyl methacrylate), containing terpyridinemoieties as well as epoxide groups, were synthesized via free-radical polymerization. The products were cross-linked non-covalently with iron(II) ions and covalently by treatment with AlCl3. Both steps could be combined in

Non-Covalent Functionalisation of C30 Fullerene by Pyrrole-n-Carboxylic Acid (n=2, 3): Density Functional Theory Studies

Science.gov (United States)

Harismah, Kun; Mirzaei, Mahmoud; Ghasemi, Nahid; Nejati, Mohammad

2017-12-01

For functionalisation of a representative C30 fullerene nanostructure by pyrrole-n-carboxylic acid (PnCA; n=2, 3) their stabilities and properties were investigated based on density functional theory calculations. Parallel calculations were also done for C60 fullerene as evidence for comparing the results. Non-covalent interactions are considered to make the functionalised structures. In contrast with the spherical shape of C60, the shape of C30 fullerene is elliptical; therefore, the functionalisation processes were done for both axial and equatorial elliptical positions (AC30 and EC30). The results indicated that both the positions of C30 have almost equivalent chances to be functionalised by PnCA; but functionalisation by P2CA is slightly more favourable than P3CA, either for C60. The illustrated molecular orbitals' distributions indicated that the direction of charge transfer could be considered from PnCA counterparts to fullerene counterparts. The molecular properties indicated more reactivity for C30 than for C60 fullerene. Finally, the atomic scale quadrupole coupling constants indicated different roles for N and O atoms of PnCA in the functionalised models.

Covalent magnetism, exchange interactions and anisotropy of the high temperature layered antiferromagnet MnB₂.

Science.gov (United States)

Khmelevskyi, S; Mohn, P

2012-01-11

The investigation of the electronic structure and magnetism for the compound MnB(2) with crystal structure type AlB(2) has been revisited to resolve contradictions between various experimental and theoretical results present in the literature. We find that MnB(2) exhibits an interesting example of a Kübler's covalent magnetism (Williams et al 1981 J. Appl. Phys. 52 2069). The covalent magnetism also appears to be the source of some disagreement between the calculated values of the magnetic moments and those given by neutron diffraction experiments. We show that this shortcoming is due to the atomic sphere approximation applied in earlier calculations. The application of the disordered local moment approach and the calculation of the inter-atomic exchange interactions within the Liechtenstein formalism reveal strong local moment antiferromagnetism with a high Néel temperature predicted from Monte Carlo simulations. A fully relativistic band structure calculation and then the application of the torque method yields a strong in-plane anisotropy of the Mn magnetic moments. The agreement of these results with neutron diffraction studies rules out any possible weak itinerant electron magnetism scenarios as proposed earlier for MnB(2).

Combination of supramolecular cross-linking with covalent cross-linking through epoxide ring-opening including gel studies

NARCIS (Netherlands)

Hofmeier, H.; El-Ghayoury, A.; Schubert, U.S.

2003-01-01

Terpolymers based on poly(methyl methacrylate), containing terpyridine-moieties as well as epoxide groups, were synthesized via free-radical polymeri-zation. The products were cross-linked non-covalently with iron(II) ions and cova-lently by treatment with AlCl3. Both steps could be combined in

Molecular electrostatic potential analysis of non-covalent complexes

Indian Academy of Sciences (India)

Chemical Sciences and Technology Division and Academy of Scientific & Innovative Research (AcSIR), ... workers proposed the electrostatic-covalent model of hydrogen bonding. ..... tain degree of electron donation and acceptance occurs.

Covalent Organic

DEFF Research Database (Denmark)

Vutti, Surendra

chemistry of silicon, InAs and GaAs materials, covalentsurface functionalization using organosilanes, liquid-phase, and vapor-phasefunctionalizations, diazo-transfer reaction, CuAAC click chemistry, different types ofbiorthogonal chemistries, SPAAC chemistry, and cellular interactions of chemically...... immobilization of D-amino acid adhesion peptideson azide functionalized silicon, GaAs and InAs materials by using CuAAC-click chemistry.The covalent immobilization of penetration peptide (TAT) on gold nanotips of InAs NWs isalso demonstrated.In chapter four, the covalent immobilization of GFP on silicon wafers......, GaAs wafers andGaAs NWs is demonstrated. Series of Fmoc-Pra-OH, NHS-PEG5-NHS and BCN-NHSfunctionalized silicon surfaces has been prepared, whereby GFP-N3 and GFP-bicyclononyneare immobilized by using CuAAC and SPAAC chemistry. The specific and covalentimmobilization of GFP-N3 on bicyclononyne...

A covalent attraction between two molecular cation TTF·~+

Institute of Scientific and Technical Information of China (English)

WANG FangFang; WANG Yi; WANG BingQiang; WANG YinFeng; MA Fang; Li ZhiRu

2009-01-01

The optimized structure of the tetrathiafulvalence radical-cation dimer (TTF·~+-TTF·~+) with all-real frequencies is obtained at MP2/6-311G level,which exhibits the attraction between two molecular cation TTF·~+.The new attraction interaction is a 20-center-2-electron intermolecular covalent π/π bonding with a telescope shape.The covalent π/π bonding has the bonding energy of about-21 kcal·mol~(-1) and is concealed by the Coulombic repulsion between two TTF·~+ cations.This intermolecular covalent attraction also influences the structure of the TTF·~+ subunit,I.e.,its molecular plane is bent by an angle θ=5.6°.This work provides new knowledge on intermolecular interaction.

A covalent attraction between two molecular cation TTF·~+

Institute of Scientific and Technical Information of China (English)

无

2009-01-01

The optimized structure of the tetrathiafulvalence radical-cation dimer(TTF·+-TTF·+) with all-real frequencies is obtained at MP2/6-311G level,which exhibits the attraction between two molecular cation TTF·+.The new attraction interaction is a 20-center-2-electron intermolecular covalent π /π bonding with a telescope shape.The covalent π /π bonding has the bonding energy of about -21 kcal·mol-1 and is concealed by the Coulombic repulsion between two TTF·+ cations.This intermolecular covalent attraction also influences the structure of the TTF·+ subunit,i.e.,its molecular plane is bent by an angle θ=5.6°.This work provides new knowledge on intermolecular interaction.

The rat IgGFcγBP and Muc2 C-terminal domains and TFF3 in two intestinal mucus layers bind together by covalent interaction.

Directory of Open Access Journals (Sweden)

Hao Yu

Full Text Available The secreted proteins from goblet cells compose the intestinal mucus. The aims of this study were to determine how they exist in two intestinal mucus layers.The intestinal mucosa was fixed with Carnoy solution and immunostained. Mucus from the loose layer, the firm layer was gently suctioned or scraped, respectively, lysed in SDS sample buffer with or without DTT, then subjected to the western blotting of rTFF3, rIgGFcγBP or rMuc2. The non-reduced or reduced soluble mucus samples in RIPA buffer were co-immunoprecipitated to investigate their possible interactions. Polyclonal antibodies for rTFF3, the rIgGFcγBP C-terminal domain and the rMuc2 C-terminal domain confirmed their localization in the mucus layer and in the mucus collected from the rat intestinal loose layer or firm layer in both western blot and immunoprecipitation experiments. A complex of rTFF3, which was approximately 250 kDa, and a monomer of 6 kDa were present in both layers of the intestinal mucus; rIgGFcγBP was present in the complex (250-280 kDa under non-reducing conditions, but shifted to 164 kDa under reducing conditions in both of the layers. rMuc2 was found mainly in a complex of 214-270 kDa under non-reducing conditions, but it shifted to 140 kDa under reducing conditions. The co-immunoprecipitation experiments showed that binding occurs among rTFF3, rIgGFcγBP and rMuc2 in the RIPA buffer soluble intestinal mucus. Blocking the covalent interaction by 100 mM DTT in the RIPA buffer soluble intestinal mucus disassociated their binding.Rat goblet cell-secreted TFF3, IgGFcγBP and Muc2, existing in the two intestinal mucus layers, are bound together by covalent interactions in the soluble fraction of intestinal mucus and form heteropolymers to be one of the biochemical mechanisms of composing the net-like structure of mucus.

Covalent interactions of 1,2,3-trichloropropane with hepatic macromolecules: studies in the male F-344 rat.

Science.gov (United States)

Weber, G L; Sipes, I G

1990-07-01

Preliminary investigations into the role of biotransformation in 1,2,3-trichloropropane (TCP)-induced tumor formation have been undertaken. Male F-344 rats were administered 30 mg/kg [14C]TCP (100 microCi/kg) ip and killed 4 hr later. The extent of covalent binding to hepatic protein, DNA, and RNA was 418, 244, and 432 pmol [14C]TCP equivalents/mg, respectively. An in vivo covalent binding time course showed no significant change in [14C]TCP equivalents bound to hepatic DNA (1-48 hr), while binding to protein was maximal by 4 hr and decreased significantly by 48 hr. The binding of TCP-associated radioactivity to hepatic protein and DNA was shown to be cumulative for two and three doses when given 24 hr apart. Pretreatment of animals with phenobarbital caused a decrease while pretreatment with SKF 525-A caused an increase in covalent binding of [14C]TCP equivalents to protein and DNA. Pretreatment of rats with beta-naphthoflavone did not alter the covalent binding of [14C]TCP equivalents to protein or DNA. However, glutathione depletion with L-buthionine-(R,S)-sulfoximine increased binding to protein by 342% while it decreased binding to DNA by 56%. Intraperitoneal administration of TCP also depleted hepatic GSH by 41 and 61% 2 hr after doses of 30 and 100 mg/kg. The in vivo binding data suggest a dual role for GSH in the bioactivation of TCP. It may, in part, be that GSH is involved in the bioactivation and covalent binding of TCP to hepatic DNA. However, it also appears to detoxify a reactive intermediate(s) that binds to protein.

Non-covalent functionalisation of C{sub 30} fullerene by pyrrole-n-carboxylic acid (n=2, 3). Density functional theory studies

Energy Technology Data Exchange (ETDEWEB)

Harismah, Kun [Univ. Muhammadiyah Surakarta (Indonesia). Dept. of Chemical Engineering; Mirzaei, Mahmoud [Isfahan Univ. of Medical Sciences (Iran, Islamic Republic of). Bioinformatics Research Center; Ghasemi, Nahid [Islamic Azad Univ., Arak (Iran, Islamic Republic of). Dept. of Chemistry; Nejati, Mohammad [Islamic Azad Univ., Tehran (Iran, Islamic Republic of). Dept. of Chemistry

2018-04-01

For functionalisation of a representative C{sub 30} fullerene nanostructure by pyrrole-n-carboxylic acid (PnCA; n=2, 3) their stabilities and properties were investigated based on density functional theory calculations. Parallel calculations were also done for C{sub 60} fullerene as evidence for comparing the results. Non-covalent interactions are considered to make the functionalised structures. In contrast with the spherical shape of C{sub 60}, the shape of C{sub 30} fullerene is elliptical; therefore, the functionalisation processes were done for both axial and equatorial elliptical positions (AC{sub 30} and EC{sub 30}). The results indicated that both the positions of C{sub 30} have almost equivalent chances to be functionalised by PnCA; but functionalisation by P2CA is slightly more favourable than P3CA, either for C{sub 60}. The illustrated molecular orbitals' distributions indicated that the direction of charge transfer could be considered from PnCA counterparts to fullerene counterparts. The molecular properties indicated more reactivity for C{sub 30} than for C{sub 60} fullerene. Finally, the atomic scale quadrupole coupling constants indicated different roles for N and O atoms of PnCA in the functionalised models.

Sacrificial spacer and non-covalent routes toward the molecular imprinting of 'poorly-functionalized' N-heterocycles

International Nuclear Information System (INIS)

Kirsch, N.; Alexander, C.; Davies, S.; Whitcombe, M.J.

2004-01-01

A comparison of three different methods for the imprinting of small aromatic heterocycles containing only a single nitrogen atom, for the preparation of specific analytical phases, was carried out. A conventional non-covalent approach to the imprinting of pyridine using methacrylic acid as the functional monomer was compared with two sacrificial spacer methods, in which heterocycles were imprinted as covalent template analogues. The results of binding experiments showed that discrimination based on ligand size was possible when polymers were prepared using a silyl ester-based template. The most selective polymer was able to bind pyridine in preference to quinoline or acridine which is opposite to the trend predicted by the pK HB values for the three ligands. Curve fitting of the isotherm for pyridine binding to this polymer to the Langmuir model gave an approximate K d of 1.1±0.1 mM and a binding site concentration of 57±2 mmol g -1 . Acridine binding did not show saturation behaviour and was non-specific and cooperative in nature

Non-covalently anchored multi-walled carbon nanotubes with hexa-decafluorinated zinc phthalocyanine as ppb level chemiresistive chlorine sensor

Science.gov (United States)

Sharma, Anshul Kumar; Mahajan, Aman; Bedi, R. K.; Kumar, Subodh; Debnath, A. K.; Aswal, D. K.

2018-01-01

A cost effective solution assembly method has been explored for preparing zinc(II)1,2,3,4,8,9,10,11,15,16,17,18,22,23,24,25-hexa-decafluoro-29H,31H-phthalocyanine/multi-walled carbon nanotubes (F16ZnPc/MWCNTs-COOH) hybrid. Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, transmission electron microscopy (TEM) and field emission scanning electron microscopy (FE-SEM) investigations confirm the non-covalent anchoring of F16ZnPc onto MWCNTs-COOH through п-п stacking interactions. Further, a highly sensitive and selective chemiresistive Cl2 sensor has been fabricated using F16ZnPc/MWCNTs-COOH hybrid. The response of sensor is found to be 21.28% for 2 ppm of Cl2 with a response time of 14 s and theoretical detection limit of the sensor is found down to 0.06 ppb. The improved Cl2 sensing characteristics of hybrid are found to be originated from the synergetic interaction between F16ZnPc and MWCNTs-COOH. The underlying mechanism for improved gas sensing performance of F16ZnPc/MWCNTs-COOH sensor towards Cl2 has been explained using Raman, X-ray photoelectron spectroscopy (XPS) and electrochemical impedance spectroscopy (EIS) studies.

Non-covalent Interactions of Graphene with Polycyclic Aromatic Hydrocarbons

NARCIS (Netherlands)

Zygouri, Panagiota; Potsi, Georgia; Mouzourakis, Eleftherios; Spyrou, Konstantinos; Gournis, Dimitrios; Rudolf, Petra

2015-01-01

In this mini review we discuss the interactions of polyaromatic hydrocarbons (PAHs) with graphene and the experimental approaches developed so far to create novel graphene/PAH hybrids and composite systems. The utilization of these systems in electrical, biomedical and polymer-reinforcement

Synthesis of 1D-glyconanomaterials by a hybrid noncovalent-covalent functionalization of single wall carbon nanotubes: a study of their selective interactions with lectins and with live cells

Science.gov (United States)

Pernía Leal, M.; Assali, M.; Cid, J. J.; Valdivia, V.; Franco, J. M.; Fernández, I.; Pozo, D.; Khiar, N.

2015-11-01

To take full advantage of the remarkable applications of carbon nanotubes in different fields, there is a need to develop effective methods to improve their water dispersion and biocompatibility while maintaining their physical properties. In this sense, current approaches suffer from serious drawbacks such as loss of electronic structure together with low surface coverage in the case of covalent functionalizations, or instability of the dynamic hybrids obtained by non-covalent functionalizations. In the present work, we examined the molecular basis of an original strategy that combines the advantages of both functionalizations without their main drawbacks. The hierarchical self-assembly of diacetylenic-based neoglycolipids into highly organized and compacted rings around the nanotubes, followed by photopolymerization leads to the formation of nanotubes covered with glyconanorings with a shish kebab-type topology exposing the carbohydrate ligands to the water phase in a multivalent fashion. The glyconanotubes obtained are fully functional, and able to establish specific interactions with their cognate receptors. In fact, by taking advantage of this selective binding, an easy method to sense lectins as a working model of toxin detection was developed based on a simple analysis of TEM images. Remarkably, different experimental settings to assess cell membrane integrity, cell growth kinetics and cell cycle demonstrated the cellular biocompatibility of the sugar-coated carbon nanotubes compared to pristine single-walled carbon nanotubes.To take full advantage of the remarkable applications of carbon nanotubes in different fields, there is a need to develop effective methods to improve their water dispersion and biocompatibility while maintaining their physical properties. In this sense, current approaches suffer from serious drawbacks such as loss of electronic structure together with low surface coverage in the case of covalent functionalizations, or instability of

Non-covalent functionalization of carbon nanotubes: Controlling Chirality Selectivity via Alkyl Groups of Conjugated Co-Polymers

Science.gov (United States)

Weight, Braden; Gifford, Brendan; Kilina, Svetlana

Carbon nanotubes (CNTs) play an important role in nanotechnology, including electronics, chemical sensors, and solar cells. Their electronic and optical properties depend on the size and geometry (chirality) of the nanotube. However, one main concern regarding nanotube application in optoelectronic devices is the difficulty of separating them based upon chirality after synthesis, as all known synthesis methods produce more than one chirality simultaneously. To get around this, one method is the functionalization of the CNTs via non-covalent bonding of co-polymers by wrapping them around the tube. We use force field simulations to explore the effects of various structural manipulations to the co-polymer 9,9-dialkylfluorenyl-2,7-diyl bipyridine (PFO-BPY) to find the preferential mechanisms of selective interactions between the PFO-BPY and CNTs of various chiralities. In particular, we focus on the effect of the branching in alkyl side-groups of PFO-BPY on their binding to the CNT surface. We have observed correlations between the side-group structures and their wrapping morphology on the CNT-Polymer interactions. Our calculations demonstrate that the branching in the position closest to the conjugated backboned results in the strongest interaction with all CNT. This research was supported by the National Science Foundation (CHE 1413614) and the Center for Computationally-Assisted Science and Technology at NDSU.

Host-Guest Complexes of Cyclodextrins and Nanodiamonds as a Strong Non-Covalent Binding Motif for Self-Assembled Nanomaterials.

Science.gov (United States)

Schibilla, Frauke; Voskuhl, Jens; Fokina, Natalie A; Dahl, Jeremy E P; Schreiner, Peter R; Ravoo, Bart Jan

2017-11-13

We report the inclusion of carboxy- and amine-substituted molecular nanodiamonds (NDs) adamantane, diamantane, and triamantane by β-cyclodextrin and γ-cyclodextrin (β-CD and γ-CD), which have particularly well-suited hydrophobicity and symmetry for an optimal fit of the host and guest molecules. We studied the host-guest interactions in detail and generally observed 1:1 association of the NDs with the larger γ-CD cavity, but observed 1:2 association for the largest ND in the series (triamantane) with β-CD. We found higher binding affinities for carboxy-substituted NDs than for amine-substituted NDs. Additionally, cyclodextrin vesicles (CDVs) were decorated with d-mannose by using adamantane, diamantane, and triamantane as non-covalent anchors, and the resulting vesicles were compared with the lectin concanavalin A in agglutination experiments. Agglutination was directly correlated to the host-guest association: adamantane showed lower agglutination than di- or triamantane with β-CDV and almost no agglutination with γ-CDV, whereas high agglutination was observed for di- and triamantane with γ-CDV. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The non-covalent decoration of self-assembling protein fibers.

Science.gov (United States)

Mahmoud, Zahra N; Grundy, Daniel J; Channon, Kevin J; Woolfson, Derek N

2010-10-01

The design of self-assembling fibers presents challenges in basic science, and has potential for developing materials for applications in areas such as tissue engineering. A contemporary issue in the field is the construction of multi-component, functionalized systems. Previously, we have developed peptide-based fibers, the SAF system, that comprises two complementary peptides, which affords considerable control over assembly and morphology. Here we present a straightforward route to functionalizing the SAFs with small molecules and, subsequently, other moieties. This is achieved via non-covalent recruitment of charged peptide tags, which offers advantages such as further control, reversibility, and future prospects for developing recombinant tags. We demonstrate the concept by appending fluorescent labels and biotin (and thence gold nanoparticles) to the peptides, and visualising the resulting decorated SAFs by light and electron microscopy. The peptide tags bind in the nm-mum range, and show specificity compared with control peptides, and for the SAFs over similar alpha-helix-based peptide fibers. 2010 Elsevier Ltd. All rights reserved.

Crystal Structure of the Dithiol Oxidase DsbA Enzyme from Proteus Mirabilis Bound Non-covalently to an Active Site Peptide Ligand

Science.gov (United States)

Kurth, Fabian; Duprez, Wilko; Premkumar, Lakshmanane; Schembri, Mark A.; Fairlie, David P.; Martin, Jennifer L.

2014-01-01

The disulfide bond forming DsbA enzymes and their DsbB interaction partners are attractive targets for development of antivirulence drugs because both are essential for virulence factor assembly in Gram-negative pathogens. Here we characterize PmDsbA from Proteus mirabilis, a bacterial pathogen increasingly associated with multidrug resistance. PmDsbA exhibits the characteristic properties of a DsbA, including an oxidizing potential, destabilizing disulfide, acidic active site cysteine, and dithiol oxidase catalytic activity. We evaluated a peptide, PWATCDS, derived from the partner protein DsbB and showed by thermal shift and isothermal titration calorimetry that it binds to PmDsbA. The crystal structures of PmDsbA, and the active site variant PmDsbAC30S were determined to high resolution. Analysis of these structures allows categorization of PmDsbA into the DsbA class exemplified by the archetypal Escherichia coli DsbA enzyme. We also present a crystal structure of PmDsbAC30S in complex with the peptide PWATCDS. The structure shows that the peptide binds non-covalently to the active site CXXC motif, the cis-Pro loop, and the hydrophobic groove adjacent to the active site of the enzyme. This high-resolution structural data provides a critical advance for future structure-based design of non-covalent peptidomimetic inhibitors. Such inhibitors would represent an entirely new antibacterial class that work by switching off the DSB virulence assembly machinery. PMID:24831013

Dispersive and Covalent Interactions between Graphene and Metal Surfaces from the Random Phase Approximation

DEFF Research Database (Denmark)

Olsen, Thomas; Yan, Jun; Mortensen, Jens Jørgen

2011-01-01

We calculate the potential energy surfaces for graphene adsorbed on Cu(111), Ni(111), and Co(0001) using density functional theory and the random phase approximation (RPA). For these adsorption systems covalent and dispersive interactions are equally important and while commonly used approximations...... for exchange-correlation functionals give inadequate descriptions of either van der Waals or chemical bonds, RPA accounts accurately for both. It is found that the adsorption is a delicate competition between a weak chemisorption minimum close to the surface and a physisorption minimum further from the surface....

Atomic Covalent Functionalization of Graphene

Science.gov (United States)

Johns, James E.; Hersam, Mark C.

2012-01-01

-dimensional materials with fundamentally different electronic and physical properties. Specifically, we focus on recent studies of the addition of atomic hydrogen, fluorine, and oxygen to the basal plane of graphene. In each of these reactions a high energy, activating step initiates the process, breaking the local π structure and distorting the surrounding lattice. Scanning tunneling microscopy experiments reveal that substrate mediated interactions often dominate when the initial binding event occurs. We then compare these substrate effects with the results of theoretical studies that typically assume a vacuum environment. As the surface coverage increases, clusters often form around the initial distortion, and the stoichiometric composition of the saturated end product depends strongly on both the substrate and reactant species. In addition to these chemical and structural observations, we review how covalent modification can extend the range of physical properties that are achievable in two-dimensional materials. PMID:23030800

Sacrificial spacer and non-covalent routes toward the molecular imprinting of 'poorly-functionalized' N-heterocycles

Energy Technology Data Exchange (ETDEWEB)

Kirsch, N.; Alexander, C.; Davies, S.; Whitcombe, M.J

2004-02-16

A comparison of three different methods for the imprinting of small aromatic heterocycles containing only a single nitrogen atom, for the preparation of specific analytical phases, was carried out. A conventional non-covalent approach to the imprinting of pyridine using methacrylic acid as the functional monomer was compared with two sacrificial spacer methods, in which heterocycles were imprinted as covalent template analogues. The results of binding experiments showed that discrimination based on ligand size was possible when polymers were prepared using a silyl ester-based template. The most selective polymer was able to bind pyridine in preference to quinoline or acridine which is opposite to the trend predicted by the pK{sub HB} values for the three ligands. Curve fitting of the isotherm for pyridine binding to this polymer to the Langmuir model gave an approximate K{sub d} of 1.1{+-}0.1 mM and a binding site concentration of 57{+-}2 mmol g{sup -1}. Acridine binding did not show saturation behaviour and was non-specific and cooperative in nature.

Covalently linked bisporphyrins bearing tetraphenylporphyrin and ...

Indian Academy of Sciences (India)

Covalently linked bisporphyrins bearing tetraphenylporphyrin and perbromoporphyrin units: Synthesis and their properties. Puttaiah Bhyrappa V Krishnan ... yields of the TPP moiety. Electrochemical redox and fluorescence data seem to suggest the possible existence of intramolecular interactions in these bisporphyrins.

Accuracy of the DLPNO-CCSD(T) method for non-covalent bond dissociation enthalpies from coinage metal cation complexes

KAUST Repository

Minenkov, Yury; Chermak, Edrisse; Cavallo, Luigi

2015-01-01

The performance of the domain based local pair-natural orbital coupled-cluster (DLPNO-CCSD(T)) method has been tested to reproduce the experimental gas phase ligand dissociation enthalpy in a series of Cu+, Ag+ and Au+ complexes. For 33 Cu+ - non-covalent ligand dissociation enthalpies all-electron calculations with the same method result in MUE below 2.2 kcal/mol, although a MSE of 1.4 kcal/mol indicates systematic underestimation of the experimental values. Inclusion of scalar relativistic effects for Cu either via effective core potential (ECP) or Douglass-Kroll-Hess Hamiltonian, reduces the MUE below 1.7 kcal/mol and the MSE to -1.0 kcal/mol. For 24 Ag+ - non-covalent ligand dissociation enthalpies the DLPNO-CCSD(T) method results in a mean unsigned error (MUE) below 2.1 kcal/mol and vanishing mean signed error (MSE). For 15 Au+ - non-covalent ligand dissociation enthalpies the DLPNO-CCSD(T) methods provides larger MUE and MSE, equal to 3.2 and 1.7 kcal/mol, which might be related to poor precision of the experimental measurements. Overall, for the combined dataset of 72 coinage metal ion complexes DLPNO-CCSD(T) results in a MUE below 2.2 kcal/mol and an almost vanishing MSE. As for a comparison with computationally cheaper density functional theory (DFT) methods, the routinely used M06 functional results in MUE and MSE equal to 3.6 and -1.7 kca/mol. Results converge already at CC-PVTZ quality basis set, making highly accurate DLPNO-CCSD(T) estimates to be affordable for routine calculations (single-point) on large transition metal complexes of > 100 atoms.

Accuracy of the DLPNO-CCSD(T) method for non-covalent bond dissociation enthalpies from coinage metal cation complexes

KAUST Repository

Minenkov, Yury

2015-08-27

The performance of the domain based local pair-natural orbital coupled-cluster (DLPNO-CCSD(T)) method has been tested to reproduce the experimental gas phase ligand dissociation enthalpy in a series of Cu+, Ag+ and Au+ complexes. For 33 Cu+ - non-covalent ligand dissociation enthalpies all-electron calculations with the same method result in MUE below 2.2 kcal/mol, although a MSE of 1.4 kcal/mol indicates systematic underestimation of the experimental values. Inclusion of scalar relativistic effects for Cu either via effective core potential (ECP) or Douglass-Kroll-Hess Hamiltonian, reduces the MUE below 1.7 kcal/mol and the MSE to -1.0 kcal/mol. For 24 Ag+ - non-covalent ligand dissociation enthalpies the DLPNO-CCSD(T) method results in a mean unsigned error (MUE) below 2.1 kcal/mol and vanishing mean signed error (MSE). For 15 Au+ - non-covalent ligand dissociation enthalpies the DLPNO-CCSD(T) methods provides larger MUE and MSE, equal to 3.2 and 1.7 kcal/mol, which might be related to poor precision of the experimental measurements. Overall, for the combined dataset of 72 coinage metal ion complexes DLPNO-CCSD(T) results in a MUE below 2.2 kcal/mol and an almost vanishing MSE. As for a comparison with computationally cheaper density functional theory (DFT) methods, the routinely used M06 functional results in MUE and MSE equal to 3.6 and -1.7 kca/mol. Results converge already at CC-PVTZ quality basis set, making highly accurate DLPNO-CCSD(T) estimates to be affordable for routine calculations (single-point) on large transition metal complexes of > 100 atoms.

σ-Hole Interactions of Covalently-Bonded Nitrogen, Phosphorus and Arsenic: A Survey of Crystal Structures

Directory of Open Access Journals (Sweden)

Peter Politzer

2014-02-01

Full Text Available Covalently-bonded atoms of Groups IV–VII tend to have anisotropic charge distributions, the electronic densities being less on the extensions of the bonds (σ-holes than in the intervening regions. These σ-holes often give rise to positive electrostatic potentials through which the atom can interact attractively and highly directionally with negative sites (e.g., lone pairs, π electrons and anions, forming noncovalent complexes. For Group VII this is called “halogen bonding” and has been widely studied both computationally and experimentally. For Groups IV–VI, it is only since 2007 that positive σ-holes have been recognized as explaining many noncovalent interactions that have in some instances long been known experimentally. There is considerable experimental evidence for such interactions involving groups IV and VI, particularly in the form of surveys of crystal structures. However we have found less extensive evidence for Group V. Accordingly we have now conducted a survey of the Cambridge Structural Database for crystalline close contacts of trivalent nitrogen, phosphorus and arsenic with six different types of electronegative atoms in neighboring molecules. We have found numerous close contacts that fit the criteria for σ-hole interactions. Some of these are discussed in detail; in two instances, computed molecular electrostatic potentials are presented.

Comparative study on collaborative interaction in non-immersive and immersive systems

Science.gov (United States)

Shahab, Qonita M.; Kwon, Yong-Moo; Ko, Heedong; Mayangsari, Maria N.; Yamasaki, Shoko; Nishino, Hiroaki

2007-09-01

This research studies the Virtual Reality simulation for collaborative interaction so that different people from different places can interact with one object concurrently. Our focus is the real-time handling of inputs from multiple users, where object's behavior is determined by the combination of the multiple inputs. Issues addressed in this research are: 1) The effects of using haptics on a collaborative interaction, 2) The possibilities of collaboration between users from different environments. We conducted user tests on our system in several cases: 1) Comparison between non-haptics and haptics collaborative interaction over LAN, 2) Comparison between non-haptics and haptics collaborative interaction over Internet, and 3) Analysis of collaborative interaction between non-immersive and immersive display environments. The case studies are the interaction of users in two cases: collaborative authoring of a 3D model by two users, and collaborative haptic interaction by multiple users. In Virtual Dollhouse, users can observe physics law while constructing a dollhouse using existing building blocks, under gravity effects. In Virtual Stretcher, multiple users can collaborate on moving a stretcher together while feeling each other's haptic motions.

Non-equilibrium fluctuation-induced interactions

International Nuclear Information System (INIS)

Dean, David S

2012-01-01

We discuss non-equilibrium aspects of fluctuation-induced interactions. While the equilibrium behavior of such interactions has been extensively studied and is relatively well understood, the study of these interactions out of equilibrium is relatively new. We discuss recent results on the non-equilibrium behavior of systems whose dynamics is of the dissipative stochastic type and identify a number of outstanding problems concerning non-equilibrium fluctuation-induced interactions.

CovalentDock Cloud: a web server for automated covalent docking.

Science.gov (United States)

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-07-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

Non-covalent attachment of silver nanoclusters onto single-walled carbon nanotubes with human serum albumin as linking molecule

Energy Technology Data Exchange (ETDEWEB)

Rodríguez-Galván, Andrés, E-mail: andres.rodriguez@nucleares.unam.mx [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito Exterior C.U., 04510 México D.F. (Mexico); Instituto de Física, Dpto. Física Experimental, Universidad Nacional Autónoma de México, Coyoacán, México, DF 04510 (Mexico); Unidad de Investigación Biomédica en Cáncer INCan-UNAM, Instituto Nacional de Cancerología, México, DF 14080 (Mexico); Heredia, Alejandro [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito Exterior C.U., 04510 México D.F. (Mexico); Amelines-Sarria, Oscar; Rivera, Margarita [Instituto de Física, Dpto. Materia Condensada, Universidad Nacional Autónoma de México, Coyoacán, 04510 México D.F. (Mexico); and others

2015-03-15

The attachment of silver nanoclusters (AgNCs) onto single-walled carbon nanotubes (SWNTs) for the formation of integrated fluorescence sites has attracted much attention due their potential applications as biological probes and nanovectors in theragnosis. Here, we report the preparation through assembly of fluorescent quasi 1-D nanomaterial based on SWNTs and silver nanoclusters (AgNCs) non-covalently attached to human serum albumin as biological linker. The fluorescent SWNT–AgNCs–HSA conjugates were characterized by atomic force microscopy, high-resolution transmission electron microscopy (HRTEM), high angle annular dark field scanning TEM (HAADF-STEM), fluorescent and UV–vis spectroscopy. The above techniques confirmed that AgNCs were non-covalently attached onto the external surface of SWNTs. In addition, it was observed that the modification did not affect the optical properties of the synthesized AgNCs since the absorption spectra and fluorescence under UV irradiation (λ = 365 nm) remain the same. The effect of the functionalized systems was tested on mammal red blood cells (RBCs) and it was found that their structural integrity was compromised by the conjugates, limiting their biological and medical applications.

Non-covalent attachment of silver nanoclusters onto single-walled carbon nanotubes with human serum albumin as linking molecule

International Nuclear Information System (INIS)

Rodríguez-Galván, Andrés; Heredia, Alejandro; Amelines-Sarria, Oscar; Rivera, Margarita

2015-01-01

The attachment of silver nanoclusters (AgNCs) onto single-walled carbon nanotubes (SWNTs) for the formation of integrated fluorescence sites has attracted much attention due their potential applications as biological probes and nanovectors in theragnosis. Here, we report the preparation through assembly of fluorescent quasi 1-D nanomaterial based on SWNTs and silver nanoclusters (AgNCs) non-covalently attached to human serum albumin as biological linker. The fluorescent SWNT–AgNCs–HSA conjugates were characterized by atomic force microscopy, high-resolution transmission electron microscopy (HRTEM), high angle annular dark field scanning TEM (HAADF-STEM), fluorescent and UV–vis spectroscopy. The above techniques confirmed that AgNCs were non-covalently attached onto the external surface of SWNTs. In addition, it was observed that the modification did not affect the optical properties of the synthesized AgNCs since the absorption spectra and fluorescence under UV irradiation (λ = 365 nm) remain the same. The effect of the functionalized systems was tested on mammal red blood cells (RBCs) and it was found that their structural integrity was compromised by the conjugates, limiting their biological and medical applications

Review: peripheral nerve regeneration using non-tubular alginate gel crosslinked with covalent bonds.

Science.gov (United States)

Hashimoto, Tadashi; Suzuki, Yoshihisa; Suzuki, Kyoko; Nakashima, Toshihide; Tanihara, Masao; Ide, Chizuka

2005-06-01

We have developed a nerve regeneration material consisting of alginate gel crosslinked with covalent bonds. in the first part of this study, we attempted to analyze nerve regeneration through alginate gel in the early stages within 2 weeks. in the second part, we tried to regenerate cat peripheral nerve by using alginate tubular or non-tubular nerve regeneration devices, and compared their efficacies. Four days after surgery, regenerating axons grew without Schwann cell investment through the partially degraded alginate gel, being in direct contact with the alginate without a basal lamina covering. One to 2 weeks after surgery, regenerating axons were surrounded by common Schwann cells, forming small bundles, with some axons at the periphery being partly in direct contact with alginate. At the distal stump, numerous Schwann cells had migrated into the alginate 8-14 days after surgery. Remarkable restorations of the 50-mm gap in cat sciatic nerve were obtained after a long term by using tubular or non-tubular nerve regeneration material consisting mainly of alginate gel. However, there was no significant difference between both groups at electrophysiological and morphological evaluation. Although, nowadays, nerve regeneration materials being marketed mostly have a tubular structure, our results suggest that the tubular structure is not indispensable for peripheral nerve regeneration.

Covalent bond force profile and cleavage in a single polymer chain

Science.gov (United States)

Garnier, Lionel; Gauthier-Manuel, Bernard; van der Vegte, Eric W.; Snijders, Jaap; Hadziioannou, Georges

2000-08-01

We present here the measurement of the single-polymer entropic elasticity and the single covalent bond force profile, probed with two types of atomic force microscopes (AFM) on a synthetic polymer molecule: polymethacrylic acid in water. The conventional AFM allowed us to distinguish two types of interactions present in this system when doing force spectroscopic measurements: the first interaction is associated with adsorption sites of the polymer chains onto a bare gold surface, the second interaction is directly correlated to the rupture process of a single covalent bond. All these bridging interactions allowed us to stretch the single polymer chain and to determine the various factors playing a role in the elasticity of these molecules. To obtain a closer insight into the bond rupture process, we moved to a force sensor stable in position when measuring attractive forces. By optimizing the polymer length so as to fulfill the elastic stability conditions, we were able for the first time to map out the entire force profile associated with the cleavage of a single covalent bond. Experimental data coupled with molecular quantum mechanical calculations strongly suggest that the breaking bond is located at one end of the polymer chain.

Study on immobilization enzyme using radiation grafting and condensation covalent

International Nuclear Information System (INIS)

Cao Jin; Su Zongxian; Gao Jianfeng

1989-01-01

The immobilization of gluecose oxidase (GOD) on polyethylene and F 46 is described by radiation grafting and condensation covalent. The GOD on polyethylene film is characterized with IR-spectrum. The results show that the enzyme activity on F 46 film is high when dose rate and covalent yield are low. When covalent yield is 4.3% the enzyme relative activity achieves the greatest value for F 46 film. The experiment also demonstrates that acrylic acid affects the relative activity of enzyme and the method of IR-pectrum character is convenient and efficient for GOD on polyethylene film

Covalent Bonding of Pyrrolobenzodiazepines (PBDs) to Terminal Guanine Residues within Duplex and Hairpin DNA Fragments

Science.gov (United States)

Mantaj, Julia; Jackson, Paul J. M.; Karu, Kersti; Rahman, Khondaker M.; Thurston, David E.

2016-01-01

Pyrrolobenzodiazepines (PBDs) are covalent-binding DNA-interactive agents with growing importance as payloads in Antibody Drug Conjugates (ADCs). Until now, PBDs were thought to covalently bond to C2-NH2 groups of guanines in the DNA-minor groove across a three-base-pair recognition sequence. Using HPLC/MS methodology with designed hairpin and duplex oligonucleotides, we have now demonstrated that the PBD Dimer SJG-136 and the C8-conjugated PBD Monomer GWL-78 can covalently bond to a terminal guanine of DNA, with the PBD skeleton spanning only two base pairs. Control experiments with the non-C8-conjugated anthramycin along with molecular dynamics simulations suggest that the C8-substituent of a PBD Monomer, or one-half of a PBD Dimer, may provide stability for the adduct. This observation highlights the importance of PBD C8-substituents, and also suggests that PBDs may bind to terminal guanines within stretches of DNA in cells, thus representing a potentially novel mechanism of action at the end of DNA strand breaks. PMID:27055050

Covalent docking of selected boron-based serine beta-lactamase inhibitors

Science.gov (United States)

Sgrignani, Jacopo; Novati, Beatrice; Colombo, Giorgio; Grazioso, Giovanni

2015-05-01

AmpC β-lactamase is a hydrolytic enzyme conferring resistance to β-lactam antibiotics in multiple Gram-negative bacteria. Therefore, identification of non-β-lactam compounds able to inhibit the enzyme is crucial for the development of novel antibacterial therapies. In general, AmpC inhibitors have to engage the highly solvent-exposed catalytic site of the enzyme. Therefore, understanding the implications of ligand-protein induced-fit and water-mediated interactions behind the inhibitor-enzyme recognition process is fundamental for undertaking structure-based drug design process. Here, we focus on boronic acids, a promising class of beta-lactamase covalent inhibitors. First, we optimized a docking protocol able to reproduce the experimentally determined binding mode of AmpC inhibitors bearing a boronic group. This goal was pursued (1) performing rigid and flexible docking calculations aiming to establish the role of the side chain conformations; and (2) investigating the role of specific water molecules in shaping the enzyme active site and mediating ligand protein interactions. Our calculations showed that some water molecules, conserved in the majority of the considered X-ray structures, are needed to correctly predict the binding pose of known covalent AmpC inhibitors. On this basis, we formalized our findings in a docking and scoring protocol that could be useful for the structure-based design of new boronic acid AmpC inhibitors.

Fabrication of molecular hybrid films of gold nanoparticle and polythiophene by covalent assembly

Energy Technology Data Exchange (ETDEWEB)

Sundaramurthy, Jayaraman, E-mail: jsu2@np.edu.sg [Department of Chemical & Biomolecular Engineering, National University of Singapore, Block E5, 4 Engineering Drive 4, 117576 (Singapore); Environmental & Water Technology Centre of Innovation, Ngee Ann Polytechnic, 599489 (Singapore); Dharmarajan, Rajarathnam [CERAR, University of South Australia, Mawson Lakes, SA 5095 (Australia); Srinivasan, M.P., E-mail: chesmp@nus.edu.sg [Department of Chemical & Biomolecular Engineering, National University of Singapore, Block E5, 4 Engineering Drive 4, 117576 (Singapore)

2015-08-31

This work demonstrates the fabrication of molecular hybrid films comprising gold nanoparticles (AuNPs) incorporated in covalently assembled, substituted polythiophene (poly(3-(2-bromoethoxy)ethoxymethylthiophene-2,5-diyl (PBrEEMT))) films by different surface chemistry routes. AuNPs are incorporated in the immobilized polythiophene matrix due to its affinity for amine and sulfur. The amount of AuNPs present depends on the nature of the incorporation, the extent of film coverage and interaction of thiophene and amine groups. PBrEEMT films functionalized with amine rich polyallylamine immobilize greater numbers of AuNPs due to more extensive gold–amine interactions. Covalent binding between AuNP and PBrEEMT films was accomplished by using pre-functionalised AuNPs (4-aminothiophenol functionalized AuNPs). Atomic force microscopy, field emission scanning electron microscopy and X-ray photoelectron spectroscopy were used to study the morphology and chemical constituents of assembled films. These approaches will pave the way for developing facile methods for nanoparticle incorporation and will also facilitate direct interaction of nanoparticles with the conducting polymer matrix and enhance the electrical properties of the films. - Highlights: • Covalent molecular assembly enabled the fabrication of molecular hybrid films. • Monomeric and polymeric species were employed as intermediate linkers. • Adopted approaches facilitated the direct interaction of gold nanoparticle in films. • The amount of nanoparticle incorporation depended on the extent of film coverage.

Antioxidative activity and emulsifying properties of cuttlefish skin gelatin–tannic acid complex as influenced by types of interaction

NARCIS (Netherlands)

Aewsiri, T.; Benjakul, S.; Visessanguan, W.; Wierenga, P.A.; Gruppen, H.

2010-01-01

The non-covalent interaction between cuttlefish skin gelatin and tannic acid was observed in gelatin modified with unoxidized tannic acid at pH 7, whereas covalent interaction was found in gelatin modified with oxidized tannic acid at pH 9. Degree of tannic acid incorporation into gelatin via

Rooster comb hyaluronate-protein, a non-covalently linked complex.

Science.gov (United States)

Tsiganos, C P; Vynios, D H; Kalpaxis, D L

1986-01-01

Hyaluronate from rooster comb was isolated by ion-exchange chromatography on DEAE-cellulose from tissue extracts and papain digests. The preparations were labelled with [14C]acetic anhydride and subjected to CsCl-density-gradient centrifugation in 4 M-guanidinium chloride in the presence and absence of 4% ZwittergentTM 3-12. A radioactive protein fraction was separated from the hyaluronate when the zwitterionic detergent was also present. The protein could also be separated from the glycosaminoglycan by chromatography on Sepharose CL-6B eluted with the same solvent mixture. The protein fraction contained three protein bands of Mr 15,000-17,000 as assessed by polyacrylamide-gel electrophoresis in 0.1% SDS, and seemed to lack lysozyme activity. No evidence of other protein or amino acid(s) covalently linked with the hyaluronate was obtained. The hyaluronate-protein complex may be re-formed upon mixing the components, the extent of its formation depending on the conditions used. The results show that, as in chondrosarcoma [Mason, d'Arville, Kimura & Hascall (1982) Biochem. J. 207, 445-457] and teratocarcinoma cells [Prehm (1983) Biochem. J. 211, 191-198] the rooster comb hyaluronate also is not linked covalently to a core protein. PMID:3741374

[Noncovalent cation-π interactions--their role in nature].

Science.gov (United States)

Fink, Krzysztof; Boratyński, Janusz

2014-11-07

Non-covalent interactions play an extremely important role in organisms. The main non-covalent interactions in nature are: ion-ion interactions, dipole-dipole interactions, hydrogen bonds, and van der Waals interactions. A new kind of intermolecular interactions--cation-π interactions--is gaining increasing attention. These interactions occur between a cation and a π system. The main contributors to cation-π interactions are electrostatic, polarization and, to a lesser extent, dispersion interactions. At first, cation-π interactions were studied in a gas phase, with metal cation-aromatic system complexes. The characteristics of these complexes are as follows: an increase of cation atomic number leads to a decrease of interaction energy, and an increase of cation charge leads to an increase of interaction energy. Aromatic amino acids bind with metal cations mainly through interactions with their main chain. Nevertheless, cation-π interaction with a hydrophobic side chain significantly enhances binding energy. In water solutions most cations preferentially interact with water molecules rather than aromatic systems. Cation-π interactions occur in environments with lower accessibility to a polar solvent. Cation-π interactions can have a stabilizing role on the secondary, tertiary and quaternary structure of proteins. These interactions play an important role in substrate or ligand binding sites in many proteins, which should be taken into consideration when the screening of effective inhibitors for these proteins is carried out. Cation-π interactions are abundant and play an important role in many biological processes.

Bioelectrochemistry of non-covalent immobilized alcohol dehydrogenase on oxidized diamond nanoparticles.

Science.gov (United States)

Nicolau, Eduardo; Méndez, Jessica; Fonseca, José J; Griebenow, Kai; Cabrera, Carlos R

2012-06-01

Diamond nanoparticles are considered a biocompatible material mainly due to their non-cytotoxicity and remarkable cellular uptake. Model proteins such as cytochrome c and lysozyme have been physically adsorbed onto diamond nanoparticles, proving it to be a suitable surface for high protein loading. Herein, we explore the non-covalent immobilization of the redox enzyme alcohol dehydrogenase (ADH) from Saccharomyces cerevisiae (E.C.1.1.1.1) onto oxidized diamond nanoparticles for bioelectrochemical applications. Diamond nanoparticles were first oxidized and physically characterized by X-ray diffraction (XRD), FT-IR and TEM. Langmuir isotherms were constructed to investigate the ADH adsorption onto the diamond nanoparticles as a function of pH. It was found that a higher packing density is achieved at the isoelectric point of the enzyme. Moreover, the relative activity of the immobilized enzyme on diamond nanoparticles was addressed under optimum pH conditions able to retain up to 70% of its initial activity. Thereafter, an ethanol bioelectrochemical cell was constructed by employing the immobilized alcohol dehydrogenase onto diamond nanoparticles, this being able to provide a current increment of 72% when compared to the blank solution. The results of this investigation suggest that this technology may be useful for the construction of alcohol biosensors or biofuel cells in the near future. Copyright © 2011 Elsevier B.V. All rights reserved.

Carbon dioxide capture using covalent organic frameworks (COFs) type material-a theoretical investigation.

Science.gov (United States)

Dash, Bibek

2018-04-26

The present work deals with a density functional theory (DFT) study of porous organic framework materials containing - groups for CO 2 capture. In this study, first principle calculations were performed for CO 2 adsorption using N-containing covalent organic framework (COFs) models. Ab initio and DFT-based methods were used to characterize the N-containing porous model system based on their interaction energies upon complexing with CO 2 and nitrogen gas. Binding energies (BEs) of CO 2 and N 2 molecules with the polymer framework were calculated with DFT methods. Hybrid B3LYP and second order MP2 methods combined with of Pople 6-31G(d,p) and correlation consistent basis sets cc-pVDZ, cc-pVTZ and aug-ccVDZ were used to calculate BEs. The effect of linker groups in the designed covalent organic framework model system on the CO 2 and N 2 interactions was studied using quantum calculations.

Application of the Covalent Bond Classification Method for the Teaching of Inorganic Chemistry

Science.gov (United States)

Green, Malcolm L. H.; Parkin, Gerard

2014-01-01

The Covalent Bond Classification (CBC) method provides a means to classify covalent molecules according to the number and types of bonds that surround an atom of interest. This approach is based on an elementary molecular orbital analysis of the bonding involving the central atom (M), with the various interactions being classified according to the…

Potent and Selective Covalent Quinazoline Inhibitors of KRAS G12C

Energy Technology Data Exchange (ETDEWEB)

Zeng, Mei; Lu, Jia; Li, Lianbo; Feru, Frederic; Quan, Chunshan; Gero, Thomas W.; Ficarro, Scott B.; Xiong, Yuan; Ambrogio, Chiara; Paranal, Raymond M.; Catalano, Marco; Shao, Jay; Wong, Kwok-Kin; Marto, Jarrod A.; Fischer, Eric S.; Jänne, Pasi A.; Scott, David A.; Westover, Kenneth D.; Gray, Nathanael S. (DFCI); (UTSMC); (Harvard-Med); (NYUSM)

2017-08-01

Targeted covalent small molecules have shown promise for cancers driven by KRAS G12C. Allosteric compounds that access an inducible pocket formed by movement of a dynamic structural element in KRAS, switch II, have been reported, but these compounds require further optimization to enable their advancement into clinical development. We demonstrate that covalent quinazoline-based switch II pocket (SIIP) compounds effectively suppress GTP loading of KRAS G12C, MAPK phosphorylation, and the growth of cancer cells harboring G12C. Notably we find that adding an amide substituent to the quinazoline scaffold allows additional interactions with KRAS G12C, and remarkably increases the labeling efficiency, potency, and selectivity of KRAS G12C inhibitors. Structural studies using X-ray crystallography reveal a new conformation of SIIP and key interactions made by substituents located at the quinazoline 2-, 4-, and 7-positions. Optimized lead compounds in the quinazoline series selectively inhibit KRAS G12C-dependent signaling and cancer cell growth at sub-micromolar concentrations.

Synergistic effect of non-covalent interaction in colloidal nematic liquid crystal doped with magnetic functionalized single-walled carbon nanotubes

Science.gov (United States)

Dalir, Nima; Javadian, Soheila

2018-03-01

Single-walled carbon nanotubes (SWCNTs), CNT@Fe3O4, and Fe3O4 nanocomposites were doped to eutectic uniaxial nematic liquid crystal (NLC's) (E5CN7) to improve physiochemical properties such as phase transition temperature, activation energy (Ea), dielectric anisotropy, and electro-optical properties. The thermal study of nematic phase shows a decrease in the nematic to isotropic phase transition temperature as CNT is doped. However, higher doping concentration of CNTs leads to the further increase in transition temperature. The anchoring effect or π-π interaction plays a key role in N-I phase transition. The functionalization of SWCNTs with Fe3O4 diminishes the CNT aggregation while the magnetic susceptibility is increased. The functionalized CNT doping to NLC's decrease significantly the phase transition temperature compared to doping of non-functionalized CNTs. Attractive interaction between guest and host molecules by magnetic and geometry effect increased the enthalpy and entropy of phase transition in the SWCNT@Fe3O4 sample compared to non-functionalized CNT doped system. Also, the Ea values are decreased as SWCNT@Fe3O4 is doped to pure E5CN7. The difference of N-I phase transition temperature was observed in Fe3O4 and CNT@Fe3O4 compared to SWCNT doped systems. Finally, dielectric anisotropy was increased in the doped system compared to pure NLC.

Detection of free and covalently bound microcystins in animal tissues by liquid chromatography-tandem mass spectrometry

International Nuclear Information System (INIS)

Neffling, Milla-Riina; Lance, Emilie; Meriluoto, Jussi

2010-01-01

Microcystins are cyanobacterial hepatotoxins capable of accumulation into animal tissues. The toxins act by inhibiting specific protein phosphatases and both non-covalent and covalent interactions occur. The 2-methyl-3-methoxy-4-phenylbutyric acid (MMPB) method determines the total, i.e. the sum of free and protein-bound microcystin in tissues. The aim of the method development in this paper was to tackle the problems with the MMPB methodology: the rather laborious workflow and the loss of material during different steps of the method. In the optimised workflow the oxidation recovery was of acceptable level (29-40%), the extraction efficiency good (62-97%), but the signal suppression effect from the matrix remained severe in our system (16-37% signal left). The extraction efficiency for the determination of the free, extractable microcystins, was found to be good, 52-100%, depending on the sample and the toxin variant and concentration. - The study concerns method development for the LC-MS-MS analysis of both free and protein-bound microcystin in tissue materials.

Detection of free and covalently bound microcystins in animal tissues by liquid chromatography-tandem mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Neffling, Milla-Riina, E-mail: mneffling@gmail.co [Department of Biochemistry and Pharmacy, Abo Akademi University, Tykistoekatu 6 A, Biocity 3rd floor, FI-20520, Turku (Finland); Lance, Emilie [UMR CNRS Ecobio 6553, University of Rennes 1, Avenue du General Leclerc, 35042, Rennes Cedex (France); Meriluoto, Jussi [Department of Biochemistry and Pharmacy, Abo Akademi University, Tykistoekatu 6 A, Biocity 3rd floor, FI-20520, Turku (Finland)

2010-03-15

Microcystins are cyanobacterial hepatotoxins capable of accumulation into animal tissues. The toxins act by inhibiting specific protein phosphatases and both non-covalent and covalent interactions occur. The 2-methyl-3-methoxy-4-phenylbutyric acid (MMPB) method determines the total, i.e. the sum of free and protein-bound microcystin in tissues. The aim of the method development in this paper was to tackle the problems with the MMPB methodology: the rather laborious workflow and the loss of material during different steps of the method. In the optimised workflow the oxidation recovery was of acceptable level (29-40%), the extraction efficiency good (62-97%), but the signal suppression effect from the matrix remained severe in our system (16-37% signal left). The extraction efficiency for the determination of the free, extractable microcystins, was found to be good, 52-100%, depending on the sample and the toxin variant and concentration. - The study concerns method development for the LC-MS-MS analysis of both free and protein-bound microcystin in tissue materials.

Introduction to a Protein Interaction System Used for Quantitative Evaluation of Biomolecular Interactions

OpenAIRE

Yamniuk, Aaron

2013-01-01

A central goal of molecular biology is the determination of biomolecular function. This comes largely from a knowledge of the non-covalent interactions that biological small and macro-molecules experience. The fundamental mission of the Molecular Interactions Research Group (MIRG) of the ABRF is to show how solution biophysical tools are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core t...

Non-natural and photo-reactive amino acids as biochemical probes of immune function.

Directory of Open Access Journals (Sweden)

Marta Gómez-Nuñez

Full Text Available Wilms tumor protein (WT1 is a transcription factor selectively overexpressed in leukemias and cancers; clinical trials are underway that use altered WT1 peptide sequences as vaccines. Here we report a strategy to study peptide-MHC interactions by incorporating non-natural and photo-reactive amino acids into the sequence of WT1 peptides. Thirteen WT1 peptides sequences were synthesized with chemically modified amino acids (via fluorination and photo-reactive group additions at MHC and T cell receptor binding positions. Certain new non-natural peptide analogs could stabilize MHC class I molecules better than the native sequences and were also able to elicit specific T-cell responses and sometimes cytotoxicity to leukemia cells. Two photo-reactive peptides, also modified with a biotin handle for pull-down studies, formed covalent interactions with MHC molecules on live cells and provided kinetic data showing the rapid clearance of the peptide-MHC complex. Despite "infinite affinity" provided by the covalent peptide bonding to the MHC, immunogenicity was not enhanced by these peptides because the peptide presentation on the surface was dominated by catabolism of the complex and only a small percentage of peptide molecules covalently bound to the MHC molecules. This study shows that non-natural amino acids can be successfully incorporated into T cell epitopes to provide novel immunological, biochemical and kinetic information.

Unexpected covalency from actinide 5f orbital interactions (An = Th, U, Np, Pu) determined from chlorine K-edge X-ray absorption spectroscopy and electronic structure theory

International Nuclear Information System (INIS)

Clark, D.L.; Batista, E.R.; Boland, K.S.

2010-01-01

We have employed Cl K-edge XAS and multiple levels of sophisticated electronic structure calculations on a series of simple octahedral light actinide (Th, U, Np, Pu) chloride salts, AnCl 6 n- in order to assess the relative roles of the valence 5f and 6d orbitals in chemical bonding. Chlorine K-edge X-ray absorption spectroscopy on AnCl 6 n- (An = Th, U, Np, Pu) systems indicates the presence of covalent interactions between both Cl 3p and An 5f and 6d orbitals, with the relative contributions changing across the series. Electronic structure calculations indicate the predominant covalent interactions are expected to occur through An-Cl bonding via t 1u and t 2u interactions with the An 5f orbitals, and through t 2g and e g interactions with An 6d orbitals. For the Cl K-edge data therefore, we expect bound state transitions from Cl 1s → e g (σ), t 2g (π), and t 1u (σ + π) orbitals. Qualitatively, the Cl K-edge data fulfills these expectations

Temperature Scanning Stress Relaxation of an Autonomous Self-Healing Elastomer Containing Non-Covalent Reversible Network Junctions

Directory of Open Access Journals (Sweden)

Amit Das

2018-01-01

Full Text Available In this work, we report about the mechanical relaxation characteristics of an intrinsically self-healable imidazole modified commercial rubber. This kind of self-healing rubber was prepared by melt mixing of 1-butyl imidazole with bromo-butyl rubber (bromine modified isoprene-isobutylene copolymer, BIIR. By this melt mixing process, the reactive allylic bromine of bromo-butyl rubber was converted into imidazole bromide salt. The resulting development of an ionic character to the polymer backbone leads to an ionic association of the groups which ultimately results to the formation of a network structure of the rubber chains. The modified BIIR thus behaves like a robust crosslinked rubber and shows unusual self-healing properties. The non-covalent reversible network has been studied in detail with respect to stress relaxation experiments, scanning electron microscopic and X-ray scattering.

Non-Covalent Interactions: Complexes of Guanidinium with DNA and RNA Nucleobases

Czech Academy of Sciences Publication Activity Database

Blanco, F.; Kelly, B.; Sanchez-Sanz, Goar; Trujillo, Cristina; Alkorta, I.; Elguero, J.; Rozas, I.

2013-01-01

Roč. 117, č. 39 (2013), s. 11608-11616 ISSN 1520-6106 Grant - others:Seventh Framework Programme of the European Union(XE) FP7-274988 People Institutional support: RVO:61388963 Keywords : molecular -orbital methods * cation-pi interactions * minor-groove binders Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.377, year: 2013

Molecular insight on the non-covalent interactions between carbapenems and uc(l,d)-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study

Science.gov (United States)

Ntombela, Thandokuhle; Fakhar, Zeynab; Ibeji, Collins U.; Govender, Thavendran; Maguire, Glenn E. M.; Lamichhane, Gyanu; Kruger, Hendrik G.; Honarparvar, Bahareh

2018-05-01

Tuberculosis remains a dreadful disease that has claimed many human lives worldwide and elimination of the causative agent Mycobacterium tuberculosis also remains elusive. Multidrug-resistant TB is rapidly increasing worldwide; therefore, there is an urgent need for improving the current antibiotics and novel drug targets to successfully curb the TB burden. uc(l,d)-Transpeptidase 2 is an essential protein in Mtb that is responsible for virulence and growth during the chronic stage of the disease. Both uc(d,d)- and uc(l,d)-transpeptidases are inhibited concurrently to eradicate the bacterium. It was recently discovered that classic penicillins only inhibit uc(d,d)-transpeptidases, while uc(l,d)-transpeptidases are blocked by carbapenems. This has contributed to drug resistance and persistence of tuberculosis. Herein, a hybrid two-layered ONIOM (B3LYP/6-31G+(d): AMBER) model was used to extensively investigate the binding interactions of LdtMt2 complexed with four carbapenems (biapenem, imipenem, meropenem, and tebipenem) to ascertain molecular insight of the drug-enzyme complexation event. In the studied complexes, the carbapenems together with catalytic triad active site residues of LdtMt2 (His187, Ser188 and Cys205) were treated at with QM [B3LYP/6-31+G(d)], while the remaining part of the complexes were treated at MM level (AMBER force field). The resulting Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) for all complexes showed that the carbapenems exhibit reasonable binding interactions towards LdtMt2. Increasing the number of amino acid residues that form hydrogen bond interactions in the QM layer showed significant impact in binding interaction energy differences and the stabilities of the carbapenems inside the active pocket of LdtMt2. The theoretical binding free energies obtained in this study reflect the same trend of the experimental observations. The electrostatic, hydrogen bonding and Van der Waals interactions between the carbapenems and Ldt

Aryloxyalkanoic Acids as Non-Covalent Modifiers of the Allosteric Properties of Hemoglobin

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Abdelsattar M. Omar

2016-08-01

Full Text Available Hemoglobin (Hb modifiers that stereospecifically inhibit sickle hemoglobin polymer formation and/or allosterically increase Hb affinity for oxygen have been shown to prevent the primary pathophysiology of sickle cell disease (SCD, specifically, Hb polymerization and red blood cell sickling. Several such compounds are currently being clinically studied for the treatment of SCD. Based on the previously reported non-covalent Hb binding characteristics of substituted aryloxyalkanoic acids that exhibited antisickling properties, we designed, synthesized and evaluated 18 new compounds (KAUS II series for enhanced antisickling activities. Surprisingly, select test compounds showed no antisickling effects or promoted erythrocyte sickling. Additionally, the compounds showed no significant effect on Hb oxygen affinity (or in some cases, even decreased the affinity for oxygen. The X-ray structure of deoxygenated Hb in complex with a prototype compound, KAUS-23, revealed that the effector bound in the central water cavity of the protein, providing atomic level explanations for the observed functional and biological activities. Although the structural modification did not lead to the anticipated biological effects, the findings provide important direction for designing candidate antisickling agents, as well as a framework for novel Hb allosteric effectors that conversely, decrease the protein affinity for oxygen for potential therapeutic use for hypoxic- and/or ischemic-related diseases.

Non-Covalent Fluorescent Labeling of Hairpin DNA Probe Coupled with Hybridization Chain Reaction for Sensitive DNA Detection.

Science.gov (United States)

Song, Luna; Zhang, Yonghua; Li, Junling; Gao, Qiang; Qi, Honglan; Zhang, Chengxiao

2016-04-01

An enzyme-free signal amplification-based assay for DNA detection was developed using fluorescent hairpin DNA probes coupled with hybridization chain reaction (HCR). The hairpin DNAs were designed to contain abasic sites in the stem moiety. Non-covalent labeling of the hairpin DNAs was achieved when a fluorescent ligand was bound to the abasic sites through hydrogen bonding with the orphan cytosine present on the complementary strand, accompanied by quench of ligand fluorescence. As a result, the resultant probes, the complex formed between the hairpin DNA and ligand, showed almost no fluorescence. Upon hybridization with target DNA, the probe underwent a dehybridization of the stem moiety containing an abasic site. The release of ligand from the abasic site to the solution resulted in an effective fluorescent enhancement, which can be used as a signal. Compared with a sensing system without HCR, a 20-fold increase in the sensitivity was achieved using the sensing system with HCR. The fluorescent intensity of the sensing system increased with the increase in target DNA concentration from 0.5 nM to 100 nM. A single mismatched target ss-DNA could be effectively discriminated from complementary target DNA. Genotyping of a G/C single-nucleotide polymorphism of polymerase chain reaction (PCR) products was successfully demonstrated with the sensing system. Therefore, integrating HCR strategy with non-covalent labeling of fluorescent hairpin DNA probes provides a sensitive and cost-effective DNA assay. © The Author(s) 2016.

Self-Healing Supramolecular Hydrogels Based on Reversible Physical Interactions

Directory of Open Access Journals (Sweden)

Satu Strandman

2016-04-01

Full Text Available Dynamic and reversible polymer networks capable of self-healing, i.e., restoring their mechanical properties after deformation and failure, are gaining increasing research interest, as there is a continuous need towards extending the lifetime and improving the safety and performance of materials particularly in biomedical applications. Hydrogels are versatile materials that may allow self-healing through a variety of covalent and non-covalent bonding strategies. The structural recovery of physical gels has long been a topic of interest in soft materials physics and various supramolecular interactions can induce this kind of recovery. This review highlights the non-covalent strategies of building self-repairing hydrogels and the characterization of their mechanical properties. Potential applications and future prospects of these materials are also discussed.

Effect of density variation and non-covalent functionalization on the compressive behavior of carbon nanotube arrays

Energy Technology Data Exchange (ETDEWEB)

Misra, A [Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012 (India); Raney, J R; Craig, A E; Daraio, C, E-mail: daraio@caltech.edu [Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125 (United States)

2011-10-21

Arrays of aligned carbon nanotubes (CNTs) have been proposed for different applications, including electrochemical energy storage and shock-absorbing materials. Understanding their mechanical response, in relation to their structural characteristics, is important for tailoring the synthesis method to the different operational conditions of the material. In this paper, we grow vertically aligned CNT arrays using a thermal chemical vapor deposition system, and we study the effects of precursor flow on the structural and mechanical properties of the CNT arrays. We show that the CNT growth process is inhomogeneous along the direction of the precursor flow, resulting in varying bulk density at different points on the growth substrate. We also study the effects of non-covalent functionalization of the CNTs after growth, using surfactant and nanoparticles, to vary the effective bulk density and structural arrangement of the arrays. We find that the stiffness and peak stress of the materials increase approximately linearly with increasing bulk density.

Inorganic Materials as Supports for Covalent Enzyme Immobilization: Methods and Mechanisms

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Paolo Zucca

2014-09-01

Full Text Available Several inorganic materials are potentially suitable for enzymatic covalent immobilization, by means of several different techniques. Such materials must meet stringent criteria to be suitable as solid matrices: complete insolubility in water, reasonable mechanical strength and chemical resistance under the operational conditions, the capability to form manageable particles with high surface area, reactivity towards derivatizing/functionalizing agents. Non-specific protein adsorption should be always considered when planning covalent immobilization on inorganic solids. A huge mass of experimental work has shown that silica, silicates, borosilicates and aluminosilicates, alumina, titania, and other oxides, are the materials of choice when attempting enzyme immobilizations on inorganic supports. More recently, some forms of elemental carbon, silicon, and certain metals have been also proposed for certain applications. With regard to the derivatization/functionalization techniques, the use of organosilanes through silanization is undoubtedly the most studied and the most applied, although inorganic bridge formation and acylation with selected acyl halides have been deeply studied. In the present article, the most common inorganic supports for covalent immobilization of the enzymes are reviewed, with particular focus on their advantages and disadvantages in terms of enzyme loadings, operational stability, undesired adsorption, and costs. Mechanisms and methods for covalent immobilization are also discussed, focusing on the most widespread activating approaches (such as glutaraldehyde, cyanogen bromide, divinylsulfone, carbodiimides, carbonyldiimidazole, sulfonyl chlorides, chlorocarbonates, N-hydroxysuccinimides.

Isoelectric focusing of small non-covalent metal species from plants.

Science.gov (United States)

Köster, Jessica; Hayen, Heiko; von Wirén, Nicolaus; Weber, Günther

2011-03-01

IEF is known as a powerful electrophoretic separation technique for amphoteric molecules, in particular for proteins. The objective of the present work is to prove the suitability of IEF also for the separation of small, non-covalent metal species. Investigations are performed with copper-glutathione complexes, with the synthetic ligand ethylenediamine-N,N'-bis(o-hydroxyphenyl)acetic acid (EDDHA) and respective metal complexes (Fe, Ga, Al, Ni, Zn), and with the phytosiderophore 2'-deoxymugineic acid (DMA) and its ferric complex. It is shown that ethylenediamine-N,N'-bis(o-hydroxyphenyl)acetic acid and DMA species are stable during preparative scale IEF, whereas copper-glutathione dissociates considerably. It is also shown that preparative scale IEF can be applied successfully to isolate ferric DMA from real plant samples, and that multidimensional separations are possible by combining preparative scale IEF with subsequent HPLC-MS analysis. Focusing of free ligands and respective metal complexes with di- and trivalent metals results in different pIs, but CIEF is usually needed for a reliable estimation of pI values. Limitations of the proposed methods (preparative IEF and CIEF) and consequences of the results with respect to metal speciation in plants are discussed. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Meta-study of musicians' non-verbal interaction

DEFF Research Database (Denmark)

Jensen, Karl Kristoffer; Marchetti, Emanuela

2010-01-01

interruptions. Hence, despite the fact that the skill to engage in a non-verbal interaction is described as tacit knowledge, it is fundamental for both musicians and teachers (Davidson and Good 2002). Typical observed non-verbal cues are for example: physical gestures, modulations of sound, steady eye contact...

Electron population uncertainty and atomic covalency

International Nuclear Information System (INIS)

Chesnut, D.B.

2006-01-01

The atoms-in-molecules (AIM) index of atomic covalency is directly related to the AIM atomic population uncertainty. The covalent bond order, delocalization index, and, therefore, the atomic covalency are maximal when electron pairs are equally shared by the atoms involved. When polarization effects are present, these measures of covalent bond character decrease. We present atomic covalences for the single- and double-heavy atom hydrides of elements of the first and second low rows of the periodic table to illustrate these effects. Some usual behavior is seen in hydrogen-bridged species due in some cases to stronger than expected multicenter bonds and in other cases to many atoms contributing to the covalency index

Quantum chemical investigation of attractive non-covalent interactions between halomethanes and rare gases.

Science.gov (United States)

McAllister, Linda J; Bruce, Duncan W; Karadakov, Peter B

2012-11-01

The interaction between rare gas atoms and trifluoromethylhalides and iodomethane is investigated using ab initio and density functional theory (DFT) methods: MP2, CCSD, B3LYP, M06, M06-L, M06-2X, M06-HF, X3LYP, PBE, B97-D, B3LYP-D3, and M06-L-D3, in combination with the aug-cc-pVTZ and aug-cc-pVTZ-PP basis sets. A weakly attractive interaction is observed for all complexes, whose strength increases as the rare gas and halogen bond donor become more polarizable, and as the group bound to the halogen bond donor becomes more electron-withdrawing. The separation between iodine and krypton in the complex CF(3)I···Kr, calculated at the MP2 and B3LYP-D3 levels of theory, agrees very well with recent experimental results (Stephens, S. L.; Walker, N. R.; Legon, A. C. J. Chem. Phys. 2011, 135, 224309). Analysis of the ability of theoretical methods to account for the dispersion interaction present in these complexes leads to the conclusion that MP2 and B3LYP-D3, which produce very similar results, are the better performing methods, followed by B97-D and the M06 suite of functionals; the popular B3LYP as well as X3LYP perform poorly and significantly underestimate the interaction strength. The orbitals responsible for the interaction are identified through Edmiston-Ruedenberg localization; it is shown that, by combining the key orbitals, it is possible to observe a molecular orbital picture of a σ-hole interaction.

The Role of Wheat and Egg Constituents in the Formation of a Covalent and Non-covalent Protein Network in Fresh and Cooked Egg Noodles.

Science.gov (United States)

Lambrecht, Marlies A; Rombouts, Ine; Nivelle, Mieke A; Delcour, Jan A

2017-01-01

Noodles of constant protein content and flour-to-egg protein ratio were made with whole egg, egg white, or egg yolk. The optimal cooking time, water absorption, and cooking loss of salted whole egg noodles was respectively lower and higher than of egg white and egg yolk noodles. However, cooked whole egg noodles showed the best Kieffer-rig extensibility. Differences in noodle properties were linked to protein network formation. Disulfide bonds in whole egg noodles developed faster and to a larger extent during cooking than in egg yolk noodles but slower and to a lower extent than in egg white noodles. The balance between the rate of protein cross-linking and starch swelling determines cooked noodle properties. Ionic and hydrophobic protein interactions increase the optimum cooking time and total work in Kieffer-rig extensibility testing of fresh noodles. Hydrogen bonds and covalent cross-links are probably the main determinants of the extensibility of cooked noodles. © 2016 Institute of Food Technologists®.

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

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Shunichi Kosugi

Full Text Available Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in 'targeted' alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/.

Dislocations in materials with mixed covalent and metallic bonding

International Nuclear Information System (INIS)

Nguyen-Manh, D.; Cawkwell, M.J.; Groeger, R.; Mrovec, M.; Porizek, R.; Pettifor, D.G.; Vitek, V.

2005-01-01

Environment-dependent bond-order potentials have been developed for L1 0 TiAl, bcc Mo and fcc Ir. They comprise both the angular character of bonding and the screening effect of nearly free electrons. These potentials have been employed in atomistic studies of screw dislocations that revealed the non-planar character of their cores. It is argued that both covalent as well as metallic character of bonding govern these structures, which in turn control the mechanical behaviour

Water-soluble light-emitting nanoparticles prepared by non-covalent bond self-assembly of a hydroxyl group functionalized oligo(p-phenyleneethynylene) with different water-soluble polymers

Institute of Scientific and Technical Information of China (English)

无

2010-01-01

Water-soluble light-emitting nanoparticles were prepared from hydroxyl group functionalized oligos(p-phenyleneethynylene) (OHOPEL) and water-soluble polymers(PEG,PAA,and PG) by non-covalent bond self-assembly.Their structure and optoelectronic properties were investigated through dynamic light scattering(DLS) ,UV and PL spectroscopy.The optical properties of OHOPEL-based water-soluble nanoparticles exhibited the same properties as that found in OHOPEL films,indicating the existence of interchain-aggregation of OHOPELs in the nanoparticles.OHOPEL-based nanoparticles prepared from conjugated oligomers show smaller size and lower dispersity than nanoparticles from conjugated polymers,which means that the structures of water-soluble nanoparticles are linked to the conjugated length.Furthermore,the OHOPEL/PG and OHOPEL/PAA systems produced smaller particles and lower polydispersity than the OHOPEL/PEG system,indicating that there may exist influence of the strength of non-covalent bonds on the size and degree of dispersity of the nanoparticles.

Detection of free and covalently bound microcystins in animal tissues by liquid chromatography-tandem mass spectrometry.

Science.gov (United States)

Neffling, Milla-Riina; Lance, Emilie; Meriluoto, Jussi

2010-03-01

Microcystins are cyanobacterial hepatotoxins capable of accumulation into animal tissues. The toxins act by inhibiting specific protein phosphatases and both non-covalent and covalent interactions occur. The 2-methyl-3-methoxy-4-phenylbutyric acid (MMPB) method determines the total, i.e. the sum of free and protein-bound microcystin in tissues. The aim of the method development in this paper was to tackle the problems with the MMPB methodology: the rather laborious workflow and the loss of material during different steps of the method. In the optimised workflow the oxidation recovery was of acceptable level (29-40%), the extraction efficiency good (62-97%), but the signal suppression effect from the matrix remained severe in our system (16-37% signal left). The extraction efficiency for the determination of the free, extractable microcystins, was found to be good, 52-100%, depending on the sample and the toxin variant and concentration. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

Binding matter with antimatter: the covalent positron bond.

Science.gov (United States)

Charry, Jorge Alfonso; Varella, Marcio T Do N; Reyes, Andrés

2018-05-16

We report sufficient theoretical evidence of the energy stability of the e⁺H₂²⁻ molecule, formed by two H⁻ anions and one positron. Analysis of the electronic and positronic densities of the latter compound undoubtedly points out the formation of a positronic covalent bond between the otherwise repelling hydride anions. The lower limit for the bonding energy of the e⁺H₂²⁻ molecule is 74 kJ/mol (0.77 eV), accounting for the zero-point vibrational correction. The formation of a non electronic covalent bond is fundamentally distinct from positron attachment to stable molecules, as the latter process is characterized by a positron affinity, analogous to the electron affinity. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A non-covalent peptide-based strategy for ex vivo and in vivo oligonucleotide delivery.

Science.gov (United States)

Crombez, Laurence; Morris, May C; Heitz, Frederic; Divita, Gilles

2011-01-01

The dramatic acceleration in identification of new nucleic acid-based therapeutic molecules such as short interfering RNA (siRNA) and peptide-nucleic acid (PNA) analogues has provided new perspectives for therapeutic targeting of specific genes responsible for pathological disorders. However, the poor cellular uptake of nucleic acids together with the low permeability of the cell membrane to negatively charged molecules remain major obstacles to their clinical development. Several non-viral strategies have been proposed to improve the delivery of synthetic short oligonucleotides both in cultured cells and in vivo. Cell-penetrating peptides constitute very promising tools for non-invasive cellular import of oligonucleotides and analogs. We recently described a non-covalent strategy based on short amphiphatic peptides (MPG8/PEP3) that have been successfully applied ex vivo and in vivo for the delivery of therapeutic siRNA and PNA molecules. PEP3 and MPG8 form stable nanoparticles with PNA analogues and siRNA, respectively, and promote their efficient cellular uptake, independently of the endosomal pathway, into a wide variety of cell lines, including primary and suspension lines, without any associated cytotoxicity. This chapter describes easy-to-handle protocols for the use of MPG-8 or PEP-3-nanoparticle technologies for PNA and siRNA delivery into adherent and suspension cell lines as well as in vivo into cancer mouse models.

Hydrophobic and electrostatic interactions between cell penetrating peptides and plasmid DNA are important for stable non-covalent complexation and intracellular delivery.

Science.gov (United States)

Upadhya, Archana; Sangave, Preeti C

2016-10-01

Cell penetrating peptides are useful tools for intracellular delivery of nucleic acids. Delivery of plasmid DNA, a large nucleic acid, poses a challenge for peptide mediated transport. The paper investigates and compares efficacy of five novel peptide designs for complexation of plasmid DNA and subsequent delivery into cells. The peptides were designed to contain reported DNA condensing agents and basic cell penetrating sequences, octa-arginine (R 8 ) and CHK 6 HC coupled to cell penetration accelerating peptides such as Bax inhibitory mutant peptide (KLPVM) and a peptide derived from the Kaposi fibroblast growth factor (kFGF) membrane translocating sequence. A tryptophan rich peptide, an analogue of Pep-3, flanked with CH 3 on either ends was also a part of the study. The peptides were analysed for plasmid DNA complexation, protection of peptide-plasmid DNA complexes against DNase I, serum components and competitive ligands by simple agarose gel electrophoresis techniques. Hemolysis of rat red blood corpuscles (RBCs) in the presence of the peptides was used as a measure of peptide cytotoxicity. Plasmid DNA delivery through the designed peptides was evaluated in two cell lines, human cervical cancer cell line (HeLa) and (NIH/3 T3) mouse embryonic fibroblasts via expression of the secreted alkaline phosphatase (SEAP) reporter gene. The importance of hydrophobic sequences in addition to cationic sequences in peptides for non-covalent plasmid DNA complexation and delivery has been illustrated. An alternative to the employment of fatty acid moieties for enhanced gene transfer has been proposed. Comparison of peptides for plasmid DNA complexation and delivery of peptide-plasmid DNA complexes to cells estimated by expression of a reporter gene, SEAP. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

A theoretical study of adsorbate-adsorbate interactions on Ru(0001)

DEFF Research Database (Denmark)

Mortensen, Jens Jørgen; Hammer, Bjørk; Nørskov, Jens Kehlet

1998-01-01

the barrier for dissociation, whereas S will increase it. The interaction with alkali atoms is mainly of an electrostatic nature. The poisoning by S is due to two kinds of repulsive interactions: a Pauli repulsion and a reduced covalent bond strength between the adsorbate and the surface d-electrons. In order...... to investigate these different interactions in more detail, we look at three different species (N atoms, and terminally bonded N(2) and CO) and use them as probes to study their interaction with two modifier atoms (Na and S). The two modifier atoms have very different properties, which allows us to decouple...

Multiscale Study of Hydrogen Adsorption on Six Designed Covalent Organic Frameworks Based on Porphyrazine, Cyclobutane and Scandium

International Nuclear Information System (INIS)

Li Le-Le; Gao Teng-Fei; Zhang Ruan-Yu; Zhang Hong

2014-01-01

The first-principles method of hydrogen adsorption is used to investigate the interaction of H_2 with the scandium-porphyrazine (Sc-Pz) and porphyrazine (Pz) clusters. The result shows that the interaction of H_2 with Sc-Pz is stronger than with Pz. Then grand canonical Monte Carlo simulations are used to investigate hydrogen adsorption in six designed covalent organic frameworks (COFs), which are designed based on porphyrazine, cyclobutane and scandium. When the pressure is from 0.1 to 100 bar and the temperature is 298 K and 77 K, the hydrogen adsorption capacities of the six COFs are calculated. We further study the importance of Sc and fillers to improve the H_2 uptake in the modified COFs by analyzing the isosteric heat of hydrogen adsorption. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Tissue Plasminogen Activator Binding to Superparamagnetic Iron Oxide Nanoparticle—Covalent Versus Adsorptive Approach

Science.gov (United States)

Friedrich, Ralf P.; Zaloga, Jan; Schreiber, Eveline; Tóth, Ildikó Y.; Tombácz, Etelka; Lyer, Stefan; Alexiou, Christoph

2016-06-01

Functionalized superparamagnetic iron oxide nanoparticles are frequently used to develop vehicles for drug delivery, hyperthermia, and photodynamic therapy and as tools used for magnetic separation and purification of proteins or for biomolecular imaging. Depending on the application, there are various possible covalent and non-covalent approaches for the functionalization of particles, each of them shows different advantages and disadvantages for drug release and activity at the desired location.

Surface functionalization of PLGA nanoparticles by non-covalent insertion of a homo-bifunctional spacer for active targeting in cancer therapy

Energy Technology Data Exchange (ETDEWEB)

Thamake, S I; Raut, S L [Department of Biomedical Sciences, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX 76107 (United States); Ranjan, A P; Vishwanatha, J K [Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, TX 76107 (United States); Gryczynski, Z, E-mail: jamboor.vishwanatha@unthsc.edu [Center for Commercialization of Fluorescence Technology, University of North Texas Health Science Center, Fort Worth, TX 76107 (United States)

2011-01-21

This work reports the surface functionalization of polymeric PLGA nanoparticles by non-covalent insertion of a homo-bifunctional chemical crosslinker, bis(sulfosuccinimidyl) suberate (BS3) for targeted cancer therapy. We dissolved BS3 in aqueous solution of PVA during formulation of nanoparticles by a modified solid/oil/water emulsion solvent evaporation method. The non-covalent insertion of BS3 was confirmed by Fourier transform infrared (FTIR) spectroscopy. Curcumin and annexin A2 were used as a model drug and a cell specific target, respectively. Nanoparticles were characterized for particle size, zeta potential and surface morphology. The qualitative assessment of antibody attachment was performed by transmission electron microscopy (TEM) as well as confocal microscopy. The optimized formulation showed antibody attachment of 86%. However, antibody attachment was abolished upon blocking the functional groups of BS3. The availability of functional antibodies was evaluated by the presence of a light chain fraction after gel electrophoresis. We further evaluated the in vitro release kinetics of curcumin from antibody coated and uncoated nanoparticles. The release of curcumin is enhanced upon antibody attachment and followed an anomalous release pattern. We also observed that the cellular uptake of nanoparticles was significantly higher in annexin A2 positive cells than in negative cells. Therefore, these results demonstrate the potential use of this method for functionalization as well as to deliver chemotherapeutic agents for treating cancer.

Surface functionalization of PLGA nanoparticles by non-covalent insertion of a homo-bifunctional spacer for active targeting in cancer therapy

Science.gov (United States)

Thamake, S. I.; Raut, S. L.; Ranjan, A. P.; Gryczynski, Z.; Vishwanatha, J. K.

2011-01-01

This work reports the surface functionalization of polymeric PLGA nanoparticles by non-covalent insertion of a homo-bifunctional chemical crosslinker, bis(sulfosuccinimidyl) suberate (BS3) for targeted cancer therapy. We dissolved BS3 in aqueous solution of PVA during formulation of nanoparticles by a modified solid/oil/water emulsion solvent evaporation method. The non-covalent insertion of BS3 was confirmed by Fourier transform infrared (FTIR) spectroscopy. Curcumin and annexin A2 were used as a model drug and a cell specific target, respectively. Nanoparticles were characterized for particle size, zeta potential and surface morphology. The qualitative assessment of antibody attachment was performed by transmission electron microscopy (TEM) as well as confocal microscopy. The optimized formulation showed antibody attachment of 86%. However, antibody attachment was abolished upon blocking the functional groups of BS3. The availability of functional antibodies was evaluated by the presence of a light chain fraction after gel electrophoresis. We further evaluated the in vitro release kinetics of curcumin from antibody coated and uncoated nanoparticles. The release of curcumin is enhanced upon antibody attachment and followed an anomalous release pattern. We also observed that the cellular uptake of nanoparticles was significantly higher in annexin A2 positive cells than in negative cells. Therefore, these results demonstrate the potential use of this method for functionalization as well as to deliver chemotherapeutic agents for treating cancer.

Covalent modification and exfoliation of graphene oxide using ferrocene

Science.gov (United States)

Avinash, M. B.; Subrahmanyam, K. S.; Sundarayya, Y.; Govindaraju, T.

2010-09-01

Large scale preparation of single-layer graphene and graphene oxide is of great importance due to their potential applications. We report a simple room temperature method for the exfoliation of graphene oxide using covalent modification of graphene oxide with ferrocene to obtain single-layer graphene oxide sheets. The samples were characterized by FESEM, HRTEM, AFM, EDAX, FT-IR, Raman and Mössbauer spectroscopic studies. HRTEM micrograph of the covalently modified graphene oxide showed increased interlayer spacing of ~2.4 nm due to ferrocene intercalation. The presence of single-layer graphene oxide sheets were confirmed by AFM studies. The covalently modified ferrocene-graphene oxide composite showed interesting magnetic behavior.Large scale preparation of single-layer graphene and graphene oxide is of great importance due to their potential applications. We report a simple room temperature method for the exfoliation of graphene oxide using covalent modification of graphene oxide with ferrocene to obtain single-layer graphene oxide sheets. The samples were characterized by FESEM, HRTEM, AFM, EDAX, FT-IR, Raman and Mössbauer spectroscopic studies. HRTEM micrograph of the covalently modified graphene oxide showed increased interlayer spacing of ~2.4 nm due to ferrocene intercalation. The presence of single-layer graphene oxide sheets were confirmed by AFM studies. The covalently modified ferrocene-graphene oxide composite showed interesting magnetic behavior. Electronic supplementary information (ESI) available: Magnetic data; AFM images; TEM micrographs; and Mössbauer spectroscopic data. See DOI: 10.1039/c0nr00024h

Surface Modification of Carbon Nanotubes with Conjugated Polyelectrolytes: Fundamental Interactions and Applications in Composite Materials, Nanofibers, Electronics, and Photovoltaics

KAUST Repository

Ezzeddine, Alaa

2015-10-01

Ever since their discovery, Carbon nanotubes (CNTs) have been renowned to be potential candidates for a variety of applications. Nevertheless, the difficulties accompanied with their dispersion and poor solubility in various solvents have hindered CNTs potential applications. As a result, studies have been developed to address the dispersion problem. The solution is in modifying the surfaces of the nanotubes covalently or non-covalently with a desired dispersant. Various materials have been employed for this purpose out of which polymers are the most common. Non-covalent functionalization of CNTs via polymer wrapping represents an attractive method to obtain a stable and homogenous CNTs dispersion. This method is able to change the surface properties of the nanotubes without destroying their intrinsic structure and preserving their properties. This thesis explores and studies the surface modification and solublization of pristine single and multiwalled carbon nanotubes via a simple solution mixing technique through non-covalent interactions of CNTs with various anionic and cationic conjugated polyelectrolytes (CPEs). The work includes studying the interaction of various poly(phenylene ethynylene) electrolytes with MWCNTs and an imidazolium functionalized poly(3-hexylthiophene) with SWCNTs. Our work here focuses on the noncovalent modifications of carbon nanotubes using novel CPEs in order to use these resulting CPE/CNT complexes in various applications. Upon modifying the CNTs with the CPEs, the resulting CPE/CNT complex has been proven to be easily dispersed in various organic and aqueous solution with excellent homogeneity and stability for several months. This complex was then used as a nanofiller and was dispersed in another polymer matrix (poly(methyl methacrylate), PMMA). The PMMA/CPE/CNT composite materials were cast or electrospun depending on their desired application. The presence of the CPE modified CNTs in the polymer matrix has been proven to enhance

Interactions of hemin with bovine serum albumin and human hemoglobin: A fluorescence quenching study

Science.gov (United States)

Makarska-Bialokoz, Magdalena

2018-03-01

The binding interactions between hemin (Hmi) and bovine serum albumin (BSA) or human hemoglobin (HHb), respectively, have been examined in aqueous solution at pH = 7.4, applying UV-vis absorption, as well as steady-state, synchronous and three-dimensional fluorescence spectra techniques. Representative results received for both BSA and HHb intrinsic fluorescence proceeding from the interactions with hemin suggest the formation of stacking non-covalent and non-fluorescent complexes in both the Hmi-BSA and Hmi-HHb systems, with highly possible concurrent formation of a coordinate bond between a group on the protein surface and the metal in Hmi molecule. All the values of calculated parameters, the binding, fluorescence quenching and bimolecular quenching rate constants point to the involvement of static quenching in both the systems studied. The blue shift in the synchronous fluorescence spectra imply the participation of both tryptophan and tyrosine residues in quenching of BSA and HHb intrinsic fluorescence. Depicted outcomes suggest that hemin is supposedly able to influence the physiological functions of BSA and HHb, the most important blood proteins, particularly in case of its overuse.

The significant role of covalency in determining the ground state of cobalt phthalocyanines molecule

Directory of Open Access Journals (Sweden)

Jing Zhou

2016-03-01

Full Text Available To shed some light on the metal 3d ground state configuration of cobalt phthalocyanines system, so far in debate, we present an investigation by X-ray absorption spectroscopy (XAS at Co L2,3 edge and theoretical calculation. The density functional theory calculations reveal highly anisotropic covalent bond between central cobalt ion and nitrogen ligands, with the dominant σ donor accompanied by weak π-back acceptor interaction. Our combined experimental and theoretical study on the Co-L2,3 XAS spectra demonstrate a robust ground state of 2A1g symmetry that is built from 73% 3d7 character and 27% 3 d 8 L ¯ ( L ¯ denotes a ligand hole components, as the first excited-state with 2Eg symmetry lies about 158 meV higher in energy. The effect of anisotropic and isotropic covalency on the ground state was also calculated and the results indicate that the ground state with 2A1g symmetry is robust in a large range of anisotropic covalent strength while a transition of ground state from 2A1g to 2Eg configuration when isotropic covalent strength increases to a certain extent. Here, we address a significant anisotropic covalent effect of short Co(II-N bond on the ground state and suggest that it should be taken into account in determining the ground state of analogous cobalt complexes.

Production of recombinant cholesterol oxidase containing covalently bound FAD in Escherichia coli

Directory of Open Access Journals (Sweden)

Molla Gianluca

2010-04-01

Full Text Available Abstract Background Cholesterol oxidase is an alcohol dehydrogenase/oxidase flavoprotein that catalyzes the dehydrogenation of C(3-OH of cholesterol. It has two major biotechnological applications, i.e. in the determination of serum (and food cholesterol levels and as biocatalyst providing valuable intermediates for industrial steroid drug production. Cholesterol oxidases of type I are those containing the FAD cofactor tightly but not covalently bound to the protein moiety, whereas type II members contain covalently bound FAD. This is the first report on the over-expression in Escherichia coli of type II cholesterol oxidase from Brevibacterium sterolicum (BCO. Results Design of the plasmid construct encoding the mature BCO, optimization of medium composition and identification of the best cultivation/induction conditions for growing and expressing the active protein in recombinant E. coli cells, concurred to achieve a valuable improvement: BCO volumetric productivity was increased from ~500 up to ~25000 U/L and its crude extract specific activity from 0.5 up to 7.0 U/mg protein. Interestingly, under optimal expression conditions, nearly 55% of the soluble recombinant BCO is produced as covalently FAD bound form, whereas the protein containing non-covalently bound FAD is preferentially accumulated in insoluble inclusion bodies. Conclusions Comparison of our results with those published on non-covalent (type I COs expressed in recombinant form (either in E. coli or Streptomyces spp., shows that the fully active type II BCO can be produced in E. coli at valuable expression levels. The improved over-production of the FAD-bound cholesterol oxidase will support its development as a novel biotool to be exploited in biotechnological applications.

Reversible and formaldehyde-mediated covalent binding of a bis-amino mitoxantrone analogue to DNA.

Science.gov (United States)

Konda, Shyam K; Kelso, Celine; Pumuye, Paul P; Medan, Jelena; Sleebs, Brad E; Cutts, Suzanne M; Phillips, Don R; Collins, J Grant

2016-05-18

The ability of a bis-amino mitoxantrone anticancer drug (named WEHI-150) to form covalent adducts with DNA, after activation by formaldehyde, has been studied by electrospray ionisation mass spectrometry and HPLC. Mass spectrometry results showed that WEHI-150 could form covalent adducts with d(ACGCGCGT)2 that contained one, two or three covalent links to the octanucleotide, whereas the control drugs (daunorubicin and the anthracenediones mitoxantrone and pixantrone) only formed adducts with one covalent link to the octanucleotide. HPLC was used to examine the extent of covalent bond formation of WEHI-150 with d(CGCGCG)2 and d(CG(5Me)CGCG)2. Incubation of WEHI-150 with d(CG(5Me)CGCG)2 in the presence of formaldehyde resulted in the formation of significantly greater amounts of covalent adducts than was observed with d(CGCGCG)2. In order to understand the observed increase of covalent adducts with d(CG(5Me)CGCG)2, an NMR study of the reversible interaction of WEHI-150 at both CpG and (5Me)CpG sites was undertaken. Intermolecular NOEs were observed in the NOESY spectra of d(ACGGCCGT)2 with added WEHI-150 that indicated that the drug selectively intercalated at the CpG sites and from the major groove. In particular, NOEs were observed from the WEHI-150 H2,3 protons to the H1' protons of G3 and G7 and from the H6,7 protons to the H5 protons of C2 and C6. By contrast, intermolecular NOEs were observed between the WEHI-150 H2,3 protons to the H2'' proton of the (5Me)C3 in d(CG(5Me)CGCG)2, and between the drug aliphatic protons and the H1' proton of G4. This demonstrated that WEHI-150 preferentially intercalates at (5Me)CpG sites, compared to CpG sequences, and predominantly via the minor groove at the (5Me)CpG site. The results of this study demonstrate that WEHI-150 is likely to form interstrand DNA cross-links, upon activation by formaldehyde, and consequently exhibit greater cytotoxicity than other current anthracenedione drugs.

Th-Based Endohedral Metallofullerenes: Anomalous Metal Position and Significant Metal-Cage Covalent Interactions with the Involvement of Th 5f Orbitals.

Science.gov (United States)

Li, Ying; Yang, Le; Liu, Chang; Hou, Qinghua; Jin, Peng; Lu, Xing

2018-05-29

Endohedral metallofullerenes (EMFs) containing actinides are rather intriguing due to potential 5f-orbital participation in the metal-metal or metal-cage bonding. In this work, density functional theory calculations first characterized the structure of recently synthesized ThC 74 as Th@ D 3 h (14246)-C 74 . We found that the thorium atom adopts an unusual off-axis position inside cage due to small metal ion size and the requirement of large coordination number, which phenomenon was further extended to other Th-based EMFs. Significantly, besides the strong metal-cage electrostatic attractions, topological and orbital analysis revealed that all the investigated Th-based EMFs exhibit obvious covalent interactions between metal and cage with substantial contribution from the Th 5f orbitals. The encapsulation by fullerenes is thus proposed as a practical pathway toward the f-orbital covalency for thorium. Interestingly, the anomalous internal position of Th led to a novel three-dimensional metal trajectory at elevated temperatures in the D 3 h -C 74 cavity, as elucidated by the static computations and molecular dynamic simulations.

Determination of the major tautomeric form of the covalently modified adenine in the (+)-CC-1065-DNA adduct by 1H and 15N NMR studies

International Nuclear Information System (INIS)

Lin, Chin Hsiung; Hurley, L.H.

1990-01-01

(+)-CC-1065 is an extremely potent antitumor antibiotic produced by Streptomyces zelensis. The potent cytotoxic effects of the drug are thought to be due to the formation of a covalent adduct with DNA through N3 of adenine. Although the covalent linkage sites between (+)-CC-1065 and DNA have been determined, the tautomeric form of the covalently modified adenine in the (+)-CC-1065-DNA duplex adduct was not defined. The [6- 15 N]deoxyadenosine-labeled 12-mer duplex adduct was then studied by 1 H and 15 N NMR. One-dimensional NOE difference and two-dimensional NOESY 1 H NMR experiments on the nonisotopically labeled 12-mer duplex adduct demonstrate that the 6-amino protons of the covalently modified adenine exhibit two signals at 9.19 and 9.08 ppm. Proton NMR experiments on the [6- 15 N]deoxyadenosine-labeled 12-mer duplex adduct show that the two resonance signals for adenine H6 observed on the nonisotopically labeled duplex adduct were split into doublets by the 15 N nucleus with coupling constants of 91.3 Hz for non-hydrogen-bonded and 86.8 Hz for hydrogen-bonded amino protons. The authors conclude that the covalently modified adenine N6 of the (+)-CC-1065-12-mer duplex adduct is predominantly in the doubly protonated form, in which calculations predict that the C6-N6 bond is shortened and the positive charge is delocalized over the entire adenine molecule

4fn-15d centroid shift in lanthanides and relation with anion polarizability, covalency, and cation electronegativity

International Nuclear Information System (INIS)

Dorenbos, P.; Andriessen, J.; Eijk, C.W.E. van

2003-01-01

Data collected on the centroid shift of the 5d-configuration of Ce 3+ in oxide and fluoride compounds were recently analyzed with a model involving the correlated motion between 5d-electron and ligand electrons. The correlation effects are proportional to the polarizability of the anion ligands and it leads, like covalency, to lowering of the 5d-orbital energies. By means of ab initio Hartree-Fock-LCAO calculations including configuration interaction the contribution from covalency and correlated motion to the centroid shift are determined separately for Ce 3+ in various compounds. It will be shown that in fluoride compounds, covalency provides an insignificant contribution. In oxides, polarizability appears to be of comparable importance as covalency

Mononuclear non-heme iron(III) complexes of linear and tripodal ...

Indian Academy of Sciences (India)

The rate of oxygenation depends on the solvent and the. Lewis acidity of iron(III) ... has been achieved by non-heme iron enzymes and their ..... oxygen atoms of nitrate ion (figure 3). ... enhanced covalency of iron-catecholate interaction and.

Weak interactions and cooperativity effects on disiloxane: a look at the building block of silicones

Science.gov (United States)

Martín-Fernández, Carlos; Montero-Campillo, M. Merced; Alkorta, Ibon; Elguero, José

2018-06-01

The behaviour of disiloxane 1 towards a set of Lewis acids (LA) and Lewis bases (LB) forming complexes through its oxygen and silicon atoms, respectively, was studied at the MP2/aug‧-cc-pVTZ level of theory, exploring a wide variety of non-covalent interactions. Disiloxane is a moderate electron acceptor and a good electron donor, exhibiting in the latter case binding energies up to almost -100 kJ/mol with BeCl2. Cooperativity effects were also analysed by looking at ternary 1:LA:LB complexes. Shorter intermolecular distances than in the corresponding binary complexes and a negative contribution of the three-body term to the binding energy indicate that the non-covalent interactions allowed by disiloxane through its acid and basic centres cooperate between them to reinforce both donor-acceptor pairs. These effects are particularly strong in complexes involving beryllium and triel bonds, but are also relevant for complexes containing hydrogen bonds.

Covalent Strategies for Targeting Messenger and Non-Coding RNAs: An Updated Review on siRNA, miRNA and antimiR Conjugates

Directory of Open Access Journals (Sweden)

Santiago Grijalvo

2018-02-01

Full Text Available Oligonucleotide-based therapy has become an alternative to classical approaches in the search of novel therapeutics involving gene-related diseases. Several mechanisms have been described in which demonstrate the pivotal role of oligonucleotide for modulating gene expression. Antisense oligonucleotides (ASOs and more recently siRNAs and miRNAs have made important contributions either in reducing aberrant protein levels by sequence-specific targeting messenger RNAs (mRNAs or restoring the anomalous levels of non-coding RNAs (ncRNAs that are involved in a good number of diseases including cancer. In addition to formulation approaches which have contributed to accelerate the presence of ASOs, siRNAs and miRNAs in clinical trials; the covalent linkage between non-viral vectors and nucleic acids has also added value and opened new perspectives to the development of promising nucleic acid-based therapeutics. This review article is mainly focused on the strategies carried out for covalently modifying siRNA and miRNA molecules. Examples involving cell-penetrating peptides (CPPs, carbohydrates, polymers, lipids and aptamers are discussed for the synthesis of siRNA conjugates whereas in the case of miRNA-based drugs, this review article makes special emphasis in using antagomiRs, locked nucleic acids (LNAs, peptide nucleic acids (PNAs as well as nanoparticles. The biomedical applications of siRNA and miRNA conjugates are also discussed.

Investigating the Non-Covalent Functionalization and Chemical Transformation of Graphene

Science.gov (United States)

Sham, Chun-Hong

Trend in device miniatures demands capabilities to produce rationally designed patterns in ever-shrinking length scale. The research community has examined various techniques to push the current lithography resolution to sub-10nm scale. One of the ideas is to utilize the natural nanoscale patterns of molecular assemblies. In this thesis, the self-assembling phenomenon of a photoactive molecule on epitaxial graphene (EG) grown on SiC was discussed. This molecular assembly enables manipulation of chemical contrast in nanoscale through UV exposure or atomic layer deposition. Future development of nanoelectronics industry will be fueled by innovations in electronics materials, which could be discovered through covalent modification of graphene. In a study reported in this thesis, silicon is deposited onto EG. After annealing, a new surface reconstruction, identified to be (3x3)-SiC, was formed. Raman spectroscopy finds no signature of graphene after annealing, indicating a complete chemical transformation of graphene. DFT calculations reveal a possible conversion mechanism. Overall, these studies provide insights for future device miniaturization; contribute to the search of novel materials and help bridging the gap between graphene and current silicon-based industrial infrastructures.

Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays.

Directory of Open Access Journals (Sweden)

Michael A Cook

Full Text Available BACKGROUND: Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base unique sequence tags, or "barcodes", associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5'-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM, we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. CONCLUSIONS/SIGNIFICANCE: These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.

Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

Science.gov (United States)

Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

2018-04-01

The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

Non-covalent association of protein and capsular polysaccharide on bacteria-sized latex beads as a model for polysaccharide-specific humoral immunity to intact Gram-positive extracellular bacteria1

Science.gov (United States)

Colino, Jesus; Duke, Leah; Snapper, Clifford M.

2013-01-01

Intact Streptococcus pneumoniae, expressing type 14 capsular polysaccharide (PPS14) and type III Streptococcus agalactiae containing a PPS14 core capsule identical to PPS14, exhibit non-covalent associations of PPS14 and bacterial protein, in contrast to soluble covalent conjugates of these respective antigens. Both bacteria and conjugates induce murine PPS14-specific IgG responses dependent on CD4+ T cells. Further, secondary immunization with conjugate and S. agalactiae, although not S. pneumoniae, results in a boosted response. However, in contrast to conjugate, PPS14-specific IgG responses to bacteria lack affinity maturation, utilize the 44.1-idiotype and are dependent on marginal zone B cells. To better understand the mechanism underlying this dichotomy we developed a minimal model of intact bacteria in which PPS14 and pneumococcal surface protein A (PspA) were stably attached to 1 μm (bacteria-sized) latex beads, but not directly linked to each other, in contrast to PPS14-PspA conjugate. PPS14+[PspA] beads, similar to conjugate, induced in mice boosted PPS14-specific IgG secondary responses, dependent on T cells and ICOS-dependent costimulation, and in which priming could be achieved with PspA alone. In contrast to conjugate, but similar to intact bacteria, the primary PPS14-specific IgG response to PPS14+[PspA] beads peaked rapidly, with the secondary response highly enriched for the 44.1-idiotype and lacking affinity maturation. These results demonstrate that non-covalent association in a particle, of polysaccharide and protein, recapitulates essential immunologic characteristics of intact bacteria that are distinct from soluble covalent conjugates of these respective antigens. PMID:23926322

An Optimal Non-Interactive Message Authentication Protocol

OpenAIRE

Pasini, Sylvain; Vaudenay, Serge

2006-01-01

Vaudenay recently proposed a message authentication protocol which is interactive and based on short authenticated strings (SAS). We study here SAS-based non-interactive message authentication protocols (NIMAP). We start by the analysis of two popular non-interactive message authentication protocols. The first one is based on a collision-resistant hash function and was presented by Balfanz et al. The second protocol is based on a universal hash function family and was proposed by Gehrmann, Mi...

The interplay of covalency, hydrogen bonding, and dispersion leads to a long range chiral network: The example of 2-butanol

Energy Technology Data Exchange (ETDEWEB)

Liriano, Melissa L.; Lewis, Emily A.; Murphy, Colin J.; Lawton, Timothy J.; Marcinkowski, Matthew D.; Therrien, Andrew J.; Sykes, E. Charles H., E-mail: charles.sykes@tufts.edu [Department of Chemistry, Tufts University, Medford, Massachusetts 02155 (United States); Carrasco, Javier [CIC Energigune, Albert Einstein 48, 01510 Miñano, Álava (Spain); Michaelides, Angelos [Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT (United Kingdom)

2016-03-07

The assembly of complex structures in nature is driven by an interplay between several intermolecular interactions, from strong covalent bonds to weaker dispersion forces. Understanding and ultimately controlling the self-assembly of materials requires extensive study of how these forces drive local nanoscale interactions and how larger structures evolve. Surface-based self-assembly is particularly amenable to modeling and measuring these interactions in well-defined systems. This study focuses on 2-butanol, the simplest aliphatic chiral alcohol. 2-butanol has recently been shown to have interesting properties as a chiral modifier of surface chemistry; however, its mode of action is not fully understood and a microscopic understanding of the role non-covalent interactions play in its adsorption and assembly on surfaces is lacking. In order to probe its surface properties, we employed high-resolution scanning tunneling microscopy and density functional theory (DFT) simulations. We found a surprisingly rich degree of enantiospecific adsorption, association, chiral cluster growth and ultimately long range, highly ordered chiral templating. Firstly, the chiral molecules acquire a second chiral center when adsorbed to the surface via dative bonding of one of the oxygen atom lone pairs. This interaction is controlled via the molecule’s intrinsic chiral center leading to monomers of like chirality, at both chiral centers, adsorbed on the surface. The monomers then associate into tetramers via a cyclical network of hydrogen bonds with an opposite chirality at the oxygen atom. The evolution of these square units is surprising given that the underlying surface has a hexagonal symmetry. Our DFT calculations, however, reveal that the tetramers are stable entities that are able to associate with each other by weaker van der Waals interactions and tessellate in an extended square network. This network of homochiral square pores grows to cover the whole Au(111) surface. Our

The interplay of covalency, hydrogen bonding, and dispersion leads to a long range chiral network: The example of 2-butanol

International Nuclear Information System (INIS)

Liriano, Melissa L.; Lewis, Emily A.; Murphy, Colin J.; Lawton, Timothy J.; Marcinkowski, Matthew D.; Therrien, Andrew J.; Sykes, E. Charles H.; Carrasco, Javier; Michaelides, Angelos

2016-01-01

The assembly of complex structures in nature is driven by an interplay between several intermolecular interactions, from strong covalent bonds to weaker dispersion forces. Understanding and ultimately controlling the self-assembly of materials requires extensive study of how these forces drive local nanoscale interactions and how larger structures evolve. Surface-based self-assembly is particularly amenable to modeling and measuring these interactions in well-defined systems. This study focuses on 2-butanol, the simplest aliphatic chiral alcohol. 2-butanol has recently been shown to have interesting properties as a chiral modifier of surface chemistry; however, its mode of action is not fully understood and a microscopic understanding of the role non-covalent interactions play in its adsorption and assembly on surfaces is lacking. In order to probe its surface properties, we employed high-resolution scanning tunneling microscopy and density functional theory (DFT) simulations. We found a surprisingly rich degree of enantiospecific adsorption, association, chiral cluster growth and ultimately long range, highly ordered chiral templating. Firstly, the chiral molecules acquire a second chiral center when adsorbed to the surface via dative bonding of one of the oxygen atom lone pairs. This interaction is controlled via the molecule’s intrinsic chiral center leading to monomers of like chirality, at both chiral centers, adsorbed on the surface. The monomers then associate into tetramers via a cyclical network of hydrogen bonds with an opposite chirality at the oxygen atom. The evolution of these square units is surprising given that the underlying surface has a hexagonal symmetry. Our DFT calculations, however, reveal that the tetramers are stable entities that are able to associate with each other by weaker van der Waals interactions and tessellate in an extended square network. This network of homochiral square pores grows to cover the whole Au(111) surface. Our

Covalent functionalization of graphene with reactive intermediates.

Science.gov (United States)

Park, Jaehyeung; Yan, Mingdi

2013-01-15

Graphene, a material made exclusively of sp(2) carbon atoms with its π electrons delocalized over the entire 2D network, is somewhat chemically inert. Covalent functionalization can enhance graphene's properties including opening its band gap, tuning conductivity, and improving solubility and stability. Covalent functionalization of pristine graphene typically requires reactive species that can form covalent adducts with the sp(2) carbon structures in graphene. In this Account, we describe graphene functionalization reactions using reactive intermediates of radicals, nitrenes, carbenes, and arynes. These reactive species covalently modify graphene through free radical addition, CH insertion, or cycloaddition reactions. Free radical additions are among the most common reaction, and these radicals can be generated from diazonium salts and benzoyl peroxide. Electron transfer from graphene to aryl diazonium ion or photoactivation of benzoyl peroxide yields aryl radicals that subsequently add to graphene to form covalent adducts. Nitrenes, electron-deficient species generated by thermal or photochemical activation of organic azides, can functionalize graphene very efficiently. Because perfluorophenyl nitrenes show enhanced bimolecular reactions compared with alkyl or phenyl nitrenes, perfluorophenyl azides are especially effective. Carbenes are used less frequently than nitrenes, but they undergo CH insertion and C═C cycloaddition reactions with graphene. In addition, arynes can serve as a dienophile in a Diels-Alder type reaction with graphene. Further study is needed to understand and exploit the chemistry of graphene. The generation of highly reactive intermediates in these reactions leads to side products that complicate the product composition and analysis. Fundamental questions remain about the reactivity and regioselectivity of graphene. The differences in the basal plane and the undercoordinated edges of graphene and the zigzag versus arm-chair configurations

Towards 4th generation biomaterials: a covalent hybrid polymer-ormoglass architecture

Science.gov (United States)

Sachot, N.; Mateos-Timoneda, M. A.; Planell, J. A.; Velders, A. H.; Lewandowska, M.; Engel, E.; Castaño, O.

2015-09-01

Hybrid materials are being extensively investigated with the aim of mimicking the ECM microenvironment to develop effective solutions for bone tissue engineering. However, the common drawbacks of a hybrid material are the lack of interactions between the scaffold's constituents and the masking of its bioactive phase. Conventional hybrids often degrade in a non-homogeneous manner and the biological response is far from optimal. We have developed a novel material with strong interactions between constituents. The bioactive phase is directly exposed on its surface mimicking the structure of the ECM of bone. Here, polylactic acid electrospun fibers have been successfully and reproducibly coated with a bioactive organically modified glass (ormoglass, Si-Ca-P2 system) covalently. In comparison with the pure polymeric mats, the fibers obtained showed improved hydrophilicity and mechanical properties, bioactive ion release, exhibited a nanoroughness and enabled good cell adhesion and spreading after just one day of culture (rMSCs and rEPCs). The fibers were coated with different ormoglass compositions to tailor their surface properties (roughness, stiffness, and morphology) by modifying the experimental parameters. Knowing that cells modulate their behavior according to the exposed physical and chemical signals, the development of this instructive material is a valuable advance in the design of functional regenerative biomaterials.Hybrid materials are being extensively investigated with the aim of mimicking the ECM microenvironment to develop effective solutions for bone tissue engineering. However, the common drawbacks of a hybrid material are the lack of interactions between the scaffold's constituents and the masking of its bioactive phase. Conventional hybrids often degrade in a non-homogeneous manner and the biological response is far from optimal. We have developed a novel material with strong interactions between constituents. The bioactive phase is directly exposed

Mechanisms for Covalent Immobilization of Horseradish Peroxidase on Ion-Beam-Treated Polyethylene

Directory of Open Access Journals (Sweden)

Alexey V. Kondyurin

2012-01-01

Full Text Available The surface of polyethylene was modified by plasma immersion ion implantation. Structure changes including carbonization and oxidation were observed. High surface energy of the modified polyethylene was attributed to the presence of free radicals on the surface. The surface energy decay with storage time after treatment was explained by a decay of the free radical concentration while the concentration of oxygen-containing groups increased with storage time. Horseradish peroxidase was covalently attached onto the modified surface by the reaction with free radicals. Appropriate blocking agents can block this reaction. All aminoacid residues can take part in the covalent attachment process, providing a universal mechanism of attachment for all proteins. The native conformation of attached protein is retained due to hydrophilic interactions in the interface region. The enzymatic activity of covalently attached protein remained high. The long-term activity of the modified layer to attach protein is explained by stabilisation of unpaired electrons in sp2 carbon structures. A high concentration of free radicals can give multiple covalent bonds to the protein molecule and destroy the native conformation and with it the catalytic activity. The universal mechanism of protein attachment to free radicals could be extended to various methods of radiation damage of polymers.

Design of a covalently bonded glycosphingolipid microarray

DEFF Research Database (Denmark)

Arigi, Emma; Blixt, Klas Ola; Buschard, Karsten

2012-01-01

, the major classes of plant and fungal GSLs. In this work, a prototype "universal" GSL-based covalent microarray has been designed, and preliminary evaluation of its potential utility in assaying protein-GSL binding interactions investigated. An essential step in development involved the enzymatic release...... of the fatty acyl moiety of the ceramide aglycone of selected mammalian GSLs with sphingolipid N-deacylase (SCDase). Derivatization of the free amino group of a typical lyso-GSL, lyso-G(M1), with a prototype linker assembled from succinimidyl-[(N-maleimidopropionamido)-diethyleneglycol] ester and 2...

Conformers and non-covalent interactions studied by laser spectroscopies and ab initio calculations

Energy Technology Data Exchange (ETDEWEB)

Ullrich, Susanne

2001-07-01

The model peptides, formanilide and acetanilide, and their weakly bound complexes were studied in the gas-phase using resonance enhanced multi-photon ionisation (REMPI) and zero electron kinetic energy (ZEKE) photoelectron spectroscopy. Both, cis- and trans-isomers of formanilide, were observed under molecular beam conditions. Trans-formanilide displayed predominantly in-plane vibrational excitation indicative of a planar geometry with modest geometry changes upon excitation and ionisation. In cis-formanilide the side-chain is twisted compared to the phenyl plane in the S{sub 0} state, but planar in the S{sub 1} and D{sub 0} states, revealed in characteristic side-chain torsional and out-of-plane bending excitations. Additionally, the ZEKE spectra provide evidence that excess cationic charge is delocalised from the aromatic ring to the side chain. The work on trans-formanilide was extended to its van der Waals complex with Argon with the purpose of investigating the torsional potential of the side-chain and probing charge delocalisation. Complexation of amides with water is of considerable interest since water is not only present as a bulk solvent surrounding a peptide but also attached to specific binding sites in its interior. Evidence was found for the existence of a NH- and CO-bound isomer of trans-formanilide in the neutral, S{sub 0} and S{sub 1}, states, with the ZEKE spectrum of the cationic 'CO-bound' complex indicating a strong preference for the NH binding site. (author)

Diazonium-derived aryl films on gold nanoparticles: evidence for a carbon-gold covalent bond.

Science.gov (United States)

Laurentius, Lars; Stoyanov, Stanislav R; Gusarov, Sergey; Kovalenko, Andriy; Du, Rongbing; Lopinski, Gregory P; McDermott, Mark T

2011-05-24

Tailoring the surface chemistry of metallic nanoparticles is generally a key step for their use in a wide range of applications. There are few examples of organic films covalently bound to metal nanoparticles. We demonstrate here that aryl films are formed on gold nanoparticles from the spontaneous reduction of diazonium salts. The structure and the bonding of the film is probed with surface-enhanced Raman scattering (SERS). Extinction spectroscopy and SERS show that a nitrobenzene film forms on gold nanoparticles from the corresponding diazonium salt. Comparison of the SERS spectrum with spectra computed from density functional theory models reveals a band characteristic of a Au-C stretch. The observation of this stretch is direct evidence of a covalent bond. A similar band is observed in high-resolution electron energy loss spectra of nitrobenzene layers on planar gold. The bonding of these types of films through a covalent interaction on gold is consistent with their enhanced stability observed in other studies. These findings provide motivation for the use of diazonium-derived films on gold and other metals in applications where high stability and/or strong adsorbate-substrate coupling are required.

Fabrication and non-covalent modification of highly oriented thin films of a zeolite-like metal-organic framework (ZMOF) with rho topology

KAUST Repository

Shekhah, Osama

2015-01-01

Here we report the fabrication of the first thin film of a zeolite-like metal-organic framework (ZMOF) with rho topology (rho-ZMOF-1, ([In48(HImDC)96]48-)n) in a highly oriented fashion on a gold-functionalized substrate. The oriented rho-ZMOF-1 film was functionalized by non-covalent modification via post-synthetic exchange of different probe molecules, such as acridine yellow, methylene blue, and Nile red. In addition, encapsulation of a porphyrin moiety was achieved via in situ synthesis and construction of the rho-ZMOF. Adsorption kinetics of volatile organic compounds on rho-ZMOF-1 thin films was also investigated. This study suggests that rho-ZMOF-1 thin films can be regarded as a promising platform for various applications such as sensing and catalysis. This journal is

High covalence in CuSO4 and the radicalization of sulfate: an X-ray absorption and density functional study.

Science.gov (United States)

Szilagyi, Robert K; Frank, Patrick; DeBeer George, Serena; Hedman, Britt; Hodgson, Keith O

2004-12-27

Sulfur K-edge X-ray absorption spectroscopy (XAS) of anhydrous CuSO(4) reveals a well-resolved preedge transition feature at 2478.8 eV that has no counterpart in the XAS spectra of anhydrous ZnSO(4) or copper sulfate pentahydrate. Similar but weaker preedge features occur in the sulfur K-edge XAS spectra of [Cu(itao)SO(4)] (2478.4 eV) and [Cu[(CH(3))(6)tren]SO(4)] (2477.7 eV). Preedge features in the XAS spectra of transition metal ligands are generally attributed to covalent delocalization of a metal d-orbital hole into a ligand-based orbital. Copper L-edge XAS of CuSO(4) revealed that 56% of the Cu(II) 3d hole is delocalized onto the sulfate ligand. Hybrid density functional calculations on the two most realistic models of the covalent delocalization pathways in CuSO(4) indicate about 50% electron delocalization onto the sulfate oxygen-based 2p orbitals; however, at most 14% of that can be found on sulfate sulfur. Both experimental and computational results indicated that the high covalence of anhydrous CuSO(4) has made sulfate more like the radical monoanion, inducing an extensive mixing and redistribution of sulfur 3p-based unoccupied orbitals to lower energy in comparison to sulfate in ZnSO(4). It is this redistribution, rather than a direct covalent interaction between Cu(II) and sulfur, that is the origin of the observed sulfur XAS preedge feature. From pseudo-Voigt fits to the CuSO(4) sulfur K-edge XAS spectrum, a ground-state 3p character of 6% was quantified for the orbital contributing to the preedge transition, in reasonable agreement with the DFT calculation. Similar XAS fits indicated 2% sulfur 3p character for the preedge transition orbitals in [Cu(itao)SO(4)] and [Cu[(CH(3))(6)tren]SO(4)]. The covalent radicalization of ligands similar to sulfate, with consequent energy redistribution of the virtual orbitals, represents a new mechanism for the induction of ligand preedge XAS features. The high covalence of the Cu sites in CuSO(4) was found to be

Chemistry of Covalent Organic Frameworks.

Science.gov (United States)

Waller, Peter J; Gándara, Felipe; Yaghi, Omar M

2015-12-15

Linking organic molecules by covalent bonds into extended solids typically generates amorphous, disordered materials. The ability to develop strategies for obtaining crystals of such solids is of interest because it opens the way for precise control of the geometry and functionality of the extended structure, and the stereochemical orientation of its constituents. Covalent organic frameworks (COFs) are a new class of porous covalent organic structures whose backbone is composed entirely of light elements (B, C, N, O, Si) that represent a successful demonstration of how crystalline materials of covalent solids can be achieved. COFs are made by combination of organic building units covalently linked into extended structures to make crystalline materials. The attainment of crystals is done by several techniques in which a balance is struck between the thermodynamic reversibility of the linking reactions and their kinetics. This success has led to the expansion of COF materials to include organic units linked by these strong covalent bonds: B-O, C-N, B-N, and B-O-Si. Since the organic constituents of COFs, when linked, do not undergo significant change in their overall geometry, it has been possible to predict the structures of the resulting COFs, and this advantage has facilitated their characterization using powder X-ray diffraction (PXRD) techniques. It has also allowed for the synthesis of COF structures by design and for their formation with the desired composition, pore size, and aperture. In practice, the modeled PXRD pattern for a given expected COF is compared with the experimental one, and depending on the quality of the match, this is used as a starting point for solving and then refining the crystal structure of the target COF. These characteristics make COFs an attractive class of new porous materials. Accordingly, they have been used as gas storage materials for energy applications, solid supports for catalysis, and optoelectronic devices. A large and

Non-Linear Dynamics and Fundamental Interactions

CERN Document Server

Khanna, Faqir

2006-01-01

The book is directed to researchers and graduate students pursuing an advanced degree. It provides details of techniques directed towards solving problems in non-linear dynamics and chos that are, in general, not amenable to a perturbative treatment. The consideration of fundamental interactions is a prime example where non-perturbative techniques are needed. Extension of these techniques to finite temperature problems is considered. At present these ideas are primarily used in a perturbative context. However, non-perturbative techniques have been considered in some specific cases. Experts in the field on non-linear dynamics and chaos and fundamental interactions elaborate the techniques and provide a critical look at the present status and explore future directions that may be fruitful. The text of the main talks will be very useful to young graduate students who are starting their studies in these areas.

Studies on the metabolism of chlorotrianisene to a reactive intermediate and subsequent covalent binding to microsomal proteins

International Nuclear Information System (INIS)

Juedes, M.J.

1989-01-01

The studies on chlorotrianisene were conducted to determine whether metabolism of chlorotrianisene occurs via the cytochrome P450 monooxygenase system and whether a reactive intermediate is being formed that is capable of binding covalently to microsomal proteins. [ 3 H]-chlorotrianisene was incubated with liver microsomes supplemented with NADPH. At the termination of the incubation, the protein was trapped on a glass filter and the unbound chlorotrianisene was removed by extensive washing of the protein with organic solvent. A dramatic stimulation of covalent binding was demonstrated in microsomes from rats treated with methylcholanthrene (60 fold increase) versus control or phenobarbital treatment. Verification of covalent binding was achieved by localization of radiolabeled bands following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of the macromolecules in the incubation mixture. Further analysis of the radiolabeled macromolecules separated on SDS-PAGE revealed that these macromolecules were degraded by protease degradation indicating that the macromolecules were proteins. Further investigations were done to determine the cause of the dramatic stimulation of covalent binding detected in microsomes from methylcholanthrene treated rats versus control or phenobarbital treated rats. Further evidence for the participation of P-450c was obtained with a reconstituted cytochrome P-450 system. Incubations of chlorotrianisene with reconstituted P-450c and NADPH-cytochrome P-450 reductase exhibited covalent binding characteristics comparable to those seen in microsomal incubations. Investigations into the nature of the binding site and the reactive intermediate are currently being conducted. By analyzing the BSA adduct, the author intends to isolate the specific amino acid binding site(s)

Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives.

Science.gov (United States)

Goins, Christopher M; Dajnowicz, Steven; Thanna, Sandeep; Sucheck, Steven J; Parks, Jerry M; Ronning, Donald R

2017-05-12

Previous studies identified ebselen as a potent in vitro and in vivo inhibitor of the Mycobacterium tuberculosis (Mtb) antigen 85 (Ag85) complex, comprising three homologous enzymes required for the biosynthesis of the mycobacterial cell wall. In this study, the Mtb Ag85C enzyme was cocrystallized with azido and adamantyl ebselen derivatives, resulting in two crystallographic structures of 2.01 and 1.30 Å resolution, respectively. Both structures displayed the anticipated covalent modification of the solvent accessible, noncatalytic Cys209 residue forming a selenenylsulfide bond. Continuous difference density for both thiol modifiers allowed for the assessment of interactions that influence ebselen binding and inhibitor orientation that were unobserved in previous Ag85C ebselen structures. The k inact /K I values for ebselen, adamantyl ebselen, and azido ebselen support the importance of observed constructive chemical interactions with Arg239 for increased in vitro efficacy toward Ag85C. To better understand the in vitro kinetic properties of these ebselen derivatives, the energetics of specific protein-inhibitor interactions and relative reaction free energies were calculated for ebselen and both derivatives using density functional theory. These studies further support the different in vitro properties of ebselen and two select ebselen derivatives from our previously published ebselen library with respect to kinetics and protein-inhibitor interactions. In both structures, the α9 helix was displaced farther from the enzyme active site than the previous Ag85C ebselen structure, resulting in the restructuring of a connecting loop and imparting a conformational change to residues believed to play a role in substrate binding specific to Ag85C. These notable structural changes directly affect protein stability, reducing the overall melting temperature by up to 14.5 °C, resulting in the unfolding of protein at physiological temperatures. Additionally, this structural

Evaluation of the release characteristics of covalently attached or electrostatically bound biocidal polymers utilizing SERS and UV-Vis absorption

Directory of Open Access Journals (Sweden)

G. N. Mathioudakis

2016-09-01

Full Text Available In this work, biocidal polymers with antimicrobial quaternized ammonium groups introduced in the polymer biocidal chains either through covalent attachment or electrostatic interaction have been separately incorporated in a poly (methyl methacrylate polymer matrix. The objective of present study was to highlight the release characteristics of biocidal polymers, primarily in saline but also in water ethanol solutions, utilizing UV-Vis absorption and Surface Enhanced Raman Scattering (SERS. It is shown that through the combination of UV-Vis and SERS techniques, upon the release process, it is possible the discrimination of the polymeric backbone and the electrostatically bound biocidal species. Moreover, it is found that electrostatically bound and covalently attached biocidal species show different SERS patterns. The long term aim is the development of antimicrobial polymeric materials containing both ionically bound and covalently attached quaternary ammonium thus achieving a dual functionality in a single component polymeric design.

An Exploratory Case Study of Young Children's Interactive Play Behaviours with a Non-English Speaking Child

Science.gov (United States)

Lee, Joohi; Md-Yunus, Sham'ah; Son, Won In; Meadows, Michelle

2009-01-01

This study is an examination of preschool-age English speaking children's interactive play behaviours with a non-English speaking child (NEC). The play types of a NEC were reported using the Parten's categories of solitary, parallel and interactive play. In addition, English-speaking children's interactive play with a NEC were reported in this…

Macromolecular weight specificity in covalent binding of bromobenzene

International Nuclear Information System (INIS)

Sun, J.D.; Dent, J.G.

1984-01-01

Bromobenzene is a hepatotoxicant that causes centrilobular necrosis. Pretreatment of animals with 3-methylcholanthrene decreases and phenobarbital pretreatment enhances the hepatotoxic action of this compound. We have investigated the macromolecular weight specificity of the covalent interactions of bromobenzene with liver macromolecules following incubation of [ 14 C]bromobenzene in isolated hepatocytes. Hepatocytes were prepared from Fischer-344 rats treated for 3 days with 3-methylcholanthrene, phenobarbital, or normal saline. After a 1-hr incubation, total covalent binding, as measured by sodium dodecyl sulfate-equilibrium dialysis, was twofold less in hepatocytes from 3-methylcholanthrene-treated rats and sixfold greater in hepatocytes from phenobarbital-treated rats, as compared to hepatocytes from control animals. Analysis of the arylated macromolecules by electrophoresis on 15% sodium dodecyl sulfate-polyacrylamide disc gels indicated that in the first 1 to 3 min of incubation substantial amounts of covalently bound radiolabel were associated with macromolecules of between 20,000 and 40,000. The amount of radioactivity associated with these macromolecules rapidly diminished in hepatocytes from control and 3-methylcholanthrene-treated animals. In hepatocytes from phenobarbital-treated animals, the amount of radioactivity associated with macromolecules, 20,000, increased throughout the incubation. The amount of radiolabel associated with macromolecules, 20,000, increased in all incubations. When nontoxic doses of phenylmethylsulfonyl fluoride, a specific inhibitor of serine proteases, were added to control hepatocytes incubated with [ 14 C]-bromobenzene, the decrease in radioactivity associated with larger (greater than 20,000) macromolecules was inhibited and a corresponding lack of increase in radioactivity associated with smaller macromolecules was observed

Flavin-N5 Covalent Intermediate in a Nonredox Dehalogenation Reaction Catalyzed by an Atypical Flavoenzyme.

Science.gov (United States)

Dai, Yumin; Kizjakina, Karina; Campbell, Ashley C; Korasick, David A; Tanner, John J; Sobrado, Pablo

2018-01-04

The flavin-dependent enzyme 2-haloacrylate hydratase (2-HAH) catalyzes the conversion of 2-chloroacrylate, a major component in the manufacture of acrylic polymers, to pyruvate. The enzyme was expressed in Escherichia coli, purified, and characterized. 2-HAH was shown to be monomeric in solution and contained a non-covalent, yet tightly bound, flavin adenine dinucleotide (FAD). Although the catalyzed reaction was redox-neutral, 2-HAH was active only in the reduced state. A covalent flavin-substrate intermediate, consistent with the flavin-acrylate iminium ion, was trapped with cyanoborohydride and characterized by mass spectrometry. Small-angle X-ray scattering was consistent with 2-HAH belonging to the succinate dehydrogenase/fumarate reductase family of flavoproteins. These studies establish 2-HAH as a novel noncanonical flavoenzyme. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Perspective on Reagent Diversity and Non-covalent Binding of Reactive Carbonyl Species (RCS and Effector Reagents in Non-enzymatic Glycation (NEG: Mechanistic Considerations and Implications for Future Research

Directory of Open Access Journals (Sweden)

Kenneth J. Rodnick

2017-06-01

Full Text Available This perspective focuses on illustrating the underappreciated connections between reactive carbonyl species (RCS, initial binding in the nonenzymatic glycation (NEG process, and nonenzymatic covalent protein modification (here termed NECPM. While glucose is the central species involved in NEG, recent studies indicate that the initially-bound glucose species in the NEG of human hemoglobin (HbA and human serum albumin (HSA are non-RCS ring-closed isomers. The ring-opened glucose, an RCS structure that reacts in the NEG process, is most likely generated from previously-bound ring-closed isomers undergoing concerted acid/base reactions while bound to protein. The generation of the glucose RCS can involve concomitantly-bound physiological species (e.g., inorganic phosphate, water, etc.; here termed effector reagents. Extant NEG schemes do not account for these recent findings. In addition, effector reagent reactions with glucose in the serum and erythrocyte cytosol can generate RCS (e.g., glyoxal, glyceraldehyde, etc.. Recent research has shown that these RCS covalently modify proteins in vivo via NECPM mechanisms. A general scheme that reflects both the reagent and mechanistic diversity that can lead to NEG and NECPM is presented here. A perspective that accounts for the relationships between RCS, NEG, and NECPM can facilitate the understanding of site selectivity, may help explain overall glycation rates, and may have implications for the clinical assessment/control of diabetes mellitus. In view of this perspective, concentrations of ribose, fructose, Pi, bicarbonate, counter ions, and the resulting RCS generated within intracellular and extracellular compartments may be of importance and of clinical relevance. Future research is also proposed.

Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.

Directory of Open Access Journals (Sweden)

Ching-Tai Chen

Full Text Available Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins and were tested on an independent dataset (consisting of 142 proteins. The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted

Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

Science.gov (United States)

Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with

Potent haloperidol derivatives covalently binding to the dopamine D2 receptor.

Science.gov (United States)

Schwalbe, Tobias; Kaindl, Jonas; Hübner, Harald; Gmeiner, Peter

2017-10-01

The dopamine D 2 receptor (D 2 R) is a common drug target for the treatment of a variety of neurological disorders including schizophrenia. Structure based design of subtype selective D 2 R antagonists requires high resolution crystal structures of the receptor and pharmacological tools promoting a better understanding of the protein-ligand interactions. Recently, we reported the development of a chemically activated dopamine derivative (FAUC150) designed to covalently bind the L94C mutant of the dopamine D 2 receptor. Using FAUC150 as a template, we elaborated the design and synthesis of irreversible analogs of the potent antipsychotic drug haloperidol forming covalent D 2 R-ligand complexes. The disulfide- and Michael acceptor-functionalized compounds showed significant receptor affinity and an irreversible binding profile in radioligand depletion experiments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nanostructured organic electrode materials grown on graphene with covalent-bond interaction for high-rate and ultra-long-life lithium-ion batteries

Institute of Scientific and Technical Information of China (English)

Qing Zhao; Jianbin Wang; Chengcheng Chen; Ting Ma; Jun Chen

2017-01-01

Nanostructured organic tetralithium salts of 2,5-dihydroxyterephthalic acid (Li4C8H2O6) supported on graphene were prepared via a facile recrystallization method.The optimized composite with 75 wt.％ Li4C8H2O6 was evaluated as an anode with redox couples of Li4C8H2OdLi6C8H2O6 and as a cathode with redox couples of Li4C8H2O6/Li2C8H2O6 for Li-ion batteries,exhibiting a high-rate capability (10 C) and long cycling life (1,000 cycles).Moreover,in an all-organic symmetric Li-ion battery,this dual-function electrode retained capacities of 191 and 121 mA.h·g-1 after 100 and 500 cycles,respectively.Density functional theory calculations indicated the presence of covalent bonds between Li4C8H2O6 and graphene,which affected both the morphology and electronic structure of the composite.The special nanostructures,high electronic conductivity of graphene,and covalent-bond interaction between Li4C8H2O6 and graphene contributed to the superior electrochemical properties.Our results indicate that the combination of organic salt molecules with graphene is useful for obtaining high-performance organic batteries.

Covalency in lanthanides. An X-ray absorption spectroscopy and density functional theory study of LnCl6(x-) (x = 3, 2).

Science.gov (United States)

Löble, Matthias W; Keith, Jason M; Altman, Alison B; Stieber, S Chantal E; Batista, Enrique R; Boland, Kevin S; Conradson, Steven D; Clark, David L; Lezama Pacheco, Juan; Kozimor, Stosh A; Martin, Richard L; Minasian, Stefan G; Olson, Angela C; Scott, Brian L; Shuh, David K; Tyliszczak, Tolek; Wilkerson, Marianne P; Zehnder, Ralph A

2015-02-25

Covalency in Ln-Cl bonds of Oh-LnCl6(x-) (x = 3 for Ln = Ce(III), Nd(III), Sm(III), Eu(III), Gd(III); x = 2 for Ln = Ce(IV)) anions has been investigated, primarily using Cl K-edge X-ray absorption spectroscopy (XAS) and time-dependent density functional theory (TDDFT); however, Ce L3,2-edge and M5,4-edge XAS were also used to characterize CeCl6(x-) (x = 2, 3). The M5,4-edge XAS spectra were modeled using configuration interaction calculations. The results were evaluated as a function of (1) the lanthanide (Ln) metal identity, which was varied across the series from Ce to Gd, and (2) the Ln oxidation state (when practical, i.e., formally Ce(III) and Ce(IV)). Pronounced mixing between the Cl 3p- and Ln 5d-orbitals (t2g* and eg*) was observed. Experimental results indicated that Ln 5d-orbital mixing decreased when moving across the lanthanide series. In contrast, oxidizing Ce(III) to Ce(IV) had little effect on Cl 3p and Ce 5d-orbital mixing. For LnCl6(3-) (formally Ln(III)), the 4f-orbitals participated only marginally in covalent bonding, which was consistent with historical descriptions. Surprisingly, there was a marked increase in Cl 3p- and Ce(IV) 4f-orbital mixing (t1u* + t2u*) in CeCl6(2-). This unexpected 4f- and 5d-orbital participation in covalent bonding is presented in the context of recent studies on both tetravalent transition metal and actinide hexahalides, MCl6(2-) (M = Ti, Zr, Hf, U).

The yeast cell fusion protein Prm1p requires covalent dimerization to promote membrane fusion.

Directory of Open Access Journals (Sweden)

Alex Engel

2010-05-01

Full Text Available Prm1p is a multipass membrane protein that promotes plasma membrane fusion during yeast mating. The mechanism by which Prm1p and other putative regulators of developmentally controlled cell-cell fusion events facilitate membrane fusion has remained largely elusive. Here, we report that Prm1p forms covalently linked homodimers. Covalent Prm1p dimer formation occurs via intermolecular disulfide bonds of two cysteines, Cys-120 and Cys-545. PRM1 mutants in which these cysteines have been substituted are fusion defective. These PRM1 mutants are normally expressed, retain homotypic interaction and can traffic to the fusion zone. Because prm1-C120S and prm1-C545S mutants can form covalent dimers when coexpressed with wild-type PRM1, an intermolecular C120-C545 disulfide linkage is inferred. Cys-120 is adjacent to a highly conserved hydrophobic domain. Mutation of a charged residue within this hydrophobic domain abrogates formation of covalent dimers, trafficking to the fusion zone, and fusion-promoting activity. The importance of intermolecular disulfide bonding informs models regarding the mechanism of Prm1-mediated cell-cell fusion.

Graphene and Carbon-Nanotube Nanohybrids Covalently Functionalized by Porphyrins and Phthalocyanines for Optoelectronic Properties.

Science.gov (United States)

Wang, Aijian; Ye, Jun; Humphrey, Mark G; Zhang, Chi

2018-04-01

In recent years, there has been a rapid growth in studies of the optoelectronic properties of graphene, carbon nanotubes (CNTs), and their derivatives. The chemical functionalization of graphene and CNTs is a key requirement for the development of this field, but it remains a significant challenge. The focus here is on recent advances in constructing nanohybrids of graphene or CNTs covalently linked to porphyrins or phthalocyanines, as well as their application in nonlinear optics. Following a summary of the syntheses of nanohybrids constructed from graphene or CNTs and porphyrins or phthalocyanines, explicit intraconjugate electronic interactions between photoexcited porphyrins/phthalocyanines and graphene/CNTs are introduced classified by energy transfer, electron transfer, and charge transfer, and their optoelectronic applications are also highlighted. The major current challenges for the development of covalently linked nanohybrids of porphyrins or phthalocyanines and carbon nanostructures are also presented. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relaxations of fluorouracil tautomers by decorations of fullerene-like SiCs: DFT studies

Energy Technology Data Exchange (ETDEWEB)

Kouchaki, Alireza [Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Chemistry, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Gülseren, Oğuz [Department of Physics, Faculty of Science, Bilkent University, Ankara (Turkey); Hadipour, Nasser [Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Mirzaei, Mahmoud, E-mail: mdmirzaei@pharm.mui.ac.ir [Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan (Iran, Islamic Republic of)

2016-06-03

Decorations of silicon carbide (SiC) fullerene-like nanoparticles by fluorouracil (FU) and its tautomers are investigated through density functional theory (DFT) calculations. Two models of fullerene-like particles including Si{sub 12}C{sub 8} and Si{sub 8}C{sub 12} are constructed to be counterparts of decorated hybrid structures, FU@Si{sub 12}C{sub 8} and FU@Si{sub 8}C{sub 12}, respectively. The initial models including original FU and tautomeric structures and SiC nanoparticles are individually optimized and then combined for further optimizations in the hybrid forms. Covalent bonds are observed for FU@Si{sub 12}C{sub 8} hybrids, whereas non-covalent interactions are seen for FU@Si{sub 8}C{sub 12} ones. The obtained properties indicated that Si{sub 12}C{sub 8} model could be considered as a better counterpart for interactions with FU structures than Si{sub 8}C{sub 12} model. The results also showed significant effects of interactions on the properties of atoms close to the interacting regions in nanoparticles. Finally, the tautomeric structures show different behaviors in interactions with SiC nanoparticles, in which the SiC nanoparticles could be employed to detect the situations of tautomeric processes for FU structures. - Highlights: • Possibilities of interaction between fluorouracil and silicon carbides have been recognized. • Possibilities for covalent and non-covalent interactions have been indicated. • Detections of tautomeric structures have been investigated.

Peptide carrier-mediated non-covalent delivery of unmodified cisplatin, methotrexate and other agents via intravenous route to the brain.

Directory of Open Access Journals (Sweden)

Gobinda Sarkar

Full Text Available BACKGROUND: Rapid pre-clinical evaluation of chemotherapeutic agents against brain cancers and other neurological disorders remains largely unattained due to the presence of the blood-brain barrier (BBB, which limits transport of most therapeutic compounds to the brain. A synthetic peptide carrier, K16ApoE, was previously developed that enabled transport of target proteins to the brain by mimicking a ligand-receptor system. The peptide carrier was found to generate transient BBB permeability, which was utilized for non-covalent delivery of cisplatin, methotrexate and other compounds to the brain. APPROACH: Brain delivery of the chemotherapeutics and other agents was achieved either by injecting the carrier peptide and the drugs separately or as a mixture, to the femoral vein. A modification of the method comprised injection of K16ApoE pre-mixed with cetuximab, followed by injection of a 'small-molecule' drug. PRINCIPAL FINDINGS: Seven-of-seven different small molecules were successfully delivered to the brain via K16ApoE. Depending on the method, brain uptake with K16ApoE was 0.72-1.1% for cisplatin and 0.58-0.92% for methotrexate (34-50-fold and 54-92 fold greater for cisplatin and methotrexate, respectively, with K16ApoE than without. Visually intense brain-uptake of Evans Blue, Light Green SF and Crocein scarlet was also achieved. Direct intracranial injection of EB show locally restricted distribution of the dye in the brain, whereas K16ApoE-mediated intravenous injection of EB resulted in the distribution of the dye throughout the brain. Experiments with insulin suggest that ligand-receptor signaling intrinsic to the BBB provides a natural means for passive transport of some molecules across the BBB. SIGNIFICANCE: The results suggest that the carrier peptide can non-covalently transport various chemotherapeutic agents to the brain. Thus, the method offers an avenue for pre-clinical evaluation of various small and large therapeutic molecules

Substituent Effects on the Hydrogen Bonding between 4-Substituted Phenols and HF, H2O, NH3

Institute of Scientific and Technical Information of China (English)

程宇辉; 傅尧; 刘磊; 郭庆祥

2003-01-01

Density function theory UB3LYP/6-31+g(d) calculations were performed to study the hydrogen bonds between para-substituted phenols and HF, H2O, or NH3. It revealed that many properties of the non-covalent complexes, such as the interaction energies, donor-acceptor distances, bond lengths and vibration frequencies, showed well-defined substituent effects. Therefore, from the substituent effects not only the mechanism of a certain non-covalent interaction can be better understood, but also the interaction energies and structures of a certain non-covalent complex, which otherwise might be very hard or resource-consuming to estimate, can be easily predicted.

Electronic structures in ion-surface interactions

International Nuclear Information System (INIS)

Kiuchi, Masato; Takeuchi, Takae; Yamamoto, Masao.

1997-01-01

A chemical bond generated by the interaction between low energy ion and base was investigated by ab initio molecular orbital method. The effects of ion charge were studied by calculation of this method. When carbon ion approached to graphite base (C 24 H 12 ), the positive ion and the neutral atom covalently bonded, but the negative ion did not combine with it. When carbon ion was injected into h-BN base (B 12 N 12 H 12 , hexagonal system boron nitride), the positive ion and the neutron atom formed covalent bond and the van der Waals binding, and the negative ion interacted statically with it. (S.Y.)

The impact of the self-interaction error on the density functional theory description of dissociating radical cations: ionic and covalent dissociation limits.

Science.gov (United States)

Gräfenstein, Jürgen; Kraka, Elfi; Cremer, Dieter

2004-01-08

Self-interaction corrected density functional theory was used to determine the self-interaction error for dissociating one-electron bonds. The self-interaction error of the unpaired electron mimics nondynamic correlation effects that have no physical basis where these effects increase for increasing separation distance. For short distances the magnitude of the self-interaction error takes a minimum and increases then again for decreasing R. The position of the minimum of the magnitude of the self-interaction error influences the equilibrium properties of the one-electron bond in the radical cations H2+ (1), B2H4+ (2), and C2H6+ (3), which differ significantly. These differences are explained by hyperconjugative interactions in 2 and 3 that are directly reflected by the self-interaction error and its orbital contributions. The density functional theory description of the dissociating radical cations suffers not only from the self-interaction error but also from the simplified description of interelectronic exchange. The calculated differences between ionic and covalent dissociation for 1, 2, and 3 provide an excellent criterion for determining the basic failures of density functional theory, self-interaction corrected density functional theory, and other methods. Pure electronic, orbital relaxation, and geometric relaxation contributions to the self-interaction error are discussed. The relevance of these effects for the description of transition states and charge transfer complexes is shown. Suggestions for the construction of new exchange-correlation functionals are given. In this connection, the disadvantages of recently suggested self-interaction error-free density functional theory methods are emphasized. (c) 2004 American Institute of Physics

Non-Covalent Interactions in the Crystal Structure of Methyl 4-Hydroxy-3-Nitrobenzoate

Directory of Open Access Journals (Sweden)

Jim Simpson

2012-06-01

Full Text Available Methyl 4-hydroxy-3-nitrobenzoate, (I, C8H7NO5, crystallizes with two unique molecules, A and B, in the asymmetric unit of the triclinic unit cell. The space group was assigned as P-1, with lattice parameters a = 0.72831(15, b = 1.0522(2, c = 1.1410(2 nm, α = 83.38(3, β = 80.83(3, γ = 82.02(3°, Z = 4, V = 0.8510(3 nm3, Mr = 197.15, Dc = 1.539 g/m3, µ= 0.131 mm−1, F(000 = 408, R = 0.1002 and wR = 0.2519. In the crystal structure, 12 hydrogen bonding and two p-stacking interactions link the molecules into infinite stacked sheets parallel to (101.

The use of Wannier function in the calculations of band structure of covalent crystals

International Nuclear Information System (INIS)

Lu Dong; Yang Guang

1985-10-01

A variational procedure has been used to build up Wannier functions to study the energy bands of diamond, silicon and α-tin. For the case of silicon the Wannier function, density of charge and band structure are calculated self-consistently and a simple method in a non-self-consistent way has been used to compute the band structure of diamond, silicon and α-tin. The method seems to be effective to describe the electronic properties of covalent crystals. (author)

Geometrical Aspects of non-gravitational interactions

OpenAIRE

Roldan, Omar; Barros Jr, C. C.

2016-01-01

In this work we look for a geometric description of non-gravitational forces. The basic ideas are proposed studying the interaction between a punctual particle and an electromagnetic external field. For this purpose, we introduce the concept of proper space-time, that allow us to describe this interaction in a way analogous to the one that the general relativity theory does for gravitation. The field equations that define this geometry are similar to the Einstein's equations, where in general...

A versatile strategy towards non-covalent functionalization of graphene by surface-confined supramolecular self-assembly of Janus tectons

Directory of Open Access Journals (Sweden)

Ping Du

2015-03-01

Full Text Available Two-dimensional (2D, supramolecular self-assembly at surfaces is now well-mastered with several existing examples. However, one remaining challenge to enable future applications in nanoscience is to provide potential functionalities to the physisorbed adlayer. This work reviews a recently developed strategy that addresses this key issue by taking advantage of a new concept, Janus tecton materials. This is a versatile, molecular platform based on the design of three-dimensional (3D building blocks consisting of two faces linked by a cyclophane-type pillar. One face is designed to steer 2D self-assembly onto C(sp2-carbon-based flat surfaces, the other allowing for the desired functionality above the substrate with a well-controlled lateral order. In this way, it is possible to simultaneously obtain a regular, non-covalent paving as well as supramolecular functionalization of graphene, thus opening interesting perspectives for nanoscience applications.

Privileged Electrophile Sensors: A Resource for Covalent Drug Development.

Science.gov (United States)

Long, Marcus John Curtis; Aye, Yimon

2017-07-20

This Perspective delineates how redox signaling affects the activity of specific enzyme isoforms and how this property may be harnessed for rational drug design. Covalent drugs have resurged in recent years and several reports have extolled the general virtues of developing irreversible inhibitors. Indeed, many modern pharmaceuticals contain electrophilic appendages. Several invoke a warhead that hijacks active-site nucleophiles whereas others take advantage of spectator nucleophilic side chains that do not participate in enzymatic chemistry, but are poised to bind/react with electrophiles. The latest data suggest that innate electrophile sensing-which enables rapid reaction with an endogenous signaling electrophile-is a quintessential resource for the development of covalent drugs. For instance, based on recent work documenting isoform-specific electrophile sensing, isozyme non-specific drugs may be converted to isozyme-specific analogs by hijacking privileged first-responder electrophile-sensing cysteines. Because this approach targets functionally relevant cysteines, we can simultaneously harness previously untapped moonlighting roles of enzymes linked to redox sensing. Copyright © 2017 Elsevier Ltd. All rights reserved.

Anticoagulant and antimicrobial finishing of non-woven polypropylene textiles

International Nuclear Information System (INIS)

Degoutin, S; Jimenez, M; Casetta, M; Bellayer, S; Chai, F; Blanchemain, N; Neut, C; Kacem, I; Traisnel, M; Martel, B

2012-01-01

The aim of this work is to prepare non-woven polypropylene (PP) textile functionalized with bioactive molecules in order to improve its anticoagulation and antibacterial properties. This paper describes the optimization of the grafting process of acrylic acid (AA) on low-pressure cold-plasma pre-activated PP, the characterization of the modified substrates and the effect of these modifications on the in vitro biological response towards cells. Then, the immobilization of gentamicin (aminoglycoside antibiotic) and heparin (anticoagulation agent) has been carried out on the grafted samples by either ionic interactions or covalent linkages. Their bioactivity has been investigated and related to the nature of their interactions with the substrate. For gentamicin-immobilized AA-grafted samples, an inhibition radius and a reduction of 99% of the adhesion of Escherichia coli have been observed when gentamicin was linked by ionic interactions, allowing the release of the antibiotic. By contrast, for heparin-immobilized AA-grafted PP samples, a strong increase of the anticoagulant effect up to 35 min has been highlighted when heparin was covalently bonded on the substrate, by contact with the blood drop. (paper)

Origin of the Distinct Diffusion Behaviors of Cu and Ag in Covalent and Ionic Semiconductors.

Science.gov (United States)

Deng, Hui-Xiong; Luo, Jun-Wei; Li, Shu-Shen; Wei, Su-Huai

2016-10-14

It is well known that Cu diffuses faster than Ag in covalent semiconductors such as Si, which has prevented the replacement of Ag by Cu as a contact material in Si solar cells for reducing the cost. Surprisingly, in more ionic materials such as CdTe, Ag diffuses faster than Cu despite that it is larger than Cu, which has prevented the replacement of Cu by Ag in CdTe solar cells to improve the performance. But, so far, the mechanisms behind these distinct diffusion behaviors of Cu and Ag in covalent and ionic semiconductors have not been addressed. Here we reveal the underlying mechanisms by combining the first-principles calculations and group theory analysis. We find that the symmetry controlled s-d coupling plays a critical role in determining the diffusion behaviors. The s-d coupling is absent in pure covalent semiconductors but increases with the ionicity of the zinc blende semiconductors, and is larger for Cu than for Ag, owing to its higher d orbital energy. In conjunction with Coulomb interaction and strain energy, the s-d coupling is able to explain all the diffusion behaviors from Cu to Ag and from covalent to ionic hosts. This in-depth understanding enables us to engineer the diffusion of impurities in various semiconductors.

Covalent Surface Modifications of Carbon Nanotubes.

Energy Technology Data Exchange (ETDEWEB)

Pavia Sanders, Adriana [Sandia National Lab. (SNL-CA), Livermore, CA (United States); O' Bryan, Greg [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

2017-07-01

A report meant to document the chemistries investigated by the author for covalent surface modification of CNTs. Oxidation, cycloaddition, and radical reactions were explored to determine their success at covalently altering the CNT surface. Characterization through infrared spectroscopy, Raman spectroscopy, and thermo gravimetric analysis was performed in order to determine the success of the chemistries employed. This report is not exhaustive and was performed for CNT surface modification exploration as it pertains to the "Next Gen" project.

Do native brown trout and non-native brook trout interact reproductively?

Science.gov (United States)

Cucherousset, J.; Aymes, J. C.; Poulet, N.; Santoul, F.; Céréghino, R.

2008-07-01

Reproductive interactions between native and non-native species of fish have received little attention compared to other types of interactions such as predation or competition for food and habitat. We studied the reproductive interactions between non-native brook trout ( Salvelinus fontinalis) and native brown trout ( Salmo trutta) in a Pyrenees Mountain stream (SW France). We found evidence of significant interspecific interactions owing to consistent spatial and temporal overlap in redd localizations and spawning periods. We observed mixed spawning groups composed of the two species, interspecific subordinate males, and presence of natural hybrids (tiger trout). These reproductive interactions could be detrimental to the reproduction success of both species. Our study shows that non-native species might have detrimental effects on native species via subtle hybridization behavior.

Analysis of the binding interaction in uric acid - Human hemoglobin system by spectroscopic techniques

Science.gov (United States)

Makarska-Bialokoz, Magdalena

2017-05-01

The binding interaction between human hemoglobin and uric acid has been studied for the first time, by UV-vis absorption and steady-state, synchronous and three-dimensional fluorescence techniques. Characteristic effects observed for human hemoglobin intrinsic fluorescence during interaction with uric acid at neutral pH point at the formation of stacking non-covalent and non-fluorescent complexes. All the calculated parameters, the binding, fluorescence quenching and bimolecular quenching rate constants, as well as Förster resonance energy transfer parameters confirm the existence of static quenching. The results of synchronous fluorescence measurements indicate that the fluorescence quenching of human hemoglobin originates both from Trp and Tyr residues and that the addition of uric acid could significantly hinder the physiological functions of human hemoglobin.

Photophysical studies of the interactions of poly(amidoamine) generation zero (PAMAM G0) with copper and zinc ions

Energy Technology Data Exchange (ETDEWEB)

López-Cabaña, Z.E. [Laboratory of Asymmetric Synthesis, Chemistry Institute of Natural Resources, University of Talca (Chile); Valdés, O. [Nanobiotechnology Division at University of Talca, Fraunhofer Chile Research Foundation – Center for Systems Biotechnology, FCR-CSB, P.O. Box 747 Talca (Chile); Vergara, C.E. [Laboratory of Asymmetric Synthesis, Chemistry Institute of Natural Resources, University of Talca (Chile); Camarada, M.B. [Universidad Andrés Bello, Facultad de Biología, Center for Bioinformatics and Integrative Biology (CBIB), República 239, Santiago (Chile); Fundación Fraunhofer Chile Research, M. Sánchez Fontecilla 310 piso 14, Las Condes (Chile); Nachtigall, F.M. [Nanobiotechnology Division at University of Talca, Fraunhofer Chile Research Foundation – Center for Systems Biotechnology, FCR-CSB, P.O. Box 747 Talca (Chile); González-Nilo, F.D. [Universidad Andrés Bello, Facultad de Biología, Center for Bioinformatics and Integrative Biology (CBIB), República 239, Santiago (Chile); Fundación Fraunhofer Chile Research, M. Sánchez Fontecilla 310 piso 14, Las Condes (Chile); Santos, Leonardo S., E-mail: lssantos@utalca.cl [Laboratory of Asymmetric Synthesis, Chemistry Institute of Natural Resources, University of Talca (Chile); Nanobiotechnology Division at University of Talca, Fraunhofer Chile Research Foundation – Center for Systems Biotechnology, FCR-CSB, P.O. Box 747 Talca (Chile)

2015-08-15

This study reports the photophysical behavior of poly(amidoamine) generation zero (PAMAM G0) in the presence of Cu(II) and Zn(II) ions in aqueous solutions using absorption and fluorescence spectroscopy. Theoretical and experimental results confirmed the presence of a strong covalent metal–ligand interaction between PAMAM G0 and copper ion that favored the formation of a ligand–metal charge transfer band coordination complex. In the case of Zn(II), no complex formation with PAMAM G0 was registered. Structure analysis identified the presence of aggregate like PAMAM G0–Zn moieties that generated an enhancement in the fluorescence emission of PAMAM G0. - Highlights: • Photophysical behavior of PAMAM G0 dendrimer with Cu and Zn ions was studied. • Strong covalent metal–ligand interaction was confirmed between PAMAM G0–Cu(II). • No complex formation with PAMAM G0 was registered in the case of Zn(II). • Dendrimer aggregate generated an enhancement in fluorescence emission.

Photophysical studies of the interactions of poly(amidoamine) generation zero (PAMAM G0) with copper and zinc ions

International Nuclear Information System (INIS)

López-Cabaña, Z.E.; Valdés, O.; Vergara, C.E.; Camarada, M.B.; Nachtigall, F.M.; González-Nilo, F.D.; Santos, Leonardo S.

2015-01-01

This study reports the photophysical behavior of poly(amidoamine) generation zero (PAMAM G0) in the presence of Cu(II) and Zn(II) ions in aqueous solutions using absorption and fluorescence spectroscopy. Theoretical and experimental results confirmed the presence of a strong covalent metal–ligand interaction between PAMAM G0 and copper ion that favored the formation of a ligand–metal charge transfer band coordination complex. In the case of Zn(II), no complex formation with PAMAM G0 was registered. Structure analysis identified the presence of aggregate like PAMAM G0–Zn moieties that generated an enhancement in the fluorescence emission of PAMAM G0. - Highlights: • Photophysical behavior of PAMAM G0 dendrimer with Cu and Zn ions was studied. • Strong covalent metal–ligand interaction was confirmed between PAMAM G0–Cu(II). • No complex formation with PAMAM G0 was registered in the case of Zn(II). • Dendrimer aggregate generated an enhancement in fluorescence emission

Capillary electrophoresis of covalently functionalized single-chirality carbon nanotubes.

Science.gov (United States)

He, Pingli; Meany, Brendan; Wang, Chunyan; Piao, Yanmei; Kwon, Hyejin; Deng, Shunliu; Wang, YuHuang

2017-07-01

We demonstrate the separation of chirality-enriched single-walled carbon nanotubes (SWCNTs) by degree of surface functionalization using high-performance CE. Controlled amounts of negatively charged and positively charged functional groups were attached to the sidewall of chirality-enriched SWCNTs through covalent functionalization using 4-carboxybenzenediazonium tetrafluoroborate or 4-diazo-N,N-diethylaniline tetrafluoroborate, respectively. Surfactant- and pH-dependent studies confirmed that under conditions that minimized ionic screening effects, separation of these functionalized SWCNTs was strongly dependent on the surface charge density introduced through covalent surface chemistry. For both heterogeneous mixtures and single-chirality-enriched samples, covalently functionalized SWCNTs showed substantially increased peak width in electropherogram spectra compared to nonfunctionalized SWCNTs, which can be attributed to a distribution of surface charges along the functionalized nanotubes. Successful separation of functionalized single-chirality SWCNTs by functional density was confirmed with UV-Vis-NIR absorption and Raman scattering spectroscopies of fraction collected samples. These results suggest a high degree of structural heterogeneity in covalently functionalized SWCNTs, even for chirality-enriched samples, and show the feasibility of applying CE for high-performance separation of nanomaterials based on differences in surface functional density. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interactions between non-physician clinicians and industry: a systematic review.

Directory of Open Access Journals (Sweden)

Quinn Grundy

2013-11-01

Full Text Available BACKGROUND: With increasing restrictions placed on physician-industry interactions, industry marketing may target other health professionals. Recent health policy developments confer even greater importance on the decision making of non-physician clinicians. The purpose of this systematic review is to examine the types and implications of non-physician clinician-industry interactions in clinical practice. METHODS AND FINDINGS: We searched MEDLINE and Web of Science from January 1, 1946, through June 24, 2013, according to PRISMA guidelines. Non-physician clinicians eligible for inclusion were: Registered Nurses, nurse prescribers, Physician Assistants, pharmacists, dieticians, and physical or occupational therapists; trainee samples were excluded. Fifteen studies met inclusion criteria. Data were synthesized qualitatively into eight outcome domains: nature and frequency of industry interactions; attitudes toward industry; perceived ethical acceptability of interactions; perceived marketing influence; perceived reliability of industry information; preparation for industry interactions; reactions to industry relations policy; and management of industry interactions. Non-physician clinicians reported interacting with the pharmaceutical and infant formula industries. Clinicians across disciplines met with pharmaceutical representatives regularly and relied on them for practice information. Clinicians frequently received industry "information," attended sponsored "education," and acted as distributors for similar materials targeted at patients. Clinicians generally regarded this as an ethical use of industry resources, and felt they could detect "promotion" while benefiting from industry "information." Free samples were among the most approved and common ways that clinicians interacted with industry. Included studies were observational and of varying methodological rigor; thus, these findings may not be generalizable. This review is, however, the

Interactions between non-physician clinicians and industry: a systematic review.

Science.gov (United States)

Grundy, Quinn; Bero, Lisa; Malone, Ruth

2013-11-01

With increasing restrictions placed on physician-industry interactions, industry marketing may target other health professionals. Recent health policy developments confer even greater importance on the decision making of non-physician clinicians. The purpose of this systematic review is to examine the types and implications of non-physician clinician-industry interactions in clinical practice. We searched MEDLINE and Web of Science from January 1, 1946, through June 24, 2013, according to PRISMA guidelines. Non-physician clinicians eligible for inclusion were: Registered Nurses, nurse prescribers, Physician Assistants, pharmacists, dieticians, and physical or occupational therapists; trainee samples were excluded. Fifteen studies met inclusion criteria. Data were synthesized qualitatively into eight outcome domains: nature and frequency of industry interactions; attitudes toward industry; perceived ethical acceptability of interactions; perceived marketing influence; perceived reliability of industry information; preparation for industry interactions; reactions to industry relations policy; and management of industry interactions. Non-physician clinicians reported interacting with the pharmaceutical and infant formula industries. Clinicians across disciplines met with pharmaceutical representatives regularly and relied on them for practice information. Clinicians frequently received industry "information," attended sponsored "education," and acted as distributors for similar materials targeted at patients. Clinicians generally regarded this as an ethical use of industry resources, and felt they could detect "promotion" while benefiting from industry "information." Free samples were among the most approved and common ways that clinicians interacted with industry. Included studies were observational and of varying methodological rigor; thus, these findings may not be generalizable. This review is, however, the first to our knowledge to provide a descriptive analysis

To bend or not to bend – are heteroatom interactions within conjugated molecules effective in dictating conformation and planarity?

KAUST Repository

Conboy, Gary; Spencer, Howard J.; Angioni, Enrico; Kanibolotsky, Alexander L.; Findlay, Neil J.; Coles, Simon J.; Wilson, Claire; Pitak, Mateusz B.; Risko, Chad; Coropceanu, Veaceslav; Bredas, Jean-Luc; Skabara, Peter J.

2016-01-01

We consider the roles of heteroatoms (mainly nitrogen, the halogens and the chalcogens) in dictating the conformation of linear conjugated molecules and polymers through non-covalent intramolecular interactions. Whilst hydrogen bonding is a competitive and sometimes more influential interaction, we provide unambiguous evidence that heteroatoms are able to determine the conformation of such materials with reasonable predictability.

To bend or not to bend – are heteroatom interactions within conjugated molecules effective in dictating conformation and planarity?

KAUST Repository

Conboy, Gary

2016-04-26

We consider the roles of heteroatoms (mainly nitrogen, the halogens and the chalcogens) in dictating the conformation of linear conjugated molecules and polymers through non-covalent intramolecular interactions. Whilst hydrogen bonding is a competitive and sometimes more influential interaction, we provide unambiguous evidence that heteroatoms are able to determine the conformation of such materials with reasonable predictability.

Structure-based non-canonical amino acid design to covalently crosslink an antibody–antigen complex

Science.gov (United States)

Xu, Jianqing; Tack, Drew; Hughes, Randall A.; Ellington, Andrew D.; Gray, Jeffrey J.

2014-01-01

Engineering antibodies to utilize non-canonical amino acids (NCAA) should greatly expand the utility of an already important biological reagent. In particular, introducing crosslinking reagents into antibody complementarity determining regions (CDRs) should provide a means to covalently crosslink residues at the antibody–antigen interface. Unfortunately, finding the optimum position for crosslinking two proteins is often a matter of iterative guessing, even when the interface is known in atomic detail. Computer-aided antibody design can potentially greatly restrict the number of variants that must be explored in order to identify successful crosslinking sites. We have therefore used Rosetta to guide the introduction of an oxidizable crosslinking NCAA, l-3,4-dihydroxyphenylalanine (l-DOPA), into the CDRs of the anti-protective antigen scFv antibody M18, and have measured crosslinking to its cognate antigen, domain 4 of the anthrax protective antigen. Computed crosslinking distance, solvent accessibility, and interface energetics were three factors considered that could impact the efficiency of l-DOPA-mediated crosslinking. In the end, 10 variants were synthesized, and crosslinking efficiencies were generally 10% or higher, with the best variant crosslinking to 52% of the available antigen. The results suggest that computational analysis can be used in a pipeline for engineering crosslinking antibodies. The rules learned from l-DOPA crosslinking of antibodies may also be generalizable to the formation of other crosslinked interfaces and complexes. PMID:23680795

Systematic studies of covalent functionalization of carbon nanotubes via argon plasma-assisted UV grafting

International Nuclear Information System (INIS)

Yan, Y H; Cui, J; Chan-Park, M B; Wang, X; Wu, Q Y

2007-01-01

Single-walled carbon nanotubes (SWNTs) with 1-vinylimidazole species covalently attached to their sidewalls and end caps have been prepared by ultraviolet (UV) irradiation in 1-vinylimidazole monomer. This process can be greatly assisted by argon (Ar) plasma pretreatment, which generates more defect sites at the tube ends and sidewalls acting as the active sites for the subsequent UV grafting of 1-vinylimidazole molecules. The effects of total deposited energy of Ar plasma treatment, either by change of treatment time or discharge power, on the functionalization degree and structural morphology of the resulting nanotubes are systematically studied. By control of the Ar plasma treatment time within 5 min at the discharge power of 200 W, no visible chopping of the functionalized SWNTs was observed. Under this advised optimum processing condition, the functionalization degree, estimated by x-ray photoelectron spectroscopy (XPS) measurement, is as high as around 26 wt% 1-vinylimidazole molecules grafted onto the nanotubes. This method may be extended to other reactive vinyl monomers and offers another diverse way of covalent functionalization of SWNTs

Vanillyl alcohol oxidases produced in Komagataella phaffii contain a highly stable non-covalently bound anionic FAD semiquinone

NARCIS (Netherlands)

Gygli, G.A.; Berkel, van W.J.H.

2017-01-01

Vanillyl alcohol oxidase (VAO) from Penicillium simplicissimum is a covalent flavoprotein that has emerged as a promising biocatalyst for the production of aromatic fine chemicals such as vanillin, coniferyl alcohol and enantiopure 1-(4’-hydroxyphenyl) alcohols. The largescale production of this

Design, synthesis and DNA interactions of a chimera between a platinum complex and an IHF mimicking peptide.

Science.gov (United States)

Rao, Harita; Damian, Mariana S; Alshiekh, Alak; Elmroth, Sofi K C; Diederichsen, Ulf

2015-12-28

Conjugation of metal complexes with peptide scaffolds possessing high DNA binding affinity has shown to modulate their biological activities and to enhance their interaction with DNA. In this work, a platinum complex/peptide chimera was synthesized based on a model of the Integration Host Factor (IHF), an architectural protein possessing sequence specific DNA binding and bending abilities through its interaction with a minor groove. The model peptide consists of a cyclic unit resembling the minor grove binding subdomain of IHF, a positively charged lysine dendrimer for electrostatic interactions with the DNA phosphate backbone and a flexible glycine linker tethering the two units. A norvaline derived artificial amino acid was designed to contain a dimethylethylenediamine as a bidentate platinum chelating unit, and introduced into the IHF mimicking peptides. The interaction of the chimeric peptides with various DNA sequences was studied by utilizing the following experiments: thermal melting studies, agarose gel electrophoresis for plasmid DNA unwinding experiments, and native and denaturing gel electrophoresis to visualize non-covalent and covalent peptide-DNA adducts, respectively. By incorporation of the platinum metal center within the model peptide mimicking IHF we have attempted to improve its specificity and DNA targeting ability, particularly towards those sequences containing adjacent guanine residues.

Substituent Effects on the Hydrogen Bonding Between Phenolate and HF, H2O and NH3

Institute of Scientific and Technical Information of China (English)

无

2002-01-01

B3LYP/6-31+g(d) calculations were performed on the hydrogen bonded complexes between substituted phenolates and HF, H2O as well as NH3. It was found that some properties of the non-covalent complexes, including the interaction energies, donor-acceptor (host-guest) distances, bond lengths, and vibration frequencies, could show well-defined substituent effects. Thus, from the substituent studies we can not only understand the mechanism of a particular non-covalent interaction better, but also easily predict the interaction energies and structures of a particular non-covalent complex, which might otherwise be very hard or resource-consuming to be known. This means that substituent effect is indeed a useful tool to be used in supramolecular chemistry and therefore, many valuable studies remain to be carried out.

UV-SPR biosensor for biomolecular interaction studies

Science.gov (United States)

Geiss, F. A.; Fossati, S.; Khan, I.; Gisbert Quilis, N.; Knoll, W.; Dostalek, J.

2017-05-01

UV surface plasmon resonance (SPR) for direct in situ detection of protein binding events is reported. A crossed relief aluminum grating was employed for diffraction coupling to surface plasmons as an alternative to more commonly used attenuated total reflection method. Wavelength interrogation of SPR was carried out by using transmission measurements in order to probe odorant-binding protein 14 (OBP14) of the honey bee (Apis mellifera). The native oxide layer on the top of an aluminum grating sensor chip allows for covalent coupling of protein molecules by using regular silane-based linkers. The probing of bound OBP14 protein at UV with confined field of surface plasmons holds potential for further studies of interaction with recently developed artificial fluorescent odorants.

Spectroscopic Evidence for Covalent Binding of Sulfadiazine to Natural Soils via 1,4-nucleophilic addition (Michael Type Addition) studied by Spin Labeling ESR

Science.gov (United States)

Aleksandrova, Olga

2015-04-01

Among different classes of veterinary pharmaceuticals, Sulfadiazine (SDZ) is widely used in animal husbandry. Its residues were detected in different environmental compartments. However, soil is a hot spot for SDZ as it receives a large portion of excreted compounds through the application of manure during soil fertilization. Ample studies on the fate of SDZ in soils showed that a large portion forms nonextractable residues (NER) along with transformation products and a low mineralization (Mueller et al., 2013). A common observation was an initially fast formation of NER up to 10% of the applied amount promptly after the application of SDZ to soil, and this portion increased up to 50% within a few days (Mueller et al., 2013; Nowak et al., 2011). A common finding for SDZ, as for other sulfonamides, was biphasic kinetics of the formation of NER, which was attributed to the occurrence of two reaction processes: a rapid, often reversible process and a slower, irreversible process (Weber et al., 1996). A single-phase reaction process was also established under anaerobic treatment (Gulkowska et al., 2014). A major focus of this work is to elucidate a reaction mechanism of covalent binding of SDZ to soil that is currently required to estimate a risk of NER formed by SDZ in soils for human health. Taking into account a key role of the amine functional groups of SDZ on its reactivity in soil, nitroxide radicals with the sewed aromatic or aliphatic amines labeled soil samples and then, were investigated by means of ESR spectroscopy. 2,5,5-Trimethyl-2-(3-aminophenyl)pyrrolidin-1-yloxy and 4-amino-2,2,6,6-Tetramethylpiperidin-1-oxyl modeled decomposition products of SDZ with the aromatic and aliphatic amines, respectively. The application of the defined combination of both spin labels (SL) to different soils well simulated a change of a paramagnetic signal of soil organic radicals interacted with SDZ. After their application to soil, SL were found in soil sites characterized

Covalently bound molecular states in beryllium and carbon isotopes

International Nuclear Information System (INIS)

Wolfram von, Oertzen; Hans-Gerhard, Bohlen; Wolfram von, Oertzen

2003-01-01

Nuclear clustering in N=Z nuclei has been studied since many decades. States close to the decay thresholds, as described by the Ikeda diagram, are of particular interest. Recent studies in loosely bound systems, as observed with neutron-rich nuclei has revived the interest in cluster structures in nuclei, with additional valence neutrons, which give rise to pronounced covalent molecular structures. The Beryllium isotopes represent the first example of such unique states in nuclear physics with extreme deformations. In the deformed shell model these are referred to as super- and hyper-deformation. These states can be described explicitly by molecular concepts, with neutrons in covalent binding orbits. Examples of recent experiments performed at the HMI-Berlin demonstrating the molecular structure of the rotational bands in Beryllium isotopes are presented. Further work on chain states (nuclear polymers) in the carbon isotopes is in progress, these are the first examples of deformed structures in nuclei with an axis ratio of 3:1. A threshold diagram with clusters bound via neutrons in covalent molecular configurations can be established, which can serve as a guideline for future work. (authors)

Covalent versus ionic bonding in alkalimetal fluoride oligomers

NARCIS (Netherlands)

Bickelhaupt, F.M.; Sola, M.; Fonseca Guerra, C.

2007-01-01

The most polar bond in chemistry is that between a fluorine and an alkalimetal atom. Inspired by our recent finding that other polar bonds (C - M and H - M) have important covalent contributions (i.e., stabilization due to bond overlap), we herein address the question if covalency is also essential

Eriocalyxin B Inhibits STAT3 Signaling by Covalently Targeting STAT3 and Blocking Phosphorylation and Activation of STAT3.

Directory of Open Access Journals (Sweden)

Xiaokui Yu

Full Text Available Activated STAT3 plays an important role in oncogenesis by stimulating cell proliferation and resisting apoptosis. STAT3 therefore is an attractive target for cancer therapy. We have screened a traditional Chinese herb medicine compound library and found Eriocalyxin B (EB, a diterpenoid from Isodon eriocalyx, as a specific inhibitor of STAT3. EB selectively inhibited constitutive as well as IL-6-induced phosphorylation of STAT3 and induced apoptosis of STAT3-dependent tumor cells. EB did not affect the upstream protein tyrosine kinases or the phosphatase (PTPase of STAT3, but rather interacted directly with STAT3. The effects of EB could be abolished by DTT or GSH, suggesting a thiol-mediated covalent linkage between EB and STAT3. Site mutagenesis of cysteine in and near the SH2 domain of STAT3 identified Cys712 to be the critical amino acid for the EB-induced inactivation of STAT3. Furthermore, LC/MS/MS analyses demonstrated that an α, β-unsaturated carbonyl of EB covalently interacted with the Cys712 of STAT3. Computational modeling analyses also supported a direct interaction between EB and the Cys712 of STAT3. These data strongly suggest that EB directly targets STAT3 through a covalent linkage to inhibit the phosphorylation and activation of STAT3 and induces apoptosis of STAT3-dependent tumor cells.

Negative Symptoms and Avoidance of Social Interaction: A Study of Non-Verbal Behaviour.

Science.gov (United States)

Worswick, Elizabeth; Dimic, Sara; Wildgrube, Christiane; Priebe, Stefan

2018-01-01

Non-verbal behaviour is fundamental to social interaction. Patients with schizophrenia display an expressivity deficit of non-verbal behaviour, exhibiting behaviour that differs from both healthy subjects and patients with different psychiatric diagnoses. The present study aimed to explore the association between non-verbal behaviour and symptom domains, overcoming methodological shortcomings of previous studies. Standardised interviews with 63 outpatients diagnosed with schizophrenia were videotaped. Symptoms were assessed using the Clinical Assessment Interview for Negative Symptoms (CAINS), the Positive and Negative Syndrome Scale (PANSS) and the Calgary Depression Scale. Independent raters later analysed the videos for non-verbal behaviour, using a modified version of the Ethological Coding System for Interviews (ECSI). Patients with a higher level of negative symptoms displayed significantly fewer prosocial (e.g., nodding and smiling), gesture, and displacement behaviours (e.g., fumbling), but significantly more flight behaviours (e.g., looking away, freezing). No gender differences were found, and these associations held true when adjusted for antipsychotic medication dosage. Negative symptoms are associated with both a lower level of actively engaging non-verbal behaviour and an increased active avoidance of social contact. Future research should aim to identify the mechanisms behind flight behaviour, with implications for the development of treatments to improve social functioning. © 2017 S. Karger AG, Basel.

Interaction of carbon nano tubes with DNA segments

International Nuclear Information System (INIS)

Peressinotto, Valdirene Sullas Teixeira

2007-01-01

Single- and double-stranded DNA (deoxyribonucleic acid) molecules can strongly bind to single-walled carbon nanotubes (SWNT) via non-covalent interactions. Under certain conditions, the DNA molecule spontaneously self-assembles into a helical wrapping around the tubular structure of the carbon nanotubes to form DNA/SWNT hybrids, which are both stable and soluble in water. This system has recently received extensive attention, since, besides rendering SWNTs dispersible in water as individual tubes, the DNA hybrids are very promising candidates for many applications in nanotechnology and molecular biology. All the possible applications for DNA-SWNT hybrids require, however, a fully understanding of DNA-nanotube wrapping mechanism which is still lacking in the literature. In this context, the aim of this work was to investigate the non-covalent interaction in aqueous medium between SWNTs and synthetic DNA segments having a known nucleotide sequence. Initially, the study was focused on poly d(GT)n sequences (n = 10, 30 and 45) that contain a sequence of alternating guanine and thymine bases and for which the efficiency to disperse and separate carbon nanotubes has already been demonstrated. Besides the size of GT sequences, the effects of ionic strength and pH in the interaction were also investigated. Afterwards, we studied the interaction of SWNT with DNA molecules that contain only a single type of nitrogenous base (DNA homopolymers), which has not been reported in details in the literature. We investigated homopolymers of poly dA 20 , poly dT 20 , poly dC 20 and the duplex poly dA 20 :dT 20 . Most of the study was carried out with small-diameter HiPco SWNTs (with diameters between 0.7 and 1.2 nm). In some studies, SWNTs with diameter around 1.4 nm, synthesized via laser ablation and arc-discharge methods, were also investigated. The arc-discharge nanotubes used in this study were functionalized with carboxylic groups (-COOH) due to their purification using strong

Tribology study of reduced graphene oxide sheets on silicon substrate synthesized via covalent assembly.

Science.gov (United States)

Ou, Junfei; Wang, Jinqing; Liu, Sheng; Mu, Bo; Ren, Junfang; Wang, Honggang; Yang, Shengrong

2010-10-19

Reduced graphene oxide (RGO) sheets were covalently assembled onto silicon wafers via a multistep route based on the chemical adsorption and thermal reduction of graphene oxide (GO). The formation and microstructure of RGO were analyzed by X-ray photoelectron spectroscopy (XPS), attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, Raman spectroscopy, and water contact angle (WCA) measurements. Characterization by atomic force microscopy (AFM) was performed to evaluate the morphology and microtribological behaviors of the samples. Macrotribological performance was tested on a ball-on-plate tribometer. Results show that the assembled RGO possesses good friction reduction and antiwear ability, properties ascribed to its intrinsic structure, that is, the covalent bonding to the substrate and self-lubricating property of RGO.

Improving the Thermostability and Optimal Temperature of a Lipase from the Hyperthermophilic Archaeon Pyrococcus furiosus by Covalent Immobilization

Directory of Open Access Journals (Sweden)

Roberta V. Branco

2015-01-01

Full Text Available A recombinant thermostable lipase (Pf2001Δ60 from the hyperthermophilic Archaeon Pyrococcus furiosus (PFUL was immobilized by hydrophobic interaction on octyl-agarose (octyl PFUL and by covalent bond on aldehyde activated-agarose in the presence of DTT at pH = 7.0 (one-point covalent attachment (glyoxyl-DTT PFUL and on glyoxyl-agarose at pH 10.2 (multipoint covalent attachment (glyoxyl PFUL. The enzyme’s properties, such as optimal temperature and pH, thermostability, and selectivity, were improved by covalent immobilization. The highest enzyme stability at 70°C for 48 h incubation was achieved for glyoxyl PFUL (around 82% of residual activity, whereas glyoxyl-DTT PFUL maintained around 69% activity, followed by octyl PFUL (27% remaining activity. Immobilization on glyoxyl-agarose improved the optimal temperature to 90°C, while the optimal temperature of octyl PFUL was 70°C. Also, very significant changes in activity with different substrates were found. In general, the covalent bond derivatives were more active than octyl PFUL. The E value also depended substantially on the derivative and the conditions used. It was observed that the reaction of glyoxyl-DTT PFUL using methyl mandelate as a substrate at pH 7 presented the best results for enantioselectivity E=22 and enantiomeric excess (ee (% = 91.

Supramolecular interactions in the solid state

Directory of Open Access Journals (Sweden)

Giuseppe Resnati

2015-11-01

Full Text Available In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1 an overview and historical review of halogen bonding; (2 exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3 the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4 strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials.

Transition from metal-ligand bonding to halogen bonding involving a metal as halogen acceptor a study of Cu, Ag, Au, Pt, and Hg complexes

Science.gov (United States)

Oliveira, Vytor; Cremer, Dieter

2017-08-01

Utilizing all-electron Dirac-exact relativistic calculations with the Normalized Elimination of the Small Component (NESC) method and the local vibrational mode approach, the transition from metal-halide to metal halogen bonding is determined for Au-complexes interacting with halogen-donors. The local stretching force constants of the metal-halogen interactions reveal a smooth transition from weak non-covalent halogen bonding to non-classical 3-center-4-electron bonding and finally covalent metal-halide bonding. The strongest halogen bonds are found for dialkylaurates interacting with Cl2 or FCl. Differing trends in the intrinsic halogen-metal bond strength, the binding energy, and the electrostatic potential are explained.

Specific non-monotonous interactions increase persistence of ecological networks.

Science.gov (United States)

Yan, Chuan; Zhang, Zhibin

2014-03-22

The relationship between stability and biodiversity has long been debated in ecology due to opposing empirical observations and theoretical predictions. Species interaction strength is often assumed to be monotonically related to population density, but the effects on stability of ecological networks of non-monotonous interactions that change signs have not been investigated previously. We demonstrate that for four kinds of non-monotonous interactions, shifting signs to negative or neutral interactions at high population density increases persistence (a measure of stability) of ecological networks, while for the other two kinds of non-monotonous interactions shifting signs to positive interactions at high population density decreases persistence of networks. Our results reveal a novel mechanism of network stabilization caused by specific non-monotonous interaction types through either increasing stable equilibrium points or reducing unstable equilibrium points (or both). These specific non-monotonous interactions may be important in maintaining stable and complex ecological networks, as well as other networks such as genes, neurons, the internet and human societies.

Determination and Quantification of Molecular Interactions in Protein Films: A Review

Directory of Open Access Journals (Sweden)

Felicia Hammann

2014-12-01

Full Text Available Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography and analysis of solid films (spectroscopy techniques, X-ray scattering methods. To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins.

Determination and Quantification of Molecular Interactions in Protein Films: A Review.

Science.gov (United States)

Hammann, Felicia; Schmid, Markus

2014-12-10

Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography) and analysis of solid films (spectroscopy techniques, X-ray scattering methods). To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins.

CRITIC2: A program for real-space analysis of quantum chemical interactions in solids

Science.gov (United States)

Otero-de-la-Roza, A.; Johnson, Erin R.; Luaña, Víctor

2014-03-01

We present CRITIC2, a program for the analysis of quantum-mechanical atomic and molecular interactions in periodic solids. This code, a greatly improved version of the previous CRITIC program (Otero-de-la Roza et al., 2009), can: (i) find critical points of the electron density and related scalar fields such as the electron localization function (ELF), Laplacian, … (ii) integrate atomic properties in the framework of Bader’s Atoms-in-Molecules theory (QTAIM), (iii) visualize non-covalent interactions in crystals using the non-covalent interactions (NCI) index, (iv) generate relevant graphical representations including lines, planes, gradient paths, contour plots, atomic basins, … and (v) perform transformations between file formats describing scalar fields and crystal structures. CRITIC2 can interface with the output produced by a variety of electronic structure programs including WIEN2k, elk, PI, abinit, Quantum ESPRESSO, VASP, Gaussian, and, in general, any other code capable of writing the scalar field under study to a three-dimensional grid. CRITIC2 is parallelized, completely documented (including illustrative test cases) and publicly available under the GNU General Public License. Catalogue identifier: AECB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 11686949 No. of bytes in distributed program, including test data, etc.: 337020731 Distribution format: tar.gz Programming language: Fortran 77 and 90. Computer: Workstations. Operating system: Unix, GNU/Linux. Has the code been vectorized or parallelized?: Shared-memory parallelization can be used for most tasks. Classification: 7.3. Catalogue identifier of previous version: AECB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 157 Nature of problem: Analysis of quantum

Comparing physically abusive, neglectful, and non-maltreating parents during interactions with their children: a meta-analysis of observational studies.

Science.gov (United States)

Wilson, Steven R; Rack, Jessica J; Shi, Xiaowei; Norris, Alda M

2008-09-01

To clarify the nature and extent of differences in the ways that physically abusive, neglectful, and non-maltreating parents communicate during interactions with their children. A meta-analysis was conducted of 33 observational studies comparing parent-child interactions in families where parents have a documented history of physical abuse or neglect vs. where parents have no history of child maltreatment. Parental behaviors were grouped into three clusters (positivity, aversiveness, and involvement) for comparison across studies. When comparing maltreating (physically abusive or neglectful) vs. non-maltreating parents, mean weighted effect sizes for the three behavioral clusters range from d=.46 to .62. Physically abusive parents are distinguished from non-maltreating parents more so than neglectful parents in terms of aversive behavior, whereas the reverse is true for involvement. Publication date, parent and child age, and task structure moderate the magnitude, though not direction, of differences. Parents with a documented history of child physical abuse or child neglect also are distinguished from non-maltreating parents by the levels of aversiveness, positivity, and involvement they display during interactions that constitute the parent-child relationship. Researchers and practitioners need to carefully consider sample size, length and setting of observation, and interaction tasks when using observational methods.

Interaction with the 5D3 monoclonal antibody is regulated by intramolecular rearrangements but not by covalent dimer formation of the human ABCG2 multidrug transporter

DEFF Research Database (Denmark)

Özvegy-Laczka, Csilla; Laczkó, Rozália; Hegedűs, Csilla

2008-01-01

D3 monoclonal antibody shows a function-dependent reactivity to an extracellular epitope of the ABCG2 transporter. In the current experiments we have further characterized the 5D3-ABCG2 interaction. The effect of chemical cross-linking and the modulation of extracellular S-S bridges...... on the transporter function and 5D3 reactivity of ABCG2 were investigated in depth. We found that several protein cross-linkers greatly increased 5D3 labeling in ABCG2 expressing HEK cells; however, there was no correlation between covalent dimer formation, the inhibition of transport activity, and the increase in 5...

The covalence effect of energy levels of ZnS:Mn2+

International Nuclear Information System (INIS)

Dong-Yang, Li; Mao-Lu, Du; Yi, Huang

2013-01-01

The contribution of the different covalence for t 2 and e orbitals must be considered in the investigation of the optical and magnetic properties of the transition metal ion in II–VI and III–V semiconductors. In present paper, two covalent parameters N t and N e associated with t 2 and e orbitals have been adopted to describe the covalence. The energy matrices considering the different covalence for t 2 and e orbitals have been provided for d 5 ions in crystal. These matrices show that the contribution from the Racah parameter A cannot be neglected in calculation of energy-level of d 5 ions in covalent crystal. The calculated results using the matrix show that the energy levels of 4 E and 4 A 1 states split, and the energy-level difference between 4 E and 4 A 1 states increases with increase of the different covalence between t 2 and e orbitals. These energy levels are always degenerate, when the different covalence for t 2 and e orbitals is neglected. By using the energy matrices, the energy-level of ZnS:Mn 2+ has been calculated. The calculated energy levels of ZnS:Mn 2+ are in good agreement with the experiments

Engaging the Terminal: Promoting Halogen Bonding Interactions with Uranyl Oxo Atoms.

Science.gov (United States)

Carter, Korey P; Kalaj, Mark; Surbella, Robert G; Ducati, Lucas C; Autschbach, Jochen; Cahill, Christopher L

2017-11-02

Engaging the nominally terminal oxo atoms of the linear uranyl (UO 2 2+ ) cation in non-covalent interactions represents both a significant challenge and opportunity within the field of actinide hybrid materials. An approach has been developed for promoting oxo atom participation in a range of non-covalent interactions, through judicious choice of electron donating equatorial ligands and appropriately polarizable halogen-donor atoms. As such, a family of uranyl hybrid materials was generated based on a combination of 2,5-dihalobenzoic acid and aromatic, chelating N-donor ligands. Delineation of criteria for oxo participation in halogen bonding interactions has been achieved by preparing materials containing 2,5-dichloro- (25diClBA) and 2,5-dibromobenzoic acid (25diBrBA) coupled with 2,2'-bipyridine (bipy) (1 and 2), 1,10-phenanthroline (phen) (3-5), 2,2':6',2''-terpyridine (terpy) (6-8), or 4'-chloro-2,2':6',2''-terpyridine (Cl-terpy) (9-10), which have been characterized through single crystal X-ray diffraction, Raman, Infrared (IR), and luminescence spectroscopy, as well as through density functional calculations of electrostatic potentials. Looking comprehensively, these results are compared with recently published analogues featuring 2,5-diiodobenzoic acid which indicate that although inclusion of a capping ligand in the uranyl first coordination sphere is important, it is the polarizability of the selected halogen atom that ultimately drives halogen bonding interactions with the uranyl oxo atoms. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural and biochemical analyses reveal insights into covalent flavinylation of the Escherichia coli Complex II homolog quinol:fumarate reductase

Energy Technology Data Exchange (ETDEWEB)

Starbird, C.A.; Maklashina, Elena; Sharma, Pankaj; Qualls-Histed, Susan; Cecchini, Gary; Iverson, T.M. (VA); (UCSF); (Vanderbilt)

2017-06-14

The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the E. coli QFR FrdA subunit. Using a ΔsdhE E. coli strain, we show that the requirement for the assembly factor depends on the cellular redox environment. We next identified residues important for the covalent attachment and selected the FrdAE245 residue, which contributes to proton shuttling during fumarate reduction, for detailed biophysical and structural characterization. We found that QFR complexes containing FrdAE245Q have a structure similar to that of the WT flavoprotein, but lack detectable substrate binding and turnover. In the context of the isolated FrdA subunit, the anticipated assembly intermediate during covalent flavinylation, FrdAE245 variants had stability similar to that of WT FrdA, contained noncovalent FAD, and displayed a reduced capacity to interact with SdhE. However, small-angle X-ray scattering (SAXS) analysis of WT FrdA cross-linked to SdhE suggested that the FrdAE245 residue is unlikely to contribute directly to the FrdA-SdhE protein-protein interface. We also found that no auxiliary factor is absolutely required for flavinylation, indicating that the covalent flavinylation is autocatalytic. We propose that multiple factors, including the SdhE assembly factor and bound dicarboxylates, stimulate covalent flavinylation by preorganizing the active site to stabilize the quinone-methide intermediate.

Reciprocal carbonyl-carbonyl interactions in small molecules and proteins.

Science.gov (United States)

Rahim, Abdur; Saha, Pinaki; Jha, Kunal Kumar; Sukumar, Nagamani; Sarma, Bani Kanta

2017-07-19

Carbonyl-carbonyl n→π* interactions where a lone pair (n) of the oxygen atom of a carbonyl group is delocalized over the π* orbital of a nearby carbonyl group have attracted a lot of attention in recent years due to their ability to affect the 3D structure of small molecules, polyesters, peptides, and proteins. In this paper, we report the discovery of a "reciprocal" carbonyl-carbonyl interaction with substantial back and forth n→π* and π→π* electron delocalization between neighboring carbonyl groups. We have carried out experimental studies, analyses of crystallographic databases and theoretical calculations to show the presence of this interaction in both small molecules and proteins. In proteins, these interactions are primarily found in polyproline II (PPII) helices. As PPII are the most abundant secondary structures in unfolded proteins, we propose that these local interactions may have implications in protein folding.Carbonyl-carbonyl π* non covalent interactions affect the structure and stability of small molecules and proteins. Here, the authors carry out experimental studies, analyses of crystallographic databases and theoretical calculations to describe an additional type of carbonyl-carbonyl interaction.

Positronium annihilation in liquids in the framework of non-local interaction

International Nuclear Information System (INIS)

Mukherjee, Tapas; Dutta, Dhanadeep

2012-01-01

In the bubble model of ortho positronium (o-Ps) annihilation in liquid the origin of the trapping of o-Ps is the electron-exchange repulsive interaction between the electron of o-Ps and the electron of the medium. The corresponding effective interaction is non-local in nature. However, in the prevalent bubble model, this effective interaction is usually treated as local (model) potential (sharp or smooth). In the present study, we have taken an approach to consider this trapping interaction as non-local in nature, which is included through a model separable non-local function to tackle the problem in analytically solvable manner. The analytical calculations show that this non-local interaction effectively acts as a gauge potential in the energy of the Ps atom in parameter (bubble radius) space. The computed bubble variables obtained using experimental Ps annihilation data are shown. A comparison between the present data with the calculated results using prevalent bubble model has been presented. Discussions have been made on the input parameter dependencies of the computed data. - Highlights: ► Bubble model has been modified by considering positronium-atom non-local interaction. ► No straight forward correlation between bubble size and effective potential is observed. ► Non-local potential acts as a guage potential.

Role of direct covalent bonding in enhanced heat dissipation property of flexible graphene oxide–carbon nanotube hybrid film

International Nuclear Information System (INIS)

Hwang, Yongseon; Kim, Myeongjin; Kim, Jooheon

2013-01-01

The thermal conductivity of graphene oxide/multiwalled carbon nanotube (GO/MWCNT) hybrid films with and without covalent bonding is examined in this study. To fabricate chemically bonded GO/MWCNT hybrid films, chlorinated GO and amino-functionalized MWCNTs are bonded covalently. The mixtures of surface modified GO and MWCNT were filtered and then subjected to hot pressing to fabricate stacked films. Examination of these chemically bonded hybrid films reveal that chlorine-doped GO exhibits enhanced electrical properties because it creates hole charge carriers by attracting the electrons in GO towards chlorine. Enhanced electrical conductivity and low sheet resistance are observed also with increasing MWCNT loadings. On comparing the through-plane thermal properties, the chemically bonded hybrid films were found to exhibit higher thermal conductivity than do the physically bonded hybrid films because of the synergetic interaction of functional groups in GO and MWCNTs in the former films. However, excess addition of MWCNTs to the films leads to an increasing phonon scattering density and a decreased thermal conductivity. - Highlights: • Graphene oxide/carbon nanotube (GO/CNT) films are bonded covalently. • GO/CNT hybrid films are prepared through filtering and hot-pressing method. • Chemically bonded hybrid films exhibit enhanced electrical and thermal properties. • Enhanced thermal conductivity is explained according to increasing CNT contents

Consistent structures and interactions by density functional theory with small atomic orbital basis sets.

Science.gov (United States)

Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

2015-08-07

A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods

Consistent structures and interactions by density functional theory with small atomic orbital basis sets

International Nuclear Information System (INIS)

Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

2015-01-01

A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT

New insights into the mechanism of interaction between CO2 and polymers from thermodynamic parameters obtained by in situ ATR-FTIR spectroscopy.

Science.gov (United States)

Gabrienko, Anton A; Ewing, Andrew V; Chibiryaev, Andrey M; Agafontsev, Alexander M; Dubkov, Konstantin A; Kazarian, Sergei G

2016-03-07

This work reports new physical insights of the thermodynamic parameters and mechanisms of possible interactions occurring in polymers subjected to high-pressure CO2. ATR-FTIR spectroscopy has been used in situ to determine the thermodynamic parameters of the intermolecular interactions between CO2 and different functional groups of the polymers capable of specific interactions with sorbed CO2 molecules. Based on the measured ATR-FTIR spectra of the polymer samples subjected to high-pressure CO2 (30 bar) at different temperatures (300-340 K), it was possible to characterize polymer-polymer and CO2-polymer interactions. Particularly, the enthalpy and entropy of the formation of the specific non-covalent complexes between CO2 and the hydroxy (-OH), carbonyl (C[double bond, length as m-dash]O) and hydroxyimino ([double bond, length as m-dash]N-OH) functional groups of the polymer samples have been measured. Furthermore, the obtained spectroscopic results have provided an opportunity for the structure of these complexes to be proposed. An interesting phenomenon regarding the behavior of CO2/polymer systems has also been observed. It has been found that only for the polyketone, the value of enthalpy was negative indicating an exothermic process during the formation of the CO2-polymer non-covalent complexes. Conversely, for the polyoxime and polyalcohol samples there is a positive enthalpy determined. This is a result of the initial polymer-polymer interactions requiring more energy to break than is released during the formation of the CO2-polymer complex. The effect of increasing temperature to facilitate the breaking of the polymer-polymer interactions has also been observed. Hence, a mechanism for the formation of CO2-polymer complexes was suggested based on these results, which occurs via a two-step process: (1) the breaking of the existing polymer-polymer interactions followed by (2) the formation of new CO2-polymer non-covalent interactions.

Surface passivation for tight-binding calculations of covalent solids

International Nuclear Information System (INIS)

Bernstein, N

2007-01-01

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp 3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system

Covalent modification of graphene and graphite using diazonium chemistry: tunable grafting and nanomanipulation.

Science.gov (United States)

Greenwood, John; Phan, Thanh Hai; Fujita, Yasuhiko; Li, Zhi; Ivasenko, Oleksandr; Vanderlinden, Willem; Van Gorp, Hans; Frederickx, Wout; Lu, Gang; Tahara, Kazukuni; Tobe, Yoshito; Uji-I, Hiroshi; Mertens, Stijn F L; De Feyter, Steven

2015-05-26

We shine light on the covalent modification of graphite and graphene substrates using diazonium chemistry under ambient conditions. We report on the nature of the chemical modification of these graphitic substrates, the relation between molecular structure and film morphology, and the impact of the covalent modification on the properties of the substrates, as revealed by local microscopy and spectroscopy techniques and electrochemistry. By careful selection of the reagents and optimizing reaction conditions, a high density of covalently grafted molecules is obtained, a result that is demonstrated in an unprecedented way by scanning tunneling microscopy (STM) under ambient conditions. With nanomanipulation, i.e., nanoshaving using STM, surface structuring and functionalization at the nanoscale is achieved. This manipulation leads to the removal of the covalently anchored molecules, regenerating pristine sp(2) hybridized graphene or graphite patches, as proven by space-resolved Raman microscopy and molecular self-assembly studies.

Autoradiographic evidence of 2-methylindole covalent binding to pulmonary epithelial cells in the goat

International Nuclear Information System (INIS)

Becker, G.M.; Breeze, R.G.; Carlson, J.R.

1984-01-01

3-Methylindole (3MI), the main ruminal fermentation product of L-tryptophan, causes acute pulmonary edema and interstitial emphysema in ruminants. Intravenous infusion of 3MI in goats causes necrosis and sloughing of pneumocytes and bronchial epithelial cells. Previous studies indicate that a reactive metabolite or metabolites of 3MI bind covalently to tissue macromolecules in the lung and this binding is associated with the pneumotoxicity of 3MI. We undertook this autoradiographic study of 3MI covalent binding to test the hypothesis that reactive 3MI metabolite(s) bind to the lung cells susceptible to 3MI-induced injury. We infused goats with ( 3 H)3MI and killed them either 0.5, 2 or 6 h after start of the infusion. Sections of fixed lung were extensively washed, alcohol dehydrated and embedded in plastic. Only covalently bound radioactivity remained. Silver grains were quantitated per area in the developed autoradiographs. There was a 2:1 ratio of binding to the small airway epithelium compared to the interalveolar septa in all the goats. Both ciliated and non-ciliated bronchiolar cells were labelled, as were both types I and II pneumocytes. Normal goat lung slices incubated in vitro with ( 3 H)3MI were labeled in the same pattern. Inclusion of either of the inhibitors of cytochrome P-450, SKF-525-A or piperonyl butoxide significantly reduced this binding to both the pneumocytes and the bronchiolar cells. We consider these results supportive of our hypothesis that 3MI is metabolized to reactive intermediates by the epithelial cells of the lung, where they bind to macromolecules, which may cause cellular damage. (author)

Exploring the Interaction Natures in Plutonyl (VI Complexes with Topological Analyses of Electron Density

Directory of Open Access Journals (Sweden)

Jiguang Du

2016-04-01

Full Text Available The interaction natures between Pu and different ligands in several plutonyl (VI complexes are investigated by performing topological analyses of electron density. The geometrical structures in both gaseous and aqueous phases are obtained with B3LYP functional, and are generally in agreement with available theoretical and experimental results when combined with all-electron segmented all-electron relativistic contracted (SARC basis set. The Pu– O y l bond orders show significant linear dependence on bond length and the charge of oxygen atoms in plutonyl moiety. The closed-shell interactions were identified for Pu-Ligand bonds in most complexes with quantum theory of atoms in molecules (QTAIM analyses. Meanwhile, we found that some Pu–Ligand bonds, like Pu–OH−, show weak covalent. The interactive nature of Pu–ligand bonds were revealed based on the interaction quantum atom (IQA energy decomposition approach, and our results indicate that all Pu–Ligand interactions is dominated by the electrostatic attraction interaction as expected. Meanwhile it is also important to note that the quantum mechanical exchange-correlation contributions can not be ignored. By means of the non-covalent interaction (NCI approach it has been found that some weak and repulsion interactions existed in plutonyl(VI complexes, which can not be distinguished by QTAIM, can be successfully identified.

Non-linear soil-structure interaction

International Nuclear Information System (INIS)

Wolf, J.P.

1984-01-01

The basic equation of motion to analyse the interaction of a non-linear structure and an irregular soil with the linear unbounded soil is formulated in the time domain. The contribution of the unbounded soil involves convolution integrals of the dynamic-stiffness coefficients in the time domain and the corresponding motions. As another possibility, a flexibility formulation fot the contribution of the unbounded soil using the dynamic-flexibility coefficients in the time domain, together with the direct-stiffness method for the structure and the irregular soil can be applied. As an example of a non-linear soil-structure-interaction analysis, the partial uplift of the basemat of a structure is examined. (Author) [pt

A novel environmental exposure index and its interaction with familial susceptibility on oral cancer in non-smokers and non-drinkers: a case-control study.

Science.gov (United States)

Yan, Lingjun; Chen, Fa; He, Baochang; Liu, Fengqiong; Liu, Fangping; Huang, Jiangfeng; Wu, Junfeng; Lin, Lisong; Qiu, Yu; Cai, Lin

2017-04-01

The objective of this study was to explore the collective effect of environmental factors and its interaction with familial susceptibility on oral cancer among non-smokers and non-drinkers (NSND). A hospital-based case-control study, including 319 oral cancer patients and 994 frequency-matched controls, was conducted in Fujian, China. We raised a weighed environmental exposure index according to nine significant environmental factors obtained from multivariable logistic regression model. And then, the index was classified into three categories according to the tertiles of controls (2.43). Multiplicative and additive interactions were evaluated between environmental exposure index and family cancer history. Our results showed that environmental exposure index was associated with an increased risk of oral cancer especially for those with family cancer history. Compared to subjects with low environmental exposure index and without family cancer history, those with high index and family cancer history showed the highest magnitude of OR in oral cancer risk (OR 10.40, 95% CI 5.46-19.80). Moreover, there was a multiplicative interaction between environmental exposure index and family cancer history for the risk of oral cancer (P oral cancer among NSND and may interact with family cancer history. Further studies are warranted to explore the underlying mechanisms.

Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories

Czech Academy of Sciences Publication Activity Database

Riley, K. E.; Pitoňák, Michal; Jurečka, P.; Hobza, Pavel

2010-01-01

Roč. 110, č. 9 (2010), s. 5023-5063 ISSN 0009-2665 R&D Projects: GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : non covalent interactions * wave function theories * DFT Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 33.033, year: 2010

Covalently coupled hybrid of graphitic carbon nitride with reduced graphene oxide as a superior performance lithium-ion battery anode

Science.gov (United States)

Fu, Yongsheng; Zhu, Junwu; Hu, Chong; Wu, Xiaodong; Wang, Xin

2014-10-01

An in situ chemical synthetic approach has been designed for the fabrication of a covalently coupled hybrid consisting of graphitic carbon nitride (g-C3N4) with reduced graphene oxide (rGO) with differing g-C3N4/rGO ratio. The epoxy groups of graphene oxide (GO) undergo a nucleophilic substitution reaction with dicyandiamide (C2H4N4) to form the C2H4N4-GO composite via a covalent C-N bond, and then both the in situ polymerization of C2H4N4 and the thermal reduction of GO can be achieved at higher temperatures, forming the covalently coupled g-C3N4-rGO. FT-IR, CP-MAS NMR and XPS analyses, clearly revealed a covalent interaction between the g-C3N4 and rGO sheets. The g-C3N4-rGO exhibits an unprecedented high, stable and reversible capacity of 1525 mA h g-1 at a current density of 100 mA g-1 after 50 cycles. Even at a large current density of 1000 mA g-1, a reversible capacity of 943 mA h g-1 can still be retained. The superior electrochemical performance of g-C3N4-rGO is attributed to the specific characteristics of the unique nanostructure of g-C3N4-rGO and the concerted effects of g-C3N4 and rGO, including covalent interactions between the two moieties, the good conductivity and high special surface area of the nanocomposite, as well as the template effect of the planar amino group of g-C3N4 for the dispersed decoration of Li+ ions.An in situ chemical synthetic approach has been designed for the fabrication of a covalently coupled hybrid consisting of graphitic carbon nitride (g-C3N4) with reduced graphene oxide (rGO) with differing g-C3N4/rGO ratio. The epoxy groups of graphene oxide (GO) undergo a nucleophilic substitution reaction with dicyandiamide (C2H4N4) to form the C2H4N4-GO composite via a covalent C-N bond, and then both the in situ polymerization of C2H4N4 and the thermal reduction of GO can be achieved at higher temperatures, forming the covalently coupled g-C3N4-rGO. FT-IR, CP-MAS NMR and XPS analyses, clearly revealed a covalent interaction between

Non-Covalent Interactions and Impact of Charge Penetration Effects in Linear Oligoacene Dimers and Single Crystals

KAUST Repository

Ryno, Sean; Risko, Chad; Bredas, Jean-Luc

2016-01-01

of charge penetration, which is shown to account for up to 50% of the total interaction energy in dimers extracted from the experimental single crystals; in the case of the most stable co-facial model dimers, this contribution is even larger than the total

Scanning tunneling spectroscopy of CdSe nanocrystals covalently bound to GaAs

DEFF Research Database (Denmark)

Walzer, K.; Marx, E.; Greenham, N.C.

2003-01-01

We present scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) measurements of CdSe nanocrystals covalently attached to doped GaAs substrates using monolayers of 1,6-hexanedithiol. STM measurements showed the formation of stable, densely packed, homogeneous monolayers...... of nanocrystals. STS measurements showed rectifying behaviour, with high currents at the opposite sample bias to that previously observed for CdSe nanocrystals adsorbed on Si substrates. We explain the rectifying behaviour by considering the interaction between the electronic states of the nanocrystals...

Merging constitutional and motional covalent dynamics in reversible imine formation and exchange processes.

Science.gov (United States)

Kovaříček, Petr; Lehn, Jean-Marie

2012-06-06

The formation and exchange processes of imines of salicylaldehyde, pyridine-2-carboxaldehyde, and benzaldehyde have been studied, showing that the former has features of particular interest for dynamic covalent chemistry, displaying high efficiency and fast rates. The monoimines formed with aliphatic α,ω-diamines display an internal exchange process of self-transimination type, inducing a local motion of either "stepping-in-place" or "single-step" type by bond interchange, whose rate decreases rapidly with the distance of the terminal amino groups. Control of the speed of the process over a wide range may be achieved by substituents, solvent composition, and temperature. These monoimines also undergo intermolecular exchange, thus merging motional and constitutional covalent behavior within the same molecule. With polyamines, the monoimines formed execute internal motions that have been characterized by extensive one-dimensional, two-dimensional, and EXSY proton NMR studies. In particular, with linear polyamines, nondirectional displacement occurs by shifting of the aldehyde residue along the polyamine chain serving as molecular track. Imines thus behave as simple prototypes of systems displaying relative motions of molecular moieties, a subject of high current interest in the investigation of synthetic and biological molecular motors. The motional processes described are of dynamic covalent nature and take place without change in molecular constitution. They thus represent a category of dynamic covalent motions, resulting from reversible covalent bond formation and dissociation. They extend dynamic covalent chemistry into the area of molecular motions. A major further step will be to achieve control of directionality. The results reported here for imines open wide perspectives, together with other chemical groups, for the implementation of such features in multifunctional molecules toward the design of molecular devices presenting a complex combination of

The RING 2.0 web server for high quality residue interaction networks.

Science.gov (United States)

Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

2016-07-08

Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evaluation of intensity and energy interaction parameters for the complexation of Pr(III) with selected nucleoside and nucleotide through absorption spectral studies

Science.gov (United States)

Bendangsenla, N.; Moaienla, T.; David Singh, Th.; Sumitra, Ch.; Rajmuhon Singh, N.; Indira Devi, M.

2013-02-01

The interactions of Pr(III) with nucleosides and nucleotides have been studied in different organic solvents employing absorption difference and comparative absorption spectrophotometry. The magnitudes of the variations in both energy and intensity interaction parameters were used to explore the degree of outer and inner sphere co-ordination, incidence of covalency and the extent of metal 4f-orbital involvement in chemical bonding. Various electronic spectral parameters like Slater-Condon (Fk), Racah (Ek), Lande parameter (ξ4f), Nephelauxatic ratio (β), bonding (b1/2), percentage covalency (δ) and intensity parameters like oscillator strength (P) and Judd Ofelt electronic dipole intensity parameter (Tλ, λ = 2, 4, 6) have been evaluated. The variation of these evaluated parameters were employed to interpret the nature of binding of Pr(III) with different ligands i.e. Adenosine/ATP in presence and absence of Ca2+.

Evaluation of Antimicrobial Efficiency of New Polymers Comprised by Covalently Attached and/or Electrostatically Bound Bacteriostatic Species, Based on Quaternary Ammonium Compounds.

Science.gov (United States)

Kougia, Efstathia; Tselepi, Maria; Vasilopoulos, Gavriil; Lainioti, Georgia Ch; Koromilas, Nikos D; Druvari, Denisa; Bokias, Georgios; Vantarakis, Apostolos; Kallitsis, Joannis K

2015-12-01

In the present work a detailed study of new bacteriostatic copolymers with quaternized ammonium groups introduced in the polymer chain through covalent attachment or electrostatic interaction, was performed. Different copolymers have been considered since beside the active species, the hydrophobic/hydrophilic nature of the co-monomer was also evaluated in the case of covalently attached bacteriostatic groups, aiming at achieving permanent antibacterial activity. Homopolymers with quaternized ammonium/phosphonium groups were also tested for comparison reasons. The antimicrobial activity of the synthesized polymers after 3 and 24 h of exposure at 4 and 22 °C was investigated on cultures of Gram-negative (P. aeruginosa, E. coli) and Gram-positive (S. aureus, E. faecalis) bacteria. It was found that the combination of the hydrophilic monomer acrylic acid (AA), at low contents, with the covalently attached bacteriostatic group vinyl benzyl dimethylhexadecylammonium chloride (VBCHAM) in the copolymer P(AA-co-VBCHAM88), resulted in a high bacteriostatic activity against P. aeruginosa and E. faecalis (6 log reduction in certain cases). Moreover, the combination of covalently attached VBCHAM units with electrostatically bound cetyltrimethylammonium 4-styrene sulfonate (SSAmC16) units in the P(SSAmC16-co-VBCHAMx) copolymers led to efficient antimicrobial materials, especially against Gram-positive bacteria, where a log reduction between 4.9 and 6.2 was verified. These materials remain remarkably efficient even when they are incorporated in polysulfone membranes.

Supramolecular systems chemistry

NARCIS (Netherlands)

Mattia, Elio; Otto, Sijbren

The field of supramolecular chemistry focuses on the non-covalent interactions between molecules that give rise to molecular recognition and self-assembly processes. Since most non-covalent interactions are relatively weak and form and break without significant activation barriers, many

Ibrutinib: a first in class covalent inhibitor of Bruton's tyrosine kinase.

Science.gov (United States)

Davids, Matthew S; Brown, Jennifer R

2014-05-01

Ibrutinib (formerly PCI-32765) is a potent, covalent inhibitor of Bruton's tyrosine kinase, a kinase downstream of the B-cell receptor that is critical for B-cell survival and proliferation. In preclinical studies, ibrutinib bound to Bruton's tyrosine kinase with high affinity, leading to inhibition of B-cell receptor signaling, decreased B-cell activation and induction of apoptosis. In clinical studies, ibrutinib has been well-tolerated and has demonstrated profound anti-tumor activity in a variety of hematologic malignancies, most notably chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL), leading to US FDA approval for relapsed CLL and MCL. Ongoing studies are evaluating ibrutinib in other types of non-Hodgkin's lymphoma, such as diffuse large B-cell lymphoma and Waldenström's macrogobulinemia, in larger Phase III studies in CLL and MCL, and in combination studies with monoclonal antibodies and chemotherapy. Future studies will combine ibrutinib with other promising novel agents currently in development in hematologic malignancies.

Studies on the Interaction between Zinc-Hydroxybenzoite Complex and Genomic DNA

Directory of Open Access Journals (Sweden)

Hacali Necefoglu

2006-04-01

Full Text Available Zinc-Hydroxybenzoite ([Zn (H206] (p-HO-C6H4COO22H20 complex which wassynthesized and characterized by instrumental methods and the DNA samples which hadbeen isolated from cattle were allowed to interact at 37 oC for different time periods. Theinteraction of genomic DNA with this complex has been followed by agarose gelelectrophoresis at 50 V for 2 h. When DNA samples were allowed to interact with this metalcomplex, it was found that band intensities changed with the concentrations of the complex.In the result of interaction between this complex and genomic DNA samples, it wasdetermined that the intensities of bands were changed at the different concentrations of thecomplex. The brightness of the bands was increased and mobility of the bands wasdecreased, indicating the occurrence of increased covalent binding of the metal complexwith DNA. In this study it was concluded that the damage effect of ascorbate was reducedby Zinc-Hydroxybenzoite.

Covalent Anchoring of Chloroperoxidase and Glucose Oxidase on the Mesoporous Molecular Sieve SBA-15

Directory of Open Access Journals (Sweden)

Martin Hartmann

2010-02-01

Full Text Available Functionalization of porous solids plays an important role in many areas, including heterogeneous catalysis and enzyme immobilization. In this study, large-pore ordered mesoporous SBA-15 molecular sieves were synthesized with tetraethyl orthosilicate (TEOS in the presence of the non-ionic triblock co-polymer Pluronic P123 under acidic conditions. These materials were grafted with 3 aminopropyltrimethoxysilane (ATS, 3-glycidoxypropyltrimethoxysilane (GTS and with 3 aminopropyltrimethoxysilane and glutaraldehyde (GA-ATS in order to provide covalent anchoring points for enzymes. The samples were characterized by nitrogen adsorption, powder X-ray diffraction, solid-state NMR spectroscopy, elemental analysis, diffuse reflectance fourier transform infrared spectroscopy and diffuse reflectance UV/Vis spectroscopy. The obtained grafted materials were then used for the immobilization of chloroperoxidase (CPO and glucose oxidase (GOx and the resulting biocatalysts were tested in the oxidation of indole. It is found that enzymes anchored to the mesoporous host by the organic moieties can be stored for weeks without losing their activity. Furthermore, the covalently linked enzymes are shown to be less prone to leaching than the physically adsorbed enzymes, as tested in a fixed-bed reactor under continuous operation conditions.

In situ metalation of free base phthalocyanine covalently bonded to silicon surfaces

Directory of Open Access Journals (Sweden)

Fabio Lupo

2014-11-01

Full Text Available Free 4-undecenoxyphthalocyanine molecules were covalently bonded to Si(100 and porous silicon through thermic hydrosilylation of the terminal double bonds of the undecenyl chains. The success of the anchoring strategy on both surfaces was demonstrated by the combination of X-ray photoelectron spectroscopy with control experiments performed adopting the commercially available 2,3,9,10,16,17,23,24-octakis(octyloxy-29H,31H-phthalocyanine, which is not suited for silicon anchoring. Moreover, the study of the shape of the XPS N 1s band gave relevant information on the interactions occurring between the anchored molecules and the substrates. The spectra suggest that the phthalocyanine ring interacts significantly with the flat Si surface, whilst ring–surface interactions are less relevant on porous Si. The surface-bonded molecules were then metalated in situ with Co by using wet chemistry. The efficiency of the metalation process was evaluated by XPS measurements and, in particular, on porous silicon, the complexation of cobalt was confirmed by the disappearance in the FTIR spectra of the band at 3290 cm−1 due to –NH stretches. Finally, XPS results revealed that the different surface–phthalocyanine interactions observed for flat and porous substrates affect the efficiency of the in situ metalation process.

Structural Analysis of ‘key’ Interactions in Functional RNA Molecules

KAUST Repository

Chawla, Mohit

2018-04-01

The main objective of the thesis is to carry out structural bioinformatics study along with usage of advanced quantum chemical methods to look at the structural stability and energetics of RNA building blocks. The main focus of the work described here lies on understanding the reasons behind the intrinsic stability of key interactions in nucleic acids. Crystal structures of RNA molecules exhibit fascinating variety of non-covalent interactions, which play an important role in maintaining the three dimensional structures. An accurate atomic level description of these interactions in the structural building blocks of RNA is a key to understand the structure-function relationship in these molecules. An effort has been made to link the conclusions drawn from quantum chemical computations on RNA base pairs in wide biochemical context of their occurrence in RNA structures. The initial attention was on the impact of natural and non-natural modifications of the nucleic acid bases on the structure and stability of base pairs that they are involved in. In the remaining sections we cover other molecular interactions shaping nucleic acids, as the interaction between ribose and the bases, and the fluoride sensing riboswitch system in order to investigate structure and dynamics of nucleic acids at the atomic level and to gain insight into the physical chemistry behind.

Structural Analysis of ‘key’ Interactions in Functional RNA Molecules

KAUST Repository

Chawla, Mohit

2018-01-01

The main objective of the thesis is to carry out structural bioinformatics study along with usage of advanced quantum chemical methods to look at the structural stability and energetics of RNA building blocks. The main focus of the work described here lies on understanding the reasons behind the intrinsic stability of key interactions in nucleic acids. Crystal structures of RNA molecules exhibit fascinating variety of non-covalent interactions, which play an important role in maintaining the three dimensional structures. An accurate atomic level description of these interactions in the structural building blocks of RNA is a key to understand the structure-function relationship in these molecules. An effort has been made to link the conclusions drawn from quantum chemical computations on RNA base pairs in wide biochemical context of their occurrence in RNA structures. The initial attention was on the impact of natural and non-natural modifications of the nucleic acid bases on the structure and stability of base pairs that they are involved in. In the remaining sections we cover other molecular interactions shaping nucleic acids, as the interaction between ribose and the bases, and the fluoride sensing riboswitch system in order to investigate structure and dynamics of nucleic acids at the atomic level and to gain insight into the physical chemistry behind.

Intermolecular interactions of decamethoxinum and acetylsalicylic acid in systems of various complexity levels

Directory of Open Access Journals (Sweden)

O. V. Vashchenko

2016-07-01

Full Text Available Intermolecular interactions between decamethoxinum (DEC and acetylsalicylic acid (ASА have been studied in the phospholipid-containing systems of escalating complexity levels. The host media for these substances were solvents, L-α-dipalmitoylphosphatidylcholine (DPPC membranes, and samples of human erythrocytes. Peculiar effects caused by DEC-ASА interaction have been observed in each system using appropriate techniques: (a DEC-ASА non-covalent complexes formation in DPPC-containing systems were revealed by mass spectrometry with electrospray ionization; (b joint DEC-ASА action on DPPC model membranes led to increasing of membrane melting temperature Tm, whereas individual drugs caused pronounced Tm decreasing, which was demonstrated by differential scanning calorimetry; (c deceleration of DEC-induced haemolysis of erythrocytes under joint DEC-ASА application was observed by optical microscopy.

Covalent functionalization of octagraphene with magnetic octahedral B6- and non-planar C6- clusters

Science.gov (United States)

Chigo-Anota, E.; Cárdenas-Jirón, G.; Salazar Villanueva, M.; Bautista Hernández, A.; Castro, M.

2017-10-01

The interaction between the magnetic boron octahedral (B6-) and non-planar (C6-) carbon clusters with semimetal nano-sheet of octa-graphene (C64H24) in the gas phase is studied by means of DFT calculations. These results reveal that non-planar-1 (anion) carbon cluster exhibits structural stability, low chemical reactivity, magnetic (1.0 magneton bohr) and semiconductor behavior. On the other hand, there is chemisorption phenomena when the stable B6- and C6- clusters are absorbed on octa-graphene nanosheets. Such absorption generates high polarity and the low-reactivity remains as on the individual pristine cases. Electronic charge transference occurs from the clusters toward the nanosheets, producing a reduction of the work function for the complexes and also induces a magnetic behavior on the functionalized sheets. The quantum descriptors obtained for these systems reveal that they are feasible candidates for the design of molecular circuits, magnetic devices, and nano-vehicles for drug delivery.

K- and L-edge X-ray Absorption Spectroscopy (XAS) and Resonant Inelastic X-ray Scattering (RIXS) Determination of Differential Orbital Covalency (DOC) of Transition Metal Sites.

Science.gov (United States)

Baker, Michael L; Mara, Michael W; Yan, James J; Hodgson, Keith O; Hedman, Britt; Solomon, Edward I

2017-08-15

Continual advancements in the development of synchrotron radiation sources have resulted in X-ray based spectroscopic techniques capable of probing the electronic and structural properties of numerous systems. This review gives an overview of the application of metal K-edge and L-edge X-ray absorption spectroscopy (XAS), as well as K resonant inelastic X-ray scattering (RIXS), to the study of electronic structure in transition metal sites with emphasis on experimentally quantifying 3d orbital covalency. The specific sensitivities of K-edge XAS, L-edge XAS, and RIXS are discussed emphasizing the complementary nature of the methods. L-edge XAS and RIXS are sensitive to mixing between 3d orbitals and ligand valence orbitals, and to the differential orbital covalency (DOC), that is, the difference in the covalencies for different symmetry sets of the d orbitals. Both L-edge XAS and RIXS are highly sensitive to and enable separation of and donor bonding and back bonding contributions to bonding. Applying ligand field multiplet simulations, including charge transfer via valence bond configuration interactions, DOC can be obtained for direct comparison with density functional theory calculations and to understand chemical trends. The application of RIXS as a probe of frontier molecular orbitals in a heme enzyme demonstrates the potential of this method for the study of metal sites in highly covalent coordination sites in bioinorganic chemistry.

Biofunctional Paper via Covalent Modification of Cellulose

Science.gov (United States)

Yu, Arthur; Shang, Jing; Cheng, Fang; Paik, Bradford A.; Kaplan, Justin M.; Andrade, Rodrigo B.; Ratner, Daniel M.

2012-01-01

Paper-based analytical devices are the subject of growing interest for the development of low-cost point-of-care diagnostics, environmental monitoring technologies and research tools for limited-resource settings. However, there are limited chemistries available for the conjugation of biomolecules to cellulose for use in biomedical applications. Herein, divinyl sulfone (DVS) chemistry was demonstrated to covalently immobilize small molecules, proteins and DNA onto the hydroxyl groups of cellulose membranes through nucleophilic addition. Assays on modified cellulose using protein-carbohydrate and protein-glycoprotein interactions as well as oligonucleotide hybridization showed that the membrane’s bioactivity was specific, dose-dependent, and stable over a long period of time. Use of an inkjet printer to form patterns of biomolecules on DVS-activated cellulose illustrates the adaptability of the DVS functionalization technique to pattern sophisticated designs, with potential applications in cellulose-based lateral flow devices. PMID:22708701

Influence of non-covalent modification of multiwalled carbon nanotubes on the crystallization behaviour of binary blends of polypropylene and polyamide 6.

Science.gov (United States)

Mukhopadhyay, Nabaneeta; Panwar, Ajay S; Kumar, Gulshan; Samajdar, I; Bhattacharyya, Arup R

2015-02-14

Blends of polypropylene (PP) and polyamide 6 (PA6) with multiwalled carbon nanotubes (MWNTs) were prepared using different processing strategies in a twin-screw micro-compounder. The effect of MWNTs on the crystallization behaviour of the PP phase and the PA6 phase of the blend has been investigated through non-isothermal crystallization studies by differential scanning calorimetric analysis. Furthermore, the effect of the addition of the compatibilizer (PP-g-MA) and the modification of MWNTs (m-MWNTs) with a non-covalent organic modifier (Li-salt of 6 amino hexanoic acid, Li-AHA) has also been studied in context to the crystallization behaviour of the PP and PA6 phase in the blend. The crystallization studies have indicated a significant increase in bulk crystallization temperature of the PP phase in the blend in the presence of MWNTs. Moreover, the formation of 'trans-lamellar crystalline' structure consisting of PA6 'trans-crystalline lamellae' on MWNTs surface was facilitated in the case of blends prepared via 'protocol 2' as compared to the corresponding blends prepared via 'protocol 1'. Wide angle X-ray diffraction analysis has showed the existence of a β-polymorph of the PP phase due to incorporation of the PA6 phase in the blend. Addition of MWNTs in the blends has facilitated further β-crystalline structure formation of the PP phase. In the presence of m-MWNTs, a higher β-fraction was observed in the PP phase as compared to the blend with pristine MWNTs. Addition of PP-g-MA has suppressed the β-phase formation in the PP phase in the blend. X-ray bulk texture analysis revealed that incorporation of PA6 as well as pristine/modified MWNTs has influenced the extent of orientation of the PP chains towards specific crystalline planes in various blend compositions of PP and PA6.

On the Mott transition and the new metal-insulator transitions in doped covalent and polar crystals

International Nuclear Information System (INIS)

Dzhumanov, S.; Begimkulov, U.; Kurbanov, U.T.; Yavidov, B.Y.

2001-10-01

The Mott transition and new metal-insulator transitions (MIT's) and their distinctive features in doped covalent semiconductors and polar compounds are studied within the continuum model of extrinsic carrier self-trapping, the Hubbard impurity band model (with on-site Coulomb repulsion and screening effects) and the extrinsic (bi)polaronic band model (with short- and long-range carrier-impurity, impurity-phonon and carrier-phonon interactions and intercarrier correlation) using the appropriate tight-binding approximations and variational methods. We have shown the formation possibility of large-radius localized one- and two-carrier impurity (or defect) states and narrow impurity bands in the band gap and charge transfer gap of these carrier-doped systems. The extrinsic Mott-Hubbard and (bi)polaronic insulating gaps are calculated exactly. The proper criterions for Mott transition, extrinsic excitonic and (bi)polaronic MIT's are obtained. We have demonstrated that the Mott transition occurs in doped covalent semiconductors (i.e. Si and Ge) and some insulators with weak carrier-phonon coupling near the large-radius dopants. While, in doped polar compounds (e.g. oxide high-T c superconductors (HTSC) and related materials) the MIT's are new extrinsic (or intrinsic) (bi)polaronic MIT's. We have found that the anisotropy of the dielectric (or (bi)polaronic) properties of doped cuprate HTSC is responsible for smooth (or continuous) MIT's, stripe formation and suppression of high-T c superconductivity. Various experimental results on in-gap states, bands and MIT's in doped covalent semiconductors, oxide HTSC and related materials are in good agreement with the developed theory of Mott transition and new (bi)polaronic MIT's. (author)

Dynamic nuclear polarization of membrane proteins: covalently bound spin-labels at protein–protein interfaces

International Nuclear Information System (INIS)

Wylie, Benjamin J.; Dzikovski, Boris G.; Pawsey, Shane; Caporini, Marc; Rosay, Melanie; Freed, Jack H.; McDermott, Ann E.

2015-01-01

We demonstrate that dynamic nuclear polarization of membrane proteins in lipid bilayers may be achieved using a novel polarizing agent: pairs of spin labels covalently bound to a protein of interest interacting at an intermolecular interaction surface. For gramicidin A, nitroxide tags attached to the N-terminal intermolecular interface region become proximal only when bimolecular channels forms in the membrane. We obtained signal enhancements of sixfold for the dimeric protein. The enhancement effect was comparable to that of a doubly tagged sample of gramicidin C, with intramolecular spin pairs. This approach could be a powerful and selective means for signal enhancement in membrane proteins, and for recognizing intermolecular interfaces

Covalent modification of platelet proteins by palmitate

International Nuclear Information System (INIS)

Muszbek, L.; Laposata, M.

1989-01-01

Covalent attachment of fatty acid to proteins plays an important role in association of certain proteins with hydrophobic membrane structures. In platelets, the structure of many membrane glycoproteins (GPs) has been examined in detail, but the question of fatty acid acylation of platelet proteins has not been addressed. In this study, we wished to determine (a) whether platelet proteins could be fatty acid acylated; and, if so, (b) whether these modified proteins were present in isolated platelet membranes and cytoskeletal fractions; and (c) if the pattern of fatty acid acylated proteins changed on stimulation of the platelets with the agonist thrombin. We observed that in platelets allowed to incorporate 3H-palmitate, a small percentage (1.37%) of radioactivity incorporated into the cells became covalently bound to protein. Selective cleavage of thioester, thioester plus O-ester, and amide-linked 3H-fatty acids from proteins, and their subsequent analysis by high-performance liquid chromatography (HPLC) indicated that the greatest part of 3H-fatty acid covalently bound to protein was thioester-linked 3H-palmitate. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and fluorography, at least ten major radiolabeled proteins were detected. Activation of platelets by thrombin greatly increased the quantity of 3H-palmitoylated proteins associated with the cytoskeleton. Nearly all radiolabeled proteins were recovered in the membrane fraction, indicating that these proteins are either integral or peripheral membrane proteins or proteins tightly associated to membrane constituents. Components of the GPIIb-IIIa complex were not palmitoylated. Thus, platelet proteins are significantly modified posttranslationally by 3H-palmitate, and incorporation of palmitoylated proteins into the cytoskeleton is a prominent component of the platelet response to thrombin stimulation

Oriented growth of magnetite along the carbon nanotubes via covalently bonded method in a simple solvothermal system

Energy Technology Data Exchange (ETDEWEB)

Zhan Yingqing; Zhao Rui; Meng Fanbing; Lei Yajie; Zhong Jiachun; Yang Xulin [Research Branch of Functional Materials, Institute of Microelectronic and Solid State Electronic, University of Electronic Science and Technology of China, Chengdu 610054 (China); Liu Xiaobo, E-mail: liuxb@uestc.edu.cn [Research Branch of Functional Materials, Institute of Microelectronic and Solid State Electronic, University of Electronic Science and Technology of China, Chengdu 610054 (China)

2011-06-15

Highlights: > Novel CNTs/magnetite hybrid materials were prepared via covalently bonded method. > Stable interaction between nitriles and iron ion promoted the oriented growth of magnetite. > The hybrid material exhibited higher magnetism and electromagnetic properties - Abstract: A new type of CNTs/magnetite hybrid material was prepared via covalently bonded method in a simple solvothermal system using FeCl{sub 3} as iron source, ethylene glycol as the reducing agent, and 4-aminophenoxyphthalonitrile-grafted CNTs as templates. The magnetite nanoparticles, with the diameters of 70-80 nm, were self-assembled along the CNTs. The FTIR, UV-vis and DSC revealed that a stable covalent bond between nitriles group and iron ion promoted the oriented growth of magnetite nanoparticles along the CNTs, resulting in good dispersibility and solution storage stability. The magnetic properties measurements indicated that a higher saturated magnetization (70.7 emu g{sup -1}) existed in the CNTs/magnetite hybrid material, which further enhanced the electromagnetic properties. The magnetic loss was caused mainly by natural resonance, which is in good agreement with the Kittel equation results. The novel electromagnetic hybrid material is believed to have potential applications in the microwave absorbing performances.

Oriented growth of magnetite along the carbon nanotubes via covalently bonded method in a simple solvothermal system

International Nuclear Information System (INIS)

Zhan Yingqing; Zhao Rui; Meng Fanbing; Lei Yajie; Zhong Jiachun; Yang Xulin; Liu Xiaobo

2011-01-01

Highlights: → Novel CNTs/magnetite hybrid materials were prepared via covalently bonded method. → Stable interaction between nitriles and iron ion promoted the oriented growth of magnetite. → The hybrid material exhibited higher magnetism and electromagnetic properties - Abstract: A new type of CNTs/magnetite hybrid material was prepared via covalently bonded method in a simple solvothermal system using FeCl 3 as iron source, ethylene glycol as the reducing agent, and 4-aminophenoxyphthalonitrile-grafted CNTs as templates. The magnetite nanoparticles, with the diameters of 70-80 nm, were self-assembled along the CNTs. The FTIR, UV-vis and DSC revealed that a stable covalent bond between nitriles group and iron ion promoted the oriented growth of magnetite nanoparticles along the CNTs, resulting in good dispersibility and solution storage stability. The magnetic properties measurements indicated that a higher saturated magnetization (70.7 emu g -1 ) existed in the CNTs/magnetite hybrid material, which further enhanced the electromagnetic properties. The magnetic loss was caused mainly by natural resonance, which is in good agreement with the Kittel equation results. The novel electromagnetic hybrid material is believed to have potential applications in the microwave absorbing performances.

Mathematical Analysis for Non-reciprocal-interaction-based Model of Collective Behavior

Science.gov (United States)

Kano, Takeshi; Osuka, Koichi; Kawakatsu, Toshihiro; Ishiguro, Akio

2017-12-01

In many natural and social systems, collective behaviors emerge as a consequence of non-reciprocal interaction between their constituents. As a first step towards understanding the core principle that underlies these phenomena, we previously proposed a minimal model of collective behavior based on non-reciprocal interactions by drawing inspiration from friendship formation in human society, and demonstrated via simulations that various non-trivial patterns emerge by changing parameters. In this study, a mathematical analysis of the proposed model wherein the system size is small is performed. Through the analysis, the mechanism of the transition between several patterns is elucidated.

Mutual influence between triel bond and cation-π interactions: an ab initio study

Science.gov (United States)

Esrafili, Mehdi D.; Mousavian, Parisasadat

2017-12-01

Using ab initio calculations, the cooperative and solvent effects on cation-π and B...N interactions are studied in some model ternary complexes, where these interactions coexist. The nature of the interactions and the mechanism of cooperativity are investigated by means of quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) index and natural bond orbital analysis. The results indicate that all cation-π and B...N binding distances in the ternary complexes are shorter than those of corresponding binary systems. The QTAIM analysis reveals that ternary complexes have higher electron density at their bond critical points relative to the corresponding binary complexes. In addition, according to the QTAIM analysis, the formation of cation-π interaction increases covalency of B...N bonds. The NCI analysis indicates that the cooperative effects in the ternary complexes make a shift in the location of the spike associated with each interaction, which can be regarded as an evidence for the reinforcement of both cation-π and B...N interactions in these systems. Solvent effects on the cooperativity of cation-π and B...N interactions are also investigated.

Ibrutinib: a first in class covalent inhibitor of Bruton’s tyrosine kinase

Science.gov (United States)

Davids, Matthew S; Brown, Jennifer R

2015-01-01

Ibrutinib (formerly PCI-32765) is a potent, covalent inhibitor of Bruton’s tyrosine kinase, a kinase downstream of the B-cell receptor that is critical for B-cell survival and proliferation. In preclinical studies, ibrutinib bound to Bruton’s tyrosine kinase with high affinity, leading to inhibition of B-cell receptor signaling, decreased B-cell activation and induction of apoptosis. In clinical studies, ibrutinib has been well-tolerated and has demonstrated profound anti-tumor activity in a variety of hematologic malignancies, most notably chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL), leading to US FDA approval for relapsed CLL and MCL. Ongoing studies are evaluating ibrutinib in other types of non-Hodgkin’s lymphoma, such as diffuse large B-cell lymphoma and Waldenström’s macrogobulinemia, in larger Phase III studies in CLL and MCL, and in combination studies with monoclonal antibodies and chemotherapy. Future studies will combine ibrutinib with other promising novel agents currently in development in hematologic malignancies. PMID:24941982

Modeling leukocyte-leukocyte non-contact interactions in a lymph node.

Directory of Open Access Journals (Sweden)

Nicola Gritti

Full Text Available The interaction among leukocytes is at the basis of the innate and adaptive immune-response and it is largely ascribed to direct cell-cell contacts. However, the exchange of a number of chemical stimuli (chemokines allows also non-contact interaction during the immunological response. We want here to evaluate the extent of the effect of the non-contact interactions on the observed leukocyte-leukocyte kinematics and their interaction duration. To this aim we adopt a simplified mean field description inspired by the Keller-Segel chemotaxis model, of which we report an analytical solution suited for slowly varying sources of chemokines. Since our focus is on the non-contact interactions, leukocyte-leukocyte contact interactions are simulated only by means of a space dependent friction coefficient of the cells. The analytical solution of the Keller-Segel model is then taken as the basis of numerical simulations of interactions between leukocytes and their duration. The mean field interaction force that we derive has a time-space separable form and depends on the chemotaxis sensitivity parameter as well as on the chemokines diffusion coefficient and their degradation rate. All these parameters affect the distribution of the interaction durations. We draw a successful qualitative comparison between simulated data and sets of experimental data for DC-NK cells interaction duration and other kinematic parameters. Remarkably, the predicted percentage of the leukocyte-leukocyte interactions falls in the experimental range and depends (~25% increase upon the chemotactic parameter indicating a non-negligible direct effect of the non-contact interaction on the leukocyte interactions.

Modeling leukocyte-leukocyte non-contact interactions in a lymph node.

Science.gov (United States)

Gritti, Nicola; Caccia, Michele; Sironi, Laura; Collini, Maddalena; D'Alfonso, Laura; Granucci, Francesca; Zanoni, Ivan; Chirico, Giuseppe

2013-01-01

The interaction among leukocytes is at the basis of the innate and adaptive immune-response and it is largely ascribed to direct cell-cell contacts. However, the exchange of a number of chemical stimuli (chemokines) allows also non-contact interaction during the immunological response. We want here to evaluate the extent of the effect of the non-contact interactions on the observed leukocyte-leukocyte kinematics and their interaction duration. To this aim we adopt a simplified mean field description inspired by the Keller-Segel chemotaxis model, of which we report an analytical solution suited for slowly varying sources of chemokines. Since our focus is on the non-contact interactions, leukocyte-leukocyte contact interactions are simulated only by means of a space dependent friction coefficient of the cells. The analytical solution of the Keller-Segel model is then taken as the basis of numerical simulations of interactions between leukocytes and their duration. The mean field interaction force that we derive has a time-space separable form and depends on the chemotaxis sensitivity parameter as well as on the chemokines diffusion coefficient and their degradation rate. All these parameters affect the distribution of the interaction durations. We draw a successful qualitative comparison between simulated data and sets of experimental data for DC-NK cells interaction duration and other kinematic parameters. Remarkably, the predicted percentage of the leukocyte-leukocyte interactions falls in the experimental range and depends (~25% increase) upon the chemotactic parameter indicating a non-negligible direct effect of the non-contact interaction on the leukocyte interactions.

Covalent immobilization of rabbit-antiaflatoxin-antibodies onto the poly-acrylamideacrylonitrile as well as hybrid material UREASIL and developing an optical immunosensor

Directory of Open Access Journals (Sweden)

Slavova M.

2017-03-01

Full Text Available The aim of this work is to describe a covalent immobilization of antibodies onto the poly- acrylamide-acrylonitrile or hybrid material UREASIL and creation of optical immunosensor for determination of aflatoxin Bl. For this purpose, mouse-anti-aflatoxin B1 antibodies with oxidized carbohydrate moieties were covalently immobilized on the membranes of polyacrylamide- polyacrylonitrile copolymer, as well as the hybrid material UREASIL. To determine the affinity> binding of the immobilized antibody with afatoxin Bl was used "sandwich" method. Associated with the immobilized antibody sought ingredients interact with a surplus of secondary’ signal antibodies. The described method has been developed as a model system, which can easily be applied for the determination of aflatoxins in samples of different origin. To the best of our knowledge, this is the first study to show that in the establishment of biosensor was used hybrid material UREASIL.

Bifunctional avidin with covalently modifiable ligand binding site.

Directory of Open Access Journals (Sweden)

Jenni Leppiniemi

Full Text Available The extensive use of avidin and streptavidin in life sciences originates from the extraordinary tight biotin-binding affinity of these tetrameric proteins. Numerous studies have been performed to modify the biotin-binding affinity of (streptavidin to improve the existing applications. Even so, (streptavidin greatly favours its natural ligand, biotin. Here we engineered the biotin-binding pocket of avidin with a single point mutation S16C and thus introduced a chemically active thiol group, which could be covalently coupled with thiol-reactive molecules. This approach was applied to the previously reported bivalent dual chain avidin by modifying one binding site while preserving the other one intact. Maleimide was then coupled to the modified binding site resulting in a decrease in biotin affinity. Furthermore, we showed that this thiol could be covalently coupled to other maleimide derivatives, for instance fluorescent labels, allowing intratetrameric FRET. The bifunctional avidins described here provide improved and novel tools for applications such as the biofunctionalization of surfaces.

Linear Discriminant Analysis for the in Silico Discovery of Mechanism-Based Reversible Covalent Inhibitors of a Serine Protease: Application of Hydration Thermodynamics Analysis and Semi-empirical Molecular Orbital Calculation.

Science.gov (United States)

Masuda, Yosuke; Yoshida, Tomoki; Yamaotsu, Noriyuki; Hirono, Shuichi

2018-01-01

We recently reported that the Gibbs free energy of hydrolytic water molecules (ΔG wat ) in acyl-trypsin intermediates calculated by hydration thermodynamics analysis could be a useful metric for estimating the catalytic rate constants (k cat ) of mechanism-based reversible covalent inhibitors. For thorough evaluation, the proposed method was tested with an increased number of covalent ligands that have no corresponding crystal structures. After modeling acyl-trypsin intermediate structures using flexible molecular superposition, ΔG wat values were calculated according to the proposed method. The orbital energies of antibonding π* molecular orbitals (MOs) of carbonyl C=O in covalently modified catalytic serine (E orb ) were also calculated by semi-empirical MO calculations. Then, linear discriminant analysis (LDA) was performed to build a model that can discriminate covalent inhibitor candidates from substrate-like ligands using ΔG wat and E orb . The model was built using a training set (10 compounds) and then validated by a test set (4 compounds). As a result, the training set and test set ligands were perfectly discriminated by the model. Hydrolysis was slower when (1) the hydrolytic water molecule has lower ΔG wat ; (2) the covalent ligand presents higher E orb (higher reaction barrier). Results also showed that the entropic term of hydrolytic water molecule (-TΔS wat ) could be used for estimating k cat and for covalent inhibitor optimization; when the rotational freedom of the hydrolytic water molecule is limited, the chance for favorable interaction with the electrophilic acyl group would also be limited. The method proposed in this study would be useful for screening and optimizing the mechanism-based reversible covalent inhibitors.

Competing intermolecular interactions of artemisinin-type agents and aspirin with membrane phospholipids: Combined model mass spectrometry and quantum-chemical study

International Nuclear Information System (INIS)

Pashynska, Vlada; Stepanian, Stepan; Gömöry, Agnes; Vekey, Karoly; Adamowicz, Ludwik

2015-01-01

Highlights: • Competitive binding of artemisinin agents and aspirin with phospholipids is shown. • Complexation between the antimalarial drugs and aspirin molecules is also found. • Energetically favorable structures of the model complexes are identified by DFT. • Membranotropic activity of the studied drugs can be modified under joint usage. - Abstract: Study of intermolecular interactions of antimalarial artemisinin-type drugs and aspirin with membrane phospholipids is important in term of elucidation of the drugs activity modification under their joint usage. Combined experimental and computational study of the interaction of dihydroartemisinin, α-artemether, and artesunate with aspirin (ASP) and dipalmitoylphosphatidylcholine (DPPC) is performed by electrospray ionization (ESI) mass spectrometry and by DFT B3LYP/aug-cc-pVDZ methods. The results of the ESI investigation of systems containing artemisinin-type agent, ASP and DPPC, reveal a competition between the antimalarial agents and ASP for binding with DPPC molecules. The complexation between the antimalarial drugs and ASP is also found. Observed phenomena suggest that membranotropic activity of artemisin-type agents and aspirin is modified under their combined usage. To elucidate structure-energy characteristics of the non-covalent complexes studied the model DFT calculations are performed for dihydroartemisinin · ASP complex and complexes of the each drug with phosphatidylcholine head of DPPC in neutral and cationized forms

Competing intermolecular interactions of artemisinin-type agents and aspirin with membrane phospholipids: Combined model mass spectrometry and quantum-chemical study

Energy Technology Data Exchange (ETDEWEB)

Pashynska, Vlada, E-mail: vlada@vl.kharkov.ua [B.Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, Lenin Ave., 47, 61103 Kharkov (Ukraine); Stepanian, Stepan [B.Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, Lenin Ave., 47, 61103 Kharkov (Ukraine); Gömöry, Agnes; Vekey, Karoly [Institute of Organic Chemistry of Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Magyar tudosok korutja, 2, Budapest H-1117 (Hungary); Adamowicz, Ludwik [University of Arizona, Department of Chemistry and Biochemistry, Tucson, AZ 85721 (United States)

2015-07-09

Highlights: • Competitive binding of artemisinin agents and aspirin with phospholipids is shown. • Complexation between the antimalarial drugs and aspirin molecules is also found. • Energetically favorable structures of the model complexes are identified by DFT. • Membranotropic activity of the studied drugs can be modified under joint usage. - Abstract: Study of intermolecular interactions of antimalarial artemisinin-type drugs and aspirin with membrane phospholipids is important in term of elucidation of the drugs activity modification under their joint usage. Combined experimental and computational study of the interaction of dihydroartemisinin, α-artemether, and artesunate with aspirin (ASP) and dipalmitoylphosphatidylcholine (DPPC) is performed by electrospray ionization (ESI) mass spectrometry and by DFT B3LYP/aug-cc-pVDZ methods. The results of the ESI investigation of systems containing artemisinin-type agent, ASP and DPPC, reveal a competition between the antimalarial agents and ASP for binding with DPPC molecules. The complexation between the antimalarial drugs and ASP is also found. Observed phenomena suggest that membranotropic activity of artemisin-type agents and aspirin is modified under their combined usage. To elucidate structure-energy characteristics of the non-covalent complexes studied the model DFT calculations are performed for dihydroartemisinin · ASP complex and complexes of the each drug with phosphatidylcholine head of DPPC in neutral and cationized forms.

Covalent α-synuclein dimers: chemico-physical and aggregation properties.

Directory of Open Access Journals (Sweden)

Micaela Pivato

Full Text Available The aggregation of α-synuclein into amyloid fibrils constitutes a key step in the onset of Parkinson's disease. Amyloid fibrils of α-synuclein are the major component of Lewy bodies, histological hallmarks of the disease. Little is known about the mechanism of aggregation of α-synuclein. During this process, α-synuclein forms transient intermediates that are considered to be toxic species. The dimerization of α-synuclein could represent a rate-limiting step in the aggregation of the protein. Here, we analyzed four covalent dimers of α-synuclein, obtained by covalent link of the N-terms, C-terms, tandem cloning of two sequences and tandem juxtaposition in one protein of the 1-104 and 29-140 sequences. Their biophysical properties in solution were determined by CD, FT-IR and NMR spectroscopies. SDS-induced folding was also studied. The fibrils formation was analyzed by ThT and polarization fluorescence assays. Their morphology was investigated by TEM and AFM-based quantitative morphometric analysis. All dimers were found to be devoid of ordered secondary structure under physiological conditions and undergo α-helical transition upon interaction with SDS. All protein species are able to form amyloid-like fibrils. The reciprocal orientation of the α-synuclein monomers in the dimeric constructs affects the kinetics of the aggregation process and a scale of relative amyloidogenic propensity was determined. Structural investigations by FT IR spectroscopy, and proteolytic mapping of the fibril core did not evidence remarkable difference among the species, whereas morphological analyses showed that fibrils formed by dimers display a lower and diversified level of organization in comparison with α-synuclein fibrils. This study demonstrates that although α-synuclein dimerization does not imply the acquisition of a preferred conformation by the participating monomers, it can strongly affect the aggregation properties of the molecules. The results

Using coloured roots to study root interaction and competition in intercropped legumes and non-legumes

DEFF Research Database (Denmark)

Tosti, Giacomo; Thorup-Kristensen, Kristian

2010-01-01

if a species with coloured roots can be used to examine the interaction in a legume-non-legume intercropping system; (ii) to verify the importance of initial root growth on the successive root development of mixture component plants; (iii) to test if the root interaction in the shallow layers has consequences...

Iron(II) phthalocyanine covalently functionalized graphene as a highly efficient non-precious-metal catalyst for the oxygen reduction reaction in alkaline media

International Nuclear Information System (INIS)

Liu, Ying; Wu, Yan-Ying; Lv, Guo-Jun; Pu, Tao; He, Xing-Quan; Cui, Li-Li

2013-01-01

Graphical abstract: The fabricated FePc-Gr catalyst for ORR exhibited high activity, favoring a direct 4-electron process, good stability and selectivity, all of which should be attributed to its high conductivity, the synergistic effect between FePc and graphene, as well as the formation of stable FePc-Gr composite through covalent bonding and π–π interaction. - Abstract: A novel iron(II) phthalocyanine covalently modified graphene (FePc-Gr) was synthesized by reduction of the product obtained through an amidation reaction between carboxyl-functionalized graphene oxide (CFGO) and iron(II) tetra-aminophthalocyanine (FeTAPc). The FePc-Gr hybird was characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy (RS) and X-ray photoelectron spectroscopy (XPS), respectively. The electrocatalytic properties of FePc-Gr toward the oxygen reduction reaction (ORR) were evaluated using cyclic voltammetry (CV) and linear sweep voltammetry methods. The peak potential of the ORR on the FePc-Gr catalyst was found to be about −0.12 V vs. SCE in 0.1 M NaOH solution, which was 180 and 360 mV more positive than that on FeTAPc and bare GCE, respectively. The rotating disk electrode (RDE) and rotating ring disk electrode (RRDE) measurements revealed that the ORR mechanism was nearly via a direct four-electron pathway to water on FePc-Gr. The current still remained 83.5% of its initial after chronoamperometric test for 10,000 s. Nevertheless, Pt/C catalyst only retained 40.5% of its initial current. The peak potential and peak current changed slightly when 3 M methanol was introduced. So the FePc-Gr composite catalyst for ORR exhibited high activity, good stability and methanol-tolerance, which could be used as a promising Pt-free catalyst for ORR in alkaline direct methanol fuel cell (DMFC)

Investigation of the heparin-thrombin interaction by dynamic force spectroscopy.

Science.gov (United States)

Wang, Congzhou; Jin, Yingzi; Desai, Umesh R; Yadavalli, Vamsi K

2015-06-01

The interaction between heparin and thrombin is a vital step in the blood (anti)coagulation process. Unraveling the molecular basis of the interactions is therefore extremely important in understanding the mechanisms of this complex biological process. In this study, we use a combination of an efficient thiolation chemistry of heparin, a self-assembled monolayer-based single molecule platform, and a dynamic force spectroscopy to provide new insights into the heparin-thrombin interaction from an energy viewpoint at the molecular scale. Well-separated single molecules of heparin covalently attached to mixed self-assembled monolayers are demonstrated, whereby interaction forces with thrombin can be measured via atomic force microscopy-based spectroscopy. Further these interactions are studied at different loading rates and salt concentrations to directly obtain kinetic parameters. An increase in the loading rate shows a higher interaction force between the heparin and thrombin, which can be directly linked to the kinetic dissociation rate constant (koff). The stability of the heparin/thrombin complex decreased with increasing NaCl concentration such that the off-rate was found to be driven primarily by non-ionic forces. These results contribute to understanding the role of specific and nonspecific forces that drive heparin-thrombin interactions under applied force or flow conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

Biofunctional paper via the covalent modification of cellulose.

Science.gov (United States)

Yu, Arthur; Shang, Jing; Cheng, Fang; Paik, Bradford A; Kaplan, Justin M; Andrade, Rodrigo B; Ratner, Daniel M

2012-07-31

Paper-based analytical devices are the subject of growing interest for the development of low-cost point-of-care diagnostics, environmental monitoring technologies, and research tools for limited-resource settings. However, there are limited chemistries available for the conjugation of biomolecules to cellulose for use in biomedical applications. Herein, divinyl sulfone (DVS) chemistry was demonstrated to immobilize small molecules, proteins, and DNA covalently onto the hydroxyl groups of cellulose membranes through nucleophilic addition. Assays on modified cellulose using protein-carbohydrate and protein-glycoprotein interactions as well as oligonucleotide hybridization showed that the membrane's bioactivity was specific, dose-dependent, and stable over a long period of time. The use of an inkjet printer to form patterns of biomolecules on DVS-activated cellulose illustrates the adaptability of the DVS functionalization technique to pattern sophisticated designs, with potential applications in cellulose-based lateral flow devices.

Non-Abelian monopole in the parameter space of point-like interactions

International Nuclear Information System (INIS)

Ohya, Satoshi

2014-01-01

We study non-Abelian geometric phase in N=2 supersymmetric quantum mechanics for a free particle on a circle with two point-like interactions at antipodal points. We show that non-Abelian Berry’s connection is that of SU(2) magnetic monopole discovered by Moody, Shapere and Wilczek in the context of adiabatic decoupling limit of diatomic molecule. - Highlights: • Supersymmetric quantum mechanics is an ideal playground for studying geometric phase. • We determine the parameter space of supersymmetric point-like interactions. • Berry’s connection is given by a Wu–Yang-like magnetic monopole in SU(2) Yang–Mills

Evidence for gene-environment interaction in a genome wide study of isolated, non-syndromic cleft palate

Science.gov (United States)

Beaty, Terri H.; Ruczinski, Ingo; Murray, Jeffrey C.; Marazita, Mary L.; Munger, Ronald G.; Hetmanski, Jacqueline B.; Murray, Tanda; Redett, Richard J.; Fallin, M. Daniele; Liang, Kung Yee; Wu, Tao; Patel, Poorav J.; Jin, Sheng C.; Zhang, Tian Xiao; Schwender, Holger; Wu-Chou, Yah Huei; Chen, Philip K; Chong, Samuel S; Cheah, Felicia; Yeow, Vincent; Ye, Xiaoqian; Wang, Hong; Huang, Shangzhi; Jabs, Ethylin W.; Shi, Bing; Wilcox, Allen J.; Lie, Rolv T.; Jee, Sun Ha; Christensen, Kaare; Doheny, Kimberley F.; Pugh, Elizabeth W.; Ling, Hua; Scott, Alan F.

2011-01-01

Non-syndromic cleft palate (CP) is a common birth defect with a complex and heterogeneous etiology involving both genetic and environmental risk factors. We conducted a genome wide association study (GWAS) using 550 case-parent trios, ascertained through a CP case collected in an international consortium. Family based association tests of single nucleotide polymorphisms (SNP) and three common maternal exposures (maternal smoking, alcohol consumption and multivitamin supplementation) were used in a combined 2 df test for gene (G) and gene-environment (G×E) interaction simultaneously, plus a separate 1 df test for G×E interaction alone. Conditional logistic regression models were used to estimate effects on risk to exposed and unexposed children. While no SNP achieved genome wide significance when considered alone, markers in several genes attained or approached genome wide significance when G×E interaction was included. Among these, MLLT3 and SMC2 on chromosome 9 showed multiple SNPs resulting in increased risk if the mother consumed alcohol during the peri-conceptual period (3 months prior to conception through the first trimester). TBK1 on chr. 12 and ZNF236 on chr. 18 showed multiple SNPs associated with higher risk of CP in the presence of maternal smoking. Additional evidence of reduced risk due to G×E interaction in the presence of multivitamin supplementation was observed for SNPs in BAALC on chr. 8. These results emphasize the need to consider G×E interaction when searching for genes influencing risk to complex and heterogeneous disorders, such as non-syndromic CP. PMID:21618603

Effects of non-standard interactions in the MINOS experiment

International Nuclear Information System (INIS)

Blennow, Mattias; Ohlsson, Tommy; Skrotzki, Julian

2008-01-01

We investigate the effects of non-standard interactions on the determination of the neutrino oscillation parameters Δm 31 2 , θ 23 , and θ 13 in the MINOS experiment. We show that adding non-standard interactions to the analysis lead to an extension of the allowed parameter space to larger values of Δm 31 2 and smaller θ 23 , and basically removes all predictability for θ 13 . In addition, we discuss the sensitivities to the non-standard interaction parameters of the MINOS experiment alone. In particular, we examine the degeneracy between θ 13 and the non-standard interaction parameter ε eτ . We find that this degeneracy is responsible for the removal of the θ 13 predictability and that the possible bound on |ε eτ | is competitive with direct bounds only if a more stringent external bound on θ 13 is applied

Covalent immobilization of lipase from Candida rugosa on Eupergit®

Directory of Open Access Journals (Sweden)

Bezbradica Dejan I.

2005-01-01

Full Text Available An approach is presented for the stable covalent immobilization of Upase from Candida rugosa on Eupergit® with a high retention of hydrolytic activity. It comprises covalent bonding via lipase carbohydrate moiety previously modified by periodate oxidation, allowing a reduction in the involvement of the enzyme functional groups that are probably important in the catalytic mechanism. The hydrolytic activities of the lipase immobilized on Eupergif1 by two conventional methods (via oxirane group and via glutaralde-hyde and with periodate method were compared. Results of lipase assays suggest that periodate method is superior for lipase immobilization on Eupergit® among methods applied in this study with respect to both, yield of immobilization and hydrolytic activity of the immobilized enzyme.

Spin-labelling study of interactions of ovalbumin with multilamellar liposomes and specific anti-ovalbumin antibodies.

Science.gov (United States)

Brgles, Marija; Mirosavljević, Krunoslav; Noethig-Laslo, Vesna; Frkanec, Ruza; Tomasić, Jelka

2007-03-10

Ovalbumin (OVA) has been used continuously as the model antigen in numerous studies of immune reactions and antigen processing, very often encapsulated into liposomes. The purpose of this work was to study the possible interactions of spin-labelled OVA and lipids in liposomal membranes using electron spin resonance (ESR) spectroscopy. OVA was covalently spin-labelled with 4-maleimido-2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO-maleimide), characterized and encapsulated into multilamellar, negatively charged liposomes. ESR spectra of this liposomal preparation gave evidence for the interaction of OVA with the lipid bilayers. Such an interaction was also evidenced by the ESR spectra of liposomal preparation containing OVA, where liposomes were spin-labelled with n-doxyl stearic acids. The spin-labelled OVA retains its property to bind specific anti-OVA antibodies, as shown by ESR spectroscopy, but also in ELISA for specific anti-OVA IgG.

Public-Key Encryption with Non-interactive Opening

DEFF Research Database (Denmark)

Damgård, Ivan Bjerre; Hofheinz, Dennis; Kiltz, Eike

2008-01-01

We formally define the primitive of public-key encryption with non-interactive opening (PKENO), where the receiver of a ciphertext C can, convincingly and without interaction, reveal what the result was of decrypting C, without compromising the scheme’s security. This has numerous applications...

Covalently bound conjugates of albumin and heparin: Synthesis, fractionation and characterization

NARCIS (Netherlands)

Hennink, Wim E.; Feijen, Jan; Ebert, Charles D.; Kim, Sung Wan

1983-01-01

Covalently bound conjugates of human serum albumin and heparin were prepared as compounds which could improve the blood-compatibility of polymer surfaces either by preadsorption or by covalent coupling of the conjugates onto blood contacting surfaces. The conjugates (10–16 weight % of heparin) were

The specific cleavage of lactone linkage to open-loop in cyclic lipopeptide during negative ESI tandem mass spectrometry: the hydrogen bond interaction effect of 4-ethyl guaiacol.

Directory of Open Access Journals (Sweden)

Mengzhe Guo

Full Text Available Mass spectrometry is a valuable tool for the analysis and identification of chemical compounds, particularly proteins and peptides. Lichenysins G, the major cyclic lipopeptide of lichenysin, and the non-covalent complex of lichenysins G and 4-ethylguaiacol were investigated with negative ion ESI tandem mass spectrometry. The different fragmentation mechanisms for these compounds were investigated. Our study shows the 4-ethylguaiacol hydrogen bond with the carbonyl oxygen of the ester group in the loop of lichenysins G. With the help of this hydrogen bond interaction, the ring structure preferentially opens in lactone linkage rather than O-C bond of the ester-group to produce alcohol and ketene. Isothermal titration 1H-NMR analysis verified the hydrogen bond and determined the proportion of subject and ligand in the non-covalent complex to be 1∶1. Theoretical calculations also suggest that the addition of the ligand can affect the energy of the transition structures (TS during loop opening.

Stability of stationary states of non-local equations with singular interaction potentials

KAUST Repository

Fellner, Klemens

2011-04-01

We study the large-time behaviour of a non-local evolution equation for the density of particles or individuals subject to an external and an interaction potential. In particular, we consider interaction potentials which are singular in the sense that their first derivative is discontinuous at the origin.For locally attractive singular interaction potentials we prove under a linear stability condition local non-linear stability of stationary states consisting of a finite sum of Dirac masses. For singular repulsive interaction potentials we show the stability of stationary states of uniformly bounded solutions under a convexity condition.Finally, we present numerical simulations to illustrate our results. © 2010 Elsevier Ltd.

The use of dansyl-calmodulin to study interactions with channels and other proteins.

Science.gov (United States)

Alaimo, Alessandro; Malo, Covadonga; Areso, Pilar; Aloria, Kerman; Millet, Oscar; Villarroel, Alvaro

2013-01-01

Steady-state fluorescence spectroscopy is a biophysical technique widely employed to characterize -interactions between proteins in vitro. Only a few proteins naturally fluoresce in cells, but by covalently attaching fluorophores virtually all proteins can be monitored. One of the first extrinsic fluorescent probes to be developed, and that is still in use, is dansyl chloride. We have used this method to monitor the interaction of a variety of proteins, including ion channels, with the Ca(2+)-dependent regulatory protein calmodulin. Here we describe the preparation and use of dansyl-calmodulin (D-CaM).

Plasma heating by non-linear wave-Plasma interaction | Echi ...

African Journals Online (AJOL)

We simulate the non-linear interaction of waves with magnetized tritium plasma with the aim of determining the parameter values that characterize the response of the plasma. The wave-plasma interaction has a non-conservative Hamiltonian description. The resulting system of Hamilton's equations is integrated numerically ...

Covalently Immobilised Cytochrome C Imaged by In Situ Scanning Tunnelling Microscopy

DEFF Research Database (Denmark)

Andersen, Jens Enevold Thaulov; Olesen, Klaus G.; Danilov, Alexey I.

1997-01-01

In situ scanning tunnelling microscopy (STM) imaging of cytochrome c (cyt c) on polycrystalline Pt surfaces and on Au(lll) was achieved first by covalent immobilisation of 3-aminopropyltriethoxysilane (3-APTS) brought to react with oxide present on the Pt surfaces. Covalently bound 3-APTS forms...

On-surface synthesis of covalent coordination polymers on micrometer scale

Institute of Scientific and Technical Information of China (English)

Mathieu Koudia; Elena Nardi; Olivier Siri; Mathieu Abel

2017-01-01

On-surface synthesis under ultrahigh vacuum provides a promising strategy to control matter at the atomic level,with important implications for the design of new two-dimensional materials having remarkable electronic,magnetic,or catalytic properties.This strategy must address the problem of limited extension of the domains due to the irreversible nature of covalent bonds,which prevents the ripening of defects.We show here that extended materials can be produced by a controlled co-deposition process.In particular,co-deposition of quinoid zwitterion molecules with iron atoms on a Ag(111) surface held at 570 K allows the formation of micrometer-sized domains based on covalent coordination bonds.This work opens up the construction of micrometer-scale single-layer covalent coordination materials under vacuum conditions.

Use of Functionalized Carbon Nanotubes for Covalent Attachment of Nanotubes to Silicon

Science.gov (United States)

Tour, James M.; Dyke, Christopher A.; Maya, Francisco; Stewart, Michael P.; Chen, Bo; Flatt, Austen K.

2012-01-01

The purpose of the invention is to covalently attach functionalized carbon nanotubes to silicon. This step allows for the introduction of carbon nanotubes onto all manner of silicon surfaces, and thereby introduction of carbon nano - tubes covalently into silicon-based devices, onto silicon particles, and onto silicon surfaces. Single-walled carbon nanotubes (SWNTs) dispersed as individuals in surfactant were functionalized. The nano - tube was first treated with 4-t-butylbenzenediazonium tetrafluoroborate to give increased solubility to the carbon nanotube; the second group attached to the sidewall of the nanotube has a silyl-protected terminal alkyne that is de-protected in situ. This gives a soluble carbon nanotube that has functional groups appended to the sidewall that can be attached covalently to silicon. This reaction was monitored by UV/vis/NJR to assure direct covalent functionalization.

Quantitative analysis of intermolecular interactions in orthorhombic rubrene

Directory of Open Access Journals (Sweden)

Venkatesha R. Hathwar

2015-09-01

Full Text Available Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

Fulltext PDF

Indian Academy of Sciences (India)

in π–π stacking with purine and pyrimidine bases. This can lead to complex formation with DNA subunits, which is an important target in cancer chemotherapy.8. Besides this, non-covalent interaction of palladium complexes with nucleic acids is also possible.9 This type of non-covalent interaction may inhibit the reactiv-.

Non-separable pairing interaction kernels applied to superconducting cuprates

International Nuclear Information System (INIS)

Haley, Stephen B.; Fink, Herman J.

2014-01-01

Highlights: • Non-separable interaction kernels with weak interactions produces HTS. • A probabilistic approach is used in filling the electronic states in the unit cell. • A set of coupled equations is derived which describes the energy gap. • SC properties of separable with non-separable interactions are compared. • There is agreement with measured properties of the SC and normal states. - Abstract: A pairing Hamiltonian H(Γ) with a non-separable interaction kernel Γ produces HTS for relatively weak interactions. The doping and temperature dependence of Γ(x,T) and the chemical potential μ(x) is determined by a probabilistic filling of the electronic states in the cuprate unit cell. A diverse set of HTS and normal state properties is examined, including the SC phase transition boundary T C (x), SC gap Δ(x,T), entropy S(x,T), specific heat C(x,T), and spin susceptibility χ s (x,T). Detailed x,T agreement with cuprate experiment is obtained for all properties

DFT study of the interaction between DOTA chelator and competitive alkali metal ions.

Science.gov (United States)

Frimpong, E; Skelton, A A; Honarparvar, B

2017-09-01

1, 4, 7, 10-tetraazacyclododecane-1, 4, 7, 10-tetracetic acid (DOTA) is an important chelator for radiolabeling of pharmaceuticals. The ability of alkali metals found in the body to complex with DOTA and compete with radio metal ions can alter the radiolabeling process. Non-covalent interactions between DOTA complexed with alkali metals Li + , Na + , K + and Rb + , are investigated with density functional theory using B3LYP and ωB97XD functionals. Conformational possibilities of DOTA were explored with a varying number of carboxylic pendant arms of DOTA in close proximity to the ions. It is found that the case in which four arms of DOTA are interacting with ions is more stable than other conformations. The objective of this study is to explore the electronic structure properties upon complexation of alkali metals Li + Na + , K + and Rb + with a DOTA chelator. Interaction energies, relaxation energies, entropies, Gibbs free energies and enthalpies show that the stability of DOTA, complexed with alkali metals decreases down the group of the periodic table. Implicit water solvation affects the complexation of DOTA-ions leading to decreases in the stability of the complexes. NBO analysis through the natural population charges and the second order perturbation theory, revealed a charge transfer between DOTA and alkali metals. Conceptual DFT-based properties such as HOMO/LUMO energies, ΔE HOMO-LUMO and chemical hardness and softness indicated a decrease in the chemical stability of DOTA-alkali metal complexes down the alkali metal series. This study serves as a guide to researchers in the field of organometallic chelators, particularly, radiopharmaceuticals in finding the efficient optimal match between chelators and various metal ions. Copyright © 2017 Elsevier Inc. All rights reserved.

Non-Chemical Distant Cellular Interactions as a potential confounder of Cell Biology Experiments

Directory of Open Access Journals (Sweden)

Ashkan eFarhadi

2014-10-01

Full Text Available Distant cells can communicate with each other through a variety of methods. Two such methods involve electrical and/or chemical mechanisms. Non-chemical, distant cellular interactions may be another method of communication that cells can use to modify the behavior of other cells that are mechanically separated. Moreover, non-chemical, distant cellular interactions may explain some cases of confounding effects in Cell Biology experiments. In this article, we review non-chemical, distant cellular interactions studies to try to shed light on the mechanisms in this highly unconventional field of cell biology. Despite the existence of several theories that try to explain the mechanism of non-chemical, distant cellular interactions, this phenomenon is still speculative. Among candidate mechanisms, electromagnetic waves appear to have the most experimental support. In this brief article, we try to answer a few key questions that may further clarify this mechanism.

The use of radiolabelled milk proteins to study thermally-induced interactions in milk systems

International Nuclear Information System (INIS)

Noh, B.

1988-01-01

Heat induced complexes between milk proteins are of considerable importance in determining the heat stability and rennin clottability of milk products. Thiol-disulfide interchange reactions have been suggested as the principal reaction mechanism for complex formation. Studies to data have not adequately established the mechanism and stoichiometry of complex formation in situ in total milk system. Tracer amounts of 14 C-β-lactoglobulin and α-lactalbumin were heated under various conditions. After clotting with rennet, radioactivity retained in the curd was counted to estimate extent of interaction of β-lactoglobulin with casein. 14 C- and 3 H-Methyl labelled proteins were used for the preparation of radiolabelled artificial casein micelles. These micelles with radiolabelled whey proteins were heated and heat-induced complexes were separated on Sephacryl S-300 eluting with 6 M guanidine hydrochloride to break all non-covalent bonds. Further separation of the protein complexes was obtained using CPG-10 or Sephacryl S-1000. The ratios of 3 H to 14 C labelled proteins in the protein complexes suggested that the stoichiometries of k-, α s2 -casein, β-lactoglobulin and α-lactalbumin in the heat-induced complexes varied as a function of the heat treatment

Swelling of whey and egg white protein hydrogels with stranded and particulate microstructures.

Science.gov (United States)

Li, Hui; Zhao, Lei; Chen, Xiao Dong; Mercadé-Prieto, Ruben

2016-02-01

Swelling of protein hydrogels in alkaline conditions strongly depends on the gel microstructure. Stranded transparent gels swell as predicted using a modified Flory-Rehner model with the net protein charge. Particulate opaque gels swell very differently, with a sudden increase at a narrow pH range. Its swelling is not controlled by the protein charge, but by the destruction of the non-covalent interactions. Comparable dissolution thresholds, one with pH and another with the degree of swelling, are observed in both types of microstructures. These conclusions are valid for both whey protein isolate (WPI) gels and egg white gels, suggesting that they are universal for all globular proteins that can form such microscructures. Differences are observed, however, from the prevalent chemical crosslinks in each protein system. Non-covalent interactions dominate WPI gels; when such interactions are destroyed at pH≥11.5 the gels swell extensively and eventually dissolve. In egg white gels, the higher degree of disulphide crosslinking allows extensive swelling when non-covalent interactions are destroyed, but dissolution only occurs at pH≥13 when covalent crosslinks are cleaved. The current study highlights that the microstructure of protein hydrogels, a unique particularity of protein systems compared to other synthetic hydrogels, defines swelling. Copyright © 2015 Elsevier B.V. All rights reserved.

Activity and stability studies of platinized multi-walled carbon nanotubes as fuel cell electrocatalysts

DEFF Research Database (Denmark)

Stamatin, Serban Nicolae; Borghei, Maryam; Dhiman, Rajnish

2015-01-01

A non-covalent functionalization for multi-walled carbon nanotubes has been used as an alternative to the damaging acid treatment. Platinum nanoparticles with similar particle size distribution have been deposited on the surface modified multi-walled carbon nanotubes. The interaction between...

Crystal structure of a human single domain antibody dimer formed through V(H-V(H non-covalent interactions.

Directory of Open Access Journals (Sweden)

Toya Nath Baral

Full Text Available Single-domain antibodies (sdAbs derived from human V(H are considered to be less soluble and prone to aggregate which makes it difficult to determine the crystal structures. In this study, we isolated and characterized two anti-human epidermal growth factor receptor-2 (HER2 sdAbs, Gr3 and Gr6, from a synthetic human V(H phage display library. Size exclusion chromatography and surface plasmon resonance analyses demonstrated that Gr3 is a monomer, but that Gr6 is a strict dimer. To understand this different molecular behavior, we solved the crystal structure of Gr6 to 1.6 Å resolution. The crystal structure revealed that the homodimer assembly of Gr6 closely mimics the V(H-V(L heterodimer of immunoglobulin variable domains and the dimerization interface is dominated by hydrophobic interactions.

Synthesis, structure, computational and in-silico anticancer studies of N,N-diethyl-N‧-palmitoylthiourea

Science.gov (United States)

Asegbeloyin, Jonnie Niyi; Oyeka, Ebube Evaristus; Okpareke, Obinna; Ibezim, Akachukwu

2018-02-01

A new potential ONS donor ligand N,N-diethyl-N‧-palmitoylthiourea (PACDEA) with the molecular formular C21H42N2OS has been synthesized and characterized by ESI-MS, UV, FTIR 1H and 13C NMR spectroscopy and single X-ray crystallography. The asymmetric molecules crystallized in the centrosymmetric structure of monoclinic crystal system with space group P21/c. In the crystal structure of the compound, molecules are linked in a continuous chain by intermolecular Nsbnd H⋯Odbnd C hydrogen bonds, which stabilized the crystal structure. The palmitoyl moiety and N (2)-ethyl group lie on a plane, while the thiocarbonyl moiety is twisted and lying othorgonal to the plane. Non-covalent interaction (NCI) analysis on the hydrogen bonded solid state structure of the molecule revealed the presence of a significant number of non-covalent interactions including intermolecular hydrogen bonding interactions, Csbnd Hsbnd -lone pair interactions, weak Van der Waals interactions, and steric/ring closure interactions. The NCI analysis also showed the presence of intramolecular stabilizing Csbnd H⋯Odbnd C and Csbnd H⋯Sdbnd C interactions. Docking simulation revealed that the compound interacted favourably with ten selected validated anticancer drug targets, which is an indication that the compound could possess some anticancer properties.

Can OPERA help in constraining neutrino non-standard interactions?

Energy Technology Data Exchange (ETDEWEB)

Esteban-Pretel, A.; Valle, J.W.F. [AHEP Group, Institut de Fisica Corpuscular, C.S.I.C./Universitat de Valencia, Edificio Institutos de Paterna, Apt 22085, E-46071 Valencia (Spain); Huber, P. [Theory Division, Department of Physics, CERN, CH-1211 Geneva 23 (Switzerland); Institute for Particle, Nuclear and Astronomical Sciences, Physics Department, Virgina Tech, Blacksburg, VA 24062 (United States)], E-mail: pahuber@vt.edu

2008-10-09

We study how much the unique ability of the OPERA experiment to directly detect {nu}{sub {tau}} can help in probing new, non-standard contact interactions of the third family of neutrinos. We perform a combined analysis of future, high-statistics MINOS and OPERA data. For the case of non-standard interactions in {nu}{sub {mu}} to {nu}{sub e} transitions we also include the impact of possible Double Chooz data. In all cases we find that the {nu}{sub {tau}} sample of OPERA is too small to be statistically significant, even if one doubles the nominal exposure of OPERA to 9x10{sup 19} pot. OPERA's real benefit for this measurement lies in its very high neutrino energy and hence very different L/E compared to MINOS.

Oligomerization of optineurin and its oxidative stress- or E50K mutation-driven covalent cross-linking: possible relationship with glaucoma pathology.

Directory of Open Access Journals (Sweden)

Jie Gao

Full Text Available The optineurin gene, OPTN, is one of the causative genes of primary open-angle glaucoma. Although oligomerization of optineurin in cultured cells was previously observed by gel filtration analysis and blue native gel electrophoresis (BNE, little is known about the characteristics of optineurin oligomers. Here, we aimed to analyze the oligomeric state of optineurin and factors affecting oligomerization, such as environmental stimuli or mutations in OPTN. Using BNE or immunoprecipitation followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE, we demonstrated that both endogenous and transfected optineurin exist as oligomers, rather than monomers, in NIH3T3 cells. We also applied an in situ proximity ligation assay to visualize the self-interaction of optineurin in fixed HeLaS3 cells and found that the optineurin oligomers were localized diffusely in the cytoplasm. Optineurin oligomers were usually detected as a single band of a size equal to that of the optineurin monomer upon SDS-PAGE, while an additional protein band of a larger size was observed when cells were treated with H2O2. We showed that larger protein complex is optineurin oligomers by immunoprecipitation and termed it covalent optineurin oligomers. In cells expressing OPTN bearing the most common glaucoma-associated mutation, E50K, covalent oligomers were formed even without H2O2 stimulation. Antioxidants inhibited the formation of E50K-induced covalent oligomers to various degrees. A series of truncated constructs of OPTN was used to reveal that covalent oligomers may be optineurin trimers and that the ubiquitin-binding domain is essential for formation of these trimers. Our results indicated that optineurin trimers may be the basic unit of these oligomers. The oligomeric state can be affected by many factors that induce covalent bonds, such as H2O2 or E50K, as demonstrated here; this provides novel insights into the pathogenicity of E50K. Furthermore

Molecular interactions between (--epigallocatechin gallate analogs and pancreatic lipase.

Directory of Open Access Journals (Sweden)

Shihui Wang

Full Text Available The molecular interactions between pancreatic lipase (PL and four tea polyphenols (EGCG analogs, like (--epigallocatechin gallate (EGCG, (--gallocatechin gallate (GCG, (--epicatechin gallate (ECG, and (--epigallocatechin (EC, were studied from PL activity, conformation, kinetics and thermodynamics. It was observed that EGCG analogs inhibited PL activity, and their inhibitory rates decreased by the order of EGCG>GCG>ECG>EC. PL activity at first decreased rapidly and then slowly with the increase of EGCG analogs concentrations. α-Helix content of PL secondary structure decreased dependent on EGCG analogs concentration by the order of EGCG>GCG>ECG>EC. EGCG, ECG, and EC could quench PL fluorescence both dynamically and statically, while GCG only quenched statically. EGCG analogs would induce PL self-assembly into complexes and the hydrodynamic radii of the complexes possessed a close relationship with the inhibitory rates. Kinetics analysis showed that EGCG analogs non-competitively inhibited PL activity and did not bind to PL catalytic site. DSC measurement revealed that EGCG analogs decreased the transition midpoint temperature of PL enzyme, suggesting that these compounds reduced PL enzyme thermostability. In vitro renaturation through urea solution indicated that interactions between PL and EGCG analogs were weak and non-covalent.

Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections

Energy Technology Data Exchange (ETDEWEB)

Chai, Jeng-Da; Head-Gordon, Martin

2008-06-14

We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functionals [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)] to include empirical atom-atom dispersion corrections. The resulting functional, {omega}B97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, {omega}B97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics, it performs noticeably better. Relative to our previous functionals, such as {omega}B97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.

Interaction of oxyanions with nickel (2) hydroxide

International Nuclear Information System (INIS)

Sokolova, M.M.; Vol'khin, V.V.

1997-01-01

Relative ability of oxoanions B(3), V(6), Cr(4), Mo(6), S(6), Mn(7), etc and Cl - to be contained in the basic salts by interaction with Ni(OH) 2 is deformined primarily by formation of ion-covalent bonds. The experimental series of oxoanions, characterizing the above property coincides with the calculational series, composed on the basis of notions on the ion-covalent interaction. The anions composition, their position in the structure of the basic salts, participation in formation of hydrogen bonds with OH-groups, contained in the brucite layer structure and H 2 O molecules influence the position of oxoanions in the series

STABLE STATIONARY STATES OF NON-LOCAL INTERACTION EQUATIONS

KAUST Repository

FELLNER, KLEMENS

2010-12-01

In this paper, we are interested in the large-time behaviour of a solution to a non-local interaction equation, where a density of particles/individuals evolves subject to an interaction potential and an external potential. It is known that for regular interaction potentials, stable stationary states of these equations are generically finite sums of Dirac masses. For a finite sum of Dirac masses, we give (i) a condition to be a stationary state, (ii) two necessary conditions of linear stability w.r.t. shifts and reallocations of individual Dirac masses, and (iii) show that these linear stability conditions imply local non-linear stability. Finally, we show that for regular repulsive interaction potential Wε converging to a singular repulsive interaction potential W, the Dirac-type stationary states ρ̄ ε approximate weakly a unique stationary state ρ̄ ∈ L∞. We illustrate our results with numerical examples. © 2010 World Scientific Publishing Company.

Local Electronic Structure of a Single-Layer Porphyrin-Containing Covalent Organic Framework

KAUST Repository

Chen, Chen

2017-12-20

We have characterized the local electronic structure of a porphyrin-containing single-layer covalent organic framework (COF) exhibiting a square lattice. The COF monolayer was obtained by the deposition of 2,5-dimethoxybenzene-1,4-dicarboxaldehyde (DMA) and 5,10,15,20-tetrakis(4-aminophenyl) porphyrin (TAPP) onto a Au(111) surface in ultrahigh vacuum followed by annealing to facilitate Schiff-base condensations between monomers. Scanning tunneling spectroscopy (STS) experiments conducted on isolated TAPP precursor molecules and the covalently linked COF networks yield similar transport (HOMO-LUMO) gaps of 1.85 ± 0.05 eV and 1.98 ± 0.04 eV, respectively. The COF orbital energy alignment, however, undergoes a significant downward shift compared to isolated TAPP molecules due to the electron-withdrawing nature of the imine bond formed during COF synthesis. Direct imaging of the COF local density of states (LDOS) via dI/dV mapping reveals that the COF HOMO and LUMO states are localized mainly on the porphyrin cores and that the HOMO displays reduced symmetry. DFT calculations reproduce the imine-induced negative shift in orbital energies and reveal that the origin of the reduced COF wave function symmetry is a saddle-like structure adopted by the porphyrin macrocycle due to its interactions with the Au(111) substrate.

Improved Performance of Pseudomonas fluorescens lipase by covalent immobilization onto Amberzyme

NARCIS (Netherlands)

Aslan, Yakup; Handayani, Nurrahmi; Stavila, Erythrina; Loos, Katja

2013-01-01

Objective: In this study, the conditions of covalent immobilization of Pseudomonas fluorescens lipase onto an oxirane-activated support (Amberzyme) were optimized to obtain a high activity yield. Furthermore, the operational and storage stabilities of immobilized lipase were tested. Methods: Optimum

Theoretical study for the interlamellar aminoalcohol functionalization of kaolinite

International Nuclear Information System (INIS)

Hou, Xin-Juan; Li, Huiquan; Liu, Qinfu; Cheng, Hongfei; He, Peng; Li, Shaopeng

2015-01-01

Graphical abstract: - Highlights: • The results indicated that aminoalcohols exist with a mixing of intercalation and grafting. • Aminoalcohols can form strong hydrogen bonds with Al octahedral sheet. • The interaction between aminoalcohols and Si tetrahedral sheet are mainly attributed by vdW force. • Aminoalcohols grafting or intercalating on kaolinite have strong reactivity as electron donors. - Abstract: Fundamental problems related to aminoalcohols intercalating on kaolinite were investigated by using density functional theory method. This study examines the adsorption modes of diethanolamine and triethanolamine on kaolinite, the role of hydrogen bonds and van der Waals (vdW) forces between aminoalcohols and interlayer of kaolinite, and the change of molecular orbital occupancies of functionalized kaolinite. Results show that functionalized kaolinite is physically intercalated and covalently grafted by aminoalcohols. Non-covalent interaction analysis provides a visualized description that intercalated aminoalcohols form strong hydrogen bonds with Al octahedral sheet, and the interaction between aminoalcohols and Si tetrahedral sheet is mainly attributed to weak vdW force. The analysis of molecular orbital occupancies for kaolinite complex showed that the functionalized kaolinite has strong chemical reactivity as electron donors on the sites of grafted or intercalated aminoalcohols for further chemical reaction with other materials

The covalent effect on the energy levels of d3 ions in tetragonal compounds

International Nuclear Information System (INIS)

Li, Dong-Yang; Du, Mao-Lu

2015-01-01

For d 3 ions in covalent compounds with tetragonal symmetry, this paper presents a complete energy matrix, in which the different covalence of t 2 and e orbitals is considered not only in the electrostatic repulsions part of energy matrix elements but also in the crystal-field potential part of energy matrix elements. With taking and no taking the crystal field parameter B 00 0 into account, the effect of covalence on the energy levels of d 3 ions system were investigated, respectively. The investigation shows that it is very necessary for considering the different covalence of t 2 and e orbitals in both electrostatic repulsions part and crystal-field potential part when the optical properties of d 3 ions in strong covalent compounds with tetragonal symmetry is investigated. On the other hand, the crystal field parameter B 00 0 has a significant effect on the energy levels, and should be considered in investigations of d 3 ions in strong covalent compounds with tetragonal symmetry. Application to calculating the energy levels for Co 2+ in CdGa 2 Se 4 , the calculated results are in agreement with the experiment data

Non-Unitarity, sterile neutrinos, and Non-Standard neutrino Interactions

CERN Document Server

Blennow, Mattias; Fernandez-Martinez, Enrique; Hernandez-Garcia, Josu; Lopez-Pavon, Jacobo

2017-04-27

The simplest Standard Model extension to explain neutrino masses involves the addition of right-handed neutrinos. At some level, this extension will impact neutrino oscillation searches. In this work we explore the differences and similarities between the case in which these neutrinos are kinematically accessible (sterile neutrinos) or not (mixing matrix non-unitarity). We clarify apparent inconsistencies in the present literature when using different parametrizations to describe these effects and recast both limits in the popular neutrino non-standard interaction (NSI) formal- ism. We find that, in the limit in which sterile oscillations are averaged out at the near detector, their effects at the far detector coincide with non-unitarity at leading order, even in presence of a matter potential. We also summarize the present bounds existing in both limits and compare them with the expected sensitivities of near-future facilities taking the DUNE proposal as a bench- mark. We conclude that non-unitarity effects ...

Covalent biofunctionalization of silicon nitride surfaces

NARCIS (Netherlands)

Arafat, A.; Giesbers, M.; Rosso, M.; Sudhölter, E.J.R.; Schroën, C.G.P.H.; White, R.G.; Li Yang,; Linford, M.R.; Zuilhof, H.

2007-01-01

Covalently attached organic monolayers on etched silicon nitride (SixN4; x 3) surfaces were prepared by reaction of SixN4-coated wafers with neat or solutions of 1-alkenes and 1-alkynes in refluxing mesitylene. The surface modification was monitored by measurement of the static water contact angle,

Integration and visualization of non-coding RNA and protein interaction networks

OpenAIRE

Junge, Alexander; Refsgaard, Jan Christian; Garde, Christian; Pan, Xiaoyong; Santos Delgado, Alberto; Anthon, Christian; Alkan, Ferhat; von Mering, Christian; Workman, Christopher; Jensen, Lars Juhl; Gorodkin, Jan

2015-01-01

Non-coding RNAs (ncRNAs) fulfill a diverse set of biological functions relying on interactions with other molecular entities. The advent of new experimental and computational approaches makes it possible to study ncRNAs and their associations on an unprecedented scale. We present RAIN (RNA Association and Interaction Networks) - a database that combines ncRNA-ncRNA, ncRNA-mRNA and ncRNA-protein interactions with large-scale protein association networks available in the STRING database. By int...

Interactive use of communication by verbal and non-verbal autistic children.

Science.gov (United States)

Amato, Cibelle Albuquerque de la Higuera; Fernandes, Fernanda Dreux Miranda

2010-01-01

Communication of autistic children. To assess the communication functionality of verbal and non-verbal children of the autistic spectrum and to identify possible associations amongst the groups. Subjects were 20 children of the autistic spectrum divided into two groups: V with 10 verbal children and NV with 10 non-verbal children with ages varying between 2y10m and 10y6m. All subjects were video recorded during 30 minutes of spontaneous interaction with their mothers. The samples were analyzed according to the functional communicative profile and comparisons within and between groups were conducted. Data referring to the occupation of communicative space suggest that there is an even balance between each child and his mother. The number of communicative acts per minute shows a clear difference between verbal and non-verbal children. Both verbal and non-verbal children use mostly the gestual communicative mean in their interactions. Data about the use of interpersonal communicative functions point out to the autistic children's great interactive impairment. The characterization of the functional communicative profile proposed in this study confirmed the autistic children's difficulties with interpersonal communication and that these difficulties do not depend on the preferred communicative mean.

Evidence of significant covalent bonding in Au(CN)(2)(-).

Science.gov (United States)

Wang, Xue-Bin; Wang, Yi-Lei; Yang, Jie; Xing, Xiao-Peng; Li, Jun; Wang, Lai-Sheng

2009-11-18

The Au(CN)(2)(-) ion is the most stable Au compound known for centuries, yet a detailed understanding of its chemical bonding is still lacking. Here we report direct experimental evidence of significant covalent bonding character in the Au-C bonds in Au(CN)(2)(-) using photoelectron spectroscopy and comparisons with its lighter congeners, Ag(CN)(2)(-) and Cu(CN)(2)(-). Vibrational progressions in the Au-C stretching mode were observed for all detachment transitions for Au(CN)(2)(-), in contrast to the atomic-like transitions for Cu(CN)(2)(-), revealing the Au-C covalent bonding character. In addition, rich electronic structural information was obtained for Au(CN)(2)(-) by employing 118 nm detachment photons. Density functional theory and high-level ab initio calculations were carried out to understand the photoelectron spectra and obtain insight into the nature of the chemical bonding in the M(CN)(2)(-) complexes. Significant covalent character in the Au-C bonding due to the strong relativistic effects was revealed in Au(CN)(2)(-), consistent with its high stability.

The influence of interlayer interactions on the mechanical properties of polymeric nanocomposites

Directory of Open Access Journals (Sweden)

Jabbarzadeh Mehrdad

2015-01-01

Full Text Available In this paper the influence of types of interlayer interactions on the elastic modules of multilayer graphene sheets (GS and nanocomposites is studied. The modeling and investigation of mechanical properties of graphite layers are performed using molecular mechanics (MM method. Initially, due to improving the model and decreasing the amount of computations, three types of elements such as beam, linear spring and nonlinear spring are used. To continue, the mechanical properties of multilayers and nanocomposites are compared using three types of interlayer interactions. Initially, nonlinear spring defined by Leonard Jones potential is used to define interlayer interactions (ordinary case. To continue, linear spring with certain stiffness, to obtain an equal linear spring and also to investigate the ultimate capacity of interlayer interactions in the force translation, by increasing the stiffness of linear springs, is employed (chemical change. Then once by omitting all Van der Waals interactions and defects creation in graphite layers, they are devoted to create covalent interlayer interactions (using Morse potential and another time, Van der Waals and covalent interlayer interactions are created spontaneously to study the properties of multilayers and nanocomposites (functionalization. The results are compared with other available literatures in this case to validate the modeling.

Data in support of covalent attachment of tyrosinase onto cyanuric chloride crosslinked magnetic nanoparticles

Directory of Open Access Journals (Sweden)

Kourosh Abdollahi

2016-12-01

Full Text Available Preparation and characterization of cross linked amine-functionalized magnetic nanoparticles as an appropriate support for covalent immobilization on tyrosinase was presented in the study "Covalent immobilization of tyrosinase onto cyanuric chloride crosslinked amine-functionalized superparamagnetic nanoparticles: synthesis and characterization of the recyclable nanobiocatalyst" (Abdollahi et al., 2016 [1]. Herein, complementary data regarding X-ray powder diffraction (XRD to characterize the synthesized magnetic nanoparticles, and transmission electron microscopy (TEM to determine the size and morphology of tyrosinase immobilized magnetic nanoparticles (tyrosinase-MNPs were reported. The purification results of the extracted tyrosinase from mushroom Agaricus bisporus were provided in a purification table. The covalent immobilization of tyrosinase onto cyanuric chloride functionalized magnetic nanoparticles was proved by performing thermo-gravimetric and energy-dispersive X-ray spectroscopy analyses. The operational stability of immobilized tyrosinase was investigated by incubating tyrosinase-MNPs at different pH and temperatures.

Covalent-ionically cross-linked polyetheretherketone proton exchange membrane for direct methanol fuel cell

CSIR Research Space (South Africa)

Luo, H

2010-08-01

Full Text Available cross-linked PEEK-WC membrane, this covalent-ionically cross-linked PEEK-WC membrane exhibits extremely reduced water uptake and methanol permeability, but just slightly sacrificed proton conductivity. The proton conductivity of the covalent...

Achieving enhanced hydrophobicity of graphene membranes by covalent modification with polydimethylsiloxane

Energy Technology Data Exchange (ETDEWEB)

Lei, Wei-Wei; Li, Hang [College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065 (China); Shi, Ling-Ying, E-mail: shilingying@scu.edu.cn [College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065 (China); Diao, Yong-Fu; Zhang, Yu-Lin; Ran, Rong [College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065 (China); Ni, Wei, E-mail: niwei@iccas.ac.cn [Institute of Chemical Materials, China Academy of Engineering Physics, Chengdu 610200 (China)

2017-05-15

Highlights: • The graphene oxide (GO) was covalently modified by amino terminated polydimethylsiloxane (PDMS) through amidation reaction. • Through the vacuum filtration method, the GO, RGO and PDMS-modified graphene membranes were successfully prepared respectively. • The morphology of membranes had smooth surface and well-stacked structure indicated by SEM and EDS mapping results. • The contact angle of GO-g-PDMS membrane was high to be 129.5° indicating a great enhancement of hydrophobicity. - Abstract: In this study, the graphene oxide was covalently modified by amino terminated polydimethylsiloxane (PDMS) through amidation reaction. And the membranes of the graphene oxide (GO), reduced graphene oxide (RGO) and PDMS-covalently modified graphene were prepared respectively by a vacuum filtration method, and the wettability of these membranes were investigated. Infrared spectroscopy, Raman, X-ray diffraction, X-ray photoelectron spectroscopy, and thermogravimetry analysis combined with dispersion ability indicated that PDMS chains were successfully grafted on the surface of graphene oxide sheets. The morphology of the prepared membranes had smooth surface and well-stacked structure in the cross-section indicated by the scanning electron microscope and EDS-mapping. The contact angle measurements indicated that the PDMS-modified graphene membrane with water contact angle 129.5° showed increased hydrophobicity compared with GO and RGO membranes.

Studies on synthesis, structural, luminescent and thermal properties of a new non-linear optical crystal: 4-amino-4H-1,2,4-triazol-1-ium-3-hydroxy-2,4,6-trinitrophenolate

Energy Technology Data Exchange (ETDEWEB)

Dhamodharan, P.; Sathya, K.; Dhandapani, M., E-mail: chemistrydhandapani@gmail.com

2017-03-01

A new organic proton transfer complex having NLO activity, 4-amino-4H-1,2,4-triazol-1-ium-3-hydroxy-2,4,6-trinitrophenolate (ATHTP), was crystallized to investigate the factors which stabilize the structure of the crystal. The compound crystallizes in triclinic system with space group P-1. Elemental analysis, thermal analysis, UV–Vis–NIR, FT-IR and NMR spectral analyses were carried out to characterize the crystal. Optical, spectral and thermal properties of the title crystal were analyzed to recommend the material for optical applications. Z-scan was used to measure the effective third-order nonlinear optical susceptibility and nonlinear refractive index. The crystal structure was determined using single crystal XRD method and the structure was optimized using Gaussian 09 program at B3LYP/6-311++G(d,p) level of basis set. This hydrogen bond interactions led to the increase in first-order hyperpolarizability of ATHTP and was 30 times greater than that of urea. Hirshfeld analyses surface analysis was carried out to explore intermolecular interactions in the crystalline state. - Highlights: • Single crystals were grown by slow evaporation solution growth technique. • N-H…O, O-H…O and C-H…O type of interactions lead to stable network. • The thermal stability of the compound was investigated by TG/DTA analyses. • The third-order nonlinear optical susceptibility is found to be 2.1×10{sup −7} esu. • Hirshfeld analyses explore covalent and non covalent interactions.

共价键的离子化%Ionization of Covalent Bond

Institute of Scientific and Technical Information of China (English)

王稼国; 荆西平

2017-01-01

本文用化学键理论分析和推导了共价键离子化的几种方式,包括金属和非金属单质中共价键的诱导离子化、化合物中共价键的降温和自诱导离子化以及含氢化合物和金属化合物的诱导离子化.从能量角度分析了离子化趋势的规律性,并且讨论了共价键的离子化的一些重要应用.%Several ionization patterns of covalent bond,including induced-ionization of covalent bond in metals and nonmetals,induced-ionization of covalent bond in hydrogen compounds and metal compounds,lowering temperature and self-induced ionization of compound,and so on,were dedueed and analyzed by using chemical bond theory.The trend of ionization was also analyzed on energy changing and several important applications of the ionization of covalent bond were discussed.

More about the comparison of local and non-local NN interaction models

International Nuclear Information System (INIS)

Amghar, A.; Desplanques, B.

2003-01-01

The effect of non-locality in the NN interaction with an off-energy shell character has been studied in the past in relation with the possibility that some models could be approximately phase-shifts equivalent. This work is extended to a non-locality implying terms that involve an anticommutator with the operator p 2 . It includes both scalar and tensor components. The most recent 'high accuracy' models are considered in the analysis. After studying the deuteron wave functions, electromagnetic properties of various models are compared with the idea that these ones differ by their non-locality but are equivalent up to a unitary transformation. It is found that the extra non-local tensor interaction considered in this work tends to re-enforce the role of the term considered in previous works, allowing one to explain almost completely the difference in the deuteron D-state probabilities evidenced by the comparison of the Bonn-QB and Paris models for instance. Conclusions for the effect of the non-local scalar interaction are not so clear. In many cases, it was found that these terms could explain part of the differences that the comparison of predictions for various models evidences but cases where they could not were also found. Some of these last ones have been analyzed in order to pointing out the origin of the failure

CHAPTER 1

African Journals Online (AJOL)

Dr Olaleye

form of natural DNA. .... either covalent or non-covalent bonding. In a covalent binding the reactive part of the compounds interacts with a nitrogen base of DNA such as guanine N7 e.g., ... electrostatic and groove binding of cationic metal.

Theoretical study of band gap in CuAlO2: Pressure dependence and self-interaction correction

International Nuclear Information System (INIS)

Nakanishi, Akitaka; Katayama-Yoshida, Hiroshi

2012-01-01

By using first-principles calculations, we studied the energy gaps of delafossite CuAlO 2 : (1) pressure dependence and (2) self-interaction correction (SIC). Our simulation shows that CuAlO 2 transforms from a delafossite structure to a leaning delafossite structure at 60 GPa. The energy gap of CuAlO 2 increases through the structural transition due to the enhanced covalency of Cu 3d and O 2p states. We implemented a self-interaction correction (SIC) into first-principles calculation code to go beyond local density approximation and applied it to CuAlO 2 . The energy gap calculated within the SIC is close to experimental data while one calculated without the SIC is about 1 eV smaller than the experimental data.

Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

Science.gov (United States)

2015-01-01

Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

Non-Covalent Supported of l-Proline on Graphene Oxide/Fe3O4 Nanocomposite: A Novel, Highly Efficient and Superparamagnetically Separable Catalyst for the Synthesis of Bis-Pyrazole Derivatives

Directory of Open Access Journals (Sweden)

Mosadegh Keshavarz

2018-02-01

Full Text Available A superparamagnetic graphene oxide/Fe3O4/l-proline nano hybrid that was obtained from the non-covalent immobilization of l-proline on graphene oxide/Fe3O4 nanocomposite was used as a new magnetically separable catalyst for the efficient synthesis of 4,4′-(arylmethylenebis(1H-pyrazol-5-ol derivatives. The prepared heterogeneous catalyst was characterized using FTIR, TGA, DTG, XRD, TEM, SEM, and elemental analysis techniques. Short reaction times (5–15 min, excellent yields (87–98%, and simple experimental procedure with an easy work-up are some of the advantages of the introduced catalyst.

Spectrofluorometric and thermal gravimetric study on binding interaction of thiabendazole with hemoglobin on epoxy-functionalized magnetic nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Maltas, Esra, E-mail: maltasesra@gmail.com; Ozmen, Mustafa

2015-09-01

The interaction of thiabendazole (Tbz) with hemoglobin (Hb) on epoxy-functionalized iron oxide nanoparticles was presented in this study. The binding capacity of Tbz was determined by measuring at an excitation wavelength of 299 nm using fluorescence spectroscopy. The thermodynamic parameters of the Hb–Tbz interaction were calculated from Stern–Volmer and van't Hoff equations. The values of enthalpy change, ∆H, and entropy change, ∆S, were found to be 0.20 kJ mol{sup −1} and 0.70 J mol{sup −1} K{sup −1}, respectively, which indicates that the hydrophilic interaction plays a main role in the binding process. The interaction ability was confirmed by Fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). Also, the thermal behavior of the Hb–Tbz interaction on functionalized iron oxide nanoparticles was studied by using the thermogravimetric analysis (TGA) technique in the temperature range of 25–950 °C, and then the kinetic parameters for the thermal decomposition were determined using the Horowitz–Metzger method. - Highlights: • Hb was immobilized by covalent attachment on GPTS–SPIONs. • Interaction of Tbz with Hb–GPTS–SPIONs was studied. • Thermodynamic parameters for interaction were calculated. • Hydrophilic interaction plays a main role in the binding process.

Characterization of the regions from E. coli 16 S RNA covalently linked to ribosomal proteins S4 and S20 after ultraviolet irradiation

International Nuclear Information System (INIS)

Ehresmann, B.; Backendorf, C.; Ehresmann, C.; Ebel, J.P.

1977-01-01

The use of ultraviolet irradiation to form photochemical covalent bonds between the 16 S RNA and a ribosomal protein is a reliable method to check RNA regions which are interacting with the protein. This technique was successfully used to covalently link RNA or DNA and specific proteins in several cases. In the case of ribosome, it has been shown that the irradiation of 30 S and 50 S subunits using high doses of ultraviolet light allowed the covalent binding of almost all of the ribosomal proteins to the 16 S or 23 S RNAs. Using mild conditions, only proteins S7 and L4 could be covalently linked to the 16 S and 23 S RNAs, respectively, and the 16 S RNA region linked to protein S7 has now been characterized. The specificity of the photoreaction was demonstrated earlier and the tryptic peptides from proteins S4 and S7, photochemically linked to the 16 S RNA complexes, were identified. A report is presented on the sequences of the RNA regions which can be photochemically linked to proteins S4 and S7 after ultraviolet irradiation of the specific S4-16 S RNA and 20 S-16 S RNA complexes

Clustering of carboxylated magnetite nanoparticles through polyethylenimine: Covalent versus electrostatic approach

Energy Technology Data Exchange (ETDEWEB)

Tóth, Ildikó Y., E-mail: Ildiko.Toth@chem.u-szeged.hu [Department of Physical Chemistry and Materials Science, University of Szeged, Aradi vt. square 1, Szeged (Hungary); Nesztor, Dániel [Department of Physical Chemistry and Materials Science, University of Szeged, Aradi vt. square 1, Szeged (Hungary); Novák, Levente [Department of Colloid and Environmental Chemistry, University of Debrecen, Egyetem square 1, Debrecen (Hungary); Illés, Erzsébet; Szekeres, Márta; Szabó, Tamás [Department of Physical Chemistry and Materials Science, University of Szeged, Aradi vt. square 1, Szeged (Hungary); Tombácz, Etelka, E-mail: tombacz@chem.u-szeged.hu [Department of Physical Chemistry and Materials Science, University of Szeged, Aradi vt. square 1, Szeged (Hungary)

2017-04-01

Carboxylated magnetite nanoparticles (MNPs) are frequently used to develop materials with enhanced properties for MRI and hyperthermia. The controlled clustering of MNPs via covalent or electrostatic approaches provides opportunity to prepare high quality materials. MNPs were prepared by co-precipitation and coated by poly(acrylic acid-co-maleic acid) (PAM@MNP). The clusters were synthesized from purified PAM@MNPs and polyethylenimine (PEI) solution via electrostatic interaction and covalent bond formation (ES-cluster and CB-cluster, respectively). The electrostatic adhesion (–NH{sub 3}{sup +} and –COO{sup –}) and the formed amide bond were confirmed by ATR-FTIR. The averaged area of CB-clusters was about twice as large as that of ES-cluster, based on TEM. The SAXS results showed that the surface of MNPs was smooth and the nanoparticles were close packed in both clusters. The pH-dependent aggregation state and zeta potential of clusters were characterized by DLS and electrophoresis measurements, the clusters were colloidally stable at pH>5. In hyperthermia experiments, the values of SAR were about two times larger for the chemically bonded cluster. The MRI studies showed exceptionally high transversion relaxivities, the r{sub 2} values are 457 mM{sup −1} s{sup −1} and 691 mM{sup −1} s{sup −1} for ES-cluster and CB-cluster, respectively. Based on these results, the chemically clustered product shows greater potential for feasible biomedical applications. - Highlights: • Chemically bonded clusters (CB-cluster) were prepared from PEI and PAM-coated MNPs. • The electrostatically clustered units (ES-cluster) are smaller and more compact. • The electrostatic adhesion and the amide bond formation were confirmed by ATR-FTIR. • CB-cluster dispersions are colloidally stable under physiological conditions. • CB-cluster shows great potential for application in MRI and hyperthermia.

Interatomic interaction of additive elements and their influence on the processes in the double metal solutions

Directory of Open Access Journals (Sweden)

Марина Анатоліівна Рябікіна

2016-07-01

Full Text Available Modern industry uses a lot of elements as additives to improve the service characteristics of metal products that are to be used for various purposes. These elements can be divided into two groups: the first group includes the elements interacting with iron and improving its characteristics (alloying elements, and the second group includes the elements, that modify the characteristics of the structure and properties in an undesirable direction. These are trace elements: S, P, O, As, and others in steel. The negative impact of these elements shows itself as banding, the formation of non-metallic inclusions, flakes, grain boundary segregations et al. The influence of the elements of the both groups on the properties of steel depends on the nature and level of interatomic interaction in the alloy. Computational and analytical study of the major impurity elements in steel impact on the interatomic bond strength and the probability of forming complexes, clusters, and chemical compounds with the basic alloying elements in the steel has been carried out in the work. The theoretical parameter which defines the strength of the ion-covalent bond of two atoms: non-metallic – metallic is the electronegativity of elements. The electronegativity difference of the metal and non-metallic elements increasing, the ionic bonding and thermodynamic stability of these compounds  increase. On the other hand, concentration of valent electrons is a universal characteristic of an atomic element which determines many of its properties, and especially the energy of interatomic interaction. Energy calculations of pairwise interatomic impurity elements: H, C, N, S, P, As interaction with Fe and major alloying elements in steel: Mn, Cr, Si, V, Al, Ti, W, Cu, Mo, Nb were made. It has been stated that all the impurity elements except phosphorus, hydrogen and arsenic have sufficient high adhesion with the majority of the metal elements in the modern steels. Phosphorus does

H-Bonding Cooperativity Effects in Amyloids: Quantum Mechanical and Molecular Mechanics Study

Czech Academy of Sciences Publication Activity Database

Přenosil, Ondřej; Pitoňák, Michal; Sedlák, Robert; Kabeláč, Martin; Hobza, Pavel

2011-01-01

Roč. 225, č. 5 (2011), s. 553-574 ISSN 0942-9352 R&D Projects: GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : non- covalent interaction * hydrogen bond * amyloids * DFT Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.568, year: 2011

Differences in the covalent binding of benzo(a)pyrene, safrole, 1'-hydroxysafrole, and 4-aminobiphenyl to DNA of pregnant and non-pregnant mice

International Nuclear Information System (INIS)

Lu, L.W.; Disher, R.M.; Randerath, Kurt

1986-01-01

The effects of pregnancy on the covalent binding of several carcinogens to DNA were investigated in mice. Non-pregnant or timed-pregnant (18th day of gestation) ICR mice of similar age were treated with benzo(a)pyrene (BP, 200 μmol/kg), safrole (600 μmol/kg), 1'-hydroxysafrole (400 μmol/kg), 4-aminobiphenyl (4-ABP, 800 μmol/kg) or trioctanoin (4 ml/kg) per os. Tissue DNA adduct levels at 24 h after carcinogen treatment were analyzed via a 32 P-postabeling assay. Pregnancy lowered the binding of the ultimate carcinogenic metalolite of BP, 7β, 8α-dihydroxy-9, 10α-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (BPDE I), to liver and lung DNA by 29-41%, but not the binding of other metabolites. The binding of safrole and its proximate carcinogen, 1'-hydroxysafrole, to liver and kidney DNA was increased 2.3-3.5 fold. Pregnancy decreased the binding of 4-ABP to liver DNA by approx. 18% but increased its binding to kidney DNA by 67%. The results suggest that exposure to some genotoxic compounds especially those requiring conjugation reactions for metabolic activation, may be more hazardous during pregnancy than in the non-pregnant state (author)

Covalent Functionalization of Carbon Nanotube by Tetrasubtituted Amino Manganese Phthalocyanine

Institute of Scientific and Technical Information of China (English)

Zheng Long YANG; Hong Zheng CHEN; Lei CAO; Han Yin LI; Mang WANG

2004-01-01

The multiwall carbon nanotube (MWCNT) bonded to 2, 9, 16, 23-tetraamino manganese phthalocyanine (TAMnPc) was obtained by covalent functionalization, and its chemical structure was characterized by TEM. The photoconductivity of single-layered photoreceptors, where MWCNT bonded by TAMnPc (MWCNT-b-TAMnPc) served as the charge generation material (CGM), was also studied.

Non-formal Learning through Ludic Engagement within Interactive Environments

DEFF Research Database (Denmark)

Petersson, Eva

Adaptive responsive environments that encourage interaction for children with severe disabilities offer a distinct potential for play and learning in rehabilitation. Physical training and therapy for these children is often enduring, tedious, and boring through repetition – and this is often...... the case for both the child and the facilitator/therapist. Despite this, little is yet known about how the utilization of empowering technology influences the users’ communication and learning. The aim of this thesis is twofold: to contribute to the understanding of the role of action and interaction...... in the learning involved when people with different abilities are using interactive environments, and to make a contribution to the research field by concluding at tentative generalizations on design for non-formal learning in interactive environments.      The thesis consists of seven studies which analyze...

Self-assembly of Hydrazide-based Heterodimers Driven by Hydrogen Bonding and Donor-Acceptor Interaction

Institute of Scientific and Technical Information of China (English)

FENG,Dai-Jun; WANG,Peng; LI,Xiao-Qiang; LI,Zhan-Ting

2006-01-01

A new series of hydrogen bonding-driven heterodimers have been self-assembled in chloroform from hydrazide-based monomers. Additional intermolecular donor-acceptor interaction between the electron-rich bis(p-phenylene)-34-crown-10 unit and the electron-deficient naphthalene diimide unit has been utilized to increase the stability of the dimmers, and pronounced cooperativity of the two discrete non-covalent forces to stabilize the dimer has been revealed by the quantitative 1H (2D) NMR and UV-Vis experiments.

Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?

Science.gov (United States)

Freilich, Mara A; Wieters, Evie; Broitman, Bernardo R; Marquet, Pablo A; Navarrete, Sergio A

2018-03-01

Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically based, species interaction network from the same region. We evaluated the overlap in the information provided by each network and the extent to which there is a bias for co-occurrence data to better detect known trophic or non-trophic, positive or negative interactions. We found a poor correspondence between the co-occurrence network and the known species interactions with overall sensitivity (probability of true link detection) equal to 0.469, and specificity (true non-interaction) equal to 0.527. The ability to detect interactions varied with interaction type. Positive non-trophic interactions such as commensalism and facilitation were detected at the highest rates. These results demonstrate that co-occurrence networks do not represent classical ecological networks in which interactions are defined by direct observations or experimental manipulations. Co-occurrence networks provide information about the joint spatial effects of environmental conditions, recruitment, and, to some extent, biotic interactions, and among the latter, they tend to better detect niche-expanding positive non-trophic interactions. Detection of links (sensitivity or specificity) was not higher for well-known intertidal keystone species than for the rest of consumers in the community. Thus, as observed in previous empirical and theoretical studies, patterns of interactions in co-occurrence networks must be interpreted with caution, especially when extending interaction

Curtailing the dark side in non-standard neutrino interactions

Energy Technology Data Exchange (ETDEWEB)

Coloma, Pilar [Theoretical Physics Department, Fermi National Accelerator Laboratory,P.O. Box 500, Batavia, IL 60510 (United States); Denton, Peter B. [Theoretical Physics Department, Fermi National Accelerator Laboratory,P.O. Box 500, Batavia, IL 60510 (United States); Niels Bohr International Academy, University of Copenhagen, The Niels Bohr Institute,Blegdamsvej 17, DK-2100, Copenhagen (Denmark); Gonzalez-Garcia, M.C. [Departament de Fisíca Quàntica i Astrofísica and Institut de Ciencies del Cosmos,Universitat de Barcelona, Diagonal 647, E-08028 Barcelona (Spain); Institució Catalana de Recerca i Estudis Avançats (ICREA),Pg. Lluis Companys 23, 08010 Barcelona (Spain); C.N. Yang Institute for Theoretical Physics, Stony Brook University,Stony Brook, NY 11794-3840 (United States); Maltoni, Michele [Instituto de Física Teórica UAM/CSIC, Universidad Autónoma de Madrid,Calle de Nicolás Cabrera 13-15, Cantoblanco, E-28049 Madrid (Spain); Schwetz, Thomas [Institut für Kernphysik, Karlsruher Institut für Technologie (KIT), D-76021 Karlsruhe (Germany)

2017-04-20

In presence of non-standard neutrino interactions the neutrino flavor evolution equation is affected by a degeneracy which leads to the so-called LMA-Dark solution. It requires a solar mixing angle in the second octant and implies an ambiguity in the neutrino mass ordering. Non-oscillation experiments are required to break this degeneracy. We perform a combined analysis of data from oscillation experiments with the neutrino scattering experiments CHARM and NuTeV. We find that the degeneracy can be lifted if the non-standard neutrino interactions take place with down quarks, but it remains for up quarks. However, CHARM and NuTeV constraints apply only if the new interactions take place through mediators not much lighter than the electroweak scale. For light mediators we consider the possibility to resolve the degeneracy by using data from future coherent neutrino-nucleus scattering experiments. We find that, for an experiment using a stopped-pion neutrino source, the LMA-Dark degeneracy will either be resolved, or the presence of new interactions in the neutrino sector will be established with high significance.

Non interacting control by measurement feedback

NARCIS (Netherlands)

Woude, van der J.W.

1987-01-01

In this paper we shall solve the problem of non interacting control by measurement feedback for systems that in addition to a control input and a measurement output have two exogenous inputs and two exogenous outputs. That is, we shall derive necessary and sufficient conditions that can actually be

Non-additive non-interacting kinetic energy of rare gas dimers

Science.gov (United States)

Jiang, Kaili; Nafziger, Jonathan; Wasserman, Adam

2018-03-01

Approximations of the non-additive non-interacting kinetic energy (NAKE) as an explicit functional of the density are the basis of several electronic structure methods that provide improved computational efficiency over standard Kohn-Sham calculations. However, within most fragment-based formalisms, there is no unique exact NAKE, making it difficult to develop general, robust approximations for it. When adjustments are made to the embedding formalisms to guarantee uniqueness, approximate functionals may be more meaningfully compared to the exact unique NAKE. We use numerically accurate inversions to study the exact NAKE of several rare-gas dimers within partition density functional theory, a method that provides the uniqueness for the exact NAKE. We find that the NAKE decreases nearly exponentially with atomic separation for the rare-gas dimers. We compute the logarithmic derivative of the NAKE with respect to the bond length for our numerically accurate inversions as well as for several approximate NAKE functionals. We show that standard approximate NAKE functionals do not reproduce the correct behavior for this logarithmic derivative and propose two new NAKE functionals that do. The first of these is based on a re-parametrization of a conjoint Perdew-Burke-Ernzerhof (PBE) functional. The second is a simple, physically motivated non-decomposable NAKE functional that matches the asymptotic decay constant without fitting.

Rotational Spectrum and Conformational Analysis of N-methyl-2-aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters

Science.gov (United States)

Calabrese, Camilla; Maris, Assimo; Evangelisti, Luca; Piras, Anna; Parravicini, Valentina; Melandri, Sonia

2018-02-01

Abstract We describe an experimental and quantum chemical study for the accurate determination of the conformational space of small molecular systems governed by intramolecular non-covalent interactions. The model systems investigated belong to the biological relevant aminoalcohol’s family, and include 2-aminophenylethanol, 2-methylaminophenylethanol, noradrenaline, adrenaline 2-aminoethanol and N-methyl-2-aminoethanol. For the latter molecule, the rotational spectrum in the 6-18 and 59.6-74.4 GHz ranges was recorded in the isolated conditions of a free jet expansion. Based on the analysis of the rotational spectra, two different conformational species and 11 isotopologues were observed and their spectroscopic constants, including 14N-nuclear hyperfine coupling constants and methyl internal rotation barriers, were determined. From the experimental data a structural determination was obtained, which was also used to benchmark accurate quantum chemical calculations on the whole conformational space. Atom in molecules and non-covalent interactions theories allowed the characterization of the position of the intramolecular non-covalent interactions and the energies involved, highlighting the subtle balance responsible of the stabilization of all the molecular systems.

Synthesis and Anticancer Activity of Gold(I)-Chloroquine Complexes

OpenAIRE

Navarro, Maribel; Castro, William; González, Sorenlis; Abad, María Jesús; Taylor, Peter

2013-01-01

Two new gold(I) -chloroquine complexes, Au(CQ)(Cl) (1) and Au(CQ)(tgta) (2), were prepared and their most probable structure were established through a combination of different spectroscopic and analytical techniques. Their interaction with two important targets of action, DNA and thioredoxin reductase (TrxR), were investigated. These studies showed that complexes 1 and 2 displayed two types of interaction with DNA, covalent binding through the metal center, and additionally a non-covalent in...

Building high-coverage monolayers of covalently bound magnetic nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Williams, Mackenzie G.; Teplyakov, Andrew V., E-mail: andrewt@udel.edu

2016-12-01

Graphical abstract: - Highlights: • A method for forming a layer of covalently bound nanoparticles is offered. • A nearly perfect monolayer of covalently bound magnetic nanoparticles was formed on gold. • Spectroscopic techniques confirmed covalent binding by the “click” reaction. • The influence of the functionalization scheme on surface coverage was investigated. - Abstract: This work presents an approach for producing a high-coverage single monolayer of magnetic nanoparticles using “click chemistry” between complementarily functionalized nanoparticles and a flat substrate. This method highlights essential aspects of the functionalization scheme for substrate surface and nanoparticles to produce exceptionally high surface coverage without sacrificing selectivity or control over the layer produced. The deposition of one single layer of magnetic particles without agglomeration, over a large area, with a nearly 100% coverage is confirmed by electron microscopy. Spectroscopic techniques, supplemented by computational predictions, are used to interrogate the chemistry of the attachment and to confirm covalent binding, rather than attachment through self-assembly or weak van der Waals bonding. Density functional theory calculations for the surface intermediate of this copper-catalyzed process provide mechanistic insight into the effects of the functionalization scheme on surface coverage. Based on this analysis, it appears that steric limitations of the intermediate structure affect nanoparticle coverage on a flat solid substrate; however, this can be overcome by designing a functionalization scheme in such a way that the copper-based intermediate is formed on the spherical nanoparticles instead. This observation can be carried over to other approaches for creating highly controlled single- or multilayered nanostructures of a wide range of materials to result in high coverage and possibly, conformal filling.

The molecular understanding of interfacial interactions of functionalized graphene and chitosan

International Nuclear Information System (INIS)

Zhang, Hong-ping; Luo, Xue-gang; Lin, Xiao-yan; Lu, Xiong; Tang, Youhong

2016-01-01

Graphical abstract: The type of the functional groups can be used to modulating interactions between graphene sheet and chitosan. - Highlights: • Investigate interfacial interactions between chitosan and functionalized graphene by DFT. • Observe covalent linkages between COOH-modified graphene and chitosan units. • Multi-functionalized graphene regulates the interfacial interactions with chitosan. • It is useful for guiding the preparation of graphene/chitosan composites. - Abstract: Graphene-reinforced chitosan scaffolds have been extensively studied for several years as promising hard tissue replacements. However, the interfacial interactions between graphene and chitosan are strongly related to the solubility, processability, and mechanical properties of graphene-reinforced chitosan (G–C) composites. The functionalization of graphene is regarded as the most effective way to improve the abovementioned properties of the G–C composite. In this study, the interfacial interactions between chitosan and functionalized graphene sheets with carboxylization (COOH-), amination (NH 2 -), and hydroxylation (OH-) groups were systematically studied at the electronic level using the method of ab initio simulations based on quantum mechanics theory and the observations were compared with reported experimental results. The covalent linkages between COOH-modified graphene and the chitosan units were demonstrated and the combination of multi-functionalization on graphene could regulate the interfacial interactions between graphene and the chitosan. The interfacial interactions between chitosan and properly functionalized graphene are critical for the preparation of G–C-based composites for tissue engineering scaffolds and other applications.

Interaction of carbon nano tubes with DNA segments; Interacao de nanotubos de carbono com segmentos de DNA

Energy Technology Data Exchange (ETDEWEB)

Peressinotto, Valdirene Sullas Teixeira

2007-07-01

Single- and double-stranded DNA (deoxyribonucleic acid) molecules can strongly bind to single-walled carbon nanotubes (SWNT) via non-covalent interactions. Under certain conditions, the DNA molecule spontaneously self-assembles into a helical wrapping around the tubular structure of the carbon nanotubes to form DNA/SWNT hybrids, which are both stable and soluble in water. This system has recently received extensive attention, since, besides rendering SWNTs dispersible in water as individual tubes, the DNA hybrids are very promising candidates for many applications in nanotechnology and molecular biology. All the possible applications for DNA-SWNT hybrids require, however, a fully understanding of DNA-nanotube wrapping mechanism which is still lacking in the literature. In this context, the aim of this work was to investigate the non-covalent interaction in aqueous medium between SWNTs and synthetic DNA segments having a known nucleotide sequence. Initially, the study was focused on poly d(GT)n sequences (n = 10, 30 and 45) that contain a sequence of alternating guanine and thymine bases and for which the efficiency to disperse and separate carbon nanotubes has already been demonstrated. Besides the size of GT sequences, the effects of ionic strength and pH in the interaction were also investigated. Afterwards, we studied the interaction of SWNT with DNA molecules that contain only a single type of nitrogenous base (DNA homopolymers), which has not been reported in details in the literature. We investigated homopolymers of poly dA{sub 20}, poly dT{sub 20}, poly dC{sub 20} and the duplex poly dA{sub 20}:dT{sub 20}. Most of the study was carried out with small-diameter HiPco SWNTs (with diameters between 0.7 and 1.2 nm). In some studies, SWNTs with diameter around 1.4 nm, synthesized via laser ablation and arc-discharge methods, were also investigated. The arc-discharge nanotubes used in this study were functionalized with carboxylic groups (-COOH) due to their

Tough Self-Healing Elastomers by Molecular Enforced Integration of Covalent and Reversible Networks.

Science.gov (United States)

Wu, Jinrong; Cai, Li-Heng; Weitz, David A

2017-10-01

Self-healing polymers crosslinked by solely reversible bonds are intrinsically weaker than common covalently crosslinked networks. Introducing covalent crosslinks into a reversible network would improve mechanical strength. It is challenging, however, to apply this concept to "dry" elastomers, largely because reversible crosslinks such as hydrogen bonds are often polar motifs, whereas covalent crosslinks are nonpolar motifs. These two types of bonds are intrinsically immiscible without cosolvents. Here, we design and fabricate a hybrid polymer network by crosslinking randomly branched polymers carrying motifs that can form both reversible hydrogen bonds and permanent covalent crosslinks. The randomly branched polymer links such two types of bonds and forces them to mix on the molecular level without cosolvents. This enables a hybrid "dry" elastomer that is very tough with fracture energy 13500 Jm -2 comparable to that of natural rubber. Moreover, the elastomer can self-heal at room temperature with a recovered tensile strength 4 MPa, which is 30% of its original value, yet comparable to the pristine strength of existing self-healing polymers. The concept of forcing covalent and reversible bonds to mix at molecular scale to create a homogenous network is quite general and should enable development of tough, self-healing polymers of practical usage. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interactions of neurotoxins with non-NMDA glutamate receptors: an autoradiographic study

International Nuclear Information System (INIS)

Kuenig, G.; Niedermeyer, B.; Krause, F.; Hartmann, J.; Deckert, J.; Heinsen, H.; Beckmann, H.; Riederer, P.; Ransmayr, G.

1994-01-01

Neurotoxic substances are discussed to cause neurode-generation by acting as excitotoxins on glutamate receptors. We investigated the properties of L-beta-oxalyl-amino-alanine (L-BOAA) and 3,4,6-trihydroxyphenlyalanine (6-OH-Dopa) at the alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) glutamate receptor and that of L-BOAA and domoic acid at the kainate glutamate receptor in human hippocampus. (3 H)AMPA binding in hippocampal subfields was inhibited by L-BOAA and 6-OH-Dopa with mean IC50-values in the low micromolar range. (3H)Kainate binding was inhibited by L-BOAA with similar potency as (3H)AMPA binding and by domoic acid with mean IC50-values in the low nanomolar range. These results support the notion that symptoms like anterograde amnesia and epileptic seizures seen in domoic acid intoxication and limbic symptoms, e.g. cognitive and mood impairment observed in neurolathyrism may be caused by excitotoxic action on non-NMDA receptors. The potent interaction of 6-OH-Dopa with the AMPA-receptor may point to a possible dopaminergic-glutamatergic interaction in the development of neurodegenerative diseases like Parkinson's and Huntington's disease. (author)

Molecular marriage through partner preferences in covalent cage formation and cage-to-cage transformation.

Science.gov (United States)

Acharyya, Koushik; Mukherjee, Sandip; Mukherjee, Partha Sarathi

2013-01-16

Unprecedented self-sorting of three-dimensional purely organic cages driven by dynamic covalent bonds is described. Four different cages were first synthesized by condensation of two triamines and two dialdehydes separately. When a mixture of all the components was allowed to react, only two cages were formed, which suggests a high-fidelity self-recognition. The issue of the preference of one triamine for a particular dialdehyde was further probed by transforming a non-preferred combination to either of the two preferred combinations by reacting it with the appropriate triamine or dialdehyde.

Ultrasensitive Nanoimmunosensor by coupling non-covalent functionalized graphene oxide platform and numerous ferritin labels on carbon nanotubes.

Science.gov (United States)

Akter, Rashida; Jeong, Bongjin; Choi, Jong-Soon; Rahman, Md Aminur

2016-06-15

An ultrasensitive electrochemical nanostructured immunosensor for a breast cancer biomarker carbohydrate antigen 15-3 (CA 15-3) was fabricated using non-covalent functionalized graphene oxides (GO/Py-COOH) as sensor probe and multiwalled carbon nanotube (MWCNTs)-supported numerous ferritin as labels. The immunosensor was constructed by immobilizing a monoclonal anti-CA 15-3 antibody on the GO modified cysteamine (Cys) self-assembled monolayer (SAM) on an Au electrode (Au/Cys) through the amide bond formation between the carboxylic acid groups of GO/Py-COOH and amine groups of anti-CA 15-3. Secondary antibody conjugated MWCNT-supported ferritin labels (Ab2-MWCNT-Ferritin) were prepared through the amide bond formation between amine groups of Ab2 and ferritin and carboxylic acid groups of MWCNTs. The detection of CA 15-3 was based on the enhanced bioelectrocatalytic reduction of hydrogen peroxide mediated by hydroquinone (HQ) at the GO/Py-COOH-based sensor probe. The GO/Py-COOH-based sensor probe and Ab2-MWCNT-Ferritin labels were characterized using cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), scanning electron microscope (SEM), transmission electron microscope (TEM), and x-ray photoelectron spectroscopy (XPS) techniques. Using differential pulse voltammetry (DPV) technique, CA 15-3 can be selectively detected as low as 0.01 ± 0.07 U/mL in human serum samples. Additionally, the proposed CA 15-3 immunosensor showed excellent selectivity and better stability in human serum samples, which demonstrated that the proposed immunosensor has potentials in proteomic researches and diagnostics. Copyright © 2016 Elsevier B.V. All rights reserved.

Increased Protein Structural Resolution from Diethylpyrocarbonate-based Covalent Labeling and Mass Spectrometric Detection

Science.gov (United States)

Zhou, Yuping; Vachet, Richard W.

2012-04-01

Covalent labeling and mass spectrometry are seeing increased use together as a way to obtain insight into the 3-dimensional structure of proteins and protein complexes. Several amino acid specific (e.g., diethylpyrocarbonate) and non-specific (e.g., hydroxyl radicals) labeling reagents are available for this purpose. Diethylpyrocarbonate (DEPC) is a promising labeling reagent because it can potentially probe up to 30% of the residues in the average protein and gives only one reaction product, thereby facilitating mass spectrometric analysis. It was recently reported, though, that DEPC modifications are labile for some amino acids. Here, we show that label loss is more significant and widespread than previously thought, especially for Ser, Thr, Tyr, and His residues, when relatively long protein digestion times are used. Such label loss ultimately decreases the amount of protein structural information that is obtainable with this reagent. We find, however, that the number of DEPC modified residues and, thus, protein structural information, can be significantly increased by decreasing the time between the covalent labeling reaction and the mass spectrometric analysis. This is most effectively accomplished using short (e.g., 2 h) proteolytic digestions with enzymes such as immobilized chymotrypsin or Glu-C rather than using methods (e.g., microwave or ultrasonic irradiation) that accelerate proteolysis in other ways. Using short digestion times, we show that the percentage of solvent accessible residues that can be modified by DEPC increases from 44% to 67% for cytochrome c, 35% to 81% for myoglobin, and 76% to 95% for β-2-microglobulin. In effect, these increased numbers of modified residues improve the protein structural resolution available from this covalent labeling method. Compared with typical overnight digestion conditions, the short digestion times decrease the average distance between modified residues from 11 to 7 Å for myoglobin, 13 to 10 Å for

A Comprehensive Analysis in Terms of Molecule-Intrinsic, Quasi-Atomic Orbitals. III. The Covalent Bonding Structure of Urea.

Science.gov (United States)

West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

2015-10-15

The analysis of molecular electron density matrices in terms of quasi-atomic orbitals, which was developed in previous investigations, is quantitatively exemplified by a detailed application to the urea molecule. The analysis is found to identify strong and weak covalent bonding interactions as well as intramolecular charge transfers. It yields a qualitative as well as quantitative ab initio description of the bonding structure of this molecule, which raises questions regarding some traditional rationalizations.

Electrostatic study of Alanine mutational effects on transcription: application to GATA-3:DNA interaction complex.

Science.gov (United States)

El-Assaad, Atlal; Dawy, Zaher; Nemer, Georges

2015-01-01

Protein-DNA interaction is of fundamental importance in molecular biology, playing roles in functions as diverse as DNA transcription, DNA structure formation, and DNA repair. Protein-DNA association is also important in medicine; understanding Protein-DNA binding kinetics can assist in identifying disease root causes which can contribute to drug development. In this perspective, this work focuses on the transcription process by the GATA Transcription Factor (TF). GATA TF binds to DNA promoter region represented by `G,A,T,A' nucleotides sequence, and initiates transcription of target genes. When proper regulation fails due to some mutations on the GATA TF protein sequence or on the DNA promoter sequence (weak promoter), deregulation of the target genes might lead to various disorders. In this study, we aim to understand the electrostatic mechanism behind GATA TF and DNA promoter interactions, in order to predict Protein-DNA binding in the presence of mutations, while elaborating on non-covalent binding kinetics. To generate a family of mutants for the GATA:DNA complex, we replaced every charged amino acid, one at a time, with a neutral amino acid like Alanine (Ala). We then applied Poisson-Boltzmann electrostatic calculations feeding into free energy calculations, for each mutation. These calculations delineate the contribution to binding from each Ala-replaced amino acid in the GATA:DNA interaction. After analyzing the obtained data in view of a two-step model, we are able to identify potential key amino acids in binding. Finally, we applied the model to GATA-3:DNA (crystal structure with PDB-ID: 3DFV) binding complex and validated it against experimental results from the literature.

Preparation and fluorescent recognition properties for fluoride of a nanostructured covalently bonded europium hybrid material

Institute of Scientific and Technical Information of China (English)

余旭东; 李景印; 李亚娟; 耿丽君; 甄小丽; 于涛

2015-01-01

A novel covalently bonded Eu3+-based silica hybrid material was designed and its spectrophotometric anion sensing prop-erty was studied. The fluorescent receptor (europium complex) was covalently grafted to the silica matrix via a sol-gel approach. FTIR, UV-vis spectra, scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD) and photoluminescent spectra were characterized, and the results revealed that the hybrid material with nanosphere structure displayed excellent photophysical property. In addition, the selective anion sensing property of the hybrid material was studied by UV-vis and fluorescence spectra. The results showed that the hybrid material exhibited a smart response with fluoride anions.

Encapsulation and covalent binding of molecular payload in enzymatically activated micellar nanocarriers.

Science.gov (United States)

Rosenbaum, Ido; Harnoy, Assaf J; Tirosh, Einat; Buzhor, Marina; Segal, Merav; Frid, Liat; Shaharabani, Rona; Avinery, Ram; Beck, Roy; Amir, Roey J

2015-02-18

The high selectivity and often-observed overexpression of specific disease-associated enzymes make them extremely attractive for triggering the release of hydrophobic drug or probe molecules from stimuli-responsive micellar nanocarriers. Here we utilized highly modular amphiphilic polymeric hybrids, composed of a linear hydrophilic polyethylene glycol (PEG) and an esterase-responsive hydrophobic dendron, to prepare and study two diverse strategies for loading of enzyme-responsive micelles. In the first type of micelles, hydrophobic coumarin-derived dyes were encapsulated noncovalently inside the hydrophobic core of the micelle, which was composed of lipophilic enzyme-responsive dendrons. In the second type of micellar nanocarrier the hydrophobic molecular cargo was covalently linked to the end-groups of the dendron through enzyme-cleavable bonds. These amphiphilic hybrids self-assembled into micellar nanocarriers with their cargo covalently encapsulated within the hydrophobic core. Both types of micelles were highly responsive toward the activating enzyme and released their molecular cargo upon enzymatic stimulus. Importantly, while faster release was observed with noncovalent encapsulation, higher loading capacity and slower release rate were achieved with covalent encapsulation. Our results clearly indicate the great potential of enzyme-responsive micellar delivery platforms due to the ability to tune their payload capacities and release rates by adjusting the loading strategy.

Non-unitarity, sterile neutrinos, and non-standard neutrino interactions

Energy Technology Data Exchange (ETDEWEB)

Blennow, Mattias [Department of Theoretical Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Albanova University Center, 106 91 Stockholm (Sweden); Coloma, Pilar [Theoretical Physics Department, Fermi National Accelerator Laboratory, P.O. Box 500, Batavia, IL 60510 (United States); Fernandez-Martinez, Enrique; Hernandez-Garcia, Josu [Departamento de Física Teórica, Universidad Autónoma de Madrid, Cantoblanco E-28049 Madrid (Spain); Instituto de Física Teórica UAM/CSIC, Calle Nicolás Cabrera 13-15, Cantoblanco E-28049 Madrid (Spain); Lopez-Pavon, Jacobo [INFN, Sezione di Genova, via Dodecaneso 33, 16146 Genova (Italy); CERN, Theoretical Physics Department, Geneva (Switzerland)

2017-04-27

The simplest Standard Model extension to explain neutrino masses involves the addition of right-handed neutrinos. At some level, this extension will impact neutrino oscillation searches. In this work we explore the differences and similarities between the case in which these neutrinos are kinematically accessible (sterile neutrinos) or not (mixing matrix non-unitarity). We clarify apparent inconsistencies in the present literature when using different parametrizations to describe these effects and recast both limits in the popular neutrino non-standard interaction (NSI) formalism. We find that, in the limit in which sterile oscillations are averaged out at the near detector, their effects at the far detector coincide with non-unitarity at leading order, even in presence of a matter potential. We also summarize the present bounds existing in both limits and compare them with the expected sensitivities of near-future facilities taking the DUNE proposal as a benchmark. We conclude that non-unitarity effects are too constrained to impact present or near future neutrino oscillation facilities but that sterile neutrinos can play an important role at long baseline experiments. The role of the near detector is also discussed in detail.

A FRET-based probe for epidermal growth factor receptor bound non-covalently to a pair of synthetic amphipathic helixes

International Nuclear Information System (INIS)

Itoh, Reina E.; Kurokawa, Kazuo; Fujioka, Aki; Sharma, Alok; Mayer, Bruce J.; Matsuda, Michiyuki

2005-01-01

Epidermal growth factor (EGF) receptor plays a pivotal role in a variety of cellular functions, such as proliferation, differentiation, and migration. To monitor the EGF receptor (EGFR) activity in living cells, we developed a probe for EGFR activity based on the principle of fluorescence resonance energy transfer (FRET). Previously, we developed a probe designated as Picchu (Phosphorylation indicator of the CrkII chimeric unit), which detects the tyrosine phosphorylation of the CrkII adaptor protein. We used a pair of synthetic amphipathic helixes, WinZipA2 and WinZipB1, to bind Picchu non-covalently to the carboxyl-terminus of the EGFR. Using this modified probe named Picchu-Z, the activity of EGFR was followed in EGF-stimulated Cos7 cells. We found that a high level of tyrosine phosphorylation of Picchu-Z probe remained after endocytosis until the point when the EGFR was translocated to the perinuclear region. These findings are in agreement with the previously reported 'signaling endosome' model. Furthermore, by pulse stimulation with EGF and by acute ablation of EGFR activity with AG1478, it was suggested that the phosphorylation of Picchu-Z probe, and probably the phosphorylation of EGFR also, underwent a rapid equilibrium (τ 1/2 < 2 min) between the phosphorylated and dephosphorylated states in the presence of EGF

Synthetic, XRD, non-covalent interactions and solvent dependent nonlinear optical studies of Sulfadiazine-Ortho-Vanillin Schiff base: (E)-4-((2-hydroxy-3-methoxy- benzylidene) amino)-N-(pyrimidin-2-yl)benzene-sulfonamide

Science.gov (United States)

Shahid, Muhammad; Salim, Muhammad; Khalid, Muhammad; Tahir, Muhammad Nawaz; Khan, Muhammad Usman; Braga, Ataualpa Albert Carmo

2018-06-01

In this study, Sulfadiazine-Ortho-Vanillin Schiff base namely (E)-4-((2-hydroxy-3-methoxybenzylidene)amino)sbnd N-(pyrimidin-2-yl)benzene-sulfonamide (BS) was synthesized. Chemical characterization and computational studies using different techniques like XRD, FT-IR, UV-Vis, NBO, FMO, and MEP have been employed. Density functional theory (DFT) calculations have been performed at M06-2X/6-311 + G(d,p) level of theory to obtain optimized geometry and vibrational wave numbers for (E)-4-((2-hydroxy-3-methoxybenzylidene)amino)sbnd N-(pyrimidin-2-yl)benzene-sulfonamide (BS). The DFT optimized geometry supports the experimental XRD parameters. Frontier molecular orbital (FMO) energies and molecular electrostatic potential (MEP) surfaces have been executed at M06-2X/6-311 + G(d,p) level of theory. NBO analysis has been carried out at M06-2X/6-311 + G(d,p) level which not only discovered the hyper conjugative interactions and stability in title molecule but also reconfirmed the existence of Nsbnd H⋯N hydrogen bonds between the dimer. The findings of small EHOMO-ELUMO gap shows less hardness and larger softness values which suggested the bioactiveness of the title molecule. Finally, the effect of solvent on nonlinear optical (NLO) properties has been executed using M06-2X level of theory and 6-311 + G (d,p) basis set. The solvent polarity enhanced the NLO response from 3.62 × 10-30 esu to 4.66 × 10-30 esu indicating the considerable NLO character hence in general may have potential applications in the development of non-linear optical materials.

Measure solutions for non-local interaction PDEs with two species

Energy Technology Data Exchange (ETDEWEB)

Francesco, Marco Di [Department of Mathematical and Statistical Sciences, University of Bath, Claverton Down, Bath, BA2 7AY (United Kingdom); Fagioli, Simone [DISIM—Department of Information Engineering, Computer Science and Mathematics, University of L' Aquila, Via Vetoio 1 (Coppito) 67100 L' Aquila (AQ) (Italy)

2013-10-01

This paper presents a systematic existence and uniqueness theory of weak measure solutions for systems of non-local interaction PDEs with two species, which are the PDE counterpart of systems of deterministic interacting particles with two species. The main motivations behind those models arise in cell biology, pedestrian movements, and opinion formation. In case of symmetrizable systems (i.e. with cross-interaction potentials one multiple of the other), we provide a complete existence and uniqueness theory within (a suitable generalization of) the Wasserstein gradient flow theory in Ambrosio et al (2008 Gradient Flows in Metric Spaces and in the Space of Probability Measures (Lectures in Mathematics ETH Zürich) 2nd edn (Basel: Birkhäuser)) and Carrillo et al (2011 Duke Math. J. 156 229–71), which allows the consideration of interaction potentials with a discontinuous gradient at the origin. In the general case of non-symmetrizable systems, we provide an existence result for measure solutions which uses a semi-implicit version of the Jordan–Kinderlehrer–Otto (JKO) scheme (Jordan et al 1998 SIAM J. Math. Anal. 29 1–17), which holds in a reasonable non-smooth setting for the interaction potentials. Uniqueness in the non-symmetrizable case is proven for C{sup 2} potentials using a variant of the method of characteristics. (paper)

Measure solutions for non-local interaction PDEs with two species

International Nuclear Information System (INIS)

Francesco, Marco Di; Fagioli, Simone

2013-01-01

This paper presents a systematic existence and uniqueness theory of weak measure solutions for systems of non-local interaction PDEs with two species, which are the PDE counterpart of systems of deterministic interacting particles with two species. The main motivations behind those models arise in cell biology, pedestrian movements, and opinion formation. In case of symmetrizable systems (i.e. with cross-interaction potentials one multiple of the other), we provide a complete existence and uniqueness theory within (a suitable generalization of) the Wasserstein gradient flow theory in Ambrosio et al (2008 Gradient Flows in Metric Spaces and in the Space of Probability Measures (Lectures in Mathematics ETH Zürich) 2nd edn (Basel: Birkhäuser)) and Carrillo et al (2011 Duke Math. J. 156 229–71), which allows the consideration of interaction potentials with a discontinuous gradient at the origin. In the general case of non-symmetrizable systems, we provide an existence result for measure solutions which uses a semi-implicit version of the Jordan–Kinderlehrer–Otto (JKO) scheme (Jordan et al 1998 SIAM J. Math. Anal. 29 1–17), which holds in a reasonable non-smooth setting for the interaction potentials. Uniqueness in the non-symmetrizable case is proven for C 2 potentials using a variant of the method of characteristics. (paper)

Electro-osmosis over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions

Science.gov (United States)

Ghosh, Uddipta; Chakraborty, Suman

2016-06-01

In this study, we attempt to bring out a generalized formulation for electro-osmotic flows over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions. To this end, we start with modified electro-chemical potential of the individual species and subsequently use it to derive modified Nernst-Planck equation accounting for the ionic fluxes generated because of the presence of non-electrostatic potential. We establish what we refer to as the Poisson-Helmholtz-Nernst-Planck equations, coupled with the Navier-Stokes equations, to describe the complete transport process. Our analysis shows that the presence of non-electrostatic interactions between the ions results in an excess body force on the fluid, and modifies the osmotic pressure as well, which has hitherto remained unexplored. We further apply our analysis to a simple geometry, in an effort to work out the Smoluchowski slip velocity for thin electrical double layer limits. To this end, we employ singular perturbation and develop a general framework for the asymptotic analysis. Our calculations reveal that the final expression for slip velocity remains the same as that without accounting for non-electrostatic interactions. However, the presence of non-electrostatic interactions along with ion specificity can significantly change the quantitative behavior of Smoluchowski slip velocity. We subsequently demonstrate that the presence of non-electrostatic interactions may significantly alter the effective interfacial potential, also termed as the "Zeta potential." Our analysis can potentially act as a guide towards the prediction and possibly quantitative determination of the implications associated with the existence of non-electrostatic potential, in an electrokinetic transport process.

Covalent Crosslinking of Porous Poly(Ionic Liquid) Membrane via a Triazine Network

OpenAIRE

Täuber, Karoline; Dani, Alessandro; Yuan, Jiayin

2017-01-01

Porous poly(ionic liquid) membranes that were prepared via electrostatic cross-linking were subsequently covalently cross-linked via formation of a 1,3,5-triazine network. The additional covalent cross-links do not affect the pore size and pore size distribution of the membranes and stabilize them towards salt solutions of high ionic strength, enabling the membranes to work in a broader environmental window.

NPR Lenses : Interactive Tools for Non-photorealistic Line Drawings

NARCIS (Netherlands)

Neumann, Petra; Isenberg, Tobias; Carpendale, Sheelagh

2007-01-01

NPR Lenses is an interactive technique for producing expressive non-photorealistic renderings. It provides an intuitive visual interaction tool for illustrators, allowing them to seamlessly apply a large variety of emphasis techniques. Advantages of 3D scene manipulation are combined with the

Construction of covalently coupled, concatameric dimers of 7TM receptors

DEFF Research Database (Denmark)

Terpager, Marie; Scholl, D Jason; Kubale, Valentina

2009-01-01

-Ala repeats flanked by flexible spacers and positively charged residues to ensure correct inside-out orientation plus an extracellular HA-tag to construct covalently coupled dimers of 7TM receptors. Such 15 TM concatameric homo- and heterodimers of the beta(2)-adrenergic and the NK(1) receptors, which...... for either of the protomers, which was not observed upon simple coexpression of the two receptors. It is concluded that covalently joined 7TM receptor dimers with surprisingly normal receptor properties can be constructed with use of an artificial transmembrane connector, which perhaps can be used to fuse...

Unanticipated C=C bonds in covalent monolayers on silicon revealed by NEXAFS.

Science.gov (United States)

Lee, Michael V; Lee, Jonathan R I; Brehmer, Daniel E; Linford, Matthew R; Willey, Trevor M

2010-02-02

Interfaces are crucial to material properties. In the case of covalent organic monolayers on silicon, molecular structure at the interface controls the self-assembly of the monolayers, which in turn influences the optical properties and electrical transport. These properties intrinsically affect their application in biology, tribology, optics, and electronics. We use near-edge X-ray absorption fine structure spectroscopy to show that the most basic covalent monolayers formed from 1-alkenes on silicon retain a double bond in one-fifth to two-fifths of the resultant molecules. Unsaturation in the predominantly saturated monolayers will perturb the regular order and affect the dependent properties. The presence of unsaturation in monolayers produced by two different methods also prompts the re-evaluation of other radical-based mechanisms for forming covalent monolayers on silicon.

Non-Newtonian fluid structure interaction in flexible biomimetic microchannels

Science.gov (United States)

Kiran, M.; Dasgupta, Sunando; Chakraborty, Suman

2017-11-01

To investigate the complex fluid structure interactions in a physiologically relevant microchannel with deformable wall and non-Newtonian fluid that flows within it, we fabricated cylindrical microchannels of various softness out of PDMS. Experiments to measure the transient pressure drop across the channel were carried out with high sampling frequencies to capture the intricate flow physics. In particular, we showed that the waveforms varies greatly for each of the non-Newtonian and Newtonian cases for both non-deformable and deformable microchannels in terms of the peak amplitude, r.m.s amplitude and the crest factor. In addition, we carried out frequency sweep experiments to evaluate the frequency response of the system. We believe that these results will aid in the design of polymer based microfluidic phantoms for arterial FSI studies, and in particular for studying blood analog fluids in cylindrical microchannels as well as developing frequency specific Lab-on-chip systems for medical diagnostics.

Electron Beam Modification and Functionalization of MWNT for Covalent Dispersion into Polymeric Systems

International Nuclear Information System (INIS)

Palmese, G. R.

2006-01-01

The discovery of multiwalled carbon nanotubes (MWNT) and singlewalled nanotubes (SWNT) has allowed for the development of structural and conductive reinforcement fillers for polymers and electronic systems. Due to their small diameter, high aspect ratio, strength, and conductive and semi-conductive properties, nanotubes are excellent reinforcing fillers for systems requiring enhanced electrical or material properties and may disperse into such systems at low percolation concentrations. However, despite their potential for enhanced composites properties, van der Waals interactions between nanotubes as well as their highly stable graphitic structure render them insoluble in water, organic solvents and most monomers. As a result, nanotubes separate from solution, and their excellent material properties are not realized on a macroscopic scale. Furthermore, in order for nanotube-reinforced systems to be structurally enhanced (allowing for load transfer from the bulk material to the nanotube filler), covalent interactions between nanotubes and the polymer chains are preferred. Therefore, the development of nanotube-based polymer composites with improved mechanical properties and electrical conductivity requires the covalent dispersion of carbon nanotubes. In this work, we have developed a novel method of nanotube surface modification in which dry MWNT are irradiated with a high-energy electron-beam (EB) in ambient air environment. Raman spectroscopy was performed to characterize the influence of EB irradiation on nanotubes, namely, variance of the disorder, or D band (∼1360 cm - 1) with respect to the graphitic, or G, peak (∼1580 cm - 1). Spectra show increased deformation to the graphitic structure, as well as increased strain on the carbon-carbon bonds, weakening the nanotube. Transmission Electron Microscopy (TEM) confirms that nanotubes remain intact despite high EB dose. In addition, minimal surface deformation and length reduction occurred on irradiated MWNT

Dibenzothiophene adsorption at boron doped carbon nanoribbons studied within density functional theory

Energy Technology Data Exchange (ETDEWEB)

López-Albarrán, P. [Facultad de Ingeniería en Tecnología de la Madera, Universidad Michoacana de San Nicolás de Hidalgo, Santiago Tapia 403, CP 58000, Morelia, Michoacán (Mexico); Navarro-Santos, P., E-mail: pnavarrosa@conacyt.mx [Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Santiago Tapia 403, CP 58000, Morelia, Michoacán (Mexico); Garcia-Ramirez, M. A. [Research Centre for Innovation in Aeronautical Engineering, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de los Garza, CP 66451 Nuevo León (Mexico); Ricardo-Chávez, J. L. [Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, Lomas 4" asección, CP 78216, San Luis Potosí, S. L. P. (Mexico)

2015-06-21

The adsorption of dibenzothiophene (DBT) on bare and boron-doped armchair carbon nanoribbons (ACNRs) is being investigated in the framework of the density functional theory by implementing periodic boundary conditions that include corrections from dispersion interactions. The reactivity of the ACNRs is characterized by using the Fukui functions as well as the electrostatic potential as local descriptors. Non-covalent adsorption mechanism is found when using the local Perdew-Becke-Ernzerhof functional, regardless of the DBT orientation and adsorption location. The dispersion interactions addition is a milestone to describe the adsorption process. The charge defects introduced in small number (i.e., by doping with B atoms), within the ACNRs increases the selectivity towards sulfur mainly due to the charge depletion at B sites. The DBT magnitude in the adsorption energy shows non-covalent interactions. As a consequence, the configurations where the DBT is adsorbed on a BC{sub 3} island increase the adsorption energy compared to random B arrangements. The stability of these configurations can be explained satisfactorily in terms of dipole interactions. Nevertheless, from the charge-density difference analysis and the weak Bader charge-distribution interactions cannot be ruled out completely. This is why the electronic properties of the ribbons are analyzed in order to elucidate the key role played by the B and DBT states in the adsorbed configurations.

Efficient protein immobilization on polyethersolfone electrospun nanofibrous membrane via covalent binding for biosensing applications

Energy Technology Data Exchange (ETDEWEB)

Mahmoudifard, Matin [Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran (Iran, Islamic Republic of); Soudi, Sara [Stem Cell Biology Department, Stem Cell Technology Research Center, Tehran (Iran, Islamic Republic of); Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Soleimani, Masoud [Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Hosseinzadeh, Simzar [Nanotechnology and Tissue Engineering Department, Stem Cell Technology Research Center, Tehran (Iran, Islamic Republic of); School of Advanced Medical Technologies, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Esmaeili, Elaheh [Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran (Iran, Islamic Republic of); Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Vossoughi, Manouchehr, E-mail: vosoughi@sharif.edu [Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran (Iran, Islamic Republic of); Chemical and Petroleum Engineering Department, Sharif University of Technology, Tehran (Iran, Islamic Republic of)

2016-01-01

In this paper we introduce novel strategy for antibody immobilization using high surface area electrospun nanofibrous membrane based on ethyl-3-(3-dimethylaminopropyl)-carbodiimide/N-hydroxysuccinimide (EDC/NHS) coupling chemistry. To present the high performance of proposed biosensors, anti-staphylococcus enterotoxin B (anti-SEB) was used as a model to demonstrate the utility of our proposed system. Polymer solution of polyethersolfone was used to fabricate fine nanofibrous membrane. Moreover, industrial polyvinylidene fluoride membrane and conventional microtiter plate were also used to compare the efficiency of antibody immobilization. Scanning electron microscopy images were taken to study the morphology of the membranes. The surface activation of nanofibrous membrane was done with the help of O{sub 2} plasma. PES nanofibrous membrane with carboxyl functional groups for covalent attachment of antibodies were treated by EDC/NHS coupling agent. The quantity of antibody immobilization was measured by enzyme-linked immuno sorbent assay (ELISA) method. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) spectroscopy was performed to confirm the covalent immobilization of antibody on membrane. Atomic force microscopy, scanning electron microscopy and invert fluorescence microscopy were used to analyze the antibody distribution pattern on solid surfaces. Results show that oxygen plasma treatment effectively increased the amount of antibody immobilization through EDC/NHS coupling chemistry. It was found that the use of nanofibrous membrane causes the improved detection signal of ELISA based biosensors in comparison to the standard assay carried out in the 96-well microtiter plate. This method has the potential to improve the ELISA-based biosensor and we believe that this technique can be used in various biosensing methods. - Highlights: • Introduction of novel strategy for antibody immobilization using high surface area electrospun

Functionalization of multiwalled carbon nanotubes by microwave irradiation for lysozyme attachment: comparison of covalent and adsorption methods by kinetics of thermal inactivation

Science.gov (United States)

Puentes-Camacho, Daniel; Velázquez, Enrique F.; Rodríguez-Félix, Dora E.; Castillo-Ortega, Mónica; Sotelo-Mundo, Rogerio R.; del Castillo-Castro, Teresa

2017-12-01

Proteins suffer changes in their tertiary structure when they are immobilized, and enzymatic activity is affected due to the low biocompatibility of some supporting materials. In this work immobilization of lysozyme on carbon nanotubes previously functionalized by microwave irradiation was studied. The effectiveness of the microwave-assisted acid treatment of carbon nanotubes was evaluated by XPS, TEM, Raman and FTIR spectroscopy. The carboxylic modification of nanotube surfaces by this fast, simple and feasible method allowed the physical adsorption and covalent linking of active lysozyme onto the carbonaceous material. Thermal inactivation kinetics, thermodynamic parameters and storage stability were studied for adsorbed and covalent enzyme complexes. A major stability was found for lysozyme immobilized by the covalent method, the activation energy for inactivation of the enzyme was higher for the covalent method and it was stable after 50 d of storage at 4 °C. The current study highlights the effect of protein immobilization method on the biotechnological potential of nanostructured biocatalysts.

Non-equilibrium magnetic interactions in strongly correlated systems

Energy Technology Data Exchange (ETDEWEB)

Secchi, A., E-mail: a.secchi@science.ru.nl [Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen (Netherlands); Brener, S.; Lichtenstein, A.I. [Institut für Theoretische Physik, Universitat Hamburg, Jungiusstraße 9, D-20355 Hamburg (Germany); Katsnelson, M.I. [Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen (Netherlands)

2013-06-15

We formulate a low-energy theory for the magnetic interactions between electrons in the multi-band Hubbard model under non-equilibrium conditions determined by an external time-dependent electric field which simulates laser-induced spin dynamics. We derive expressions for dynamical exchange parameters in terms of non-equilibrium electronic Green functions and self-energies, which can be computed, e.g., with the methods of time-dependent dynamical mean-field theory. Moreover, we find that a correct description of the system requires, in addition to exchange, a new kind of magnetic interaction, that we name twist exchange, which formally resembles Dzyaloshinskii–Moriya coupling, but is not due to spin–orbit, and is actually due to an effective three-spin interaction. Our theory allows the evaluation of the related time-dependent parameters as well. -- Highlights: •We develop a theory for magnetism of strongly correlated systems out of equilibrium. •Our theory is suitable for laser-induced ultrafast magnetization dynamics. •We write time-dependent exchange parameters in terms of electronic Green functions. •We find a new magnetic interaction, a “twist exchange”. •We give general expressions for magnetic noise in itinerant-electron systems.

Disorder phenomena in covalent semiconductors

International Nuclear Information System (INIS)

Popescu, M.A.

1975-01-01

The structure of the amorphous semiconductors has been investigated by means of X-ray diffraction and by computer simulation of random network models. Amorphous germanium contains mainly five and six-membered rings of atoms. In glassy state, the ternary compounds A 2 B 4 C 2 5 , such as CdGeAs 2 contain only even rings of atoms (six-membered and eight-membered rings). In the memory glasses of the type A 2 B 4 C 2 5 , such as GeAs 2 Te 7 , the valency state of every element is that from the crystal and important van der Waals forces are effective in the network. No Ge-Ge, Ge-As and As-As bonds are formed. The high pressure forms of the germanium have been simulated by computer. The force constants of the covalent bonds in Ge III and Ge IV differ from those in Ge I. The bond bending force constant decreases rapidly when the density of the crystal increases, a fact which has been imparted to a reduction of the sp 3 hybridization. The compressibility curve of the Ge I has been explained. The effect of the radial and uniaxial deformation on the non-crystalline networks has been studied. The compressibility of the amorphous germanium is by 1.5 per cent greater than that of crystalline germanium. The Poisson coefficient for a-Ge network is 0.233. The structure of the As 2 S 3 glass doped with different amounts of germanium (up to 40 at. per cent) and silver (up to 12 at. per cent) has been investigated. The As 2 S 3 Gesub(x) compositions are constituted from a disordered packing of structural units whose chemical composition and relative proportion in the glass essentially depends on the germanium content. (author)

Search for primarily non-interacting decay modes of the upsilon

International Nuclear Information System (INIS)

Leffler, J.S.

1986-03-01

The hadronic transition UPSILON(2S) → π 0 π 0 UPSILON(1S) is utilized to search for the reactions: UPSILON(1S) → non-interacting particles and UPSILON(1S) → γ + non-interacting particles. 44 pb -1 of UPSILON(2S) data were taken by the Crystal Ball detector at the DORIS II storage ring in order to perform this study. An upper limit of BR(UPSILON → Unseen) -1 of UPSILON(2S) data was available for this study. An upper limit on the branching ratio BR(UPSILON → γ + Unseen) is measured for photon energies in the range 500 MeV -3 (90% C.L.), is obtained. The compact size of the Crystal Ball detector enhances the observable branching ratio for noninteracting particles with short lifetimes such as massive axions. The identification of the recent Darmstadt events with a 1.6 MeV axion is excluded by the present result assuming the minimal Peccei-Quinn model. Limits on the spontaneous supersymmetry breaking mass scale are also derived as a function of gravitino mass

Non-linear electromagnetic interactions in thermal QED

International Nuclear Information System (INIS)

Brandt, F.T.; Frenkel, J.

1994-08-01

The behavior of the non-linear interactions between electromagnetic fields at high temperature is examined. It is shown that, in general, the log(T) dependence on the temperature of the Green functions is simply related to their UV behavior at zero-temperature. It is argued that the effective action describing the nonlinear thermal electromagnetic interactions has a finite limit as T -> ∞. This thermal action approaches, in the long wavelength limit, the negative of the corresponding zero-temperature action. (author). 12 refs, 1 fig

Covalent microcontact printing of proteins fro cell patterning

NARCIS (Netherlands)

Rozkiewicz, D.I.; Kraan, Yvonne M.; Werten, Marc W.T.; de Wolf, Frits A.; Subramaniam, Vinod; Ravoo, B.J.; Reinhoudt, David

2006-01-01

We describe a straightforward approach to the covalent immobilization of cytophilic proteins by microcontact printing, which can be used to pattern cells on substrates. Cytophilic proteins are printed in micropatterns on reactive self-assembled monolayers by using imine chemistry. An

The role of double covalent flavin binding in chito-oligosaccharide oxidase from Fusarium graminearum

NARCIS (Netherlands)

Heuts, Dominic P. H. M.; Winter, Remko T.; Damsma, Gerke E.; Janssen, Dick B.; Fraaije, Marco W.

2008-01-01

ChitO (chito-oligosaccharide oxidase) from Fusarium graminearum catalyses the regioselective oxidation of N-acetylated oligosaccharides. The enzyme harbours an FAD cofactor that is covalently attached to His(94) and Cys(154). The functional role of this unusual bi-covalent flavin-protein linkage was

Conglutinin binds the HIV-1 envelope glycoprotein gp 160 and inhibits its interaction with cell membrane CD4

DEFF Research Database (Denmark)

Andersen, Ove; Sørensen, A M; Svehag, S E

1991-01-01

The highly glycosylated envelope glycoprotein (gp 160) of human immunodeficiency virus (HIV) interacts with the CD4 molecule present on the membrane of CD4+ cells and is involved in the pathobiology of HIV infection. Lectins bind glycoproteins through non-covalent interactions with specific hexose...... residues. The mammalian C-type lectin bovine conglutinin was examined for its ability to interact with recombinant gp160 (rgp160) produced in vaccinia virus-infected BHK21 cells. Specific binding of conglutinin to rgp160 was demonstrated by ELISA. The interaction of bovine conglutinin with rgp160...... of the binding of rgp160 to the CD4 receptor on CEM 13 cells, as demonstrated by FACS analyses. These results indicate that conglutinin may inhibit the infection with HIV-1 through its interaction with the viral envelope glycoprotein....

Inhibition of interaction between epigallocatechin-3-gallate and myofibrillar protein by cyclodextrin derivatives improves gel quality under oxidative stress.

Science.gov (United States)

Zhang, Yumeng; Chen, Lin; Lv, Yuanqi; Wang, Shuangxi; Suo, Zhiyao; Cheng, Xingguang; Xu, Xinglian; Zhou, Guanghong; Li, Zhixi; Feng, Xianchao

2018-06-01

High levels of polyphenols can interact with myofibrillar proteins (MPs), causing damage to a MP emulsion gel. In this study, β-cyclodextrins were used to reduce covalent and non-covalent interaction between epigallocatechin-3-gallate (EGCG) and MPs under oxidative stress. The loss of both thiol and free amine groups and the unfolding of MPs caused by EGCG (80 μM/g protein) were significantly prevented by β-cyclodextrins, and the structural stability and solubility were improved. MP emulsion gel treated with EGCG (80 μM/g protein) had the highest cooking loss (68.64%) and gel strength (0.51 N). Addition of β-cyclodextrins significantly reduced cooking loss (26.24-58.20%) and improved gel strength (0.31-0.41 N) of MP emulsion gel jeopardized by EGCG under oxidative stress. Damage to the emulsifying properties of MPs caused by EGCG was significantly prevented by addition of β-cyclodextrins. β-cyclodextrins reduced interaction between EGCG and MPs in the order Methyl-β-cyclodextrin > (2-Hydroxypropyl)-β-cyclodextrin > β-cyclodextrin. In absence of EGCG, addition of β-cyclodextrins partly protected MPs from oxidative attack and improved its solubility. It is concluded that β-cyclodextrins does not markedly reduce the antioxidant ability of EGCG according to carbonyl analysis, and can effectively increase EGCG loading to potentially provide more durable antioxidant effect for meat products during processing, transportation and storage. Copyright © 2018 Elsevier Ltd. All rights reserved.

NON-LINEAR MODELING OF THE RHIC INTERACTION REGIONS

International Nuclear Information System (INIS)

TOMAS, R.; FISCHER, W.; JAIN, A.; LUO, Y.; PILAT, F.

2004-01-01

For RHIC's collision lattices the dominant sources of transverse non-linearities are located in the interaction regions. The field quality is available for most of the magnets in the interaction regions from the magnetic measurements, or from extrapolations of these measurements. We discuss the implementation of these measurements in the MADX models of the Blue and the Yellow rings and their impact on beam stability

The study on the non-linear soil structure interaction for nuclear power plants

International Nuclear Information System (INIS)

Tetsuya Hagiwara; Yoshio Kitada

2005-01-01

1. Introduction: JNES is planning a new project to study non-linear soil-structure interaction (SSI) effect under large earthquake ground motions equivalent to and/or over a design earthquake ground motion of S2(The extreme design earthquake). Concerning the SSI test, it is pointed out that handling of the scale effect of the specimen together with the surrounding soil on the earthquake response evaluation of the actual structure is essential issue for the scaled model test. Thus, for the test, the largest specimen possible and the biggest input motion possible are necessary. Taking into account the above issues, new test methodology, which utilizes artificial earthquake ground motion, is considered desirable if it can be performed at a realistic cost. Under this motivation, we have studied the test methodology which applying blasting power as for a big earthquake ground motion. The information from a coal mine company in the U.S.A. indicates that the works performed in the surface coal mine to blast a rock covering a coal layer generates a big artificial ground motion, which is similar to earthquake ground motion. Application of this artificial earthquake ground motion for the SSI test is considered very promising because the blasting work is carried out periodically for mining coal so that we can apply artificial motions generated by the work if we construct a building model at a closed point to the blasting work area. The major purposes of the test will be to understand (a) basic earthquake response characteristics of a Nuclear Power Plant (NPP) reactor building when a large earthquake strikes the NPP site and (b) nonlinear characteristics of SSI phenomenon during a big earthquake. In the paper, we introduce the test method and basic characteristics of measured artificial ground motions generated by the blasting works on an actual site. 2. Conclusion: It was confirmed that the artificial ground motions generated by blasting works have enough acceleration level

Synthesis, characterization, DNA/protein interaction and cytotoxicity studies of Cu(II) and Co(II) complexes derived from dipyridyl triazole ligands

Science.gov (United States)

Zhang, Wei; Yao, Di; Wei, Yi; Tang, Jie; Bian, He-Dong; Huang, Fu-Ping; Liang, Hong

2016-06-01

Four different transition metal complexes containing dipyridyl triazole ligands, namely [Cu(abpt)2Cl2]·2H2O (1), [Cu(abpt)2(ClO4)2] (2), [Co2(abpt)2(H2O)2Cl2]·Cl2·4H2O (3) and [Co2(Hbpt)2(CH3OH)2(NO3)2] (4) have been designed, synthesized and further structurally characterized by X-ray crystallography, ESI-MS, elemental analysis, IR and Raman spectroscopy. In these complexes, the both ligands act as bidentate ligands with N, N donors. DNA binding interactions with calf thymus DNA (ct-DNA) of the ligand and its complexes 1 ~ 4 were investigated via electronic absorption, fluorescence quenching, circular dichroism and viscosity measurements as well as confocal Laser Raman spectroscopy. The results show these complexes are able to bind to DNA via the non-covalent mode i.e. intercalation and groove binding or electrostatic interactions. The interactions with bovine serum albumin (BSA) were also studied using UV-Vis and fluorescence spectroscopic methods which indicated that fluorescence quenching of BSA by these compounds was the presence of both static and dynamic quenching. Moreover, the in vitro cytotoxic effects of the complexes against four cell lines SK-OV-3, HL-7702, BEL7404 and NCI-H460 showed the necessity of the coordination action on the biological properties on the respective complex and that all four complexes exhibited substantial cytotoxic activity.

Differentiated Staffing and Non-Teamed Organizational Structures as They Affect Elementary School Teacher-Pupil Interaction.

Science.gov (United States)

Petrie, Thomas A.; And Others

A study was conducted of the differences in the frequency of selected student-teacher interaction in differentiated staffs and in non-teamed schools. The interaction processes studied were synthesized from Erikson's four stages of childhood: student behaviors--information processing, choice-making, reflection, problem solving, and procedures or…

In-situ determination of amine/epoxy and carboxylic/epoxy exothermic heat of reaction on surface of modified carbon nanotubes and structural verification of covalent bond formation

Science.gov (United States)

Neves, Juliana C.; de Castro, Vinícius G.; Assis, Ana L. S.; Veiga, Amanda G.; Rocco, Maria Luiza M.; Silva, Glaura G.

2018-04-01

An effective nanofiller-matrix interaction is considered crucial to produce enhanced nanocomposites. Nevertheless, there is lack of experiments focused in the direct measurement of possible filler-matrix covalent linkage, which was the main goal of this work for a carbon nanotube (CNT)/epoxy system. CNT were functionalized with oxygenated (ox) functions and further with triethylenetetramine (TETA). An in-situ determination methodology of epoxy-CNTs heat of reaction was developed by Differential Scanning Calorimetry (DSC). Values of -(8.7 ± 0.4) and -(6.0 ± 0.6) J/g were observed for epoxy with CNT-ox and CNT-TETA, respectively. These results confirm the occurrence of covalent bonds for both functionalized CNTs, a very important information due to the literature generally disregard this possibility for oxygenated functions. The higher value obtained for CNT-ox can be attributed to a not complete amidation and to steric impediments in the CNT-TETA structure. The modified CNTs produced by DSC experiments were then characterized by X-Ray Photoelectron Spectroscopy, Transmission Electron Microscopy and Thermogravimetry, which confirmed the covalent linkage. This characterization methodology can be used to verify the occurrence of covalent bonds in various nanocomposites with a quantitative evaluation, providing data for better understanding of the role of CNT functional groups and for tailoring its interface with polymers.

Effects of multiple enzyme–substrate interactions in basic units of cellular signal processing

International Nuclear Information System (INIS)

Seaton, D D; Krishnan, J

2012-01-01

Covalent modification cycles are a ubiquitous feature of cellular signalling networks. In these systems, the interaction of an active enzyme with the unmodified form of its substrate is essential for signalling to occur. However, this interaction is not necessarily the only enzyme–substrate interaction possible. In this paper, we analyse the behaviour of a basic model of signalling in which additional, non-essential enzyme–substrate interactions are possible. These interactions include those between the inactive form of an enzyme and its substrate, and between the active form of an enzyme and its product. We find that these additional interactions can result in increased sensitivity and biphasic responses, respectively. The dynamics of the responses are also significantly altered by the presence of additional interactions. Finally, we evaluate the consequences of these interactions in two variations of our basic model, involving double modification of substrate and scaffold-mediated signalling, respectively. We conclude that the molecular details of protein–protein interactions are important in determining the signalling properties of enzymatic signalling pathways. (paper)

A binderless, covalently bulk modified electrochemical sensor: Application to simultaneous determination of lead and cadmium at trace level

Energy Technology Data Exchange (ETDEWEB)

Gunigollahalli Kempegowda, Raghu [Department of Studies in Chemistry, Bangalore University, Central College Campus, Bangalore 560001 (India); Malingappa, Pandurangappa, E-mail: mprangachem@gmail.com [Department of Studies in Chemistry, Bangalore University, Central College Campus, Bangalore 560001 (India)

2012-05-30

Highlights: Black-Right-Pointing-Pointer Proposed sensor is a new type of binderless covalent bulk modified electrode. Black-Right-Pointing-Pointer Surface can be easily renewed by simple mechanical polishing using emery sheets. Black-Right-Pointing-Pointer Free from modifier leaching during electrochemical measurements. Black-Right-Pointing-Pointer Provides long term storage stability with good reproducibility. Black-Right-Pointing-Pointer Nanomolar level detection limit achieved with selectivity. - Abstract: A new type of covalent binderless bulk modified electrode has been fabricated and used in the simultaneous determination of lead and cadmium ions at nanomolar level. The modification of graphitic carbon with 4-amino salicylic acid was carried out under microwave irradiation through the amide bond formation. The electrochemical behavior of the fabricated electrode has been carried out to decipher the interacting ability of the functional moieties present on the modifier molecules toward the simultaneous determination of Pb{sup 2+} and Cd{sup 2+} ions using cyclic and differential pulse anodic stripping voltammetry. The possible mode of interaction of functional groups with metal ions is proposed based on the pKa values of the modifier functionalities present on the surface of graphitic carbon particles. The analytical utility of the proposed sensor has been validated by measuring the lead and cadmium content from pretreated waste water samples of lead acid batteries.

Organic/inorganic electrochromic nanocomposites with various interfacial interactions: A review

Energy Technology Data Exchange (ETDEWEB)

Xiong, Shanxin, E-mail: xiongsx@xust.edu.cn; Yin, Siyuan; Wang, Yuyun; Kong, Zhenzhen; Lan, Jinpeng; Zhang, Runlan; Gong, Ming; Wu, Bohua; Chu, Jia; Wang, Xiaoqin

2017-07-15

Highlights: • We review the effects of interfacial interactions in electrochromic nanocomposites. • Interfacial interactions are useful for film fabrication and property-enhancement. • The strong interaction can enhance the electron conduction and structural strength. • The weak interactions exist widely between organic and inorganic phases. • Multiple weak interactions can provide various performance-adjusting approaches. - Abstract: Electrochromic properties of organic or inorganic materials can be improved through preparing organic/inorganic electrochromic nanocomposites. In electrochromic nanocomposites, the interfacial interactions between the organic and inorganic phases play three important roles in preparation and application of the nanocomposites. Firstly, the interfacial interactions result in stable molecular structures. Secondly, they also improve the electron conduction and ion transport process in the nanocomposites. Thirdly, they enhance the electrochemical and electrochromic properties of the nanocomposites. In this paper, we review the common interfacial interactions including covalent bond, coordination bond, electrostatic interaction, hydrogen bond and π-π stacking interaction between the organic and inorganic phases in the electrochromic nanocomposites. The preparation method, the relationship between the structure and properties, and the mechanism of modulation of electrochromic effect in the nanocomposites with various interfacial interactions are surveyed. The strong interfacial interaction, e.g., covalent bond, is helpful for obtaining electrochromic nanocomposites with high electron conduction and high structural strength. However it is very complicated to construct covalent bond between the organic and inorganic phases. Another strong interfacial interaction, the coordination bond is mainly confined to preparation of electrochromic complex of metal ion and pyridine derivative. While, the weak interfacial interactions, e

Organic/inorganic electrochromic nanocomposites with various interfacial interactions: A review

International Nuclear Information System (INIS)

Xiong, Shanxin; Yin, Siyuan; Wang, Yuyun; Kong, Zhenzhen; Lan, Jinpeng; Zhang, Runlan; Gong, Ming; Wu, Bohua; Chu, Jia; Wang, Xiaoqin

2017-01-01

Highlights: • We review the effects of interfacial interactions in electrochromic nanocomposites. • Interfacial interactions are useful for film fabrication and property-enhancement. • The strong interaction can enhance the electron conduction and structural strength. • The weak interactions exist widely between organic and inorganic phases. • Multiple weak interactions can provide various performance-adjusting approaches. - Abstract: Electrochromic properties of organic or inorganic materials can be improved through preparing organic/inorganic electrochromic nanocomposites. In electrochromic nanocomposites, the interfacial interactions between the organic and inorganic phases play three important roles in preparation and application of the nanocomposites. Firstly, the interfacial interactions result in stable molecular structures. Secondly, they also improve the electron conduction and ion transport process in the nanocomposites. Thirdly, they enhance the electrochemical and electrochromic properties of the nanocomposites. In this paper, we review the common interfacial interactions including covalent bond, coordination bond, electrostatic interaction, hydrogen bond and π-π stacking interaction between the organic and inorganic phases in the electrochromic nanocomposites. The preparation method, the relationship between the structure and properties, and the mechanism of modulation of electrochromic effect in the nanocomposites with various interfacial interactions are surveyed. The strong interfacial interaction, e.g., covalent bond, is helpful for obtaining electrochromic nanocomposites with high electron conduction and high structural strength. However it is very complicated to construct covalent bond between the organic and inorganic phases. Another strong interfacial interaction, the coordination bond is mainly confined to preparation of electrochromic complex of metal ion and pyridine derivative. While, the weak interfacial interactions, e

Interactive affective sharing versus non-interactive affective sharing in work groups : Comparative effects of group affect on work group performance and dynamics

NARCIS (Netherlands)

Klep, Annefloor; Wisse, Barbara; Van Der Flier, Henk

This study explores whether the dynamic path to group affect, which is characterized by interactive affective sharing processes, yields different effects on task performance and group dynamics than the static path to group affect, which arises from non-interactive affective sharing. The results of

Interactive affective sharing versus non-interactive affective sharing in work groups: Comparative effects of group affect on work group performance and dynamics

NARCIS (Netherlands)

Klep, A.H.M.; Wisse, B.M.; van der Flier, H.

2011-01-01

This study explores whether the dynamic path to group affect, which is characterized by interactive affective sharing processes, yields different effects on task performance and group dynamics than the static path to group affect, which arises from non-interactive affective sharing. The results of

Covalent modification of serum transferrin with phospholipid and incorporation into liposomal membranes

DEFF Research Database (Denmark)

Afzelius, P; Demant, E J; Hansen, Gert Helge

1989-01-01

A method is described for incorporation of water-soluble proteins into liposomal membranes using covalent protein-phospholipid conjugates in detergent solution. A disulfide derivative of phosphatidylethanolamine containing a reactive N-hydroxysuccinimide ester group is synthesized, and the deriva......A method is described for incorporation of water-soluble proteins into liposomal membranes using covalent protein-phospholipid conjugates in detergent solution. A disulfide derivative of phosphatidylethanolamine containing a reactive N-hydroxysuccinimide ester group is synthesized...

Nucleation and Growth of Covalent Organic Frameworks from Solution: The Example of COF-5

KAUST Repository

Li, Haoyuan

2017-10-24

The preparation of two-dimensional covalent organic frameworks (2D COFs) with large crystalline domains and controlled morphology is necessary for realizing the full potential of their atomically precise structures and uniform, tailorable porosity. Currently 2D COF syntheses are developed empirically, and most materials are isolated as insoluble and unprocessable powders with typical crystalline domain sizes smaller than 50 nm. Little is known about their nucleation and growth processes, which involve a combination of covalent bond formation, degenerate exchange, and non-covalent stacking processes. A deeper understanding of the chemical processes that lead to COF polymerization and crystallization is key to achieving improved materials quality and control. Here, we report a kinetic Monte Carlo (KMC) model that describes the formation of a prototypical boronate-ester linked 2D COF known as COF-5 from its 2,3,6,7,10,11-hexahydroxytriphenylene and 1,4-phenylene bis(boronic acid) monomers in solution. The key rate parameters for the KMC model were derived from experimental measurements when possible and complemented with reaction pathway analyses, molecular dynamics simulations, and binding free-energy calculations. The essential features of experimentally measured COF-5 growth kinetics are reproduced well by the KMC simulations. In particular, the simulations successfully captured a nucleation process followed by a subsequent growth process. The nucleating species are found to be multi-layer structures that form through multiple pathways. During the growth of COF-5, extensions in the lateral (in-plane) and vertical (stacking) directions are both seen to be linear with respect to time and are dominated by monomer addition and oligomer association, respectively. Finally, we show that the experimental observations of increased average crystallite size with the addition of water are modeled accurately by the simulations. These results will inform the rational development

A carrier for non-covalent delivery of functional beta-galactosidase and antibodies against amyloid plaques and IgM to the brain.

Directory of Open Access Journals (Sweden)

Gobinda Sarkar

Full Text Available BACKGROUND: Therapeutic intervention of numerous brain-associated disorders currently remains unrealized due to serious limitations imposed by the blood-brain-barrier (BBB. The BBB generally allows transport of small molecules, typically <600 daltons with high octanol/water partition coefficients, but denies passage to most larger molecules. However, some receptors present on the BBB allow passage of cognate proteins to the brain. Utilizing such receptor-ligand systems, several investigators have developed methods for delivering proteins to the brain, a critical requirement of which involves covalent linking of the target protein to a carrier entity. Such covalent modifications involve extensive preparative and post-preparative chemistry that poses daunting limitations in the context of delivery to any organ. Here, we report creation of a 36-amino acid peptide transporter, which can transport a protein to the brain after routine intravenous injection of the transporter-protein mixture. No covalent linkage of the protein with the transporter is necessary. APPROACH: A peptide transporter comprising sixteen lysine residues and 20 amino acids corresponding to the LDLR-binding domain of apolipoprotein E (ApoE was synthesized. Transport of beta-galactosidase, IgG, IgM, and antibodies against amyloid plques to the brain upon iv injection of the protein-transporter mixture was evaluated through staining for enzyme activity or micro single photon emission tomography (micro-SPECT or immunostaining. Effect of the transporter on the integrity of the BBB was also investigated. PRINCIPAL FINDINGS: The transporter enabled delivery to the mouse brain of functional beta-galactosidase, human IgG and IgM, and two antibodies that labeled brain-associated amyloid beta plaques in a mouse model of Alzheimer's disease. SIGNIFICANCE: The results suggest the transporter is able to transport most or all proteins to the brain without the need for chemically linking the

Non-Linear Interactive Stories in Computer Games

DEFF Research Database (Denmark)

Bangsø, Olav; Jensen, Ole Guttorm; Kocka, Tomas

2003-01-01

The paper introduces non-linear interactive stories (NOLIST) as a means to generate varied and interesting stories for computer games automatically. We give a compact representation of a NOLIST based on the specification of atomic stories, and show how to build an object-oriented Bayesian network...

The shape-memory effect in ionic elastomers: fixation through ionic interactions.

Science.gov (United States)

González-Jiménez, Antonio; Malmierca, Marta A; Bernal-Ortega, Pilar; Posadas, Pilar; Pérez-Aparicio, Roberto; Marcos-Fernández, Ángel; Mather, Patrick T; Valentín, Juan L

2017-04-19

Shape-memory elastomers based on a commercial rubber cross-linked by both ionic and covalent bonds have been developed. The elastomeric matrix was a carboxylated nitrile rubber (XNBR) vulcanized with magnesium oxide (MgO) providing ionic interactions that form hierarchical structures. The so-named ionic transition is used as the unique thermal transition responsible for the shape-memory effect (SME) in these elastomers. These ionic interactions fix the temporary shape due to their behavior as dynamic cross-links with temperature changes. Covalent cross-links were incorporated with the addition of different proportions of dicumyl peroxide (DCP) to the ionic elastomer to establish and recover the permanent shape. In this article, the SME was modulated by modifying the degree of covalent cross-linking, while keeping the ionic contribution constant. In addition, different programming parameters, such as deformation temperature, heating/cooling rate, loading/unloading rate and percentage of tensile strain, were evaluated for their effects on shape-memory behavior.

A comparative study of traditional lecture methods and interactive lecture methods in introductory geology courses for non-science majors at the college level

Science.gov (United States)

Hundley, Stacey A.

In recent years there has been a national call for reform in undergraduate science education. The goal of this reform movement in science education is to develop ways to improve undergraduate student learning with an emphasis on developing more effective teaching practices. Introductory science courses at the college level are generally taught using a traditional lecture format. Recent studies have shown incorporating active learning strategies within the traditional lecture classroom has positive effects on student outcomes. This study focuses on incorporating interactive teaching methods into the traditional lecture classroom to enhance student learning for non-science majors enrolled in introductory geology courses at a private university. Students' experience and instructional preferences regarding introductory geology courses were identified from survey data analysis. The information gained from responses to the questionnaire was utilized to develop an interactive lecture introductory geology course for non-science majors. Student outcomes were examined in introductory geology courses based on two teaching methods: interactive lecture and traditional lecture. There were no significant statistical differences between the groups based on the student outcomes and teaching methods. Incorporating interactive lecture methods did not statistically improve student outcomes when compared to traditional lecture teaching methods. However, the responses to the survey revealed students have a preference for introductory geology courses taught with lecture and instructor-led discussions and students prefer to work independently or in small groups. The results of this study are useful to individuals who teach introductory geology courses and individuals who teach introductory science courses for non-science majors at the college level.

Non-conventional screening of the Coulomb interaction in low-dimensional and finite-size systems

NARCIS (Netherlands)

van den Brink, J.; Sawatzky, G.A.

2000-01-01

We study the screening of the Coulomb interaction in non-polar systems by polarizable atoms. We show that in low dimensions and small finite-size systems this screening deviates strongly from that conventionally assumed. In fact in one dimension the short-range interaction is strongly screened and

Reversible covalent binding of neratinib to human serum albumin in vitro.

Science.gov (United States)

Chandrasekaran, Appavu; Shen, Li; Lockhead, Susan; Oganesian, Aram; Wang, Jianyao; Scatina, JoAnn

2010-12-01

Neratinib (HKI-272), an irreversible inhibitor of Her 2 tyrosine kinase, is currently in development as an alternative for first and second line therapy in metastatic breast cancer patients who overexpress Her 2. Following incubation of [(14)C]neratinib in control human plasma at 37°C for 6 hours, about 60% to 70% of the radioactivity was not extractable, due to covalent binding to albumin. In this study, factors that could potentially affect the covalent binding of neratinib to plasma proteins, specifically to albumin were investigated. When [(14)C]neratinib was incubated at 10 μg/mL in human serum albumin (HSA) or control human plasma, the percent binding increased with time; the highest percentages of binding (46 and 67%, respectively) were observed at 6 hours, the longest duration of incubation examined. Binding increased with increasing temperature; the highest percentages of binding to HSA or human plasma (59 and 78%) were observed at 45°C, the highest temperature tested. The binding also increased with increasing pH of incubation; the highest percentages of binding (56 and 65%) were observed at pH 8.5, the highest pH value tested. The percentages of binding were similar (53% to 57%) when a wide range of concentrations of [(14)C]neratinib (50 ng/mL to 10 μg/mL) were incubated with human plasma at 37°C for 6 hours, indicating that the binding was independent of the substrate concentration, especially in the therapeutic range (50 to 200 ng/mL). When human plasma proteins containing covalently bound [(14)C]neratinb were suspended in a 10 fold volume of phosphate buffer at pH 4.0, 6.0, 7.4, and 8.5, and further incubated at 37°C for ~ 16 hours, about 45%, 44%, 32%, and 12% of the total radioactivity, respectively, was released as unchanged [(14)C]neratinib, indicating that the binding is reversible in nature, with more released at pH 7.4 and below. In conclusion, the covalent binding of neratinib to serum albumin is pH, time and temperature dependent, but

Rotational Spectrum and Conformational Analysis of N-Methyl-2-Aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters

Directory of Open Access Journals (Sweden)

Camilla Calabrese

2018-02-01

Full Text Available We describe an experimental and quantum chemical study for the accurate determination of the conformational space of small molecular systems governed by intramolecular non-covalent interactions. The model systems investigated belong to the biological relevant aminoalcohol's family, and include 2-amino-1-phenylethanol, 2-methylamino-1-phenylethanol, noradrenaline, adrenaline 2-aminoethanol, and N-methyl-2-aminoethanol. For the latter molecule, the rotational spectrum in the 6–18 and 59.6–74.4 GHz ranges was recorded in the isolated conditions of a free jet expansion. Based on the analysis of the rotational spectra, two different conformational species and 11 isotopologues were observed and their spectroscopic constants, including 14N-nuclear hyperfine coupling constants and methyl internal rotation barriers, were determined. From the experimental data a structural determination was performed, which was also used to benchmark accurate quantum chemical calculations on the whole conformational space. Atom in molecules and non-covalent interactions theories allowed the characterization of the position of the intramolecular non-covalent interactions and the energies involved, highlighting the subtle balance responsible of the stabilization of all the molecular systems.

Double Dynamic Supramolecular Polymers of Covalent Oligo-Dynamers

NARCIS (Netherlands)

Schaeffer, Gaël; Buhler, Eric; Candau, Sauveur Jean; Lehn, Jean-Marie

2013-01-01

Double-dynamic polymers, incorporating both molecular and supramolecular dynamic features (“double dynamers”) have been generated, where these functions are present in a nonstoichiometric ratio in the main chain of the polymer. It has been achieved by (1) the formation of covalent oligo-dynamers in

Effect of photocurrent enhancement in porphyrin–graphene covalent hybrids

International Nuclear Information System (INIS)

Tang, Jianguo; Niu, Lin; Liu, Jixian; Wang, Yao; Huang, Zhen; Xie, Shiqiang; Huang, Linjun; Xu, Qingsong; Wang, Yuan; Belfiore, Laurence A.

2014-01-01

Graphene oxide (GO) sheets were covalently functionalized with 5-p-aminophenyl-10,15,20-triphenylporphyrin (NH 2 TPP) by an amidation reaction between the amino group in NH 2 TPP and carboxyl groups in GO. The Fourier transform infrared spectroscopy, nuclear magnetic resonance, scanning and transmission electron microscopies reveal that NH 2 TPP covalent bonds form on the double surface of graphene oxide sheets, generating a unique nano-framework, i.e., NH 2 TPP-graphene-NH 2 TPP. Its UV–visible spectroscopy reveals that the absorption spectrum is not a linear superposition of the spectra of NH 2 TPP and graphene oxide, because a 59 nm red shift of the strong graphene oxide absorption is observed from 238 to 297 nm, with significant spectral broadening between 300 and 700 nm. Fluorescence emission spectroscopy indicates efficient quenching of NH 2 TPP photoluminescence in this hybrid material, suggesting that photo-induced electron transfer occurs at the interface between NH 2 TPP and GO. A reversible on/off photo-current density of 47 mA/cm 2 is observed when NH 2 TPP-graphene-NH 2 TPP hybrid sandwiches are subjected to pulsed white-light illumination. Covalently-bound porphyrins decrease the optical HOMO/LUMO band gap of graphene oxide by ≈ 1 eV, according to UV–visible spectroscopy. Cyclic voltammetry predicts a small HOMO/LUMO band gap of 0.84 eV for NH 2 TPP-graphene-NH 2 TPP hybrid sandwiches, which is consistent with efficient electron transfer and fluorescence quenching. - Highlights: • Porphyrins are covalently bound to sheets of graphene oxide via an amidation reaction. • The formed hetero-junction interface decreases the optical band gap of graphene oxide. • Cyclic voltammetry predicts a graphene oxide band gap of 0.84 eV, which is easily photo-excited. • Its on/off photo-current density of 46 μA/cm 2 is 5-fold larger than that for physically stacked hybrid

Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization.

Directory of Open Access Journals (Sweden)

Tine N Vinther

Full Text Available An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic β-cell. Due to the transient nature of insulin dimer, direct investigation of this important form is inherently difficult. To address the relationship between insulin oligomerization and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization to form the structural equivalent of the classical hexamer. The covalently linked dimer neither bound to the insulin receptor, nor induced a metabolic response in vitro. However, it was extremely thermodynamically stable and did not form amyloid fibrils when subjected to mechanical stress, underlining the importance of oligomerization for insulin stability.

Integration and visualization of non-coding RNA and protein interaction networks

DEFF Research Database (Denmark)

Junge, Alexander; Refsgaard, Jan Christian; Garde, Christian

Non-coding RNAs (ncRNAs) fulfill a diverse set of biological functions relying on interactions with other molecular entities. The advent of new experimental and computational approaches makes it possible to study ncRNAs and their associations on an unprecedented scale. We present RAIN (RNA Associ......) co-occurrences found by text mining Medline abstracts. Each resource was assigned a reliability score by assessing its agreement with a gold standard set of microRNA-target interactions. RAIN is available at: http://rth.dk/resources/rain...

Interactions of acetylated histones with DNA as revealed by UV laser induced histone-DNA crosslinking

International Nuclear Information System (INIS)

Stefanovsky, V.Yu.; Dimitrov, S.I.; Angelov, D.; Pashev, I.G.

1989-01-01

The interaction of acetylated histones with DNA in chromatin has been studied by UV laser-induced crosslinking histones to DNA. After irradiation of the nuclei, the covalently linked protein-DNA complexes were isolated and the presence of histones in them demonstrated immunochemically. When chromatin from irradiated nuclei was treated with clostripain, which selectively cleaved the N-terminal tails of core histones, no one of them was found covalently linked to DNA, thus showing that crosslinking proceeded solely via the N-terminal regions. However, the crosslinking ability of the laser was preserved both upon physiological acetylation of histones, known to be restricted to the N-terminal tails, and with chemically acetylated chromatin. This finding is direct evidence that the postsynthetic histone acetylation does not release the N-terminal tails from interaction with DNA

Increase in covalent binding of 5-hydroxydiclofenac to hepatic tissues in rats co-treated with lipopolysaccharide and diclofenac: involvement in the onset of diclofenac-induced idiosyncratic hepatotoxicity.

Science.gov (United States)

Kishida, Tomoyuki; Onozato, Tomoya; Kanazawa, Toru; Tanaka, Satoru; Kuroda, Junji

2012-01-01

Diclofenac (DCF), a nonsteroidal anti-inflammatory drug, is well known to induce idiosyncratic hepatotoxicity. Although there remains much to be elucidated about its onset mechanism, it is widely accepted as a hypothesis that idiosyncratic hepatotoxicity arises from a specific immune response to a hapten formed by covalent binding of drugs or their reactive metabolites to hepatic tissues. In this study, we investigated the effects of covalent binding of DCF reactive metabolites to hepatic tissues using a rat model of liver injury induced by co-treatment with lipopolysaccharide (LPS) at a non-hepatotoxic dose. In studies done in vitro using hepatic microsomes prepared from rats treated with LPS alone, 4'- and 5-hydroxylation activities on DCF metabolism and adducts of reactive metabolites to dansyl glutathione (dGSH) were markedly decreased associated with a decrease in total P450 content. However, in studies done in vivo, the LPS/DCF co-treatment significantly increased adducts of 5-hydroxydiclofenac (5-OH-DCF) to rat hepatic tissues and delayed the elimination of 5-OH-DCF from plasma. Furthermore, we investigated the effects of co-treatment on hepatic GSH level in rats. A decrease of hepatic GSH was observed with the LPS/DCF co-treatment but not with LPS or DCF alone. The results suggest that covalent binding of reactive metabolites via 5-OH-DCF to hepatic tissues may play an important role in the onset of DCF-induced idiosyncratic hepatotoxicity, especially under decreased GSH conditions.

An explicit method in non-linear soil-structure interaction

International Nuclear Information System (INIS)

Kunar, R.R.

1981-01-01

The explicit method of analysis in the time domain is ideally suited for the solution of transient dynamic non-linear problems. Though the method is not new, its application to seismic soil-structure interaction is relatively new and deserving of public discussion. This paper describes the principles of the explicit approach in soil-structure interaction and it presents a simple algorithm that can be used in the development of explicit computer codes. The paper also discusses some of the practical considerations like non-reflecting boundaries and time steps. The practicality of the method is demonstrated using a computer code, PRESS, which is used to compare the treatment of strain-dependent properties using average strain levels over the whole time history (the equivalent linear method) and using the actual strain levels at every time step to modify the soil properties (non-linear method). (orig.)

The Interaction between Real Options and Financial Hedging: An Empirical Study of Danish Non-Financial Companies

DEFF Research Database (Denmark)

Aabo, Tom

The interaction between real options and financial hedging is analyzed empirically. A majority of Danish non-financial companies either (1) chooses at times not to hedge an exchange rate operating exposure financially due to the possibility of the company to react to changes in exchange rates...

The Chemistry and Biochemistry of Heme c: Functional Bases for Covalent Attachment

OpenAIRE

Bowman, Sarah E. J.; Bren, Kara L.

2008-01-01

A discussion of the literature concerning the synthesis, function, and activity of heme c-containing proteins is presented. Comparison of the properties of heme c, which is covalently bound to protein, is made to heme b, which is bound noncovalently. A question of interest is why nature uses biochemically expensive heme c in many proteins when its properties are expected to be similar to heme b. Considering the effects of covalent heme attachment on heme conformation and on the proximal histi...

Development of an enzyme-linked immunosorbent assay (ELISA)-like fluorescence assay to investigate the interactions of glycosaminoglycans to cells

Energy Technology Data Exchange (ETDEWEB)

Boucas, Rodrigo Ippolito [Disciplina de Biologia Molecular, Departamento de Bioquimica, Universidade Federal de Sao Paulo, SP (Brazil); Trindade, Edvaldo S. [Disciplina de Biologia Molecular, Departamento de Bioquimica, Universidade Federal de Sao Paulo, SP (Brazil); Departamento de Biologia Celular, Universidade Federal do Parana, Curitiba, Parana (Brazil); Tersariol, Ivarne L.S. [Disciplina de Biologia Molecular, Departamento de Bioquimica, Universidade Federal de Sao Paulo, SP (Brazil); Centro Interdisciplinar de Investigacao Bioquimica, Universidade de Mogi das Cruzes, Mogi das Cruzes, SP (Brazil); Dietrich, Carl P. [Disciplina de Biologia Molecular, Departamento de Bioquimica, Universidade Federal de Sao Paulo, SP (Brazil); Nader, Helena B. [Disciplina de Biologia Molecular, Departamento de Bioquimica, Universidade Federal de Sao Paulo, SP (Brazil)], E-mail: hbnader.bioq@epm.br

2008-06-23

Sulfated glycosaminoglycans were labeled with biotin to study their interaction with cells in culture. Thus, heparin, heparan sulfate, chondroitin 4-sulfate, chondroitin 6-sulfate and dermatan sulfate were labeled using biotin-hydrazide, under different conditions. The structural characteristics of the biotinylated products were determined by chemical (molar ratios of hexosamine, uronic acid, sulfate and biotin) and enzymatic methods (susceptibility to degradation by chondroitinases and heparitinases). The binding of biotinylated glycosaminoglycans was investigated both in endothelial and smooth muscle cells in culture, using a novel time resolved fluorometric method based on interaction of europium-labeled streptavidin with the biotin covalently linked to the compounds. The interactions of glycosaminoglycans were saturable and number of binding sites could be obtained for each individual compound. The apparent dissociation constant varied among the different glycosaminoglycans and between the two cell lines. The interactions of the biotinylated glycosaminoglycans with the cells were also evaluated using confocal microscopy. We propose a convenient and reliable method for the preparation of biotinylated glycosaminoglycans, as well as a sensitive non-competitive fluorescence-based assay for studies of the interactions and binding of these compounds to cells in culture.

Development of an enzyme-linked immunosorbent assay (ELISA)-like fluorescence assay to investigate the interactions of glycosaminoglycans to cells

International Nuclear Information System (INIS)

Boucas, Rodrigo Ippolito; Trindade, Edvaldo S.; Tersariol, Ivarne L.S.; Dietrich, Carl P.; Nader, Helena B.

2008-01-01

Sulfated glycosaminoglycans were labeled with biotin to study their interaction with cells in culture. Thus, heparin, heparan sulfate, chondroitin 4-sulfate, chondroitin 6-sulfate and dermatan sulfate were labeled using biotin-hydrazide, under different conditions. The structural characteristics of the biotinylated products were determined by chemical (molar ratios of hexosamine, uronic acid, sulfate and biotin) and enzymatic methods (susceptibility to degradation by chondroitinases and heparitinases). The binding of biotinylated glycosaminoglycans was investigated both in endothelial and smooth muscle cells in culture, using a novel time resolved fluorometric method based on interaction of europium-labeled streptavidin with the biotin covalently linked to the compounds. The interactions of glycosaminoglycans were saturable and number of binding sites could be obtained for each individual compound. The apparent dissociation constant varied among the different glycosaminoglycans and between the two cell lines. The interactions of the biotinylated glycosaminoglycans with the cells were also evaluated using confocal microscopy. We propose a convenient and reliable method for the preparation of biotinylated glycosaminoglycans, as well as a sensitive non-competitive fluorescence-based assay for studies of the interactions and binding of these compounds to cells in culture

Covalent cross-linking of insulin-like growth factor-1 to a specific inhibitor from human serum

International Nuclear Information System (INIS)

Ooi, G.T.; Herington, A.C.

1986-01-01

Previous studies have shown that a specific inhibitor of insulin-like growth factor (IGF) action in vitro can be isolated from normal human serum and subsequently partially purified on an IGF-affinity column. The ability of the inhibitor to bind the IGFs has now been confirmed directly using covalent cross-linking techniques. When 125 I-IGF-1 was cross-linked to inhibitor using disuccinimidyl suberate, five specifically labelled bands were seen on SDS-PAGE and autoradiography. Two bands (MW 21.5 K and 25.5 K) were intensely labelled, while the remaining three (MW 37 K, 34 K and 18 K) appeared as minor bands only. Inhibitor bioactivity, following further analysis by hydrophobic interaction chromatography or Con A-Sepharose affinity chromatography, was always associated with the presence of the 21.5 K and/or 25.5 K bands

Applications of covalent organic frameworks (COFs): From gas storage and separation to drug delivery

Institute of Scientific and Technical Information of China (English)

Ming-Xue Wu; Ying-Wei Yang

2017-01-01

Covalent organic frameworks (COFs) are an emerging class of porous covalent organic structures whose backbones were composed of light elements (B,C,N,O,Si) and linked by robust covalent bonds to endow such material with desirable properties,i.e.,inherent porosity,well-defined pore aperture,ordered channel structure,large surface area,high stability,and multi-dimension.As expected,the abovementioned properties of COFs broaden the applications of this class of materials in various fields such as gas storage and separation,catalysis,optoelectronics,sensing,small molecules adsorption,and drug delivery.In this review,we outlined the synthesis of COFs and highlighted their applications ranging from the initial gas storage and separation to drug delivery.

In Vitro Interactions between 17β-Estradiol and DNA Result in Formation of the Hormone-DNA Complexes

Directory of Open Access Journals (Sweden)

Zbynek Heger

2014-07-01

Full Text Available Beyond the role of 17β-estradiol (E2 in reproduction and during the menstrual cycle, it has been shown to modulate numerous physiological processes such as cell proliferation, apoptosis, inflammation and ion transport in many tissues. The pathways in which estrogens affect an organism have been partially described, although many questions still exist regarding estrogens’ interaction with biomacromolecules. Hence, the present study showed the interaction of four oligonucleotides (17, 20, 24 and/or 38-mer with E2. The strength of these interactions was evaluated using optical methods, showing that the interaction is influenced by three major factors, namely: oligonucleotide length, E2 concentration and interaction time. In addition, the denaturation phenomenon of DNA revealed that the binding of E2 leads to destabilization of hydrogen bonds between the nitrogenous bases of DNA strands resulting in a decrease of their melting temperatures (Tm. To obtain a more detailed insight into these interactions, MALDI-TOF mass spectrometry was employed. This study revealed that E2 with DNA forms non-covalent physical complexes, observed as the mass shifts for app. 270 Da (Mr of E2 to higher molecular masses. Taken together, our results indicate that E2 can affect biomacromolecules, as circulating oligonucleotides, which can trigger mutations, leading to various unwanted effects.

STABLE STATIONARY STATES OF NON-LOCAL INTERACTION EQUATIONS

KAUST Repository

FELLNER, KLEMENS; RAOUL, GAË L

2010-01-01

.r.t. shifts and reallocations of individual Dirac masses, and (iii) show that these linear stability conditions imply local non-linear stability. Finally, we show that for regular repulsive interaction potential Wε converging to a singular repulsive

Enhanced Biological Response of AVS-Functionalized Ti-6Al-4V Alloy through Covalent Immobilization of Collagen.

Science.gov (United States)

Rezvanian, Parsa; Daza, Rafael; López, Patricia A; Ramos, Milagros; González-Nieto, Daniel; Elices, Manuel; Guinea, Gustavo V; Pérez-Rigueiro, José

2018-02-20

This study presents the development of an efficient procedure for covalently immobilizing collagen molecules on AVS-functionalized Ti-6Al-4V samples, and the assessment of the survival and proliferation of cells cultured on these substrates. Activated Vapor Silanization (AVS) is a versatile functionalization technique that allows obtaining a high density of active amine groups on the surface. A procedure is presented to covalently bind collagen to the functional layer using EDC/NHS as cross-linker. The covalently bound collagen proteins are characterized by fluorescence microscopy and atomic force microscopy and their stability is tested. The effect of the cross-linker concentration on the process is assessed. The concentration of the cross-linker is optimized and a reliable cleaning protocol is developed for the removal of the excess of carbodiimide from the samples. The results demonstrate that the covalent immobilization of collagen type I on Ti-6Al-4V substrates, using the optimized protocol, increases the number of viable cells present on the material. Consequently, AVS in combination with the carbodiimide chemistry appears as a robust method for the immobilization of proteins and, for the first time, it is shown that it can be used to enhance the biological response to the material.

Constraints of a parity-conserving/time-reversal-non-conserving interaction

International Nuclear Information System (INIS)

Oers, Willem T.H. van

2002-01-01

Time-Reversal-Invariance non-conservation has for the first time been unequivocally demonstrated in a direct measurement at CPLEAR. One then can ask the question: What about tests of time-reversal-invariance in systems other than the kaon system? Tests of time-reversal-invariance can be distinguished as belonging to two classes: the first one deals with time-reversal-invariance-non-conserving (T-odd)/parity violating (P-odd) interactions, while the second one deals with T-odd/P-even interactions (assuming CPT conservation this implies C-conjugation non-conservation). Limits on a T-odd/P-odd interaction follow from measurements of the electric dipole moment of the neutron ( -26 e.cm [95% C.L.]). It provides a limit on a T-odd/P-odd pion-nucleon coupling constant which is less than 10 -4 times the weak interaction strength. Experimental limits on a T-odd/P-even interaction are much less stringent. Following the standard approach of describing the nucleon-nucleon interaction in terms of meson exchanges, it can be shown that only charged ρ-meson exchange and A 1 -meson exchange can lead to a T-odd/P-even interaction. The better constraints stem from measurements of the electric dipole moment of the neutron and from measurements of charge-symmetry breaking in neutron-proton elastic scattering. The latter experiments were executed at TRIUMF (497 and 347 MeV) and at IUCF (183 MeV). All other experiments, like detailed balance experiments, polarization - analyzing power difference determinations, and five-fold correlation experiments with polarized incident nucleons and aligned nuclear targets, have been shown to be at least an order to magnitude less sensitive. Is there room for further experimentation?

Principles of interactions in non-aqueous electrolyte solutions

NARCIS (Netherlands)

Lyklema, J.

2013-01-01

In this paper a review is presented on the molecular interactions in non-aqueous media of low dielectric permittivity. Qualitative and quantitative distinctions with aqueous solutions are emphasized. The reviewed themes include dispersion forces, dissociation and association equilibria,

Dynamic covalent chemistry of bisimines at the solid/liquid interface monitored by scanning tunnelling microscopy.

Science.gov (United States)

Ciesielski, Artur; El Garah, Mohamed; Haar, Sébastien; Kovaříček, Petr; Lehn, Jean-Marie; Samorì, Paolo

2014-11-01

Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.

Crystallization of copper(II) sulfate based minerals and MOF from ...

Indian Academy of Sciences (India)

Administrator

critical nucleus in terms of aggregation of tectons through non-covalent interactions provides chemical insights .... minerals and materials crystallized from the system ... occurs (refer figure 7). obtained from various crystallization studies. Use of.

Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization

DEFF Research Database (Denmark)

Vinther, Tine N.; Norrman, Mathias; Strauss, Holger M.

2012-01-01

An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers...... in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic ß-cell. Due to the transient nature of insulin dimer, direct investigation of this important form is inherently difficult. To address the relationship between insulin oligomerization...... and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization...

Spin interactions in Graphene-Single Molecule Magnets Hybrids

Science.gov (United States)

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Aña; Luis, Fernando; Rauschenbach, Stephan; Dressel, Martin; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2014-03-01

Graphene is a potential component of novel spintronics devices owing to its long spin diffusion length. Besides its use as spin-transport channel, graphene can be employed for the detection and manipulation of molecular spins. This requires an appropriate coupling between the sheets and the single molecular magnets (SMM). Here, we present a comprehensive characterization of graphene-Fe4 SMM hybrids. The Fe4 clusters are anchored non-covalently to the graphene following a diffusion-limited assembly and can reorganize into random networks when subjected to slightly elevated temperature. Molecules anchored on graphene sheets show unaltered static magnetic properties, whilst the quantum dynamics is profoundly modulated. Interaction with Dirac fermions becomes the dominant spin-relaxation channel, with observable effects produced by graphene phonons and reduced dipolar interactions. Coupling to graphene drives the spins over Villain's threshold, allowing the first observation of strongly-perturbative tunneling processes. Preliminary spin-transport experiments at low-temperature are further presented.

The circumnuclear environment of nearby non-interacting Seyfert galaxies

International Nuclear Information System (INIS)

Pogge, R.W.

1988-01-01

An investigation into the physical conditions prevailing in the regions immediately surrounding the active nuclei in 20 nearby, non-interacting Seyfert galaxies is reported. CCD interference-band images isolating the bright emission lines of Hα + [N II] λλ6548, 6583 and [O III] λ5007 have been obtained to search for spatially extended circumnuclear emission regions. Long-slit, low resolution spectrophotometry of interesting cases was used to probe the ionization state of the extended emission regions. For comparison, a CCD Hα + [N II] interference-band imaging survey of a statistically significant sample of 91 bright non-Seyfert spiral galaxies meeting the same non-interaction criteria has been carried out. Only three out of nine Seyfert 1s have spatially extended ionized gas regions compared with eight out of eleven Seyfert 2s. Enhanced circumnuclear star formation is uncommon to both Seyfert 1s and 2s. Extended emission in Seyfert 1s has essentially the same morphology in both Hα + [N II] and [O III] emission. In the Seyfert 2s, the Hα + [N II] and [O III] images show different extended emission morphologies. The [O III] emission regions appear as either one- or two-sided structures, four of which are resolved into two distinct cones of high-ionization gas emanating from the active nucleus. The morphology and ionization of these regions suggest collimation of the nuclear ionizing radiation field. The 91 non-interacting non-Seyfert spiral galaxies exhibit a rich variety of nuclear and circumnuclear emission-line structures ranging from no emission detected to bright stellar nuclei with complicated circumnuclear emission regions extending for many kiloparsecs

Non-standard interaction effects at reactor neutrino experiments

International Nuclear Information System (INIS)

Ohlsson, Tommy; Zhang, He

2009-01-01

We study non-standard interactions (NSIs) at reactor neutrino experiments, and in particular, the mimicking effects on θ 13 . We present generic formulas for oscillation probabilities including NSIs from sources and detectors. Instructive mappings between the fundamental leptonic mixing parameters and the effective leptonic mixing parameters are established. In addition, NSI corrections to the mixing angles θ 13 and θ 12 are discussed in detailed. Finally, we show that, even for a vanishing θ 13 , an oscillation phenomenon may still be observed in future short baseline reactor neutrino experiments, such as Double Chooz and Daya Bay, due to the existences of NSIs

The Janus Kinase (JAK) FERM and SH2 Domains: Bringing Specificity to JAK-Receptor Interactions.

Science.gov (United States)

Ferrao, Ryan; Lupardus, Patrick J

2017-01-01

The Janus kinases (JAKs) are non-receptor tyrosine kinases essential for signaling in response to cytokines and interferons and thereby control many essential functions in growth, development, and immune regulation. JAKs are unique among tyrosine kinases for their constitutive yet non-covalent association with class I and II cytokine receptors, which upon cytokine binding bring together two JAKs to create an active signaling complex. JAK association with cytokine receptors is facilitated by N-terminal FERM and SH2 domains, both of which are classical mediators of peptide interactions. Together, the JAK FERM and SH2 domains mediate a bipartite interaction with two distinct receptor peptide motifs, the proline-rich "Box1" and hydrophobic "Box2," which are present in the intracellular domain of cytokine receptors. While the general sidechain chemistry of Box1 and Box2 peptides is conserved between receptors, they share very weak primary sequence homology, making it impossible to posit why certain JAKs preferentially interact with and signal through specific subsets of cytokine receptors. Here, we review the structure and function of the JAK FERM and SH2 domains in light of several recent studies that reveal their atomic structure and elucidate interaction mechanisms with both the Box1 and Box2 receptor motifs. These crystal structures demonstrate how evolution has repurposed the JAK FERM and SH2 domains into a receptor-binding module that facilitates interactions with multiple receptors possessing diverse primary sequences.

Non-standard neutrino interactions in the mu–tau sector

Directory of Open Access Journals (Sweden)

Irina Mocioiu

2015-04-01

Full Text Available We discuss neutrino mass hierarchy implications arising from the effects of non-standard neutrino interactions on muon rates in high statistics atmospheric neutrino oscillation experiments like IceCube DeepCore. We concentrate on the mu–tau sector, which is presently the least constrained. It is shown that the magnitude of the effects depends strongly on the sign of the ϵμτ parameter describing this non-standard interaction. A simple analytic model is used to understand the parameter space where differences between the two signs are maximized. We discuss how this effect is partially degenerate with changing the neutrino mass hierarchy, as well as how this degeneracy could be lifted.

Photochemical properties and sensor applications of modified yellow fluorescent protein (YFP) covalently attached to the surfaces of etched optical fibers (EOFs).

Science.gov (United States)

Veselov, Alexey A; Abraham, Bobin George; Lemmetyinen, Helge; Karp, Matti T; Tkachenko, Nikolai V

2012-01-01

Fluorescent proteins have the inherent ability to act as sensing components which function both in vitro and inside living cells. We describe here a novel study on a covalent site-specific bonding of fluorescent proteins to form self-assembled monolayers (SAMs) on the surface of etched optical fibers (EOFs). Deposition of fluorescent proteins on EOFs gives the opportunity to increase the interaction of guided light with deposited molecules relative to plane glass surfaces. The EOF modification is carried out by surface activation using 3-aminopropylthrimethoxysilane (APTMS) and bifunctional crosslinker sulfosuccinimidyl 4-[N-maleimidomethyl]cyclohexane-1-carboxylate (sulfo-SMCC) which exposes sulfhydryl-reactive maleimide groups followed by covalent site-specific coupling of modified yellow fluorescent protein (YFP). Steady-state and fluorescence lifetime measurements confirm the formation of SAM. The sensor applications of YPF SAMs on EOF are demonstrated by the gradual increase of emission intensity upon addition of Ca(2+) ions in the concentration range from a few tens of micromolars up to a few tens of millimolars. The studies on the effect of pH, divalent cations, denaturing agents, and proteases reveal the stability of YFP on EOFs at normal physiological conditions. However, treatments with 0.5% SDS at pH 8.5 and protease trypsin are found to denaturate or cleave the YFP from fiber surfaces.

Construction of a Hierarchical Architecture of Covalent Organic Frameworks via a Postsynthetic Approach.

Science.gov (United States)

Zhang, Gen; Tsujimoto, Masahiko; Packwood, Daniel; Duong, Nghia Tuan; Nishiyama, Yusuke; Kadota, Kentaro; Kitagawa, Susumu; Horike, Satoshi

2018-02-21

Covalent organic frameworks (COFs) represent an emerging class of crystalline porous materials that are constructed by the assembly of organic building blocks linked via covalent bonds. Several strategies have been developed for the construction of new COF structures; however, a facile approach to fabricate hierarchical COF architectures with controlled domain structures remains a significant challenge, and has not yet been achieved. In this study, a dynamic covalent chemistry (DCC)-based postsynthetic approach was employed at the solid-liquid interface to construct such structures. Two-dimensional imine-bonded COFs having different aromatic groups were prepared, and a homogeneously mixed-linker structure and a heterogeneously core-shell hollow structure were fabricated by controlling the reactivity of the postsynthetic reactions. Solid-state nuclear magnetic resonance (NMR) spectroscopy and transmission electron microscopy (TEM) confirmed the structures. COFs prepared by a postsynthetic approach exhibit several functional advantages compared with their parent phases. Their Brunauer-Emmett-Teller (BET) surface areas are 2-fold greater than those of their parent phases because of the higher crystallinity. In addition, the hydrophilicity of the material and the stepwise adsorption isotherms of H 2 O vapor in the hierarchical frameworks were precisely controlled, which was feasible because of the distribution of various domains of the two COFs by controlling the postsynthetic reaction. The approach opens new routes for constructing COF architectures with functionalities that are not possible in a single phase.

The Search for Covalently Ligandable Proteins in Biological Systems

Directory of Open Access Journals (Sweden)

Syed Lal Badshah

2016-09-01

Full Text Available This commentary highlights the recent article published in Nature, June 2016, titled: “Proteome-wide covalent ligand discovery in native biological systems”. They screened the whole proteome of different human cell lines and cell lysates. Around 700 druggable cysteines in the whole proteome were found to bind the electrophilic fragments in both active and inactive states of the proteins. Their experiment and computational docking results agreed with one another. The usefulness of this study in terms of bringing a change in medicinal chemistry is highlighted here.

Reaction mechanisms for on-surface synthesis of covalent nanostructures

International Nuclear Information System (INIS)

Björk, J

2016-01-01

In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms. (topical review)

Covalent Immobilization of β-Glucosidase on Magnetic Particles for Lignocellulose Hydrolysis

DEFF Research Database (Denmark)

Alftrén, Johan; Hobley, Timothy John

2013-01-01

β-Glucosidase hydrolyzes cellobiose to glucose and is an important enzyme in the consortium used for hydrolysis of cellulosic and lignocellulosic feedstocks. In the present work, β-glucosidase was covalently immobilized on non-porous magnetic particles to enable re-use of the enzyme. It was found...... that particles activated with cyanuric chloride and polyglutaraldehyde gave the highest bead-related immobilized enzyme activity when tested with p-nitrophenyl-β-D-glucopyranoside (104.7 and 82.2 U/g particles, respectively). Furthermore, the purified β-glucosidase preparation from Megazyme gave higher bead......-related enzyme activities compared to Novozym 188 (79.0 and 9.8 U/g particles, respectively). A significant improvement in thermal stability was observed for immobilized enzyme compared to free enzyme; after 5 h (at 65 °C), 36 % of activity remained for the former, while there was no activity in the latter...

Covalent Attachment of Bent-Core Mesogens to Silicon Surfaces

NARCIS (Netherlands)

Scheres, L.; Achten, R.; Giesbers, M.; Smet, de L.; Arafat, A.; Sudhölter, E.J.R.; Marcelis, A.T.M.; Zuilhof, H.

2009-01-01

Two vinyl-terminated bent core-shaped liquid crystalline molecules that exhibit thermotropic antiferroelectric SmCPA phases have been covalently attached onto a hydrogen-terminated silicon(111) surface. The surface attachment was achieved via a mild procedure from a mesitylene solution, using

A QUANTUM MECHANICAL STUDY OF THE PROTONATION AND COVALENT HYDRATION OF QUINAZOLINE IN THE PRESENCE OF METAL CATIONS

Science.gov (United States)

We have investigated the protonation and reversible covalent hydration of quinazoline in the presence of Li+, Na+, and Ca2+ ions using ab initio quantum mechanical calculations at the MP2/6-31G**//HF/6-31G*level of theory. Proton affinities, enthalpies of hydration at 298.15K (DH...

Cold-set globular protein gels: Interactions, structure and rheology as a function of protein concentration.

NARCIS (Netherlands)

Alting, A.C.; Hamer, R.J.; Kruif, de C.G.

2003-01-01

We identified the contribution of covalent and noncovalent interactions to the scaling behavior of the structural and rheological properties in a cold gelling protein system. The system we studied consisted of two types of whey protein aggregates, equal in size but different in the amount of

Hydroxamic acid interactions with solvated cerium hydroxides in the flotation of monazite and bastnäsite—Experiments and DFT study

Energy Technology Data Exchange (ETDEWEB)

Sarvaramini, A., E-mail: amin.sarvaramini.1@ulaval.ca; Azizi, D., E-mail: dariush.azizi.1@ulaval.ca; Larachi, F., E-mail: faical.larachi@gch.ulaval.ca

2016-11-30

Highlights: • Experimental and DFT studies of hydroxamic acid adsorption on monazite and bastnäsite. • Highest bastnäsite and monazite floatability observed at pH 7–9. • First solvation layer of cerium hydroxides consisted of up to 10 water molecules. • Solvated Ce(OH){sub 2}{sup +} and Ce(OH){sup 2+} cations interact with up to 3 collector anions. • Interaction of zero-charge solvated Ce(OH){sub 3} involves up to 2 collector anions. - Abstract: Density functional theory (DFT) simulations and experiments were performed to clarify the interaction mechanisms between hydroxamic acid collectors and cerium hydroxides during the flotation of bastnäsite and monazite minerals. These minerals showed considerable floatability at moderately alkaline pH which was related to the adsorption of hydroxamic acids on their surfaces as confirmed by vibrational spectroscopic and zeta potential measurements. DFT simulations showed that at moderately alkaline pH, the interactions between solvated Ce(OH){sup 2+} and Ce(OH){sub 2}{sup +} and heptyl-hydroxamic acid (HHA) anions resulted in the formation of, respectively, [Ce(OH)(HHA){sub x}(H{sub 2}O){sub y}]{sup 2−x} (x[y = ] = 1[6],2[3],3[1]) and [Ce(OH){sub 2}(HHA){sub x}(H{sub 2}O){sub y}]{sup 1−x} (x[y = ] = 1[5],2[1],3[0]) complexes. The collector anions were found to interact directly through formation of two covalent bonds between their two polar-head oxygen atoms and cerium in the hydroxide complexes. However, formation of such new bonds resulted in breakage of a few covalent/electrostatic bonds between cerium and water molecules initially present in the first hydration shell of the rare-earth metal cation. Building up in the electric double layer of the semi-soluble minerals, these complexes, and by extension, those from other rare-earth elements belonging to monazite and bastnäsite, are speculated to play a role in the interactions between rare-earth minerals and hydroxamic acid collectors.

Drug interactions between non-rifamycin antibiotics and hormonal contraception: a systematic review.

Science.gov (United States)

Simmons, Katharine B; Haddad, Lisa B; Nanda, Kavita; Curtis, Kathryn M

2018-01-01

The purpose of this study was to determine whether interactions between non-rifamycin antibiotics and hormonal contraceptives result in decreased effectiveness or increased toxicity of either therapy. We searched MEDLINE, Embase, clinicaltrials.gov, and Cochrane libraries from database inception through June 2016. We included trials, cohort, case-control, and pharmacokinetic studies in any language that addressed pregnancy rates, pharmacodynamics, or pharmacokinetic outcomes when any hormonal contraceptive and non-rifamycin antibiotic were administered together vs apart. Of 7291 original records that were identified, 29 met criteria for inclusion. Two authors independently assessed study quality and risk of bias using the United States Preventive Services Task Force evidence grading system. Findings were tabulated by drug class. Study quality ranged from good to poor and addressed only oral contraceptive pills, emergency contraception pills, and the combined vaginal ring. Two studies demonstrated no difference in pregnancy rates in women who used oral contraceptives with and without non-rifamycin antibiotics. No differences in ovulation suppression or breakthrough bleeding were observed in any study that combined hormonal contraceptives with any antibiotic. No significant decreases in any progestin pharmacokinetic parameter occurred during co-administration with any antibiotic. Ethinyl estradiol area under the curve decreased when administered with dirithromycin, but no other drug. Evidence from clinical and pharmacokinetic outcomes studies does not support the existence of drug interactions between hormonal contraception and non-rifamycin antibiotics. Data are limited by low quantity and quality for some drug classes. Most women can expect no reduction in hormonal contraceptive effect with the concurrent use of non-rifamycin antibiotics. Copyright © 2017 Elsevier Inc. All rights reserved.

Influence of magnetic dipole and magnetoelastic interactions on the phase states of 2D non-Heisenberg ferromagnetic with complex exchange interactions

International Nuclear Information System (INIS)

Fridman, Yu.A.; Matunin, D.A.; Klevets, Ph.N.; Kosmachev, O.A.

2009-01-01

The phase states of the 2D non-Heisenberg ferromagnetic with anisotropic bilinear and biquadratic exchange interactions are investigated. The limiting cases of the system under consideration are the two-dimensional XY-model with biquadratic exchange interaction and the isotropic Heisenberg ferromagnetic. The account of the magnetic dipole interaction leads to the realization of spatially inhomogeneous quadrupolar phase. The stability regions of various phase transitions for different values of the material parameters are studied. The phase diagram is built. Besides, the temperature phase transitions are investigated. The influence of the magnetoelastic interaction on the formation of the long-range quadrupolar order is determined.

Oligomeric protein structure networks: insights into protein-protein interactions

Directory of Open Access Journals (Sweden)

Brinda KV

2005-12-01

Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

Interpersonal Interactions in Instrumental Lessons: Teacher/Student Verbal and Non-Verbal Behaviours

Science.gov (United States)

Zhukov, Katie

2013-01-01

This study examined verbal and non-verbal teacher/student interpersonal interactions in higher education instrumental music lessons. Twenty-four lessons were videotaped and teacher/student behaviours were analysed using a researcher-designed instrument. The findings indicate predominance of student and teacher joke among the verbal behaviours with…

Effect of interaction with clowns on vital signs and non-verbal communication of hospitalized children.

Science.gov (United States)

Alcântara, Pauline Lima; Wogel, Ariane Zonho; Rossi, Maria Isabela Lobo; Neves, Isabela Rodrigues; Sabates, Ana Llonch; Puggina, Ana Cláudia

2016-12-01

Compare the non-verbal communication of children before and during interaction with clowns and compare their vital signs before and after this interaction. Uncontrolled, intervention, cross-sectional, quantitative study with children admitted to a public university hospital. The intervention was performed by medical students dressed as clowns and included magic tricks, juggling, singing with the children, making soap bubbles and comedic performances. The intervention time was 20minutes. Vital signs were assessed in two measurements with an interval of one minute immediately before and after the interaction. Non-verbal communication was observed before and during the interaction using the Non-Verbal Communication Template Chart, a tool in which nonverbal behaviors are assessed as effective or ineffective in the interactions. The sample consisted of 41 children with a mean age of 7.6±2.7 years; most were aged 7 to 11 years (n=23; 56%) and were males (n=26; 63.4%). There was a statistically significant difference in systolic and diastolic blood pressure, pain and non-verbal behavior of children with the intervention. Systolic and diastolic blood pressure increased and pain scales showed decreased scores. The playful interaction with clowns can be a therapeutic resource to minimize the effects of the stressing environment during the intervention, improve the children's emotional state and reduce the perception of pain. Copyright © 2016 Sociedade de Pediatria de São Paulo. Publicado por Elsevier Editora Ltda. All rights reserved.

In vitro drug interaction of levocetirizine and diclofenac: Theoretical and spectroscopic studies.

Science.gov (United States)

Abo Dena, Ahmed S; Abdel Gaber, Sara A

2017-06-15

Levocetirizine dihydrochloride is known to interact with some anti-inflammatory drugs. We report here a comprehensive integrated theoretical and experimental study for the in vitro drug interaction between levocetirizine dihydrochloride (LEV) and diclofenac sodium (DIC). The interaction of the two drugs was confirmed by the molecular ion peak obtained from the mass spectrum of the product. Moreover, FTIR and 1 HNMR spectra of the individual drugs and their interaction product were inspected to allocate the possible sites of interaction. In addition, quantum mechanical DFT calculations were performed to search for the interaction sites and to verify the types of interactions deduced from the spectroscopic studies such as charge-transfer and non-bonding π-π interactions. It was found that the studied drugs interact with each other in aqueous solution via four types of interactions, namely, ion-pair formation, three weak hydrogen bonds, non-bonding π-π interactions and charge-transfer from DIC to LEV. Copyright © 2017 Elsevier B.V. All rights reserved.

In vitro drug interaction of levocetirizine and diclofenac: Theoretical and spectroscopic studies

Science.gov (United States)

Abo Dena, Ahmed S.; Abdel Gaber, Sara A.

2017-06-01

Levocetirizine dihydrochloride is known to interact with some anti-inflammatory drugs. We report here a comprehensive integrated theoretical and experimental study for the in vitro drug interaction between levocetirizine dihydrochloride (LEV) and diclofenac sodium (DIC). The interaction of the two drugs was confirmed by the molecular ion peak obtained from the mass spectrum of the product. Moreover, FTIR and 1HNMR spectra of the individual drugs and their interaction product were inspected to allocate the possible sites of interaction. In addition, quantum mechanical DFT calculations were performed to search for the interaction sites and to verify the types of interactions deduced from the spectroscopic studies such as charge-transfer and non-bonding π-π interactions. It was found that the studied drugs interact with each other in aqueous solution via four types of interactions, namely, ion-pair formation, three weak hydrogen bonds, non-bonding π-π interactions and charge-transfer from DIC to LEV.