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Sample records for benzimidazole probe molecules

  1. Experimental and theoretical analysis of 2-amino 1-methyl benzimidazole molecule based on DFT

    Science.gov (United States)

    Sas, E. B.; Cevik, M.; Kurt, M.

    2017-12-01

    In this work were shown spectroscopic properties, molecular structure and electronic properties of 2-amino 1 methyl benzimidazole molecule. The theoretical calculations in the title molecule were performed with density functional theory method. Experimental wavenumber of 2-amino 1 methyl benzimidazole molecule were recorded with FT-Raman, dispersive Raman and FT-IR between 4000 and 0, 4000-400 and 4000-370 cm-1, respectively. The scaled theoretical wavenumber are assigned based on total energy distribution. Other experimental spectra were recorded in specific solvents.

  2. Mass analyzed threshold ionization spectroscopy of aza-aromatic bicyclic molecules: Benzimidazole and benzotriazole

    Energy Technology Data Exchange (ETDEWEB)

    Lin, J.L.; Li, Y.C. [Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, 1 Section 4, Roosevelt Road, Taipei 10617, Taiwan (China); Tzeng, W.B. [Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, 1 Section 4, Roosevelt Road, Taipei 10617, Taiwan (China)], E-mail: wbt@po.iams.sinica.edu.tw

    2007-04-20

    We report the vibrationally resolved cation spectra of benzimidazole and benzotriazole, which give the respective adiabatic ionization energies (IEs) to be 67552 {+-} 5 cm{sup -1} and 70474 {+-} 5 cm{sup -1}. Comparing these data with that of indole, one finds that the IE of these aza-aromatic bicyclic molecules increases with the number of the N atoms. Most of the active modes of the benzimidazole cation are related to the in-plane ring vibrations. In contrast, the observed spectral bands of the benzotriazole cation correspond to the out-of-plane N2-H and skeleton N1N2N3 bending vibrations. These experimental findings may be attributed to the nature and the N atoms in the five-membered ring.

  3. Mass analyzed threshold ionization spectroscopy of aza-aromatic bicyclic molecules: Benzimidazole and benzotriazole

    Science.gov (United States)

    Lin, Jung Lee; Li, Yi Chang; Tzeng, Wen Bih

    2007-04-01

    We report the vibrationally resolved cation spectra of benzimidazole and benzotriazole, which give the respective adiabatic ionization energies (IEs) to be 67552 ± 5 cm -1 and 70474 ± 5 cm -1. Comparing these data with that of indole, one finds that the IE of these aza-aromatic bicyclic molecules increases with the number of the N atoms. Most of the active modes of the benzimidazole cation are related to the in-plane ring vibrations. In contrast, the observed spectral bands of the benzotriazole cation correspond to the out-of-plane N2-H and skeleton N1N2N3 bending vibrations. These experimental findings may be attributed to the nature and the N atoms in the five-membered ring.

  4. A turn-on supramolecular fluorescent probe for sensing benzimidazole fungicides and its application in living cell imaging

    Science.gov (United States)

    Tang, Qing; Zhang, Jing; Sun, Tao; Wang, Cheng-Hui; Huang, Ying; Zhou, Qingdi; Wei, Gang

    2018-02-01

    A cucurbit[8]uril-based turn-on supramolecular fluorescent probe between cucurbit[8]uril (Q[8]) and pyronine Y (PyY) (designated 2PyY@Q[8]) in acidic aqueous solution showed a remarkable fluorescence 'turn-on' response to benzimidazole fungicides such as thiabendazole, fuberidazole and carbendazim. The 2PyY@Q[8] fluorescent probe can be used to detect benzimidazole fungicides with high sensitivity and selectivity with a detection limit of 10- 8 mol/L. A good linear relationship of emission intensity at 580 nm for benzimidazole fungicides at concentrations of 0.4-5.0 μmol/L was observed. The proposed sensing mechanism was investigated using 1H NMR spectroscopy combined with density functional theory calculations at the B3LYP/6-31G(d) level. The cell imaging study showed that the 2PyY@Q[8] complex could be used to image benzimidazole fungicide in prostate cancer (PC3) cells, which may help to elucidate relevant biological processes at the molecular level.

  5. Two proton-conductive hybrids based on 2-(3-pyridyl)benzimidazole molecules and Keggin-type heteropolyacids

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Mei-Lin, E-mail: weimeilinhd@163.com; Wang, Yu-Xia; Wang, Xin-Jun

    2014-01-15

    Two proton-conductive organic/inorganic complexes were constructed by Keggin-type heteropolyacids and 2-(3-pyridyl)benzimidazole molecules. Single-crystal X-ray diffraction analyses revealed that two complexes crystallized in the monoclinic space group P2{sub 1}/c, exhibited different unit cell parameters, and presented different hydrogen-bonded networks constructed by 2-(3-pyridyl)benzimidazole molecules, [PMo{sub 12}O{sub 40}]{sup 3−} anions and solvent molecules. The results of thermogravimetric analyses suggest that two supramolecular complexes have different thermal stability based on the different hydrogen-bonded networks. Two complexes at 100 °C under 35–98% relative humidity showed a good proton conductivity of about 10{sup −3} S cm{sup −1}. The proton conductivities of two complexes under 98% relative humidity both increase on a logarithmic scale with temperature range from 25 to 100 °C. At 100 °C, both complexes showed poor proton conductivities of 10{sup −8}–10{sup −9} S cm{sup −1} under acetonitrile or methanol vapor. - Graphical abstract: Two molecular hybrids constructed by Keggin-type heteropolyacids and 2-(3-pyridyl)benzimidazole molecules showed good proton conductivities of 10{sup −3} S cm{sup −1} at 100 °C under 35–98% relative humidity. Display Omitted - Highlights: • 2-(3-Pyridyl)benzimidazole could form hydrogen bonds via the N–H groups. • Heteropolyacids have suitable characteristics to be used excellent proton conductors. • Two proton-conductive hybrids based on Keggin HPAs and 3-PyBim were constructed. • The structures were determined by using single-crystal X-ray diffraction data. • They showed good proton conductivities of 10{sup −3} S cm{sup −1} at 100 °C under 35–98% RH.

  6. Synthesis, Characterization and Chelating Properties of Benzimidazole-Salicylic Acid Combined Molecule

    Directory of Open Access Journals (Sweden)

    Kamlesh V. Patel

    2009-01-01

    Full Text Available Aminomethylation (i.e. Mannich reaction of benzimidazole was carried out by treating benzimidalzole with formaldehyde and 4-aminosalicylic acid. The resultant compound was designated as 1-(4-carboxy-3-hydroxyphenyl aminomethyl benzimidazole (BI-SA. The transition metal complexes of Cu2+, Co2+, Ni2+, Mn2+, Zn2+ and Fe3+ of BI-SA have been prepared and characterized by elemental analyses, spectral studies, magnetic moment determination, molar conductivity measurement and microbicidal activity.

  7. Small molecule probes for cellular death machines.

    Science.gov (United States)

    Li, Ying; Qian, Lihui; Yuan, Junying

    2017-08-01

    The past decade has witnessed a significant expansion of our understanding about the regulated cell death mechanisms beyond apoptosis. The application of chemical biological approaches had played a major role in driving these exciting discoveries. The discovery and use of small molecule probes in cell death research has not only revealed significant insights into the regulatory mechanism of cell death but also provided new drug targets and lead drug candidates for developing therapeutics of human diseases with huge unmet need. Here, we provide an overview of small molecule modulators for necroptosis and ferroptosis, two non-apoptotic cell death mechanisms, and discuss the molecular pathways and relevant pathophysiological mechanisms revealed by the judicial applications of such small molecule probes. We suggest that the development and applications of small molecule probes for non-apoptotic cell death mechanisms provide an outstanding example showcasing the power of chemical biology in exploring novel biological mechanisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Probing the Probes: Fitness Factors For Small Molecule Tools

    OpenAIRE

    Workman, Paul; Collins, Ian

    2010-01-01

    Chemical probes for interrogating biological processes are of considerable current interest. Cell permeable small molecule tools have a major role in facilitating the functional annotation of the human genome, understanding both physiological and pathological processes, and validating new molecular targets. To be valuable, chemical tools must satisfy necessary criteria and recent publications have suggested objective guidelines for what makes a useful chemical probe. Although recognizing that...

  9. Small molecule probes for plant cell wall polysaccharide imaging

    Directory of Open Access Journals (Sweden)

    Ian eWallace

    2012-05-01

    Full Text Available Plant cell walls are composed of interlinked polymer networks consisting of cellulose, hemicelluloses, pectins, proteins, and lignin. The ordered deposition of these components is a dynamic process that critically affects the development and differentiation of plant cells. However, our understanding of cell wall synthesis and remodeling, as well as the diverse cell wall architectures that result from these processes, has been limited by a lack of suitable chemical probes that are compatible with live-cell imaging. In this review, we summarize the currently available molecular toolbox of probes for cell wall polysaccharide imaging in plants, with particular emphasis on recent advances in small molecule-based fluorescent probes. We also discuss the potential for further development of small molecule probes for the analysis of cell wall architecture and dynamics.

  10. BRCA Testing by Single-Molecule Molecular Inversion Probes

    NARCIS (Netherlands)

    Neveling, K.; Mensenkamp, A.R.; Derks, R; Kwint, M.P.; Ouchene, H.; Steehouwer, M.; Lier, L.A. van; Bosgoed, E.A.J.; Rikken, A.; Tychon, M.W.J.; Zafeiropoulou, D.; Castelein, S.; Hehir-Kwa, J.Y.; Thung, G.W.; Hofste, T.; Lelieveld, S.H.; Bertens, S.M.; Adan, I.B.; Eijkelenboom, A.; Tops, B.B.J.; Yntema, H.G.; Stokowy, T.; Knappskog, P.M.; Hoberg-Vetti, H.; Steen, V.M.; Boyle, E.; Martin, B.; Ligtenberg, M.J.L.; Shendure, J.; Nelen, M.R.; Hoischen, A.

    2017-01-01

    BACKGROUND: Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the

  11. Heterobifunctional crosslinkers for tethering single ligand molecules to scanning probes

    International Nuclear Information System (INIS)

    Riener, Christian K.; Kienberger, Ferry; Hahn, Christoph D.; Buchinger, Gerhard M.; Egwim, Innocent O.C.; Haselgruebler, Thomas; Ebner, Andreas; Romanin, Christoph; Klampfl, Christian; Lackner, Bernd; Prinz, Heino; Blaas, Dieter; Hinterdorfer, Peter; Gruber, Hermann J.

    2003-01-01

    Single molecule recognition force microscopy (SMRFM) is a versatile atomic force microscopy (AFM) method to probe specific interactions of cognitive molecules on the single molecule level. It allows insights to be gained into interaction potentials and kinetic barriers and is capable of mapping interaction sites with nm positional accuracy. These applications require a ligand to be attached to the AFM tip, preferably by a distensible poly(ethylene glycol) (PEG) chain between the measuring tip and the ligand molecule. The PEG chain greatly facilitates specific binding of the ligand to immobile receptor sites on the sample surface. The present study contributes to tip-PEG-ligand tethering in three ways: (i) a convenient synthetic route was found to prepare NH 2 -PEG-COOH which is the key intermediate for long heterobifunctional crosslinkers; (ii) a variety of heterobifunctional PEG derivatives for tip-PEG-ligand linking were prepared from NH 2 -PEG-COOH; (iii) in particular, a new PEG crosslinker with one thiol-reactive end and one terminal nitrilotriacetic acid (NTA) group was synthesized and successfully used to tether His 6 -tagged protein molecules to AFM tips via noncovalent NTA-Ni 2+ -His 6 bridges. The new crosslinker was applied to link a recombinant His 6 -tagged fragment of the very-low density lipoprotein receptor to the AFM tip whereupon specific docking to the capsid of human rhinovirus particles was observed by force microscopy. In a parallel study, the specific interaction of the small GTPase Ran with the nuclear import receptor importin β1 was studied in detail by SMRFM, using the new crosslinker to link His 6 -tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557

  12. Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules.

    Science.gov (United States)

    Hendriks, Frank C; Schmidt, Joel E; Rombouts, Jeroen A; Lammertsma, Koop; Bruijnincx, Pieter C A; Weckhuysen, Bert M

    2017-05-05

    A micro-spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4-(4-diethylaminostyryl)-1-methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM-5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization-dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture-dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X-ray diffraction. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  13. Excitonic Coupling in Linear and Trefoil Trimer Perylenediimide Molecules Probed by Single-Molecule Spectroscopy

    KAUST Repository

    Yoo, Hyejin

    2012-10-25

    Perylenediimide (PDI) molecules are promising building blocks for photophysical studies of electronic interactions within multichromophore arrays. Such PDI arrays are important materials for fabrication of molecular nanodevices such as organic light-emitting diodes, organic semiconductors, and biosensors because of their high photostability, chemical and physical inertness, electron affinity, and high tinctorial strength over the entire visible spectrum. In this work, PDIs have been organized into linear (L3) and trefoil (T3) trimer molecules and investigated by single-molecule fluorescence microscopy to probe the relationship between molecular structures and interchromophoric electronic interactions. We found a broad distribution of coupling strengths in both L3 and T3 and hence strong/weak coupling between PDI units by monitoring spectral peak shifts in single-molecule fluorescence spectra upon sequential photobleaching of each constituent chromophore. In addition, we used a wide-field defocused imaging technique to resolve heterogeneities in molecular structures of L3 and T3 embedded in a PMMA polymer matrix. A systematic comparison between the two sets of experimental results allowed us to infer the correlation between intermolecular interactions and molecular structures. Our results show control of the PDI intermolecular interactions using suitable multichromophoric structures. © 2012 American Chemical Society.

  14. Probing physics beyond the standard model in diatomic molecules

    International Nuclear Information System (INIS)

    Denis, M.

    2017-01-01

    Nowadays, the incompleteness of the Standard Model of particles (SM) is largely acknowledged. One of its most obvious shortcomings is the lack of explanation for the huge surplus of matter over antimatter in the universe, the so-called baryon asymmetry of the universe. New CP (charge conjugation and spatial parity) violations absent in the SM are assumed to be responsible for this asymmetry. Such a violation could be observed, in ordinary matter through a set of interactions violating both parity and time-reversal symmetries (P, T -odd) among which the preponderant ones are the electron Electric Dipole Moment (eEDM), the electron-nucleon scalar-pseudoscalar (enSPS) and the nuclear magnetic quadrupole moment (nMQM) interactions. Hence, an experimental evidence of a non-zero P, T -odd interaction constant would be a probe of this New Physics beyond the Standard Model. The calculation of the corresponding molecular parameters is performed by making use of an elaborate four-component relativistic configuration interaction approach in polar diatomic molecules containing an actinide, that are particularly adequate systems for eEDM experiments, such as ThO that allowed for assigning the most constraining upper bound on the eEDM and ThF + that will be used in a forthcoming experiment. Those results will be of crucial importance in the interpretation of the measurements since the fundamental constants can only be evaluated if one combines both experimental energy shift measurements and theoretical molecular parameters. This manuscript proceeds as follows, after an introduction to the general background of the search of CP-violations and its consequences for the understanding of the Universe (Chapter 1), a presentation of the underlying theory of the evidence of such violation in ordinary matter, namely the P, T -odd sources of the Electric Dipole Moment of a many-electron system, as well as the relevant molecular parameters is given in Chapter 2. A similar introduction to

  15. Mass amplifying probe for sensitive fluorescence anisotropy detection of small molecules in complex biological samples.

    Science.gov (United States)

    Cui, Liang; Zou, Yuan; Lin, Ninghang; Zhu, Zhi; Jenkins, Gareth; Yang, Chaoyong James

    2012-07-03

    Fluorescence anisotropy (FA) is a reliable and excellent choice for fluorescence sensing. One of the key factors influencing the FA value for any molecule is the molar mass of the molecule being measured. As a result, the FA method with functional nucleic acid aptamers has been limited to macromolecules such as proteins and is generally not applicable for the analysis of small molecules because their molecular masses are relatively too small to produce observable FA value changes. We report here a molecular mass amplifying strategy to construct anisotropy aptamer probes for small molecules. The probe is designed in such a way that only when a target molecule binds to the probe does it activate its binding ability to an anisotropy amplifier (a high molecular mass molecule such as protein), thus significantly increasing the molecular mass and FA value of the probe/target complex. Specifically, a mass amplifying probe (MAP) consists of a targeting aptamer domain against a target molecule and molecular mass amplifying aptamer domain for the amplifier protein. The probe is initially rendered inactive by a small blocking strand partially complementary to both target aptamer and amplifier protein aptamer so that the mass amplifying aptamer domain would not bind to the amplifier protein unless the probe has been activated by the target. In this way, we prepared two probes that constitute a target (ATP and cocaine respectively) aptamer, a thrombin (as the mass amplifier) aptamer, and a fluorophore. Both probes worked well against their corresponding small molecule targets, and the detection limits for ATP and cocaine were 0.5 μM and 0.8 μM, respectively. More importantly, because FA is less affected by environmental interferences, ATP in cell media and cocaine in urine were directly detected without any tedious sample pretreatment. Our results established that our molecular mass amplifying strategy can be used to design aptamer probes for rapid, sensitive, and selective

  16. Single-molecule probes in organic field-effect transistors

    NARCIS (Netherlands)

    Nicolet, Aurélien Armel Louis

    2007-01-01

    The goal of this thesis is to study charge transport phenomena in organic materials. This is done optically by means of single-molecule spectroscopy in a field-effect transistor based on a molecular crystal. We present (in Chapter 2) a fundamental requirement for single-molecule spectroscopy

  17. Spectroscopic probes of vibrationally excited molecules at chemically significant energies

    Energy Technology Data Exchange (ETDEWEB)

    Rizzo, T.R. [Univ. of Rochester, NY (United States)

    1993-12-01

    This project involves the application of multiple-resonance spectroscopic techniques for investigating energy transfer and dissociation dynamics of highly vibrationally excited molecules. Two major goals of this work are: (1) to provide information on potential energy surfaces of combustion related molecules at chemically significant energies, and (2) to test theoretical modes of unimolecular dissociation rates critically via quantum-state resolved measurements.

  18. Single Molecule Junctions: Probing Contact Chemistry and Fundamental Circuit Laws

    Energy Technology Data Exchange (ETDEWEB)

    Hybertsen M. S.

    2013-04-11

    By exploiting selective link chemistry, formation of single molecule junctions with reproducible conductance has become established. Systematic studies reveal the structure-conductance relationships for diverse molecules. I will draw on experiments from my collaborators at Columbia University, atomic-scale calculations and theory to describe progress in two areas. First, I will describe a novel route to form single molecule junctions, based on SnMe3 terminated molecules, in which gold directly bonds to carbon in the molecule backbone resulting in near ideal contact resistance [1]. Second, comparison of the conductance of junctions formed with molecular species containing either one backbone or two backbones in parallel allows demonstration of the role of quantum interference in the conductance superposition law at the molecular scale [2].

  19. Modelling attosecond probing of electron wavepacket dynamics in non-aligned molecules

    International Nuclear Information System (INIS)

    Schmidt, J; Yakovlev, V S; Goulielmakis, E

    2008-01-01

    We propose and simulate an attosecond pump-probe scheme applied to an ensemble of non-aligned (or partially aligned) diatomic molecules. Non-dissociative dynamics initiated by an ultraviolet pump pulse are probed by photoionizing the molecule with an attosecond extreme-ultraviolet probe pulse. Photoelectron spectra recorded for different delays between the pulses exhibit signatures of streaking and sub-femtosecond quantum beating. If more than one vibrational state is excited, the nuclear motion modulates the visibility of quantum interference effects

  20. Flicker Noise as a Probe of Electronic Interaction at Metal-Single Molecule Interfaces.

    Science.gov (United States)

    Adak, Olgun; Rosenthal, Ethan; Meisner, Jeffery; Andrade, Erick F; Pasupathy, Abhay N; Nuckolls, Colin; Hybertsen, Mark S; Venkataraman, Latha

    2015-06-10

    Charge transport properties of metal-molecule interfaces depend strongly on the character of molecule-electrode interactions. Although through-bond coupled systems have attracted the most attention, through-space coupling is important in molecular systems when, for example, through-bond coupling is suppressed due to quantum interference effects. To date, a probe that clearly distinguishes these two types of coupling has not yet been demonstrated. Here, we investigate the origin of flicker noise in single molecule junctions and demonstrate how the character of the molecule-electrode coupling influences the flicker noise behavior of single molecule junctions. Importantly, we find that flicker noise shows a power law dependence on conductance in all junctions studied with an exponent that can distinguish through-space and through-bond coupling. Our results provide a new and powerful tool for probing and understanding coupling at the metal-molecule interface.

  1. Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules

    NARCIS (Netherlands)

    Hendriks, Frank C.; Schmidt, Joel E.; Rombouts, Jeroen A.; Lammertsma, Koop; Bruijnincx, Pieter C.A.; Weckhuysen, Bert M.

    2017-01-01

    A micro-spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4-(4-diethylaminostyryl)-1-methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM-5) topology and subsequent

  2. ANTIBACTERIAL ACTIVITY OF BENZIMIDAZOLES 2-THIO, 2-AMINODERIVATIVES AND COMPLEXES OF BENZIMIDAZOLES WITH TRANSITIONAL METALS

    Directory of Open Access Journals (Sweden)

    E. I. Mayboroda

    2014-01-01

    Full Text Available The literature data about antibacterial properties of benzimidazole 2-thio-, 2-aminoderivatives and benzimidazole complexes have been generalized and systematized in the review. Today prevention and treatment of diseases caused by microorganisms is an actual problem of modern therapy. Therefore, the search for active molecules, the based on them development of some new, more effective antimicrobial agents is an important task of modern pharmaceutical chemistry. Promising compounds for solving these problems are benzimidazole derivatives. They are available, functionally capable, stable and have a wide spectrum of biological activities (antiviral, anthelmintic, antibacterial, anticancer, antidiabetic.The purpose of this paper is to generalize and systematize information about the antimicrobial action of 2-thio-, 2-amino-substituted benzimidazoles and benzimidazole derivatives complexes with transition metals.These compounds and their complexes with transition metals are active against pathogenic strains Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhimurium, Proteus vulgaris, Bacillus cereus, Micrococcus luteus, Helicobacter рylori and others.

  3. Single-molecule correlated chemical probing of RNA.

    Science.gov (United States)

    Homan, Philip J; Favorov, Oleg V; Lavender, Christopher A; Kursun, Olcay; Ge, Xiyuan; Busan, Steven; Dokholyan, Nikolay V; Weeks, Kevin M

    2014-09-23

    Complex higher-order RNA structures play critical roles in all facets of gene expression; however, the through-space interaction networks that define tertiary structures and govern sampling of multiple conformations are poorly understood. Here we describe single-molecule RNA structure analysis in which multiple sites of chemical modification are identified in single RNA strands by massively parallel sequencing and then analyzed for correlated and clustered interactions. The strategy thus identifies RNA interaction groups by mutational profiling (RING-MaP) and makes possible two expansive applications. First, we identify through-space interactions, create 3D models for RNAs spanning 80-265 nucleotides, and characterize broad classes of intramolecular interactions that stabilize RNA. Second, we distinguish distinct conformations in solution ensembles and reveal previously undetected hidden states and large-scale structural reconfigurations that occur in unfolded RNAs relative to native states. RING-MaP single-molecule nucleic acid structure interrogation enables concise and facile analysis of the global architectures and multiple conformations that govern function in RNA.

  4. Benzimidazoles: A biologically active compounds

    Directory of Open Access Journals (Sweden)

    Salahuddin

    2017-02-01

    Full Text Available Synthesis of commercially available benzimidazole involves condensation of o-phenylenediamine with formic acid. The most prominent benzimidazole compound in nature is N-riosyldimethylbenzimidazole, which serves as a axial ligand for cobalt in vitamin B12. The benzimidazole and its derivatives play a very important role as a therapeutic agent e.g. antiulcer and anthelmintic drugs. Apart from this the benzimidazole derivatives exhibit pharmacological activities such as antimicrobial, antiviral, anticancer, anti-inflammatory, analgesic, etc. The substituted benzimidazoles are summarized in this review to know about the chemistry as well as pharmacological activities.

  5. UPAR targeted molecular imaging of cancers with small molecule-based probes.

    Science.gov (United States)

    Ding, Feng; Chen, Seng; Zhang, Wanshu; Tu, Yufeng; Sun, Yao

    2017-10-15

    Molecular imaging can allow the non-invasive characterization and measurement of biological and biochemical processes at the molecular and cellular levels in living subjects. The imaging of specific molecular targets that are associated with cancers could allow for the earlier diagnosis and better treatment of diseases. Small molecule-based probes play prominent roles in biomedical research and have high clinical translation ability. Here, with an emphasis on small molecule-based probes, we review some recent developments in biomarkers, imaging techniques and multimodal imaging in molecular imaging and highlight the successful applications for molecular imaging of cancers. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Probing single-molecule electron-hole transfer dynamics at a molecule-NiO semiconductor nanocrystalline interface.

    Science.gov (United States)

    Dhital, Bharat; Rao, Vishal Govind; Lu, H Peter

    2017-07-14

    Interfacial charge transfer dynamics in dye-sensitized NiO nanoparticles are being investigated for photocathodes in p-type dye-sensitized solar cells. In the photoreaction, after fast electron transfer from NiO to a molecule, the recombination of the hole in the nanoparticles with the electron in a reduced molecule plays an important role in the charge separation process and solar energy harvesting. Nevertheless, knowledge of the interfacial charge recombination (CR) rate and its mechanism is still limited due to the complex photoinduced electron and hole dynamics and lack of characterization of the inhomogeneity of the dynamics. Here, we report our work on probing interfacial charge recombination dynamics in Zn(ii)-5,10,15,20-tetra(3-carboxyphenyl)porphyrin (m-ZnTCPP) dye-sensitized NiO nanoparticles by correlating single-molecule fluorescence blinking dynamics with charge transfer dynamics using single-molecule photon-stamping spectroscopy. The correlated analyses of single-molecule fluorescence intensity, lifetime, and blinking reveal the intrinsic distribution and temporal fluctuation of interfacial charge transfer reactivity, which are closely related to site-specific molecular interactions and dynamics.

  7. Photoelectron angular distributions from polar molecules probed by intense femtosecond lasers

    DEFF Research Database (Denmark)

    Abu-Samha, Mahmoud; Madsen, Lars Bojer

    2010-01-01

    -active-electron and frozen-nuclei approximations. Our analysis shows that for the HF and LiF molecules, anisotropies in the molecular potential and the probed orbital lead to enhanced ionization during laser half cycles with the field pointing antiparallel to the permanent dipole of the dipole term in a multipolar expansion...

  8. Diffusion behaviors of fluorescence probe molecules through the stratum corneum layer under physical stress.

    Science.gov (United States)

    Lee, Ho; Kim, Jin Woong

    2013-04-01

    This study experimentally demonstrates how application of an external physical stress onto the skin membrane affects the permeation of penetrating molecules. As a proxy of active compounds, in this study, a series of fluorescence probe molecules were utilized. We observed that skin permeation could be enhanced by imparting vertical strokes from a tapping head consisting of projections onto the skin. This was confirmed with consistency from in vitro and in vivo transdermal permeation studies. After an effective physical stress was applied to the skin, the permeation depth of probe molecules remarkably increased, which was comparable to the case of topical treatment. This seems to arise from temporal disordering of the stratum corneum layer in response to the applied physical stress.

  9. A Pyrene- and Phosphonate-Containing Fluorescent Probe as Guest Molecule in a Host Polymer Matrix

    Directory of Open Access Journals (Sweden)

    Jacqueline Marchand-Brynaert

    2013-02-01

    Full Text Available New host-guest materials have been prepared by incorporation of a home-made organic probe displaying a pyrene motif and a phosphonate function into a regular amphiphilic copolymer. Using powder X-Ray diffraction, photoluminescence and FT-IR spectroscopy, we have been able to study the non-covalent interactions between the host matrix and the guest molecule in the solid state. Interestingly, we have shown that the matrix directs the guest spatial localization and alters its properties. Thanks to the comparison of pyrene vs. N-pyrenylmaleimide derivatives, the influence of the chemical nature of the guest molecules on the non-covalent interactions with the host have been studied. In addition, using polyethylene glycol as a reference host, we have been able to evidence a true matrix effect within our new insertion materials. The phosphonated guest molecule appears to be a novel probe targeting the hydrophilic domain of the host copolymer.

  10. Benzimidazole-loaded Halloysite Nanotube as a Smart Coating Application

    Directory of Open Access Journals (Sweden)

    Khairina Azmi Zahidah

    2017-09-01

    Full Text Available Smart coating has been developed for the corrosion control of surfaces exposed to corrosive environment. An important step in development of a smart coating is the successful impregnation of corrosion inhibitor into the nanocontainer as a coating pigment. In this study, halloysite was used as nanocontainer to encapsulate benzimidazole as corrosion inhibitor by vacuum method. FESEM, TEM, FTIR and TGA characterization techniques were used to confirm the loading of halloysite with benzimidazole. FESEM results indicated differences between the morphology of the unloaded-halloysite and benzimidazole loaded-halloysite. TEM results confirmed that benzimidazole molecules are loaded into halloysite. FTIR result revealed there are differences in the absorbance characteristic of peaks between peak number 1000-4000 cm-1 for loaded and unloaded samples. It is seen that the absorbance in the loaded-halloysite is higher than unloaded-halloysite, which confirms quantity/specific functional group of molecules. TGA result showed the temperature of degradation of benzimidazole-loaded HNT was higher than pure HNT. EIS was conducted to examine the protection characteristic of the developed smart coating. From EIS results, of 1, 3, and 6 days of experimental duration, it is seen that the value of coating impedance (Z’ after exposure to 3.5% NaCl environment is very height, 2.460E+07 Ω, which confirm a very good anti corrosion protection characteristic for the developed smart coating. 

  11. Force probing of individual molecules inside the living cell is now a reality.

    Science.gov (United States)

    Oddershede, Lene B

    2012-11-01

    Biological systems can be quantitatively explored using single-molecule manipulation techniques such as optical or magnetic tweezers or atomic force microscopy. Though a plethora of discoveries have been accomplished using single-molecule manipulation techniques in vitro, such investigations constantly face the criticism that conditions are too far from being physiologically relevant. Technical achievements now allow scientists to take the next step: to use single-molecule manipulation techniques quantitatively in vivo. Considerable progress has been accomplished in this realm; for example, the interaction between a protein and the membrane of a living cell has been probed, the mechanical properties of individual proteins central for cellular adhesion have been measured and even the action of molecular motors in living cells has been quantified. Here, we review the progress of in vivo single-molecule manipulation with a focus on the special challenges posed by in vivo conditions and how these can be overcome.

  12. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes.

    Science.gov (United States)

    Scheler, Ott; Kaplinski, Lauris; Glynn, Barry; Palta, Priit; Parkel, Sven; Toome, Kadri; Maher, Majella; Barry, Thomas; Remm, Maido; Kurg, Ants

    2011-02-28

    We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity. We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.

  13. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes

    Directory of Open Access Journals (Sweden)

    Toome Kadri

    2011-02-01

    Full Text Available Abstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.

  14. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes

    LENUS (Irish Health Repository)

    Scheler, Ott

    2011-02-28

    Abstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal\\/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.

  15. Adsorption of probe molecules in pillared interlayered clays: Experiment and computer simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gallardo, A., E-mail: a.gallardo@iqfr.csic.es; Guil, J. M.; Lomba, E.; Almarza, N. G.; Khatib, S. J. [Instituto de Química Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid (Spain); Cabrillo, C.; Sanz, A. [Instituto de Estructura de la Materia, CSIC, Serrano 123, E-28006 Madrid (Spain); Pires, J. [Centro de Química e Bioquímica da Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa (Portugal)

    2014-06-14

    In this paper we investigate the adsorption of various probe molecules in order to characterize the porous structure of a series of pillared interlayered clays (PILC). To that aim, volumetric and microcalorimetric adsorption experiments were performed on various Zr PILC samples using nitrogen, toluene, and mesitylene as probe molecules. For one of the samples, neutron scattering experiments were also performed using toluene as adsorbate. Various structural models are proposed and tested by means of a comprehensive computer simulation study, using both geometric and percolation analysis in combination with Grand Canonical Monte Carlo simulations in order to model the volumetric and microcalorimetric isotherms. On the basis of this analysis, we propose a series of structural models that aim at accounting for the adsorption experimental behavior, and make possible a microscopic interpretation of the role played by the different interactions and steric effects in the adsorption processes in these rather complex disordered microporous systems.

  16. Comprehensive Review in Current Developments of Benzimidazole-Based Medicinal Chemistry.

    Science.gov (United States)

    Keri, Rangappa S; Hiremathad, Asha; Budagumpi, Srinivasa; Nagaraja, Bhari Mallanna

    2015-07-01

    The properties of benzimidazole and its derivatives have been studied over more than one hundred years. Benzimidazole derivatives are useful intermediates/subunits for the development of molecules of pharmaceutical or biological interest. Substituted benzimidazole derivatives have found applications in diverse therapeutic areas such as antiulcer, anticancer agents, and anthelmintic species to name just a few. This work systematically gives a comprehensive review in current developments of benzimidazole-based compounds in the whole range of medicinal chemistry as anticancer, antibacterial, antifungal, anti-inflammatory, analgesic agents, anti-HIV, antioxidant, anticonvulsant, antitubercular, antidiabetic, antileishmanial, antihistaminic, antimalarial agents, and other medicinal agents. This review will further be helpful for the researcher on the basis of substitution pattern around the nucleus with an aim to help medicinal chemists for developing an SAR on benzimidazole drugs/compounds. © 2014 John Wiley & Sons A/S.

  17. Evidence of zeolitic-like domains in mesostructured aluminosilicates: FTIR spectroscopy of basic probe molecules

    OpenAIRE

    Sánchez, M. T.; Agúndez Rodríguez, Javier; Pérez Pariente, Joaquín; Márquez Álvarez, Carlos; Onida, B.; Garrone, E.

    2007-01-01

    The acid properties of mesostructured aluminosilicates synthesized from gel precursors of colloidal ZSM-5 zeolite have been studied by FTIR spectroscopy of basic probe molecules (ammonia, CO and propene). It is shown that these materials possess stronger acid sites with higher thermal stability than those of conventional A1-MCM-41. These results explain the enhanced m-xylene isomerization activity of these materials and are attributed to the presence of zeolitic-like domains in the aluminosil...

  18. Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging

    Science.gov (United States)

    Ha, Taekjip; Tinnefeld, Philip

    2012-05-01

    Single-molecule fluorescence spectroscopy and super-resolution microscopy are important elements of the ongoing technical revolution to reveal biochemical and cellular processes in unprecedented clarity and precision. Demands placed on the photophysical properties of the fluorophores are stringent and drive the choice of appropriate probes. Such fluorophores are not simple light bulbs of a certain color and brightness but instead have their own “personalities” regarding spectroscopic parameters, redox properties, size, water solubility, photostability, and several other factors. Here, we review the photophysics of fluorescent probes, both organic fluorophores and fluorescent proteins, used in applications such as particle tracking, single-molecule FRET, stoichiometry determination, and super-resolution imaging. Of particular interest is the thiol-induced blinking of Cy5, a curse for single-molecule biophysical studies that was later overcome using Trolox through a reducing/oxidizing system but a boon for super-resolution imaging owing to the controllable photoswitching. Understanding photophysics is critical in the design and interpretation of single-molecule experiments.

  19. X-ray Pump–Probe Investigation of Charge and Dissociation Dynamics in Methyl Iodine Molecule

    Directory of Open Access Journals (Sweden)

    Li Fang

    2017-05-01

    Full Text Available Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. We present our investigation of photoionization and nuclear dynamics in methyl iodine (CH3I molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up to 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.

  20. Mechanochromic Fluorescent Probe Molecules for Damage Detection in Aerospace Polymers and Composites

    Science.gov (United States)

    Toivola, Ryan E.

    The detection of damage in aerospace composites can be improved by incorporation of mechanochromic fluorescent probe molecules into the polymers used in composite parts. This study focuses on a novel series of mechanochromic probes, AJNDE15 and AJNDE17, which are incorporated in structural epoxy resin DGEBA-DETA. Chapter 1 details the characterization of the DGEBA-DETA epoxy system used in this study. The important characteristics of DGEBA-DETA's response to mechanical loading will be discussed within the larger field of glassy amorphous polymer deformation. The mechanical, thermal, and chemical properties of DGEBA-DETA relevant to this work will be measured using standardized techniques and instrumentation. Chapters 2 and 3 focus on the mechanochromic probes AJNDE15 and AJNDE17 in the DGEBA-DETA system. Chapter 2 presents research designed to identify the mechanism through which the probes display mechanochromism. The possible mechanochromic mechanisms are introduced in a literature review. Research on these probes in DGEBA-DETA will be presented and discussed with respect to the possible mechanisms, and the mechanism that best fits the results will be identified as a mechanochemical reaction. Chapter 3 continues the analysis of the mechanochromism of the probes in DGEBA-DETA. The kinetics of the mechanochromic reaction will be studied and compared with the current understanding of glassy polymer deformation. Possible models for the molecular interactions responsible for mechanochromism in this system will be put forward. Research will be presented to evaluate the mechanochromism kinetics and for comparison with the behavior predicted by the models.

  1. Communication: Probing the absolute configuration of chiral molecules at aqueous interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Lotze, Stephan, E-mail: lotze@amolf.nl; Versluis, Jan [FOM Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam (Netherlands); Olijve, Luuk L. C.; Schijndel, Luuk van; Milroy, Lech G.; Voets, Ilja K. [Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Bakker, Huib J., E-mail: bakker@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)

    2015-11-28

    We demonstrate that the enantiomers of chiral macromolecules at an aqueous interface can be distinguished with monolayer sensitivity using heterodyne-detected vibrational sum-frequency generation (VSFG). We perform VSFG spectroscopy with a polarization combination that selectively probes chiral molecular structures. By using frequencies far detuned from electronic resonances, we probe the chiral macromolecular structures with high surface specificity. The phase of the sum-frequency light generated by the chiral molecules is determined using heterodyne detection. With this approach, we can distinguish right-handed and left-handed helical peptides at a water-air interface. We thus show that heterodyne-detected VSFG is sensitive to the absolute configuration of complex, interfacial macromolecules and has the potential to determine the absolute configuration of enantiomers at interfaces.

  2. Probing the site-dependent Kondo response of nanostructured graphene with organic molecules.

    Science.gov (United States)

    Garnica, Manuela; Stradi, Daniele; Calleja, Fabián; Barja, Sara; Díaz, Cristina; Alcamí, Manuel; Arnau, Andrés; Vázquez de Parga, Amadeo L; Martín, Fernando; Miranda, Rodolfo

    2014-08-13

    TCNQ molecules are used as a sensitive probe for the Kondo response of the electron gas of a nanostructured graphene grown on Ru(0001) presenting a moiré pattern. All adsorbed molecules acquired an extra electron by charge transfer from the substrate, but only those adsorbed in the FCC-Top areas of the moiré show magnetic moment and Kondo resonance in the STS spectra. DFT calculations trace back this behavior to the existence of a surface resonance in the low areas of the graphene moiré, whose density distribution strongly depends on the stacking sequence of the moiré area and effectively quenches the magnetic moment for HCP-Top sites.

  3. Highly Charged Ion -- Molecule Collisions: a probe and a tool for studying complex systems

    Science.gov (United States)

    Adoui, L.; Rousseau, P.; Capron, M.; Maisonny, R.; Lawicki, A.; Domaracka, A.; Manil, B.; Mery, A.; Poully, J.-C.; Rangama, J.; Huber, B. A.; Lattouf, E.; Zettergren, H.; Johansson, H. A. B.; Seitz, F.; Rosen, S.; Schmidt, H. T.; Holm, A. I. S.; Cederquist, H.; Bari, S.; Hoekstra, R.; Schlatholter, T.; Alvarado, F.; Postma, J.

    2011-05-01

    It has already been demonstrated that collision with low energy Highly Charged Ions (HCI) provide a soft and efficient way to study the stability of complex systems. Indeed, such ions are known to remove electrons at large impact parameters resulting in a fast and gentle ionisation. We will present at this conference the different applications of these ions as: - they can be used to enlighten collision mechanisms viacompleteexperiments on fragmentation dynamics of small molecules; - they can act as a probe of the stability of the resulting charged species. We will illustrate this feature in the case of molecular clusters (for example in the case of Polycyclic Aromatic Hydrocarbons); - they can also be used, in a less conventional way, as a tool to form new bonds and induce the formation of even more complex molecules. Perspectives of this work will be discussed at the conference.

  4. Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules.

    Science.gov (United States)

    Leinen, Philipp; Green, Matthew F B; Esat, Taner; Wagner, Christian; Tautz, F Stefan; Temirov, Ruslan

    2015-01-01

    Controlled manipulation of single molecules is an important step towards the fabrication of single molecule devices and nanoscale molecular machines. Currently, scanning probe microscopy (SPM) is the only technique that facilitates direct imaging and manipulations of nanometer-sized molecular compounds on surfaces. The technique of hand-controlled manipulation (HCM) introduced recently in Beilstein J. Nanotechnol. 2014, 5, 1926-1932 simplifies the identification of successful manipulation protocols in situations when the interaction pattern of the manipulated molecule with its environment is not fully known. Here we present a further technical development that substantially improves the effectiveness of HCM. By adding Oculus Rift virtual reality goggles to our HCM set-up we provide the experimentalist with 3D visual feedback that displays the currently executed trajectory and the position of the SPM tip during manipulation in real time, while simultaneously plotting the experimentally measured frequency shift (Δf) of the non-contact atomic force microscope (NC-AFM) tuning fork sensor as well as the magnitude of the electric current (I) flowing between the tip and the surface. The advantages of the set-up are demonstrated by applying it to the model problem of the extraction of an individual PTCDA molecule from its hydrogen-bonded monolayer grown on Ag(111) surface.

  5. Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules

    Directory of Open Access Journals (Sweden)

    Philipp Leinen

    2015-11-01

    Full Text Available Controlled manipulation of single molecules is an important step towards the fabrication of single molecule devices and nanoscale molecular machines. Currently, scanning probe microscopy (SPM is the only technique that facilitates direct imaging and manipulations of nanometer-sized molecular compounds on surfaces. The technique of hand-controlled manipulation (HCM introduced recently in Beilstein J. Nanotechnol. 2014, 5, 1926–1932 simplifies the identification of successful manipulation protocols in situations when the interaction pattern of the manipulated molecule with its environment is not fully known. Here we present a further technical development that substantially improves the effectiveness of HCM. By adding Oculus Rift virtual reality goggles to our HCM set-up we provide the experimentalist with 3D visual feedback that displays the currently executed trajectory and the position of the SPM tip during manipulation in real time, while simultaneously plotting the experimentally measured frequency shift (Δf of the non-contact atomic force microscope (NC-AFM tuning fork sensor as well as the magnitude of the electric current (I flowing between the tip and the surface. The advantages of the set-up are demonstrated by applying it to the model problem of the extraction of an individual PTCDA molecule from its hydrogen-bonded monolayer grown on Ag(111 surface.

  6. Thermodynamics of the Sorption of Benzimidazoles on Octadecyl Silica Gel from Water-Methanol Eluents

    Science.gov (United States)

    Shafigulin, R. V.; Bulanova, A. V.

    2018-02-01

    The standard enthalpy and entropy component of transferring benzimidazoles from water-methanol solutions to surfaces of octadecyl silica gel are determined using reversed-phase high-performance liquid chromatography (RP HPLC). The dependences between the enthalpy and polarizability of the molecules of the studied benzimidazoles, the enthalpy and the entropy factor are studied, and the influence of the quantitative composition of the water-methanol solution on the enthalpy are studied.

  7. Charge Transport in Metal-Molecule-Metal Junctions Probed by Conducting Atomic Force Microscopy

    International Nuclear Information System (INIS)

    Lee, Min Hyung; Song, Hyunwook

    2013-01-01

    We have demonstrated a proof of intrinsic charge transport properties in alkanedithiol molecular junctions using a multiprobe approach combining a variety of transport techniques. The temperature-independent I(V) behavior and the correct exponential decay of conductance with respect to molecular length shows that the dominant charge transport mechanism is off-resonant tunneling. Length-dependent TVS measurements for the saturated alkane-dithiol series indicate that we did indeed probe a molecular system with CAFM. These results can provide stringent criteria to establish a valid molecular transport junction via a probabilistic measurement technique. In this study, we report a study of charge transport in alkanedithiol SAMs formed in metal-molecule-metal junctions using CAFM in combination with a variety of molecular transport techniques including temperature-and length-variable transport measurements and transition voltage spectroscopy. The main goal of this study is to probe the intrinsic transport properties of component molecules using CAFM, but not parasitic or defect-related effects

  8. Infrared-pump-x-ray-probe spectroscopy of vibrationally excited molecules

    Science.gov (United States)

    Ignatova, Nina; da Cruz, Vinícius V.; Couto, Rafael C.; Ertan, Emilie; Odelius, Michael; Ågren, Hans; Guimarães, Freddy F.; Zimin, Andrei; Polyutov, Sergey P.; Gel'mukhanov, Faris; Kimberg, Victor

    2017-04-01

    We develop a theory of infrared (IR)-pump-x-ray-probe spectroscopy for molecular studies. We illustrate advantages of the proposed scheme by means of numerical simulations employing a vibrational wave packet technique applied to x-ray absorption and resonant inelastic x-ray scattering (RIXS) spectra of the water molecule vibrationally excited by a preceding IR field. The promotion of the vibrationally excited molecule to the dissociative 1 a1-14 a1 and bound 1 a1-12 b2 core-excited states with qualitatively different shapes of the potential energy surfaces creates nuclear wave packets localized along and between the OH bonds, respectively. The projection of these wave packets on the final vibrational states, governed by selection and propensity rules, results in spatial selectivity of RIXS sensitive to the initial vibrationally excited state, which makes it possible to probe selectively the ground state properties along different modes. In addition, we propose to use RIXS as a tool to study x-ray absorption from a selected vibrational level of the ground state when the spectral resolution is sufficiently high to resolve vibrational overtones. The proposed technique has potential applications for advanced mapping of multidimensional potential energy surfaces of ground and core-excited molecular states, for symmetry-resolved spectroscopy, and for steering chemical reactions.

  9. Probing Protein Multidimensional Conformational Fluctuations by Single-Molecule Multiparameter Photon Stamping Spectroscopy

    Science.gov (United States)

    2015-01-01

    Conformational motions of proteins are highly dynamic and intrinsically complex. To capture the temporal and spatial complexity of conformational motions and further to understand their roles in protein functions, an attempt is made to probe multidimensional conformational dynamics of proteins besides the typical one-dimensional FRET coordinate or the projected conformational motions on the one-dimensional FRET coordinate. T4 lysozyme hinge-bending motions between two domains along α-helix have been probed by single-molecule FRET. Nevertheless, the domain motions of T4 lysozyme are rather complex involving multiple coupled nuclear coordinates and most likely contain motions besides hinge-bending. It is highly likely that the multiple dimensional protein conformational motions beyond the typical enzymatic hinged-bending motions have profound impact on overall enzymatic functions. In this report, we have developed a single-molecule multiparameter photon stamping spectroscopy integrating fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic approach enables simultaneous observations of both FRET-related site-to-site conformational dynamics and molecular rotational (or orientational) motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have further observed wide-distributed rotational flexibility along orientation coordinates by recording fluorescence anisotropy and simultaneously identified multiple intermediate conformational states along FRET coordinate by monitoring time-dependent donor lifetime, presenting a whole picture of multidimensional conformational dynamics in the process of T4 lysozyme open-close hinge-bending enzymatic turnover motions under enzymatic reaction conditions. By analyzing the autocorrelation functions of both lifetime and anisotropy trajectories, we have also observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional conformational fluctuation dynamics, providing a fundamental

  10. Probing symmetry and symmetry breaking in resonant soft-x-ray fluorescence spectra of molecules

    Energy Technology Data Exchange (ETDEWEB)

    Glans, P.; Gunnelin, K.; Guo, J. [Uppsala Univ. (Sweden)] [and others

    1997-04-01

    Conventional non-resonant soft X-ray emission brings about information about electronic structure through its symmetry and polarization selectivity, the character of which is governed by simple dipole rules. For centro-symmetric molecules with the emitting atom at the inversion center these rules lead to selective emission through the required parity change. For the more common classes of molecules which have lower symmetry or for systems with degenerate core orbitals (delocalized over identical sites), it is merely the local symmetry selectivity that provides a probe of the local atomic orbital contribution to the molecular orbital. For instance, in X-ray spectra of first row species the intensities essentially map the p-density at each particular atomic site, and, in a molecular orbital picture, the contribution of the local p-type atomic orbitals in the LCAO description of the molecular orbitals. The situation is different for resonant X-ray fluorescence spectra. Here strict parity and symmetry selectivity gives rise to a strong frequency dependence for all molecules with an element of symmetry. In addition to symmetry selectivity the strong frequency dependence of resonant X-ray emission is caused by the interplay between the shape of a narrow X-ray excitation energy function and the lifetime and vibrational broadenings of the resonantly excited core states. This interplay leads to various observable effects, such as linear dispersion, resonance narrowing and emission line (Stokes) doubling. Also from the point of view of polarization selectivity, the resonantly excited X-ray spectra are much more informative than the corresponding non-resonant spectra. Examples are presented for nitrogen, oxygen, and carbon dioxide molecules.

  11. Small-Molecule Theranostic Probes: A Promising Future in Neurodegenerative Diseases

    Directory of Open Access Journals (Sweden)

    Suzana Aulić

    2013-01-01

    Full Text Available Prion diseases are fatal neurodegenerative illnesses, which include Creutzfeldt-Jakob disease in humans and scrapie, chronic wasting disease, and bovine spongiform encephalopathy in animals. They are caused by unconventional infectious agents consisting primarily of misfolded, aggregated, β-sheet-rich isoforms, denoted prions, of the physiological cellular prion protein (PrPC. Many lines of evidence suggest that prions (PrPSc act both as a template for this conversion and as a neurotoxic agent causing neuronal dysfunction and cell death. As such, PrPSc may be considered as both a neuropathological hallmark of the disease and a therapeutic target. Several diagnostic imaging probes have been developed to monitor cerebral amyloid lesions in patients with neurodegenerative disorders (such as Alzheimer’s disease, Parkinson’s disease, and prion disease. Examples of these probes are Congo red, thioflavin T, and their derivatives. We synthesized a series of styryl derivatives, denoted theranostics, and studied their therapeutic and/or diagnostic potentials. Here we review the salient traits of these small molecules that are able to detect and modulate aggregated forms of several proteins involved in protein misfolding diseases. We then highlight the importance of further studies for their practical implications in therapy and diagnostics.

  12. Quantum chemical assessment of benzimidazole derivatives as corrosion inhibitors.

    Science.gov (United States)

    Obayes, Hasan R; Alwan, Ghadah H; Alobaidy, Abdul Hameed Mj; Al-Amiery, Ahmed A; Kadhum, Abdul Amir H; Mohamad, Abu Bakar

    2014-03-27

    The majority of well-known inhibitors are organic compounds containing multiple bonds and heteroatoms, such as O, N or S, which allow adsorption onto the metal surface. These compounds can adsorb onto the metal surface and block active surface sites, reducing the rate of corrosion. A comparative theoretical study of three benzimidazole isomers, benzimidazole (BI), 2-methylbenzimidazole (2-CH3-BI), and 2-mercaptobenzimidazole (2-SH-BI), as corrosion inhibitors was performed using density functional theory (DFT) with the B3LYP functional basis set. Nitro and amino groups were selected for investigation as substituents of the three corrosion inhibitors. Nitration of the corrosion inhibitor molecules led to a decrease in inhibition efficiency, while reduction of the nitro group led to an increase in inhibition efficiency. These aminobenzimidazole isomers represent a significant improvement in the inhibition efficiency of corrosion inhibitor molecules.

  13. Infrared-x-ray pump-probe spectroscopy of the NO molecule

    International Nuclear Information System (INIS)

    Guimaraes, F.F.; Felicissimo, V.C.; Kimberg, V.; Gel'mukhanov, F.; Aagren, H.; Cesar, A.

    2005-01-01

    Two color infrared-x-ray pump-probe spectroscopy of the NO molecule is studied theoretically and numerically in order to obtain a deeper insight of the underlying physics and of the potential of this suggested technology. From the theoretical investigation a number of conclusions could be drawn: It is found that the phase of the infrared field strongly influences the trajectory of the nuclear wave packet, and hence, the x-ray spectrum. The trajectory experiences fast oscillations with the vibrational frequency with a modulation due to the anharmonicity of the potential. The dependences of the x-ray spectra on the delay time, the duration, and the shape of the pulses are studied in detail. It is shown that the x-ray spectrum keep memory about the infrared phase after the pump field left the system. This memory effect is sensitive to the time of switching-off the pump field and the Rabi frequency. The phase effect takes maximum value when the duration of the x-ray pulse is one-fourth of the infrared field period, and can be enhanced by a proper control of the duration and intensity of the pump pulse. The manifestation of the phase is different for oriented and disordered molecules and depends strongly on the intensity of the pump radiation

  14. Vibrational Probes: From Small Molecule Solvatochromism Theory and Experiments to Applications in Complex Systems.

    Science.gov (United States)

    Błasiak, Bartosz; Londergan, Casey H; Webb, Lauren J; Cho, Minhaeng

    2017-04-18

    The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies. To fully utilize IR probe functional groups for quantitative bioassays, a variety of biological and chemical techniques have been developed to site-specifically introduce vibrational probe groups into proteins and nucleic acids. These IR-probe-labeled biomolecules and chemically reactive systems are subject to linear and nonlinear vibrational spectroscopic investigations and provide information on the local electric field, conformational changes, site-site protein contacts, and/or function-defining features of biomolecules. A rapidly expanding library of data from such experiments requires an interpretive method with atom-level chemical accuracy. However, despite prolonged efforts to develop an all-encompassing theory for describing vibrational solvatochromism and electrochromism as well as dynamic fluctuations of instantaneous vibrational frequencies, purely empirical and highly approximate theoretical models have often been used to interpret experimental results. They are, in many cases, based on the simple assumption that the vibrational frequency of an IR reporter is solely dictated by electric potential or field distribution around the vibrational chromophore. Such simplified description of vibrational solvatochromism generally referred to as

  15. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    Energy Technology Data Exchange (ETDEWEB)

    Karayel, A., E-mail: matchlessjimmy@163.com, E-mail: yccaoh@hotmail.com; Özbey, S. [Hacettepe University, Physics Engineering Department (Turkey); Ayhan-Kılcıgil, G.; Kuş, C. [Ankara University, Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Turkey)

    2015-12-15

    The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

  16. In Silico Mechanistic Profiling to Probe Small Molecule Binding to Sulfotransferases

    Science.gov (United States)

    Martiny, Virginie Y.; Carbonell, Pablo; Lagorce, David; Villoutreix, Bruno O.; Moroy, Gautier; Miteva, Maria A.

    2013-01-01

    Drug metabolizing enzymes play a key role in the metabolism, elimination and detoxification of xenobiotics, drugs and endogenous molecules. While their principal role is to detoxify organisms by modifying compounds, such as pollutants or drugs, for a rapid excretion, in some cases they render their substrates more toxic thereby inducing severe side effects and adverse drug reactions, or their inhibition can lead to drug–drug interactions. We focus on sulfotransferases (SULTs), a family of phase II metabolizing enzymes, acting on a large number of drugs and hormones and showing important structural flexibility. Here we report a novel in silico structure-based approach to probe ligand binding to SULTs. We explored the flexibility of SULTs by molecular dynamics (MD) simulations in order to identify the most suitable multiple receptor conformations for ligand binding prediction. Then, we employed structure-based docking-scoring approach to predict ligand binding and finally we combined the predicted interaction energies by using a QSAR methodology. The results showed that our protocol successfully prioritizes potent binders for the studied here SULT1 isoforms, and give new insights on specific molecular mechanisms for diverse ligands’ binding related to their binding sites plasticity. Our best QSAR models, introducing predicted protein-ligand interaction energy by using docking, showed accuracy of 67.28%, 78.00% and 75.46%, for the isoforms SULT1A1, SULT1A3 and SULT1E1, respectively. To the best of our knowledge our protocol is the first in silico structure-based approach consisting of a protein-ligand interaction analysis at atomic level that considers both ligand and enzyme flexibility, along with a QSAR approach, to identify small molecules that can interact with II phase dug metabolizing enzymes. PMID:24039991

  17. In silico mechanistic profiling to probe small molecule binding to sulfotransferases.

    Directory of Open Access Journals (Sweden)

    Virginie Y Martiny

    Full Text Available Drug metabolizing enzymes play a key role in the metabolism, elimination and detoxification of xenobiotics, drugs and endogenous molecules. While their principal role is to detoxify organisms by modifying compounds, such as pollutants or drugs, for a rapid excretion, in some cases they render their substrates more toxic thereby inducing severe side effects and adverse drug reactions, or their inhibition can lead to drug-drug interactions. We focus on sulfotransferases (SULTs, a family of phase II metabolizing enzymes, acting on a large number of drugs and hormones and showing important structural flexibility. Here we report a novel in silico structure-based approach to probe ligand binding to SULTs. We explored the flexibility of SULTs by molecular dynamics (MD simulations in order to identify the most suitable multiple receptor conformations for ligand binding prediction. Then, we employed structure-based docking-scoring approach to predict ligand binding and finally we combined the predicted interaction energies by using a QSAR methodology. The results showed that our protocol successfully prioritizes potent binders for the studied here SULT1 isoforms, and give new insights on specific molecular mechanisms for diverse ligands' binding related to their binding sites plasticity. Our best QSAR models, introducing predicted protein-ligand interaction energy by using docking, showed accuracy of 67.28%, 78.00% and 75.46%, for the isoforms SULT1A1, SULT1A3 and SULT1E1, respectively. To the best of our knowledge our protocol is the first in silico structure-based approach consisting of a protein-ligand interaction analysis at atomic level that considers both ligand and enzyme flexibility, along with a QSAR approach, to identify small molecules that can interact with II phase dug metabolizing enzymes.

  18. Laser assisted anticancer activity of benzimidazole based metal organic nanoparticles.

    Science.gov (United States)

    Praveen, P A; Ramesh Babu, R; Balaji, P; Murugadas, A; Akbarsha, M A

    2018-03-01

    Recent studies showed that the photothermal therapy can be effectively used for the targeted cancerous cells destruction. Hence, in the present study, benzimidazole based metal organic complex nanoparticles, dichloro cobalt(II) bis-benzimidazole (Co-BMZ) and dichloro copper(II) bis-benzimidazole (Cu-BMZ), were synthesized by reprecipitation method and their anti-cancer activity by means of photothermal effect has been studied. Transmission electron microscopy analysis shows that the particle size of Cu-BMZ is ∼100 nm and Co-BMZ is in the range between 100 and 400 nm. Zeta potential analysis ensures the stability of the synthesized nanoparticles. It is found that the nonlinear absorption of the nanoparticles increases with increase in laser power intensity. Phototoxicity of human lung cancer (A549) and the normal mouse embryonic fibroblast (NIH-3T3) cells was studied using a 650 nm laser. Even though both the cell lines were affected by laser irradiation, A549 cells show higher cell destruction and lower IC 50 values than the normal cells. Docking studies were used to analyse the interaction site and the results showed that the Cu-BMZ molecules have higher dock score than the Co-BMZ molecules. The obtained results indicate that Cu-BMZ samples have lesser particle size, higher nonlinear absorption and higher interaction energy than the Co-BMZ samples. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Single molecule mapping of the optical field distribution of probes for near-field microscopy

    NARCIS (Netherlands)

    Veerman, J.A.; Garcia Parajo, M.F.; Kuipers, L.; van Hulst, N.F.

    1999-01-01

    The most difficult task in near-field scanning optical microscopy (NSOM) is to make a high quality subwavelength aperture probe, Recently we have developed high definition NSOM probes by focused ion beam (FIB) milling. These probes have a higher brightness, better polarization characteristics,

  20. Benzimidazoles diminish ERE transcriptional activity and cell growth in breast cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Payton-Stewart, Florastina [Department of Chemistry, College of Arts and Sciences, Xavier University of Louisiana, New Orleans, LA (United States); Tilghman, Syreeta L. [Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA (United States); Williams, LaKeisha G. [Division of Clinical and Administrative Sciences, College of Pharmacy Xavier University of Louisiana, New Orleans, LA (United States); Winfield, Leyte L., E-mail: lwinfield@spelman.edu [Department of Chemistry, Spelman College, Atlanta, GA (United States)

    2014-08-08

    Highlights: • The methyl-substituted benzimidazole was more effective at inhibiting growth in MDA-MB 231 cells. • The naphthyl-substituted benzimidazole was more effective at inhibiting growth in MCF-7 cells than ICI. • The benzimidazole molecules demonstrated a dose-dependent reduction in ERE transcriptional activity. • The benzimidazole molecules had binding mode in ERα and ERβ comparable to that of the co-crystallized ligand. - Abstract: Estrogen receptors (ERα and ERβ) are members of the nuclear receptor superfamily. They regulate the transcription of estrogen-responsive genes and mediate numerous estrogen related diseases (i.e., fertility, osteoporosis, cancer, etc.). As such, ERs are potentially useful targets for developing therapies and diagnostic tools for hormonally responsive human breast cancers. In this work, two benzimidazole-based sulfonamides originally designed to reduce proliferation in prostate cancer, have been evaluated for their ability to modulate growth in estrogen dependent and independent cell lines (MCF-7 and MDA-MB 231) using cell viability assays. The molecules reduced growth in MCF-7 cells, but differed in their impact on the growth of MDA-MB 231 cells. Although both molecules reduced estrogen response element (ERE) transcriptional activity in a dose dependent manner, the contrasting activity in the MDA-MB-231 cells seems to suggest that the molecules may act through alternate ER-mediated pathways. Further, the methyl analog showed modest selectivity for the ERβ receptor in an ER gene expression array panel, while the naphthyl analog did not significantly alter gene expression. The molecules were docked in the ligand binding domains of the ERα-antagonist and ERβ-agonist crystal structures to evaluate the potential of the molecules to interact with the receptors. The computational analysis complimented the results obtained in the assay of transcriptional activity and gene expression suggesting that the molecules

  1. 1-[2,2-Bis(1,3-benzimidazol-1-ylmethyl-3-bromopropyl]-1,3-benzimidazole

    Directory of Open Access Journals (Sweden)

    Tai-Bao Wei

    2011-07-01

    Full Text Available The title compound, C26H23BrN6, has been synthesized as a potential ligand for the construction of metal–organic frameworks. The three benzimidazolyl groups present three potential coordination nodes. The dihedral angles between the benzimidazole ring systems are 74.03 (10, 66.49 (9 and 74.09 (9°. The structure contains large voids, which contain highly disordered solvent molecules that may be CH3CH2OH. Since the solvent molecules could not be located, the PLATON/SQUEEZE procedure [Spek (2009. Acta Cryst. D65, 148–155] was used.

  2. Theoretical Investigation of Dynamic Properties of Magnetic Molecule Systems as Probed by NMR and Pulsed Fields Experiments

    Energy Technology Data Exchange (ETDEWEB)

    Rousochatzakis, Ioannis [Iowa State Univ., Ames, IA (United States)

    2005-12-17

    The field of molecular magnetism[l-6] has become a subject of intense theoretical and experimental interest and has rapidly evolved during the last years. This inter-disciplinary field concerns magnetic systems at the molecular or "nanoscopic" level, whose realization has become feasible due to recent advances in the field of chemical synthesis. The present theoretical work provides a first step towards exploiting the possibilities that are offered by probing magnetic molecules using external magnetic fields with high sweep rates. These probes, apart for providing information specific to magnetic molecules, offer the possibility of conducting a detailed study of the relaxational behavior of interacting spin systems as a result of their coupling with a "heat bath" and in particular the excitations of the host lattice. Development of a broad theoretical framework for dealing with relaxational phenomena induced by dynamical magnetic fields is indeed a worthy goal.

  3. Probing the local environment of a single OPE3 molecule using inelastic tunneling electron spectroscopy

    NARCIS (Netherlands)

    Frisenda, R.; Perrin, M.L.; Van der Zant, H.S.J.

    2015-01-01

    We study single-molecule oligo(phenylene ethynylene)dithiol junctions by means of inelastic electron tunneling spectroscopy (IETS). The molecule is contacted with gold nano-electrodes formed with the mechanically controllable break junction technique. We record the IETS spectrum of the molecule from

  4. Synthesis of Some Benzimidazole-substituted Benzotriazoles

    African Journals Online (AJOL)

    NJD

    2-Alkylsubstituted benzimidazoles (3a–h) were prepared from the acid-catalyzed reaction of 4-methyl-1,2-phenylenediamine with corresponding carboxylic acids. Addition of these benzimidazoles to N-chloromethylbenzotriazole in the presence of sodium amide under reflux conditions gave the novel ...

  5. Probing the local environment of a single OPE3 molecule using inelastic tunneling electron spectroscopy.

    Science.gov (United States)

    Frisenda, Riccardo; Perrin, Mickael L; van der Zant, Herre S J

    2015-01-01

    We study single-molecule oligo(phenylene ethynylene)dithiol junctions by means of inelastic electron tunneling spectroscopy (IETS). The molecule is contacted with gold nano-electrodes formed with the mechanically controllable break junction technique. We record the IETS spectrum of the molecule from direct current measurements, both as a function of time and electrode separation. We find that for fixed electrode separation the molecule switches between various configurations, which are characterized by different IETS spectra. Similar variations in the IETS signal are observed during atomic rearrangements upon stretching of the molecular junction. Using quantum chemistry calculations, we identity some of the vibrational modes which constitute a chemical fingerprint of the molecule. In addition, changes can be attributed to rearrangements of the local molecular environment, in particular at the molecule-electrode interface. This study shows the importance of taking into account the interaction with the electrodes when describing inelastic contributions to transport through single-molecule junctions.

  6. Probing the local environment of a single OPE3 molecule using inelastic tunneling electron spectroscopy

    Directory of Open Access Journals (Sweden)

    Riccardo Frisenda

    2015-12-01

    Full Text Available We study single-molecule oligo(phenylene ethynylenedithiol junctions by means of inelastic electron tunneling spectroscopy (IETS. The molecule is contacted with gold nano-electrodes formed with the mechanically controllable break junction technique. We record the IETS spectrum of the molecule from direct current measurements, both as a function of time and electrode separation. We find that for fixed electrode separation the molecule switches between various configurations, which are characterized by different IETS spectra. Similar variations in the IETS signal are observed during atomic rearrangements upon stretching of the molecular junction. Using quantum chemistry calculations, we identity some of the vibrational modes which constitute a chemical fingerprint of the molecule. In addition, changes can be attributed to rearrangements of the local molecular environment, in particular at the molecule–electrode interface. This study shows the importance of taking into account the interaction with the electrodes when describing inelastic contributions to transport through single-molecule junctions.

  7. Effect of substituents on polarizability and hyperpolarizability values of benzimidazole metal complexes

    Energy Technology Data Exchange (ETDEWEB)

    Praveen, P. A.; Babu, R. Ramesh, E-mail: rampap2k@yahoo.co.in [Crystal Growth and Thin films Laboratory, Department of Physics, Bharathidasan University, Tiruchirappalli - 620 024, Tamilnadu (India)

    2016-05-23

    In this report, the polarizability and first and second order hyperpolarizability values of bis benzimidazole Zn(II)-2R and bis benzimidazole Cd(II)-2R complexes, with different electron donating moieties R (R= Cl, Br, I, Acetate) were calculated using time dependent Hartree-Fock (TDHF) formalism embedded in MOPAC2012 package. Further the role of substituents on polarizability and hyperpolarizability values is investigated for the first time by analyzing the frontier molecular orbitals of the complexes with respect to the electronegativity of the substituents. It is found that the increase in electronegativity of the substituents correspondingly increases the energy gap of the molecules, which in turn reduces the polarizability values of both Zn and Cd benzimidazole complexes. Similarly, increase in electronegativity reduces the electric quadrupole moments of both the metal complexes, which in turn reduces the hyperpolarizability values.

  8. Bis(1-benzyl-1H-benzimidazole-κN3dichloridozinc

    Directory of Open Access Journals (Sweden)

    Rachid Bouhfid

    2014-03-01

    Full Text Available In the title compound, [ZnCl2(C14H12N22], the ZnII atom exhibits a distorted tetrahedral coordination geometry involving two chloride anions and two N-atom donors from 1-benzyl-1H-benzimidazole ligands. In both ligands, the benzyl and benzimidazole rings are nearly perpendicular [dihedral angles = 81.7 (2 and 81.5 (2°]. The two benzimidazole systems are essentially planar [maximum deviations = 0.015 (3 and 0.020 (2 Å] and form a dihedral angle of 78.09 (8°. In the crystal, centrosymmetrically related molecules are linked by pairs of C—H...Cl hydrogen bonds into chains parallel to the a axis.

  9. Ionic conducting poly-benzimidazoles

    International Nuclear Information System (INIS)

    Jouanneau, J.

    2006-11-01

    Over the last years, many research works have been focused on new clean energy systems. Hydrogen fuel cell seems to be the most promising one. However, the large scale development of this technology is still limited by some key elements. One of them is the polymer electrolyte membrane 'Nafion' currently used, for which the ratio performance/cost is too low. The investigations we carried out during this thesis work are related to a new class of ionic conducting polymer, the sulfonated poly-benzimidazoles (sPBI). Poly-benzimidazoles (PBI) are aromatic heterocyclic polymers well-known for their excellent thermal and chemical stability. Ionic conduction properties are obtained by having strong acid groups (sulfonic acid SO 3 H) on the macromolecular structure. For that purpose, we first synthesized sulfonated monomers. Their poly-condensation with an appropriate non-sulfonated co-monomer yields to sPBI with sulfonation range from 0 to 100 per cent. Three different sPBI structures were obtained, and verified by appropriate analytical techniques. We also showed that the protocol used for the synthesis resulted in high molecular weights polymers. We prepared ionic conducting membrane by casting sPBI solutions on glass plates. Their properties of stability, water swelling and ionic conductivity were investigated. Surprisingly, the behaviour of sPBI was quite different from the other sulfonated aromatic polymers with same amount of SO 3 H, their stability was much higher, but their water swelling and ionic conductivity were quite low. We attributed these differences to strong ionic interactions between the sulfonic acid groups and the basic benzimidazole groups of our polymers. However, we managed to solve this problem synthesizing very highly sulfonated PBI, obtaining membranes with a good balance between all the properties necessary. (author)

  10. Probing force-induced unfolding intermediates of a single staphylococcal nuclease molecule and the effect of ligand binding

    International Nuclear Information System (INIS)

    Ishii, Takaaki; Murayama, Yoshihiro; Katano, Atsuto; Maki, Kosuke; Kuwajima, Kunihiro; Sano, Masaki

    2008-01-01

    Single-molecule manipulation techniques have given experimental access to unfolding intermediates of proteins that are inaccessible in conventional experiments. A detailed characterization of the intermediates is a challenging problem that provides new possibilities for directly probing the energy landscape of proteins. We investigated single-molecule mechanical unfolding of a small globular protein, staphylococcal nuclease (SNase), using atomic force microscopy. The unfolding trajectories of the protein displayed sub-molecular and stochastic behavior with typical lengths corresponding to the size of the unfolded substructures. Our results support the view that the single protein unfolds along multiple pathways as suggested in recent theoretical studies. Moreover, we found the drastic change, caused by the ligand and inhibitor bindings, in the mechanical unfolding dynamics

  11. Voltammetric Determination of a Benzimidazole Anthelmintic Mixture ...

    African Journals Online (AJOL)

    2002-10-17

    Oct 17, 2002 ... KEYWORDS. Electrochemistry, square-wave voltammetry, benzimidazole anthelmintics, poly(3-methylthiophene) electrode. 1. Introduction .... electrode and. (2) unmodified electrode. A, fenbendazole; B, mebendazole, C, oxibendazole, and D, thiabendazole. Arrows indicate the direction of potential scan.

  12. Quinoline Fluorescent Probes for Zinc - from Diagnostic to Therapeutic Molecules in Treating Neurodegenerative Diseases.

    Science.gov (United States)

    Czaplinska, Barbara; Spaczynska, Ewelina; Musiol, Robert

    2018-01-01

    Fluorescent compounds had gained strong attention due to their wide and appealing applications. Microscopic techniques and visualization are good examples among others. Introduction of fluorescent dyes into microbiology opens the possibility to observe tissues, organisms or organelle with exceptional sensitivity and resolution. Probes for detection of biologically relevant metals as zinc, iron or copper seems to be particularly important for drug design and pharmaceutical sciences. Quinoline derivatives are well known for their good metal affinity and wide spectrum of biological activity. In this regard, molecular sensors built on this scaffold may be useful not only as analytical but also as therapeutic agents. In the present review, application of quinoline moiety in designing of novel fluorescent probes for zinc is presented and discussed. Zinc cations are relevant for vast majority of processes and recently attract a great deal of attention for their role in neurodegenerative diseases. Compounds interacting with Zn2+ may be used for early diagnosis of such disorders, for example the Alzheimer disease. Quinoline-based zinc probes may exert some beneficial role in organism acting as theranostic agents. First preliminary drugs for Alzheimer therapy that are based on quinoline moiety are good example of this trend. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  13. Biological Activity and Molecular Structures of Bis(benzimidazole and Trithiocyanurate Complexes

    Directory of Open Access Journals (Sweden)

    Pavel Kopel

    2015-06-01

    Full Text Available 1-(1H-Benzimidazol-2-yl-N-(1H-benzimidazol-2-ylmethylmethanamine (abb and 2-(1H-benzimidazol-2-ylmethylsulfanylmethyl-1H-benzimidazole (tbb have been prepared and characterized by elemental analysis. These bis(benzimidazoles have been further used in combination with trithiocyanuric acid for the preparation of complexes. The crystal and molecular structures of two of them have been solved. Each nickel atom in the structure of trinuclear complex [Ni3(abb3(H2O3(μ-ttc](ClO43·3H2O·EtOH (1, where ttcH3 = trithiocyanuric acid, is coordinated with three N atoms of abb, the N,S donor set of ttc anion and an oxygen of a water molecule. The crystal of [(tbbH2(ttcH22(ttcH3(H2O] (2 is composed of a protonated bis(benzimidazole, two ttcH2 anions, ttcH3 and water. The structure is stabilized by a network of hydrogen bonds. These compounds were primarily synthesized for their potential antimicrobial activity and hence their possible use in the treatment of infections caused by bacteria or yeasts (fungi. The antimicrobial and antifungal activity of the prepared compounds have been evaluated on a wide spectrum of bacterial and yeast strains and clinical specimens isolated from patients with infectious wounds and the best antimicrobial properties were observed in strains after the use of ligand abb and complex 1, when at least 80% growth inhibition was achieved.

  14. How to probe transverse magnetic anisotropy of a single-molecule magnet by electronic transport?

    Science.gov (United States)

    Misiorny, M.; Burzuri, E.; Gaudenzi, R.; Park, K.; Leijnse, M.; Wegewijs, M.; Paaske, J.; Cornia, A.; van der Zant, H.

    We propose an approach for in-situ determination of the transverse magnetic anisotropy (TMA) of an individual molecule by electronic transport measurements, see Phys. Rev. B 91, 035442 (2015). We study a Fe4 single-molecule magnet (SMM) captured in a gateable junction, a unique tool for addressing the spin in different redox states of a molecule. We show that, due to mixing of the spin eigenstates of the SMM, the TMA significantly manifests itself in transport. We predict and experimentally observe the pronounced intensity modulation of the Coulomb peak amplitude with the magnetic field in the linear-response transport regime, from which the TMA parameter E can be estimated. Importantly, the method proposed here does not rely on the small induced tunnelling effects and, hence, works well at temperatures and electron tunnel broadenings by far exceeding the tunnel splittings and even E itself. We deduce that the TMA for a single Fe4 molecule captured in a junction is substantially larger than the bulk value. Work supported by the Polish Ministry of Science and Education as `Iuventus Plus' project (IP2014 030973) in years 2015-2016.

  15. Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET

    NARCIS (Netherlands)

    Hohlbein, J.; Kapanidis, A.N.

    2016-01-01

    Monitoring conformational changes in DNA polymerases using single-molecule Förster resonance energy transfer (smFRET) has provided new tools for studying fidelity-related mechanisms that promote the rejection of incorrect nucleotides before DNA synthesis. In addition to the previously known open

  16. RNA structure probing : biochemical structure analysis of autoimmune-related RNA molecules

    NARCIS (Netherlands)

    Teunissen, A.W.M.

    1999-01-01

    Next to the well known messenger, ribosomal and transfer RNAs, a large number of small structural RNA molecules exist. These RNAs are bound to proteins, forming ribonucleoprotein particles (RNPs). RNPs are often targets for autoantibodies occurring in an autoimmune disease.Chapter 1 introduces

  17. Real-time spectral interferometry probes the internal dynamics of femtosecond soliton molecules.

    Science.gov (United States)

    Herink, G; Kurtz, F; Jalali, B; Solli, D R; Ropers, C

    2017-04-07

    Solitons, particle-like excitations ubiquitous in many fields of physics, have been shown to exhibit bound states akin to molecules. The formation of such temporal soliton bound states and their internal dynamics have escaped direct experimental observation. By means of an emerging time-stretch technique, we resolve the evolution of femtosecond soliton molecules in the cavity of a few-cycle mode-locked laser. We track two- and three-soliton bound states over hundreds of thousands of consecutive cavity roundtrips, identifying fixed points and periodic and aperiodic molecular orbits. A class of trajectories acquires a path-dependent geometrical phase, implying that its dynamics may be topologically protected. These findings highlight the importance of real-time detection in resolving interactions in complex nonlinear systems, including the dynamics of soliton bound states, breathers, and rogue waves. Copyright © 2017, American Association for the Advancement of Science.

  18. Probing strong-field electron-nuclear dynamics of polyatomic molecules using proton motion

    International Nuclear Information System (INIS)

    Markevitch, Alexei N.; Smith, Stanley M.; Levis, Robert J.; Romanov, Dmitri A.

    2007-01-01

    Proton ejection during Coulomb explosion is studied for several structure-related organic molecules (anthracene, anthraquinone, and octahydroanthracene) subjected to 800 nm, 60 fs laser pulses at intensities from 0.50 to 4.0x10 14 W cm -2 . The proton kinetic energy distributions are found to be markedly structure specific. The distributions are bimodal for anthracene and octahydroanthracene and trimodal for anthraquinone. Maximum (cutoff) energies of the distributions range from 50 eV for anthracene to 83 eV for anthraquinone. The low-energy mode (∼10 eV) is most pronounced in octahydroanthracene. The dependence of the characteristic features of the distributions on the laser intensity provides insights into molecular specificity of such strong-field phenomena as (i) nonadiabatic charge localization and (ii) field-mediated restructuring of polyatomic molecules polarized by a strong laser field

  19. Mapping the electrostatic force field of single molecules from high-resolution scanning probe images

    Czech Academy of Sciences Publication Activity Database

    Hapala, Prokop; Švec, Martin; Stetsovych, Oleksandr; van der Heijden, N.J.; Ondráček, Martin; van der Lit, J.; Mutombo, Pingo; Swart, I.; Jelínek, Pavel

    2016-01-01

    Roč. 7, May (2016), 1-8, č. článku 11560. ISSN 2041-1723 R&D Projects: GA MŠk LM2015087; GA ČR(CZ) GC14-16963J Institutional support: RVO:68378271 Keywords : generalized gradient approximation * submolecular resolution * tunneling microscope * chemical-structure * co molecules Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 12.124, year: 2016

  20. Probing the conductance superposition law in single-molecule circuits with parallel paths.

    Science.gov (United States)

    Vazquez, H; Skouta, R; Schneebeli, S; Kamenetska, M; Breslow, R; Venkataraman, L; Hybertsen, M S

    2012-10-01

    According to Kirchhoff's circuit laws, the net conductance of two parallel components in an electronic circuit is the sum of the individual conductances. However, when the circuit dimensions are comparable to the electronic phase coherence length, quantum interference effects play a critical role, as exemplified by the Aharonov-Bohm effect in metal rings. At the molecular scale, interference effects dramatically reduce the electron transfer rate through a meta-connected benzene ring when compared with a para-connected benzene ring. For longer conjugated and cross-conjugated molecules, destructive interference effects have been observed in the tunnelling conductance through molecular junctions. Here, we investigate the conductance superposition law for parallel components in single-molecule circuits, particularly the role of interference. We synthesize a series of molecular systems that contain either one backbone or two backbones in parallel, bonded together cofacially by a common linker on each end. Single-molecule conductance measurements and transport calculations based on density functional theory show that the conductance of a double-backbone molecular junction can be more than twice that of a single-backbone junction, providing clear evidence for constructive interference.

  1. Momentum mapping spectrometer for probing the fragmentation dynamics of molecules induced by keV electrons

    International Nuclear Information System (INIS)

    Singh, Raj; Bhatt, Pragya; Yadav, Namita; Shanker, R

    2011-01-01

    We describe a new experimental setup for studying the fragmentation dynamics of molecules induced by the impact of keV electrons using the well-known technique of recoil ion momentum spectroscopy. The apparatus consists of mainly a time- and position-sensitive multi-hit particle detector for ion analysis and a channel electron multiplier detector for detecting the ejected electrons. Different components of the setup and the relevant electronics for data acquisition are described in detail with their working principles. In order to verify the reliable performance of the setup, we have recorded the collision-induced ionic spectra of the CO 2 molecule by the impact of keV electrons. Information about the ion pairs of CO + :O + , C + :O + and O + :O + resulting from dissociative ionizing collisions of 20 and 26 keV electrons with a dilute gaseous target of CO 2 molecules has been obtained. Under conditions of the present experiment, the momentum resolutions of the spectrometer for the combined momenta of CO + and O + ions in the direction of the time-of-flight axis and perpendicular to the direction of an electron beam are found to be 10.0 ± 0.2 and 15.0 ± 0.3 au, respectively

  2. Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface.

    Science.gov (United States)

    Leinen, Philipp; Green, Matthew F B; Esat, Taner; Wagner, Christian; Tautz, F Stefan; Temirov, Ruslan

    2016-10-02

    Considering organic molecules as the functional building blocks of future nanoscale technology, the question of how to arrange and assemble such building blocks in a bottom-up approach is still open. The scanning probe microscope (SPM) could be a tool of choice; however, SPM-based manipulation was until recently limited to two dimensions (2D). Binding the SPM tip to a molecule at a well-defined position opens an opportunity of controlled manipulation in 3D space. Unfortunately, 3D manipulation is largely incompatible with the typical 2D-paradigm of viewing and generating SPM data on a computer. For intuitive and efficient manipulation we therefore couple a low-temperature non-contact atomic force/scanning tunneling microscope (LT NC-AFM/STM) to a motion capture system and fully immersive virtual reality goggles. This setup permits "hand controlled manipulation" (HCM), in which the SPM tip is moved according to the motion of the experimenter's hand, while the tip trajectories as well as the response of the SPM junction are visualized in 3D. HCM paves the way to the development of complex manipulation protocols, potentially leading to a better fundamental understanding of nanoscale interactions acting between molecules on surfaces. Here we describe the setup and the steps needed to achieve successful hand-controlled molecular manipulation within the virtual reality environment.

  3. Modeling single molecule junction mechanics as a probe of interface bonding

    Science.gov (United States)

    Hybertsen, Mark S.

    2017-03-01

    Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. A set of exemplary model junction structures has been analyzed using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond to the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N-Au and S-Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor

  4. Probing non polar interstellar molecules through their protonated form: Detection of protonated cyanogen (NCCNH+).

    Science.gov (United States)

    Agúndez, M; Cernicharo, J; de Vicente, P; Marcelino, N; Roueff, E; Fuente, A; Gerin, M; Guélin, M; Albo, C; Barcia, A; Barbas, L; Bolaño, R; Colomer, F; Diez, M C; Gallego, J D; Gómez-González, J; López-Fernández, I; López-Fernández, J A; López-Pérez, J A; Malo, I; Serna, J M; Tercero, F

    2015-07-01

    Cyanogen (NCCN) is the simplest member of the series of dicyanopolyynes. It has been hypothesized that this family of molecules can be important constituents of interstellar and circumstellar media, although the lack of a permanent electric dipole moment prevents its detection through radioastronomical techniques. Here we present the first solid evidence of the presence of cyanogen in interstellar clouds through the detection of its protonated form toward the cold dark clouds TMC-1 and L483. Protonated cyanogen (NCCNH + ) has been identified through the J = 5 - 4 and J = 10 - 9 rotational transitions using the 40m radiotelescope of Yebes and the IRAM 30m telescope. We derive beam averaged column densities for NCCNH + of (8.6 ± 4.4) × 10 10 cm -2 in TMC-1 and (3.9 ± 1.8) × 10 10 cm -2 in L483, which translate to fairly low fractional abundances relative to H 2 , in the range (1-10) × 10 -12 . The chemistry of protonated molecules in dark clouds is discussed, and it is found that, in general terms, the abundance ratio between the protonated and non protonated forms of a molecule increases with increasing proton affinity. Our chemical model predicts an abundance ratio NCCNH + /NCCN of ~ 10 -4 , which implies that the abundance of cyanogen in dark clouds could be as high as (1-10) × 10 -8 relative to H 2 , i.e., comparable to that of other abundant nitriles such as HCN, HNC, and HC 3 N.

  5. The small molecule probe PT-Yellow labels the renal proximal tubules in zebrafish.

    Science.gov (United States)

    Sander, Veronika; Patke, Shantanu; Sahu, Srikanta; Teoh, Chai Lean; Peng, Zhenzhen; Chang, Young-Tae; Davidson, Alan J

    2015-01-01

    We report the development of a small fluorescent molecule, BDNCA3-D2, herein referred to as PT-Yellow. Soaking zebrafish embryos in PT-Yellow or intraperitoneal injection into adults results in non-toxic in vivo fluorescent labeling of the renal proximal tubules, the major site of blood filtrate reabsorption and a common target of injury in acute kidney injury. We demonstrate the applicability of this new compound as a rapid and simple readout for zebrafish kidney filtration and proximal tubule reabsorption function.

  6. Solvent additive effects on small molecule crystallization in bulk heterojunction solar cells probed during spin casting

    KAUST Repository

    Pérez, Louis A.

    2013-09-04

    Solvent additive processing can lead to drastic improvements in the power conversion efficiency (PCE) in solution processable small molecule (SPSM) bulk heterojunction solar cells. In situ grazing incidence wide-angle X-ray scattering is used to investigate the kinetics of crystallite formation during and shortly after spin casting. The additive is shown to have a complex effect on structural evolution invoking polymorphism and enhanced crystalline quality of the donor SPSM. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Fast sensitive amplifier for two-probe conductance measurements in single molecule break junctions

    Science.gov (United States)

    Johnson, Tyler K.; Ivie, Jeffrey A.; Jaruvang, Jason; Monti, Oliver L. A.

    2017-03-01

    We demonstrate an amplifier based on the Wheatstone bridge designed specifically for use in single molecule break junctions. This amplifier exhibits superior performance due to its large bandwidth, flat frequency response, and high sensitivity. The amplifier is capable of measuring conductance values from 102 to 10-6G0 (G0 = 2e2/h), while maintaining a bandwidth in excess of 20 kHz, and shows remarkable resolution in the molecular conductance regime of 10-2 to 10-5 G0.

  8. Dissociative electron attachment to CO molecule probed by velocity slice imaging technique

    Science.gov (United States)

    Nag, Pamir; Nandi, Dhananjay

    2017-11-01

    We have studied dissociative electron attachment to CO molecule using the well-established velocity slice imaging spectrometer. We have conclusively determined the symmetries of the TNI states involved in both the channels producing O‑ ions. In contrast to a recent report, we observed additional forwards lobes in the angular distribution data and we claim there is no need to invoke coherent interference between different states as introduced previously. Recent R-matrix calculations and momentum imaging study by other groups strongly support our claims.

  9. A Fluorogenic Probe for the Catalyst-Free Detection of Azide-Tagged Molecules

    Science.gov (United States)

    Friscourt, Frédéric; Fahrni, Christoph J.; Boons, Geert-Jan

    2012-01-01

    Fluorogenic reactions in which non- or weakly-fluorescent reagents produce highly fluorescent products can be exploited to detect a broad range of compounds including biomolecules and materials. We describe a modified dibenzocyclooctyne that under catalyst-free conditions undergoes fast strain-promoted cycloadditions with azides to yield strongly fluorescent triazoles. The cycloaddition products are more than 1000-fold brighter compared to the starting cyclooctyne, exhibit large Stokes shift, and can be excited above 350 nm, which is required for many applications. Quantum mechanical calculations indicate that the fluorescence increase upon triazole formation is due to large differences in oscillator strengths of the S0 S1 transitions in the planar C2v-symmetric starting material compared to the symmetry-broken and non-planar cycloaddition products. The new fluorogenic probe was successfully employed for labeling of proteins modified by an azide moiety. PMID:23095037

  10. Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

    Science.gov (United States)

    Kuo, Tzu-Ling; Garcia-Manyes, Sergi; Li, Jingyuan; Barel, Itay; Lu, Hui; Berne, Bruce J; Urbakh, Michael; Klafter, Joseph; Fernández, Julio M

    2010-06-22

    The widely used Arrhenius equation describes the kinetics of simple two-state reactions, with the implicit assumption of a single transition state with a well-defined activation energy barrier DeltaE, as the rate-limiting step. However, it has become increasingly clear that the saddle point of the free-energy surface in most reactions is populated by ensembles of conformations, leading to nonexponential kinetics. Here we present a theory that generalizes the Arrhenius equation to include static disorder of conformational degrees of freedom as a function of an external perturbation to fully account for a diverse set of transition states. The effect of a perturbation on static disorder is best examined at the single-molecule level. Here we use force-clamp spectroscopy to study the nonexponential kinetics of single ubiquitin proteins unfolding under force. We find that the measured variance in DeltaE shows both force-dependent and independent components, where the force-dependent component scales with F(2), in excellent agreement with our theory. Our study illustrates a novel adaptation of the classical Arrhenius equation that accounts for the microscopic origins of nonexponential kinetics, which are essential in understanding the rapidly growing body of single-molecule data.

  11. Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET.

    Science.gov (United States)

    Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis

    2017-12-01

    Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. We have employed a DNA fragment with two NgoMIV recognition sites and a FRET dye pair such that upon protein-induced DNA looping the dyes are brought to close proximity resulting in a FRET signal. The dynamics of DNA-NgoMIV interactions proved to be heterogeneous, with individual smFRET trajectories exhibiting broadly different average looped state durations. Distinct types of the dynamics were attributed to different types of DNA-protein complexes, mediated either by one NgoMIV tetramer simultaneously bound to two specific sites ("slow" trajectories) or by semi-specific interactions of two DNA-bound NgoMIV tetramers ("fast" trajectories), as well as to conformational heterogeneity of individual NgoMIV molecules. © 2017 Wiley Periodicals, Inc.

  12. Virus-based surface patterning of biological molecules, probes, and inorganic materials.

    Science.gov (United States)

    Ahn, Suji; Jeon, Seongho; Kwak, Eun-A; Kim, Jong-Man; Jaworski, Justyn

    2014-10-01

    An essential requirement for continued technological advancement in many areas of biology, physics, chemistry, and materials science is the growing need to generate custom patterned materials. Building from recent achievements in the site-specific modification of virus for covalent surface tethering, we show in this work that stable 2D virus patterns can be generated in custom geometries over large area glass surfaces to yield templates of biological, biochemical, and inorganic materials in high density. As a nanomaterial building block, filamentous viruses have been extensively used in recent years to produce materials with interesting properties, owing to their ease of genetic and chemical modification. By utilizing un-natural amino acids generated at specific locations on the filamentous fd bacteriophage protein coat, surface immobilization is carried out on APTES patterned glass resulting in precise geometries of covalently linked virus material. This technique facilitated the surface display of a high density of virus that were labeled with biomolecules, fluorescent probes, and gold nanoparticles, thereby opening the possibility of integrating virus as functional components for surface engineering. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. From Sensors to Silencers: Quinoline- and Benzimidazole-Sulfonamides as Inhibitors for Zinc Proteases

    Science.gov (United States)

    2010-01-01

    Derived from the extensive work in the area of small molecule zinc(II) ion sensors, chelating fragment libraries of quinoline- and benzimidazole-sulfonamides have been prepared and screened against several different zinc(II)-dependent matrix metalloproteinases (MMPs). The fragments show impressive inhibition of these metalloenzymes and preferences for different MMPs based on the nature of the chelating group. The findings show that focused chelator libraries are a powerful strategy for the discovery of lead fragments for metalloprotein inhibition. PMID:20507095

  14. Ethyl 1-(2-hydroxyethyl-2-p-tolyl-1H-benzimidazole-5-carboxylate

    Directory of Open Access Journals (Sweden)

    Natarajan Arumugam

    2010-07-01

    Full Text Available The asymmetric unit of the title compound, C19H20N2O3, contains two molecules (A and B with slightly different orientations of the ethyl groups with respect to the attached carboxylate groups. Intramolecular C—H...O hydrogen bonds generate S(8 ring motifs in both molecules A and B. In each molecule, the benzimidazole ring system is essentially planar, with maximum deviations of 0.023 (1 and 0.020 (1 Å, respectively, for molecules A and B. The dihedral angle between the benzimidazole ring system and the phenyl ring is 37.34 (5° for molecule A and 42.42 (5° for molecule B. In the crystal, O—H...N and C—H...O hydrogen bonds link the molecules into [100] columns with a cross-section of two-molecule by two-molecule wide, and further stabilization is provided by weak C—H...π and π–π interactions [centroid separations = 3.5207 (7 and 3.6314 (8 Å].

  15. QSAR STUDY OF BENZIMIDAZOLE DERIVATIVES INHIBITION ON ...

    African Journals Online (AJOL)

    Preferred Customer

    The paper describes a quantitative structure-activity relationship (QSAR) study of IC50 values of benzimidazole ... neural network model is a fully-connected, feed forward back propagation network with a 5-4-1 architecture. Standard ... volume, molecular surface area, hydrophobicity (Log P), hydration energy and molecular.

  16. Probing the interactions of organic molecules, nanomaterials, and microbes with solid surfaces using quartz crystal microbalances: methodology, advantages, and limitations.

    Science.gov (United States)

    Huang, Rixiang; Yi, Peng; Tang, Yuanzhi

    2017-06-21

    Quartz crystal microbalances (QCMs) provide a new analytical opportunity and prospect to characterize many environmental processes at solid/liquid interfaces, thanks to their almost real-time measurement of physicochemical changes on their quartz sensor. This work reviews the applications of QCMs in probing the interactions of organic molecules, nanomaterials (NMs) and microbes with solid surfaces. These interfacial interactions are relevant to critical environmental processes such as biofilm formation, fate and transport of NMs, fouling in engineering systems and antifouling practices. The high sensitivity, real-time monitoring, and simultaneous frequency and dissipation measurements make QCM-D a unique technique that helps reveal the interaction mechanisms for the abovementioned processes (e.g., driving forces, affinity, kinetics, and the interplay between surface chemistry and solution chemistry). On the other hand, QCM measurement is nonselective and spatially-dependent. Thus, caution should be taken during data analysis and interpretation, and it is necessary to cross-validate the results using complementary information from other techniques for more quantitative and accurate interpretation. This review summarizes the general methodologies for collecting and analyzing raw QCM data, as well as for evaluating the associated uncertainties. It serves to help researchers gain deeper insights into the fundamentals and applications of QCMs, and provides new perspectives on future research directions.

  17. 2-(4-Hydroxyphenyl-1H-benzimidazol-3-ium chloride monohydrate

    Directory of Open Access Journals (Sweden)

    Jazmin E. González-Padilla

    2013-09-01

    Full Text Available The title molecular salt, C13H11N2O+·Cl−·H2O, crystallizes as a monohydrate. In the cation, the phenol and benzimidazole rings are almost coplanar, making a dihedral angle of 3.18 (4°. The chloride anion and benzimidazole cation are linked by two N+—H...Cl− hydrogen bonds, forming chains propagating along [010]. These chains are linked through O—H...Cl hydrogen bonds involving the water molecule and the chloride anion, which form a diamond core, giving rise to the formation of two-dimensional networks lying parallel to (10-2. Two π–π interactions involving the imidazolium ring with the benzene and phenol rings [centroid–centroid distances = 3.859 (3 and 3.602 (3 Å, respectively], contribute to this second dimension. A strong O—H...O hydrogen bond involving the water molecule and the phenol substituent on the benzimidazole unit links the networks, forming a three-dimensional structure.

  18. Orthorhombic polymorph of 4-[(1H-benzimidazol-1-ylmethyl]benzoic acid

    Directory of Open Access Journals (Sweden)

    Hai-Wei Kuai

    2011-11-01

    Full Text Available We reported recently the first polymorph of the title compound [Kuai & Cheng (2011a. Acta Cryst., E67, o2787]. A second polymorph of the title compound, C15H12N2O2, was unexpectedly obtained by the hydrothermal reaction of the title compound with manganese chloride in the presence of potassium hydroxide at 413 K. The benzimidazole ring system is almost planar, with a maximum deviation from the mean plane of 0.015 (2 Å. The benzimidazole and benzene rings are inclined at a dihedral angle of 79.00 (1°. In the crystal, adjacent molecules are connected through O—H...N hydrogen bonds into a one-dimensional chain along the [001] direction.

  19. Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.

    Directory of Open Access Journals (Sweden)

    Zach Hensel

    Full Text Available DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R and O(L (separated by 2.3 kb, mediated by the λ repressor CI (accession number P03034, play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.

  20. Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response

    Energy Technology Data Exchange (ETDEWEB)

    Crnolatac, Ivo; Rogan, Iva; Majić, Boris; Tomić, Sanja [Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb (Croatia); Deligeorgiev, Todor [Faculty of Chemistry and Pharmacy, University of Sofia (Bulgaria); Horvat, Gordan [Department of Physical Chemistry, Faculty of Science/Chemistry, Horvatovac 102A, HR-10000 Zagreb (Croatia); Makuc, Damjan; Plavec, Janez [Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana (Slovenia); EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, Ljubljana (Slovenia); Pescitelli, Gennaro [Department of Chemistry, University of Pisa, Via Moruzzi 13, Pisa (Italy); Piantanida, Ivo, E-mail: pianta@irb.hr [Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb (Croatia)

    2016-10-12

    Two small molecules showed intriguing properties of analytical multipurpose probes, whereby one chromophore gives different signal for many different DNA/RNA by application of several highly sensitive spectroscopic methods. Dyes revealed pronounced fluorescence ratiomeric differentiation between ds-AU-RNA, AT-DNA and GC-DNA in approximate order 10:8:1. Particularly interesting, dyes showed specific fluorimetric response for poly rA even at 10-fold excess of any other ss-RNA, and moreover such emission selectivity is preserved in multicomponent ss-RNA mixtures. The dyes also showed specific chiral recognition of poly rU in respect to the other ss-RNA by induced CD (ICD) pattern in visible range (400–500 nm), which was attributed to the dye-side-chain contribution to binding (confirmed by absence of any ICD band for reference compound lacking side-chain). Most intriguingly, minor difference in the side-chain attached to dye chromophore resulted in opposite sign of dye-ICD pattern, whereby differences in NMR NOESY contacts and proton chemical shifts between two dye/oligo rU complexes combined with MD simulations and CD calculations attributed observed bisignate ICD to the dimeric dye aggregate within oligo rU. - Highlights: • Novel dyes emit fluorescence only for poly rA even at high excess of all other ss-RNA. • Fluorescence response for AT-DNA is 8 times stronger than for GC-DNA. • Florescence induced by ds-RNA is 20% stronger that emission induced by ds-DNA. • Intrinsically non-chiral, dyes show strong and characteristic ICD response for poly rU.

  1. Design of a low-temperature plasma (LTP) probe with adjustable output temperature and variable beam diameter for the direct detection of organic molecules.

    Science.gov (United States)

    Martínez-Jarquín, Sandra; Winkler, Robert

    2013-03-15

    The direct detection of organic molecules by mass spectrometry requires ionization methods which are compatible with ambient conditions. A relatively new strategy is the use of a free low-temperature plasma beam for ionization. The objective is to design a safe and adjustable plasma beam to enable optimal ionization and desorption parameters for specific molecules. A plasma probe based on a dielectric barrier discharge was designed, where the plasma is guided through an internal second tube. This setup permits different beam diameter settings and the control of the plasma temperature. The ionization and desorption of pure organic compounds, as well as their direct detection from roasted coffee beans, were tested. The presented plasma probe provides improved safety with respect to arcing, ozone generation and electric shock, compared with conventional designs. The functionality of previously reported devices is expanded. A defined plasma diameter can be set by choosing the appropriate insert, while the input voltage controls the plasma temperature. The variation of measurement parameters enables the optimized direct detection of target compounds from roasted coffee beans, such as caffeine, guaiacol and vanillin. The presented low-temperature plasma probe allows the fine-tuning of ionization and desorption parameters, according to the target molecules. Possible applications include: (1) The ambient ionization and desorption of organic compounds with different volatility and (2) The direct analysis of food products such as roasted coffee beans. Copyright © 2013 John Wiley & Sons, Ltd.

  2. Simple, mild, and highly efficient synthesis of 2-substituted benzimidazoles and bis-benzimidazoles

    Energy Technology Data Exchange (ETDEWEB)

    Eren, Bilge, E-mail: bilge.eren@bilecik.edu.tr [Faculty of Science and Arts, Department of Chemistry, Bilecik Seyh Edebali University, (Turkey); Bekdemir, Yunus [Faculty of Science and Arts, Canik Basari University, Samsun (Turkey)

    2014-07-01

    A new convenient method for preparation of 2-substituted benzimidazoles and bis-benzimidazoles is presented. In this method, o-phenylenediamines were condensed with bisulfite adducts of various aldehydes and di-aldehydes under neat conditions by microwave heating. The results were also compared with results of synthesis by conventional heating under reflux. Structures of the products were confirmed by infrared, {sup 1}H- and {sup 13}C-NMR spectroscopy. Short reaction times, good yields, easy purification of products, and mild reaction conditions are the main advantages of this method. (author)

  3. Morphology, molecular dynamics and electric conductivity of carbohydrate polymer films based on alginic acid and benzimidazole.

    Science.gov (United States)

    Rachocki, Adam; Pogorzelec-Glaser, Katarzyna; Pawlaczyk, Czesław; Tritt-Goc, Jadwiga

    2011-12-13

    The present paper describes a preparation method and molecular investigations of new biodegradable proton-conducting carbohydrate polymer films based on alginic acid and benzimidazole. Electric conductivity was studied in a wide temperature range in order to check the potential application of these compounds as membranes for electrochemical devices. Compared to pure alginic acid powder or its film, the biodegradable film of alginic acid with an addition of benzimidazole exhibits considerably higher conductivity in the range above water boiling temperature (up to approximately 10(-3) S/cm at 473 K). Due to this important feature the obtained films can be considered as candidates for application in high-temperature electrochemical devices. The microscopic nature and mechanism of the conduction in alginate based materials were studied by proton nuclear magnetic resonance (NMR). The results show specific changes in morphology and molecular dynamics between pure alginate powders and the films obtained without and with the addition of benzimidazole molecules. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. Probing the emitter site of Renilla luciferase using small organic molecules; an attempt to understand the molecular architecture of the emitter site.

    Science.gov (United States)

    Salehi, Farajollah; Emamzadeh, Rahman; Nazari, Mahboobeh; Rasa, Seyed Mohammad Mahdi

    2016-12-01

    Renilla luciferase is a sensitive enzyme and has wide applications in biotechnology such as drug screening. Previous studies have tried to show the catalytic residues, nevertheless, the accurate architecture and molecular behavior of its emitter site remains uncharacterized. In this study, the activity of Renilla luciferase, in the presence of two small organic molecules including dimethyl sulfoxide (DMSO) and isopropanol was considered and the structure was studied by circular dichroism (CD) and fluorescence spectroscopy. Moreover, the interaction of small organic molecules with the Renilla luciferase was studied using molecular dynamics simulations. Kinetics studies showed that at low concentration of DMSO (16.6-66mM) and isopropanol (19.3-76mM) the K m changed and a competitive inhibition pattern was observed. Moreover, spectroscopy studies reveled that the changes of activity of Renilla luciferase in the presence of low concentrations of small organic molecules was not associated with structural collapse or severe changes in the enzyme conformation. Molecular dynamics simulations indicated that DMSO and isopropanol, as probing molecules, were both able to bind to the emitter site and remained with the residues of the emitter site. Based on the probing data, the architecture of the emitter site in the "non-binding" model was proposed. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Bis(pyrrole-benzimidazole) conjugates as novel colorimetric sensor ...

    Indian Academy of Sciences (India)

    Sanjeev Pran Mahanta

    Abstract. Novel bis(pyrrole-benzimidazole) (PYBI) conjugates were investigated as colorimetric anion recognition motif by employing multiple donor sites. In this regard, PYBI derivatives where pyrrole unit is connected to the C2 position of benzimidazole via its α-position were synthesized and their anion recognition.

  6. 2-Heteroaryl Benzimidazole Derivatives as Melanin Concentrating Hormone Receptor 1 (MCH-R1) Antagonists

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Chae Jo; Kim, Jeong Young; Lee, Byung Ho; Oh, Kwangseok; Yi, Kyu Yang [Korea Research Institute of Chemical Technology, Daejeon (Korea, Republic of)

    2013-08-15

    A novel series of 2-heteroaryl substituted benzimidazole derivatives, containing the piperidinylphenyl acetamide group at the 1-position, were synthesized and evaluated as MCH-R1 antagonists. Extensive SAR investigation probing the effects of C-2 heteroaryl group led to the identification of 2-[2-(pyridin-3-yl)ethyl] analog 3o, which exhibits highly potent MCH-R1 binding activity with an IC{sub 50} value of 1 nM. This substance 3o also has low hERG binding activity, good metabolic stability, and favorable pharmacokinetic properties.

  7. New substituted benzimidazole derivatives: a patent review (2013 - 2014).

    Science.gov (United States)

    Wang, Miao; Han, Xiaofeng; Zhou, Zhiming

    2015-05-01

    The benzimidazole nucleus is found in a variety of naturally occurring compounds and is of significant importance in medicinal chemistry. Owing to its conspicuous pharmacological properties, benzimidazoles have become an important pharmacophore and sub-structure in drug design and have been screened for a wide range of biological activities. Areas covered in this paper include a review of the biological effects, mechanisms and synthesis of benzimidazole derivatives in the past 2 years based on patents. The patent databases Scifinder and esp@cenet were used to locate patent applications that were published between 2013 to present. Information from articles published is also included. Benzimidazole derivatives are remarkably effective compounds to many diseases and may have the potential to be the first effective therapy against Ebola virus. Therefore, it is of great importance to develop specific design software and sustainable industrial synthetic routes for the development of effective and clinically relevant benzimidazole compounds.

  8. Subunits of highly Fluorescent Protein R-Phycoerythrin as Probes for Cell Imaging and Single-Molecule Detection

    Energy Technology Data Exchange (ETDEWEB)

    Isailovic, Dragan [Iowa State Univ., Ames, IA (United States)

    2005-01-01

    The purposes of our research were: (1) To characterize subunits of highly fluorescent protein R-Phycoerythrin (R-PE) and check their suitability for single-molecule detection (SMD) and cell imaging, (2) To extend the use of R-PE subunits through design of similar proteins that will be used as probes for microscopy and spectral imaging in a single cell, and (3) To demonstrate a high-throughput spectral imaging method that will rival spectral flow cytometry in the analysis of individual cells. We first demonstrated that R-PE subunits have spectroscopic and structural characteristics that make them suitable for SMD. Subunits were isolated from R-PE by high-performance liquid chromatography (HPLC) and detected as single molecules by total internal reflection fluorescence microscopy (TIRFM). In addition, R-PE subunits and their enzymatic digests were characterized by several separation and detection methods including HPLC, capillary electrophoresis, sodium dodecyl sulfate-polyacrilamide gel electrophoresis (SDS-PAGE) and HPLC-electrospray ionization mass spectrometry (ESI-MS). Favorable absorption and fluorescence of the R-PE subunits and digest peptides originate from phycoerythrobilin (PEB) and phycourobilin (PUB) chromophores that are covalently attached to cysteine residues. High absorption coefficients and strong fluorescence (even under denaturing conditions), broad excitation and emission fluorescence spectra in the visible region of electromagnetic spectrum, and relatively low molecular weights make these molecules suitable for use as fluorescence labels of biomolecules and cells. We further designed fluorescent proteins both in vitro and in vivo (in Escherichia coli) based on the highly specific attachment of PEB chromophore to genetically expressed apo-subunits of R-PE. In one example, apo-alpha and apo-beta R-PE subunits were cloned from red algae Polisiphonia boldii (P. boldii), and expressed in E. coli. Although expressed apo-subunits formed inclusion

  9. Synthesis and quantitative structure activity relationship (QSAR) of arylidene (benzimidazol-1-yl)acetohydrazones as potential antibacterial agents.

    Science.gov (United States)

    El-Kilany, Yeldez; Nahas, Nariman M; Al-Ghamdi, Mariam A; Badawy, Mohamed E I; El Ashry, El Sayed H

    2015-01-01

    Ethyl (benzimidazol-1-yl)acetate was subjected to hydrazinolysis with hydrazine hydrate to give (benzimidazol-1-yl)acetohydrazide. The latter was reacted with various aromatic aldehydes to give the respective arylidene (1H-benzimidazol-1-yl)acetohydrazones. Solutions of the prepared hydrazones were found to contain two geometric isomers. Similarly (2-methyl-benzimidazol-1-yl)acetohydrazide was reacted with various aldehydes to give the corresponding hydrazones. The antibacterial activity was evaluated in vitro by minimum inhibitory concentration (MIC) against Agrobacterium tumefaciens (A. tumefaciens), Erwinia carotovora (E. carotovora), Corynebacterium fascians (C. fascians) and Pseudomonas solanacearum (P. solanacearum). MIC result demonstrated that salicylaldehyde(1H-benzimidazol-1-yl)acetohydrazone (4) was the most active compound (MIC = 20, 35, 25 and 30 mg/L against A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively). Quantitative structure activity relationship (QSAR) investigation using Hansch analysis was applied to find out the correlation between antibacterial activity and physicochemical properties. Various physicochemical descriptors and experimentally determined MIC values for different microorganisms were used as independent and dependent variables, respectively. pMICs of the compounds exhibited good correlation (r = 0.983, 0.914, 0.960 and 0.958 for A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively) with the prediction made by the model. QSAR study revealed that the hydrophobic parameter (ClogP), the aqueous solubility (LogS), calculated molar refractivity, topological polar surface area and hydrogen bond acceptor were found to have overall significant correlation with antibacterial activity. The statistical results of training set, correlation coefficient (r and r (2)), the ratio between regression and residual variances (f, Fisher's statistic), the standard error of estimates and

  10. Thermostability and photophysical properties of mixed-ligand carboxylate/benzimidazole Zn(II)-coordination polymers

    Energy Technology Data Exchange (ETDEWEB)

    Barros, Bráulio Silva, E-mail: brauliobarros@ect.ufrn.br [School of Science and Technology, Federal University of Rio Grande do Norte (UFRN), Campus Universitário Lagoa Nova, 59078-970 Natal, RN (Brazil); Chojnacki, Jaroslaw [Department of Inorganic Chemistry, Chemical Faculty, Gdansk University of Technology, G. Narutowicza 11/12, 80-233 Gdansk (Poland); Macêdo Soares, Antonia Alice; Kulesza, Joanna; Lourenço da Luz, Leonis; Júnior, Severino Alves [Department of Fundamental Chemistry, Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 – Cidade Universitária, 50670-901 Recife, PE (Brazil)

    2015-07-15

    The reaction between Zn(NO{sub 3}){sub 2}·6H{sub 2}O or Zn(CH{sub 3}COO){sub 2}·2H{sub 2}O and isophthalic acid (1,3-H{sub 2}bdc) in the presence of benzimidazole (Hbzim) in dimethylformamide (DMF)/ethanol (EtOH)/H{sub 2}O solvent mixture at room temperature yielded two structurally different coordination polymers: [Zn{sub 2}(1,3-bdc){sub 2}(Hbzim){sub 2}] (1) and [Zn{sub 2}(1,3-bdc)(bzim){sub 2}] (2). (1) is a 2D-layered framework with a molecule of benzimidazole coordinated to the Zn center, whereas (2) is a 3D framework with benzimidazolate species acting as a co-ligand and bridging two Zn(II) ions. Reactions performed at 90 °C led to the formation of coordination polymers structurally similar to (2), independently of the Zn(II) source used. In the absence of benzimidazole, the reaction between ZnAc{sub 2}.2H{sub 2}O and 1,3-H{sub 2}bdc at 90 °C resulted in the formation of (3), a 3D coordination polymer Zn(HCOO){sub 3}(Me{sub 2}NH{sub 2}{sup +}). It was observed that the thermostability and the photophysical properties of (1) and (2) are strongly dependent on the coordination modes and packing of benzimidazole in the solid state. These materials present photoluminescence in the wide range of the spectrum, from UV to IR. A full understanding of a physical process occurring in these intriguing systems, including complete energy level diagrams with possible transitions were provided. - Graphical abstract: Display Omitted - Highlights: • Structurally different Zn(II)-coordination polymers were prepared. • The formation of frameworks was counter anion and temperature dependent. • Photoluminescence in the wide range of the spectrum, from UV to IR was observed. • Thermostability and luminescence depended on bzim packing in the structure.

  11. A third polymorph of 1,4-bis(1H-benzimidazol-2-ylbenzene

    Directory of Open Access Journals (Sweden)

    Wei-Wei Fu

    2014-06-01

    Full Text Available The title compound, C20H14N4, is a new polymorph of the previously reported structures, which were orthorhombic, space group Pbca [Bei et al. (2000. Acta Cryst. C56, 718–719] and monoclinic, space group P21/c [Dudd et al. (2003. Green Chem. 5, 187–192]. The asymmetric unit consists of two independent molecules in which the dihedral angels between the central benzene ring and the outer benzimidazole ring systems are 16.81 (10 and 14.23 (10° in one molecule and 26.09 (10 and 37.29 (10° in the other. In the crystal, molecules are linked by N—H...N and C—H...N hydrogen bonds into a tape running along the c-axis direction.

  12. Derivatives of benzimidazole: vasodilator activity of 2-(p-chloro-alpha-hydroxybenzyl)-benzimidazole hydrochloride. Preliminary study.

    Science.gov (United States)

    Demenge, P; Carraz, G; Luu Duc, C; Silice, C

    1979-01-01

    The effects of 2-(p-chloro-alpha-hydroxybenzyl)-benzimidazole hydrochloride (HBBPC) have been studied in the rabbit and rat. Most of these studies were performed comparatively with reference vasodilators and papaverine. HBBPC vasodilator activity is nearly the same as that of papaverine in the isolated rabbit ear. The characteristic of the vasoactive action of HBBPC seems to reside in its duration. The mechanism of action of HBBPC seems of peripheral type, that is to say it acts on the vascular smooth muscle.

  13. Multimodal Probes: Superresolution and Transmission Electron Microscopy Imaging of Mitochondria, and Oxygen Mapping of Cells, Using Small-Molecule Ir(III) Luminescent Complexes.

    Science.gov (United States)

    Shewring, Jonathan R; Cankut, Ahmet J; McKenzie, Luke K; Crowston, Bethany J; Botchway, Stanley W; Weinstein, Julia A; Edwards, Elizabeth; Ward, Michael D

    2017-12-18

    We describe an Ir(III)-based small-molecule, multimodal probe for use in both light and electron microscopy. The direct correlation of data between light- and electron-microscopy-based imaging to investigate cellular processes at the ultrastructure level is a current challenge, requiring both dyes that must be brightly emissive for luminescence imaging and scatter electrons to give contrast for electron microscopy, at a single working concentration suitable for both methods. Here we describe the use of Ir(III) complexes as probes that provide excellent image contrast and quality for both luminescence and electron microscopy imaging, at the same working concentration. Significant contrast enhancement of cellular mitochondria was observed in transmission electron microscopy imaging, with and without the use of typical contrast agents. The specificity for cellular mitochondria was also confirmed with MitoTracker using confocal and 3D-structured illumination microscopy. These phosphorescent dyes are part of a very exclusive group of transition-metal complexes that enable imaging beyond the diffraction limit. Triplet excited-state phosphorescence was also utilized to probe the O 2 concentration at the mitochondria in vitro, using lifetime mapping techniques.

  14. Nanostructures and Self-Assembly of Organogels via Benzimidazole/Benzothiazole Imide Derivatives with Different Alkyl Substituent Chains

    Directory of Open Access Journals (Sweden)

    Xihai Shen

    2013-01-01

    Full Text Available New benzimidazole/benzothiazole imide derivatives with different alkyl substituent chains were designed and synthesized. Their gelation behaviors in 22 solvents were tested as novel low-molecular-mass organic gelators. The test showed that the alkyl substituent chains and headgroups of benzimidazole/benzothiazole residues in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. More alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. SEM and AFM observations revealed that the gelator molecules self-assemble into different aggregates from wrinkle, lamella and belt to dot with change of solvents. Spectral studies indicated that there existed different H-bond formation between imide groups and hydrophobic force of alkyl substituent chains in molecular skeletons. The present work may give some insights into design and character of new organogelators and soft materials with special molecular structures.

  15. Structure of HIV-1 nonnucleoside reverse transcriptase inhibitors derivatives of N-benzyl-benzimidazole with different substituents in position 4

    Science.gov (United States)

    Ziółkowska, Natasza E.; Michejda, Christopher J.; Bujacz, Grzegorz D.

    2010-01-01

    The constant development of new drugs against HIV-1 is necessary due to global expansion of AIDS and HIV-1 drug resistance. Nonnucleoside reverse transcriptase inhibitors of HIV-1 (NNRTIs) are potentially effective and nontoxic drugs in AIDS therapy. The crystal structures of six nonnucleoside inhibitors of HIV-1 reverse transcriptase (RT) derivatives of N-benzyl-benzimidazole are reported here. The investigated compounds belong to the group of so called "butterfly like" inhibitors with characteristic two π-electron moieties with an angled orientation. The structural data show the influence of the substituents of the benzimidazole ring on the geometry of the molecule and correlation between the structure of the inhibitor and its biological activity.

  16. Single molecule FRET data analysis procedures for FRET efficiency determination: probing the conformations of nucleic acid structures.

    Science.gov (United States)

    Krüger, Asger Christian; Birkedal, Victoria

    2013-11-01

    Single molecule FRET microscopy is an attractive technique for studying structural dynamics and conformational diversity of nucleic acid structures. Some of its strengths are that it can follow structural changes on a fast time scale and identify conformation distributions arising from dynamic or static population heterogeneity. Here, we give a description of the experiment and data analysis procedures of this method and detail what parameters are needed for FRET efficiency calculation. Using single molecule FRET data obtained on G-quadruplex DNA structures that exhibit large conformation diversity, we illustrate that the shape of the FRET distribution changes depending on what parameters are included in the data analysis procedure. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Crystal structure of ethyl 2-(1H-benzimidazol-2-yl-2-[2-(4-nitrophenylhydrazinylidene]acetate

    Directory of Open Access Journals (Sweden)

    Mohamed Loughzail

    2015-04-01

    Full Text Available The title compound, C17H15N5O4, was obtained via the condensation of 3-ethoxy-2-[2-(4-nitrophenylhydrazono]-3-oxopropanoic acid with 1,2-diaminobenzene. In the molecule, the dihedral angles between the acetate group and the two aromatic subunits (benzimidazole and nitrophenylhydrazone are 7.35 (9 and 18.23 (9°, respectively. Intramolecular N—H...O and N—H...N contacts occur. In the crystal, C—H...O and N—H...O hydrogen bonds link the molecules into chains along the b-axis direction.

  18. Adipic acid–2,6-bis(1H-benzimidazol-2-ylpyridine–water (1/2/4

    Directory of Open Access Journals (Sweden)

    Songzhu Lin

    2012-12-01

    Full Text Available The asymmetric unit of the title hydrated co-crystal, 2C19H13N5·C6H10O4·4H2O, consists of one 2,6-bis(1H-benzimidazol-2-ylpyridine molecule, half of an adipic acid molecule (bisected by an inversion center and two water solvates. In the crystal, N—H...O, O—H...O and O—H...N hydrogen bonds and π–π interactions [centroid–centroid distances = 3.769 (2 and 3.731 (2 Å] form a three-dimensional supramolecular structure.

  19. Poly[μ2-aqua-aqua(μ3-1H-benzimidazole-5,6-dicarboxylato-κ3N3:O5:O5′manganese(II

    Directory of Open Access Journals (Sweden)

    Tan Zheng-De

    2010-05-01

    Full Text Available In the title complex, [Mn(C9H4N2O4(H2O2]n, the MnII atom is in a distorted octahedral coordination completed by one N atom from one 1H-benzimidazole-5,6-dicarboxylate ligand, two O atoms from two different 1H-benzimidazole-5,6-dicarboxylate ligands, and three O atoms from three water molecules. Two bridging water molecules and two bridging carboxylate groups from a 1H-benzimidazole-5,6-dicarboxylate ligand connect two MnII ions into a dimeric structure. In the crystal, extensive intermolecular O—H...O, N—H...O and C—H...O hydrogen bonding forms a three-dimensional network.

  20. cyclo-Tetra-μ-malato-κ16O,O′,O′′:O′′′-tetrakis[bis(1H-benzimidazole-κN3cobalt(II] eicosahydrate

    Directory of Open Access Journals (Sweden)

    Duan-Jun Xu

    2008-04-01

    Full Text Available The title compound, [Co4(C4H4O54(C7H6N28]·20H2O, consists of tetranuclear CoII complexes and disordered uncoordinated water molecules. The tetrameric complex molecule has overline{4} symmetry. While two benzimidazole molecules and a tridentate malate dianion coordinate a CoII ion, the carboxylate O atom from an adjacent malate dianion bridges the CoII ions to complete a distorted octahedral coordination geometry. The tridentate malate dianion chelates the CoII ion, and the chelate six- and five-membered rings show half-chair and envelope configurations, respectively. A face-to-face separation of 3.494 (9 Å between parallel benzimidazole ligands indicates the existence of π–π stacking between adjacent complexes. The crystal structure also involves N—H...O and O—H...O hydrogen bonds.

  1. FEMVib, an ab initio multi-dimensional solver for probing vibrational dynamics in polyatomic molecules and free radicals

    Science.gov (United States)

    Xu, Dong

    Accurate prediction of the vibrational spectra in polyatomic molecules and free radicals depends on obtaining high quality solutions to the vibrational Schrodinger equation. The quantum simple harmonic oscillator provides the traditional first approximation for modeling molecular vibrational states. Rarely does a vibrational analysis extend beyond this first approximation, and harmonic energy levels are routinely used to predict the infrared spectra and other dynamical properties of molecules. However, there are many large-amplitude molecular motions that are extremely anharmonic, including internal torsions about atom-atom single bonds, bending and stretching of weak bonds in van der Waals complexes, and isomerization along relocalization coordinates in free radicals. In these cases, the harmonic treatment provided by electronic structure quantum chemistry packages is completely inadequate. Furthermore, the anharmonicity often includes strong coupling among two or more distinct vibrational coordinates, necessitating a multi-dimensional analysis of the vibrational Schrodinger equation along the coupled coordinates. A novel ab initio solver package, FEMVib, is developed within the finite element method (FEM) framework. A mixed programming paradigm that combines C++, Fortran and Python is employed to take advantage of existing numerical libraries. FEMVib has been rigorously tested to resolve the eigenvalues and wavefunctions of hundreds of vibrational energy states to high accuracy and precision. It may be used to calculate the complete vibrational spectra of triatomic molecules or to approximate larger systems through a "relaxed" model that allows complete coupling of up to three selected vibrational coordinates. FEMVib provides physical chemists with a general, robust and accurate computational tool for molecular vibrational analysis.

  2. Using Force to Probe Single-Molecule Receptor-Cytoskeletal Anchoring Beneath the Surface of a Living Cell

    DEFF Research Database (Denmark)

    Evans, Evan; Kinoshita, Koji

    2007-01-01

    , K. (2005). Nano-to-micro scale dynamics of P-selectin detachment from leukocyte interfaces: I. Separation of PSGL-1 from the cell cytoskeleton. Biophys. J. 88, 2288-2298]. Retracting cells from receptor-surface attachments at many different speeds revealed that the kinetic rate for receptor......The ligation of cell surface receptors often communicates a signal that initiates a cytoplasmic chemical cascade to implement an important cell function. Less well understood is how physical stress applied to a cell surface adhesive bond propagates throughout the cytostructure to catalyze...... or trigger important steps in these chemical processes. Probing the nanoscale impact of pulling on cell surface bonds, we discovered that receptors frequently detach prematurely from the interior cytostructure prior to failure of the exterior adhesive bond [Evans, E., Heinrich, V., Leung, A., and Kinoshita...

  3. Look fast: Crystallization of conjugated molecules during solution shearing probed in-situ and in real time by X-ray scattering

    KAUST Repository

    Smilgies, Detlef Matthias

    2012-12-20

    High-speed solution shearing, in which a drop of dissolved material is spread by a coating knife onto the substrate, has emerged as a versatile, yet simple coating technique to prepare high-mobility organic thin film transistors. Solution shearing and subsequent drying and crystallization of a thin film of conjugated molecules is probed in situ using microbeam grazing incidence wide-angle X-ray scattering (μGIWAXS). We demonstrate the advantages of this approach to study solution based crystal nucleation and growth, and identify casting parameter combinations to cast highly ordered and laterally aligned molecular thin films. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Detection of benzimidazole carbamates and amino metabolites in liver by surface plasmon resonance-biosensor

    Science.gov (United States)

    Two surface plasmon resonance (SPR) biosensor screening assays were developed and validated to detect 11 benzimidazole carbamate (BZT) and four amino-benzimidazole veterinary drug residues in liver tissue. The assays used polyclonal antibodies, raised in sheep, to detect BZTs and amino-benzimidazole...

  5. Probing the origin of elliptical high-order harmonic generation from aligned molecules in linearly polarized laser fields

    International Nuclear Information System (INIS)

    Son, Sang-Kil; Telnov, Dmitry A.; Chu, Shih-I.

    2010-01-01

    A recent experiment [Phys. Rev. Lett. 102, 073902 (2009)] has demonstrated that elliptically polarized high-order harmonic generation can be produced from linearly polarized driving fields for aligned molecular systems. In order to reveal the underlying physical mechanisms of elliptical harmonics, we present fully ab initio and high-precision calculations and analyses of the amplitude, phase, and polarization state of the harmonic radiation from molecular hydrogen ions with arbitrary orientation. We find that high ellipticity arises from molecular orbital symmetry and two-center interference effects. Our ab initio exploration and findings lead to a general rule that the ellipticity becomes high for molecular orbitals represented by a symmetric combination of atomic orbitals, whereas it becomes low for molecular orbitals represented by an antisymmetric combination. This finding also applies to the general case of aligned linear molecules.

  6. Probing the rate-determining region of the potential energy surface for a prototypical ion-molecule reaction.

    Science.gov (United States)

    Xie, Changjian; Liu, Xinguo; Sweeny, Brendan C; Miller, Thomas M; Ard, Shaun G; Shuman, Nicholas S; Viggiano, Albert A; Guo, Hua

    2018-03-13

    We report a joint experimental-theoretical study of the F -  + HCl → HF + Cl - reaction kinetics. The experimental measurement of the rate coefficient at several temperatures was made using the selected ion flow tube method. Theoretical rate coefficients are calculated using the quasi-classical trajectory method on a newly developed global potential energy surface, obtained by fitting a large number of high-level ab initio points with augmentation of long-range electrostatic terms. In addition to good agreement between experiment and theory, analyses suggest that the ion-molecule reaction rate is significantly affected by shorter-range interactions, in addition to the traditionally recognized ion-dipole and ion-induced dipole terms. Furthermore, the statistical nature of the reaction is assessed by comparing the measured and calculated HF product vibrational state distributions to that predicted by the phase space theory.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Author(s).

  7. Infrared absorption by molecular gases as a probe of nanoporous silica xerogel and molecule-surface collisions: Low-pressure results

    Science.gov (United States)

    Vander Auwera, J.; Ngo, N. H.; El Hamzaoui, H.; Capoen, B.; Bouazaoui, M.; Ausset, P.; Boulet, C.; Hartmann, J.-M.

    2013-10-01

    Transmission spectra of gases confined (but not adsorbed) within the pores of a 1.4-cm-thick silica xerogel sample have been recorded between 2.5 and 5 μm using a high-resolution Fourier transform spectrometer. This was done for pure CO, CO2, N2O, H2O, and CH4 at room temperature and pressures of a few hectopascals. Least-squares fits of measured absorption lines provide the optical-path lengths within the confined (LC) and free (LF) gas inside the absorption cell and the half width at half maximum ΓC of the lines of the confined gases. The values of LC and LF retrieved using numerous transitions of all studied species are very consistent. Furthermore, LC is in satisfactory agreement with values obtained from independent measurements, thus showing that reliable information on the open porosity volume can be retrieved from an optical experiment. The values of ΓC, here resulting from collisions of the molecules with the inner surfaces of the xerogel pores, are practically independent of the line for each gas and inversely proportional to the square root of the probed-molecule molar mass. This is a strong indication that, for the studied transitions, a single collision of a molecule with a pore surface is sufficient to change its rotational state. A previously proposed simple model, used for the prediction of the line shape, leads to satisfactory agreement with the observations. It also enables a determination of the average pore size, bringing information complementary to that obtained from nitrogen adsorption porosimetry.

  8. Potential radiosensitizing agents. 5. 2-Substituted benzimidazole derivatives

    International Nuclear Information System (INIS)

    Gupta, R.P.; Larroquette, C.A.; Agrawal, K.C.

    1982-01-01

    A series of 2-substituted benzimidazoles and their derivatives have been synthesized and tested for their ability to selectively sensitize hypoxic Chinese hamster cells (V-79) toward the lethal effect of ionizing radiation. These compounds were prepared by reacting the 2-substituted benzimidazoles with 1,2-epoxy-3-methoxypropane in the presence of potassium carbonate. Reaction of the 2-nitro and 2-methylfonyl analogue with the epoxide also yielded a cyclized material, which was confirmed to be a benzimidazo[2,1-b]oxazole. In an attempt to increase the electron affinity, 5- or 6-nitro-2-substituted-benzimidazoles were also synthesized and then reacted with the epoxide to yield the corresponding 1-substituted derivatives. The results of the biological tests for the radiosensitizing activity of these agents against Chinese hamster cells (V-79) in culture indicated that the 2-nitro-substituted analogues were the most effective sensitizers in this series

  9. Synthesis and biological evaluation of 2-substituted benzimidazole derivatives

    Directory of Open Access Journals (Sweden)

    Gurusamy Mariappan

    2015-09-01

    Full Text Available A novel series of 2-substituted benzimidazole derivatives (3a–3j were synthesized by the reaction of 2-chloro methyl benzimidazole with substituted primary aromatic amines. All the compounds were characterized by UV, IR, 1H NMR, mass spectral data and CHN elemental analysis. The synthesized derivatives were screened for analgesic and anti-inflammatory activities. All the compounds showed significant effect at 100 mg/kg p.o. and the experimental data are statistically significant at p < 0.01 level.

  10. Probing Interactions of N-Donor Molecules with Open Metal Sites within Paramagnetic Cr-MIL-101: A Solid-State NMR Spectroscopic and Density Functional Theory Study.

    Science.gov (United States)

    Wittmann, Thomas; Mondal, Arobendo; Tschense, Carsten B L; Wittmann, Johannes J; Klimm, Ottokar; Siegel, Renée; Corzilius, Björn; Weber, Birgit; Kaupp, Martin; Senker, Juergen

    2018-02-14

    Understanding host-guest interactions is one of the key requirements for adjusting properties in metal-organic frameworks (MOFs). In particular, systems with coordinatively unsaturated Lewis acidic metal sites feature highly selective adsorption processes. This is attributed to strong interactions with Lewis basic guest molecules. Here we show that a combination of 13 C MAS NMR spectroscopy with state-of-the-art density functional theory (DFT) calculations allows one to unravel the interactions of water, 2-aminopyridine, 3-aminopyridine, and diethylamine with the open metal sites in Cr-MIL-101. The 13 C MAS NMR spectra, obtained with ultrafast magic-angle spinning, are well resolved, with resonances distributed over 1000 ppm. They present a clear signature for each guest at the open metal sites. Based on competition experiments this leads to the following binding preference: water open metal sites, the NMR data offer additional information about the guest and framework dynamics. We expect that our strategy has the potential for probing the binding situation of adsorbate mixtures at the open metal sites of MOFs in general and thus accesses the microscopic interaction mechanisms for this important material class, which is essential for deriving structure-property relationships.

  11. (E-1,2-Bis(1-propyl-5,6-dimethyl-1H-benzimidazol-2-ylethene

    Directory of Open Access Journals (Sweden)

    Joseph A. Potenza

    2010-03-01

    Full Text Available In the title compound, C26H32N4, the essentially planar (r.m.s. deviations of 0.0053 and 0.0242 Å benzimidazole fragments are trans with respect to a central ethene fragment, and are canted in opposite directions by 2.78 (6 and 5.87 (6° with respect to the ethene plane, giving the molecule a propeller conformation. The terminal ethyl fragments of the pendant n-propyl groups protrude to either side of the benzimidazole planes. Overall, the molecule exhibits a pseudo-center of symmetry at the mid-point of the ethene fragment. Both π–π stacking and typical C—H...π interactions are notably absent, as are intermolecular hydrogen bonds. When viewed along the a axis, the structure appears as criss-crossed layers of molecules with the planar fragments separated along the c-cell direction by the protruding ethyl groups.

  12. Crystal structures of HIV-1 nonnucleoside reverse transcriptase inhibitors: N-benzyl-4-methyl-benzimidazoles

    Science.gov (United States)

    Ziółkowska, Natasza E.; Michejda, Christopher J.; Bujacz, Grzegorz D.

    2009-07-01

    HIV-1 nonnucleoside reverse transcriptase inhibitors are potentially specific and effective drugs in AIDS therapy. The presence of two aromatic systems with an angled orientation in the molecule of the inhibitor is crucial for interactions with HIV-1 RT. The inhibitor drives like a wedge into the cluster of aromatic residues of RT HIV-1 and restrains the enzyme in a conformation that blocks the chemical step of nucleotide incorporation. Structural studies provide useful information for designing new, more active inhibitors. The crystal structures of four NNRTIs are presented here. The investigated compounds are derivatives of N-benzyl-4-methyl-benzimidazole with various aliphatic and aromatic substituents at carbon 2 positions and a 2,6-dihalogeno-substituted N-benzyl moiety. Structural data reported here show that the conformation of the investigated compounds is relatively rigid. Such feature is important for the nonnucleoside inhibitor binding to HIV-1 reverse transcriptase.

  13. Low power optical limiting studies on nanocrystalline benzimidazole ...

    Indian Academy of Sciences (India)

    Home; Journals; Bulletin of Materials Science; Volume 38; Issue 3. Low power optical limiting studies on nanocrystalline benzimidazole thin films prepared by modified liquid phase growth technique. P A Praveen S P Prabhakaran R Ramesh Babu K Sethuraman K Ramamurthi. Volume 38 Issue 3 June 2015 pp 645-651 ...

  14. Benzimidazole grafted polybenzimidazoles for proton exchange membrane fuel cells

    DEFF Research Database (Denmark)

    Yang, Jingshuai; Aili, David; Li, Qingfeng

    2013-01-01

    High molecular weight polybenzimidazole (PBI) was synthesized and grafted with benzimidazole pendant groups. The high molecular weight of PBI resulted in good film-forming properties and superior tensile strength. With a phosphoric acid doping level (ADL) of 13.1, a tensile strength of 16 MPa was...... humidification. © 2013 The Royal Society of Chemistry....

  15. QSAR study of benzimidazole derivatives inhibition on escherichia ...

    African Journals Online (AJOL)

    The paper describes a quantitative structure-activity relationship (QSAR) study of IC50 values of benzimidazole derivatives on escherichia coli methionine aminopeptidase. The activity of the 32 inhibitors has been estimated by means of multiple linear regression (MLR) and artificial neural network (ANN) techniques.

  16. Activation of peroxyl and molecular oxygen using bis-benzimidazole ...

    Indian Academy of Sciences (India)

    New tetradentate bis-benzimidazole ligands have been synthesized and utilized to prepare copper (II) complexes. Some of these copper (II) complexes have been characterized structurally. The copper (II) in these complexes is found to possess varying geometries. A distorted octahedral geometry is found with a highly ...

  17. Bis (pyrrole-benzimidazole) conjugates as novel colorimetric sensor ...

    Indian Academy of Sciences (India)

    PYBI selectively interacts with fluoride ion, whereas introduction of nitro group on the benzimidazole moiety enhances the binding affinity by at least one order, albeit at the expense of the selectivity. Bridging of two PYBIs led to interesting cooperative effect between the two subunits, which gets enhanced upon changing the ...

  18. Low power optical limiting studies on nanocrystalline benzimidazole ...

    Indian Academy of Sciences (India)

    Low power optical limiting studies on nanocrystalline benzimidazole thin films prepared by modified liquid phase growth technique. P A PRAVEEN1, S P PRABHAKARAN1, R RAMESH BABU1,∗, K SETHURAMAN2 and K RAMAMURTHI3. 1Crystal Growth and Thin Film Laboratory, Department of Physics, Bharathidasan ...

  19. Glutathione transferase-mediated benzimidazole-resistance in Fusarium graminearum.

    Science.gov (United States)

    Sevastos, A; Labrou, N E; Flouri, F; Malandrakis, A

    2017-09-01

    Fusarium graminearum laboratory mutants moderately (MR) and highly (HR) benzimidazole-resistant, carrying or not target-site mutations at the β 2 -tubulin gene were utilized in an attempt to elucidate the biochemical mechanism(s) underlying the unique BZM-resistance paradigm of this fungal plant pathogen. Relative expression analysis in the presence or absence of carbendazim (methyl-2-benzimidazole carbamate) using a quantitative Real Time qPCR (RT-qPCR) revealed differences between resistant and the wild-type parental strain although no differences in expression levels of either β 1 - or β 2 -tubulin homologue genes were able to fully account for two of the highly resistant phenotypes. Glutathione transferase (GST)-mediated detoxification was shown to be -at least partly- responsible for the elevated resistance levels of a HR isolate bearing the β 2 -tubulin Phe200Tyr resistance mutation compared with another MR isolate carrying the same mutation. This benzimidazole-resistance mechanism is reported for the first time in F. graminearum. No indications of detoxification involved in benzimidazole resistance were found for the rest of the isolates as revealed by GST and glutathione peroxidase (GPx) activities and bioassays using monoxygenase and hydrolase detoxification enzyme inhibiting synergists. Interestingly, besides the Phe200Tyr mutation-carrying HR isolate, the remaining highly-carbendazim resistant phenotypes could not be associated with any of the target site modification/overproduction, detoxification or reduced uptake-increased efflux mechanisms. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Bis(pyrrole-benzimidazole) conjugates as novel colorimetric sensor ...

    Indian Academy of Sciences (India)

    Sanjeev Pran Mahanta

    Bis(pyrrole-benzimidazole) conjugates as novel colorimetric sensor for anions. SANJEEV PRAN MAHANTAa,b,∗ and PRADEEPTA KUMAR PANDAb,∗. aDepartment of Chemical Sciences, Tezpur University, Napaam, Assam 784 028, India. bSchool of Chemistry, University of Hyderabad, Hyderabad, Telengana 500 046, ...

  1. Synthesis of a Spirocyclic Oxetane-Fused Benzimidazole

    Directory of Open Access Journals (Sweden)

    Michael Gurry

    2015-07-01

    Full Text Available A new synthesis of 2-oxa-7-azaspiro[3.5]nonane is described. Spirocyclic oxetanes, including 2-oxa-6-azaspiro[3.3]heptane were converted into o-cycloalkylaminoacetanilides for oxidative cyclizations using Oxone® in formic acid. The expanded spirocyclic oxetane successfully gave the [1,2-a] ring-fused benzimidazole. X-ray crystal structure of the resultant new tetracyclic system, 1ʹ,2ʹ-dihydro-4ʹH-spiro[oxetane-3,3ʹ-pyrido[1,2-a]benzimidazole] and the azetidine ring-opened adduct, N-(2-acetamido-4-bromophenyl-N-{[3-(chloromethyl oxetan-3-yl]methyl}acetamide are disclosed.

  2. ECOLOGICALLY SAFE BENZIMIDAZOLE-BASED ANTHELMINTIC DRUGS: SYNTHESIS, PROPERTIES, MEDICATION

    Directory of Open Access Journals (Sweden)

    S. S. Khalikov

    2016-01-01

    Full Text Available The aim is to study the process of mechanochemical modification of the physico-chemical and anthelmintic benzimidazole properties of drugs to change their water solubility and increase their efficiency.Methods. We have used the technology of solid phase mechanical processing of substances with polysaccharides to obtain the supramolecular complexes, which are characterized by a complex of physico-chemical methods (IR spectroscopy, DTA, XRF, solubility, etc. as well as tested for anthelmintic effect in laboratory models and experiments on sheep.Results. The drug has a high efficiency in laboratory models of helminthes and in experiments on sheep infested spontaneously with nematodes of gastrointestinal tract lowering the dosages of substance.Conclusion. Solid phase mechanochemical processing of certain substances of benzimidazole anthelmintic drugs with polysaccharides shows the possibility of obtaining environmentally friendly products with improved solubility, bioavailability and increased biological activity against nematodes.

  3. Adipic acid-2,6-bis-(1H-benzimidazol-2-yl)pyridine-water (1/2/4).

    Science.gov (United States)

    Lin, Songzhu; Jia, Ruokun; Gao, Feng; Zhou, Xiaoqing

    2012-12-01

    The asymmetric unit of the title hydrated co-crystal, 2C19H13N5·C6H10O4·4H2O, consists of one 2,6-bis-(1H-benzimidazol-2-yl)pyridine mol-ecule, half of an adipic acid mol-ecule (bis-ected by an inversion center) and two water solvates. In the crystal, N-H⋯O, O-H⋯O and O-H⋯N hydrogen bonds and π-π inter-actions [centroid-centroid distances = 3.769 (2) and 3.731 (2) Å] form a three-dimensional supra-molecular structure.

  4. Methyl 2-Benzamido-2-(1H-benzimidazol-1-ylmethoxyacetate

    Directory of Open Access Journals (Sweden)

    Alami Anouar

    2012-09-01

    Full Text Available The heterocyclic carboxylic α-aminoester methyl 2-benzamido-2-(1H-benzimidazol-1-ylmethoxyacetate is obtained by O-alkylation of methyl α-azido glycinate N-benzoylated with 1H-benzimidazol-1-ylmethanol.

  5. A bioassay for the detection of benzimidazoles reveals their presence in a range of environmental samples

    Directory of Open Access Journals (Sweden)

    Terence S Crofts

    2014-11-01

    Full Text Available Cobamides are a family of enzyme cofactors that include vitamin B12 (cobalamin and are produced solely by prokaryotes. Structural variability in the lower axial ligand has been observed in cobamides produced by diverse organisms. Of the three classes of lower ligands, the benzimidazoles are uniquely found in cobamides, whereas the purine and phenolic bases have additional biological functions. Many organisms acquire cobamides by salvaging and remodeling cobamides or their precursors from the environment. These processes require free benzimidazoles for incorporation as lower ligands, though the presence of benzimidazoles in the environment has not been previously investigated. Here, we report a new purification method and bioassay to measure the total free benzimidazole content of samples from microbial communities and laboratory media components. The bioassay relies on the calcofluor-bright phenotype of a bluB mutant of the model cobalamin-producing bacterium Sinorhizobium meliloti. The concentrations of individual benzimidazoles in these samples were measured by liquid chromatography-tandem mass spectrometry. Several benzimidazoles were detected in subpicomolar to subnanomolar concentrations in host-associated and environmental samples. In addition, benzimidazoles were found to be common contaminants of laboratory media components. These results suggest that benzimidazoles present in the environment and in laboratory media have the potential to influence microbial metabolic activities.

  6. Benzimidazole acrylonitriles as multifunctional push-pull chromophores: Spectral characterisation, protonation equilibria and nanoaggregation in aqueous solutions

    Science.gov (United States)

    Horak, Ema; Vianello, Robert; Hranjec, Marijana; Krištafor, Svjetlana; Zamola, Grace Karminski; Steinberg, Ivana Murković

    2017-05-01

    Heterocyclic donor-π-acceptor molecular systems based on an N,N-dimethylamino phenylacrylonitrile benzimidazole skeleton have been characterised and are proposed for potential use in sensing applications. The benzimidazole moiety introduces a broad spectrum of useful multifunctional properties to the system including electron accepting ability, pH sensitivity and compatibility with biomolecules. The photophysical characterisation of the prototropic forms of these chromophores has been carried out in both solution and on immobilisation in polymer films. The experimental results are further supported by computational determination of pKa values. It is noticed that compound 3 forms nanoaggregates in aqueous solutions with aggregation-induced emission (AIE) at 600 nm. All the systems demonstrate spectral pH sensitivity in acidic media which shifts towards near-neutral values upon immobilisation in polymer films or upon aggregation in an aqueous environment (compound 3). The structure-property relationships of these functional chromophores, involving their spectral characteristics, acid-base equilibria, pKa values and aggregation effects have been determined. Potential applications of the molecules as pH and biomolecular sensors are proposed based on their pH sensitivity and AIE properties.

  7. Dichlorido{2-[(5-methyl-1H-pyrazol-3-yl-κN2methyl]-1H-1,3-benzimidazole-κN3}zinc

    Directory of Open Access Journals (Sweden)

    Karim Chkirate

    2017-01-01

    Full Text Available The asymmetric unit of the title complex, [ZnCl2(C12H12N4], contains two independent molecules having similar conformations. The coordination about the ZnII atom is distorted tetrahedral, with the geometrical constraints of the chelating ligand responsible for the observed distortion. Each of the independent molecules forms chains in the crystal through pairs of N—H...Cl hydrogen bonds, using the pyrazole and benzimidazole N—H groups as donors. The first molecule forms chains running parallel to the b axis, while the other molecule affords the same kind of one-dimensional supramolecular structure parallel to the a axis. The structure was refined as a two-component twin with BASF = 0.0437 (4.

  8. Evaluation of the membrane permeability (PAMPA and skin) of benzimidazoles with potential cannabinoid activity and their relation with the Biopharmaceutics Classification System (BCS).

    Science.gov (United States)

    Alvarez-Figueroa, M Javiera; Pessoa-Mahana, C David; Palavecino-González, M Elisa; Mella-Raipán, Jaime; Espinosa-Bustos, Cristián; Lagos-Muñoz, Manuel E

    2011-06-01

    The permeability of five benzimidazole derivates with potential cannabinoid activity was determined in two models of membranes, parallel artificial membrane permeability assay (PAMPA) and skin, in order to study the relationship of the physicochemical properties of the molecules and characteristics of the membranes with the permeability defined by the Biopharmaceutics Classification System. It was established that the PAMPA intestinal absorption method is a good predictor for classifying these molecules as very permeable, independent of their thermodynamic solubility, if and only if these have a Log P(oct) value <3.0. In contrast, transdermal permeability is conditioned on the solubility of the molecule so that it can only serve as a model for classifying the permeability of molecules that possess high solubility (class I: high solubility, high permeability; class III: high solubility, low permeability).

  9. Design, synthesis, pharmacological evaluation and in silico ADMET prediction of novel substituted benzimidazole derivatives as angiotensin II-AT1 receptor antagonists based on predictive 3D QSAR models.

    Science.gov (United States)

    Vyas, V K; Gupta, N; Ghate, M; Patel, S

    2014-01-01

    In this study we designed novel substituted benzimidazole derivatives and predicted their absorption, distribution, metabolism, excretion and toxicity (ADMET) properties, based on a predictive 3D QSAR study on 132 substituted benzimidazoles as AngII-AT1 receptor antagonists. The two best predicted compounds were synthesized and evaluated for AngII-AT1 receptor antagonism. Three different alignment tools for comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used. The best 3D QSAR models were obtained using the rigid body (Distill) alignment method. CoMFA and CoMSIA models were found to be statistically significant with leave-one-out correlation coefficients (q(2)) of 0.630 and 0.623, respectively, cross-validated coefficients (r(2)cv) of 0.651 and 0.630, respectively, and conventional coefficients of determination (r(2)) of 0.848 and 0.843, respectively. 3D QSAR models were validated using a test set of 24 compounds, giving satisfactory predicted results (r(2)pred) of 0.727 and 0.689 for the CoMFA and CoMSIA models, respectively. We have identified some key features in substituted benzimidazole derivatives, such as lipophilicity and H-bonding at the 2- and 5-positions of the benzimidazole nucleus, respectively, for AT1 receptor antagonistic activity. We designed 20 novel substituted benzimidazole derivatives and predicted their activity. In silico ADMET properties were also predicted for these designed molecules. Finally, the compounds with best predicted activity were synthesized and evaluated for in vitro angiotensin II-AT1 receptor antagonism.

  10. Ionic conducting poly-benzimidazoles; Polybenzimidazoles conducteurs ioniques

    Energy Technology Data Exchange (ETDEWEB)

    Jouanneau, J

    2006-11-15

    Over the last years, many research works have been focused on new clean energy systems. Hydrogen fuel cell seems to be the most promising one. However, the large scale development of this technology is still limited by some key elements. One of them is the polymer electrolyte membrane 'Nafion' currently used, for which the ratio performance/cost is too low. The investigations we carried out during this thesis work are related to a new class of ionic conducting polymer, the sulfonated poly-benzimidazoles (sPBI). Poly-benzimidazoles (PBI) are aromatic heterocyclic polymers well-known for their excellent thermal and chemical stability. Ionic conduction properties are obtained by having strong acid groups (sulfonic acid SO{sub 3}H) on the macromolecular structure. For that purpose, we first synthesized sulfonated monomers. Their poly-condensation with an appropriate non-sulfonated co-monomer yields to sPBI with sulfonation range from 0 to 100 per cent. Three different sPBI structures were obtained, and verified by appropriate analytical techniques. We also showed that the protocol used for the synthesis resulted in high molecular weights polymers. We prepared ionic conducting membrane by casting sPBI solutions on glass plates. Their properties of stability, water swelling and ionic conductivity were investigated. Surprisingly, the behaviour of sPBI was quite different from the other sulfonated aromatic polymers with same amount of SO{sub 3}H, their stability was much higher, but their water swelling and ionic conductivity were quite low. We attributed these differences to strong ionic interactions between the sulfonic acid groups and the basic benzimidazole groups of our polymers. However, we managed to solve this problem synthesizing very highly sulfonated PBI, obtaining membranes with a good balance between all the properties necessary. (author)

  11. Proton conduction in adipic acid/benzimidazole hybrid electrolytes

    Science.gov (United States)

    Karadedeli, B.; Bozkurt, A.; Baykal, A.

    2005-07-01

    Anhydrous proton conducting organic electrolytes were prepared by doping of adipic acid (AA) with benzimidazole (BnIm) at various stoichiometric ratios to form BnIm xAA ( x is the mol ratio of BnIm to -COOH unit). The AA-BnIm interactions were investigated with Fourier transform infrared spectroscopy (FT-IR) and X-ray diffraction (XRD). Thermal properties were characterized by means of thermogravimetry analysis (TG) and differential scanning calorimetry (DSC). The proton conductivity of these materials was studied by dielectric spectroscopy. The blends exhibit a maximum proton conductivity of 4×10 -3 S/cm at 130 °C.

  12. Proton conduction in adipic acid/benzimidazole hybrid electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Karadedeli, B. [Department of Chemistry, Fatih University, 34500 Buyukcekmece-Istanbul (Turkey); Bozkurt, A. [Department of Chemistry, Fatih University, 34500 Buyukcekmece-Istanbul (Turkey)]. E-mail: bozkurt@fatih.edu.tr; Baykal, A. [Department of Chemistry, Fatih University, 34500 Buyukcekmece-Istanbul (Turkey)

    2005-07-15

    Anhydrous proton conducting organic electrolytes were prepared by doping of adipic acid (AA) with benzimidazole (BnIm) at various stoichiometric ratios to form BnIm {sub x} AA (x is the mol ratio of BnIm to -COOH unit). The AA-BnIm interactions were investigated with Fourier transform infrared spectroscopy (FT-IR) and X-ray diffraction (XRD). Thermal properties were characterized by means of thermogravimetry analysis (TG) and differential scanning calorimetry (DSC). The proton conductivity of these materials was studied by dielectric spectroscopy. The blends exhibit a maximum proton conductivity of 4x10{sup -3} S/cm at 130 deg C.

  13. Pulse radiolysis of 2-mercapto benzimidazole in aqueous solutions

    International Nuclear Information System (INIS)

    Dey, G.R.; Naik, D.B.; Kishore, K.; Moorthy, P.N.

    1994-01-01

    The initial e aq - /H adducts of 2-mercapto benzimidazole(MBZ) (λ max ∼ 370 nm) which are mild reductants react with parent compound to give an intermolecular 3-electron bonded species with λ max at 590 nm. The rate constants for the reactions of MBZ with e aq - and OH radicals at pH 7 and with H-atoms at pH 2 were determined. OH radical reaction with MBZ gives an intramolecular 3-electron bonded species. (author). 2 refs., 2 figs., 1 tab

  14. Optical, thermal and electrical properties of polybenzimidazoles derived from substituted benzimidazoles

    Science.gov (United States)

    Anand, Siddeswaran; Muthusamy, Athianna

    2017-11-01

    Three benzimidazole monomers synthesized by condensing various substituted phenolic aldehydes with 4-methylphenylenediamine were converted in to polymers by oxidative polycondensation. The structure of the monomers and polymers were confirmed by various spectroscopic techniques. Electronic distribution of molecular frontier orbitals and optimized geometries of monomers were calculated by Gaussian 09 package. The spectral results showed that the repeating units are connected through both Csbnd C and Csbnd Osbnd C linkages. Both polymers and monomers are showing good fluorescence emission in blue region. The electrical conductivity of I2 doped PBIs was measured using two point probe technique. The conductivities of PBIs were compared on the basis of the charge densities obtained from Huckel method on imidazole nitrogen which is involved in iodine coordination. The conductivity of polymers increases with increase in iodine vapour contact time. The dielectric properties of the synthesized polymers have been investigated at different temperature and frequency. Among the PBIs, PBIOP is having greater thermal stability and is shown by high carbines residues of around 50% at 500 °C in thermogravimetric analysis.

  15. Benzimidazole as corrosion inhibitor for heat treated 6061 Al- SiCp composite in acetic acid

    Science.gov (United States)

    Chacko, Melby; Nayak, Jagannath

    2015-06-01

    6061 Al-SiCpcomposite was solutionizedat 350 °C for 30 minutes and water quenched. It was then underaged at 140 °C (T6 treatment). The aging behaviour of the composite was studied using Rockwell B hardness measurement. Corrosion behaviour of the underaged sample was studied in different concentrations of acetic acid and at different temperatures. Benzimidazole at different concentrations was used for the inhibition studies. Inhibition efficiency of benzimidazole was calculated for different experimental conditions. Thermodynamic parameters were found out which suggested benzimidazole is an efficient inhibitor and it adsorbed on to the surface of composite by mixed adsorption where chemisorption is predominant.

  16. (Salicylato[tris(1-methyl-1H-benzimidazol-2-ylmethylamine]copper(II perchlorate dimethylformamide disolvate

    Directory of Open Access Journals (Sweden)

    Huilu Wu

    2008-01-01

    Full Text Available In the title complex, [Cu(C7H5O3(C27H27N7]ClO4·2C3H7NO, the CuII ion is five-coordinated by four N atoms from the tris(1-methyl-1H-benzimidazol-2-ylmethylamine ligand and an O atom of the monodentate salicylate ligand. The N4O donor set defines a coordination geometry intermediate between square-pyramidal and trigonal–bipyramidal. The crystal structure is stabilized by O—H...O interactions. The atoms of the aromatic ring of the salicylate ligand are disordered over two sites of equal occupancy. In addition, one of the dimethylformamide solvent molecules is partially disordered over two positions, of approximately equal occupancy.

  17. Probing into hybrid organic-molecule and InAs quantum-dots nanosystem with multistacked dots-in-a-well units

    DEFF Research Database (Denmark)

    Chen, Miaoxiang Max; Kobashi, Kazufumi

    2012-01-01

    Hybridizing air-stable organic-molecules with advanced III-V semiconductor quantum-dots (QDs) structures can be utilized to create a new generation of biochemical sensing devices. In order to enhance their optical performances, the active regions in these QDs structures commonly consist...... of multistacked dots-in-a-well (DWELL) units. The effects of grafted molecules on the performances of the QDs structures with multistacked DWELLs, however, still remain unclear. Here, we show the significant improvements in the optical properties of InAs QDs in a hybrid nanosystem obtained by grafting...

  18. Synthesis and anticancer activity of novel water soluble benzimidazole carbamates.

    Science.gov (United States)

    Cheong, Jae Eun; Zaffagni, Michela; Chung, Ivy; Xu, Yingjie; Wang, Yiqiang; Jernigan, Finith E; Zetter, Bruce R; Sun, Lijun

    2018-01-20

    Metastases account for more than 90% of all cancer deaths and respond poorly to most therapies. There remains an urgent need for new therapeutic modalities for the treatment of advanced metastatic cancers. The benzimidazole methylcarbamate drugs, commonly used as anti-helmitics, have been suggested to have anticancer activity, but progress has been stalled by their poor water solubility and poor suitability for systemic delivery to disseminated cancers. We synthesized and characterized the anticancer activity of novel benzimidazoles containing an oxetane or an amine group to enhance solubility. Among them, the novel oxetanyl substituted compound 18 demonstrated significant cytotoxicity toward a variety of cancer cell types including prostate, lung, and ovarian cancers with strong activity toward highly aggressive cancer lines (IC 50 : 0.9-3.8 μM). Compound 18 achieved aqueous solubility of 361 μM. In a mouse xenograft model of a highly metastatic human prostate cancer, compound 18 (30 mg/kg) significantly inhibited the growth of established tumors (T/C: 0.36) without noticeable toxicity. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  19. New fluorescent probes of the hydroxyl radical: characterisation and modelization of the reactivity of coumarin derivatives with HO; Developpement de sondes fluorescentes du radical hydroxyle: caracterisation et modelisation de la reactivite de molecules derivees de la coumarine avec HO

    Energy Technology Data Exchange (ETDEWEB)

    Louit, G.

    2005-10-15

    The hydroxyl radical is involved in a wide range of different fields, from oxidative stress to atmospheric chemistry. In addition to the study of oxidative damage in biological media, the hydroxyl radical detection allows to perform a dosimetry when it is produced by ionising radiation. The aims of this work have been double: - to improve the detection of the hydroxyl radical by the design of new probes - to improve knowledge on the reactive pathways in which the hydroxyl radical is involved. We have studied the coumarin molecule, as well as 6 derivatives that we have synthesised, as fluorescent probes of the hydroxyl radical. Firstly, fluorescence spectroscopy and HPLC chromatography have allowed the evaluation of the sensibility and selectivity of detection of the probes. Consequently to this study, two applications have been developed, concerning the determination of rate constants by competition kinetics and bidimensional dosimetry. Secondly, we have studied the reactivity of the hydroxyl radical through the regioselectivity of its addition on the aromatic cycle. This problem was addressed by the combined use of experimental methods such as time resolved kinetics and HPLC along with interpretation from classical and ab initio modelization. (author)

  20. Correlation between the molecular structure and the inhibiting effect of some benzimidazole derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Niamien, P.M., E-mail: niamienfr@yahoo.fr [Laboratoire de chimie physique, Universite de Cocody-Abidjan, 22 BP 582 Abidjan (Cote d' Ivoire); Essy, F.K.; Trokourey, A.; Yapi, A.; Aka, H.K. [Laboratoire de chimie physique, Universite de Cocody-Abidjan, 22 BP 582 Abidjan (Cote d' Ivoire); Diabate, D. [Laboratoire de chimie physique, Universite de Cocody-Abidjan, 22 BP 582 Abidjan (Cote d' Ivoire); Institut UTINAM-UMR CNRS 6213 Equipe capteurs et membranes 25013 Besancon cedex, 22 BP 582 Abidjan 22 (Cote d' Ivoire)

    2012-09-14

    Quantum chemical parameters of 2-thiobenzylbenzimidazole (TBBI), 2-thiomethylbenzimidazole (TMBI), and 2-mercaptobenzimidazole (MBI) were calculated. The correlation between molecular structure of these compounds and their inhibition efficiency IE (%) against copper corrosion in 1 M HNO{sub 3} was found by considering Density Functional Theory DFT/B3LYP/6-31G (d, p) level. The properties most relevant to their potential action as corrosion inhibitors have been calculated: highest occupied molecular orbital energy (E{sub HOMO}), lowest unoccupied molecular orbital energy (E{sub LUMO}), energy gap ({Delta}E), dipole moment ({mu}) and parameters that provide informations about the chemical reactivity: electronegativity ({chi}), global hardness ({eta}), global softness ({sigma}) and electrophilicity index ({omega}). All calculations have been performed using the Gaussian 03W suite of programs. It was found that theoretical data support experimental results. -- Highlights: Black-Right-Pointing-Pointer Benzimidazole derivatives (TBBI, TMBI, MBI) as corrosion inhibitors of copper in 1 M HNO{sub 3}. Black-Right-Pointing-Pointer The inhibition process evaluated by weight loss indicates that the investigated compounds are good inhibitors of copper. Black-Right-Pointing-Pointer The inhibition efficiency is found to be in the following order: TBBI > TMBI > MBI. Black-Right-Pointing-Pointer The studied molecules adsorbed on the metal surface according to the Langmuir adsorption isotherm. Black-Right-Pointing-Pointer Most of the calculated molecular parameters by DFT/B3LYP/6-31G (d, p) show excellent correlation with the inhibition efficiency.

  1. Triaryl Benzimidazoles as a New Class of Antibacterial Agents against Resistant Pathogenic Microorganisms.

    Science.gov (United States)

    Picconi, Pietro; Hind, Charlotte; Jamshidi, Shirin; Nahar, Kazi; Clifford, Melanie; Wand, Matthew E; Sutton, J Mark; Rahman, Khondaker Miraz

    2017-07-27

    A new class of nontoxic triaryl benzimidazole compounds, derived from existing classes of DNA minor groove binders, were designed, synthesized, and evaluated for their antibacterial activity against multidrug resistant (MDR) Gram-positive and Gram-negative species. Molecular modeling experiments suggest that the newly synthesized class cannot be accommodated within the minor groove of DNA due to a change in the shape of the molecules. Compounds 8, 13, and 14 were found to be the most active of the series, with MICs in the range of 0.5-4 μg/mL against the MDR Staphylococci and Enterococci species. Compound 13 showed moderate activity against the MDR Gram-negative strains, with MICs in the range of 16-32 μg/mL. Active compounds showed a bactericidal mode of action, and a mechanistic study suggested the inhibition of bacterial gyrase as the mechanism of action (MOA) of this chemical class. The MOA was further supported by the molecular modeling study.

  2. In Vitro Pharmacodynamics of Benzimidazole and Tetrahydropyrimidine Derivatives in European Bison Gastro-Intestinal Nematodes

    Directory of Open Access Journals (Sweden)

    Laura CĂTANĂ

    2017-11-01

    Full Text Available The present study was aimed to evaluate the efficacy of anthelmintic agents against intestinal nematodes found in European bison. It was performed between October 2016 and May 2017, using Egg Hatch Assay (EHA and Larval Development Assay (LDA. The parasites were obtained from faecal samples, harvested from bisons in Romania and Sweden. The efficacy of albendazole (ABZ, mebendazole (MBZ thiabendazole (TBZ and pyrantel (PYR was tested. In EHA, the maximum efficacy was observed in MBZ (EC50 = - 0.227 μg/ml, and then TBZ (EC50 = - 0.2228. ABZ had a weaker result, EC50 being 0.326 μg/ml. All tested benzimidazoles registered hatching percentages below 50%, reflecting the lack of parasitic resistance. MIC obtained in the LDA tests were 0.2144 μg/ml for TBZ, 0.2792 μg/ml for PYR, 0.5429 μg/ml for MBZ, while ABZ came last (MIC = 0.8187 μg/ml. The in vitro tests proved the antiparasitic molecules efficacy against bisons nematode population and a limited risk of inducing resistance phenomena.

  3. A Benzimidazole Proton Pump Inhibitor Increases Growth and Tolerance to Salt Stress in Tomato

    Directory of Open Access Journals (Sweden)

    Michael J. Van Oosten

    2017-07-01

    Full Text Available Pre-treatment of tomato plants with micromolar concentrations of omeprazole (OP, a benzimidazole proton pump inhibitor in mammalian systems, improves plant growth in terms of fresh weight of shoot and roots by 49 and 55% and dry weight by 54 and 105% under salt stress conditions (200 mM NaCl, respectively. Assessment of gas exchange, ion distribution, and gene expression profile in different organs strongly indicates that OP interferes with key components of the stress adaptation machinery, including hormonal control of root development (improving length and branching, protection of the photosynthetic system (improving quantum yield of photosystem II and regulation of ion homeostasis (improving the K+:Na+ ratio in leaves and roots. To our knowledge OP is one of the few known molecules that at micromolar concentrations manifests a dual function as growth enhancer and salt stress protectant. Therefore, OP can be used as new inducer of stress tolerance to better understand molecular and physiological stress adaptation paths in plants and to design new products to improve crop performance under suboptimal growth conditions.Highlight: Omeprazole enhances growth of tomato and increases tolerance to salinity stress through alterations of gene expression and ion uptake and transport.

  4. Fixation of carbon dioxide into dimethyl carbonate over titanium-based zeolitic thiophene-benzimidazolate framework

    Data.gov (United States)

    U.S. Environmental Protection Agency — A titanium-based zeolitic thiophene-benzimidazolate framework has been designed for the direct synthesis of dimethyl carbonate (DMC) from methanol and carbon...

  5. L-shaped benzimidazole fluorophores: synthesis, characterization and optical response to bases, acids and anions.

    Science.gov (United States)

    Lirag, Rio Carlo; Le, Ha T M; Miljanić, Ognjen Š

    2013-05-14

    Nine L-shaped benzimidazole fluorophores have been synthesized, computationally evaluated and spectroscopically characterized. These "half-cruciform" fluorophores respond to bases, acids and anions through changes in fluorescence that vary from moderate to dramatic.

  6. Localization microscopy of DNA in situ using Vybrant{sup ®} DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution

    Energy Technology Data Exchange (ETDEWEB)

    Żurek-Biesiada, Dominika [Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków (Poland); Szczurek, Aleksander T. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Prakash, Kirti [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg (Germany); Mohana, Giriram K. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Lee, Hyun-Keun [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany); Roignant, Jean-Yves [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Birk, Udo J. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany); Dobrucki, Jurek W., E-mail: jerzy.dobrucki@uj.edu.pl [Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków (Poland); Cremer, Christoph, E-mail: c.cremer@imb-mainz.de [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany)

    2016-05-01

    Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant{sup ®} DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10{sup 6} signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100 nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. - Highlights: • Super-resolution imaging of nuclear DNA with Vybrant Violet and blue excitation. • 90nm resolution images of DNA structures in optically thick eukaryotic nuclei. • Enhanced resolution confirms the existence of DNA-free regions inside the nucleus. • Optimized imaging conditions enable multicolor super-resolution imaging.

  7. Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube and in a computer.

    Science.gov (United States)

    Wollman, Adam J M; Miller, Helen; Zhou, Zhaokun; Leake, Mark C

    2015-04-01

    DNA-interacting proteins have roles in multiple processes, many operating as molecular machines which undergo dynamic meta-stable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and the proteins that bind to it must ideally be interrogated at a single molecule level in their native in vivo environments, in a time-resolved manner, fast enough to sample the molecular transitions across the free-energy landscape. Progress has been made over the past decade in utilizing cutting-edge tools of the physical sciences to address challenging biological questions concerning the function and modes of action of several different proteins which bind to DNA. These physiologically relevant assays are technically challenging but can be complemented by powerful and often more tractable in vitro experiments which confer advantages of the chemical environment with enhanced detection signal-to-noise of molecular signatures and transition events. In the present paper, we discuss a range of techniques we have developed to monitor DNA-protein interactions in vivo, in vitro and in silico. These include bespoke single-molecule fluorescence microscopy techniques to elucidate the architecture and dynamics of the bacterial replisome and the structural maintenance of bacterial chromosomes, as well as new computational tools to extract single-molecule molecular signatures from live cells to monitor stoichiometry, spatial localization and mobility in living cells. We also discuss recent developments from our laboratory made in vitro, complementing these in vivo studies, which combine optical and magnetic tweezers to manipulate and image single molecules of DNA, with and without bound protein, in a new super-resolution fluorescence microscope.

  8. Study of the 14C benzimidazole distribution in mice after inter-peritoneal injection

    International Nuclear Information System (INIS)

    Tyortyalian, C.

    1965-01-01

    In order to provide further information on the mechanism of benzimidazole radioprotective activity, this work studies the tissual repartition in mice of this compound labelled with carbon 14. Experiments have showed that benzimidazole distribution is fast and homogeneous in all the tissues, but however affinity appears at the level of stomach and gastric content. Elimination is made through the urinary system and is very fast. (author) [fr

  9. Synthesis of N-Alkyl-2-thiomethyl Benzimidazoles: A Green Approach

    OpenAIRE

    Rao, S. Srinivas; Reddy, Ch. Venkata Ramana; Dubey, P. K.

    2014-01-01

    A green approach for the synthesis of N-alkyl-2-thiomethyl benzimidazoles 2 (R=CH3, C2H5, CH2Ph) under different conditions has been developed from N-alkyl-2-chloromethyl benzimidazole (i.e., CH3, C2H5, CH2Ph) 1 by reaction with thiourea by physical grinding, or by using green solvents like ethanol and PEG-600, or by using microwave irradiation technique.

  10. Oxidative polycondensation of benzimidazole using NaOCl: Synthesis, characterization, optical, thermal and electrical properties of polybenzimidazoles

    Science.gov (United States)

    Anand, Siddeswaran; Muthusamy, Athianna; Dineshkumar, Sengottuvelu; Chandrasekaran, J.

    2017-11-01

    A series of polybenzimidazole polymers, poly-2-(1H-benzo[d] imidazole-2-yl) phenol (PBIP2), poly-3-(1H-benzo[d] imidazole-2-yl) phenol (PBIP3) and poly-4-(1H-benzo[d] imidazole-2-yl) phenol (PBIP4) were synthesized by oxidative polycondensation of benzimidazole monomers 2-(1H-benzo [d] imidazole-2-yl) phenol (BIP2), 3-(1H-benzo [d] imidazole-2-yl) phenol (BIP3) and 4-(1H-benzo [d] imidazole-2-yl) phenol (BIP4). The structure of benzimidazoles monomers and polybenzimidazoles (PBI) were confirmed by various spectroscopic techniques. The quantum theoretical calculations of band gap energy values of monomers were done with DFT and are compared with its optical band gap energy values. Fluorescence spectra of these compounds showed maximum emission in blue region. The electrical conductivity of PBIs was measured by four-point probe technique and showed good electrical response on iodine doping and conductivity increases with increase iodine doping time. The differences in conductivities among the three PBIs are in accordance with the charge density on imidazole nitrogens calculated by Huckel method. The high carbines residue (∼40%) at 500 °C in thermo gravimetric analysis shows that the PBIs are having reasonably good thermal stability. Polymers have recorded high dielectric constant at low applied frequency of 50 Hz at 393 K. The I-V characteristics of polybenzimidazoles p-n diodes showed rectifying nature with a typical forward to reverse current in the range -4 to 4 V. The high n values are caused by non homogeneities and effect of series resistance.

  11. Passing Current through Touching Molecules

    DEFF Research Database (Denmark)

    Schull, G.; Frederiksen, Thomas; Brandbyge, Mads

    2009-01-01

    The charge flow from a single C-60 molecule to another one has been probed. The conformation and electronic states of both molecules on the contacting electrodes have been characterized using a cryogenic scanning tunneling microscope. While the contact conductance of a single molecule between two...

  12. A single molecule assay to probe monovalent and multivalent bonds between hyaluronan and its key leukocyte receptor CD44 under force

    Science.gov (United States)

    Bano, Fouzia; Banerji, Suneale; Howarth, Mark; Jackson, David G.; Richter, Ralf P.

    2016-09-01

    Glycosaminoglycans (GAGs), a category of linear, anionic polysaccharides, are ubiquitous in the extracellular space, and important extrinsic regulators of cell function. Despite the recognized significance of mechanical stimuli in cellular communication, however, only few single molecule methods are currently available to study how monovalent and multivalent GAG·protein bonds respond to directed mechanical forces. Here, we have devised such a method, by combining purpose-designed surfaces that afford immobilization of GAGs and receptors at controlled nanoscale organizations with single molecule force spectroscopy (SMFS). We apply the method to study the interaction of the GAG polymer hyaluronan (HA) with CD44, its receptor in vascular endothelium. Individual bonds between HA and CD44 are remarkably resistant to rupture under force in comparison to their low binding affinity. Multiple bonds along a single HA chain rupture sequentially and independently under load. We also demonstrate how strong non-covalent bonds, which are versatile for controlled protein and GAG immobilization, can be effectively used as molecular anchors in SMFS. We thus establish a versatile method for analyzing the nanomechanics of GAG·protein interactions at the level of single GAG chains, which provides new molecular-level insight into the role of mechanical forces in the assembly and function of GAG-rich extracellular matrices.

  13. Nanostructured poly(benzimidazole membranes by N-alkylation

    Directory of Open Access Journals (Sweden)

    J. Weber

    2014-01-01

    Full Text Available Modification of poly(benzimidazole (PBI by N-alkylation leads to polymers capable of undergoing microphase separation. Polymers with different amounts of C18 alkyl chains have been prepared. The polymers were analyzed by spectroscopy, thermal analysis, electron microscopy and X-ray scattering. The impact of the amount of alkyl chains on the observed microphase separation was analyzed. Membranes prepared from the polymers do show microphase separation, as evidenced by scattering experiments. While no clear morphology could be derived for the domains in the native state, evidence for the formation of lamellar morphologies upon doping with phosphoric acid is provided. Finally, the proton conductivity of alkyl-modified PBI is compared with that of pure PBI, showing that the introduction of alkyl side chains does not result in significant conductivity changes.

  14. Antituberculosis: Synthesis and Antimycobacterial Activity of Novel Benzimidazole Derivatives

    Directory of Open Access Journals (Sweden)

    Yeong Keng Yoon

    2013-01-01

    Full Text Available A total of seven novel benzimidazoles were synthesized by a 4-step reaction starting from 4-fluoro-3-nitrobenzoic acid under relatively mild reaction conditions. The synthesized compounds were screened for their antimycobacterial activity against M. tuberculosis H37Rv (MTB-H37Rv and INH-resistant M. tuberculosis (INHR-MTB strains using agar dilution method. Three of them displayed good activity with MIC of less than 0.2 μM. Compound ethyl 1-(2-(4-(4-(ethoxycarbonyl-2-aminophenylpiperazin-1-ylethyl-2-(4-(5-(4-fluorophenylpyridin-3-ylphenyl-1H-benzo[d]imidazole-5-carboxylate (5g was found to be the most active with MIC of 0.112 μM against MTB-H37Rv and 6.12 μM against INHR-MTB, respectively.

  15. QSAR MODELING OF ANTIBACTERIAL ACTIVITY OF SOME BENZIMIDAZOLE DERIVATIVES

    Directory of Open Access Journals (Sweden)

    SANJA O. PODUNAVAC-KUZMANOVIĆ

    2011-03-01

    Full Text Available A quantitative structure-activity relationship (QSAR study has been carried out for a training set of 12 benzimidazole derivatives to correlate and predict the antibacterial activity of studied compounds against Gram-negative bacteria Pseudomonas aeruginosa. Multiple linear regression was used to select the descriptors and to generate the best prediction model that relates the structural features to inhibitory activity. The predictivity of the model was estimated by cross-validation with the leave-one-out method. Our results suggest a QSAR model based on the following descriptors: parameter of lipophilicity (logP and hydration energy (HE. Good agreement between experimental and predicted inhibitory values, obtained in the validation procedure, indicated the good quality of the generated QSAR model.

  16. Characterisation of the acidity and the basicity of transition alumina by NMR and FTIR spectroscopy of adsorption of probe molecules; Caracterisation par RMN et infrarouge de molecules sondes adsorbees, de l'acidite et de la basicite d'alumines de transition

    Energy Technology Data Exchange (ETDEWEB)

    Mathonneau, E.

    2003-04-01

    This work has been devoted to characterization of the acidity and the basicity of the surface of transition alumina. Three different alumina (Alumina-{gamma}, -{delta} et -{theta} ({gamma}-Al, {delta}-Al, {theta}-Al)) have been studied by adsorption of probe molecules such trimethyl phosphine and carbon monoxide (acidity study); and tri-ethyl borane (basicity study). We emphasized that the acidity increases with an increasing pretreatment temperature where as the basicity decreases. Comparing quantitative results from the different probe molecules we could show an increasing strength acidity following: {gamma}-Al > {theta}-Al > {delta}-Al, and basicity following: {delta}-Al > {gamma}-Al > {theta}-Al. We could evaluate on a qualitative (nature and repartition) and on a quantitative point of view the impact of the transformations {gamma}-Al {yields} {delta}-Al and {gamma}-Al > {theta}-Al on the acid-basicity of the surface. We could also explain catalytic reactivity differences between alumina for the position isomerization of butene-1. (author)

  17. Controllable synthesis of nucleotide complex based on pH control: a small-molecule fluorescent probe as an auxiliary ligand to indicate the pre-organization of the nucleotide complex in solution.

    Science.gov (United States)

    Zhou, Pei; Wang, Chong; Qiu, Qi-Ming; Yao, Jian-Feng; Sheng, Chuan-Fang; Li, Hui

    2015-10-28

    Different CMP-bpe-M(ii) (CMP = cytidine monophosphate, bpe = bis(4-pyridyl)ethylene, M(ii) = Mn(2+) and Co(2+)) complexes are synthesized controllably based on pH control and well studied by X-ray single-crystal diffraction analysis. Interestingly, the suitable pH conditions are explored by considering the pre-organization modes of CMP, bpe, and M(2+) in aqueous solution by fluorescence spectroscopy based on acid/basic titration. The organic base bpe serves as a small-molecule fluorescent probe to indicate the changes of pre-organization modes along with the changes of the solution acidity. Furthermore, a perfect self-complementary sugar-base hydrogen bond is first reported based on the crystal structure analysis in this work, and different chiralities and SHG activities of CMP-bpe-Mn(ii) complexes obtained at different pH values are studied.

  18. Mobile Probing and Probes

    DEFF Research Database (Denmark)

    Duvaa, Uffe; Ørngreen, Rikke; Weinkouff, Anne-Gitte

    2012-01-01

    Mobile probing is a method, which has been developed for learning about digital work situations, as an approach to discover new grounds. The method can be used when there is a need to know more about users and their work with certain tasks, but where users at the same time are distributed (in time...... and space). Mobile probing was inspired by the cultural probe method, and was influenced by qualitative interview and inquiry approaches. The method has been used in two subsequent projects, involving school children (young adults at 15-17 years old) and employees (adults) in a consultancy company. Findings...... point to mobile probing being a flexible method for uncovering the unknowns, as a way of getting rich data to the analysis and design phases. On the other hand it is difficult to engage users to give in depth explanations, which seem easier in synchronous dialogs (whether online or face2face...

  19. Mobile Probing and Probes

    DEFF Research Database (Denmark)

    Duvaa, Uffe; Ørngreen, Rikke; Weinkouff Mathiasen, Anne-Gitte

    2013-01-01

    Mobile probing is a method, developed for learning about digital work situations, as an approach to discover new grounds. The method can be used when there is a need to know more about users and their work with certain tasks, but where users at the same time are distributed (in time and space......). Mobile probing was inspired by the cultural probe method, and was influenced by qualitative interview and inquiry approaches. The method has been used in two subsequent projects, involving school children (young adults at 15-17 years old) and employees (adults) in a consultancy company. Findings point...... to mobile probing being a flexible method for uncovering the unknowns, as a way of getting rich data to the analysis and design phases. On the other hand it is difficult to engage users to give in depth explanations, which seem easier in synchronous dialogs (whether online or face2face). The development...

  20. Probing the role of metal cations on the aggregation behavior of amyloid β-peptide at a single molecule level by AFM

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Yang; Wang, Jianhua, E-mail: wjh@cqu.edu.cn; Liu, Chundong [Chongqing University, Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering (China)

    2016-09-15

    With the development of nanotechnology, understanding of intermolecular interactions on a single molecule level by atomic force spectroscopy (AFM) has played an important role in molecular biology and biomedical science. In recent years, some research suggested that the presence of metal cations is an important regulator in the processes of misfolding and aggregation of the amyloid β-protein (Aβ), which may be an important etiological factor of Alzheimer’s disease. However, the knowledge on the principle of interactions between Aβ and metal cations at the single molecule level is still poor understood. In this paper, the amyloid β-protein (Aβ) was fabricated on substrate of mixed thiol-modified gold nanoparticles using self-assembled monolayer method and the adhesion force in the longitudinal direction between metal cations and Aβ42 were investigated by AFM. The role of metal ions on Aβ aggregation is discussed from the perspective of single molecular force. The force results showed that the specific adhesion force F{sub i} and the nonspecific force F{sub 0} between a single Aβ–Aβ pair in control experiment were calculated as 42 ± 3 and 80 pN, respectively. However, F{sub i} between a single Aβ–Aβ pair in the presence of Cu{sup 2+}, Zn{sup 2+}, Ca{sup 2+} and Al{sup 3+} increased dramatically to 84 ± 6, 89 ± 3, 73 ± 5, 95 ± 5 pN successively, which indicated that unbinding between Aβ proteins is accelerated in the presence of metal cations. What is more, the imaging results showed that substoichiometric copper cations accelerate the formation of fibrils within 3 days. The combined atomic force spectroscopy and imaging analysis indicate that metal cations play a role in promoting the aggregating behavior of Aβ42.

  1. Probing the role of metal cations on the aggregation behavior of amyloid β-peptide at a single molecule level by AFM

    Science.gov (United States)

    Xie, Yang; Wang, Jianhua; Liu, Chundong

    2016-09-01

    With the development of nanotechnology, understanding of intermolecular interactions on a single molecule level by atomic force spectroscopy (AFM) has played an important role in molecular biology and biomedical science. In recent years, some research suggested that the presence of metal cations is an important regulator in the processes of misfolding and aggregation of the amyloid β-protein (Aβ), which may be an important etiological factor of Alzheimer's disease. However, the knowledge on the principle of interactions between Aβ and metal cations at the single molecule level is still poor understood. In this paper, the amyloid β-protein (Aβ) was fabricated on substrate of mixed thiol-modified gold nanoparticles using self-assembled monolayer method and the adhesion force in the longitudinal direction between metal cations and Aβ42 were investigated by AFM. The role of metal ions on Aβ aggregation is discussed from the perspective of single molecular force. The force results showed that the specific adhesion force F i and the nonspecific force F 0 between a single Aβ-Aβ pair in control experiment were calculated as 42 ± 3 and 80 pN, respectively. However, F i between a single Aβ-Aβ pair in the presence of Cu2+, Zn2+, Ca2+ and Al3+ increased dramatically to 84 ± 6, 89 ± 3, 73 ± 5, 95 ± 5 pN successively, which indicated that unbinding between Aβ proteins is accelerated in the presence of metal cations. What is more, the imaging results showed that substoichiometric copper cations accelerate the formation of fibrils within 3 days. The combined atomic force spectroscopy and imaging analysis indicate that metal cations play a role in promoting the aggregating behavior of Aβ42.

  2. Process design of high-concentration benzimidazole wastewater treatment based on the molecular structure of contaminants.

    Science.gov (United States)

    Li, Chenru; Qian, Kun; Liu, Qinyao; Zhang, Qianyi; Yao, Chen; Song, Wei; Wang, Yihong

    2018-04-01

    Benzimidazole is an important intermediate in industry and it is usually difficult to be degraded by many treatment technologies. Looking for a highly effective, environment-friendly degradation process for benzimidazole wastewater is of great significance to reduce pollution. Based on the structure of contaminants, the micro-electrolysis (ME) coupled with the Fenton technique was chosen to degrade the industrial benzimidazole wastewater. Special feeding was applied to maintain the suitable hydrogen peroxide (H 2 O 2 ) concentration to produce the hydroxyl radicals (•OH) as much as possible and protect •OH from being quenched by excess H 2 O 2 according to the reaction mechanism. The results showed that this combined technique was highly efficient to decompose benzimidazole compounds. More chemical oxygen demand (COD) could be reduced when flow control was used, compared to the flow not being controlled. The COD removal rate could reach 85.2% at optimal parameters. Then the effluent of this process was combined with the existing biochemical system for further degradation. The studies of Ultraviolet Spectrophotometry, Fourier Transform Infrared Spectroscopy and Liquid Chromatography Mass Spectrometry showed that both 2-(a-Hydroxyethyl) benzimidazole and 2-Acetylbenzimidazole were decomposed to the isopropanolamine and aniline after the ME treatment; then the intermediates were oxidized into oxalic acid after the Fenton reaction.

  3. Evaluation of chromatographic columns packed with semi- and fully porous particles for benzimidazoles separation.

    Science.gov (United States)

    Gonzalo-Lumbreras, Raquel; Sanz-Landaluze, Jon; Cámara, Carmen

    2015-07-01

    The behavior of 15 benzimidazoles, including their main metabolites, using several C18 columns with standard or narrow-bore diameters and different particle size and type were evaluated. These commercial columns were selected because their differences could affect separation of benzimidazoles, and so they can be used as alternative columns. A simple screening method for the analysis of benzimidazole residues and their main metabolites was developed. First, the separation of benzimidazoles was optimized using a Kinetex C18 column; later, analytical performances of other columns using the above optimized conditions were compared and then individually re-optimized. Critical pairs resolution, analysis run time, column type and characteristics, and selectivity were considered for chromatographic columns comparison. Kinetex XB was selected because it provides the shortest analysis time and the best resolution of critical pairs. Using this column, the separation conditions were re-optimized using a factorial design. Separations obtained with the different columns tested can be applied to the analysis of specific benzimidazoles residues or other applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Synthesis, characterisation and evaluation of N-mannich bases of 2-substituted Benzimidazole derivatives

    Science.gov (United States)

    Vinoth Kumar, Sekar; Subramanian, Mohan Raj; Chinnaiyan, Santhosh Kumar

    2013-01-01

    Rationale Benzimidazoles and its derivatives represent one of the mainly biological active classes of literature. Aim In this present study aimed to synthesize N-mannich bases derivatives compounds bearing of 2-substituted benzimidazole moiety, in order to investigate their possible biological activity. Method Benzimidazole compounds were prepared from the condensation reaction between ortho phenylene diamine and various acids. Mannich base of newly synthesized Benzimidazole derivatives were synthesized from 2-substituted Benzimidazoles by reacting with secondary amines. The purity of the compounds was ascertained by melting point (m.p) and thin layer chromatography (TLC). Structures of the synthesized compounds were elucidated by spectral data. Antimicrobial assay was performed by microbroth dilution method. Bacterial genomic DNA cleavage was assessed by Agarose gel electrophoresis. Toxicity of the most effective compounds was studied by Brine-shrimp lethality assay. Result Among the synthesized compounds, compound 5E (a) and (b) was establish to be the most potent against all tested microorganisms. This two compounds exhibited complete bacterial DNA cleavage and non-toxic. Conclusion These results suggest that it an interesting compound compared to the current therapeutic agents and are considered to investigate further for the same. PMID:24563595

  5. Synthesis, crystal structure, spectroscopic characterization, Hirshfeld surface analysis, and DFT calculations of 1,4-dimethyl-2-oxo-pyrimido[1,2-a]benzimidazole hydrate

    Science.gov (United States)

    El Bakri, Youness; Anouar, El Hassane; Ramli, Youssef; Essassi, El Mokhtar; Mague, Joel T.

    2018-01-01

    Imidazopyrimidine derivatives are organic synthesized compounds with a pyrimido[1,2-a]benzimidazole as basic skeleton. They are known for their various biological properties and as an important class of compounds in medicinal chemistry. A new 1,4-dimethyl-2-oxo-pyrimido[1,2-a]benzimidazole hydrate derivative of the tilted group has been synthesized and characterized by spectroscopic techniques NMR and FT-IR; and by a single crystal X-ray diffraction. The X-ray results showed that the tricyclic core of the title compound, C12H11N3O·H2O, is almost planar. The molecules stack along the a-axis direction in head-to- tail fashion through π-stacking interactions involving all three rings. The stacks are tied together by direct Csbnd H⋯O hydrogen bonds and by Osbnd H⋯O, Osbnd N⋯N and Csbnd H⋯O hydrogen bonds with the lattice water. DFT calculations at B3LYP/6-311++G(d,p) in gas phase an polarizable continuum model have been carried out to predict the spectral and geometrical data of the tilted compound. The obtained results showed relatively good correlations between the predicted and experimental data with correlation coefficients higher than 98%.

  6. Lipase-Catalyzed Kinetic Resolution of Novel Antifungal N-Substituted Benzimidazole Derivatives.

    Science.gov (United States)

    Łukowska-Chojnacka, Edyta; Staniszewska, Monika; Bondaryk, Małgorzata; Maurin, Jan K; Bretner, Maria

    2016-04-01

    A series of new N-substituted benzimidazole derivatives was synthesized and their antifungal activity against Candida albicans was evaluated. The chemical step included synthesis of appropriate ketones containing benzimidazole ring, reduction of ketones to the racemic alcohols, and acetylation of alcohols to the esters. All benzimidazole derivatives were obtained with satisfactory yields and in relatively short times. All synthesized compounds exhibit significant antifungal activity against Candida albicans 900028 ATCC (% cell inhibition at 0.25 μg concentration > 98%). Additionally, racemic mixtures of alcohols were separated by lipase-catalyzed kinetic resolution. In the enzymatic step a transesterification reaction was applied and the influence of a lipase type and solvent on the enantioselectivity of the reaction was studied. The most selective enzymes were Novozyme SP 435 and lipase Amano AK from Pseudomonas fluorescens (E > 100). © 2016 Wiley Periodicals, Inc.

  7. JVG9, a benzimidazole derivative, alters the surface and cytoskeleton of Trypanosoma cruzi bloodstream trypomastigotes.

    Science.gov (United States)

    Díaz-Chiguer, Dylan L; Hernández-Luis, Francisco; Nogueda-Torres, Benjamín; Castillo, Rafael; Reynoso-Ducoing, Olivia; Hernández-Campos, Alicia; Ambrosio, Javier R

    2014-09-01

    Trypanosoma cruzi has a particular cytoskeleton that consists of a subpellicular network of microtubules and actin microfilaments. Therefore, it is an excellent target for the development of new anti-parasitic drugs. Benzimidazole 2-carbamates, a class of well-known broad-spectrum anthelmintics, have been shown to inhibit the in vitro growth of many protozoa. Therefore, to find efficient anti-trypanosomal (trypanocidal) drugs, our group has designed and synthesised several benzimidazole derivatives. One, named JVG9 (5-chloro-1H-benzimidazole-2-thiol), has been found to be effective against T. cruzi bloodstream trypomastigotes under both in vitro and in vivo conditions. Here, we present the in vitro effects observed by laser scanning confocal and scanning electron microscopy on T. cruzi trypomastigotes. Changes in the surface and the distribution of the cytoskeletal proteins are consistent with the hypothesis that the trypanocidal activity of JVG9 involves the cytoskeleton as a target.

  8. JVG9, a benzimidazole derivative, alters the surface and cytoskeleton of Trypanosoma cruzi bloodstream trypomastigotes

    Directory of Open Access Journals (Sweden)

    Dylan L Díaz-Chiguer

    2014-09-01

    Full Text Available Trypanosoma cruzi has a particular cytoskeleton that consists of a subpellicular network of microtubules and actin microfilaments. Therefore, it is an excellent target for the development of new anti-parasitic drugs. Benzimidazole 2-carbamates, a class of well-known broad-spectrum anthelmintics, have been shown to inhibit the in vitro growth of many protozoa. Therefore, to find efficient anti-trypanosomal (trypanocidal drugs, our group has designed and synthesised several benzimidazole derivatives. One, named JVG9 (5-chloro-1H-benzimidazole-2-thiol, has been found to be effective against T. cruzi bloodstream trypomastigotes under both in vitro and in vivo conditions. Here, we present the in vitro effects observed by laser scanning confocal and scanning electron microscopy on T. cruzi trypomastigotes. Changes in the surface and the distribution of the cytoskeletal proteins are consistent with the hypothesis that the trypanocidal activity of JVG9 involves the cytoskeleton as a target.

  9. Antiproliferative activity of synthesized some new benzimidazole carboxamidines against MCF-7 breast carcinoma cells.

    Science.gov (United States)

    Karaaslan, Cigdem; Bakar, Filiz; Goker, Hakan

    2018-02-23

    Breast cancer is the most endemic cause of cancer among women in both developed and developing countries. Benzimidazole derivatives exemplify one of the chemical classes that show strong cytotoxic activity especially against breast cancer cells (MCF-7). Aromatic amidine derivatives are known as a group of DNA interactive compounds that bind minor groove of the genome, especially A-T base pairs, and show significant in vitro and in vivo toxicity toward cancer cells. In light of these studies, some new mono/dicationic amidino benzimidazole derivatives were synthesized and evaluated for cytotoxic activity on cultured MCF-7 breast cancer cells. Some of these compounds have strongly inhibited MCF-7 cell viability in a dose-dependent manner compared with clinically used reference compounds, imatinib mesylate and docetaxel. Among them, 4-[(5(6)-bromo-1H-benzimidazole-2-yl)amino]benzene-1-carboxamidine (30) showed the best inhibitory activity with IC50 value of 4.6 nM.

  10. 99mTc labeled benzimidazole for detecting brain application

    International Nuclear Information System (INIS)

    Kumar, Nitin; Srivastava, V.; Tiwari, A.K.; Mishra, A.K.

    2010-01-01

    Full text: The synthesis and structure-activity relationship of a new class of Benzimidazole/Benzthiazole derivatives with low-nanomolar affinity for the Dopaminergic catachol and high selectivity versus the MAO receptor were found. Based on their chemical structure, four new derivatives which contain atoms to afford future labeling with PET isotopes, were synthesized and evaluated for enzyme activity. All the compound were tested for radiopharmaceutical efficacy. The % radiolabeling efficacy were found more than 95% after 24 hrs. The blood kinetics were found fast in nature which shows that this drug can be utilized for such application in which drug will go in longer time. The % reach in brain were found 3 to 5% which confirms that it can be utilized as brain imaging agent. The Enzyme kinetics of this compound has been studied spectrophotometrically at 25.0 deg C and at constant ionic strength of 0.10 mol dm-3. The products were identified by LCESI-MS technique and other spectral studies

  11. Benzimidazole and imidazole lithium salts for battery electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Scheers, Johan; Johansson, Patrik; Jacobsson, Per [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden); Szczecinski, Przemyslaw; Wieczorek, Wladyslaw [Polymer Ionics Research Group, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, PL-00664 Warsaw (Poland); Armand, Michel [Laboratoire de Reactivite et de Chimie des Solides, Universite de Picardie Jules Verne, 33 rue St. Leu, 80089 Amiens (France)

    2010-09-15

    The intrinsic anion oxidation potential ({delta}E{sub v}) and lithium ion pair dissociation energy ({delta}E{sub d}) are two important properties for predicting the potential use of new lithium salts for battery electrolytes. In this work several cyano substituted fluoroalkylated benzimidazole and imidazole anions have been investigated computationally to obtain {delta}E{sub v} and {delta}E{sub d}. Varying the number and position of cyano substituents results in large effects on the electrochemical stability of the anion and on the possible lithium ion pair configurations. The lengthening of the fluoroalkyl group introduces several new stable ion pair configurations and a small increase in anion oxidation stability. The most promising fluoroalkylated anions in the present work are the 4,5,6,7-tetracyano-2-fluoroalkylated benzimidazolides (TTB and PTB), with oxidation potentials suitable for high voltage Li-ion battery applications (<4.2 V) and much improved {delta}E{sub d} compared to PF{sub 6}{sup -} - a benchmark for commercially available anions. Further improvements in {delta}E{sub d}, with maintained stability towards oxidation, are obtainable by replacing the fluoroalkyl group by an additional cyano group, but possibly demanding increased synthesis efforts. (author)

  12. Identification and Optimization of Benzimidazole Sulfonamides as Orally Bioavailable Sphingosine 1-Phosphate Receptor 1 Antagonists with in Vivo Activity.

    Science.gov (United States)

    Hennessy, Edward J; Oza, Vibha; Adam, Ammar; Byth, Kate; Castriotta, Lillian; Grewal, Gurmit; Hamilton, Geraldine A; Kamhi, Victor M; Lewis, Paula; Li, Danyang; Lyne, Paul; Öster, Linda; Rooney, Michael T; Saeh, Jamal C; Sha, Li; Su, Qibin; Wen, Shengua; Xue, Yafeng; Yang, Bin

    2015-09-10

    We report here a novel series of benzimidazole sulfonamides that act as antagonists of the S1P1 receptor, identified by exploiting an understanding of the pharmacophore of a high throughput screening (HTS)-derived series of compounds described previously. Lead compound 2 potently inhibits S1P-induced receptor internalization in a cell-based assay (EC50 = 0.05 μM), but has poor physical properties and metabolic stability. Evolution of this compound through structure-activity relationship development and property optimization led to in vivo probes such as 4. However, this compound was unexpectedly found to be a potent CYP3A inducer in human hepatocytes, and thus further chemistry efforts were directed at addressing this liability. By employing a pregnane X receptor (PXR) reporter gene assay to prioritize compounds for further testing in human hepatocytes, we identified lipophilicity as a key molecular property influencing the likelihood of P450 induction. Ultimately, we have identified compounds such as 46 and 47, which demonstrate the desired S1P1 antagonist activity while having greatly reduced risk of CYP3A induction in humans. These compounds have excellent oral bioavailability in preclinical species and exhibit pharmacodynamic effects of S1P1 antagonism in several in vivo models following oral dosing. Relatively modest antitumor activity was observed in multiple xenograft models, however, suggesting that selective S1P1 antagonists would have limited utility as anticancer therapeutics as single agents.

  13. Molecule Matters

    Indian Academy of Sciences (India)

    is a very stable and inert molecule due to the formation of a triple bond between the two atoms. Surpris- ingly isoelectronic molecules are quite reactive making dinitrogen very useful and unique. Dinitrogen (N. 2. ) is such an innocuous molecule that you might not think it worthy of special attention. We take this molecule for.

  14. Chloridobis[2-(1,3-thiazol-4-yl-κN-1H-benzimidazole-κN3]cobalt(II chloride dihydrate

    Directory of Open Access Journals (Sweden)

    Zhan-Wang Shi

    2012-08-01

    Full Text Available In the title compound, [CoCl(C10H7N3S2]Cl·2H2O, the CoII atom is five-coordinated by four N atoms from two chelating 2-(1,3-thiazol-4-yl-1H-benzimidazole ligands and one Cl atom in a distorted trigonal–bipyramidal geometry. In the crystal, N—H...O and O—H...Cl hydrogen bonds and π–π interactions between the thiazole, imidazole and benzene rings [centroid-to-centroid distances 3.546 (2, 3.683 (2 and 3.714 (2 Å] link the complex cations, chloride anions and uncoordinating water molecules into a three-dimensional network.

  15. Bis[2-(2-aminoethyl-1H-benzimidazole-κ2N2,N3](nitrato-κ2O,O′cobalt(II chloride trihydrate

    Directory of Open Access Journals (Sweden)

    Jing Zhao

    2012-06-01

    Full Text Available In the title compound, [Co(NO3(C9H11N32]Cl·3H2O, the CoII atom is coordinated by four N atoms from two chelating 2-(2-aminoethyl-1H-benzimidazole ligands and two O atoms from one nitrate anion in a distorted octahedral coordination environment. In the crystal, N—H...Cl, N—H...O, O—H...Cl and O—H...O hydrogen bonds link the complex cations, chloride anions and solvent water molecules into a three-dimensional network. π–π interactions between the imidazole and benzene rings and between the benzene rings are observed [centroid–centroid distances = 3.903 (3, 3.720 (3, 3.774 (3 and 3.926 (3 Å].

  16. Probing the molecules of the mind

    African Journals Online (AJOL)

    Adele

    2005-01-10

    Jan 10, 2005 ... molecular medicine and molecular biology, the reader is re- ferred to recent ... Abstract. The molecular dimension of biology has been finding practical applications in all fields of medicine over the last few decades, but arguably one of the .... vironmental niches, such as the bone marrow, where cells com-.

  17. SAR of PXR transactivation in benzimidazole-based IGF-1R kinase inhibitors.

    Science.gov (United States)

    Zimmermann, Kurt; Wittman, Mark D; Saulnier, Mark G; Velaparthi, Upender; Sang, Xiaopeng; Frennesson, David B; Struzynski, Charles; Seitz, Steven P; He, Liqi; Carboni, Joan M; Li, Aixin; Greer, Ann F; Gottardis, Marco; Attar, Ricardo M; Yang, Zheng; Balimane, Praveen; Discenza, Lorell N; Lee, Francis Y; Sinz, Michael; Kim, Sean; Vyas, Dolatrai

    2010-03-01

    The SAR of PXR transactivation by 3-(benzimidazol-2-yl)-pyridine-2-one based ATP competitive inhibitors of Insulin-like Growth Factor 1 Receptor kinase (IGF-1R) is discussed. Compounds without PXR transactivation, with in vivo antitumor activity, reduced protein binding and improved oral exposure are presented. Copyright 2010 Elsevier Ltd. All rights reserved.

  18. Potassium hydroxide/dimethyl sulfoxide promoted intramolecular cyclization for the synthesis of benzimidazol-2-ones.

    Science.gov (United States)

    Beyer, Astrid; Reucher, Christine M M; Bolm, Carsten

    2011-06-03

    A new protocol for intramolecular N-arylations of ureas to form benzimidazol-2-ones has been developed. The cyclization reaction occurs in the presence of KOH and DMSO at close to ambient temperature. Under these conditions the yields are high and a wide range of functional groups are tolerated.

  19. Resistance to benzimidazoles and levamisole in nematode parasites of sheep in Nyandarua district of Kenya

    DEFF Research Database (Denmark)

    Maingi, N.; Bjørn, H.; Gichohi, V.M.

    1998-01-01

    The occurrence of anthelmintic resistance on 25 sheep farms in the Nyandarua District of Kenya was investigated, using the faecal egg count reduction test (FECRT), the egg hatch assay (EHA) and a larval development assay (LDA). In the FECRT, resistance to both benzimidazoles (BZs) and levamisole...

  20. Fixation of carbon dioxide into dimethyl carbonate over titanium-based zeolitic thiophene-benzimidazolate framework

    Science.gov (United States)

    A titanium-based zeolitic thiophene-benzimidazolate framework has been designed for the direct synthesis of dimethyl carbonate (DMC) from methanol and carbon dioxide. The developed catalyst activates carbon dioxide and delivers over 16% yield of DMC without the use of any dehydra...

  1. Stability of rare earth complexes with 2-(o-hydroxyphenyl)benzimidazole in aqueous-dioxane medium

    International Nuclear Information System (INIS)

    Akhrimenko, Z.M.; Panyushkin, V.T.; Fedorova, M.V.

    1990-01-01

    Method of potentiometric titration was used to determine protonation constants of 2-(-hydroxyphenyl)benzimidazole (pK 1 =4.5; pK 2 =11.30) and stability constants of Pr,Nd,Sm,Eu,Tb,Dy complexes with this ligand. Nonmonotonous change of lgK 1 with increase of ordinal number of rare earth element was revealed

  2. In vitro evaluation of selected benzimidazole derivatives as an antioxidant and xanthine oxidase inhibitors.

    Science.gov (United States)

    Nile, Shivraj H; Kumar, Brajesh; Park, Se W

    2013-09-01

    2-Aryl-1-arylmethyl-1H-benzimidazole derivatives having different side chains on the structure were examined in vitro for their antioxidant abilities by 2,2-diphenyl-1-picryl hydrazine radical scavenging activity, reducing ability, OH radical scavenging activity, inhibition of polyphenol oxidase and xanthine oxidase. Overall, with few exceptions, all the 2-aryl-1-arylmethyl-1H-benzimidazoles showed moderate biological activity with all parameters examined. The 2-aryl-1-arylmethyl-1H-benzimidazoles were found to be reactive toward 2,2-diphenyl-1-picryl hydrazine radical and had considerable reducing ability, with significant xanthine oxidase inhibition. With few exceptions, all the compounds under study were found to possess moderate-to-poor OH radical scavenging activity and inhibited polyphenol oxidase significantly. These findings suggest that these 2-aryl-1-arylmethyl-1H-benzimidazoles can be considered as potential antioxidant and xanthine oxidase inhibitory agents, those might be further, explored for the design of lead antioxidant and antigout drug candidates using in vivo trials. © 2013 John Wiley & Sons A/S.

  3. Novel fluorinated benzimidazole-based scaffolds and their anticancer activity in vitro

    Czech Academy of Sciences Publication Activity Database

    Bhambra, A.S.; Edgar, M.; Elsegood, M.R.J.; Horsburgh, L.; Kryštof, Vladimír; Lucas, P.D.; Mojally, M.; Teat, S. J.; Warwick, T.G.; Weaver, G.W.; Zeinali, F.

    2016-01-01

    Roč. 188, AUG (2016), s. 99-109 ISSN 0022-1139 R&D Projects: GA ČR(CZ) GA15-15264S Institutional support: RVO:61389030 Keywords : Anticancer activity * Benzimidazole * C-F activation Subject RIV: FR - Pharmacology ; Medidal Chemistry Impact factor: 2.101, year: 2016

  4. Cobalt and Nickel Complexes Bearing 2-(2-pyridyl)-Benzimidazole: Synthesis and Ethylene Oligomerization

    OpenAIRE

    Du, Jian-Long; Li-Jun-Li

    2005-01-01

    A series of cobalt and nickel complexes MLX2 (M=Co or Ni, X=Cl) bearing 2-(2-pyridyl)benzimidazole ligands were synthesized. Treatment of the complexes with methylaluminoxane (MAO) leads to active catalysts for ethylene oligomerization. The oligomers were olefins from C2 to C6.

  5. Anion exchange membrane based on alkali doped poly(2,5-benzimidazole) for fuel cell

    CSIR Research Space (South Africa)

    Luo, H

    2012-02-01

    Full Text Available The properties of alkali doped poly(2,5-benzimidazole) membrane with different alkali doping level for fuel cell application is reported in this work. The alkali doping level played an important role for the ion conductivity of the membrane. The ion...

  6. Silica Sulfuric Acid: An Eco-Friendly and Reusable Catalyst for Synthesis of Benzimidazole Derivatives

    Directory of Open Access Journals (Sweden)

    Bahareh Sadeghi

    2013-01-01

    Full Text Available Silica sulfuric acid (SiO2-OSO3H as an eco-friendly, readily available, and reusable catalyst is applied to benzimidazole derivatives synthesis under reflux in ethanol. The procedure is very simple and the products are isolated with an easy workup in good-to-excellent yields.

  7. 2-aryl benzimidazole conjugate induced apoptosis in human breast cancer MCF-7 cells through caspase independent pathway.

    Science.gov (United States)

    Nayak, V Lakshma; Nagesh, Narayana; Ravikumar, A; Bagul, Chandrakant; Vishnuvardhan, M V P S; Srinivasulu, Vunnam; Kamal, Ahmed

    2017-01-01

    Apoptosis is a representative form of programmed cell death, which has been assumed to be critical for cancer prevention. Thus, any agent that can induce apoptosis may be useful for cancer treatment and apoptosis induction is arguably the most potent defense against cancer promotion. In our previous studies, 2-aryl benzimidazole conjugates were synthesized and evaluated for their antiproliferative activity and one of the new molecule (2f) was considered as a potential lead. This lead molecule showed significant antiproliferative activity against human breast cancer cell line, MCF-7. The results of the present study revealed that this compound arrested the cell cycle at G2/M phase. Topoisomerase II inhibition assay and Western blot analysis suggested that this compound effectively inhibits topoisomerase II activity which leads to apoptotic cell death. Apoptosis induction in MCF-7 cells was further confirmed by loss of mitochondrial membrane potential (∆Ψm), release of cytochrome c from mitochondria, an increase in the level of apoptosis inducing factor (AIF), generation of reactive oxygen species (ROS), up regulation of proapoptotic protein Bax and down regulation of anti apoptotic protein Bcl-2. Apoptosis assay using Annexin V-FITC assay also suggested that this compound induced cell death by apoptosis. However, compound 2f induced apoptosis could not be reversed by Z-VAD-FMK (a pan-caspase inhibitor) demonstrated that the 2f induced apoptosis was caspase independent. Further, 2f treatment did not activate caspase-7 and caspase-9 activity, suggesting that this compound induced apoptosis in breast cancer cells via a caspase independent pathway. Most importantly, this compound was less toxic towards non-tumorigenic breast epithelial cells, MCF-10A. Furthermore, docking studies also support the potentiality of this molecule to bind to the DNA topoisomerase II.

  8. Poly[(acetato-κ2O,O′aqua(μ4-1H-benzimidazole-5,6-dicarboxylato-κ5N3:O5,O5′:O5,O6:O6′praseodymium(III

    Directory of Open Access Journals (Sweden)

    Yi-Fan Luo

    2010-10-01

    Full Text Available In the title complex, [Pr(C9H4N2O4(C2H3O2(H2O]n, the PrIII ion is coordinated by five O atoms and one N atom from four benzimidazole-5,6-dicarboxylate ligands, two O atoms from an acetate ligand and one water molecule, giving a tricapped trigonal-prismatic geometry. The benzimidazole-5,6-dicarboxylate and acetate ligands connect the PrIII ions, forming a layer in the ac plane; the layers are further linked by N—H...O and O—H...O hydrogen bonding and π–π stacking interactions between neighboring pyridine rings [the centroid–centroid distance is 3.467 (1 Å], assembling a three-dimensional supramolecular network. The acetate methyl group is disordered over two positions with site-occupancy factors of 0.75 and 0.25.

  9. Molecule nanoweaver

    Science.gov (United States)

    Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  10. Photoactive layer based on T-shaped benzimidazole dyes used for solar cell: from photoelectric properties to molecular design

    OpenAIRE

    Beibei Xu; Yuanzuo Li; Peng Song; Fengcai Ma; Mengtao Sun

    2017-01-01

    Three benzimidazole-based organic dyes, possessing the same triphenylamine donors and cyanoacrylic acid acceptors with the bithiophene ?-bridges combined in different nuclear positions of benzimidazole, were investigated in the utility of dye-sensitizer solar cells. The structure, molecular orbital and energy, absorption spectra and some important parameters (such as light harvesting efficiency (LHE), electron injection driving force, the electron injection time, chemical reactivity parameter...

  11. Vibrationally resolved ¹Lb (¹A')↔S0 (¹A') electronic spectra of benzimidazole and indene: Influence of Duschinsky and Herzberg-Teller effects on weak dipole-allowed transitions.

    Science.gov (United States)

    Yang, Pan; Pang, Min; Li, Ming; Shen, Wei; He, Rongxing

    2015-12-05

    Geometrical optimizations of the ground and first excited states of benzimidazole and indene were performed using the density functional theory (DFT) and its time-dependent extension methods (TD-DFT), respectively. Their vibrationally resolved (1)Lb ((1)A')↔S0 ((1)A') absorption and fluorescence spectra were simulated within the Franck-Condon approximation including the Herzberg-Teller (HT) and Duschinsky effects. Calculated results revealed that, with the HT and Duschinsky effects getting involved, the simulated weak (1)Lb ((1)A')↔S0 ((1)A') electronic spectra of the two molecules excellently reproduce the experimental findings. Based on the experimental data and other theoretical results, we tentatively assigned most of the vibrational normal modes which emerged in the experimental spectra of the two molecules. The present theoretical insights are expected to help us understand the nature of electronic transitions in the vibrationally resolved absorption and fluorescence spectra of benzimidazole and its analogues. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Bis(benzimidazole)amine vanadium catalysts for olefin polymerisation and co-polymerisation: thermally robust, single-site catalysts activated by simple alkylaluminium reagents.

    Science.gov (United States)

    Tomov, Atanas K; Gibson, Vernon C; Zaher, Damien; Elsegood, Mark R J; Dale, Sophie H

    2004-09-07

    Vanadium complexes containing bis(benzimidazole)amine ligands, upon activation by simple alkylaluminium reagents, give unusually robust, single-site, catalysts for olefin polymerisation/co-polymerisation.

  13. Exploring 2D and 3D QSARs of benzimidazole derivatives as transient receptor potential melastatin 8 (TRPM8 antagonists using MLR and kNN-MFA methodology

    Directory of Open Access Journals (Sweden)

    Kamlendra Singh Bhadoriya

    2016-09-01

    Full Text Available TRPM8 is now best known as a cold- and menthol-activated channel implicated in thermosensation. TRPM8 is specifically expressed in a subset of pain- and temperature-sensing neuron. TRPM8 plays a major role in the sensation of cold and cooling substances. TRPM8 is a potential new target for the treatment of painful conditions. Thus, TRPM8 antagonists represent a new, novel and potentially useful treatment strategy to treat various disease states such as urological disorders, asthma, COPD, prostate and colon cancers, and painful conditions related to cold, such as cold allodynia and cold hyperalgesia. Better tools such as potent and specific TRPM8 antagonists are mandatory as high unmet medical need for such progress. To achieve this objective quantitative structure–activity relationship (QSAR studies were carried out on a series of 25 benzimidazole-containing TRPM8 antagonists to investigate the structural requirements of their inhibitory activity against cTRPM8. The statistically significant best 2D-QSAR model having correlation coefficient r2 = 0.88 and cross-validated squared correlation coefficient q2 = 0.64 with external predictive ability of pred_r2 = 0.69 was developed by SW-MLR. The physico-chemical descriptors such as polarizabilityAHP, kappa2, XcompDipole, +vePotentialSurfaceArea, XKMostHydrophilic were found to show a significant correlation with biological activity in benzimidazole derivatives. Molecular field analysis was used to construct the best 3D-QSAR model using SW-kNN method, showing good correlative and predictive capabilities in terms of q2 = 0.81 and pred_r2 = 0.55. Developed kNN-MFA model highlighted the importance of shape of the molecules, i.e., steric & electrostatic descriptors at the grid points S_774 & E_1024 for TRPM8 receptor binding. These models (2D & 3D were found to yield reliable clues for further optimization of benzimidazole derivatives in the data set. The information rendered by 2D- and 3D

  14. Microwave-assisted RAFT polymerization of well-constructed magnetic surface molecularly imprinted polymers for specific recognition of benzimidazole residues

    Science.gov (United States)

    Chen, Fangfang; Wang, Jiayu; Chen, Huiru; Lu, Ruicong; Xie, Xiaoyu

    2018-03-01

    Magnetic nanoparticles have been widely used as support core for fast separation, which could be directly separated from complicated matrices using an external magnet in few minutes. Surface imprinting based on magnetic core has shown favorable adsorption and separation performance, including good adsorption capacity, fast adsorption kinetics and special selectivity adsorption. Reversible addition-fragmentation chain transfer (RAFT) is an ideal choice for producing well-defined complex architecture with mild reaction conditions. We herein describe the preparation of well-constructed magnetic molecularly imprinted polymers (MMIPs) for the recognition of benzimidazole (BMZ) residues via the microwave-assisted RAFT polymerization. The merits of RAFT polymerization assisting with microwave heating allowed successful and more efficient preparation of well-constructed imprinted coats. Moreover, the polymerization time dramatically shortened and was just 1/24th of the time taken by conventional heating. The results indicated that a uniform nanoscale imprinted layer was formed on the Fe3O4 core successfully, and enough saturation magnetization of MMIPs (16.53 emu g-1) was got for magnetic separation. The desirable adsorption capacity (30.18 μmol g-1) and high selectivity toward template molecule with a selectivity coefficient (k) of 13.85 of MMIPs were exhibited by the adsorption isothermal assay and competitive binding assay, respectively. A solid phase extraction enrichment approach was successfully established for the determination of four BMZ residues from apple samples using MMIPs coupled to HPLC. Overall, this study provides a versatile approach for highly efficient fabrication of well-constructed MMIPs for enrichment and determination of target molecules from complicated samples.

  15. Synthesis and Biological Evaluation of Benzimidazole Phenylhydrazone Derivatives as Antifungal Agents against Phytopathogenic Fungi

    Directory of Open Access Journals (Sweden)

    Xing Wang

    2016-11-01

    Full Text Available A series of benzimidazole phenylhydrazone derivatives (6a–6ai were synthesized and characterized by 1H-NMR, ESI-MS, and elemental analysis. The structure of 6b was further confirmed by single crystal X-ray diffraction as (E-configuration. All the compounds were screened for antifungal activity against Rhizoctonia solani and Magnaporthe oryzae employing a mycelium growth rate method. Compound 6f exhibited significant inhibitory activity against R. solani and M. oryzae with the EC50 values of 1.20 and 1.85 μg/mL, respectively. In vivo testing demonstrated that 6f could effectively control the development of rice sheath blight (RSB and rice blast (RB caused by the above two phytopathogens. This work indicated that the compound 6f with a benzimidazole phenylhydrazone scaffold could be considered as a leading structure for the development of novel fungicides.

  16. Suspicion de la résistance aux benzimidazoles chez les strongles ...

    African Journals Online (AJOL)

    Suspicion de la résistance aux benzimidazoles chez les strongles gastrointestinaux du caprin à Lubumbashi, R.D. Congo. EV Okombe, SEW Pongombo. Abstract. Cent vingt-quatre caprins sélectionnés dans deux fermes de la région de Lubumbashi en R.D. Congo, ont été examinés en utilisant le test de réduction de ...

  17. Polybenzimidazole Membranes Containing Benzimidazole Side Groups for High Temprature Polymer Electrolyte Membrane Fuel Cells

    DEFF Research Database (Denmark)

    Yang, Jingshuai; Li, Xueyuan; Xu, Yizin

    2013-01-01

    temperatures without humidification. At an acid doping level of 13.1 mol H3PO4 per average molar repeat unit, the PBI membranes with a benzimidazole grafting degree of 10.6% demonstrated a conductivity of 0.15 S cm-1 and a H2-air fuel cell peak power density of 378 mW cm-2 at 180 oC at ambient pressure without...

  18. Halide/pseudohalide complexes of cadmium(II) with benzimidazole: Synthesis, crystal structures and fluorescence properties

    Science.gov (United States)

    Zhao, Hai-Yan; Yang, Fu-Li; Li, Na; Wang, Xiao-Jing

    2017-11-01

    Two new dinuclear Cd(II) complexes, [CdL1Cl2]2·H2O (1) and [CdL1(N3)2]2·CH3OH (2) and one dicyanamide bridged one-dimensional polynuclear network [CdL1(μ1,5-dca)dca]n (3) of the potentially tridentate NNN-donor Schiff base 2-((1H-benzimidazol-2-yl-ethylimino)-methyl)pyridine (L1) and another dinucler Cd(II) complex [CdL2Cl(dca)]2 (4) of a similar NNN-donor Schiff base ligand 2-((1H-benzimidazol-2-yl-propylimino)-methyl)pyridine (L2), have been synthesized and characterized by elemental analyses, IR and single crystal X-ray crystallography. The ligands L1 and L2 are [1 + 1] condensation products of pyridine-2-carbaldehyde with 2-aminoethyl-1H-benzimidazole and 2-aminopropyl-1H-benzimidazole, respectively. In the complexes 1 and 4 the two Cd(II) centers are held together by the bridged chloride ligands, while in 2 the two Cd(II) centers are bridged by μ1,1-azide ions. Complex 3 has a one-dimensional infinite chain structure in which Cd(II) ions are bridged by single dicyanamide groups in end-to-end fashion. All the metal centers have a distorted octahedral geometry and H-bonding or π⋯π interactions are operative to bind the complex units in the solid state. Furthermore, these complexes have been investigated by thermogravimetric analyses and fluorescence spectra.

  19. Cultural probes

    DEFF Research Database (Denmark)

    Madsen, Jacob Østergaard

    The aim of this study was thus to explore cultural probes (Gaver, Boucher et al. 2004), as a possible methodical approach, supporting knowledge production on situated and contextual aspects of occupation.......The aim of this study was thus to explore cultural probes (Gaver, Boucher et al. 2004), as a possible methodical approach, supporting knowledge production on situated and contextual aspects of occupation....

  20. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 4. Molecule Matters – van der Waals Molecules - History and Some Perspectives on Intermolecular Forces ... Author Affiliations. E Arunan1. Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India.

  1. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 4. Molecule Matters – van der Waals Molecules - History and Some Perspectives on Intermolecular Forces. E Arunan. Feature Article Volume 14 Issue 4 April 2009 pp 346-356 ...

  2. MALDI-TOF MS Analysis of Native and Permethylated or Benzimidazole-Derivatized Polysaccharides

    Directory of Open Access Journals (Sweden)

    Chung-Hsuan Chen

    2012-04-01

    Full Text Available MALDI-TOF MS provides rapid and sensitive analyses of larger biomolecules. However, MS analyses of polysaccharide have been reported to have lower sensitivity compared to peptides and proteins. Here, we investigated some polysaccharides chemically derivatized by permethylation and ortho-phenylene diamine (OPD tagging. Methylated glycan is obviously able to improve the sensitivity for mass spectrometry detection. Oxidative condensation by UV-activation tagging to saccharides by OPD and peptide-OPD also improve the sensitivity of MALDI-TOF MS analyses. Polysaccharides including dextran, glucomannan, arabinoxylan, arabinogalactan and beta-1,3-glucan, isolated from nutritional supplements of Ganoderma lucidum and Saccharomyces pastorianus were measured using MALDI-TOF MS with 2,5-dihydroxybenzoic acid (2,5-DHB as the matrix. These glycans were also derivatized to methylated and benzimidazole-tagged glycans by chemical transformation for molecular weight analysis. The derivatized polysaccharides showed excellent MALDI-TOF MS signal enhancement in the molecular weight range from 1 to 5 kDa. Here, we demonstrate an efficient method to give glycan-benzimidazole (glycan-BIM derivatives for polysaccharide determination in MALDI-TOF MS. Therefore, permethylated or benzimidazole-derivatized polysaccharides provide a new option for polysaccharide analysis using MALDI-TOF MS.

  3. Novel organic dyes based on phenyl-substituted benzimidazole for dye sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Saltan, Gözde Murat [Department of Chemistry, Faculty of Arts and Science, Celal Bayar University, Yunus Emre, 45140 Manisa (Turkey); Dinçalp, Haluk, E-mail: haluk.dincalp@cbu.edu.tr [Department of Chemistry, Faculty of Arts and Science, Celal Bayar University, Yunus Emre, 45140 Manisa (Turkey); Kıran, Merve; Zafer, Ceylan [Solar Energy Institute, Ege University, Bornova, 35100 Izmir (Turkey); Erbaş, Seçil Çelik [Celal Bayar University, Materials Engineering Department, Faculty of Engineering, Yunus Emre, 45140 Manisa (Turkey)

    2015-08-01

    Two new sensitizers derived from benzimidazole core for dye-sensitized solar cell (DSSC) applications were designed and synthesized as D–π–A structures, in which two phenyl-substituted benzimidazole group, a phenyl ring and a cyanoacrylic acid were used as the electron donor, π-conjugated linkage and the electron acceptor, respectively. Effect of methoxy- and N,N-dimetylamino- moieties attached to the phenyl groups of benzimidazole were investigated by means of optical and photovoltaic measurements. The compounds exhibit broad absorption maximum at 387 nm with the tail extending up to 500 nm on TiO{sub 2}-coated thin film. The longer wavelength absorption band around 360 nm and the much longer decay components could be attributed to the existence of charge transfer state of the dyes in solutions. DSSC device fabricated by using methoxy substituted dye (BI5a) as a sensitizer shows much better incident photon-to-current conversion efficiency (IPCE) of 64% giving cell efficiency of 2.68%. - Graphical abstract: Display Omitted - Highlights: • Long decay times suggest the delayed fluorescence caused by the existence of ICT. • The best solar energy conversion efficiency was obtained for BI5a dye (2.68%). • More fluorescent BI5a dye gives higher photocurrent generation.

  4. Design, synthesis, α-glucosidase inhibitory activity, molecular docking and QSAR studies of benzimidazole derivatives

    Science.gov (United States)

    Dinparast, Leila; Valizadeh, Hassan; Bahadori, Mir Babak; Soltani, Somaieh; Asghari, Behvar; Rashidi, Mohammad-Reza

    2016-06-01

    In this study the green, one-pot, solvent-free and selective synthesis of benzimidazole derivatives is reported. The reactions were catalyzed by ZnO/MgO containing ZnO nanoparticles as a highly effective, non-toxic and environmentally friendly catalyst. The structure of synthesized benzimidazoles was characterized using spectroscopic technics (FT-IR, 1HNMR, 13CNMR). Synthesized compounds were evaluated for their α-glucosidase inhibitory potential. Compounds 3c, 3e, 3l and 4n were potent inhibitors with IC50 values ranging from 60.7 to 168.4 μM. In silico studies were performed to explore the binding modes and interactions between enzyme and synthesized benzimidazoles. Developed linear QSAR model based on density and molecular weight could predict bioactivity of newly synthesized compounds well. Molecular docking studies revealed the availability of some hydrophobic interactions. In addition, the bioactivity of most potent compounds had good correlation with estimated free energy of binding (ΔGbinding) which was calculated according to docked best conformations.

  5. A trisubstituted benzimidazole cell division inhibitor with efficacy against Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Susan E Knudson

    Full Text Available Trisubstituted benzimidazoles have demonstrated potency against Gram-positive and Gram-negative bacterial pathogens. Previously, a library of novel trisubstituted benzimidazoles was constructed for high throughput screening, and compounds were identified that exhibited potency against M. tuberculosis H37Rv and clinical isolates, and were not toxic to Vero cells. A new series of 2-cyclohexyl-5-acylamino-6-N, N-dimethylaminobenzimidazoles derivatives has been developed based on SAR studies. Screening identified compounds with potency against M. tuberculosis. A lead compound from this series, SB-P17G-A20, was discovered to have an MIC of 0.16 µg/mL and demonstrated efficacy in the TB murine acute model of infection based on the reduction of bacterial load in the lungs and spleen by 1.73 ± 0.24 Log10 CFU and 2.68 ± Log10 CFU, respectively, when delivered at 50 mg/kg by intraperitoneal injection (IP twice daily (bid. The activity of SB-P17G-A20 was determined to be concentration dependent and to have excellent stability in mouse and human plasma, and liver microsomes. Together, these studies demonstrate that SB-P17G-A20 has potency against M. tuberculosis clinical strains with varying susceptibility and efficacy in animal models of infection, and that trisubstituted benzimidazoles continue to be a platform for the development of novel inhibitors with efficacy.

  6. Synthesis, antimicrobial and cytotoxic activity of novel azetidine-2-one derivatives of 1H-benzimidazole

    Directory of Open Access Journals (Sweden)

    Malleshappa Noolvi

    2014-04-01

    Full Text Available A series of 1-methyl-N-[(substituted-phenylmethylidene-1H-benzimidazol-2-amines (4a–4g were prepared via the formation of 1-methyl-1H-benzimidazol-2-amine (3, which was prepared by the cycloaddition of o-phenylenediamine (1 with cyanogen bromide in the presence of aqueous base followed by N-methylation with methyl iodide in the presence of anhydrous potassium carbonate in dry acetonitrile. Moreover, the four-membered β-lactam ring was introduced by the cycloaddition of 4a–4g and chloroacetyl chloride in the presence of triethylamine catalyst to give 3-chloro-1-(1-methyl-1H-benzimidazol-2-yl-(4′-substituted-phenylazetidin-2-one 5a–5g. A total of 14 compounds were synthesized and characterized by IR, 1H NMR, 13C NMR and Mass spectral technique, in addition they were evaluated for anti-bacterial and cytotoxic properties. Among the chemicals tested 4a, 4b, 5a, 5b, 5g exhibited good antibacterial activity and 5f, 5g shown good cytotoxic activity in vitro.

  7. 1-Methyl-2-methylsulfanyl-6-nitro-1H-benzimidazole

    Directory of Open Access Journals (Sweden)

    Mohamed El Ghozlani

    2014-04-01

    Full Text Available The molecule of the title compound, C9H9N3O2S, is built up from fused five- and six-membered rings connected to methylsulfanyl and nitro groups, respectively. The mean plane through the fused ring system is inclined slightly relative to the plane passing through the nitro group [dihedral angle = 3.6 (2°]. In the crystal, molecules are linked by C—H...O hydrogen bonds and π–π interactions between imidazole rings [inter-centroid distance = 3.667 (3 Å], forming a three-dimensional network.

  8. Electrophoresis-mass spectrometry probe

    Science.gov (United States)

    Andresen, Brian D.; Fought, Eric R.

    1987-01-01

    The invention involves a new technique for the separation of complex mixtures of chemicals, which utilizes a unique interface probe for conventional mass spectrometers which allows the electrophoretically separated compounds to be analyzed in real-time by a mass spectrometer. This new chemical analysis interface, which couples electrophoresis with mass spectrometry, allows complex mixtures to be analyzed very rapidly, with much greater specificity, and with greater sensitivity. The interface or probe provides a means whereby large and/or polar molecules in complex mixtures to be completely characterized. The preferred embodiment of the probe utilizes a double capillary tip which allows the probe tip to be continually wetted by the buffer, which provides for increased heat dissipation, and results in a continually operating interface which is more durable and electronically stable than the illustrated single capillary tip probe interface.

  9. Atkins' molecules

    CERN Document Server

    Atkins, Peters

    2003-01-01

    Originally published in 2003, this is the second edition of a title that was called 'the most beautiful chemistry book ever written'. In it, we see the molecules responsible for the experiences of our everyday life - including fabrics, drugs, plastics, explosives, detergents, fragrances, tastes, and sex. With engaging prose Peter Atkins gives a non-technical account of an incredible range of aspects of the world around us, showing unexpected connections, and giving an insight into how this amazing world can be understood in terms of the atoms and molecules from which it is built. The second edition includes dozens of extra molecules, graphical presentation, and an even more accessible and enthralling account of the molecules themselves.

  10. Interstellar Molecules

    Science.gov (United States)

    Solomon, Philip M.

    1973-01-01

    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  11. Mobile probes

    DEFF Research Database (Denmark)

    Ørngreen, Rikke; Jørgensen, Anna Neustrup; Noesgaard, Signe Schack

    2016-01-01

    to in an interview. This method provided valuable insight into the contextual use, i.e. how did the online resource transfer to the work practice. However, the research team also found that mobile probes may provide the scaffolding necessary for individual and peer learning at a very local (intra-school) community...... level. This paper is an initial investigation of how the mobile probes process proved to engage teachers in their efforts to improve teaching. It also highlights some of the barriers emerging when applying mobile probes as a scaffold for learning.......A project investigating the effectiveness of a collection of online resources for teachers' professional development used mobile probes as a data collection method. Teachers received questions and tasks on their mobile in a dialogic manner while in their everyday context as opposed...

  12. Counting probe

    International Nuclear Information System (INIS)

    Matsumoto, Haruya; Kaya, Nobuyuki; Yuasa, Kazuhiro; Hayashi, Tomoaki

    1976-01-01

    Electron counting method has been devised and experimented for the purpose of measuring electron temperature and density, the most fundamental quantities to represent plasma conditions. Electron counting is a method to count the electrons in plasma directly by equipping a probe with the secondary electron multiplier. It has three advantages of adjustable sensitivity, high sensitivity of the secondary electron multiplier, and directional property. Sensitivity adjustment is performed by changing the size of collecting hole (pin hole) on the incident front of the multiplier. The probe is usable as a direct reading thermometer of electron temperature because it requires to collect very small amount of electrons, thus it doesn't disturb the surrounding plasma, and the narrow sweep width of the probe voltage is enough. Therefore it can measure anisotropy more sensitively than a Langmuir probe, and it can be used for very low density plasma. Though many problems remain on anisotropy, computer simulation has been carried out. Also it is planned to provide a Helmholtz coil in the vacuum chamber to eliminate the effect of earth magnetic field. In practical experiments, the measurement with a Langmuir probe and an emission probe mounted to the movable structure, the comparison with the results obtained in reverse magnetic field by using a Helmholtz coil, and the measurement of ionic sound wave are scheduled. (Wakatsuki, Y.)

  13. 2-(1H-Benzimidazol-2-ylphenol

    Directory of Open Access Journals (Sweden)

    S. M. Prakash

    2014-02-01

    Full Text Available The title molecule, C13H10N2O, is essentially planar, the maximum deviation from the plane of the non-H atoms being 0.016 (2 Å. The imidazole ring makes a dihedral angle of 0.37 (13° with the attached benzene ring. An intramolecular O—H...N hydrogen bond generates an S(6 ring motif. In the crystal, molecules are linked through N—H...O hydrogen bonds, forming chains propagating in [001]. The crystal packing also features four π–π stacking interactions involving the imidazole ring, fused benzene ring and attached benzene ring system [centroid–centroid distances = 3.6106 (17, 3.6108 (17, 3.6666 (17 and 3.6668 (17 Å].

  14. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  15. Synthesis of potent and tissue-selective androgen receptor modulators (SARMs): 2-(2,2,2)-Trifluoroethyl-benzimidazole scaffold.

    Science.gov (United States)

    Ng, Raymond A; Lanter, James C; Alford, Vernon C; Allan, George F; Sbriscia, Tifanie; Lundeen, Scott G; Sui, Zhihua

    2007-03-15

    The synthesis and in vivo SAR of 2-(2,2,2)-trifluoroethyl-benzimidazoles are described. Prostate antagonism and/or levator ani agonism can be modulated by varying the substitution at the 2-position of 5,6-dichloro-benzimidazoles. Potent androgen agonists on the muscle were discovered that strongly bind to the androgen receptor (2-17 nM) and show potent in vivo efficacy (0.03-0.11 mg/day). True SARMs showing both prostate antagonism and levator ani agonism were revealed.

  16. Adhesion molecules

    CERN Document Server

    Preedy, Victor R

    2016-01-01

    This book covers the structure and classification of adhesion molecules in relation to signaling pathways and gene expression. It discusses immunohistochemical localization, neutrophil migration, and junctional, functional, and inflammatory adhesion molecules in pathologies such as leukocyte decompression sickness and ischemia reperfusion injury. Highlighting the medical applications of current research, chapters cover diabetes, obesity, and metabolic syndrome; hypoxia; kidney disease; smoking, atrial fibrillation, and heart disease, the brain and dementia; and tumor proliferation. Finally, it looks at molecular imaging and bioinformatics, high-throughput technologies, and chemotherapy.

  17. Conductivity Probe

    Science.gov (United States)

    2008-01-01

    The Thermal and Electrical Conductivity Probe (TECP) for NASA's Phoenix Mars Lander took measurements in Martian soil and in the air. The needles on the end of the instrument were inserted into the Martian soil, allowing TECP to measure the propagation of both thermal and electrical energy. TECP also measured the humidity in the surrounding air. The needles on the probe are 15 millimeters (0.6 inch) long. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  18. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule Matters - Dinitrogen. A G Samuelson J Jabadurai. Volume 16 Issue 12 ... Author Affiliations. A G Samuelson1 J Jabadurai1. Department of Inroganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India.

  19. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 5. Molecule Matters - N-Heterocyclic Carbenes - The Stable Form of R2 C: Anil J Elias. Feature Article Volume 13 Issue 5 May 2008 pp 456-467. Fulltext. Click here to view fulltext PDF. Permanent link:

  20. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 9. Molecule Matters - A Chromium Compound with a Quintuple Bond. K C Kumara Swamy. Feature Article Volume 11 Issue 9 September 2006 pp 72-75. Fulltext. Click here to view fulltext PDF. Permanent link:

  1. Glycerol Containing Triacetylborate Mediated Syntheses of Novel 2-Heterostyryl Benzimidazole Derivatives: A Green Approach

    Directory of Open Access Journals (Sweden)

    Ashok Kumar Taduri

    2014-01-01

    Full Text Available A very simple, mild, efficient, and novel green methodology has been developed for the syntheses of some 2-hetero/styryl-benzimidazoles. Title compounds were synthesized by the condensation of o-phenylenediamine with cinnamic acids at 150–180°C for 5-6 h using glycerol containing triacetylborate (10–20 mol% as the reaction medium. In an alternative approach, condensation of 2-methylbenzimidazole derivatives with aromatic aldehydes was done using glycerol containing triacetylborate (10–20 mol% as the reaction medium.

  2. Sulfonated copolyimide membranes derived from a novel diamine monomer with pendant benzimidazole groups for fuel cells

    DEFF Research Database (Denmark)

    Li, Wei; Guo, Xiaoxia; Aili, David

    2015-01-01

    Sulfonated polyimides are among the most interesting proton exchange membrane materials with high proton conductivity and good mechanical characteristics. As a major challenge the hydrolytic instability of the polymer backbone is addressed by introducing basic moieties in the polymer main chain....... A series of sulfonated copolyimides (SPI) are prepared via random copolymerizatio of 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTDA) with a new diamine monomer with pendant benzimidazole groups, 2,2'-bis(4-(1H-benzo[d]imidazol-2-yl)phenoxy)benzidine (BIPOB), and a sulfonated diamine monomer 4,4'-bis...

  3. (S-2-(2-Pyrrolidinio-1H-benzimidazol-3-ium dichloride monohydrate

    Directory of Open Access Journals (Sweden)

    Dai Jing

    2009-06-01

    Full Text Available In the title compound, C11H15N32+·2Cl−·H2O, one N atom of the imidazole ring and the N atom of the pyrrolidine ring are protonated. The crystal structure is stabilized by aromatic π–π interactions between the benzene rings of neighbouring benzimidazole systems [centroid–centroid duistance = 3.712 (2 Å]. The crystal structure is further stabilized by intermolecular N—H...Cl, O—H...Cl and N—H...O hydrogen bonds.

  4. 2-(2'-pyridyl) benzimidazole complexes of dioxouranium (VI) and thorium(VI)

    International Nuclear Information System (INIS)

    Dash, K.C.; Mohanta, H.

    1978-01-01

    The bidentate ligand, 2-(2'-pyridyl) benzimidazole (PBH), forms a variety of complexes with dioxouranium(VI) and thorium(IV) of the type, U0 2 (PBH)sub(n)X 2 (n = l, X Cl, I, NO 3 , O.5SO 4 : n = 2, X = NCS), UO 2 (PBH) 3 (ClO 4 ) 2 , Th(PBH) 2 X 4 = Cl, NCS, NO 3 ) and Th(PBH) 4 (ClO 4 ) 4 . Microanalysis, electric conductivity in various non-aqueous media, electronic and IR (down to 200 cm -1 ) spectra, mass spectra and the TGA, DTA measurements on the complexes are reported. (author)

  5. Unprecedented chemosensing behavior of novel tetra-substituted benzimidazole zinc(II) phthalocynine for selective detection of Bi3 + ion: Synthesis, characterization and ROS generation

    Science.gov (United States)

    Ullah, Azeem; Shah, Faheem; Khan, Imran; Anwar, Muhammad; Shah, Kiramat; Muhammad, Munira Taj; Ahmad, Farid

    2018-03-01

    In this work, synthesis of novel symmetrical 4-(2-bromo-4-(5-bromo-1H-benzo[d] imidazol-2-yl) phenoxy) tetra substituted zinc phthalocyanine has been reported. The novel benzimidazole zinc phthlocynine compound (3) has been characterized by MALDI-TOF MS, FT-IR, UV-vis, and 1H NMR spectroscopy. This new compound 3 displayed excellent selectivity towards Bi3 + ion in the presence of other competitive ions including Ca2 +, Cd2 +, Co2 + Cu2 +, Fe3 +, Hg2 +, Sn2 +, Mg2 +, Na+, Ni2 + and Pb2 + respectively. Upon addition of Bi3 + into the solution of compound 3 in DMSO, dramatic change was observed in the Q- and the B-bands in UV-visible spectra as a result of donor acceptor interactions. Reactive oxygen species (ROS) were also studied using 2,7-dichlorofluorescin diacetate (DCFH-DA) a fluorescent probe which is converted to highly fluorescent dichlorofluorescein (DCF) in the presence of ROS. This property of non-aggregating zinc phthalocyanine is promising as a photosensitizer in photodynamic therapy of cancer.

  6. Pollution Probe.

    Science.gov (United States)

    Chant, Donald A.

    This book is written as a statement of concern about pollution by members of Pollution Probe, a citizens' anti-pollution group in Canada. Its purpose is to create public awareness and pressure for the eventual solution to pollution problems. The need for effective government policies to control the population explosion, conserve natural resources,…

  7. Probe specificity

    International Nuclear Information System (INIS)

    Laget, J.M.

    1986-11-01

    Specificity and complementarity of hadron and electron probes must be systematically developed to answer three questions currently asked in intermediate energy nuclear physics: what is nucleus structure at short distances, what is nature of short range correlations, what is three body force nature [fr

  8. 1-Methyl-6-nitro-1H-benzimidazole

    Directory of Open Access Journals (Sweden)

    Svetozar Katuščák

    2008-04-01

    Full Text Available The title compound, C8H7N3O2, a potential antitumour drug and an antioxidant agent, was studied in order to give more insight into structure–function relationships. The 1-methylbenzimidazole unit of the molecule was found to be exactly planar and the nitro group is inclined at an angle of 10.4 (2° to the plane of the heterocycle. The bond lengths in the present derivative were analyzed in details and compared with those of the parent unsubstituted analogues in the Cambridge Structural Database. The results have shown that the additional nitro group is not involved in conjugation with the adjacent π-system and hence has no effect on the charge distribution of the heterocyclic ring.

  9. From A Fundamental Study on Hydrogen Bond Network and Chain Mobility in Benzimidazole Model Compounds to Various Designs and Development of Benzimidazole-based Anhydrous Membranes for Proton Exchange Membrane Fuel Cell

    Directory of Open Access Journals (Sweden)

    Suwabun Chirachanchai

    2011-12-01

    Full Text Available A series of N-containing heterocycles i.e., imidazole and benzimidazole are systematically designed to study how proton transfer in anhydrous system is related to hydrogen bond network and molecular mobility. The work extends to polymers containing heterocycles to clarify the proton conductivity in proton exchange membrane fuel cell (PEMFC.

  10. Synthesis and properties of mixed-ligand ruthenium(II) complexes containing 2-(2-pyridyl)-benzimidazole and related ligands

    International Nuclear Information System (INIS)

    Haga, Masaaki; Tanaka, Toshio.

    1979-01-01

    Mixed-ligand ruthenium(II) complexes of the [Ru(bpy) 2 L]sup(n+) (ClO 4 )sub(n) type, where bpy= 2,2'-bipyridine; L= 2-(2-pyridyl)-benzimidazole (PBImH) when n= 2, and L= 2-(2-pyridyl)-benzimidazolate (PBIm) and 2-(o-hydroxyphenyl)-benzimidazole (OBImH) when n= 1, were prepared. Anodic peak potentials and ruthenium-to-bipyridine charge transfer bands of these complexes are rationalized in terms of the donor ability of L. (author)

  11. Benzimidazole derivative M084 extends the lifespan of Caenorhabditis elegans in a DAF-16/FOXO-dependent way.

    Science.gov (United States)

    Ding, Ai-Jun; Wu, Gui-Sheng; Tang, Bin; Hong, Xuechuan; Zhu, Michael X; Luo, Huai-Rong

    2017-02-01

    With the growth of aging population, there is increasing demand to develop strategy to improve the aging process and aging-related diseases. Benzimidazole and its derivatives are crucial heterocyclic backbone of many drugs and compounds with diverse therapeutic applications, including alleviation of aging-related diseases. Here, we investigate if the benzimidazole derivative n-butyl-[1H]-benzimidazol-2-amine (M084), a novel inhibitor of TRPC4 and TRPC5 channels and antidepressant, could affect the lifespan of Caenorhabditis elegans (C. elegans). Our results showed that M084 could extend the lifespan of C. elegans, delay age-related decline of phenotypes, and improve stress resistance. M084 could not extend the lifespan of the loss-of-function mutants of daf-16, daf-2, pdk-1, aak-2, clk-1, isp-1, sir-2.1, and skn-1. M084 could decrease the ATP level and increase the gene expression of mitochondrial unfolded protein response factors. Thus, M084 might inhibit the mitochondrial respiration, activate mitochondrial unfolded protein response and AMPK, recruite SIR-2.1 and SKN-1, and finally through the transcription factor DAF-16, delay the aging process of C. elegans. Our findings reveal the new pharmaceutical potential of benzimidazole derivatives and provide clue for developing novel anti-aging agents.

  12. Synthesis and optical properties of novel pyrido[1,2-a]benzimidazole-containing 1,3,4-oxadiazole derivatives

    International Nuclear Information System (INIS)

    Yang He; Ge Yanqing; Jia Jiong; Wang Jianwu

    2011-01-01

    A series of novel substituted 1,3,4-oxadiazole derivatives containing pyrido[1,2-a]benzimidazole moiety were synthesized and characterized using FTIR, 1 H NMR, 13 C NMR, and HRMS. An efficient tandem reaction was employed as a key step in constructing the pyrido[1,2-a]benzimidazole moiety under very mild condition. The structure of compound 4a was established by X-ray crystallography. The UV-vis absorption and fluorescence spectral characteristics of these compounds were investigated in several solvents. Compounds 4a-i display similar absorptions, with absorption peaks ranging from 330 to 339 nm in acetonitrile, while the absorption maxima of compound 4j bearing a diphenylamino group on the benzene ring is red-shifted distinctly to 377 nm due to the strong electron-donating property of its substituent and extended π-conjugated system. All these target heterocyclic compounds present blue-green emissions (461-487 nm) in dilute solutions and show high quantum yields of fluorescence (φ PL =0.65-0.99) in dichloromethane. - Research Highlights: → The first report about the unique optical properties of pyrido[1,2-a]benzimidazole heteroaromatic compounds containing 1,3,4-oxadiazole unit. → Synthesis of pyrido[1,2-a]benzimidazole moiety via a novel efficient tandem reaction. → The target heterocyclic compounds showing high quantum yields of fluorescence, with great potential for use as fluorescent pigments and in optical/electro devices.

  13. Design, synthesis, molecular docking and biological evaluation of new dithiocarbamates substituted benzimidazole and chalcones as possible chemotherapeutic agents.

    Science.gov (United States)

    Bacharaju, Keerthana; Jambula, Swathi Reddy; Sivan, Sreekanth; Jyostnatangeda, Saritha; Manga, Vijjulatha

    2012-05-01

    A series of novel dithiocarbamates with benzimidazole and chalcone scaffold have been designed synthesised and evaluated for their antimitotic activity. Compounds 4c and 9d display the most promising antimitotic activity with IC(50) of 1.66 μM and 1.52 μM respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Novel sulfonated poly(arylene ether ketone) copolymers bearing carboxylic or benzimidazole pendant groups for proton exchange membranes

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Haidan; Zhao, Chengji; Ma, Wenjia; Fu, Tiezhu; Na, Hui [Alan G. MacDiarmid Institute, College of Chemistry, Jilin University, Changchun 130012 (China); Cui, Zhiming; Xing, Wei [Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022 (China)

    2009-09-05

    A novel strategy in which the benzimidazole group and sulfonic group are simultaneously attached to an aromatic polymer has been reported in this paper. For this purpose, sulfonated poly(arylene ether ketone) copolymers containing carboxylic acid groups (SPAEK-x-COOH, x refers to the molar percentage of sulfonated repeating units) are prepared by the aromatic nucleophilic polycondensation of sodium 5,5'-carbonyl-bis(2-fluobenzene-sulfonate) (SDFBP), 4,4'-difluorobenzophenone (DFBP) and phenolphthalin (PPL). Then the carboxylic acid groups attached to the SPAEK-x-COOH are transformed to benzimidazole units through condensation reactions (referred to as SPAEK-x-BI). Fourier transform infrared spectroscopy and {sup 1}H NMR measurements are used to characterize and confirm the structures of these copolymers. SPAEK-x-COOH membranes exhibit superior mechanical properties with maximum elongations at break up to 133%, meanwhile SPAEK-x-BI also shows good thermal and mechanical stability. The proton conductivity, swelling ratio and methanol permeability of the polymers with benzimidazole are lower than those with carboxylic groups, which indicated that there is an acid-base complex between benzimidazole and sulfonic acid groups. A balance of proton conductivity, methanol permeability, thermal and mechanical stabilities can be designed by incorporation of functional groups to meet the requirements for the applications in direct methanol fuel cells. (author)

  15. Ionization probes of molecular structure and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, P.M. [State Univ. of New York, Stony Brook (United States)

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  16. Microwave-assisted Synthesis of Benzimidazole Derivatives from Citronellal in Kaffir Lime (Citrus hystrix DC.) Oil

    Science.gov (United States)

    Sapri Ramadhan, Dwi; Warsito; Dhiaul Iftitah, Elvina

    2018-01-01

    Benzimidazoles are an important group of heterocyclic aromatic organic compound in the field of medicinal chemistry. It plays a very important role in pharmacological activity such as, analgesic, antiinflammatory, antibacterial, anti ungal, anti iral, antithelmenthic, anti convulsant, antihypertensive, and antiulcer. The synthesis of benzimidazole derivative under microwave irradiation of citronellal as raw material which is extracted from Citrus hystrix DC. (kaffir lime) leaves. The reaction using methanol and dichloromethane as solvent with variation of reaction time at 30, 40, 50, 60, and 70 minutes and mole ratio of citronellal to 1,2-phenylenediamine, 1:1, 1:1.5, and 1:2, respectively. Synthesis products was characterized by FT-IR and GC-MS. The optimum reaction time was obtained at 60 minutes in the present of dichloromethane and 1:2 mole ratio of citronellal to 1,2-phenylenediamine. The yield of the product is 42.19%. Structure of the synthesized compound were assigned on spectrum bands for C=N str at 1661 cm-1, C-N str at 1271 cm-1, C=C str of benzene ring at 1622 and 1456 cm-1 and C=C str of alkene at 1379 cm-1. GC-MS analysis showed single peak with retention time of 15.339 minute and m/z 242.

  17. Neutral alkaline-metal and alkaline-earth-metal derivatives of imidazole and benzimidazole.

    Science.gov (United States)

    Blanco, Fernando; Lloyd, David G; Alkorta, Ibon; Elguero, José

    2014-06-12

    A theoretical study of the minima and connecting transition states of the neutral complexes formed by alkaline-metal and alkaline-earth-metal derivatives of imidazolate and benzimidazolate anions has been carried out using B3LYP/6-31+G(d,p), B3LYP/6-311+G(3df,2p), and G3B3 methods. Two and three nondegenerated minima and two and four TS structures have been identified for imidazole and benzimidazole derivatives, respectively. The most stable minima of the alkaline-metal derivatives of both systems correspond to the metal interacting with the imidazole ring, whereas in the alkaline-earth-metal derivatives, the preferred minima depend on the substituent. A remarkable feature of some minima is the fact that some of the metal-aromatic interactions follow the classical π-cation pattern, even though the global structure corresponds to a neutral salt, constituting a class of noncovalent interaction of great interest in the chemistry of aromatic and heterocyclic complexes. A CSD search has confirmed that the two bonding modes, N-σ and π, are present in the solid phase. The π mode has been analyzed by comparison with other azoles.

  18. Hybrid imidazole (benzimidazole)/pyridine (quinoline) derivatives and evaluation of their anticancer and antimycobacterial activity.

    Science.gov (United States)

    Mantu, Dorina; Antoci, Vasilichia; Moldoveanu, Costel; Zbancioc, Gheorghita; Mangalagiu, Ionel I

    2016-01-01

    The design, synthesis, structure, and in vitro anticancer and antimycobacterial activity of new hybrid imidazole (benzimidazole)/pyridine (quinoline) derivatives are described. The strategy adopted for synthesis is straight and efficient, involving a three-step setup procedure: N-acylation, N-alkylation, and quaternization of nitrogen heterocycle. The solubility in microbiological medium and anticancer and antimycobacterial activity of a selection of new synthesized compounds were evaluated. The hybrid derivatives have an excellent solubility in microbiological medium, which make them promising from the pharmacological properties point of view. One of the hybrid compounds, 9 (with a benzimidazole and 8-aminoquinoline skeleton), exhibits a very good and selective antitumor activity against Renal Cancer A498 and Breast Cancer MDA-MB-468. Moreover, the anticancer assay suggests that the hybrid Imz (Bimz)/2-AP (8-AQ) compounds present a specific affinity to Renal Cancer A498. Concerning the antimycobacterial activity, only the hybrid compound, 9, has a significant activity. SAR correlations have been performed.

  19. Optoelectronic performance comparison of new thiophene linked benzimidazole conjugates with diverse substitution patterns

    Science.gov (United States)

    Saltan, Gözde Murat; Dinçalp, Haluk; Kırmacı, Eser; Kıran, Merve; Zafer, Ceylan

    2018-01-01

    In an approach to develop efficient organic optoelectronic devices to be used in light-driven systems, a series of three thiophene linked benzimidazole conjugates were synthesized and characterized. The combination of two thiophene rings to a benzimidazole core decorated with different functional groups (such as sbnd OCH3, sbnd N(CH3)2, sbnd CF3) resulted in donor-acceptor type molecular scaffold. The effect of the electronic behavior of the substituents on the optical, electrochemical, morphological and electron/hole transporting properties of the dyes were systematically investigated. DTBI2 dye exhibited distinct absorption properties among the other studied dyes because N,N-dimethylamino group initiated intramolecular charge transfer (ICT) process in the studied solvents. In solid state, the dyes exhibit peaks extending up to 600 nm. Depending on the solvent polarities, dyes show significant wavelength changes on their fluorescence emission spectra in the excited states. Morphological parameters of the thin films spin-coated from CHCl3 solution were investigated by using AFM instrument; furthermore photovoltaic responses are reported, even though photovoltaic performances of the fabricated solar cells with different configurations are quite low.

  20. Adsorption and desorption characteristic of benzimidazole based fungicide carbendazim in pakistani soils

    International Nuclear Information System (INIS)

    Ahmad, K.S.; Rashid, N.; Tazaiyen, S.; Nazar, M.F.

    2013-01-01

    A versatile cost-effective Benzimidazole based fungicide, Carbendazim (methyl 1H-benzimidazole-2 carboxylate ) has been utilized to investigate its sorption-desorption behaviour on physicochemical properties of geographical soils, ranging from hilly to desert areas of Pakistan, via batch equilibrium method. The data obtained in all tests showed that adsorption co-efficient isotherm for Carbendazim in four tested soil were well fitted the freundlich equation. Distribution co-efficient (K d ) parameters are low (3.59 to 11.60 ml micro g/sup -1/) indicating low adsorption. It was observed that Carbendazim showed a relatively greater degree of adsorption on soil samples (Soil 4) that were collected from northern hilly areas Ayubia, Khyber Pakhton khaw (KPK) (Silt loam) i.e.11.60 ml mu g/sup -1/ and least adsorption on sandy Soil of Multan Punjab(Soil 2). While other two soils 1 were collected from Murree region, a boarder of Punjab and KPK mountain area and Soil 3 from Tarnol, Islamabad. Desorption studies reveal that the adsorbed fungicide is firmly retained by soil particles and their adsorption are almost irreversible. The results indicate that soil organic matter (SOM) and appropriate pH also play key role in sorption capacity. (author)

  1. Experimental and Theoretical Study of the Reactivity of Gold Nanoparticles Towards Benzimidazole-2-ylidene Ligands.

    Science.gov (United States)

    Rodríguez-Castillo, María; Lugo-Preciado, Gustavo; Laurencin, Danielle; Tielens, Frederik; van der Lee, Arie; Clément, Sébastien; Guari, Yannick; López-de-Luzuriaga, José M; Monge, Miguel; Remacle, Françoise; Richeter, Sébastien

    2016-07-18

    The reactivity of benzimidazol-2-ylidenes with respect to gold nanoparticles (AuNPs) has been investigated using a combined experimental and computational approach. First, the grafting of benzimidazol-2-ylidenes bearing benzyl groups on the nitrogen atoms is described, and comparisons are made with structurally similar N-heterocyclic carbenes (NHCs) bearing other N-groups. Similar reactivity was observed for all NHCs, with 1) the erosion of the AuNPs under the effect of the NHC and 2) the formation of bis(NHC) gold complexes. DFT calculations were performed to investigate the modes of grafting of such ligands, to determine adsorption energies, and to rationalize the spectroscopic data. Two types of computational models were developed to describe the grafting onto large or small AuNPs, with either periodic or cluster-type DFT calculations. Calculations of NMR parameters were performed on some of these models, and discussed in light of the experimental data. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Silane Cross-Linked Sulfonted Poly(Ether Ketone/Ether Benzimidazoles for Fuel Cell Applications

    Directory of Open Access Journals (Sweden)

    Zilu Yao

    2017-11-01

    Full Text Available γ-(2,3-epoxypropoxy propyltrimethoxysilane (KH-560 was incorporated in various proportions into side-chain-type sulfonated poly(ether ketone/ether benzimidazole (SPEKEBI as a crosslinker, to make membranes with high ion exchange capacities and excellent performance for direct methanol fuel cells (DMFCs. Systematical measurements including Fourier transform infrared (FT-IR, scanning electron microscopy-energy-dispersive and X-ray photoelectron spectroscopy (XPS proved the complete disappearance of epoxy groups in KH-560 and the existence of Si in the membranes. The resulting membranes showed increased mechanical strength and thermal stability compared to the unmodified sulfonated poly(ether ketone/ether benzimidazole membrane in appropriate doping amount. Meanwhile, the methanol permeability has decreased, leading to the increase of relative selectivities of SPEKEBI-x-SiO2 membranes. Furthermore, the H2/O2 cell performance of SPEKEBI-2.5-SiO2 membrane showed a much higher peak power density compared with the pure SPEKEBI memrbrane.

  3. An effective colorimetric and ratiometric fluorescent probe for bisulfite in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Xi [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Zhang, Tao [Institute of Developmental Biology, School of Life Science, Shandong University, Jinan 250100 (China); Du, Zhi-Fang; Cao, Xiang-Jian; Chen, Ming-Yu [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Taishan College, Shandong University, Jinan 250100 (China); Hu, Sheng-Wen [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Miao, Jun-Ying, E-mail: miaojy@sdu.edu.cn [Institute of Developmental Biology, School of Life Science, Shandong University, Jinan 250100 (China); Zhao, Bao-Xiang, E-mail: bxzhao@sdu.edu.cn [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China)

    2015-08-12

    We have developed the first two-photon colorimetric and ratiometric fluorescent probe, BICO, for the detection of bisulfite (HSO{sub 3}{sup −}) in aqueous solution. The probe contains coumarin and benzimidazole moieties and can detect HSO{sub 3}{sup −} based on the Michael addition reaction with a limit of detection 5.3 × 10{sup −8} M in phosphate-buffered saline solution. The probe was used to detect bisulfite in tap water, sugar and dry white wine. Moreover, test strips were made and used easily. We successfully applied the probe to image living cells, using one-photon fluorescence imaging. BICO overcomes the limitations in sensitivity of previously reported probes and the solvation effect of bisulfite, which demonstrates its excellent value in practical application. - Highlights: • A colorimetric and ratiometric fluorescent probe was developed. • The probe could detect bisulfite in PBS buffer solution and real samples. • Bisulfite test paper was made to naked-eye detect bisulfite. • This probe successfully used to living cell imaging in ratiometric manner.

  4. An effective colorimetric and ratiometric fluorescent probe for bisulfite in aqueous solution

    International Nuclear Information System (INIS)

    Dai, Xi; Zhang, Tao; Du, Zhi-Fang; Cao, Xiang-Jian; Chen, Ming-Yu; Hu, Sheng-Wen; Miao, Jun-Ying; Zhao, Bao-Xiang

    2015-01-01

    We have developed the first two-photon colorimetric and ratiometric fluorescent probe, BICO, for the detection of bisulfite (HSO 3 − ) in aqueous solution. The probe contains coumarin and benzimidazole moieties and can detect HSO 3 − based on the Michael addition reaction with a limit of detection 5.3 × 10 −8  M in phosphate-buffered saline solution. The probe was used to detect bisulfite in tap water, sugar and dry white wine. Moreover, test strips were made and used easily. We successfully applied the probe to image living cells, using one-photon fluorescence imaging. BICO overcomes the limitations in sensitivity of previously reported probes and the solvation effect of bisulfite, which demonstrates its excellent value in practical application. - Highlights: • A colorimetric and ratiometric fluorescent probe was developed. • The probe could detect bisulfite in PBS buffer solution and real samples. • Bisulfite test paper was made to naked-eye detect bisulfite. • This probe successfully used to living cell imaging in ratiometric manner

  5. Benzimidazole derivative small-molecule 991 enhances AMPK activity and glucose uptake induced by AICAR or contraction in skeletal muscle

    DEFF Research Database (Denmark)

    Bultot, Laurent; Jensen, Thomas Elbenhardt; Lai, Yu-Chiang

    2016-01-01

    AMP-activated protein kinase (AMPK) plays diverse roles and coordinates complex metabolic pathways for maintenance of energy homeostasis. This could be explained by the fact that AMPK exists as multiple heterotrimer complexes comprising a catalytic α-subunit (α1 and α2) and regulatory β (β1 and β...

  6. Visualizing Chemical Bonds in Synthetic Molecules

    Science.gov (United States)

    Collins, Laura C.; Ruth, Anthony; Green, David B.; Janko, Boldizsar; Gomes, Kenjiro K.

    The use of synthetic quantum systems makes it possible to study phenomena that cannot be probed by conventional experiments. We created synthetic molecules using atomic manipulation and directly imaged the chemical bonds using tunneling spectroscopy. These synthetic systems allow us to probe the structure and electronic properties of chemical bonds in molecules, including those that would be unstable in nature, with unprecedented detail. The experimental images of electronic states in our synthetic molecules show a remarkable match to the charge distribution predicted by density functional theory calculations. The statistical analysis of the spectroscopy of these molecules can be adapted in the future to quantify aromaticity, which has been difficult to quantify universally thus far due to vague definitions. We can also study anti-aromatic molecules which are unstable naturally, to illuminate the electronic consequences of antiaromaticity.

  7. Application of a Reverse Line Blot hybridisation assay for the species-specific identification of cyathostomins (Nematoda, Strongylida) from benzimidazole-treated horses in the Slovak Republic.

    Science.gov (United States)

    Cernanská, Dana; Paoletti, Barbara; Králová-Hromadová, Ivica; Iorio, Raffaella; Cudeková, Patrícia; Milillo, Piermarino; Traversa, Donato

    2009-03-09

    Five horse farms located in eastern Slovakia were investigated for the presence of benzimidazole-resistant strongyles by faecal egg count reduction test and egg hatch assay. Coprocultures were prepared for each farm from faecal samples taken pre- and post-treatment and harvested larvae were molecularly examined with a Reverse Line Blot assay. Faecal egg count reduction values ranged from 0 to 52.5% and all farms were positive for benzimidazole-resistant cyathostomins. Seven benzimidazole-resistant cyathostomin species were molecularly identified on farms before and also after treatment. These data demonstrate that resistance to benzimidazoles is well established in cyathostomin populations from horse farms in the Slovak Republic and that the molecular assay was able to determine the species-specific distribution of resistant cyathostomins under field conditions.

  8. The Synthesis and Biological Evaluation of N-Substituted 1H-Benzimidazol-2-yl-1H-pyrazole-3,5-diamines

    Czech Academy of Sciences Publication Activity Database

    Jedinák, L.; Kryštof, Vladimír; Cankař, P.

    2016-01-01

    Roč. 53, č. 2 (2016), s. 499-507 ISSN 0022-152X Institutional support: RVO:61389030 Keywords : ONE-POT SYNTHESIS * BENZIMIDAZOLE DERIVATIVES * EFFICIENT SYNTHESIS Subject RIV: CE - Biochemistry Impact factor: 0.893, year: 2016

  9. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 12. Molecule Matters van der Waals Molecules - Noble Gas Clusters are London Molecules! E Arunan. Feature Article Volume 14 Issue 12 December 2009 pp 1210-1222 ...

  10. Synthesis and evaluation of benzimidazole carbamates bearing indole moieties for antiproliferative and antitubulin activities.

    Science.gov (United States)

    Guan, Qi; Han, Chunming; Zuo, Daiying; Zhai, Min'an; Li, Zengqiang; Zhang, Qian; Zhai, Yanpeng; Jiang, Xuewei; Bao, Kai; Wu, Yingliang; Zhang, Weige

    2014-11-24

    A series of novel benzimidazole carbamates bearing indole moieties with sulphur or selenium atoms connecting the aromatic rings were synthesised and evaluated for their antiproliferative activities against three human cancer cell lines (SGC-7901, A-549 and HT-1080) using an MTT assay. Compounds 10a, 10b, 7a, 7b and 7f showed significant activities against these cell lines. The most potent compound in this series, 10a, was selected to investigate its antitumour mechanism. In addition, molecular docking studies suggested that compound 10a interacts very closely with the nocodazole docking pose through hydrogen bonds at the colchicine binding site of tubulin. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  11. Direct Synthesis of 7 nm Thick Zinc(II)-Benzimidazole-Acetate Metal-Organic Framework Nanosheets

    Energy Technology Data Exchange (ETDEWEB)

    Xue, Feng; Kumar, Prashant; Xu, Wenqian; Mkhoyan, K. Andre; Tsapatsis, Michael

    2018-01-09

    Two-dimensional metal-organic frameworks (MOFs) are promising candidates for high performance gas sepa-ration membranes. Currently, MOF nanosheets are mostly fabricated through delamination of layered MOFs, which often re-sults in a low yield of intact free-standing nanosheets. In this work, we present a direct synthesis method for zinc(II)-benzimidazole-acetate (Zn(Bim)OAc) MOF nanosheets. The obtained nanosheets have a lateral dimension of 600 nm when synthesized at room temperature. By adjusting the synthesis temperature, the morphology of obtained nanosheets can be readily tuned from nanosheets to nanobelts. A thickness of 7 nm is determined for Zn(Bim)OAc using high-angle annular dark-field scanning transmission electron microscopy, which makes these nanosheets promising building blocks of gas sepa-ration membranes.

  12. Efficient fluorescent deep-blue and hybrid white emitting devices based on carbazole/benzimidazole compound

    KAUST Repository

    Yang, Xiaohui

    2011-07-28

    We report the synthesis, photophysics, and electrochemical characterization of carbazole/benzimidazole-based compound (Cz-2pbb) and efficient fluorescent deep-blue light emitting devices based on Cz-2pbb with the peak external quantum efficiency of 4.1% and Commission Internationale dÉnclairage coordinates of (0.16, 0.05). Efficient deep-blue emission as well as high triplet state energy of Cz-2pbb enables fabrication of hybrid white organic light emitting diodes with a single emissive layer. Hybrid white emitting devices based on Cz-2pbb show the peak external quantum efficiency exceeding 10% and power efficiency of 14.8 lm/W at a luminance of 500 cd/m2. © 2011 American Chemical Society.

  13. Synthesis and antimicrobial activity of novel 2-substituted benzimidazole, benzoxazole and benzothiazole derivatives

    Directory of Open Access Journals (Sweden)

    Vikas S. Padalkar

    2016-11-01

    Full Text Available In an endeavor to find a new class of antimicrobial agents, a series of 2-(1H-benzimidazol-2-yl-5-(diethylaminophenol, 2-(1,3-benzoxazol-2-yl-5-(diethylaminophenol, 2-(1,3-benzothiazol-2-yl-5-(diethylaminophenol and their derivatives were synthesized starting from p-N,N-diethyl amino salicylaldehyde with different substituted o-phenylenediamine or o-aminophenol or o-aminothiophenol. The newly synthesized compounds were characterized by FT-IR, 1H NMR and LC–MS analysis. All compounds were evaluated for in vitro antibacterial activities against Escherichia coli and Staphylococcus aureus strains and in vitro antifungal activity against Candida albicans and Aspergillus niger strains by using serial dilution method. The antibacterial activities were expressed as the minimum inhibitory concentration (MIC in μg/mL.

  14. 2-(2{prime}-hydroxyphenyl)benzothiazoles, -benzoxazoles, and -benzimidazoles for plastic scintillation applications

    Energy Technology Data Exchange (ETDEWEB)

    Pla-Dalmau, A. [Fermi National Accelerator Lab., Batavia, IL (United States)

    1995-08-25

    A new series of fluorescent compounds has been tested as dopants for plastic scintillation applications. Several 2-(2{prime}-hydroxyphenyl)benzothiazole, -benzoxazole, and -benzimidazole derivatives have been prepared and studied in a polystyrene matrix. Each derivative has been added to a styrene solution which has been thermally polymerized. The transmittance, fluorescence, and light yield characteristics of these compounds in polystyrene have been determined. Their emission time distributions have also been measured, and the decay time constants have been calculated from these data. In addition, the doped polystyrene samples have been irradiated to a total dose of 10 Mrad, utilizing a {sup 60}Co source in order to evaluate their susceptibility to radiation-induced damage. 6 figs., 1 tab.

  15. Watching single molecules dance

    Science.gov (United States)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  16. (2-Benzoyl-1-phenylethenolato-κ2O,O′bis[2-(1-phenyl-1H-benzimidazol-2-ylphenyl-κC1]iridium(III dichloromethane disolvate

    Directory of Open Access Journals (Sweden)

    Stanislav I. Bezzubov

    2016-12-01

    Full Text Available We present here synthesis and crystal structure of a neutral IrIII complex, [Ir(C19H13N22(C15H11O2]·2CH2Cl2 or [Ir(C^N2O^O]·2CH2Cl2, where C^N is 1,2-diphenyl-1H-benzimidazole and O^O is 2-benzoyl-1-phenylethenolate. The coordination sphere of the IrIII atom, located on a twofold rotation axis, is that of a slighlty distorted C2N2O2 octahedron, with the N atoms in a trans configuration. In the crystal, complex molecules assemble through weak C—H...π interactions in the range 2.699 (3–2.892 (3 Å. The solvent CH2Cl2 molecules reside in channels aligned along the a axis and are connected to the complex molecules by C—H...O interactions.

  17. Impact of zeolite-Y framework on the geometry and reactivity of Ru (III) benzimidazole complexes - A DFT study

    Science.gov (United States)

    Selvaraj, Tamilmani; Rajalingam, Renganathan; Balasubramanian, Viswanathan

    2018-03-01

    A detailed comparative Density Functional Theory (DFT) study is made to understand the structural changes of the guest complex due to steric and electronic interactions with the host framework. In this study, Ru(III) benzimidazole and 2- ethyl Ru(III) benzimidazole complexes encapsulated in a supercage of zeolite Y. The zeolitic framework integrity is not disturbed by the intrusion of the large guest complex. A blue shift in the d-d transition observed in the UV-Visible spectroscopic studies of the zeolite encapsulated complexes and they shows a higher catalytic efficiency. Encapsulation of zeolite matrix makes the metal center more viable to nucleophilic attack and favors the phenol oxidation reaction. Based on the theoretical calculations, transition states and structures of reaction intermediates involved in the catalytic cycles are derived.

  18. Crystal structure of {bis[(1H-benzimidazol-2-yl-κN3methyl]sulfane}dichloridomercury(II

    Directory of Open Access Journals (Sweden)

    Mehdi Bouchouit

    2015-12-01

    Full Text Available In the asymmetric unit of the title compound, [HgCl2(C16H14N4S], the HgII cation is linked to two Cl atoms and two imidazole N atoms of the chelating bis[(1H-benzimidazol-2-ylmethyl]sulfane ligand, forming a slightly distorted tetrahedral environment. The substitued imidazole rings of the ligand are almost perfectly planar [with maximum deviations of 0.017 (3 and 0.012 (3 Å] and form a dihedral angle of 42.51 (5°. The crystal packing can be described as alternating layers parallel to (010. In this arrangement, N—H...Cl hydrogen bonds between the N—H groups of the benzimidazole moieties and chloride ligands are responsible for the formation of the chain-like packing pattern along [010] exhibiting a C(6 graph-set motif.

  19. Quantitative structure-activity relationship (QSAR) study of a series of benzimidazole derivatives as inhibitors of Saccharomyces cerevisiae.

    Science.gov (United States)

    Podunavac-Kuzmanović, Sonja O; Cvetković, Dragoljub D; Jevrić, Lidija R; Uzelac, Natasa J

    2013-01-01

    A quantitative structure activity relationship (QSAR) has been carried out on a series of benzimidazole derivatives to identify the structural requirements for their inhibitory activity against yeast Saccharomyces cerevisiae. A multiple linear regression (MLR) procedure was used to model the relationships between various physicochemical, steric, electronic, and structural molecular descriptors and antifungal activity of benzimidazole derivatives. The QSAR expressions were generated using a training set of 16 compounds and the predictive ability of the resulting models was evaluated against a test set of 8 compounds. The best QSAR models were further validated by leave one out technique as well as by the calculation of statistical parameters for the established theoretical models. Therefore, satisfactory relationships between antifungal activity and molecular descriptors were found. QSAR analysis reveals that lipophilicity descriptor (logP), dipole moment (DM) and surface area grid (SAG) govern the inhibitory activity of compounds studied against Saccharomyces cerevisiae.

  20. 1-Benzyl-2-Phenylbenzimidazole (BPB, a Benzimidazole Derivative, Induces Cell Apoptosis in Human Chondrosarcoma through Intrinsic and Extrinsic Pathways

    Directory of Open Access Journals (Sweden)

    Ju-Fang Liu

    2012-12-01

    Full Text Available In this study, we investigated the anticancer effects of a new benzimidazole derivative, 1-benzyl-2-phenyl -benzimidazole (BPB, in human chondrosarcoma cells. BPB-mediated apoptosis was assessed by the MTT assay and flow cytometry analysis. The in vivo efficacy was examined in a JJ012 xenograft model. Here we found that BPB induced apoptosis in human chondrosarcoma cell lines (JJ012 and SW1353 but not in primary chondrocytes. BPB induced upregulation of Bax, Bad and Bak, downregulation of Bcl-2, Bid and Bcl-XL and dysfunction of mitochondria in chondrosarcoma. In addition, BPB also promoted cytosolic releases AIF and Endo G. Furthermore, it triggered extrinsic death receptor-dependent pathway, which was characterized by activating Fas, FADD and caspase-8. Most importantly, animal studies revealed a dramatic 40% reduction in tumor volume after 21 days of treatment. Thus, BPB may be a novel anticancer agent for the treatment of chondrosarcoma.

  1. Synthesis and Biological Evaluation of Novel Benzimidazole Derivatives Bearing a Heterocyclic Ring at 4/5 Position

    Energy Technology Data Exchange (ETDEWEB)

    Wubulikasimu, Reyila; Yang, Yanbing; Xue, Fei; Luo, Xianjin; Shao, Dongping [Shanghai Jiaotong Univ., Shanghai (China); Li, Yuhuan; Gao, Rongmei [Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China); Ye, Weidong [Zhejiang Medicine Co. Ltd., Zhejiang (China)

    2013-08-15

    A series of novel benzimidazole derivatives bearing a heterocyclic ring as oxadiazole (21-32), thiadiazole (33-34), triazole (35-36) were synthesized and evaluated for their activities against Coxsackie virus B3 and B6 in Vero cells. Compounds 21-26, 31-36 with moieties of 2'-pyridyl, 3'-pyridyl and 4'-pyridyl at the 2-position and oxadiazoles, thiadiazole, or triazole substituent at the 4- or 5-position generally displayed activities against CVB3 and CVB6. Especially compound 24 (IC{sub 50} = 1.08 μg/mL, SI = 61.7 against CVB3) was the promising candidate as lead compound for anti-enteroviral drug. It was observed in the incorporation of heterocyclic rings in benzimidazole at the 5-position could enhance their biological activities.

  2. Poly[μ-aqua-diaqua(μ3-1H-benzimidazole-5-carboxylato-κ3N3:O,O′(μ2-1H-benzimidazole-5-carboxylato-κ3N3:O:O′-μ5-sulfato-μ4-sulfato-tricadmium

    Directory of Open Access Journals (Sweden)

    Lai-Chen Chen

    2011-09-01

    Full Text Available The asymmetric unit of the title compound, [Cd3(C8H5N2O22(SO42(H2O3]n, contains three CdII ions, two sulfate anions, two 1H-benzimidazole-5-carboxylate (H2bic ligands and three coordinated water molecules. One CdII ion is six-coordinated and exhibits a distorted octahedral geometry, while the other two CdII ions are seven-coordinated, displaying a distorted pentagonal–bipyramidal geometry. The CdII ions are bridged by two types of sulfate anions, producing inorganic chains along [100]. These chains are further connected by the H2bic ligands, leading to a three-dimensional framework. N—H...O and O—H...O hydrogen bonds and π–π interactions between the imidazole and benzene rings [centroid–centroid distances = 3.953 (2, 3.507 (2, 3.407 (2 and 3.561 (2 Å] further stabilize the crystal structure.

  3. Reactive Chemical Probes: Beyond the Kinase Cysteinome.

    Science.gov (United States)

    Jones, Lyn H

    2018-04-12

    The reaction of small molecule chemical probes with proteins has been harnessed to develop covalent inhibitor drugs and protein profiling technologies. This Essay discusses some of the recent enhancements to the chemical biology toolkit that are enabling the study of previously unchartered areas of chemoproteomic space. An analysis of the kinome is used to illustrate the potential for these approaches to pursue new targets using reactive chemical probes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. 1,3-Bis[(1H-benzotriazol-1-yl)methyl]-2,3-dihydro-1H-benzimidazole

    Czech Academy of Sciences Publication Activity Database

    Rivera, A.; Maldonado, M.; Casas, J.L.; Dušek, Michal; Fejfarová, Karla

    2011-01-01

    Roč. 67, Part 4 (2011), o990-u1533 ISSN 1600-5368 Grant - others:AV ČR(CZ) AP0701 Program:Akademická prémie - Praemium Academiae Institutional research plan: CEZ:AV0Z10100521 Keywords : benzimidazole * benzotriazol * X-ray diffraction * structure determination * Jana2006 Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.347, year: 2011

  5. Polystyrene-supported pyridinium chloroaluminate ionic liquid as a new heterogeneous Lewis acid catalyst for selective synthesis of benzimidazoles

    Directory of Open Access Journals (Sweden)

    Parvanak Boroujeni Kaveh

    2013-01-01

    Full Text Available Polystyrene-supported pyridinium chloroaluminate ionic liquid was prepared from the reaction of Merrifield resin with pyridine followed by reaction with aluminium chloride. This catalyst was used as a new chemoselective Lewis acid catalyst for the exclusive synthesis of 2-substituted benzimidazoles from the reaction of aldehydes with o-phenylenediamines. The catalyst is stable (as a bench top catalyst and can be easily recovered and reused without appreciable change in its efficiency.

  6. NaHSO4-SiO2-Promoted Solvent-Free Synthesis of Benzoxazoles, Benzimidazoles, and Benzothiazole Derivatives

    Directory of Open Access Journals (Sweden)

    K. Ravi Kumar

    2013-01-01

    Full Text Available An efficient protocol has been developed for the preparation of a library of benzoxazole, benzimidazole, and benzothiazole derivatives from reactions of acyl chlorides with o-substituted aminoaromatics in the presence of catalytic amount of silica-supported sodium hydrogen sulphate under solvent-free conditions. Simple workup procedure, high yield, easy availability, reusability, and use of ecofriendly catalyst are some of the striking features of the present protocol.

  7. Recent advances in developing small molecules targeting RNA.

    Science.gov (United States)

    Guan, Lirui; Disney, Matthew D

    2012-01-20

    RNAs are underexploited targets for small molecule drugs or chemical probes of function. This may be due, in part, to a fundamental lack of understanding of the types of small molecules that bind RNA specifically and the types of RNA motifs that specifically bind small molecules. In this review, we describe recent advances in the development and design of small molecules that bind to RNA and modulate function that aim to fill this void.

  8. Alternative energy production pathways in Taenia crassiceps cysticerci in vitro exposed to a benzimidazole derivative (RCB20).

    Science.gov (United States)

    Fraga, Carolina Miguel; Da Costa, Tatiane Luiza; De Castro, Ana Maria; Reynoso-Ducoing, Olivia; Ambrosio, Javier; Hernández-Campos, Alicia; Castillo, Rafael; Vinaud, Marina Clare

    2016-04-01

    Biochemical studies of benzimidazole derivatives are important to determine their mode of action and activity against parasites. The lack of antihelminthic alternatives to treat parasitic infections and albendazole resistance cases make the search for new antiparasitary drugs of utmost importance. The 6-chloro-5-(1-naphthyloxy)-2-(trifluoromethyl)-1H-benzimidazole (RCB20) is a benzimidazole derivative with promising effect. This study evaluated the effect of different concentrations of RCB20 in the alternative energetic pathway of in vitro Taenia crassiceps cysticerci. The parasites were in vitro exposed to 6.5 and 13 µM of RCB20 and albendazole sulfoxide (ABZSO). The quantification of acetate, acetoacetate, β-hydroxybutyrate, fumarate and propionate was performed by high-performance liquid chromatography. The quantification of urea, creatinine and total proteins was performed by spectrophotometry. The increase in β-hydroxybutyrate reflects the enhancement of the fatty acid oxidation in the treated groups. Volatile fatty acids secretion, acetate and propionate, was increased in the treated groups. The secretion mechanisms of the treated parasites were impaired due to organic acids increased concentrations in the cysticerci. It is possible to conclude that the metabolic effect on alternative energetic pathways is slightly increased in the parasites treated with RCB20 than the ones treated with ABZSO.

  9. Studies on the thermal and radiolytic resistance of an anion exchanger with benzimidazole functional groups in nitric acid solution

    International Nuclear Information System (INIS)

    Iwasa, Satoru; Murata, Kiyoshi; Takeda, Kunihiko; Arai, Tsuyoshi; Wei, Y.Z.; Kumagai, Mikio

    2001-01-01

    Thermal and radiolytic resistance of AR-01R anion exchanger containing benzimidazole groups as exchange sites in nitric acid solution has been studied. Changes in its exchange capacity (EC), structure and shape were investigated and compared with those of a commercial Amberlite IRA-900 anion exchanger with quaternary ammonium group. Compared to the IRA-900, the AR-01R anion exchanger showed significantly higher thermal resistance and its decrease in EC was less than 10% after immersion in 9 mol·dm -3 solution for 72 h. On the other hand, it was found that the EC decrease of these two anion exchangers induced by γ-ray irradiation was almost the same; their EC decreased by 20-25% after irradiation in 9 mol·dm -3 HNO 3 solution at room temperature with absorption dose of 3.0 MGy. The change of the strong-base benzimidazole group to weak-base benzimidazole group in AR-01 was found to be the main damage by heat and γ-ray irradiation. (author)

  10. Proximal Probes Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Proximal Probes Facility consists of laboratories for microscopy, spectroscopy, and probing of nanostructured materials and their functional properties. At the...

  11. Slow, spontaneous degradation of lansoprazole, omeprazole and pantoprazole tablets: isolation and structural characterization of the toxic antioxidants 3H-benzimidazole-2-thiones.

    Science.gov (United States)

    Rajab, A; Touma, M; Rudler, H; Afonso, C; Seuleiman, M

    2013-09-01

    The spontaneous degradation of lansoprazole, omeprazole and pantoprazole tablets upon long-term and forced storage conditions was determined by high performance liquid chromatography (HPLC). The more abundant products could be isolated by liquid chromatography and their molecular weights determined by Mass Spectrometry (MS). Their structures, established according to their spectroscopic data, were compared to those of either the literature or of authentic samples. Thus lansoprazole led mainly to a mixture of 3H-benzimidazole-2-thione (2a) and 3H-benzimidazole-2-one (2c), omeprazole mainly to a mixture of 5-methoxy-3H-benzimidazole-2-thione (1a) and 2-hydroxymethyl-3, 5-dimethyl-4-methoxypyridine (1b), and pantoprazole, to 5-difluoromethoxy-3H-benzimidazole-2-thione (3a) and 2-hydroxymethyl-3, 4-dimethoxypyridine (3b). Although some of the degradation products had already been observed under different conditions, the detection of benzimidazole-2-thiones is unprecedented and their involvement as possible physiological, yet toxic antioxidants must be emphasized. Plausible, unified mechanisms for the formation of the different degradation products observed herein and in previous papers from the literature are suggested.

  12. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Safvan, C.P.; Sakai, H.

    1999-01-01

    Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed...... by mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....

  13. Inhibiting properties of benzimidazole films for Cu(II)/Cu(I) reduction in chloride media studied by RDE and EQCN techniques

    International Nuclear Information System (INIS)

    Scendo, M.; Hepel, M.

    2007-01-01

    The effects of benzimidazole (BIM) and 2-methylbenzimidazole (MBIM) on the electroreduction of Cu(II) on a rotating Pt disk electrode in chloride media were investigated. These studies were undertaken in conjunction with earlier observation that these imidazole derivatives act as inhibitors of copper corrosion processes and are non-toxic. We have found that BIM and MBIM also form adsorption films on Pt, which are able to inhibit one-electron reduction of Cu(II) to Cu(I) and prevent the development of convective diffusion limiting current wave. The inhibition was found to be controlled by field-assisted mass transfer in the film. The ingress of Cu(II) species into the film was detected using the EQCN technique. The EQCN measurements indicate that small fraction of Cu(I) formed in the film by reduction of Cu(II) is retained in the film, most likely in the form of CuCl. The uptake of CuCl by inhibitor films diminishes in strongly inhibiting films (e.g., in acidic medium). The inhibition effectiveness of Cu(II) reduction process by Pt vertical bar BIM and Pt vertical bar MBIM films increases strongly with increasing acidity of the medium in the pH range from 3.0 to 1.0. The mechanism of this remarkable pH effect has been proposed. It is based on charge and pH-induced film restructuring, including changes in orientation and protonation of BIM molecules in the film

  14. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Molecule Matters van der Waals Molecules - Rg•••HF Complexes are Debye Molecules! E Arunan. Feature Article Volume 15 Issue 7 July 2010 pp 667-674. Fulltext. Click here to view fulltext PDF. Permanent link:

  15. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 12. Molecule Matters van der Waals Molecules - Noble Gas Clusters are London Molecules! E Arunan ... Author Affiliations. E Arunan1. Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India.

  16. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Molecule Matters van der Waals Molecules - Rg•••HF Complexes are Debye Molecules! E Arunan ... Author Affiliations. E Arunan1. Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India.

  17. In situ temperature monitoring in single-molecule FRET experiments

    Science.gov (United States)

    Hartmann, Andreas; Berndt, Frederic; Ollmann, Simon; Krainer, Georg; Schlierf, Michael

    2018-03-01

    Thermodynamic properties of single molecules including enthalpic and entropic contributions are often determined from experiments by a direct control and precise measurement of the local temperature. However, common temperature monitoring techniques using, for example, ultrafine temperature probes can lead to uncertainties as the probe cannot be placed in the vicinity of the molecule of interest. Here, we devised an approach to measure the local temperature in freely diffusing confocal single-molecule Förster Resonance Energy Transfer (smFRET) experiments in situ by directly adding the temperature-sensitive fluorescent dye Rhodamine B, whose fluorescence lifetime serves as a probe of the local temperature in the confocal volume. We demonstrate that the temperature and FRET efficiencies of static and dynamic molecules can be extracted within one measurement simultaneously, without the need of a reference chamber. We anticipate this technique to be particularly useful in the physicochemical analyses of temperature-dependent biomolecular processes from single-molecule measurements.

  18. The first reported case of resistance of gastrointestinal nematodes to benzimidazole anthelmintic in goats in Poland

    Science.gov (United States)

    Mickiewicz, Marcin; Czopowicz, Michał; Górski, Paweł; Kaba, Jarosław

    2017-01-01

    Fecal egg count reduction (FECR) test with albendazole and egg hatch test (EHT) with thiabendazole (TBZ) were performed in a dairy goat herd suspected of anthelmintic resistance to benzimidazoles. The herd had been regularly dewormed with fenbendazole for 5 previous years and despite that it remained infected with several species of gastrointestinal nematodes (Trichostrongylus colubriformis, Teladorsagia circumcincta, and Haemonchus contortus). Albendazole was administered per os at dose of 20 mg/kg to 10 goats (treated group), while 10 other goats remained untreated (control group). Fecal egg count (FEC) was determined using McMaster egg counting method before and 7 days after the treatment in the treated group, and once (at the latter moment) in the control group. EHT was performed on the pooled rectal sample collected from treated goats. EHT comprised the negative control and 7 consecutive concentrations of TBZ (0.05, 0.1, 0.2, 0.3, 0.5, 1.0, 2.0 μg/ml) according to the standard procedure. Two hundred eggs/larvae were counted to determine percentage of unhatched eggs, which was adjusted by the natural mortality. TBZ dose effective in preventing hatching of 50% of eggs (ED50) was determined using the log-probit transformation. Median FEC (range) before the treatment was 1000 (250–3450) epg in the treated group and dropped to 150 (50–500) epg after the treatment (p=0.005). Median FEC (range) after the treatment was also significantly lower in the treated than in control group (p=0.009), where it was 725 (0–5050) epg. FECR between the treated and control group was 81% (95% CI: 49%, 93%). FECR in the treated group was 83% and 74% based on average and individual approach, respectively. ED50 value of TBZ was 0.78 μg/ml. Only H. contortus persisted in the treated group after treatment. The results indicate resistance of H. contortus to a benzimidazole anthelmintic, which is the first such case reported in Polish goats.

  19. Design, synthesis and antimicrobial evaluation of novel benzimidazole type of Fluconazole analogues and their synergistic effects with Chloromycin, Norfloxacin and Fluconazole.

    Science.gov (United States)

    Zhang, Hui-Zhen; Damu, Guri L V; Cai, Gui-Xin; Zhou, Cheng-He

    2013-06-01

    A novel series of benzimidazole type of Fluconazole analogues were synthesized and characterized by (1)H NMR, (13)C NMR, IR, MS and HRMS spectra. All the new compounds were screened for their antimicrobial activities in vitro by two-fold serial dilution technique. The bioactive evaluation showed that 3,5-bis(trifluoromethyl)phenyl benzimidazoles gave comparable or even stronger antibacterial and antifungal efficiency in comparison with reference drugs Chloromycin, Norfloxacin and Fluconazole. The combination of 2,4-difluorobenzyl benzimidazole derivative 5m and its hydrochloride 7 respectively with antibacterial Chloromycin, Norfloxacin or antifungal Fluconazole showed better antimicrobial efficiency with less dosage and broader antimicrobial spectrum than the separated use of them alone. Notably, these combined systems were more sensitive to Fluconazole-insensitive Aspergillus flavus and methicillin-resistant MRSA. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  20. Genetically encoded fluorescent probe to visualize phosphatidylinositol

    Czech Academy of Sciences Publication Activity Database

    Eisenreichová, Andrea; Humpolíčková, Jana; Bouřa, Evžen

    2017-01-01

    Roč. 284, Suppl 1 (2017), s. 364-365 ISSN 1742-464X. [FEBS Congress /42./ From Molecules to Cells and Back. 10.09.2017-14.09.2017, Jerusalem] R&D Projects: GA ČR GJ15-21030Y; GA MŠk LO1302 Institutional support: RVO:61388963 Keywords : phosphatidylinositol * fluorescent probe Subject RIV: CE - Biochemistry

  1. Estimation of the cost of large-scale school deworming programmes with benzimidazoles.

    Science.gov (United States)

    Montresor, A; Gabrielli, A F; Diarra, A; Engels, D

    2010-02-01

    This study estimates the cost of distributing benzimidazole tablets in the context of school deworming programmes: we analysed studies reporting the cost of school deworming from seven countries in four WHO regions. The estimated cost for drug procurement to cover one million children (including customs clearance and international transport) is approximately US$20000. The estimated financial costs (including the cost of training of personnel, drug transport, social mobilization and monitoring) is, on average, equivalent to US$33000 per million school-age children with minimal variation in different countries and continents. The estimated economic costs of distribution (including the time spent by teachers, and health personnel at central, provincial and district level) to cover one million children approximately corresponds to US$19000. This study shows the minimal cost of school deworming activities, but also shows the significant contribution (corresponding to a quarter of the entire cost of the programme) provided by health and education systems in endemic countries even in the case of drug donations and donor support of distribution costs. Copyright 2009 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

  2. Synthesis of benzimidazole-grafted graphene oxide/multi-walled carbon nanotubes composite for supercapacitance application

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, Rajesh Kr., E-mail: r05bhu@gmail.com [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore (Singapore); Xingjue, Wang [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore (Singapore); Kumar, Vinod [Department of Zoology, Banaras Hindu University, Varanasi (India); Srivastava, Anchal [Department of Physics, Banaras Hindu University, Varanasi (India); Singh, Vidya Nand [CSIR-National Physical Laboratory, New Delhi (India)

    2014-11-05

    Highlights: • We are reporting supercapacitance performance of BI-GO/MWCNTs composite. • The specific capacitance of BI-GO/MWCNTs is 275 and 460 F/g at 200 and 5 mV/s scan rate. • This composite has shown 224 F/g capacitance after 1300 cycles at 200 mV/s scan rate. - Abstract: We are reporting the fabrication, characterizations and supercapacitance performance of benzimidazole-grafted graphene oxide/multi-walled carbon nanotubes (BI-GO/MWCNTs) composite. The synthesis of BI-GO materials involves cyclization reaction of carboxylic groups on GO among the hydroxyl and amino groups on o-phenylenediamine. The BI-GO/MWCNTs composite has been fabricated via in situ reduction of BI-GO using hydrazine in presence of MWCNTs. Scanning electron microscopy (SEM), Transmission electron microscopy (TEM), Raman spectroscopy, X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) have been used to characterize its surface and elemental composition. The uniform dispersion of MWCNTs with BI-GO helps to improve the charge transfer reaction during electrochemical process. The specific capacitance of BI-GO/MWCNTs composite is 275 and 460 F/g at 200 and 5 mV/s scan rate in 1 mol/L aqueous solution of H{sub 2}SO{sub 4}. This BI-GO/MWCNTs composite has shown 224 F/g capacitance after 1300 cycles at 200 mV/s scan rate, which represents its good electrochemical stability.

  3. Structural investigation of HIV-1 nonnucleoside reverse transcriptase inhibitors: 2-Aryl-substituted benzimidazoles

    Science.gov (United States)

    Ziółkowska, Natasza E.; Michejda, Christopher J.; Bujacz, Grzegorz D.

    2009-11-01

    Acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) is one of the most destructive epidemics in history. Inhibitors of HIV enzymes are the main targets to develop drugs against that disease. Nonnucleoside reverse transcriptase inhibitors of HIV-1 (NNRTIs) are potentially effective and nontoxic. Structural studies provide information necessary to design more active compounds. The crystal structures of four NNRTI derivatives of 2-aryl-substituted N-benzyl-benzimidazole are presented here. Analysis of the geometrical parameters shows that the structures of the investigated inhibitors are rigid. The important geometrical parameter is the dihedral angle between the planes of the π-electron systems of the benzymidazole and benzyl moieties. The values of these dihedral angles are in a narrow range for all investigated inhibitors. There is no significant difference between the structure of the free inhibitor and the inhibitor in the complex with RT HIV-1. X-ray structures of the investigated inhibitors are a good basis for modeling enzyme-inhibitor interactions in rational drug design.

  4. Distant polypharmacology among MLP chemical probes.

    Science.gov (United States)

    Antolín, Albert A; Mestres, Jordi

    2015-02-20

    Small molecules are essential tool compounds to probe the role of proteins in biology and advance toward more efficient therapeutics. However, they are used without a complete knowledge of their selectivity across the entire proteome, at risk of confounding their effects due to unknown off-target interactions. Current state-of-the-art computational approaches to predicting the affinity profile of small molecules offer a means to anticipate potential nonobvious selectivity liabilities of chemical probes. The application of in silico target profiling on the full set of chemical probes from the NIH Molecular Libraries Program (MLP) resulted in the identification of biologically relevant in vitro affinities for proteins distantly related to the primary targets of ML006, ML123, ML141, and ML204, helping to lower the risk of their further use in chemical biology.

  5. Asymmetric Ring Opening/Cyclization/Retro-Mannich Reaction of Cyclopropyl Ketones with Aryl 1,2-Diamines for the Synthesis of Benzimidazole Derivatives.

    Science.gov (United States)

    Xia, Yong; Lin, Lili; Chang, Fenzhen; Liao, Yuting; Liu, Xiaohua; Feng, Xiaoming

    2016-09-26

    A highly efficient asymmetric ring-opening/cyclization/retro-Mannich reaction of cyclopropyl ketones with aryl 1,2-diamines has been realized using a chiral N,N'-dioxide/Sc(III) catalyst. Benzimidazoles containing chiral side chains were generated under mild reaction conditions in excellent outcomes (up to 99 % yield and 97 % ee). This method also provides efficient access to chiral benzimidazole-substituted amide and cycloheptene derivatives. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Determination of benzimidazoles in meat samples by capillary zone electrophoresis tandem mass spectrometry following dispersive liquid-liquid microextraction.

    Science.gov (United States)

    Tejada-Casado, Carmen; Moreno-González, David; Lara, Francisco J; García-Campaña, Ana M; Del Olmo-Iruela, Monsalud

    2017-03-24

    A novel method based on capillary zone electrophoresis-tandem mass spectrometry has been proposed and validated for the identification and simultaneous quantification of twelve benzimidazoles in meat samples. Electrophoretic separation was carried out using 500mM formic acid (pH 2.2) as background electrolyte and applying a voltage of 25kV at 25°C. In order to improve the sensitivity, stacking mode injection was applied, using as injection solvent a mixture of 30:70 acetonitrile/water at 50mbar for 75s. Sensitivity enhancement factors from 74 to 317 were obtained under these conditions. Detection using an ion trap as analyzer, operating in multiple reactions monitoring mode was employed. The main MS/MS parameters as well as the composition of the sheath liquid and other electrospray variables were optimized in order to obtain the highest sensitivity and precision in conjunction with an unequivocal identification. The method was applied to poultry and pork muscle samples. The deproteinization of samples and extraction of benzimidazoles was carried out with acetonitrile. MgSO 4 and NaCl were added as salting-out agents. Subsequently, dispersive liquid-liquid microextraction was applied as clean up procedure. The organic layer (acetonitrile, used as dispersant) containing the benzimidazoles was mixed with the extractant (chloroform) and both were injected in water, producing a cloudy solution. Recoveries for fortified samples were higher than 70%, with relative standard deviations lower than 16% were obtained in all cases. The limits of detection were below 3μgkg -1 , demonstrating the applicability of this fast, simple, and environmentally friendly method. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Aromatic carboxylate effect on dimensionality of three bis(benzimidazole)-based cobalt(II) coordination polymers: Syntheses, structures and properties

    International Nuclear Information System (INIS)

    Zhang, Ju-Wen; Gong, Chun-Hua; Hou, Li-Li; Tian, Ai-Xiang; Wang, Xiu-Li

    2013-01-01

    Three new metal-organic coordination polymers [Co(4-bbc) 2 (bbbm)] (1), [Co(3,5-pdc)(bbbm)]·2H 2 O (2) and [Co(1,4-ndc)(bbbm)] (3) (4-Hbbc=4-bromobenzoic acid, 3,5-H 2 pdc=3,5-pyridinedicarboxylic acid, 1,4-H 2 ndc=1,4-naphthalenedicarboxylic acid and bbbm=1,1-(1,4-butanediyl)bis-1H-benzimidazole) were hydrothermally synthesized and structurally characterized. Polymer 1 is a 1D chain formed by the bbbm ligands and Co II ions. Polymer 2 exhibits a 2D network with a (3·4·5)(3 2 ·4·5·6 2 ·7 4 ) topology. Polymer 3 possesses a 3D three-fold interpenetrating framework. The versatile structures of title polymers indicate that the aromatic carboxylates have an important influence on the dimensionality of 1–3. Moreover, the thermal stability, electrochemical and luminescent properties of 1–3 were investigated. - graphical abstract: Three bis(benzimidazole)-based cobalt(II) coordination polymers tuned by aromatic carboxylates were hydrothermally synthesized and structurally characterized. The aromatic carboxylates play a key role in the dimensionality of three polymers. The electrochemical and luminescent properties of three polymers were investigated. Display Omitted - Highlights: • Three bis(benzimidazole)-based cobalt(II) coordination polymers tuned by aromatic carboxylates were obtained. • The aromatic carboxylates have an important influence on the dimensionality of three polymers. • The electrochemical and luminescent properties of three polymers were investigated

  8. ERK-dependent phosphorylation of HSF1 mediates chemotherapeutic resistance to benzimidazole carbamates in colorectal cancer cells.

    Science.gov (United States)

    Wales, Christina T K; Taylor, Frederick R; Higa, Allan T; McAllister, Harvey A; Jacobs, Aaron T

    2015-07-01

    Drugs containing the benzimidazole carbamate scaffold include anthelmintic and antifungal agents, and they are now also recognized as having potential applications in the treatment of colorectal and other cancers. These agents act by binding to β-tubulin, and in doing so they disrupt microtubules, arrest cell division, and promote apoptotic cell death in malignant cells. We have evaluated several commercially available benzimidazole carbamates for cytotoxic activity in colorectal cancer cells. In addition to cytotoxicity, we also observe activation of the transcription factor, heat shock factor-1 (HSF1). HSF1 is well known to mediate a cytoprotective response that promotes tumor cell survival and drug resistance. Here, we show that biochemical inhibition with the HSF1 inhibitor KRIBB11 or siRNA-based silencing of HSF1 results in a significant enhancement of drug potency, causing an approximately two-fold decrease in IC50 values of parbendazole and nocodazole. We also define a mechanism for drug-induced HSF1 activation, which results from a phosphorylation event at Ser326 that is dependent on the activation of the extracellular regulated protein kinase-1/2 (ERK-1/2) mitogen-activated protein kinase pathway. Inhibition of the upstream kinase MEK-1/2 with U0126 attenuates the phosphorylation of both ERK-1/2 and HSF1, and significantly enhances drug cytotoxicity. From these data we propose a unique model whereby the ERK-1/2-dependent activation of HSF1 promotes chemotherapeutic resistance to benzimidazole carbamates. Therefore, targeting the ERK-1/2 signaling cascade is a potential strategy for HSF1 inhibition and a means of enhancing the cytotoxicity of these agents.

  9. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    RESONANCE. February 2015. GENERAL ARTICLE. Single-Molecule Spectroscopy. Every Molecule is Different! Kankan Bhattacharyya. Keywords. Single-molecule ..... Resonance Energy. Transfer (FRET) is an elegant technique to measure the distance between a donor and an acceptor molecule. FRET refers to the.

  10. Molecule of the Month.

    Indian Academy of Sciences (India)

    Molecule of the Month. Corannulene - A Bucky Bowl. H Surya Prakash Rao. The structure, properties and synthesis of a bowl shaped molecule, which resembles a fragment of fullerene, are described here. Chemistry of aromatic molecules has a long history. Many molecules made up of multiple benzene-like rings have ...

  11. THE ORNL ATOM PROBE

    OpenAIRE

    Miller, M.

    1986-01-01

    The ORNL Atom Probe is a microanalytical tool for studies in materials science. The instrument is a combination of a customized version of the vacuum system of the VG FIM-100 atom probe, an ORNL-designed microcomputer-controlled digital timing system, and a double curved CEMA Imaging Atom Probe detector. The atom probe combines four instruments into one - namely a field ion microscope, an energy compensated time-of-flight mass spectrometer, an imaging atom probe, and a pulsed laser atom probe.

  12. Mobile Game Probes

    DEFF Research Database (Denmark)

    Borup Lynggaard, Aviaja

    2006-01-01

    This paper will examine how probes can be useful for game designers in the preliminary phases of a design process. The work is based upon a case study concerning pervasive mobile phone games where Mobile Game Probes have emerged from the project. The new probes are aimed towards a specific target...... group and the goal is to specify the probes so they will cover the most relevant areas for our project. The Mobile Game Probes generated many interesting results and new issues occurred, since the probes came to be dynamic and favorable for the process in new ways....

  13. [Substituted 1,5,6,7-tetrahydro-4H-benzimidazol-4-ones as inhibitors of urease].

    Science.gov (United States)

    Tarun, E I; Zheldakova, T A; Metelitsa, D I

    2008-01-01

    A comparative kinetic study of the inhibition of urea hydrolysis by 9 substituted 1,5,6,7-tetrahydro-4H-benzimidazol-4-ones (BI I-IX) has been carried out. The inhibition had reversibl competitive character; the inhibition constants K(i), varied from 29 up to 754 microM in dependence of the structure of BI I-IX. Three BI I-III, having the K(i) values from 29 to 82 microM, may be used as the potential therapeutic agents for gastroenterology for treatment of stomach and duodenal ulcers.

  14. Probing the molecules of the mind | Mendelow | African Journal of ...

    African Journals Online (AJOL)

    The molecular dimension of biology has been finding practical applications in all fields of medicine over the last few decades, but arguably one of the most challenging and exciting areas is that of molecular psychiatry. Much progress has been gained from traditional linkage studies into gene candidates for various ...

  15. Probing the molecules of the mind | Mendelow | African Journal of ...

    African Journals Online (AJOL)

    The PDF file you selected should load here if your Web browser has a PDF reader plug-in installed (for example, a recent version of Adobe Acrobat Reader). If you would like more information about how to print, save, and work with PDFs, Highwire Press provides a helpful Frequently Asked Questions about PDFs.

  16. Computational probing protein-protein interactions targeting small molecules.

    Science.gov (United States)

    Wang, Yong-Cui; Chen, Shi-Long; Deng, Nai-Yang; Wang, Yong

    2016-01-15

    With the booming of interactome studies, a lot of interactions can be measured in a high throughput way and large scale datasets are available. It is becoming apparent that many different types of interactions can be potential drug targets. Compared with inhibition of a single protein, inhibition of protein-protein interaction (PPI) is promising to improve the specificity with fewer adverse side-effects. Also it greatly broadens the drug target search space, which makes the drug target discovery difficult. Computational methods are highly desired to efficiently provide candidates for further experiments and hold the promise to greatly accelerate the discovery of novel drug targets. Here, we propose a machine learning method to predict PPI targets in a genomic-wide scale. Specifically, we develop a computational method, named as PrePPItar, to Predict PPIs as drug targets by uncovering the potential associations between drugs and PPIs. First, we survey the databases and manually construct a gold-standard positive dataset for drug and PPI interactions. This effort leads to a dataset with 227 associations among 63 PPIs and 113 FDA-approved drugs and allows us to build models to learn the association rules from the data. Second, we characterize drugs by profiling in chemical structure, drug ATC-code annotation, and side-effect space and represent PPI similarity by a symmetrical S-kernel based on protein amino acid sequence. Then the drugs and PPIs are correlated by Kronecker product kernel. Finally, a support vector machine (SVM), is trained to predict novel associations between drugs and PPIs. We validate our PrePPItar method on the well-established gold-standard dataset by cross-validation. We find that all chemical structure, drug ATC-code, and side-effect information are predictive for PPI target. Moreover, we can increase the PPI target prediction coverage by integrating multiple data sources. Follow-up database search and pathway analysis indicate that our new predictions are worthy of future experimental validation. In conclusion, PrePPItar can serve as a useful tool for PPI target discovery and provides a general heterogeneous data integrative framework. PrePPItar is available at http://doc.aporc.org/wiki/PrePPItar. ycwang@nwipb.cas.cn or ywang@amss.ac.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Small Molecules from Spiders Used as Chemical Probes

    DEFF Research Database (Denmark)

    Olsen, Christian Adam; Kristensen, Anders S.; Strømgaard, Kristian

    2011-01-01

    Spiders are important species in ecological systems and as major predators of insects they are endowed with a plethora of low‐molecular‐weight natural products having intriguing biological activities. The isolation and biological characterization of these entities are well established, however, o...... the area of pheromones and allomones from spiders. Herein, we recapitulate these recent results, put them into perspective with previous findings, and provide an outlook for future studies of these chemotypes....

  18. Biological mechanisms, one molecule at a time

    Science.gov (United States)

    Tinoco, Ignacio; Gonzalez, Ruben L.

    2011-01-01

    The last 15 years have witnessed the development of tools that allow the observation and manipulation of single molecules. The rapidly expanding application of these technologies for investigating biological systems of ever-increasing complexity is revolutionizing our ability to probe the mechanisms of biological reactions. Here, we compare the mechanistic information available from single-molecule experiments with the information typically obtained from ensemble studies and show how these two experimental approaches interface with each other. We next present a basic overview of the toolkit for observing and manipulating biology one molecule at a time. We close by presenting a case study demonstrating the impact that single-molecule approaches have had on our understanding of one of life's most fundamental biochemical reactions: the translation of a messenger RNA into its encoded protein by the ribosome. PMID:21685361

  19. Molecular characterization, fitness and mycotoxin production of Fusarium graminearum laboratory strains resistant to benzimidazoles.

    Science.gov (United States)

    Sevastos, A; Markoglou, A; Labrou, N E; Flouri, F; Malandrakis, A

    2016-03-01

    Six benzimidazole (BMZ)-resistant Fusarium graminearum strains were obtained after UV mutagenesis and selection on carbendazim (MBC)-amended medium. In vitro bioassays resulted in the identification of two resistant phenotypes that were highly HR (Rf: 40-170, based on EC50) and moderately MR (Rf: 10-20) resistant to carbendazim. Cross resistance studies with other fungicides showed that all mutant strains tested were also resistant to other BMZs, such as benomyl and thiabendazole, but retained their parental sensitivity to fungicides belonging to other chemical groups. A point mutation at codon 6 (His6Asn) was found in the β2-tubulin gene of MR isolates while another mutation at codon 200 (Phe200Tyr) was present in one MR and one HR isolates. Interestingly, low temperatures suppressed MBC-resistance in all isolates bearing the H6N mutation. The three-dimensional homology model of the wild-type and mutants of β-tubulins were constructed, and the possible carbendazim binding site was analyzed. Studies on fitness parameters showed that the mutation(s) for resistance to BMZs did not affect the mycelial growth rate whereas adverse effects were found in sporulation and conidial germination in most of the resistant mutants. Pathogenicity tests on corn cobs revealed that mutants were less or equally aggressive to the wild-type strain but expressed their BMZ-resistance after inoculation on maize cobs treated with MBC. Analysis of mycotoxin production by high performance liquid chromatography revealed that only two HR strains produced zearalenone (ZEA) at concentrations similar to that of the wild-type strain, while no ZEA levels were detected in the rest of the mutants. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. New Benzimidazole-1,2,4-Triazole Hybrid Compounds: Synthesis, Anticandidal Activity and Cytotoxicity Evaluation

    Directory of Open Access Journals (Sweden)

    Hülya Karaca Gençer

    2017-03-01

    Full Text Available Owing to the growing need for antifungal agents, we synthesized a new series 2-((5-(4-(5-substituted-1H-benzimidazol-2-ylphenyl-4-substituted-4H-1,2,4-triazol-3-ylthio-1-(substitutedphenylethan-1-one derivatives, which were tested against Candida species. The synthesized compounds were characterized and elucidated by FT-IR, 1H-NMR, 13C-NMR and HR-MS spectroscopies. The synthesized compounds were screened in vitro anticandidal activity against Candida species by broth microdiluation methods. In vitro cytotoxic effects of the final compounds were determined by MTT assay. Microbiological studies revealed that compounds 5m, 5o, 5r, 5t, 5y, 5ab, and 5ad possess a good antifungal profile. Compounds 5w was the most active derivative and showed comparable antifungal activity to those of reference drugs ketoconazole and fluconazole. Cytotoxicity evaluation of compounds 5m, 5o, 5r, 5w, 5y, 5ab and 5ad showed that compounds 5w and 5ad were the least cytotoxic agents. Effects of these two compounds against ergosterol biosynthesis were observed by LC-MS-MS method, which is based on quantification of ergosterol level in C. albicans. Compounds 5w and 5d inhibited ergosterol biosynthesis concentration dependently. A fluorescence microscopy study was performed to visualize effect of compound 5w against C. albicans at cellular level. It was determined that compound 5w has a membrane damaging effect, which may be related with inhibition of biosynthesis of ergosterol.

  1. Separation of lanthanides and actinides(III) using tridentate benzimidazole, benzoxazole and benzothiazole ligands

    Energy Technology Data Exchange (ETDEWEB)

    Drew, M.G.B.; Hudson, M.J.; Iveson, P.B.; Vaillant, L.; Youngs, T.G.A. [Reading Univ. (United Kingdom). Dept. of Chemistry; Hill, C.; Madic, Ch. [CEA Valrho, Dir. de l' Energie Nucleaire, Departement RadioChimie et Procedes, Service de Chimie des Procedes de Separation (DEN/DRCP/SCPS/LCSE), 30 - Marcoule (France)

    2004-04-01

    The ability of new hydrophobic tridentate ligands based on 2,6-bis(benzimidazole-2-yl)pyridine, 2,6-bis(benzoxazole-2-yl)pyridine and 2,6-bis(benzothiazole-2-yl)pyridine to selectively extract americium(III) from europium(III) was measured. The most promising ligand - 2,6-bis(benzoxazole-2-yl)-4-(2-decyl-1-tetra-decyl-oxy)pyridine L{sup 9} was found to give separation factors (SF{sub Am/Eu}) of up to 70 when used to extract cations from 0.02-0.10 M HNO{sub 3} into TPH in synergy with 2-bromo-decanoic acid. Six structures of lanthanide complexes with 2,6-bis(benzoxazole-2-yl)pyridine L{sup 6} were then determined to evaluate the types of species that are likely to be involved in the separation process. Three structural types were observed, namely [LnL{sup 6}(NO{sub 3}){sub 3}(H{sub 2}O){sub 2}), 11-coordinate only for La, [LnL{sup 6}(NO{sub 3})3 (CH{sub 3}CN)], 10-coordinate for Pr, Nd and Eu and [LnL{sup 6}(NO{sub 3}){sub 3}(H{sub 2}O)], L 10-coordinate for Eu and Gd. Quantum Mechanics calculations were carried out on the tridentate ligands to elucidate the conformational preferences of the ligands in the free state and protonated and di-protonated forms and to assess the electronic properties of the ligands for comparison with other ter-dentate ligands used in lanthanide/actinide separation processes. (authors)

  2. Mechanism of the pharmacokinetic interaction between methotrexate and benzimidazoles: potential role for breast cancer resistance protein in clinical drug-drug interactions

    NARCIS (Netherlands)

    Breedveld, Pauline; Zelcer, Noam; Pluim, Dick; Sönmezer, Ozgür; Tibben, Matthijs M.; Beijnen, Jos H.; Schinkel, Alfred H.; van Tellingen, Olaf; Borst, Piet; Schellens, Jan H. M.

    2004-01-01

    The antifolate drug methotrexate (MTX) is transported by breast cancer resistance protein (BCRP; ABCG2) and multidrug resistance-associated protein1-4 (MRP1-4; ABCC1-4). In cancer patients, coadministration of benzimidazoles and MTX can result in profound MTX-induced toxicity coinciding with an

  3. Preparation and characterisation of porous poly(2,5benzimidazole) (ABPBI) membranes using surfactants as templates for polymer electrolyte membrane fuel cells

    CSIR Research Space (South Africa)

    Zheng, H

    2010-04-01

    Full Text Available The first instance synthesis of porous poly(2,5benzimidazole) (ABPBI) membranes using sodium dodecyl sulfate (SDS) surfactants as templates is reported. The membranes were characterised by SEM, TGA, DSC and tensile tests. The tensile test results...

  4. Dimethylplatinum(II) and Tetramethylplatinum(IV) Complexes of 1-Methyl-(2-alkylthiomethyl)-1H-benzimidazoles: Experimental and DFT-Calculated Structures and NMR Spectra

    Czech Academy of Sciences Publication Activity Database

    Knödler, A.; Kaim, W.; Jain, V. K.; Záliš, Stanislav

    2002-01-01

    Roč. 655, 1/2 (2002), s. 218-226 ISSN 0022-328X R&D Projects: GA MŠk OC D14.20 Institutional research plan: CEZ:AV0Z4040901 Keywords : platinum compounds * benzimidazole ligands * NMR spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.901, year: 2002

  5. Anchoring of Cu(II) onto surface of porous metal-organic framework through post-synthesis modification for the synthesis of benzimidazoles and benzothiazoles

    Energy Technology Data Exchange (ETDEWEB)

    Kardanpour, Reihaneh; Tangestaninejad, Shahram, E-mail: stanges@sci.ui.ac.ir; Mirkhani, Valiollah, E-mail: mirkhani@sci.ui.ac.ir; Moghadam, Majid, E-mail: moghadamm@sci.ui.ac.ir; Mohammadpoor-Baltork, Iraj; Zadehahmadi, Farnaz

    2016-03-15

    Efficient synthesis of various benzimidazoles and benzothiazoles under mild conditions catalyzed by Cu(II) anchored onto UiO-66–NH{sub 2} metal organic framework is reported. In this manner, first, the aminated UiO-66 was modified with thiophene-2-carbaldehyde and then the prepared Schiff base was reacted with CuCl{sub 2}. The prepared catalyst was characterized by FT-IR, UV–vis, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), N{sub 2} adsorption, inductively coupled plasma atomic emission spectroscopy (ICP-AES) and field emission scanning electron microscopy (FE-SEM). The UiO-66–NH{sub 2}–TC–Cu was applied as a highly efficient catalyst for synthesis of benzimidazole and benzothiazole derivatives by the reaction of aldehydes with 1,2-diaminobenzene or 2-aminothiophenol. The Cu(II)-containing MOF was reused several times without any appreciable loss of its efficiency. - Graphical abstract: Efficient synthesis of benzimidazoles and benzothiazoles catalyzed by Cu(II) anchored onto UiO-66–NH{sub 2} metal organic framework is reported. - Highlights: • A copper Schiff base was immobilized on UiO-66 via postsynthetic modification. • The modified MOFs were fully characterized by a variety of methods. • The catalyst was used for the preparation of benzimidazoles and benzothiazoles. • In comparison of other catalysts, our catalyst was more efficient and forceful.

  6. Highly Efficient and Facile Method for Synthesis of 2-Substituted Benzimidazoles via Reductive Cyclization of O-Nitroaniline and Aryl Aldehydes

    Directory of Open Access Journals (Sweden)

    Hossein Naeimi

    2012-01-01

    Full Text Available A versatile and convenient synthesis of 2-substituted benzimidazoles, using o-nitroaniline as starting material with several aryl aldehydes, has been accomplished by using a small amount of a reluctant agent. The reaction was carried out under very mild conditions at room temperature. The yields obtained are very good in reasonably short reaction times.

  7. Highly Efficient and Facile Method for Synthesis of 2-Substituted Benzimidazoles via Reductive Cyclization of O-Nitroaniline and Aryl Aldehydes

    OpenAIRE

    Hossein Naeimi; Nasrin Alishahi

    2012-01-01

    A versatile and convenient synthesis of 2-substituted benzimidazoles, using o-nitroaniline as starting material with several aryl aldehydes, has been accomplished by using a small amount of a reluctant agent. The reaction was carried out under very mild conditions at room temperature. The yields obtained are very good in reasonably short reaction times.

  8. Donated chemical probes for open science.

    Science.gov (United States)

    Müller, Susanne; Ackloo, Suzanne; Arrowsmith, Cheryl H; Bauser, Marcus; Baryza, Jeremy L; Blagg, Julian; Böttcher, Jark; Bountra, Chas; Brown, Peter J; Bunnage, Mark E; Carter, Adrian J; Damerell, David; Dötsch, Volker; Drewry, David H; Edwards, Aled M; Edwards, James; Elkins, Jon M; Fischer, Christian; Frye, Stephen V; Gollner, Andreas; Grimshaw, Charles E; IJzerman, Adriaan; Hanke, Thomas; Hartung, Ingo V; Hitchcock, Steve; Howe, Trevor; Hughes, Terry V; Laufer, Stefan; Li, Volkhart Mj; Liras, Spiros; Marsden, Brian D; Matsui, Hisanori; Mathias, John; O'Hagan, Ronan C; Owen, Dafydd R; Pande, Vineet; Rauh, Daniel; Rosenberg, Saul H; Roth, Bryan L; Schneider, Natalie S; Scholten, Cora; Singh Saikatendu, Kumar; Simeonov, Anton; Takizawa, Masayuki; Tse, Chris; Thompson, Paul R; Treiber, Daniel K; Viana, Amélia Yi; Wells, Carrow I; Willson, Timothy M; Zuercher, William J; Knapp, Stefan; Mueller-Fahrnow, Anke

    2018-04-20

    Potent, selective and broadly characterized small molecule modulators of protein function (chemical probes) are powerful research reagents. The pharmaceutical industry has generated many high-quality chemical probes and several of these have been made available to academia. However, probe-associated data and control compounds, such as inactive structurally related molecules and their associated data, are generally not accessible. The lack of data and guidance makes it difficult for researchers to decide which chemical tools to choose. Several pharmaceutical companies (AbbVie, Bayer, Boehringer Ingelheim, Janssen, MSD, Pfizer, and Takeda) have therefore entered into a pre-competitive collaboration to make available a large number of innovative high-quality probes, including all probe-associated data, control compounds and recommendations on use (https://openscienceprobes.sgc-frankfurt.de">https://openscienceprobes.sgc-frankfurt.dehttps://openscienceprobes.sgc-frankfurt.de/">/). Here we describe the chemical tools and target-related knowledge that have been made available, and encourage others to join the project. © 2018, Müller et al.

  9. The status of molecules

    International Nuclear Information System (INIS)

    Barnes, T.

    1994-01-01

    The experimental and theoretical status of hadronic molecules, which are weakly-bound states of two or more hadrons are summarized. A brief history of the subject is given, and a few good candidates are discussed. Some signatures for molecules which may be of interest in the classification of possible molecule states are studied. It is shown that a more general understanding of 2 → 2 hadron-hadron scattering amplitudes will be crucial for molecule searches. A few more recent molecule candidates which are not well established as molecules but satisfy some of the expected signatures are also discussed. (author). 50 refs

  10. Photoactive layer based on T-shaped benzimidazole dyes used for solar cell: from photoelectric properties to molecular design

    Science.gov (United States)

    Xu, Beibei; Li, Yuanzuo; Song, Peng; Ma, Fengcai; Sun, Mengtao

    2017-03-01

    Three benzimidazole-based organic dyes, possessing the same triphenylamine donors and cyanoacrylic acid acceptors with the bithiophene π-bridges combined in different nuclear positions of benzimidazole, were investigated in the utility of dye-sensitizer solar cells. The structure, molecular orbital and energy, absorption spectra and some important parameters (such as light harvesting efficiency (LHE), electron injection driving force, the electron injection time, chemical reactivity parameters, vertical dipole moment as well as interaction models of dye-I2) were obtained according to Newns-Anderson model and DFT calculation. The process and strength of charge transfer and separation were visualized with charge different density and index of spatial extent (S, D and Δq). Current work paid attention to the new T-shaped dyes to reveal the relation between the structure and photoelectric performance. Furthermore, nine dyes (substitution of alkyl chains and π-bridges) have been designed and characterized to screen promising sensitizer candidates with excellent photo-electronic properties.

  11. Sonochemical synthesis of two nanostructured silver(I) coordination polymers based on semi-rigid bis(benzimidazole) ligands.

    Science.gov (United States)

    Hao, Shao Yun; Li, Yue Hua; Hao, Zeng Chuan; Cui, Guang Hua

    2017-11-01

    Nanoparticles of two silver(I) coordination polymers (CPs), [Ag 2 (L1) 2 (DCTP)] n (1) and [Ag 2 (L2)(DCTP)] n (2) (L1=1,3-bis(5,6-dimethylbenzimidazol-1-ylmethyl)benzene, L2=1,4-bis(benzimidazol-1-yl)-2-butene, H 2 DCTP=2,5-dichloroterephthalic acid), were synthesized by the sonochemical approach and hydrothermal method. Both CPs were characterized by elemental analysis, IR spectra, single-crystal X-ray diffraction, scanning electron microscopy (SEM), and thermogravimetric analyses (TGA). CP 1 exhibits a 2D 4-connected sql net with the point symbol {4 4 .6 2 }. While CP 2 displays a 2D 3,4-connected 3,4L13 net with the point symbol {4.6 2 } 2 {4 2 .6 2 .8 2 }. The structural diversity indicates that semi-rigid bis(benzimidazole) co-ligands play important roles in tuning the structures of the mixed Ag(I) CPs. The ultrasound irradiation time, temperature, and power showed significant effects on the morphology and growth process of the nanoparticles of two silver(I) CPs. The luminescence and photocatalytic properties of the nanoparticles of CPs 1-2 on the degradation of methyl blue (MB) were also investigated in detail. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Determination of benzimidazole residues and their metabolites in raw milk using high performance liquid chromatography-diode array detection

    Directory of Open Access Journals (Sweden)

    Marija Denžić Lugomer

    2017-01-01

    Full Text Available A new analytical method using high performance liquid chromatography-diode array detector (HPLC-DAD was developed for the analysis of 18 benzimidazoles and their metabolites in milk. Samples were extracted with acetonitrile and n-hexane and purified by polymer cation exchange (PCX solid phase extraction cartridges. LC separation was performed on Xbridge C18 with gradient elution using acetonitrile and ammonium acetate buffer. The DAD detection was set at 298, 312, 254 and 290 nm. The method was validated according to the criteria of Commission Decision 2002/657/EC. The following validation parameters were set: accuracy (expressed as recovery 31.7-137.6 %, limit of decision (CCα 6.0-120.6 μg kg-1, detection capability (CCβ 6.1-120.8 μg kg-1, limit of detection (LOD 1-4 μg kg-1, limit of quantification (LOQ 4-18 μg kg-1, precision as CV 7.0-22.5 %, withinlaboratory reproducibility expressed as CV 8.8-30.6 %. Finally, the developed method was applied to the analysis of collected milk samples. A total of 50 milk samples was analysed for benzimidazole residues. All obtained concentrations for all compounds were below the LOQ values.

  13. Raman Optical Activity of Biological Molecules

    Science.gov (United States)

    Blanch, Ewan W.; Barron, Laurence D.

    Now an incisive probe of biomolecular structure, Raman optical activity (ROA) measures a small difference in Raman scattering from chiral molecules in right- and left-circularly polarized light. As ROA spectra measure vibrational optical activity, they contain highly informative band structures sensitive to the secondary and tertiary structures of proteins, nucleic acids, viruses and carbohydrates as well as the absolute configurations of small molecules. In this review we present a survey of recent studies on biomolecular structure and dynamics using ROA and also a discussion of future applications of this powerful new technique in biomedical research.

  14. Hadronic molecules with hidden charm and bottom

    Directory of Open Access Journals (Sweden)

    Guo Feng-Kun

    2016-01-01

    Full Text Available Many of the new structures observed since 2003 in experiments in the heavy quarkonium mass region, such as the X(3872 and Zc (3900, are rather close to certain thresholds, and thus can be good candidates of hadronic molecules, which are loose bound systems of hadrons. We will discuss the consequences of heavy quark symmetry for hadronic molecules with heavy quarks. We will also emphasize that the hadronic molecular component of a given structure can be directly probed in long-distance processes, while the short-distance processes are not sensitive to it.

  15. Imaging of tautomerism in a single molecule.

    Science.gov (United States)

    Piwoński, Hubert; Stupperich, Clemens; Hartschuh, Achim; Sepioł, Jerzy; Meixner, Alfred; Waluk, Jacek

    2005-04-20

    Fluorescence imaging is used to visualize directly the transfer of two inner hydrogen atoms in single porphycene molecules. This reaction leads to a chemically equivalent but differently oriented structure and hence results in a rotation of the transition dipole moments. By probing single immobilized molecules with an azimuthally polarized laser beam in the focal spot of a confocal microscope we observe ring-like emission patterns, possible only for a chromophore with two nearly orthogonal transition dipole moments. Numerical simulations of the observed emission patterns yield a value of 72 degrees for the angle between the S0-S1 transition moments in the two tautomeric forms.

  16. Organo Luminescent semiconductor nanocrystal probes for biological applications and process for making and using such probes

    Science.gov (United States)

    Weiss, Shimon; Bruchez, Jr., Marcel; Alivisatos, Paul

    1999-01-01

    A luminescent semiconductor nanocrystal compound is described which is capable of linking to an affinity molecule. The compound comprises (1) a semiconductor nanocrystal capable of emitting electromagnetic radiation (luminescing) in a narrow wavelength band and/or absorbing energy, and/or scattering or diffracting electromagnetic radiation--when excited by an electromagnetic radiation source (of narrow or broad bandwidth) or a particle beam; and (2) at least one linking agent, having a first portion linked to the semiconductor nanocrystal and a second portion capable of linking to an affinity molecule. The luminescent semiconductor nanocrystal compound is linked to an affinity molecule to form an organo luminescent semiconductor nanocrystal probe capable of bonding with a detectable substance in a material being analyzed, and capable of emitting electromagnetic radiation in a narrow wavelength band and/or absorbing, scattering, or diffracting energy when excited by an electromagnetic radiation source (of narrow or broad bandwidth) or a particle beam. The probe is stable to repeated exposure to light in the presence of oxygen and/or other radicals. Further described is a process for making the luminescent semiconductor nanocrystal compound and for making the organo luminescent semiconductor nanocrystal probe comprising the luminescent semiconductor nanocrystal compound linked to an affinity molecule capable of bonding to a detectable substance. A process is also described for using the probe to determine the presence of a detectable substance in a material.

  17. Short-time solvation dynamics probed by phase-locked heterodyne detected pump-probe

    NARCIS (Netherlands)

    de Boeij, W.P.; Pshenichnikov, M.S; Wiersma, D. A.

    1995-01-01

    Phase-locked heterodyne detected pump-probe experiments are reported on solutions of a dye molecule in ethylene glycol, methanol and acetonitrile. By performing experiments at different phase-lock wavelengths, the real and imaginary parts of the line broadening function g(t) could be mapped out. The

  18. Structural Requirements of Some 2-(1-Propylpiperidin-4-yl)-1H-benzimidazole-4-carboxamide Derivatives as Poly (ADP-Ribose) Polymerase (PARP) for the Treatment of Cancer: QSAR Approach.

    Science.gov (United States)

    Sharma, Mukesh C

    2016-03-01

    The present study is aimed to elucidate the structural features of substituted 2-(1-propylpiperidin-4-yl)-1H-benzimidazole-4-carboxamide required for poly (ADP-ribose) polymerase inhibition and to obtain predictive 2D QSAR models to guide the rational synthesis of novel poly (ADP-ribose) polymerase inhibitors. The statistical analysis has shown that excellent results are obtained by using partial least regression based on simulated annealing method. The best model was selected based on the highest correlation coefficient r (2) = 0.8590, and cross-validated squared correlation coefficient q (2) = 0.7875 with external predictive ability of [Formula: see text] was developed by stepwise PLS method with the descriptors like T_N_F_1, SdsCHcount, and Rotatable Bond Count. The generated models provide insight into the influence of various interactive fields on the activity and, thus, can help in designing and forecasting the inhibition activity of novel (ADP-ribose) polymerase molecules.

  19. Electrical resistivity probes

    Science.gov (United States)

    Lee, Ki Ha; Becker, Alex; Faybishenko, Boris A.; Solbau, Ray D.

    2003-10-21

    A miniaturized electrical resistivity (ER) probe based on a known current-voltage (I-V) electrode structure, the Wenner array, is designed for local (point) measurement. A pair of voltage measuring electrodes are positioned between a pair of current carrying electrodes. The electrodes are typically about 1 cm long, separated by 1 cm, so the probe is only about 1 inch long. The electrodes are mounted to a rigid tube with electrical wires in the tube and a sand bag may be placed around the electrodes to protect the electrodes. The probes can be positioned in a borehole or on the surface. The electrodes make contact with the surrounding medium. In a dual mode system, individual probes of a plurality of spaced probes can be used to measure local resistance, i.e. point measurements, but the system can select different probes to make interval measurements between probes and between boreholes.

  20. New Benzimidazole-Based Bipolar Hosts: Highly Efficient Phosphorescent and Thermally Activated Delayed Fluorescent Organic Light-Emitting Diodes Employing the Same Device Structure.

    Science.gov (United States)

    Zhao, Yali; Wu, Chao; Qiu, Panlong; Li, Xiaoping; Wang, Qiang; Chen, Jiangshan; Ma, Dongge

    2016-02-03

    The rapid development of the thermally activated delayed fluorescence (TADF) emitters makes it necessary to produce new versatile host materials for both phosphorescent and TADF emitters. Three new bipolar host materials, 9,9'-(2'-(1H-benzimidazol-1-yl)-[1,1'-biphenyl]-3,5-diyl)bis(9H-carbazole) (o-mCPBI), 9,9'-(3'-(1H-benzimidazol-1-yl)-[1,1'-biphenyl]-3,5-diyl)bis(9H-carbazole) (m-mCPBI), and 9,9'-(4'-(1H-benzimidazol-1-yl)-[1,1'-biphenyl]-3,5-diyl)bis(9H-carbazole) (p-mCPBI), are designed and synthesized by integrating mCP with benzimidazole moiety via the ortho-, meta-, and para-positions of N-phenyl. The influence of different linking modes on the thermal, photophysical, electrochemical, and charge transport properties of the compounds is studied. By employing the same device structure except the emitting layer, the device performances of the blue, green, yellow, red, white phosphorescent and blue, green TADF organic light-emitting diodes (OLEDs) based on the three hosts are investigated. Among these three hosts, o-mCPBI exhibits the best device performance with external quantum efficiencies of over 20% for phosphorescent OLEDs and enhanced efficiencies for TADF devices. All these devices show relatively low efficiency roll-offs at high brightness. The versatility of the benzimidazole-based bipolar host o-mCPBI, such as an extremely high triplet energy level, suitable molecular orbital energy levels, improved thermal and charge transport properties, and excellent device performances for various colors, makes it a universal host material for highly efficient both phosphorescent and TADF OLEDs.

  1. Microsatellite marker analysis of Haemonchus contortus populations from Pakistan suggests that frequent benzimidazole drug treatment does not result in a reduction of overall genetic diversity.

    Science.gov (United States)

    Chaudhry, Umer; Redman, E M; Ashraf, Kamran; Shabbir, Muhammad Zubair; Rashid, Muhammad Imran; Ashraf, Shoaib; Gilleard, John S

    2016-06-17

    The impact of drug selection pressure on the overall genetic diversity of parasitic nematode populations in the field is poorly understood. In this study, we address this issue for the small ruminant parasite Haemonchus contortus in the Punjab, Pakistan. This region provides an opportunity to compare H. contortus populations that have been subjected to a prolonged period of frequent benzimidazole drug treatments on government farms with parasite populations that have been exposed to little or no drug treatment in neighbouring pastoral herds. Adult H. contortus worms were collected from the abomasa of small ruminants from three government farms frequently using benzimidazole drugs, and closed to animal movement, for over 30 years and also from from eighteen pastoral herds subject to minimal drug selection. The frequency of three known benzimidazole resistance associated mutations was determined in each parasite population. For the seven parasite populations in which resistance mutations were found, the diversity, geographical distribution and phylogenetic relationships of isotype-1 β-tubulin benzimidazole resistance haplotypes were determined. In addition, the genetic diversity of the parasite populations on the three government farms were compared with those from four pastoral herds. The F200Y (TAC) resistance mutation was present at a very high frequency in H. contortus populations from government herds, but not from pastoral herds, consistent with their respective drug selection histories. Population genetic analysis, using a panel of microsatellite markers, revealed that there was little genetic differentiation among the parasite populations with no significant difference in the overall genetic diversity between government and pastoral herds. In addition, sequence analysis of the isotype-1 β-tubulin locus revealed multiple F200Y (TAC) haplotypes demonstrating soft selective sweeps even in government herds with little or no contemporary parasite migration. The

  2. CD molecules 2005: human cell differentiation molecules

    Czech Academy of Sciences Publication Activity Database

    Zola, H.; Swart, B.; Nicholson, I.; Aasted, B.; Bensussan, A.; Boumsell, L.; Buckley, C.; Clark, G.; Drbal, Karel; Engel, P.; Hart, D.; Hořejší, Václav; Isacke, C.; Macardle, P.; Malavasi, F.; Mason, D.; Olive, D.; Saalmüller, A.; Schlossman, S.F.; Schwartz-Albiez, R.; Simmons, P.; Tedder, T.F.; Uguccioni, M.; Warren, H.

    2005-01-01

    Roč. 106, č. 9 (2005), s. 3123-3126 ISSN 0006-4971 Institutional research plan: CEZ:AV0Z5052915 Keywords : CD molecules * leukocyte antigen Subject RIV: EC - Immunology Impact factor: 10.131, year: 2005

  3. Single Molecule Spectroscopy of Electron Transfer

    International Nuclear Information System (INIS)

    Holman, Michael; Zang, Ling; Liu, Ruchuan; Adams, David M.

    2009-01-01

    The objectives of this research are threefold: (1) to develop methods for the study electron transfer processes at the single molecule level, (2) to develop a series of modifiable and structurally well defined molecular and nanoparticle systems suitable for detailed single molecule/particle and bulk spectroscopic investigation, (3) to relate experiment to theory in order to elucidate the dependence of electron transfer processes on molecular and electronic structure, coupling and reorganization energies. We have begun the systematic development of single molecule spectroscopy (SMS) of electron transfer and summaries of recent studies are shown. There is a tremendous need for experiments designed to probe the discrete electronic and molecular dynamic fluctuations of single molecules near electrodes and at nanoparticle surfaces. Single molecule spectroscopy (SMS) has emerged as a powerful method to measure properties of individual molecules which would normally be obscured in ensemble-averaged measurement. Fluctuations in the fluorescence time trajectories contain detailed molecular level statistical and dynamical information of the system. The full distribution of a molecular property is revealed in the stochastic fluctuations, giving information about the range of possible behaviors that lead to the ensemble average. In the case of electron transfer, this level of understanding is particularly important to the field of molecular and nanoscale electronics: from a device-design standpoint, understanding and controlling this picture of the overall range of possible behaviors will likely prove to be as important as designing ia the ideal behavior of any given molecule.

  4. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    GENERAL ARTICLE. Single-Molecule Spectroscopy. Every Molecule is Different! Kankan Bhattacharyya. Keywords. Single-molecule spectroscopy. (SMS), confocal microscopy,. FCS, sm-FRET, FLIM. 1 High-resolution spectrum re- fers to a spectrum consisting of very sharp lines. The sharp lines clearly display transitions to ...

  5. Site-Specific Infrared Probes of Proteins

    Science.gov (United States)

    Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

    2015-04-01

    Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.

  6. Site-Specific Infrared Probes of Proteins

    Science.gov (United States)

    Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

    2015-01-01

    Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

  7. Retarded Local Dynamics of Single Fluorescent Probes in Polymeric Glass due to Interaction Strengthening

    Science.gov (United States)

    Zhang, Hao; Yang, Jingfa; Zhao, Jiang

    The effect of strengthening of interaction between single fluorescent probes and polymer matrix to the probes dynamics is investigated using single molecule fluorescence defocus microscopy. By introducing multiple hydroxyl groups to the fluorescent probes, which builds up hydrogen bonds between the probe and polymer matrix, the dynamics is discovered to be retarded. This is evidenced by the lowering of the frequency of the vibrational modes in the power spectra of the rotation trajectories of individual fluorescent probes, and also by the lowering of population of rotating probes. The results show that by strengthening the probe-matrix interaction, the local dynamics detected by the probes is equivalent to that detected by a bigger probe, due to the enhanced friction between the probe and the polymer matrix. the National Basic Research Program of China (2012CB821500).

  8. Precision control of single-molecule electrical junctions.

    Science.gov (United States)

    Haiss, Wolfgang; Wang, Changsheng; Grace, Iain; Batsanov, Andrei S; Schiffrin, David J; Higgins, Simon J; Bryce, Martin R; Lambert, Colin J; Nichols, Richard J

    2006-12-01

    There is much discussion of molecules as components for future electronic devices. However, the contacts, the local environment and the temperature can all affect their electrical properties. This sensitivity, particularly at the single-molecule level, may limit the use of molecules as active electrical components, and therefore it is important to design and evaluate molecular junctions with a robust and stable electrical response over a wide range of junction configurations and temperatures. Here we report an approach to monitor the electrical properties of single-molecule junctions, which involves precise control of the contact spacing and tilt angle of the molecule. Comparison with ab initio transport calculations shows that the tilt-angle dependence of the electrical conductance is a sensitive spectroscopic probe, providing information about the position of the Fermi energy. It is also shown that the electrical properties of flexible molecules are dependent on temperature, whereas those of molecules designed for their rigidity are not.

  9. Benzimidazole-resistant gastrointestinal nematodes in indigenous Chiapas and Pelibuey sheep breeds from Chiapas, Mexico.

    Science.gov (United States)

    Liébano-Hernández, E; González-Olvera, M; Vázquez-Peláez, C; Mendoza-de-Gives, P; Ramírez-Vargas, G; Peralta-Lailson, M; Reyes-García, M E; Osorio, J; Sánchez-Pineda, H; López-Arellano, M E

    2015-01-01

    Because of the natural adaptation of Mexican sheep, the aim of the present study was to identify the presence or absence of gastrointestinal parasitic nematodes (GIN) resistant to benzimidazole (BZ) in both Chiapas and Pelibuey sheep breeds on local farms. Both male and female GIN-infected grazing sheep of the two breeds were selected. Sheep faecal samples were collected to obtain infective larvae (L3). This evolving stage of the parasite was used for taxonomic identification of the genus, based on its morphological characteristics. BZ anthelmintic resistance was evaluated using a nematode-compound in vitro interaction bioassay and the allele-specific polymerase chain reaction technique to detect mutations of residues 198 and 200 on isotype 1 of the β-tubulin gene. Three BZ-based compounds (febendazole (FBZ), tiabendazole (TBZ) and albendazole (ABZ)) at concentrations of 1, 0.5, 0.25, 0.125, 0.062 and 0.03 mg/ml were used to estimate the anthelmintic efficacy and lethal dose (LD50, LD90 and LD99) of the drugs. Two parasitic nematodes, Haemonchus and Teladorsagia, were identified in both isolates. Also, the proportions of anthelmintic resistance identified in GIN of the two sheep breeds were 68% in isolates from the Chiapas breed and 71.8% in the Pelibuey breed. The specific lethal activity obtained with FBZ was higher than 90%. However, TBZ and ABZ showed a lethal activity lower than 50%. High variability in the discriminating dose values was found among the BZ drugs. For example, FBZ LD ranged from 0.01 to 1.20 mg/ml; on the other hand, TBZ and ABZ required a dose ranging from 0.178 to 759 mg/ml. In addition, amino acid changes of Phe (TTC) to Tyr (TAC) at codon 200 of the β-tubulin gene, showing resistance to BZ, and no changes at codon 198 Glu (GAA) to Ala (GCA) were observed for both isolates. These results confirmed the presence of a genetic mutation associated with BZ in both Chiapas and Pelibuey nematode isolates.

  10. Protein recognition by a pattern-generating fluorescent molecular probe

    Science.gov (United States)

    Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M.; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M.; Motiei, Leila; Margulies, David

    2017-12-01

    Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

  11. High temperature probe

    Science.gov (United States)

    Swan, Raymond A.

    1994-01-01

    A high temperature probe for sampling, for example, smokestack fumes, and is able to withstand temperatures of 3000.degree. F. The probe is constructed so as to prevent leakage via the seal by placing the seal inside the water jacket whereby the seal is not exposed to high temperature, which destroys the seal. The sample inlet of the probe is also provided with cooling fins about the area of the seal to provide additional cooling to prevent the seal from being destroyed. Also, a heated jacket is provided for maintaining the temperature of the gas being tested as it passes through the probe. The probe includes pressure sensing means for determining the flow velocity of an efficient being sampled. In addition, thermocouples are located in various places on the probe to monitor the temperature of the gas passing there through.

  12. Microneurosurgical water probe.

    Science.gov (United States)

    Pogády, P; Wurm, G

    2005-04-01

    When constructing the micro-neurosurgical water ball probe, the authors have simply combined the properties of a ball probe with an irrigational function and the supportive role of water current to form a new irrigating ball dissector. The micro-instrument has an outlet mechanism with which the surgeon can regulate the flow of physiological solution into the operational field. Its point has the properties of a ball probe, and the overall bayonet shape facilitates surgical interventions in deep tissues under microscopic control. The water probe therefore enables the surgeon to perform precise mechanical preparation supported by a regulated current of water and a targeted irrigation in the operational field. The physiological solution in the pressure infusion cuff is under minimal pressure and directly connected to the probe. Due to the fact that one device can be used for various purposes the water ball probe represents an advantageous alternative to conventional micro-neurosurgical preparation.

  13. Synthesis, interaction with DNA and antiproliferative activities of two novel Cu(II) complexes with Schiff base of benzimidazole

    Science.gov (United States)

    Song, Wen-Ji; Cheng, Jian-Ping; Jiang, Dong-Hua; Guo, Li; Cai, Meng-Fei; Yang, Hu-Bin; Lin, Qiu-Yue

    2014-03-01

    Two novel copper(II) complexes with Schiff base of benzimidazole [Cu(L)Cl]2·CH3OH have been synthesized. HL1 (N-(benzimidazol-2-ymethyl)-5-chlorosalicylideneimine, C15H11ClN3O) and HL2 (N-(benzimidazol-2-ymethyl)-salicylideneimine, C15H12N3O) are ligands of complex (1) and complex (2), respectively. The complexes were characterized by elemental analysis, IR, UV-Vis, TGA and X-ray diffraction. Within the complexes, Cu(II) ions were four coordinated by two nitrogen atom of azomethine and imine, one phenolic oxygen atom from HL and one chloride atom. A distorted quadrilateral structure was formed. Complex (1) crystallized in the triclinic crystal system. Results showed that π-π stacking effect occurred due to the existence of aromatic ring from Schiff base and hydrogen bonding between methanol and adjacent atoms. The DNA binding properties of the complexes were investigated by electronic absorption spectra, fluorescence spectra and viscosity measurements. Results indicated that complexes bound to DNA via partial intercalation mode. The DNA binding constants Kb/(L mol-1) were 1.81 × 104 (1), 1.37 × 104 (2), 6.27 × 103 (HL1) and 3.14 × 103 (HL2) at 298 K. The title complexes could quench the emission intensities of EB-DNA system significantly. The results of agarose gel electrophoresis indicated complex (1) could cleave supercoiled DNA through the oxidative mechanism. The inhibition ratios revealed that complex (1) and HL1 had strong antiproliferative activities against human breast cancer cells (MCF-7) lines and human colorectal cancer cells (COLO205) lines in vitro. The antiproliferative activities of complex (1) against MCF-7 lines (IC50 = 16.9 ± 1.5 μmol L-1) and against COLO205 lines (IC50 = 16.5 ± 3.4 μmol L-1) is much stronger than that of HL1, which had the potential to develop anti-cancer drug.

  14. Formation of Ultracold Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cote, Robin [Univ. of Connecticut, Storrs, CT (United States)

    2016-01-28

    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

  15. Small molecule inhibitors of anthrax edema factor.

    Science.gov (United States)

    Jiao, Guan-Sheng; Kim, Seongjin; Moayeri, Mahtab; Thai, April; Cregar-Hernandez, Lynne; McKasson, Linda; O'Malley, Sean; Leppla, Stephen H; Johnson, Alan T

    2018-01-15

    Anthrax is a highly lethal disease caused by the Gram-(+) bacteria Bacillus anthracis. Edema toxin (ET) is a major contributor to the pathogenesis of disease in humans exposed to B. anthracis. ET is a bipartite toxin composed of two proteins secreted by the vegetative bacteria, edema factor (EF) and protective antigen (PA). Our work towards identifying a small molecule inhibitor of anthrax edema factor is the subject of this letter. First we demonstrate that the small molecule probe 5'-Fluorosulfonylbenzoyl 5'-adenosine (FSBA) reacts irreversibly with EF and blocks enzymatic activity. We then show that the adenosine portion of FSBA can be replaced to provide more drug-like molecules which are up to 1000-fold more potent against EF relative to FSBA, display low cross reactivity when tested against a panel of kinases, and are nanomolar inhibitors of EF in a cell-based assay of cAMP production. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. The status of molecules

    International Nuclear Information System (INIS)

    Barnes, T.; Oak Ridge National Lab., TN; Tennessee Univ., Knoxville, TN

    1994-06-01

    This report summarizes the experimental and theoretical status of hadronic molecules, which are weakly-bound states of two or more hadrons. We begin with a brief history of the subject and discuss a few good candidates, and then abstract some signatures for molecules which may be of interest in the classification of possible molecule states. Next we argue that a more general understanding of 2 → 2 hadron-hadron scattering amplitudes will be crucial for molecule searches, and discuss some of our recent work in this area. We conclude with a discussion of a few more recent molecule candidates (notably the f o (1710)) which are not well established as molecules but satisfy some of the expected signatures. (Author)

  17. Searching for novel N1-substituted benzimidazol-2-ones as non-nucleoside HIV-1 RT inhibitors.

    Science.gov (United States)

    Ferro, Stefania; Buemi, Maria Rosa; De Luca, Laura; Agharbaoui, Fatima E; Pannecouque, Christophe; Monforte, Anna-Maria

    2017-07-15

    Non-nucleoside reverse transcriptase inhibitors (NNRTIs) represent an integral part of the currently available combination antiretroviral therapy (cART) contributing to reduce the AIDS-mortality and turned the disease from lethal to chronic. In this context we recently reported a series of 6-chloro-1-(3-methylphenylsulfonyl)-1,3-dihydro-2H-benzimidazol-2-ones as potent non-nucleoside HIV-1 reverse transcriptase inhibitors. In this paper, we describe the design and the synthesis of two novel series of benzimidazolone analogues in which the linker moiety between the phenyl ring and the sulfonyl group was modified and new small lipophilic groups on the benzyl sulfonyl pendant were introduced. All the new obtained compounds were evaluated as RT inhibitors and were also tested against RTs containing single amino acid mutations. Finally, molecular docking studies were performed in order to rationalize the observed activity of the most promising compound. Copyright © 2017. Published by Elsevier Ltd.

  18. Benzimidazole-functionalized Zr-UiO-66 nanocrystals for luminescent sensing of Fe{sup 3+} in water

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Yingying; Zhang, Hanzhuo; Lei, Fan; Liang, Mei; Qian, Xuefeng; Shen, Peilian [The Key laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, National Engineering Lab for Textile Fiber Materials and Processing Technology (Zhejiang), College of Materials and Textiles, Zhejiang Sci-Tech University, Hangzhou 310018 (China); Xu, Hui, E-mail: huixu@cjlu.edu.cn [Institute of Coordination Bond Metrology and Engineering, College of Materials Science and Engineering, China Jiliang University, Hangzhou 310018 (China); Chen, Zhihui, E-mail: huixu.chen@gmail.com [The Key laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, National Engineering Lab for Textile Fiber Materials and Processing Technology (Zhejiang), College of Materials and Textiles, Zhejiang Sci-Tech University, Hangzhou 310018 (China); Key Lab of Advanced Transducers and Intelligent Control System, Ministry of Education and Shanxi Province, College of Physics and Optoelectronics, Taiyuan University of Technology, Taiyuan 030024 (China); Gao, Junkuo, E-mail: jkgao@zstu.edu.cn [The Key laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, National Engineering Lab for Textile Fiber Materials and Processing Technology (Zhejiang), College of Materials and Textiles, Zhejiang Sci-Tech University, Hangzhou 310018 (China); Yao, Juming [The Key laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, National Engineering Lab for Textile Fiber Materials and Processing Technology (Zhejiang), College of Materials and Textiles, Zhejiang Sci-Tech University, Hangzhou 310018 (China)

    2017-01-15

    Zr-based MOF structure UiO-66 exhibits unprecedented high thermal and chemical stability, making it to be one of the most used MOFs in various applications. Yet, the poor photoluminescent (PL) properties of UiO-66 limit its applications in luminescent sensing. Herein, a new benzimidazole-functionalized UiO-66 nanocrystal (UiO-66-BI) was successfully fabricated via microwave synthesis. UiO-66-BI displayed octahedral nanocrystal morphology with a diameter smaller than 200 nm and could disperse well in water and common organic solvents. UiO-66-BI demonstrated extended optical absorption in the visible-light region and efficiently improved PL emission compared with UiO-66 pristine. The sensing properties of UiO-66-BI nanocrystals towards different ions were studied, and the results demonstrated that UiO-66-BI showed excellent selective luminescent sensing of Fe{sup 3+} ions in water.

  19. Synthesis and properties of poly(aryl sulfone benzimidazole) and its copolymers for high temperature membrane electrolytes for fuel cells

    DEFF Research Database (Denmark)

    Yang, Jingshuai; Li, Qingfeng; Cleemann, Lars Nilausen

    2012-01-01

    Poly(aryl sulfone benzimidazole) (SO2PBI) and its copolymers with poly[2,2′-p-(phenylene)-5,5′-bibenzimidazole] (pPBI), termed as Co-SO2PBI, were synthesized with varied feeding ratios of 4,4′-sulfonyldibenzoic acid (SDBA) to terephthalic acid (TPA). Incorporation of the stiff para......, the membrane swelling was reduced and the mechanical strength was improved, as compared with their meta structured analogues. At an acid doping level of 11 mol H3PO4 per average molar repeat unit, the Co-20%SO2PBI membrane exhibited a tensile strength of 16 MPa at room temperature and an H2-air fuel cell peak...

  20. Discovery of membrane active benzimidazole quinolones-based topoisomerase inhibitors as potential DNA-binding antimicrobial agents.

    Science.gov (United States)

    Zhang, Ling; Addla, Dinesh; Ponmani, Jeyakkumar; Wang, Ao; Xie, Dan; Wang, Ya-Nan; Zhang, Shao-Lin; Geng, Rong-Xia; Cai, Gui-Xin; Li, Shuo; Zhou, Cheng-He

    2016-03-23

    A series of novel benzimidazole quinolones as potential antimicrobial agents were designed and synthesized. Most of the prepared compounds exhibited good or even stronger antimicrobial activities in comparison with reference drugs. The most potent compound 15m was membrane active and did not trigger the development of resistance in bacteria. It not only inhibited the formation of biofilms but also disrupted the established Staphylococcus aureus and Escherichia coli biofilms. It was able to inhibit the relaxation activity of E. coli topoisomerase IV at 10 μM concentration. Moreover, this compound also showed low toxicity against mammalian cells. Molecular modeling and experimental investigation of compound 15m with DNA suggested that this compound could effectively bind with DNA to form a steady 15m-DNA complex which might further block DNA replication to exert the powerful bioactivities. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  1. Ultracold Polar Molecules

    Science.gov (United States)

    2016-04-01

    AFRL-AFOSR-UK-TR-2016-0005 Ultracold Polar Molecules Jeremy Hutson UNIVERSITY OF DURHAM Final Report 04/01/2016 DISTRIBUTION A: Distribution approved...DATES COVERED (From - To) 15-Jan-2010 to 14-Jul-2015 4. TITLE AND SUBTITLE Final Report on Grant FA8655-10-1-3033 on Ultracold Polar Molecules 5a...formation of ultracold 87RbCs molecules in their rovibrational ground state by magnetoassociation followed by STIRAP, resulting in 14 papers acknowledging

  2. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    D)> HBr (0.83 D) > HI (0.45 D) [8]. Hence, these molecules can and do induce a dipole moment in the rare gas atoms when the two interact. The induced dipole moment is proportional to the inducing field E and the proportionality constant is the polariz- ability, i.e., μ i. = αE. However, as mentioned above, dispersion.

  3. Cold Rydberg molecules

    Science.gov (United States)

    Raithel, Georg; Zhao, Jianming

    2017-04-01

    Cold atomic systems have opened new frontiers at the interface of atomic and molecular physics. These include research on novel types of Rydberg molecules. Three types of molecules will be reviewed. Long-range, homonuclear Rydberg molecules, first predicted in [1] and observed in [2], are formed via low-energy electron scattering of the Rydberg electron from a ground-state atom within the Rydberg atom's volume. The binding mostly arises from S- and P-wave triplet scattering. We use a Fermi model that includes S-wave and P-wave singlet and triplet scattering, the fine structure coupling of the Rydberg atom and the hyperfine structure coupling of the 5S1/2 atom (in rubidium [3]). The hyperfine structure gives rise to mixed singlet-triplet potentials for both low-L and high-L Rydberg molecules [3]. A classification into Hund's cases [3, 4, 5] will be discussed. The talk further includes results on adiabatic potentials and adiabatic states of Rydberg-Rydberg molecules in Rb and Cs. These molecules, which have even larger bonding length than Rydberg-ground molecules, are formed via electrostatic multipole interactions. The leading interaction term of neutral Rydberg-Rydberg molecules is between two dipoles, while for ionic Rydberg molecules it is between a dipole and a monopole. NSF (PHY-1506093), NNSF of China (61475123).

  4. Synthesis of New Fluoro-Benzimidazole Derivatives as an Approach towards the Discovery of Novel Intestinal Antiseptic Drug Candidates.

    Science.gov (United States)

    Cevik, Ulviye Acar; Saglik, Begum Nurpelin; Ozkay, Yusuf; Canturk, Zerrin; Bueno, Juan; Demirci, Fatih; Koparal, Ali Savas

    2017-01-01

    In the present study, nineteen new fluoro-benzimidazole derivatives, including nifuroxazide analogs, were synthesized by microwave-supported reactions and tested against a panel of pathogenic microorganisms consisting of resistant strains. The synthesized compounds were characterized and identified by FT-IR, 1H- and 13C-NMR, mass spectroscopy, and elemental analyses, respectively. In vitro antimicrobial and cytotoxic effects of the synthesized compounds were determined by microdilution and by [3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyltetrazolium bromide] (MTT) assay. The compound 4-[5(6)-fluoro-1H-benzimidazol-2-yl)-N'-(2- methylbenzylidene)]benzohydrazide (18) showed particularly high inhibitory activity against the gastro-intestinal pathogens, such as Escherichia coli O157:H7, Escherichiacoli ATCC 8739, Escherichia coli ATCC 35218 and Salmonella typhimurium ATCC 13311 standard strains, with minimum inhibitory concentrations (MIC90) ranging from 0.49-0.98 μg/mL. The microbial panel contained a total of ten pathogens including Klebsiella sp., Mycobacterium sp., MRSA, etc., for which the level of inhibitory activity measured was higher than that exhibited by the tested concentrations (MIC > 1000 μg/mL). In vitro cytotoxicity results revealed that the inhibitory concentration (IC50) value (210.23 μg/mL) of compound 18 against CCD 841 CoN cells (human intestinal epithelial cell line) is about 430 times higher than its MIC90 value against the tested Escherichia coli strains. Furthermore, the docking study of compound 18 suggested that its structure is very compatible with the active site pocket of the phosphofructokinase-2 enzyme. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  5. Molecular diagnosis of benzimidazole resistance in Haemonchus contortus in sheep from different geographic regions of North India

    Directory of Open Access Journals (Sweden)

    S. Chandra

    2014-05-01

    Full Text Available Aim: To monitor the benzimidazole resistance in Haemonchus contortus in sheep from different agro climatic zones of India reared in extensive or intensive managemental conditions. Materials and Methods: Faecal materials were collected from sheep from organized as well as private farms located in Rohilkhand region, Bundelkhand region, and eastern Utter Pradesh. Larvae were obtained by coproculture and identified as L3 of Haemonchus contortus. Exsheathment of larvae was done by incubating them in 180 µl of sodium hypochlorite for 5-20 minutes. Genomic DNA was isolated from single larvae and amplification of -tubulin of Haemonchus contortus was done by primary and nested PCR. PCR-RFLP was done with RsaI enzyme for species identification. Genotyping was done by Allele specific PCR using Nested PCR product as template and resulting fragments were separated by gel electrophoresis in a 1.5% agarose gel in TAE buffer. Results: Primary PCR size of -tubulin gene of H. contortus was 840 bp, whereas nested PCR amplified 774 bp size product. Species was confirmed as H. contortus by PCR-RFLP which shows three fragments at 440 bp, 190 bp, and 150 bp. From Rohilkhand region out of 30 larvae, 19 (63% were homozygous resistant (RR, 6 (20% were homozygous susceptible (SS, and 5 (17% were heterozygous (RS. From Bundelkhand 34 (85% were RR, 4 (10% were SS, and 2 (5% were RS out of 40 larvae screened. From Eastern UP (Jaunpur and Varanasi 30 larvae each from Jaunpur and Varanasi were genotyped;larvae from Jaunpur revealed 53% RR, 27% SS, and 20% RS whereas larvae from Varanasi genotyped showed 57% RR, 17% SS, and 26% RS. Conclusion: Due to indiscriminate use of Benzimidazole group of drugs in organized and private farms, resistance to this group of drugs is increasing at the field level.

  6. Probe tests microweld strength

    Science.gov (United States)

    1965-01-01

    Probe is developed to test strength of soldered, brazed or microwelded joints. It consists of a spring which may be adjusted to the desired test pressure by means of a threaded probe head, and an indicator lamp. Device may be used for electronic equipment testing.

  7. Molecule of the Month

    Indian Academy of Sciences (India)

    dimensional structure of a chemical ... used as probes to understand many aspects of structure, bonding and reactivity. I shall give a few examples. ... While electronic stabilization is provided by the π electrons in the ring, the adamantyl groups ...

  8. Chromosome-specific DNA Repeat Probes

    Energy Technology Data Exchange (ETDEWEB)

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  9. Evaluation of synthetic linear motor-molecule actuation energetics

    OpenAIRE

    Brough, Branden; Northrop, Brian H.; Schmidt, Jacob J.; Tseng, Hsian-Rong; Houk, Kendall N.; Stoddart, J. Fraser; Ho, Chih-Ming

    2006-01-01

    By applying atomic force microscope (AFM)-based force spectroscopy together with computational modeling in the form of molecular force-field simulations, we have determined quantitatively the actuation energetics of a synthetic motor-molecule. This multidisciplinary approach was performed on specifically designed, bistable, redox-controllable [2]rotaxanes to probe the steric and electrostatic interactions that dictate their mechanical switching at the single-molecule level. The fusion of expe...

  10. Metastable Helium Molecules as Tracers in Superfluid 4He

    International Nuclear Information System (INIS)

    Guo, W.; Wright, J. D.; Cahn, S. B.; Nikkel, J. A.; McKinsey, D. N.

    2009-01-01

    Metastable helium molecules generated in a discharge near a sharp tungsten tip immersed in superfluid 4 He are imaged using a laser-induced-fluorescence technique. By pulsing the tip, a small cloud of He 2 * molecules is produced. We can determine the normal-fluid velocity in a heat-induced counterflow by tracing the position of a single molecule cloud. As we run the tip in continuous field-emission mode, a normal-fluid jet from the tip is generated and molecules are entrained in the jet. A focused 910 nm pump laser pulse is used to drive a small group of molecules to the first excited vibrational level of the triplet ground state. Subsequent imaging of the tagged molecules with an expanded 925 nm probe laser pulse allows us to measure the flow velocity of the jet. The techniques we developed provide new tools in quantitatively studying the normal fluid flow in superfluid helium.

  11. Synthesis of novel tripodal-benzimidazole from 2,4,6-tris(p-formylphenoxy)-1,3,5-triazine: Structural, electrochemical and antimicrobial studies

    International Nuclear Information System (INIS)

    Koc, Ziya Erdem; Bingol, Haluk; Saf, Ahmet O.; Torlak, Emrah; Coskun, Ahmet

    2010-01-01

    Four new tripodal-benzimidazole derivatives were synthesized by Schiff base reaction between 2,4,6-tris(p-formylphenoxy)-1,3,5-triazine (TRIPOD) and different diamine derivatives. The structures of the obtained compounds were identified by FT-IR, 1 H NMR, 13 C NMR and UV-vis spectral data, thermal analysis and elemental analysis. Electrochemical behaviors of the compounds were studied by cyclic voltammetry in DMF including 0.1 M [NBu 4 ] [PF 6 ]. The voltammograms showed peaks having similar characteristics except tripodal-benzimidazole including -NO 2 derivative. In addition, their antimicrobial activities were evaluated by using the standard disk diffusion method in dimethylformamide media. The activities were determined against 4 bacteria cultures by comparing to those of gentamycin.

  12. Identification of novel benzimidazole derivatives as anti-Trypanosoma cruzi agents: solid-phase synthesis, structure-activity relationships and molecular docking studies.

    Science.gov (United States)

    Ríos, Natalia; Varela, Javier; Birriel, Estefania; González, Mercedes; Cerecetto, Hugo; Merlino, Alicia; Porcal, Williams

    2013-10-01

    In this paper, we report the solid-phase synthesis of 33 novel 1,2,5-tri-substituted benzimidazole derivatives and their in vitro activity on cruzipain and Trypanosoma cruzi epimastigotes. Seven compounds were potent inhibitors of T. cruzi growth with IC50 values in the range 6-16 µM. Applying structure-activity relationships and principal component analysis strategies we were able to determine ring substituent effects and physicochemical properties that are important for the antichagasic activity of these novel derivatives, as well as get an insight into their possible mechanisms of action. Molecular docking studies revealed the binding orientation of the ligands in the active site of cruzipain providing new guidelines for the further design of better inhibitors. Compound 2a constitute a promising hit compound for novel anti-T. cruzi agents showing that the benzimidazole scaffold may represent an interesting therapeutic alternative for the treatment of Chagas disease.

  13. Solid-phase synthesis and spectral properties of 2-alkylthio-6H-pyrano[2,3-f]benzimidazole-6-ones: a combinatorial approach for 2-alkylthioimidazocoumarins.

    Science.gov (United States)

    Song, Aimin; Zhang, Jinhua; Lebrilla, Carlito B; Lam, Kit S

    2004-01-01

    The solid-phase synthesis of 2-alkylthio-6H-pyrano[2,3-f]benzimidazole-6-ones (2-alkylthioimidazocoumarins) is described. 7-Fluoro-4-methyl-6-nitro-2-oxo-2H-1-benzopyran-3-carboxylic acid was coupled to Rink amide resin via its carboxyl group. The resin-bound scaffold then underwent aromatic nucleophilic substitution with primary amines, followed by reduction of the nitro group with tin (II) chloride. Subsequent cyclization of the o-dianilino intermediates with thiocarbonyldiimidazole (TCD) afforded resin-bound 1,3-dihydro-2-thioxo-6H-pyrano[2,3-f]benzimidazole-6-ones, which were then S-alkylated with alkyl halides in the presence of N,N-diisopropylethylamine (DIEA). The desired products were obtained in good yield with high purity after trifluoroacetic acid cleavage. The unique spectral properties of 2-alkylthioimidazocoumarins indicate that they may be useful in photodynamic therapy.

  14. Proton-conducting membranes based on benzimidazole-containing sulfonated poly(ether ether ketone) compared with their carboxyl acid form

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hongtao; Wu, Jing; Zhao, Chengji; Zhang, Gang; Zhang, Yang; Shao, Ke; Xu, Dan; Lin, Haidan; Han, Miaomiao; Na, Hui [Alan G MacDiarmid Institute, College of Chemistry, Jilin University, Changchun 130012 (China)

    2009-10-15

    A series of sulfonated poly(ether ether ketone) containing pendant carboxyl (C-SPEEKs) have been synthesized using a nucleophilic polycondesation reaction. A condensation reaction between 1,2-diaminobenzene and carboxyl resulted in a new series of copolymers containing benzimidazole groups (SPEEK-BIms). The expected structures of the sulfonated copolymers are confirmed by {sup 1}H NMR. The dependence of ion exchange capacity, water uptake, proton conductivity and methanol diffusion coefficient of SPEEK-BIm membranes has been studied and compared with their carboxyl acid form. The results suggest that the introduction of benzimidazole groups may be responsible for many excellent properties of the membranes for fuel cell. It is noticeable that the markedly improved oxidative stability is benefit for the application of membrane. (author)

  15. Novel sulfonated poly(ether ether ketone) with pendant benzimidazole groups as a proton exchange membrane for direct methanol fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yang; Shao, Ke; Zhao, Chengji; Zhang, Gang; Li, Hongtao; Fu, Tiezhu; Na, Hui [Alan G MacDiarmid Institute, College of Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, Jilin (China)

    2009-10-20

    A series of sulfonated poly(ether ether ketone)s bearing pendant carboxylic acid groups (C-SPEEKs) have been prepared and subsequently react with 1,2-diaminobenzene to obtain sulfonated poly(ether ether ketone)s with pendant benzimidazole groups (BI-SPEEKs). The expected structures of the sulfonated copolymers are confirmed by {sup 1}H NMR. The resulting copolymers all show good thermal and mechanical properties. It should be noted that the introduction of benzimidazole groups into the copolymer improves its thermal and oxidative stability obviously. Meanwhile, compared to C-SPEEK, BI-SPEEK membranes show much lower water uptake and methanol permeability with the same sulfonation degree (DS). In order to study morphological changes of C-SPEEK and BI-SPEEK membranes, hydrophilic domains sizes from an atomic force microscopy (AFM) are investigated. (author)

  16. Microwave assisted, one-pot synthesis of 5-nitro- 2-aryl substituted-1H-benzimidazole libraries: screening in vitro for antimicrobial activity.

    Science.gov (United States)

    Hosamani, Kallappa Mahadevappa; Seetharamareddy, Harisha Reddy; Keri, Rangappa Sangappa; Hanamanthagouda, Manohar Shirugumbi; Moloney, Mark G

    2009-10-01

    The efficient and rapid synthesis of 5-nitro-2-aryl substituted-1H-benzimidazole libraries (1a-1j) has been established. Thus, both microwave and conventional cyclo-condensation of 4-nitro ortho-phenylenediamine with various phenoxyacetic acids were carried out in the presence of HCl catalyst. The microwave synthesis route afforded advantages, such as good to excellent yields, shorter reaction time (2.5-3.5 min), readily available starting material, and simple purification procedure, which distinguish the present protocol from other existing methods used for the synthesis of benzimidazole libraries. Bioassay indicated that all the compounds showed in vitro antimicrobial activity against Vancomycin resistant enteroccoccus, Staphylococcus aureus, Micrococcus, Bacillus subtilis (gram-positive bacteria) and Shigella dysentery, Escherichia coli (gram-negative bacteria) and Candida albicans, Aspergillus niger, Penicillium (fungi). The minimum inhibitory concentration (MIC) was determined for test compounds as well as for reference standards.

  17. A green and efficient protocol for the synthesis of quinoxaline, benzoxazole and benzimidazole derivatives using heteropolyanion-based ionic liquids: as a recyclable solid catalyst.

    Science.gov (United States)

    Vahdat, Seyed Mohammad; Baghery, Saeed

    2013-09-01

    In this paper, we introduce two nonconventional ionic liquid compounds which are composed of propane sulfonate functionalized organic cations and heteropolyanions as green solid acid catalysts for the highly efficient and green synthesis of 2,3-disubstitutedquinoxaline derivatives. These ionic liquids are in the solid state at room temperature and the synthesis is carried out via the one-pot condensation reaction of various o-phenylenediamine with 1,2-diketone derivatives. Benzoxazole and benzimidazole derivatives were also synthesized by these novel catalysts via the one-pot condensation from reaction orthoester with o-aminophenol (synthesis of benzoxazole derivatives) and ophenylenediamine (synthesis of benzimidazole derivatives). All experiments successfully resulted in the desired products. The described novel synthesis method has several advantages of safety, mild condition, high yields, short reaction times, simplicity and easy workup compared to the traditional method of synthesis.

  18. Molecule of the Month

    Indian Academy of Sciences (India)

    Atoms in a molecule generally prefer, particularly among the neighbouring ones, certain optimmn geometrical relationships. These are manifested in specific ranges of bond lengths, bond angles, torsion angles etc. As it always happens, chemists are interested in making molecules where these 'standard relationships' are ...

  19. Molecule of the Month

    Indian Academy of Sciences (India)

    Cyclo bu tadiene (1) has been one of the most popular molecules for experimentalists and theoreticians. This molecule is unstable as . it is antiaromatic ( 4,n electrons in a cyclic array). Even though some highly substituted cyclobutadienes, for example, compound 2 and the Fe(CO)3 complex of cyclobutadiene (3) are ...

  20. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! Kankan Bhattacharyya. General Article Volume 20 Issue 2 February 2015 pp 151-164. Fulltext. Click here to view fulltext PDF. Permanent link:

  1. Algebraic theory of molecules

    CERN Document Server

    Iachello, F

    1995-01-01

    1. The Wave Mechanics of Diatomic Molecules. 2. Summary of Elements of Algebraic Theory. 3. Mechanics of Molecules. 4. Three-Body Algebraic Theory. 5. Four-Body Algebraic Theory. 6. Classical Limit and Coordinate Representation. 8. Prologue to the Future. Appendices. Properties of Lie Algebras; Coupling of Algebras; Hamiltonian Parameters

  2. Molecule of the Month.

    Indian Academy of Sciences (India)

    described here. Chemistry of aromatic molecules has a long history. Many molecules made up of multiple benzene-like rings have been isolated or made in the laboratory over the years. These are called polycondensed aromatic hydrocarbons (PAH for short). ... a bowl like symmetric polycyclic aromatic hydrocarbon of the.

  3. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! ... Author Affiliations. Kankan Bhattacharyya1. Department of Physical Chemistry, Indian Association for the Cultivation of Science Jadavpur, Kolkata 700 032 India.

  4. Electrons in Molecules

    Indian Academy of Sciences (India)

    “What are electrons doing in molecules?” This is a deceptively simple question that scientists have been trying to answer for more than eighty years. With the advent of quantum mechanics in 1926, it became clear that we must understand the dynamics of electronic motion in atoms, molecules and solids in order to explain ...

  5. ISOLATED MOLECULES IN METALS

    NARCIS (Netherlands)

    1992-01-01

    In this paper, some results obtained on the formation of isolated molecules of composition SnOx in silver and SnFx in copper-are reviewed. Hyperfine interaction and ion beam interaction techniques were used for the identification of these molecules.

  6. Molecule of the Month

    Indian Academy of Sciences (India)

    Nature is an excellent synthetic organic chemist. Using mild reaction conditions and a few elemental combinations, a large variety of complex molecules are made in and around us. The atoms are put together in precise arrangements to enable the molecules to carry out different tasks with remarkable specificity.

  7. Synthesis of a novel series of 4-arylpiperazinyl derivatives linked to a 2-(pyridin-3-yl)-1H-benzimidazole as new Delavirdine analogues

    Energy Technology Data Exchange (ETDEWEB)

    Pessoa-Mahana, David; Nunez, Andres; Espinosa, Christian; Mella-Raipn, Jaime [Pontificia Universidad Catolica de Chile, Santiago (Chile). Facultad de Quimica. Dept. de Farmacia; Pessoa-Mahana, Hernan [Universidad de Chile, Santiago (Chile). Facultad de Ciencias Quimicas. Dept. de Quimica Organica y Fisico-Quimica

    2010-07-01

    The synthesis of a series of substituted arylpiperazines linked to a 2-(pyridin-3-yl)-1H-benzo[d]imidazole scaffold through an alkylic linker is reported. The novel 1-(2-(4-arylpiperazin-1-yl)alkyl)-2-(pyridin-3-yl)-1H-benzimidazole derivatives are structurally related to the anti-HIV-1 drug Delavirdine and belong to the bis(heteroaryl)piperazines family (BHAPs), a well known HIV-1 reverse transcriptase inhibitors group. (author)

  8. Novel product ions of 2-aminoanilide and benzimidazole Ag(I) complexes using electrospray ionization with multi-stage tandem mass spectrometry.

    Science.gov (United States)

    Johnson, Byron S; Burinsky, David J; Burova, Svetlana A; Davis, Roman; Fitzgerald, Russ N; Matsuoka, Richard T

    2012-05-15

    The 2-aminoaniline scaffold is of significant value to the pharmaceutical industry and is embedded in a number of pharmacophores including 2-aminoanilides and benzimidazoles. A novel application of coordination ion spray mass spectrometry (CIS-MS) for interrogating the silver ion (Ag(+)) complexes of a homologous series of these compounds using multi-stage tandem mass spectrometry is described. Unlike the ubiquitous alkali metal ion complexes, Ag(+) complexes of 2-aminoanilides and benzimidazoles were found to yield [M - H](+) ions in significant abundance via gas-phase elimination of the metal hydride (AgH) resulting in unique product ion cascades. Sample introduction was by liquid chromatography with mass spectrometry analysis performed on a hybrid linear ion trap/orbitrap instrument capable of high-resolution measurements. Rigorous structural characterization by multi-stage tandem mass spectrometry using [M +  H](+), [M - H](-) and [M - H](+) precursor ions derived from ESI and CIS experiments was performed for the homologous series of 2-aminoanilide and benzimidazole compounds. A full tabular comparison of structural information resulting from these product ion cascades was produced. Multi-stage tandem mass spectrometry of [M - H](+) ions resulting from Ag(+) complexes of 2-aminoanilides and benzimidazoles in CIS-MS experiments produced unique product ion cascades that exhibited complementary structural information to that obtained from tandem mass spectrometry of [M  +  H](+) and [M - H](-) ions by electrospray ionization (ESI). These observations may be broadly applicable to other compounds that are observed to form Ag(+) complexes and eliminate AgH. Copyright © 2012 John Wiley & Sons, Ltd.

  9. Application of Recognition Tunneling in Single Molecule Identification

    Science.gov (United States)

    Zhao, Yanan

    Single molecule identification is one essential application area of nanotechnology. The application areas including DNA sequencing, peptide sequencing, early disease detection and other industrial applications such as quantitative and quantitative analysis of impurities, etc. The recognition tunneling technique we have developed shows that after functionalization of the probe and substrate of a conventional Scanning Tunneling Microscope with recognition molecules ("tethered molecule-pair" configuration), analyte molecules trapped in the gap that is formed by probe and substrate will bond with the reagent molecules. The stochastic bond formation/breakage fluctuations give insight into the nature of the intermolecular bonding at a single molecule-pair level. The distinct time domain and frequency domain features of tunneling signals were extracted from raw signals of analytes such as amino acids and their enantiomers. The Support Vector Machine (a machine-learning method) was used to do classification and predication based on the signal features generated by analytes, giving over 90% accuracy of separation of up to seven analytes. This opens up a new interface between chemistry and electronics with immediate implications for rapid Peptide/DNA sequencing and molecule identification at single molecule level.

  10. Optical Probes for Neurobiological Sensing and Imaging.

    Science.gov (United States)

    Kim, Eric H; Chin, Gregory; Rong, Guoxin; Poskanzer, Kira E; Clark, Heather A

    2018-04-13

    probing entire neurobiological units with high spatiotemporal resolution. Thus, we introduce selected applications for ion and neurotransmitter detection to investigate both neurons and non-neuronal brain cells. We focus on families of optical probes because of their ability to sense a wide array of molecules and convey spatial information with minimal damage to tissue. We start with a discussion of currently available molecular probes, highlight recent advances in genetically modified fluorescent probes for ions and small molecules, and end with the latest research in nanosensors for biological imaging. Customizable, nanoscale optical sensors that accurately and dynamically monitor the local environment with high spatiotemporal resolution could lead to not only new insights into the function of all cell types but also a broader understanding of how diverse neural signaling systems act in conjunction with neighboring cells in a spatially relevant manner.

  11. Development of novel (1-H benzimidazole bearing pyrimidine-trione based MAO-A inhibitors: Synthesis, docking studies and antidepressant activity

    Directory of Open Access Journals (Sweden)

    Bijo Mathew

    2016-09-01

    Full Text Available The synthesis of some novel (1-H benzimidazole bearing pyrimidine-trione based MAO-A inhibitors were achieved by the reaction between 2E-1-(1H-benzimidazol-2-yl-3-phenylprop-2-en-1-ones(4a–f and barbituric acid in the presence of a catalytic amount of acetic acid medium. All the final structures were assigned on the basis of IR, 1HNMR and mass spectra analyses. All the synthesized derivatives showed good antidepressant activity when compared to the standard clomipiramine at a dose level of 20 mg/kg. The compound (5d 5-{(2E-1-(1H-benzimidazol-2-yl-3-[4-(dimethylaminophenyl] prop-2-en-1-ylidene} pyrimidine-2, 4, 6(1H,3H,5H-trione significantly reduced the duration of immobility times at 50 mg/kg−1 dose level when compared to the standard drug. Molecular docking studies revealed the need for an extra hydrophobic interaction in the titled scaffold for acquiring the promising experimental values. It has been concluded that the computational values obtained after the docking calculation are in good agreement with the experimental values.

  12. Single-molecule tracking in living cells using single quantum dot applications.

    Science.gov (United States)

    Baba, Koichi; Nishida, Kohji

    2012-01-01

    Revealing the behavior of single molecules in living cells is very useful for understanding cellular events. Quantum dot probes are particularly promising tools for revealing how biological events occur at the single molecule level both in vitro and in vivo. In this review, we will introduce how single quantum dot applications are used for single molecule tracking. We will discuss how single quantum dot tracking has been used in several examples of complex biological processes, including membrane dynamics, neuronal function, selective transport mechanisms of the nuclear pore complex, and in vivo real-time observation. We also briefly discuss the prospects for single molecule tracking using advanced probes.

  13. Toward Generalization of Iterative Small Molecule Synthesis.

    Science.gov (United States)

    Lehmann, Jonathan W; Blair, Daniel J; Burke, Martin D

    2018-02-01

    Small molecules have extensive untapped potential to benefit society, but access to this potential is too often restricted by limitations inherent to the customized approach currently used to synthesize this class of chemical matter. In contrast, the "building block approach", i.e., generalized iterative assembly of interchangeable parts, has now proven to be a highly efficient and flexible way to construct things ranging all the way from skyscrapers to macromolecules to artificial intelligence algorithms. The structural redundancy found in many small molecules suggests that they possess a similar capacity for generalized building block-based construction. It is also encouraging that many customized iterative synthesis methods have been developed that improve access to specific classes of small molecules. There has also been substantial recent progress toward the iterative assembly of many different types of small molecules, including complex natural products, pharmaceuticals, biological probes, and materials, using common building blocks and coupling chemistry. Collectively, these advances suggest that a generalized building block approach for small molecule synthesis may be within reach.

  14. Dynamics of Activated Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Mullin, Amy S. [Univ. of Maryland, College Park, MD (United States)

    2016-11-16

    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  15. Electron correlation in molecules

    CERN Document Server

    Wilson, S

    2007-01-01

    Electron correlation effects are of vital significance to the calculation of potential energy curves and surfaces, the study of molecular excitation processes, and in the theory of electron-molecule scattering. This text describes methods for addressing one of theoretical chemistry's central problems, the study of electron correlation effects in molecules.Although the energy associated with electron correlation is a small fraction of the total energy of an atom or molecule, it is of the same order of magnitude as most energies of chemical interest. If the solution of quantum mechanical equatio

  16. Neutrons as a probe

    International Nuclear Information System (INIS)

    Iizumi, Masashi

    1993-01-01

    As an introduction to the symposium a brief overview will be given about the features of neutrons as a probe. First it will be pointed out that the utilization of neutrons as a probe for investigating the structural and dynamical properties of condensed matters is a benign gift eventuated from the release of atomic energy initiated by Enrico Fermi exactly half century ago. Features of neutrons as a probe are discussed in accordance with the four basic physical properties of neutrons as an elementary particle; (1) no electric charge (the interaction with matter is nuclear), (2) the mass of neutron is 1 amu, (3) spin is 1/2 and (4) neutrons have magnetic dipole moment. Overview will be given on the uniqueness of neutrons as a probe and on the variety in the way they are used in the wide research area from the pure science to the industrial applications. (author)

  17. Imaging and controlling proton motion in molecules

    Science.gov (United States)

    Ibrahim, H.; Beaulieu, S.; Wanie, V.; Endo, T.; Wales, B.; Tong, X.-M.; Schuurman, M. S.; Sanderson, J.; Légaré, F.

    2017-11-01

    How do atoms move within a molecule? What are the paths they take? Coulomb Explosion Imaging combined with a multi-color pump probe scheme allows us to address these questions with a table top setup. Since the momentum information of molecular fragments is preserved at the moment of explosion, we can deduce the fragment's momentary position, representing the structure of the molecule. We have studied isomerization and dissociation events through the movement of protons, deuterons and electrons, taking advantage of the rich statistics this technique provides. In the case of proton migration in the acetylene cation, we were able to identify an isotope dependent to- and fro isomerization behavior [1]. Presently, we are expanding our studies on more complex processes. Aside from passively studying dynamics, we have also actively controlled the electron localization in small molecules [2] using two-color mid-infrared asymmetric laser fields. The manipulation of protons, the lightest atomic fragments in molecules, is of great interest due to the tremendous diversity of molecules containing them, in combination with the generality of how protons behave within molecules. Their detection involves certain challenges since they move extremely fast compared to heavier atoms. Here, we focus on two different proton motions which are triggered by excitation with ultrashort laser pulses and imaged with the Coulomb explosion imaging (CEI) technique. First, we will discuss proton migration dynamics in the acetylene cation launched due to strong field multiphoton ionization with UV pulses in a rather simple table top approach. Second, we will concentrate on controlling electron localization - and thus proton localization - in the cation of the hydrogen molecule by using an asymmetric two color field in the mid-infrared (MIR).

  18. Noninvasive ultrasonic probes

    International Nuclear Information System (INIS)

    Barnes, S.R.; Galer, D.R.; Leard, R.S.

    1987-01-01

    An ultrasonic probe is described for insonifying the ascending aorta of a supine or reclining human patient from a location within the suprasternal notch of the patient. The probe comprises: a transducer head and an elongated handle; housing propagates ultrasonic energy and for intercept-frequency-shifted, reflected radiant energy; the handle has a proximate portion and a distal portion and a non-circular cross-sectional configuration with at least one longitudinal edge which furnishes a gripping surface; this facilitates tactile positioning of the probe; the transducer head is integral with the handle of the probe at the exposed end of the proximate portion; the transducer head has a generally arcuate cross-sectional configuration and a generally trapezoidal profile; the transducer head is oriented at right angles to the proximate portion of the handle and has an exposed, patient contacting end in which the transducer means are located; this facilitates the orientation of the transducer means housed in the head relative to the ascending aorta of the patient; and the distal end portion of the elongated probe handle is integral with and immovably oriented at a severe angle relative to the proximate end of that handle, and lies in the same plane as the proximate end of the handle; the transducer head of the probe is placed with facility within the suprasternal notch of the patient by an operator positioned behind the head of the patient

  19. Single molecules and nanotechnology

    CERN Document Server

    Vogel, Horst

    2007-01-01

    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  20. Quantum dot molecules

    CERN Document Server

    Wu, Jiang

    2014-01-01

    This book reviews recent advances in the exciting and rapidly growing field of quantum dot molecules (QDMs). It offers state-of-the-art coverage of novel techniques and connects fundamental physical properties with device design.

  1. Electron-molecule collisions

    CERN Document Server

    Takayanagi, Kazuo

    1984-01-01

    Scattering phenomena play an important role in modern physics. Many significant discoveries have been made through collision experiments. Amongst diverse kinds of collision systems, this book sheds light on the collision of an electron with a molecule. The electron-molecule collision provides a basic scattering problem. It is scattering by a nonspherical, multicentered composite particle with its centers having degrees of freedom of motion. The molecule can even disintegrate, Le., dissociate or ionize into fragments, some or all of which may also be molecules. Although it is a difficult problem, the recent theoretical, experimental, and computational progress has been so significant as to warrant publication of a book that specializes in this field. The progress owes partly to technical develop­ ments in measurements and computations. No less important has been the great and continuing stimulus from such fields of application as astrophysics, the physics of the earth's upper atmosphere, laser physics, radiat...

  2. Vibrations of a molecule in an external force field.

    Science.gov (United States)

    Okabayashi, Norio; Peronio, Angelo; Paulsson, Magnus; Arai, Toyoko; Giessibl, Franz J

    2018-05-01

    The oscillation frequencies of a molecule on a surface are determined by the mass distribution in the molecule and the restoring forces that occur when the molecule bends. The restoring force originates from the atomic-scale interaction within the molecule and with the surface, which plays an essential role in the dynamics and reactivity of the molecule. In 1998, a combination of scanning tunneling microscopy with inelastic tunneling spectroscopy revealed the vibrational frequencies of single molecules adsorbed on a surface. However, the probe tip itself exerts forces on the molecule, changing its oscillation frequencies. Here, we combine atomic force microscopy with inelastic tunneling spectroscopy and measure the influence of the forces exerted by the tip on the lateral vibrational modes of a carbon monoxide molecule on a copper surface. Comparing the experimental data to a mechanical model of the vibrating molecule shows that the bonds within the molecule and with the surface are weakened by the proximity of the tip. This combination of techniques can be applied to analyze complex molecular vibrations and the mechanics of forming and loosening chemical bonds, as well as to study the mechanics of bond breaking in chemical reactions and atomic manipulation.

  3. Discovering Small Molecule Inhibitors Targeted to Ligand-Stimulated RAGE-DIAPH1 Signaling Transduction

    Science.gov (United States)

    Pan, Jinhong

    The receptor of advanced glycation end product (RAGE) is a multiligand receptor of the immunoglobulin superfamily of cell surface molecules, which plays an important role in immune responses. Full-length RAGE includes three extracellular immunoglobulin domains, a transmembrane domain and an intracellular domain. It is a pattern recognition receptor that can bind diverse ligands. NMR spectroscopy and x-ray crystallization studies of the extracellular domains of RAGE indicate that RAGE ligands bind by distinct charge- and hydrophobicity-dependent mechanisms. It is found that calgranulin binding to the C1C2 domain or AGEs binding to the V domain activates extracellular signaling, which triggers interactions of the RAGE cytoplasmic tail (ctRAGE) with intracellular effector, such as diaphanous 1 (DIAPH1), to initiate signal transduction cascades. ctRAGE is essential for RAGE-ligand-mediated signal transduction and consequent modulation of gene expression and cellular properties. RAGE is over-expressed in diseased tissues of most RAGE-associated pathogenic conditions, such as complications of Alzheimer's diseases, diabetes, vascular diseases, inflammation, cancers and neurodegeneration. They are the major diseases affecting a large population worldwide. RAGE can function as a biomarker or drug target for these diseases. The cytoplasmic tail of RAGE can be used as a drug target to inhibit RAGE-induced intracellular signaling by small molecule inhibitors to treat RAGE-associated diseases. We developed a high throughput screening assay with which we probed a small molecule library of 58,000 compounds to find that 777 small molecules displayed 50% inhibition and 97 compounds demonstrated dose-dependent inhibition of the binding of ctRAGE-DIAPH1. Eventually, there were 13 compounds which displayed dose-dependent inhibition of ctRAGE binding to DIAPH1 and direct binding to ctRAGE analyzed by 15N HSQC-NMR and native tryptophan fluorescence titration experiments; thus, they were

  4. Free enthalpies of replacing water molecules in protein binding pockets.

    Science.gov (United States)

    Riniker, Sereina; Barandun, Luzi J; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F

    2012-12-01

    Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH(3) group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH(3) at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.

  5. UV and VUV spectroscopy and photochemistry of small molecules in a supersonic jet

    Science.gov (United States)

    Ruehl, E.; Vaida, V.

    1990-01-01

    UV and VUV absorption and emission spectroscopy is used to probe jet cooled molecules, free radicals, and clusters in the gas phase. Due to efficient cooling inhomogeneous effects on spectral line widths are eliminated. Therefore from these spectra, both structural and dynamical information is obtained. The photoproducts of these reactions are probed by resonance enhanced multiphoton ionization.

  6. Effect of H4R antagonist N-(2-aminoethyl)-5-chloro-1H-indol-2-carboxamides and 5-chloro-2-(piperazin-1-ylmethyl)-1H-benzimidazole on histamine and 4-methylhistamine-induced mast cell response.

    Science.gov (United States)

    Nagarajan, Gomathi; Mariappanadar, Vairamani; Tamizh, Muthu; Kaliappan, Ilango; Elden, Berla Thangam

    2017-06-01

    The histamine plays a decisive role in acute and chronic inflammatory responses and is regulated through its four types of distinct receptors designated from H1 to H4. Recently histamine 4 receptor (H4R) antagonists have been reported to possess various pharmacological effects against various allergic diseases. To investigate the inhibitory effect of N-(2-aminoethyl)-5-chloro-1H-indol-2-carboxamide (Compound A) and 5-chloro-2-(piperazin-1-ylmethyl)-1H-benzimidazole (Compound L) on H4R-mediated calcium mobilization, cytokine IL-13 production, ERK1/2, Akt and NF-κB activation in human mastocytoma cells-1 (HMC-1). Compounds A and L were synthesized chemically and their inhibitory effect on intracellular calcium release was analyzed by Fluo-4 calcium assay, cytokine measurement through ELISA and activation of signaling molecules by western blot. Pre-treatment with compounds A and L significantly reduced the H4R-mediated intracellular calcium release. Histamine and 4-methylhistamine (4-MH) induced Th2 cytokine IL-13 production in HMC-1 cells, was inhibited by compound A (77.61%, 74.25% at 1 μM concentration) and compound L (79.63%, 81.70% at 1 μM concentration). Furthermore, histamine induced the phosphorylation of ERK1/2, Akt and NF-κB was suppressed by compounds A and L at varying levels, ERK1/2 (88%, 86%), Akt (88%, 89%) and NF-κB (89%, 87%) in HMC-1 cells. Taken together these data demonstrate that compound A and compound L may block H4R-mediated downstream signaling events.

  7. Model for resonant plasma probe.

    Energy Technology Data Exchange (ETDEWEB)

    Warne, Larry Kevin; Johnson, William Arthur; Hebner, Gregory Albert; Jorgenson, Roy E.; Coats, Rebecca Sue

    2007-04-01

    This report constructs simple circuit models for a hairpin shaped resonant plasma probe. Effects of the plasma sheath region surrounding the wires making up the probe are determined. Electromagnetic simulations of the probe are compared to the circuit model results. The perturbing effects of the disc cavity in which the probe operates are also found.

  8. Single-Molecule Electronics: Chemical and Analytical Perspectives.

    Science.gov (United States)

    Nichols, Richard J; Higgins, Simon J

    2015-01-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

  9. SCANNING PROBE MICROSCOPY STUDY OF MOLECULAR NANOSTRUCTURES ON 2D MATERIALS

    OpenAIRE

    Chen, Chuanhui

    2017-01-01

    Molecules adsorbed on two-dimensional (2D) materials can show interesting physical and chemical properties. This thesis presents scanning probe microscopy (SPM) investigation of emerging 2D materials, molecular nanostructures on 2D substrates at the nanometer scale, and biophysical processes on the biological membrane. Two main techniques of nano-probing are used: scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The study particularly emphasizes on self-assembled molecul...

  10. Single-Molecule Fluorescence Microscopy Reveals Local Diffusion Coefficients in the Pore Network of an Individual Catalyst Particle

    NARCIS (Netherlands)

    Hendriks, Frank|info:eu-repo/dai/nl/412642697; Meirer, Florian; Kubarev, Alexey V.; Ristanovic, Zoran|info:eu-repo/dai/nl/328233005; Roeffaers, Maarten B J; Vogt, Eelco T. C.|info:eu-repo/dai/nl/073717398; Bruijnincx, Pieter C. A.|info:eu-repo/dai/nl/33799529X; Weckhuysen, Bert M.|info:eu-repo/dai/nl/285484397

    2017-01-01

    We used single-molecule fluorescence microscopy to study self-diffusion of a feedstock-like probe molecule with nanometer accuracy in the macropores of a micrometer-sized, real-life fluid catalytic cracking (FCC) particle. Movies of single fluorescent molecules allowed their movement through the

  11. Antibody Fragments as Probe in Biosensor Development

    Directory of Open Access Journals (Sweden)

    Serge Muyldermans

    2008-08-01

    Full Text Available Today’s proteomic analyses are generating increasing numbers of biomarkers, making it essential to possess highly specific probes able to recognize those targets. Antibodies are considered to be the first choice as molecular recognition units due to their target specificity and affinity, which make them excellent probes in biosensor development. However several problems such as difficult directional immobilization, unstable behavior, loss of specificity and steric hindrance, may arise from using these large molecules. Luckily, protein engineering techniques offer designed antibody formats suitable for biomarker analysis. Minimization strategies of antibodies into Fab fragments, scFv or even single-domain antibody fragments like VH, VL or VHHs are reviewed. Not only the size of the probe but also other issues like choice of immobilization tag, type of solid support and probe stability are of critical importance in assay development for biosensing. In this respect, multiple approaches to specifically orient and couple antibody fragments in a generic one-step procedure directly on a biosensor substrate are discussed.

  12. Continuously tunable nucleic acid hybridization probes.

    Science.gov (United States)

    Wu, Lucia R; Wang, Juexiao Sherry; Fang, John Z; Evans, Emily R; Pinto, Alessandro; Pekker, Irena; Boykin, Richard; Ngouenet, Celine; Webster, Philippa J; Beechem, Joseph; Zhang, David Yu

    2015-12-01

    In silico-designed nucleic acid probes and primers often do not achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. We present a novel, on-the-fly method of tuning probe affinity and selectivity by adjusting the stoichiometry of auxiliary species, which allows for independent and decoupled adjustment of the hybridization yield for different probes in multiplexed assays. Using this method, we achieved near-continuous tuning of probe effective free energy. To demonstrate our approach, we enforced uniform capture efficiency of 31 DNA molecules (GC content, 0-100%), maximized the signal difference for 11 pairs of single-nucleotide variants and performed tunable hybrid capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples.

  13. Convective heat flow probe

    Science.gov (United States)

    Dunn, James C.; Hardee, Harry C.; Striker, Richard P.

    1985-01-01

    A convective heat flow probe device is provided which measures heat flow and fluid flow magnitude in the formation surrounding a borehole. The probe comprises an elongate housing adapted to be lowered down into the borehole; a plurality of heaters extending along the probe for heating the formation surrounding the borehole; a plurality of temperature sensors arranged around the periphery of the probe for measuring the temperature of the surrounding formation after heating thereof by the heater elements. The temperature sensors and heater elements are mounted in a plurality of separate heater pads which are supported by the housing and which are adapted to be radially expanded into firm engagement with the walls of the borehole. The heat supplied by the heater elements and the temperatures measured by the temperature sensors are monitored and used in providing the desired measurements. The outer peripheral surfaces of the heater pads are configured as segments of a cylinder and form a full cylinder when taken together. A plurality of temperature sensors are located on each pad so as to extend along the length and across the width thereof, with a heating element being located in each pad beneath the temperature sensors. An expansion mechanism driven by a clamping motor provides expansion and retraction of the heater pads and expandable packer-type seals are provided along the probe above and below the heater pads.

  14. Small molecule screening identifies targetable zebrafish pigmentation pathways

    DEFF Research Database (Denmark)

    Colanesi, Sarah; Taylor, Kerrie L; Temperley, Nicholas D

    2012-01-01

    Small molecules complement genetic mutants and can be used to probe pigment cell biology by inhibiting specific proteins or pathways. Here, we present the results of a screen of active compounds for those that affect the processes of melanocyte and iridophore development in zebrafish and investig......Small molecules complement genetic mutants and can be used to probe pigment cell biology by inhibiting specific proteins or pathways. Here, we present the results of a screen of active compounds for those that affect the processes of melanocyte and iridophore development in zebrafish...... and investigate the effects of a few of these compounds in further detail. We identified and confirmed 57 compounds that altered pigment cell patterning, number, survival, or differentiation. Additional tissue targets and toxicity of small molecules are also discussed. Given that the majority of cell types...

  15. Single-Molecule Interfacial Electron Transfer

    Energy Technology Data Exchange (ETDEWEB)

    Ho, Wilson [Univ. of California, Irvine, CA (United States)

    2018-02-03

    Interfacial electron transfer (ET) plays an important role in many chemical and biological processes. Specifically, interfacial ET in TiO2-based systems is important to solar energy technology, catalysis, and environmental remediation technology. However, the microscopic mechanism of interfacial ET is not well understood with regard to atomic surface structure, molecular structure, bonding, orientation, and motion. In this project, we used two complementary methodologies; single-molecule fluorescence spectroscopy, and scanning-tunneling microscopy and spectroscopy (STM and STS) to address this scientific need. The goal of this project was to integrate these techniques and measure the molecular dependence of ET between adsorbed molecules and TiO2 semiconductor surfaces and the ET induced reactions such as the splitting of water. The scanning probe techniques, STM and STS, are capable of providing the highest spatial resolution but not easily time-resolved data. Single-molecule fluorescence spectroscopy is capable of good time resolution but requires further development to match the spatial resolution of the STM. The integrated approach involving Peter Lu at Bowling Green State University (BGSU) and Wilson Ho at the University of California, Irvine (UC Irvine) produced methods for time and spatially resolved chemical imaging of interfacial electron transfer dynamics and photocatalytic reactions. An integral aspect of the joint research was a significant exchange of graduate students to work at the two institutions. This project bridged complementary approaches to investigate a set of common problems by working with the same molecules on a variety of solid surfaces, but using appropriate techniques to probe under ambient (BGSU) and ultrahigh vacuum (UCI) conditions. The molecular level understanding of the fundamental interfacial electron transfer processes obtained in this joint project will be important for developing efficient light harvesting

  16. Imaging and force probing RNA by atomic force microscopy

    NARCIS (Netherlands)

    Schön, Peter Manfred

    2016-01-01

    In the past 30 years, the atomic force microscope (AFM) has become a true enabling platform in the life sciences opening entire novel avenues for structural and dynamic studies of biological systems. It enables visualization, probing and manipulation across the length scales, from single molecules

  17. Multispectral imaging probe

    Science.gov (United States)

    Sandison, David R.; Platzbecker, Mark R.; Descour, Michael R.; Armour, David L.; Craig, Marcus J.; Richards-Kortum, Rebecca

    1999-01-01

    A multispectral imaging probe delivers a range of wavelengths of excitation light to a target and collects a range of expressed light wavelengths. The multispectral imaging probe is adapted for mobile use and use in confined spaces, and is sealed against the effects of hostile environments. The multispectral imaging probe comprises a housing that defines a sealed volume that is substantially sealed from the surrounding environment. A beam splitting device mounts within the sealed volume. Excitation light is directed to the beam splitting device, which directs the excitation light to a target. Expressed light from the target reaches the beam splitting device along a path coaxial with the path traveled by the excitation light from the beam splitting device to the target. The beam splitting device directs expressed light to a collection subsystem for delivery to a detector.

  18. A Chemical Probe that Labels Human Pluripotent Stem Cells

    Directory of Open Access Journals (Sweden)

    Nao Hirata

    2014-03-01

    Full Text Available A small-molecule fluorescent probe specific for human pluripotent stem cells would serve as a useful tool for basic cell biology research and stem cell therapy. Screening of fluorescent chemical libraries with human induced pluripotent stem cells (iPSCs and subsequent evaluation of hit molecules identified a fluorescent compound (Kyoto probe 1 [KP-1] that selectively labels human pluripotent stem cells. Our analyses indicated that the selectivity results primarily from a distinct expression pattern of ABC transporters in human pluripotent stem cells and from the transporter selectivity of KP-1. Expression of ABCB1 (MDR1 and ABCG2 (BCRP, both of which cause the efflux of KP-1, is repressed in human pluripotent stem cells. Although KP-1, like other pluripotent markers, is not absolutely specific for pluripotent stem cells, the identified chemical probe may be used in conjunction with other reagents.

  19. Using a redox-sensitive phosphorescent probe for optical evaluation of an intracellular redox environment.

    Science.gov (United States)

    Liu, Shujuan; Zhou, Na; Chen, Zejing; Wei, Huanjie; Zhu, Yana; Guo, Song; Zhao, Qiang

    2017-01-01

    A reducing intracellular environment is necessary for living cells. Here a redox-sensitive phosphorescent probe Ir-NO has been developed for evaluating the redox environment in living cells. Upon addition of reducing molecules, such as glutathione and ascorbic acid, the phosphorescent intensity of the probe is turned on, and the emission lifetime is elongated evidently. Furthermore, this probe has been used for optical imaging of the intracellular reducing environment by utilizing confocal laser scanning microscopy and phosphorescence lifetime imaging microscopy.

  20. MOLECULES IN {eta} CARINAE

    Energy Technology Data Exchange (ETDEWEB)

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf [Max-Planck Institut fuer Radioastronomie, Auf dem Huegel 69, 53121 Bonn (Germany); Zapata, Luis A.; Rodriguez, Luis F. [Centro de Radioastronomia y Astrofisica, Universidad Nacional Autonoma de Mexico, Apartado Postal 3-72, 58090 Morelia, Michoacan (Mexico)

    2012-04-10

    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  1. Photochemistry of interstellar molecules

    Science.gov (United States)

    Stief, L. J.

    1971-01-01

    The photochemistry of two diatomic and eight polyatomic molecules is discussed quantitatively. For an interstellar molecule, the lifetime against photodecomposition depends upon the absorption cross section, the quantum yield or probability of dissociation following photon absorption, and the interstellar radiation field. The constant energy density of Habing is used for the unobserved regions of interstellar radiation field, and the field in obscuring clouds is estimated by combining the constant flux with the observed interstellar extinction curve covering the visible and ultraviolet regions. Lifetimes against photodecomposition in the unobscured regions and as a function of increasing optical thickness in obscuring clouds are calculated for the ten species. The results show that, except for CO, all the molecules have comparable lifetimes of less than one hundred years. Thus they can exist only in dense clouds and can never have been exposed to the unobscured radiation. The calculations further show that the lifetimes in clouds of moderate opacity are of the order of one million years.

  2. MOLECULES IN η CARINAE

    International Nuclear Information System (INIS)

    Loinard, Laurent; Menten, Karl M.; Güsten, Rolf; Zapata, Luis A.; Rodríguez, Luis F.

    2012-01-01

    We report the detection toward η Carinae of six new molecules, CO, CN, HCO + , HCN, HNC, and N 2 H + , and of two of their less abundant isotopic counterparts, 13 CO and H 13 CN. The line profiles are moderately broad (∼100 km s –1 ), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO + do not appear to be underabundant in η Carinae. On the other hand, molecules containing nitrogen or the 13 C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of η Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  3. Dissociation dynamics of diatomic molecules in intense fields

    Science.gov (United States)

    Magrakvelidze, Maia

    We study the dynamics of diatomic molecules (dimers) in intense IR and XUV laser fields theoretically and compare the results with measured data in collaboration with different experimental groups worldwide. The first three chapters of the thesis cover the introduction and the background on solving time-independent and time-dependent Schrodinger equation. The numerical results in this thesis are presented in four chapters, three of which are focused on diatomic molecules in IR fields. The last one concentrates on diatomic molecules in XUV pulses. The study of nuclear dynamics of H2 or D2 molecules in IR pulses is given in Chapter 4. First, we investigate the optimal laser parameters for observing field-induced bond softening and bond hardening in D2+. Next, the nuclear dynamics of H2 + molecular ions in intense laser fields are investigated by analyzing their fragment kinetic-energy release (KER) spectra as a function of the pump-probe delay τ Lastly, the electron localization is studied for long circularly polarized laser pulses. Chapter 5 covers the dissociation dynamics of O2+ in an IR laser field. The fragment KER spectra are analyzed as a function of the pump-probe delay τ Within the Born-Oppenheimer approximation, we calculate ab-initio adiabatic potential-energy curves and their electric dipole couplings, using the quantum chemistry code GAMESS. In Chapter 6, the dissociation dynamics of the noble gas dimer ions He 2+, Ne2+, Ar2 +, Kr2+, and Xe2 + is investigated in ultrashort pump and probe laser pulses of different wavelengths. We observe a striking "delay gap" in the pump-probe-delay-dependent KER spectrum only if the probe-pulse wavelength exceeds the pump-pulse wavelength. Comparing pump-probe-pulse-delay dependent KER spectra for different noble gas dimer cations, we quantitatively discuss quantum-mechanical versus classical aspects of the nuclear vibrational motion as a function of the nuclear mass. Chapter 7 focuses on diatomic molecules in XUV

  4. Hadron Molecules Revisted

    Energy Technology Data Exchange (ETDEWEB)

    Longacre, R. S. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2013-12-10

    Hadron Molecules are particles made out of hadrons that are held together by self interactions. In this report we discuss seven such molecules and their self interactions. The f0(980), a0(980), f1(1400), ΔN(2150) and π1(1400) molecular structure is given. We predict that two more states the $K\\bar{K}K$(1500) and a1(1400) should be found.

  5. Electron Accumulative Molecules.

    Science.gov (United States)

    Buades, Ana B; Sanchez Arderiu, Víctor; Olid-Britos, David; Viñas, Clara; Sillanpää, Reijo; Haukka, Matti; Fontrodona, Xavier; Paradinas, Markos; Ocal, Carmen; Teixidor, Francesc

    2018-02-28

    With the goal to produce molecules with high electron accepting capacity and low reorganization energy upon gaining one or more electrons, a synthesis procedure leading to the formation of a B-N(aromatic) bond in a cluster has been developed. The research was focused on the development of a molecular structure able to accept and release a specific number of electrons without decomposing or change in its structural arrangement. The synthetic procedure consists of a parallel decomposition reaction to generate a reactive electrophile and a synthesis reaction to generate the B-N(aromatic) bond. This procedure has paved the way to produce the metallacarboranylviologen [M(C 2 B 9 H 11 )(C 2 B 9 H 10 )-NC 5 H 4 -C 5 H 4 N-M'(C 2 B 9 H 11 )(C 2 B 9 H 10 )] (M = M' = Co, Fe and M = Co and M' = Fe) and semi(metallacarboranyl)viologen [3,3'-M(8-(NC 5 H 4 -C 5 H 4 N-1,2-C 2 B 9 H 10 )(1',2'-C 2 B 9 H 11 )] (M = Co, Fe) electron cumulative molecules. These molecules are able to accept up to five electrons and to donate one in single electron steps at accessible potentials and in a reversible way. By targeted synthesis and corresponding electrochemical tests each electron transfer (ET) step has been assigned to specific fragments of the molecules. The molecules have been carefully characterized, and the electronic communication between both metal centers (when this situation applies) has been definitely observed through the coplanarity of both pyridine fragments. The structural characteristics of these molecules imply a low reorganization energy that is a necessary requirement for low energy ET processes. This makes them electronically comparable to fullerenes, but on their side, they have a wide range of possible solvents. The ET from one molecule to another has been clearly demonstrated as well as their self-organizing capacity. We consider that these molecules, thanks to their easy synthesis, ET, self-organizing capacity, wide range of solubility, and easy processability, can

  6. Spectral characteristics of 2-(2?-hydroxy-3?-pyridyl)benzimidazole: effects of solvents and acid or base concentrations

    Science.gov (United States)

    Dogra, S. K.

    2005-01-01

    Absorption, fluorescence and fluorescence excitation spectroscopy and time dependent fluorimetry have been used to study the spectral characteristics of 2-(2'-hydroxy-3'-pyridyl)benzimidazole (2-H3PyBI) in different solvents and at different acid-base concentrations. Observation of only one small Stokes shifted fluorescence band reveals the absence of excited state intramolecular proton transfer (ESIPT). 2-H3PyBI is mainly present as the keto form even in cyclohexane. First site of protonation is imidazole nitrogen atom in both ground (S 0) and first excited singlet state (S 1). Dication in S 0 state is formed by protonating exo carbonyl group and pyridine nitrogen in S 1 state. Deprotonation occurs from >N-H moiety of pyridone, followed by structural reorganization to yield enolate ion. AM1 semi-empirical quantum mechanical and density functional theory (DFT) calculations have been used to assign the structure of neutral species and the site of protonation and deprotonation of 2-H3PyBI. Dissociation constants of various prototropic equilibria were determined and discussed. Theoretical calculations have been carried out to find the cause for the absence of ESIPT.

  7. Synthesis and biological evaluation of imidazo[2,1-b]thiazole-benzimidazole conjugates as microtubule-targeting agents.

    Science.gov (United States)

    Baig, Mirza Feroz; Nayak, V Lakshma; Budaganaboyina, Prasad; Mullagiri, Kishore; Sunkari, Satish; Gour, Jitendra; Kamal, Ahmed

    2018-02-12

    A series of imidazo[2,1-b]thiazole-benzimidazole conjugates were synthesized and evaluated for their antiproliferative activity against four human cancer cell lines i.e.; HeLa (cervical), A549 (lung), MCF-7 (breast) and DU-145 (prostate) along with normal HEK-293 cell line. Amongst them, conjugate 6d displayed significant cytotoxicity against human lung cancer cell line, A549 with IC 50 value 1.08 µM. Further, cell cycle analysis revealed that this compound arrested the cell cycle at G2/M phase in A549 cells. Furthermore, the tubulin polymerization assay results suggest that this conjugate (6d) exhibits significant inhibitory effect on the tubulin assembly with an IC50 value of 1.68 µM. Moreover, the apoptotic inducing properties of compound 6d was confirmed by Hoechst staining, measurement of mitochondrial membrane potential (ΔΨm) and annexin V-FITC assay. Further, molecular docking studies revealed that compound 6d occupied the colchicine binding site. Copyright © 2018. Published by Elsevier Inc.

  8. Effect of Mercapto and Methyl Groups on the Efficiency of Imidazole and Benzimidazole-based Inhibitors of Iron Corrosion.

    Science.gov (United States)

    Milošev, Ingrid; Kovačević, Nataša; Kokalj, Anton

    2016-01-01

    We report on the combined experimental and computational study of imidazole- and benzimidazole-based corrosion inhibitors containing methyl and/or mercapto groups. Electrochemical measurements and long-term immersion tests were performed on iron in NaCl solution, whilst computational study explicitly addresses the molecular level details of the bonding on iron surface by means of density functional theory calculations (DFT). Experimental data were the basis for the determination of inhibition efficiency and mechanism. Methyl group combined with mercapto group has a beneficial effect on corrosion inhibition at all inhibitor concentrations. The beneficial effect of mercapto group combined with benzene group is not so pronounced as when combined with methyl group. The latter is in stark contrast with the behaviour found previously on copper, where the effect of methyl group was detrimental and that of mercapto and benzene beneficial. Explicit DFT calculations reveal that methyl-group has a small effect on the inhibitor-surface interaction. In contrast, the presence of mercapto group involves the strong S-surface bonding and consequently the adsorption of inhibitors with mercapto group is found to be more exothermic.

  9. Newly synthesized bis-benzimidazole compound 8 induces apoptosis, autophagy and reactive oxygen species generation in HeLa cells.

    Science.gov (United States)

    Chu, Naying; Yao, Guodong; Liu, Yuan; Cheng, Maosheng; Ikejima, Takashi

    2016-09-01

    Compound 8 (C8) is a newly synthesized bis-benzimidazole derivative and exerts significant anti-tumor activity in vitro. Previous studies demonstrated that C8 induced apoptosis and autophagy in human promyelocytic leukemia HL60 cells. However, cytotoxicity study on human peripheral blood mononuclear cells (hPBMC) showed that C8 exhibited less toxicity in normal cells. In this study, the molecular mechanism of C8 on human cervical carcinoma HeLa cells was investigated. The results showed that C8 inhibited the growth of HeLa cells and triggered both apoptotic and autophagic cell death. Subsequent experiment also indicated that reactive oxygen species (ROS) generation was induced in C8-treated HeLa cells. Since ROS scavenger decreased the ratio of apoptotic and autophagic cells, ROS generation contributed to C8-induced apoptosis and autophagy. Furthermore, inhibitors of apoptosis and autophagy also reduced ROS generation, respectively. Autophagy inhibition increased cell growth compared to C8-treated group and attenuated apoptotic cell death, indicating that C8-induced autophagy promoted apoptosis for cell death. However, the percentage of autophagic cells was enhanced when limiting apoptosis process. Taken together, C8 induced ROS-mediated apoptosis and autophagy in HeLa cells, autophagy promoted apoptosis but the former was antagonized by the latter. The data also gave us a new perspective on the anti-tumor effect of C8. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Ruthenium and iron complexes with benzotriazole and benzimidazole derivatives as simple models for proton-coupled electron transfer systems

    Directory of Open Access Journals (Sweden)

    Rocha Reginaldo C.

    2001-01-01

    Full Text Available Iron and ruthenium complexes of the type [M-LH]n (where M = RuII,III(NH35(2+,3+, RuII,III(edta2-,- [edta = ethylenedinitrilotetraacetate], or FeII,III(CN5(3-,2- and LH = benzotriazole or benzimidazole were prepared and characterized in aqueous solutions by means of electrochemical and spectroelectrochemical methods. Special emphasis was given to the pH-dependent redox processes, exhibited by all the investigated complexes. From their related Pourbaix diagrams, which displayed a typically Nernstian behavior, the pKa and formal reduction potential values were extracted. In addition, these E1/2 versus pH curves were also used to illustrate the partitioning relationship concerning the redox and acid-base species, and their interconversion equilibria. The active area in which the dependence of the M III/M II couple on the pH takes place, as delimited by pKaIII and pKaII, was taken into account in order to evaluate the usefulness of such simple complexes as models for proton-coupled electron transfer (PCET. The results were interpreted in terms of the acceptor/donor electronic character of the ligands and sigma,pi-metal-ligand interactions in both redox states of the metal ion.

  11. Novel Benzothiazole, Benzimidazole and Benzoxazole Derivatives as Potential Antitumor Agents: Synthesis and Preliminary in Vitro Biological Evaluation

    Directory of Open Access Journals (Sweden)

    Li Yang

    2012-01-01

    Full Text Available In a previous hit-to-lead research program targeting anticancer agents, two promising lead compounds, 1a and 1b, were found. However, the poor solubility of 1a and 1b made difficult further in vivo studies. To solve this problem, a lead optimization was conducted through introducing N-methyl-piperazine groups at the 2-position and 6-position. To our delight, the optimized analogue 1d showed comparable antiproliferative activity in vitro with better solubility, compared with 1a. Based on this result, the replacement of the benzothiazole scaffold with benzimidazole and benzoxazole moieties afforded 1f and 1g, whose activities were fundamentally retained. In the preliminary in vitro biological evaluation, the immunofluorescence staining of HCT116 cells indicated that 1d, 1f and 1g led to cytosolic vacuolization which was not induced by 1a at low micromolecular concentrations. These results suggest that these optimized compounds might potentially constitute a novel class of anticancer agents, which merit further studies.

  12. Single Molecule Screening of Disease DNA Without Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ji-Young [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    The potential of single molecule detection as an analysis tool in biological and medical fields is well recognized today. This fast evolving technique will provide fundamental sensitivity to pick up individual pathogen molecules, and therefore contribute to a more accurate diagnosis and a better chance for a complete cure. Many studies are being carried out to successfully apply this technique in real screening fields. In this dissertation, several attempts are shown that have been made to test and refine the application of the single molecule technique as a clinical screening method. A basic applicability was tested with a 100% target content sample, using electrophoretic mobility and multiple colors as identification tools. Both electrophoretic and spectral information of individual molecule were collected within a second, while the molecule travels along the flow in a capillary. Insertion of a transmission grating made the recording of the whole spectrum of a dye-stained molecule possible without adding complicated instrumental components. Collecting two kinds of information simultaneously and combining them allowed more thorough identification, up to 98.8% accuracy. Probing mRNA molecules with fluorescently labeled cDNA via hybridization was also carried out. The spectral differences among target, probe, and hybrid were interpreted in terms of dispersion distances after transmission grating, and used for the identification of each molecule. The probes were designed to have the least background when they are free, but have strong fluorescence after hybridization via fluorescence resonance energy transfer. The mRNA-cDNA hybrids were further imaged in whole blood, plasma, and saliva, to test how far a crude preparation can be tolerated. Imaging was possible with up to 50% of clear bio-matrix contents, suggesting a simple lysis and dilution would be sufficient for imaging for some cells. Real pathogen DNA of human papillomavirus (HPV) type-I6 in human genomic DNA

  13. Hybridization-based biosensor containing hairpin probes and use thereof

    Science.gov (United States)

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2010-10-12

    A sensor chip that includes: a fluorescence quenching surface; a nucleic acid probe that contains first and second ends with the first end bound to the fluorescence quenching surface, and is characterized by being able to self-anneal into a hairpin conformation; and a first fluorophore bound to the second end of the first nucleic acid molecule. When the first nucleic acid molecule is in the hairpin conformation, the fluorescence quenching surface substantially quenches fluorescent emissions by the first fluorophore; and when the first nucleic acid molecule is in a non-hairpin conformation, fluorescent emissions by the fluorophore are substantially free of quenching by the fluorescence quenching surface. Various nucleic acid probes, methods of making the sensor chip, biological sensor devices that contain the sensor chip, and their methods of use are also disclosed.

  14. Molecule of the Month

    Indian Academy of Sciences (India)

    The electronic absorption spectrum of a molecule often depends on the solvent used. The change in position (and, sometimes, intensity) of the UV/Vis band accompanying a change in the polarity of the medium is called solvatochromism. The phenomenon has its origins in intermolecular solute–solvent interactions, such as ...

  15. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 2. Molecule of the Month Isomers of Benzene - Still Pursuing Dreams. J Chandrasekhar. Feature Article Volume 1 Issue 2 February 1996 pp 80-83. Fulltext. Click here to view fulltext PDF. Permanent link:

  16. Molecule of the Month

    Indian Academy of Sciences (India)

    Molecule of the Month. A Dicopper (II) Complex Hydrolyzes the Phosphate Diester Bond! R N Mukherjee is with the Department of. Chemistry at Indian. Institute of Technology,. Kanpur. 1 DNA: Deoxyribonucleic Acid;. RNA: Ribonucleic Acid; HPNP: 2-Hydroxypropyl-p-nitrophenyl phosphate; Phosphodiester: Di- ester of ...

  17. Molecule-based magnets

    Indian Academy of Sciences (India)

    The design of molecule-based magnets has also been extended to the design of poly-functional molecular magnets, such as those exhibiting second-order optical nonlinearity, liquid crystallinity, or chirality simultaneously with long-range magnetic order. Solubility, low density and biocompatibility are attractive features of ...

  18. Molecule of the Month

    Indian Academy of Sciences (India)

    Michael Faraday opened up a new chapter in chemistry when he isolated benzene from the distillate of coal tar. The deceptively simple molecule with the formula C6H6 has triggered many experiments and theoretical proposals. The correct ring struc- ture, shown in 1 (see Figure 1), was assigned by Kekule after his.

  19. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule of the Month - Adamantane - A Plastic Piece of Diamond. J Chandrasekhar. Volume 16 Issue 12 December 2011 pp 1232-1237. Fulltext. Click here to view fulltext PDF. Permanent link:

  20. Molecules to Materials

    Indian Academy of Sciences (India)

    coordination polymers and molecular systems in which metal ions serve as the source of the ... cobalt, nickel and gadolinium which are themselves ferromagnetic in their bulk state (Box 1). ... their complexes, organic free and ion radicals and molecules such as 02 and NO are good examples of paramagnetic systems.

  1. Excitons: Molecules in flatland

    Science.gov (United States)

    Yao, Wang

    2015-06-01

    Forming molecules from atoms is commonplace in dense atomic gases. But it now seems that some two-dimensional materials provide a suitable environment for creating complex molecular states from the hydrogen-like electron-hole pairs that form in semiconductors.

  2. Quantum Interference of Molecules

    Indian Academy of Sciences (India)

    IAS Admin

    C60, the third allotropic form of carbon was discovered in 1985 by Kroto and colleagues. These carbon mole- cules have a structure of a truncated icosahedron (see. Figure 5). The truncated icosahedron has 12 pentagon and 20 hexagon rings and has 60 vertices { the shape of a soccer ball. These molecules have been ...

  3. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 5. Molecule of the Month Molecular–Chameleon: Solvatochromism at its Iridescent Best! Photon Rao. Feature Article Volume 2 Issue 5 May 1997 pp 69-72. Fulltext. Click here to view fulltext PDF. Permanent link:

  4. Molecules to Materials

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 3; Issue 5. Molecules to Materials Liquid Crystals and Molecular Conductors. T P Radhakrishnan. Series Article Volume 3 Issue 5 May 1998 pp 6-23. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. Atoms, Molecules, and Compounds

    CERN Document Server

    Manning, Phillip

    2007-01-01

    Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.

  6. Atoms, Molecules and Radiation

    Indian Academy of Sciences (India)

    IAS Admin

    A Refresher Course in Applications of Quantum Mechanics to 'Atoms, Molecules and Radiation' will be held at the Indian Academy of Sciences, Bangalore from December 8 to 20. 2014. The Course is primarily aimed at teachers teaching quantum mechanics and/ or atomic and molecular physics at the UG / PG level.

  7. Diversity in Biological Molecules

    Science.gov (United States)

    Newbury, H. John

    2010-01-01

    One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…

  8. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 9. Molecule of the Month Adamantane - A Plastic Piece of Diamond. J Chandrasekhar. Feature Article Volume 1 Issue 9 September 1996 pp 66-71. Fulltext. Click here to view fulltext PDF. Permanent link:

  9. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule of the Month - A Stable Dibismuthene - A Compound with a Bi-Bi Double Bond. V Chandrasekhar. Volume 16 ... Author Affiliations. V Chandrasekhar1. Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India.

  10. Probing the Solar Interior

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 3; Issue 3. Probing the Solar Interior Hearing the Heartbeats of the Sun. Ashok Ambastha. General ... Author Affiliations. Ashok Ambastha1. Joint In-Charge Udaipur Solar Observatory Physical Research laboratory P.O. Box No. 198 Udaipur 313 001, India ...

  11. Probing the Solar Interior

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 3; Issue 3. Probing the Solar Interior Hearing the Heartbeats of the Sun. Ashok Ambastha. General Article Volume 3 Issue 3 March 1998 pp 18-31. Fulltext. Click here to view fulltext PDF. Permanent link:

  12. Terahertz scanning probe microscope

    NARCIS (Netherlands)

    Klapwijk, T.M.

    2014-01-01

    The invention provides aterahertz scanning probe microscope setup comprising (i) a terahertz radiation source configured to generate terahertz radiation; (ii) a terahertz lens configured to receive at least part of the terahertz radiation from the terahertz radiation source; (iii) a cantilever unit

  13. One-Probe Search

    DEFF Research Database (Denmark)

    Östlin, Anna; Pagh, Rasmus

    2002-01-01

    We consider dictionaries that perform lookups by probing a single word of memory, knowing only the size of the data structure. We describe a randomized dictionary where a lookup returns the correct answer with probability 1 - e, and otherwise returns don't know. The lookup procedure uses an expan...

  14. Probing the Solar System

    Science.gov (United States)

    Wilkinson, John

    2013-01-01

    Humans have always had the vision to one day live on other planets. This vision existed even before the first person was put into orbit. Since the early space missions of putting humans into orbit around Earth, many advances have been made in space technology. We have now sent many space probes deep into the Solar system to explore the planets and…

  15. Thermal conductivity probe

    Science.gov (United States)

    Navickas, J.

    1969-01-01

    Low-mass probe accurately measures the thermal conductivity of polyurethane foam /and other thermal insulating materials/ while exposed to either hydrogen of helium permeation in temperature ranges from ambient to cryogenic. The thermal conductivity of a specimen is determined from an experimentally determined increase in temperature.

  16. 1,3-Bis(pyridin-2-yl-1H-benzimidazol-3-ium tetrafluoridoborate

    Directory of Open Access Journals (Sweden)

    Gabriele Grieco

    2011-08-01

    Full Text Available The asymmetric unit of the title compound, C17H13N4+·BF4−, contains one half of the benzimidazolium cation and one half of the tetrafluoridoborate anion, with crystallographic mirror planes bisecting the molecules. One F atom of the tetrafluoridoborate is equally disordered about a crystallographic mirror plane. In the crystal, C—H...F interactions link the cations and anions into layers parallel to (100. The crystal packing is further stabilized by F...π contacts involving the tetrafluoridoborate anions and the five-membered rings [F...centroid = 2.811 (2 Å].

  17. Bis[μ-3-(1H-benzimidazol-2-ylbenzoato]dicopper(I

    Directory of Open Access Journals (Sweden)

    Zheng-Yu Su

    2010-12-01

    Full Text Available The dimeric title complex, [Cu2(C14H9N2O22], resides on a center of symmetry. In the crystal, the molecules are packed via π–π stacking interactions alternating between imidazole and benzene rings [mean interplanar distances = 3.754 (3 and 3.624 (3 Å]. An intermolecular N—H...O hydrogen bond links the dimers together. The two-coordinate CuI atom displays an O—Cu—N bond angle of 176.3 (2°. The Cu...Cu distance within the dimer is 5.100 (2 Å.

  18. Voltage-Driven Conformational Switching with Distinct Raman Signature in a Single-Molecule Junction.

    Science.gov (United States)

    Bi, Hai; Palma, Carlos-Andres; Gong, Yuxiang; Hasch, Peter; Elbing, Mark; Mayor, Marcel; Reichert, Joachim; Barth, Johannes V

    2018-04-11

    Precisely controlling well-defined, stable single-molecule junctions represents a pillar of single-molecule electronics. Early attempts to establish computing with molecular switching arrays were partly challenged by limitations in the direct chemical characterization of metal-molecule-metal junctions. While cryogenic scanning probe studies have advanced the mechanistic understanding of current- and voltage-induced conformational switching, metal-molecule-metal conformations are still largely inferred from indirect evidence. Hence, the development of robust, chemically sensitive techniques is instrumental for advancement in the field. Here we probe the conformation of a two-state molecular switch with vibrational spectroscopy, while simultaneously operating it by means of the applied voltage. Our study emphasizes measurements of single-molecule Raman spectra in a room-temperature stable single-molecule switch presenting a signal modulation of nearly 2 orders of magnitude.

  19. A new three-dimensional bis(benzimidazole)-based cadmium(II) coordination polymer

    Science.gov (United States)

    Hao, Shao Yun; Hou, Suo Xia; Hao, Zeng Chuan; Cui, Guang Hua

    2018-01-01

    A new coordination polymer (CP), formulated as [Cd(L)(DCTP)]n (1) (L = 1,1‧-(1,4-butanediyl)bis(2-methylbenzimidazole), H2DCTP = 2,5-dichloroterephthalic acid), was synthesized under hydrothermal conditions and the performance as luminescent probe was also investigated. Single-crystal X-ray diffraction reveals CP 1 is a 3D 3-fold interpenetrated dia network with large well-defined pores. It is found that CP 1 revealed highly sensitive luminescence sensing for Fe3 + ions in acetonitrile solution with a high quenching efficiency of KSV = 2541.238 L·mol- 1 and a low detection limit of 3.2 μM (S/N = 3). Moreover, the photocatalytic efficiency of 1 for degradation of methylene blue could reach 82.8% after 135 min. Therefore, this coordination polymer could be viewed as multifunctional material for selectively sensing Fe3 + ions and effectively degrading dyes.

  20. OMG: Open Molecule Generator.

    Science.gov (United States)

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-09-17

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

  1. An environmental transfer hub for multimodal atom probe tomography.

    Science.gov (United States)

    Perea, Daniel E; Gerstl, Stephan S A; Chin, Jackson; Hirschi, Blake; Evans, James E

    2017-01-01

    Environmental control during transfer between instruments is required for samples sensitive to air or thermal exposure to prevent morphological or chemical changes prior to analysis. Atom probe tomography is a rapidly expanding technique for three-dimensional structural and chemical analysis, but commercial instruments remain limited to loading specimens under ambient conditions. In this study, we describe a multifunctional environmental transfer hub allowing controlled cryogenic or room-temperature transfer of specimens under atmospheric or vacuum pressure conditions between an atom probe and other instruments or reaction chambers. The utility of the environmental transfer hub is demonstrated through the acquisition of previously unavailable mass spectral analysis of an intact organic molecule made possible via controlled cryogenic transfer into the atom probe using the hub. The ability to prepare and transfer specimens in precise environments promises a means to access new science across many disciplines from untainted samples and allow downstream time-resolved in situ atom probe studies.

  2. Light emission probing quantum shot noise and charge fluctuations at a biased molecular junction

    DEFF Research Database (Denmark)

    Schneider, N.L.; Lu, Jing Tao; Brandbyge, M.

    2012-01-01

    The emission of plasmonic light from a single C60 molecule on Cu(111) is probed in a scanning tunneling microscope from the weak-coupling, tunneling range to strong coupling of the molecule to the electrodes at contact. At positive sample voltage the photon yield decreases owing to shot...

  3. Single Molecule Electrochemical Detection in Aqueous Solutions and Ionic Liquids.

    Science.gov (United States)

    Byers, Joshua C; Paulose Nadappuram, Binoy; Perry, David; McKelvey, Kim; Colburn, Alex W; Unwin, Patrick R

    2015-10-20

    Single molecule electrochemical detection (SMED) is an extremely challenging aspect of electroanalytical chemistry, requiring unconventional electrochemical cells and measurements. Here, SMED is reported using a "quad-probe" (four-channel probe) pipet cell, fabricated by depositing carbon pyrolytically into two diagonally opposite barrels of a laser-pulled quartz quadruple-barreled pipet and filling the open channels with electrolyte solution, and quasi-reference counter electrodes. A meniscus forms at the end of the probe covering the two working electrodes and is brought into contact with a substrate working electrode surface. In this way, a nanogap cell is produced whereby the two carbon electrodes in the pipet can be used to promote redox cycling of an individual molecule with the substrate. Anticorrelated currents generated at the substrate and tip electrodes, at particular distances (typically tens of nanometers), are consistent with the detection of single molecules. The low background noise realized in this droplet format opens up new opportunities in single molecule electrochemistry, including the use of ionic liquids, as well as aqueous solution, and the quantitative assessment and analysis of factors influencing redox cycling currents, due to a precisely known gap size.

  4. ProbeZT: Simulation of transport coefficients of molecular electronic junctions under environmental effects using Büttiker's probes

    Science.gov (United States)

    Korol, Roman; Kilgour, Michael; Segal, Dvira

    2018-03-01

    We present our in-house quantum transport package, ProbeZT. This program provides linear response coefficients: electrical and electronic thermal conductances, as well as the thermopower of molecular junctions in which electrons interact with the surrounding thermal environment. Calculations are performed based on the Büttiker probe method, which introduces decoherence, energy exchange and dissipation effects phenomenologically using virtual electrode terminals called probes. The program can realize different types of probes, each introducing various environmental effects, including elastic and inelastic scattering of electrons. The molecular system is described by an arbitrary tight-binding Hamiltonian, allowing the study of different geometries beyond simple one-dimensional wires. Applications of the program to study the thermoelectric performance of molecular junctions are illustrated. The program also has a built-in functionality to simulate electron transport in double-stranded DNA molecules based on a tight-binding (ladder) description of the junction.

  5. A novel series of N-acyl substituted indole-linked benzimidazoles and naphthoimidazoles as potential anti inflammatory, anti biofilm and anti microbial agents.

    Science.gov (United States)

    Abraham, Rajan; Prakash, Periakaruppan; Mahendran, Karthikeyan; Ramanathan, Murugappan

    2018-01-01

    A novel N-acyl substituted indole-linked benzimidazoles and naphthoimidazoles were synthesized. Their chemical structures were confirmed using spectroscopic tools including 1 H NMR, 13 C NMR and CHN-elemental analyses. Anti inflammatory activity for all target compounds was evaluated in-vitro. The synthesized compounds hinder the biofilm formation and control the growth of the pathogen, Staphylococcus epidermis. Anti microbial activity of the compounds was evaluated against both Gram negative and Gram positive bacteria such as Staphylococcus aureus (MTCC 2940), Pseudomonas aeruginosa (MTCC424), Escherchia coli (MTCC 443) and Enterococcus fecalis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Bis(acetylacetonato-κ2O,O′(2-amino-1-methyl-1H-benzimidazole-κN3oxidovanadium(IV

    Directory of Open Access Journals (Sweden)

    Zukhra Ch. Kadirova

    2009-07-01

    Full Text Available The title mixed-ligand oxidovanadium(IV compound, [VO(C5H7O22(C8H9N3], contains a VIV atom in a distorted octahedral coordination, which is typical for such complexes. The vanadyl group and the N-heterocyclic ligand are cis to each other. The coordination bond is located at the endocyclic N atom of the benzimidazole ligand. Intramolecular hydrogen bonds between the exo-NH2 group H atoms and acetylacetonate O atoms stabilize the crystal structure.

  7. Calibration Fixture For Anemometer Probes

    Science.gov (United States)

    Lewis, Charles R.; Nagel, Robert T.

    1993-01-01

    Fixture facilitates calibration of three-dimensional sideflow thermal anemometer probes. With fixture, probe oriented at number of angles throughout its design range. Readings calibrated as function of orientation in airflow. Calibration repeatable and verifiable.

  8. Zero-mode waveguide nanophotonic structures for single molecule characterization

    Science.gov (United States)

    Crouch, Garrison M.; Han, Donghoon; Bohn, Paul W.

    2018-05-01

    Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (µM–mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer, and fluorescence correlation spectroscopy for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs. In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.

  9. Single-Molecule Nanomagnets

    Science.gov (United States)

    Friedman, Jonathan R.; Sarachik, Myriam P.

    2010-04-01

    Single-molecule magnets straddle the classical and quantum mechanical worlds, displaying many fascinating phenomena. They may have important technological applications in information storage and quantum computation. We review the physical properties of two prototypical molecular nanomagnets, Mn12-acetate and Fe8: Each behaves as a rigid, spin-10 object and exhibits tunneling between up and down directions. As temperature is lowered, the spin-reversal process evolves from thermal activation to pure quantum tunneling. At low temperatures, magnetic avalanches occur in which the magnetization of an entire sample rapidly reverses. We discuss the important role that symmetry-breaking fields play in driving tunneling and in producing Berry-phase interference. Recent experimental advances indicate that quantum coherence can be maintained on timescales sufficient to allow a meaningful number of quantum computing operations to be performed. Efforts are under way to create monolayers and to address and manipulate individual molecules.

  10. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    Energy Technology Data Exchange (ETDEWEB)

    Greulich-Bode, Karin; Wang, Mei; Rhein, Andreas; Weier, Jingly; Weier, Heinz-Ulli

    2008-12-16

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-?B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  11. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    Energy Technology Data Exchange (ETDEWEB)

    Greulich-Bode, Karin M.; Wang, Mei; Rhein, Andreas P.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-12-04

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-{kappa}B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  12. Atoms, molecules & elements

    CERN Document Server

    Graybill, George

    2007-01-01

    Young scientists will be thrilled to explore the invisible world of atoms, molecules and elements. Our resource provides ready-to-use information and activities for remedial students using simplified language and vocabulary. Students will label each part of the atom, learn what compounds are, and explore the patterns in the periodic table of elements to find calcium (Ca), chlorine (Cl), and helium (He) through hands-on activities.

  13. 1-Decyl-6-nitro-1H-benzimidazol-2(3H-one

    Directory of Open Access Journals (Sweden)

    Younes Ouzidan

    2011-11-01

    Full Text Available The title molecule, C17H25N3O3, is built up from fused six- and five-membered rings linked to a –C10H21 chain. The fused-ring system is essentially planar, the largest deviation from the mean plane being 0.009 (2 Å. The chain is roughly perpendicular to this plane, making a dihedral angle of 79.5 (2°. In the crystal, N—H...O hydrogen bonds build infinite chains along [010]. There are channels in the structure containing disordered hexane. The contribution of this solvent to the scattering power was suppressed using the SQUEEZE option in PLATON [Spek (2009. Acta Cryst. D65, 148–155].

  14. Controlled Clustering of Gold Nanoparticles using Solid-support for Surface-enhanced Raman Spectroscopic Probes

    International Nuclear Information System (INIS)

    Chang, Hyejin; Chae, Jinjoo; Jeong, Hong; Kang, Homan; Lee, Yoonsik

    2014-01-01

    We fabricated small clusters of gold nanoparticles by using solid-supported aggregation of gold nanoparticles. The fabricated Au nanoclusters consisting mainly of dimers showed homogeneous characteristics in cluster size and SERS intensity. The SERS enhancement of 4-ABT molecules in an effective area within 2-nm gap appeared to be approximately 10. Detachment process by ultrasonication was successively carried out in order to use the nanoclusters as SERS probes. The possibility of these clusters as SERS probe was proved in terms of signal and cluster size. Single molecule-level sensitivity of surface-enhanced Raman scattering (SERS) was known approximately fifteen years ago. Ever since there have been many different applications benefiting from the ultra-high sensitivity such as single molecule detection, chemical sensing and bio-molecular probes. Especially, SERS has drawn much attention in bio-multiplexing probes owing to its unique optical characteristics claiming extremely narrow bandwidth, high sensitivity of light signals, and non-bleaching feature

  15. Photonic Molecule Lasers Revisited

    Science.gov (United States)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.

    2014-05-01

    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  16. Heavy ion beam probing

    Energy Technology Data Exchange (ETDEWEB)

    Hickok, R L

    1980-07-01

    This report consists of the notes distributed to the participants at the IEEE Mini-Course on Modern Plasma Diagnostics that was held in Madison, Wisconsin in May 1980. It presents an overview of Heavy Ion Beam Probing that briefly describes the principles and discuss the types of measurements that can be made. The problems associated with implementing beam probes are noted, possible variations are described, estimated costs of present day systems, and the scaling requirements for large plasma devices are presented. The final chapter illustrates typical results that have been obtained on a variety of plasma devices. No detailed calculations are included in the report, but a list of references that will provide more detailed information is included.

  17. Heavy ion beam probing

    International Nuclear Information System (INIS)

    Hickok, R.L.

    1980-07-01

    This report consists of the notes distributed to the participants at the IEEE Mini-Course on Modern Plasma Diagnostics that was held in Madison, Wisconsin in May 1980. It presents an overview of Heavy Ion Beam Probing that briefly describes the principles and discuss the types of measurements that can be made. The problems associated with implementing beam probes are noted, possible variations are described, estimated costs of present day systems, and the scaling requirements for large plasma devices are presented. The final chapter illustrates typical results that have been obtained on a variety of plasma devices. No detailed calculations are included in the report, but a list of references that will provide more detailed information is included

  18. Gravity Probe B Inspection

    Science.gov (United States)

    2000-01-01

    The space vehicle Gravity Probe B (GP-B) is the relativity experiment developed at Stanford University to test two extraordinary predictions of Albert Einstein's general theory of relativity. The experiment will measure, very precisely, the expected tiny changes in the direction of the spin axes of four gyroscopes contained in an Earth-orbiting satellite at a 400-mile altitude. So free are the gyroscopes from disturbance that they will provide an almost perfect space-time reference system. They will measure how space and time are very slightly warped by the presence of the Earth, and, more profoundly, how the Earth's rotation very slightly drags space-time around with it. These effects, though small for the Earth, have far-reaching implications for the nature of matter and the structure of the Universe. GP-B is among the most thoroughly researched programs ever undertaken by NASA. This is the story of a scientific quest in which physicists and engineers have collaborated closely over many years. Inspired by their quest, they have invented a whole range of technologies that are already enlivening other branches of science and engineering. In this photograph, engineer Gary Reynolds is inspecting the inside of the probe neck during probe thermal repairs. GP-B is scheduled for launch in April 2004 and managed for NASA by the Marshall Space Flight Center. Development of the GP-B is the responsibility of Stanford University along with major subcontractor Lockheed Martin Corporation. (Image credit to Russ Leese, Gravity Probe B, Stanford University)

  19. Novel Eddycurrent Probe Development.

    Science.gov (United States)

    1981-12-01

    oVCut MVc AVu inc F C -- -(1)(-jlOOO AZC (23)0 --2--M F1 (23) If the Thevenin source voltages, V0, are adjusted so that Vinc is the same for both the...as small as 1.2 cm. The differential probe assembly was spring loaded about a pivot post (see Figure 12) so it could scan noncircular or eccentric

  20. Induced current heating probe

    International Nuclear Information System (INIS)

    Thatcher, G.; Ferguson, B.G.; Winstanley, J.P.

    1984-01-01

    An induced current heating probe is of thimble form and has an outer conducting sheath and a water flooded flux-generating unit formed from a stack of ferrite rings coaxially disposed in the sheath. The energising coil is made of solid wire which connects at one end with a coaxial water current tube and at the other end with the sheath. The stack of ferrite rings may include non-magnetic insulating rings which help to shape the flux. (author)

  1. Atom probe crystallography

    OpenAIRE

    Gault, Baptiste; Moody, Michael P.; Cairney, Julie M.; Ringer, Simon P.

    2012-01-01

    This review addresses new developments in the emerging area of “atom probe crystallography”, a materials characterization tool with the unique capacity to reveal both composition and crystallographic structure at the atomic scale. This information is crucial for the manipulation of microstructure for the design of both structural and functional materials with optimized mechanical, electric, optoelectronic, magnetic, or superconducting properties that will find application in, for example, nan...

  2. Probing gravitation with pulsars

    Science.gov (United States)

    Kramer, Michael

    2013-03-01

    Radio pulsars are fascinating and extremely useful objects. Despite our on-going difficulties in understanding the details of their emission physics, they can be used as precise cosmic clocks in a wide-range of experiments - in particular for probing gravitational physics. While the reader should consult the contributions to these proceedings to learn more about this exciting field of discovering, exploiting and understanding pulsars, we will concentrate here on on the usage of pulsars as gravity labs.

  3. Nanoscale thermal probing

    Directory of Open Access Journals (Sweden)

    Yanan Yue

    2012-03-01

    Full Text Available Nanoscale novel devices have raised the demand for nanoscale thermal characterization that is critical for evaluating the device performance and durability. Achieving nanoscale spatial resolution and high accuracy in temperature measurement is very challenging due to the limitation of measurement pathways. In this review, we discuss four methodologies currently developed in nanoscale surface imaging and temperature measurement. To overcome the restriction of the conventional methods, the scanning thermal microscopy technique is widely used. From the perspective of measuring target, the optical feature size method can be applied by using either Raman or fluorescence thermometry. The near-field optical method that measures nanoscale temperature by focusing the optical field to a nano-sized region provides a non-contact and non-destructive way for nanoscale thermal probing. Although the resistance thermometry based on nano-sized thermal sensors is possible for nanoscale thermal probing, significant effort is still needed to reduce the size of the current sensors by using advanced fabrication techniques. At the same time, the development of nanoscale imaging techniques, such as fluorescence imaging, provides a great potential solution to resolve the nanoscale thermal probing problem.

  4. Einstein Inflationary Probe (EIP)

    Science.gov (United States)

    Hinshaw, Gary

    2004-01-01

    I will discuss plans to develop a concept for the Einstein Inflation Probe: a mission to detect gravity waves from inflation via the unique signature they impart to the cosmic microwave background (CMB) polarization. A sensitive CMB polarization satellite may be the only way to probe physics at the grand-unified theory (GUT) scale, exceeding by 12 orders of magnitude the energies studied at the Large Hadron Collider. A detection of gravity waves would represent a remarkable confirmation of the inflationary paradigm and set the energy scale at which inflation occurred when the universe was a fraction of a second old. Even a strong upper limit to the gravity wave amplitude would be significant, ruling out many common models of inflation, and pointing to inflation occurring at much lower energy, if at all. Measuring gravity waves via the CMB polarization will be challenging. We will undertake a comprehensive study to identify the critical scientific requirements for the mission and their derived instrumental performance requirements. At the core of the study will be an assessment of what is scientifically and experimentally optimal within the scope and purpose of the Einstein Inflation Probe.

  5. Benzimidazoles Promote Anti-TNF Mediated Induction of Regulatory Macrophages and Enhance Therapeutic Efficacy in a Murine Model.

    Science.gov (United States)

    Wildenberg, Manon E; Levin, Alon D; Ceroni, Alessandro; Guo, Zhen; Koelink, Pim J; Hakvoort, Theodorus B M; Westera, Liset; Bloemendaal, Felicia M; Brandse, Johannan F; Simmons, Alison; D'Haens, Geert R; Ebner, Daniel; van den Brink, Gijs R

    2017-12-04

    Regulatory macrophages play a critical role in tissue repair, and we have previously shown that anti-tumour necrosis factor [TNF] antibodies induce these macrophages in vitro and in vivo in IBD patients. The induction of regulatory macrophages can be potentiated using the combination of anti-TNF and thiopurines, consistent with the enhanced efficacy of this combination therapy described in clinical trials. As thiopurines are unfortunately associated with significant side effects, we here aimed to identify alternatives for combination therapy with anti-TNF, using the macrophage induction model as a screening tool. Mixed lymphocyte reactions were treated with anti-TNF and a library of 1600 drug compounds. Induction of CD14+CD206+ macrophages was analysed by flow cytometry. Positive hits were validated in vitro and in the T cell transfer model of colitis. Among the 98 compounds potentiating the induction of regulatory macrophages by anti-TNF were six benzimidazoles, including albendazole. Albendazole treatment in the presence of anti-TNF resulted in alterations in the tubulin skeleton and signalling though AMPK, which was required for the enhanced induction. Combination therapy also increased expression levels of the immunoregulatory cytokine IL-10. In vivo, albendazole plus anti-TNF combination therapy was superior to monotherapy in a model of colitis, in terms of both induction of regulatory macrophages and improvement of clinical symptoms. Albendazole enhances the induction of regulatory macrophages by anti-TNF and potentiates clinical efficacy in murine colitis. Given its favourable safety profile, these data indicate that the repurposing of albendazole may be a novel option for anti-TNF combination therapy in IBD.

  6. Nine New Fluorescent Probes

    Science.gov (United States)

    Lin, Tsung-I.; Jovanovic, Misa V.; Dowben, Robert M.

    1989-06-01

    Absorption and fluorescence spectroscopic studies are reported here for nine new fluorescent probes recently synthesized in our laboratories: four pyrene derivatives with substituents of (i) 1,3-diacetoxy-6,8-dichlorosulfonyl, (ii) 1,3-dihydroxy-6,8-disodiumsulfonate, (iii) 1,3-disodiumsulfonate, and (iv) l-ethoxy-3,6,8-trisodiumsulfonate groups, and five [7-julolidino] coumarin derivatives with substituents of (v) 3-carboxylate-4-methyl, (vi) 3- methylcarboxylate, (vii) 3-acetate-4-methyl, (viii) 3-propionate-4-methyl, and (ix) 3-sulfonate-4-methyl groups. Pyrene compounds i and ii and coumarin compounds v and vi exhibit interesting absorbance and fluorescence properties: their absorption maxima are red shifted compared to the parent compound to the blue-green region, and the band width broadens considerably. All four blue-absorbing dyes fluoresce intensely in the green region, and the two pyrene compounds emit at such long wavelengths without formation of excimers. The fluorescence properties of these compounds are quite environment-sensitive: considerable spectral shifts and fluorescence intensity changes have been observed in the pH range from 3 to 10 and in a wide variety of polar and hydrophobic solvents with vastly different dielectric constants. The high extinction and fluorescence quantum yield of these probes make them ideal fluorescent labeling reagents for proteins, antibodies, nucleic acids, and cellular organelles. The pH and hydrophobicity-dependent fluorescence changes can be utilized as optical pH and/or hydrophobicity indicators for mapping environmental difference in various cellular components in a single cell. Since all nine probes absorb in the UV, but emit at different wavelengths in the visible, these two groups of compounds offer an advantage of utilizing a single monochromatic light source (e.g., a nitrogen laser) to achieve multi-wavelength detection for flow cytometry application. As a first step to explore potential application in

  7. Negative ions of polyatomic molecules

    International Nuclear Information System (INIS)

    Christophorou, LG.

    1980-01-01

    In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules are discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to hot molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules (electron affinity), and the basic and the applied significance of negative-ion studies

  8. Three dimensional alignment of molecules using elliptically polarized laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Bjerre, N.; Hald, K.

    2000-01-01

    We demonstrate, theoretically and experimentally, that an intense, elliptically polarized, nonresonant laser field can simultaneously force all three axes of a molecule to align along given axes fixed in space, thus inhibiting the free rotation in all three Euler angles. Theoretically, the effect...... is illustrated through time dependent quantum mechanical calculations. Experimentally, 3, 4-dibromothiophene molecules are aligned with a nanosecond laser pulse. The alignment is probed by 2D ion imaging of the fragments from a 20 fs laser pulse induced Coulomb explosion....

  9. Development of Mackintosh Probe Extractor

    Science.gov (United States)

    Rahman, Noor Khazanah A.; Kaamin, Masiri; Suwandi, Amir Khan; Sahat, Suhaila; Jahaya Kesot, Mohd

    2016-11-01

    Dynamic probing is a continuous soil investigation technique, which is one of the simplest soil penetration test. It basically consist of repeatedly driving a metal tipped probe into the ground using a drop weight of fixed mass and travel. Testing was carried out continuously from ground level to the final penetration depth. Once the soil investigation work done, it is difficult to pull out the probe rod from the ground, due to strong soil structure grip against probe cone and prevent the probe rod out from the ground. Thus, in this case, a tool named Extracting Probe was created to assist in the process of retracting the probe rod from the ground. In addition, Extracting Probe also can reduce the time to extract the probe rod from the ground compare with the conventional method. At the same time, it also can reduce manpower cost because only one worker involve to handle this tool compare with conventional method used two or more workers. From experiment that have been done we found that the time difference between conventional tools and extracting probe is significant, average time difference is 155 minutes. In addition the extracting probe can reduce manpower usage, and also labour cost for operating the tool. With all these advantages makes this tool has the potential to be marketed.

  10. A novel magnetic core-shell nanocomposite Fe3O4@chitosan@ZnO for the green synthesis of 2-benzimidazoles

    Science.gov (United States)

    Tian, Fei; Niu, Libo; Chen, Bo; Gao, Xuejia; Lan, Xingwang; Huo, Li; Bai, Guoyi

    2017-10-01

    A novel magnetic core-shell nanocomposite Fe3O4@Chitosan@ZnO was successfully prepared by in situ chemical precipitation method. It has a clear core-shell structure with magnetic Fe3O4 (about 160 nm in diameter) as core, chitosan as the inner shell, and ZnO as the outer shell, as demonstrated by the transmission electron microscopy and the related elemental mapping. Moreover, this nanocomposite has high magnetization (43.6 emu g-1) so that it can be easily separated from the reaction mixture within 4 s by an external magnetic field. The introduction of the natural chitosan shell, instead of the conventional SiO2 shell, and its combination with the active ZnO ensures this novel nanocomposite green character and good catalytic performance in the synthesis of 2-benzimidazoles with moderate to excellent isolated yields at room temperature. Notably, it can be recycled seven times without appreciable loss of its initial catalytic activity, demonstrating its good stability and making it an attractive candidate for the green synthesis of 2-benzimidazoles. [Figure not available: see fulltext.

  11. Biological evaluation of a cytotoxic 2-substituted benzimidazole copper(II) complex: DNA damage, antiproliferation and apoptotic induction activity in human cervical cancer cells.

    Science.gov (United States)

    Qiao, Xin; Ma, Zhong-Ying; Shao, Jia; Bao, Wei-Guo; Xu, Jing-Yuan; Qiang, Zhao-Yan; Lou, Jian-Shi

    2014-02-01

    Exploring novel chemotherapeutic agents is a great challenge in cancer medicine. To that end, 2-substituted benzimidazole copper(II) complex, [Cu(BMA)Cl2]·(CH3OH) (1) [BMA = N,N'-bis(benzimidazol-2-yl-methyl)amine], was synthesized and its cytotoxicity was characterized. The interaction between complex 1 and calf thymus DNA was detected by spectroscopy methods. The binding constant (K b = 1.24 × 10(4 )M(-1)) and the apparent binding constant (K app = 6.67 × 10(6 )M(-1)) of 1 indicated its moderate DNA affinity. Complex 1 induced single strand breaks of pUC19 plasmid DNA in the presence of H2O2 through an oxidative pathway. Cytotoxicity studies proved that complex 1 could inhibit the proliferation of human cervical carcinoma cell line HeLa in both time- and dose-dependent manners. The results of nuclei staining by Hoechst 33342 and alkaline single-cell gel electrophoresis proved that complex 1 caused cellular DNA damage in HeLa cells. Furthermore, treatment of HeLa cells with 1 resulted in S-phase arrest, loss of mitochondrial potential, and up-regulation of caspase-3 and -9 in HeLa cells, suggesting that complex 1 was capable of inducing apoptosis in cancer cells through the intrinsic mitochondrial pathway.

  12. Synthesis and PASS-assisted in silico approach of some novel 2-substituted benzimidazole bearing a pyrimidine-2, 4, 6(trione system as mucomembranous protector

    Directory of Open Access Journals (Sweden)

    Bijo Mathew

    2013-01-01

    Full Text Available Purpose: The present paper demonstrates the utility of PASS computer-aided program and makes a clear comparison of predicted and observed pharmacological properties of some novel 5-[(2E-1-(1H-benzimidazol-2-yl-3-substituted phenylprop-2-en-1-ylidene] pyrimidine-2, 4, 6 (1H, 3H, 5H-triones (5a-f. Materials and Methods: The synthesis of the titled derivatives were achieved by the reaction between 2E-1-(1H-benzimidazol-2-yl-3-phenylprop-2-en-1-ones (4a-f and barbituric acid in the presence of catalytic amount of acetic acid medium. All the final structures were assigned on the basis of IR, 1 HNMR and mass spectra analysis. All the newly synthesized compounds were screened for their antiulcer activity in the pylorus-ligated rats. Results: Compounds 5b, 5e and 5c showed a percentage protection of (69.58, 69.56 and 67.17 at a dose of 50 mg/kg b.w. when compared to standard omeprazole (77.37%, 2 mg/kg b.w.. Conclusion: Scanning of stomach specimens using electron microscope revealed that the mice treated with standard and synthetic derivatives had no injury observed in stomach mucosa, which is identical to that of the control animal.

  13. Measurements of H-atom density by a catalytic probe

    International Nuclear Information System (INIS)

    Vesel, A.; Drenik, A.; Mozetic, M.

    2006-01-01

    One of the important plasma parameters in tokamaks is the density of neutral hydrogen atoms which can be measured by catalytic probes. The method is based on the catalytic recombination of H atoms on the metal surface. In order to prevent a substantial drain of atoms by the probe, it should be made as small as possible. But still this effect can not be neglected. Therefore a study of the influence of a catalytic probe on the H-atom density was performed. The source of neutral H-atoms was inductively coupled RF hydrogen plasma. The gas from the discharge vessel was leaked to an experimental chamber through a narrow tube with the diameter of 5 mm and the length of 6 cm. Charged particles created in the discharge vessel were recombined on the walls of the narrow tube, so that the gas entering the experimental chamber was a mixture of hydrogen atoms and molecules only. The density of H-atoms in the experimental chamber was measured with two nickel catalytic probes. One probe was at fixed position and the other one was made movable. A change in the probe signal of the fixed probe was measured versus the position of the movable probe. The measurements were performed at the pressures between 10 Pa and 200 Pa and at two different RF powers 200 W and 300 W. It was found that the density of neutral hydrogen atoms was reduced for about 20% due to the presence of the probe. This result was independent from the pressure in the experimental chamber. (author)

  14. Nucleic acid-based fluorescent probes and their analytical potential.

    Science.gov (United States)

    Juskowiak, Bernard

    2011-03-01

    It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.

  15. The influence of morphology on excitons in single conjugated molecules

    Science.gov (United States)

    Thiessen, Alexander

    The electronic properties of pi-conjugated molecules are strongly related to their molecular shape and morphology of assembly in three-dimensional space. Understanding the various structure-property relationships is relevant to the applications of these materials in optoelectronic devices such as organic light-emitting diodes, field effect transistors and photovoltaic cells. The fact that conjugated systems interact with visible light opens these materials to a plethora of noninvasive spectroscopic investigation techniques. In this work, electronic properties of different pi-conjugated systems are studied spectroscopically on the ensemble and the single molecule levels. Single molecule spectroscopy is advantageous in that it allows the investigation of the individual nuclear building blocks that contribute to the properties of the ensemble. Additionally, transient photoluminescence spectroscopy methods can provide useful insight into the temporal evolution of the emissive states. In combination with these methods, novel pi-conjugated model molecules are used to probe processes related to exciton dynamics. For the first time, the spatial localization of excited states is probed experimentally in a molecule with a circular chromophoric structure. In addition, a set of model molecules with different geometries is employed to study exciton relaxation in pi-conjugated systems. The molecular morphology is utilized to distinguish between processes such as nuclear reorganization and torsional relaxation. Furthermore, single molecule spectroscopy is used to study the electronic structure of individual polymer chains in the photovoltaic cell material poly-(3-hexylthiophene). Optical spectra of this polymer are known to change with the morphology of the bulk film. Single molecule studies reveal that individual polymer chains exhibit similar behavior and indicate that spectral diversity is an intrinsic property of single P3HT molecules. The main results of this work are the

  16. Ultra-cold molecule production

    International Nuclear Information System (INIS)

    Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.

    2005-01-01

    The production of Ultra-cold molecules is a goal of many laboratories through out the world. Here we are pursuing a unique technique that utilizes the kinematics of atomic and molecular collisions to achieve the goal of producing substantial numbers of sub Kelvin molecules confined in a trap. Here a trap is defined as an apparatus that spatially localizes, in a known location in the laboratory, a sample of molecules whose temperature is below one degree absolute Kelvin. Further, the storage time for the molecules must be sufficient to measure and possibly further cool the molecules. We utilize a technique unique to Sandia to form cold molecules from near mass degenerate collisions between atoms and molecules. This report describes the progress we have made using this novel technique and the further progress towards trapping molecules we have cooled

  17. Organic molecule fluorescence as an experimental test-bed for quantum jumps in thermodynamics.

    Science.gov (United States)

    Browne, Cormac; Farrow, Tristan; Dahlsten, Oscar C O; Taylor, Robert A; Vlatko, Vedral

    2017-08-01

    We demonstrate with an experiment how molecules are a natural test bed for probing fundamental quantum thermodynamics. Single-molecule spectroscopy has undergone transformative change in the past decade with the advent of techniques permitting individual molecules to be distinguished and probed. We demonstrate that the quantum Jarzynski equality for heat is satisfied in this set-up by considering the time-resolved emission spectrum of organic molecules as arising from quantum jumps between states. This relates the heat dissipated into the environment to the free energy difference between the initial and final state. We demonstrate also how utilizing the quantum Jarzynski equality allows for the detection of energy shifts within a molecule, beyond the relative shift.

  18. Playing with molecules.

    Science.gov (United States)

    Toon, Adam

    2011-12-01

    Recent philosophy of science has seen a number of attempts to understand scientific models by looking to theories of fiction. In previous work, I have offered an account of models that draws on Kendall Walton's 'make-believe' theory of art. According to this account, models function as 'props' in games of make-believe, like children's dolls or toy trucks. In this paper, I assess the make-believe view through an empirical study of molecular models. I suggest that the view gains support when we look at the way that these models are used and the attitude that users take towards them. Users' interaction with molecular models suggests that they do imagine the models to be molecules, in much the same way that children imagine a doll to be a baby. Furthermore, I argue, users of molecular models imagine themselves viewing and manipulating molecules, just as children playing with a doll might imagine themselves looking at a baby or feeding it. Recognising this 'participation' in modelling, I suggest, points towards a new account of how models are used to learn about the world, and helps us to understand the value that scientists sometimes place on three-dimensional, physical models over other forms of representation.

  19. A Brief Introduction to Single-Molecule Fluorescence Methods.

    Science.gov (United States)

    van den Wildenberg, Siet M J L; Prevo, Bram; Peterman, Erwin J G

    2018-01-01

    One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster Resonance Energy Transfer and orientation measurements with fluorescence polarization.

  20. Mapping the Small Molecule Interactome by Mass Spectrometry.

    Science.gov (United States)

    Flaxman, Hope A; Woo, Christina M

    2018-01-16

    Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.