WorldWideScience

Sample records for protein-small molecule interactions

  1. Detection of protein-small molecule binding using a self-referencing external cavity laser biosensor.

    Science.gov (United States)

    Meng Zhang; Peh, Jessie; Hergenrother, Paul J; Cunningham, Brian T

    2014-01-01

    High throughput screening of protein-small molecule binding interactions using label-free optical biosensors is challenging, as the detected signals are often similar in magnitude to experimental noise. Here, we describe a novel self-referencing external cavity laser (ECL) biosensor approach that achieves high resolution and high sensitivity, while eliminating thermal noise with sub-picometer wavelength accuracy. Using the self-referencing ECL biosensor, we demonstrate detection of binding between small molecules and a variety of immobilized protein targets with binding affinities or inhibition constants in the sub-nanomolar to low micromolar range. The demonstrated ability to perform detection in the presence of several interfering compounds opens the potential for increasing the throughput of the approach. As an example application, we performed a "needle-in-the-haystack" screen for inhibitors against carbonic anhydrase isozyme II (CA II), in which known inhibitors are clearly differentiated from inactive molecules within a compound library.

  2. Antidiabetic effects of glucokinase regulatory protein small-molecule disruptors

    Science.gov (United States)

    Lloyd, David J.; St Jean, David J.; Kurzeja, Robert J. M.; Wahl, Robert C.; Michelsen, Klaus; Cupples, Rod; Chen, Michelle; Wu, John; Sivits, Glenn; Helmering, Joan; Komorowski, Renée; Ashton, Kate S.; Pennington, Lewis D.; Fotsch, Christopher; Vazir, Mukta; Chen, Kui; Chmait, Samer; Zhang, Jiandong; Liu, Longbin; Norman, Mark H.; Andrews, Kristin L.; Bartberger, Michael D.; van, Gwyneth; Galbreath, Elizabeth J.; Vonderfecht, Steven L.; Wang, Minghan; Jordan, Steven R.; Véniant, Murielle M.; Hale, Clarence

    2013-12-01

    Glucose homeostasis is a vital and complex process, and its disruption can cause hyperglycaemia and type II diabetes mellitus. Glucokinase (GK), a key enzyme that regulates glucose homeostasis, converts glucose to glucose-6-phosphate in pancreatic β-cells, liver hepatocytes, specific hypothalamic neurons, and gut enterocytes. In hepatocytes, GK regulates glucose uptake and glycogen synthesis, suppresses glucose production, and is subject to the endogenous inhibitor GK regulatory protein (GKRP). During fasting, GKRP binds, inactivates and sequesters GK in the nucleus, which removes GK from the gluconeogenic process and prevents a futile cycle of glucose phosphorylation. Compounds that directly hyperactivate GK (GK activators) lower blood glucose levels and are being evaluated clinically as potential therapeutics for the treatment of type II diabetes mellitus. However, initial reports indicate that an increased risk of hypoglycaemia is associated with some GK activators. To mitigate the risk of hypoglycaemia, we sought to increase GK activity by blocking GKRP. Here we describe the identification of two potent small-molecule GK-GKRP disruptors (AMG-1694 and AMG-3969) that normalized blood glucose levels in several rodent models of diabetes. These compounds potently reversed the inhibitory effect of GKRP on GK activity and promoted GK translocation both in vitro (isolated hepatocytes) and in vivo (liver). A co-crystal structure of full-length human GKRP in complex with AMG-1694 revealed a previously unknown binding pocket in GKRP distinct from that of the phosphofructose-binding site. Furthermore, with AMG-1694 and AMG-3969 (but not GK activators), blood glucose lowering was restricted to diabetic and not normoglycaemic animals. These findings exploit a new cellular mechanism for lowering blood glucose levels with reduced potential for hypoglycaemic risk in patients with type II diabetes mellitus.

  3. Biophysical characterization of membrane protein-small molecule interactions

    NARCIS (Netherlands)

    Chen, Dan

    2015-01-01

    Membrane proteins are account for up to two thirds of known druggable targets. Traditionally, new drugs against this class of proteins have been discovered through HTS. However, not all GPCRs are amenable to traditional screening methods. Recently, fragment-based drug discovery (FBDD) has emerged as

  4. Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking.

    Science.gov (United States)

    Wang, Hongrui; Liu, Hongwei; Cai, Leixin; Wang, Caixia; Lv, Qiang

    2017-07-10

    In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein-small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (MC) and REMC sampling methods, these methods use multi-objective optimization Pareto front information to facilitate the selection of replicas for exchange. The Pareto front information generated to select lower energy conformations as representative conformation structure replicas can facilitate the convergence of the available conformational space, including available near-native structures. Furthermore, our approach directly provides min-min scenario Pareto optimal solutions, as well as a hybrid of the min-min and max-min scenario Pareto optimal solutions with lower energy conformations for use as structure templates in the REMC sampling method. These methods were validated based on a thorough analysis of a benchmark data set containing 16 benchmark test cases. An in-depth comparison between MC, REMC, multi-objective optimization-REMC (MO-REMC), and hybrid MO-REMC (HMO-REMC) sampling methods was performed to illustrate the differences between the four conformational search strategies. Our findings demonstrate that the MO-REMC and HMO-REMC conformational sampling methods are powerful approaches for obtaining protein-small molecule docking conformational predictions based on the binding energy of complexes in RosettaLigand.

  5. Electron-excited molecule interactions

    International Nuclear Information System (INIS)

    Christophorou, L.G.; Tennessee Univ., Knoxville, TN

    1991-01-01

    In this paper the limited but significant knowledge to date on electron scattering from vibrationally/rotationally excited molecules and electron scattering from and electron impact ionization of electronically excited molecules is briefly summarized and discussed. The profound effects of the internal energy content of a molecule on its electron attachment properties are highlighted focusing in particular on electron attachment to vibrationally/rotationally and to electronically excited molecules. The limited knowledge to date on electron-excited molecule interactions clearly shows that the cross sections for certain electron-molecule collision processes can be very different from those involving ground state molecules. For example, optically enhanced electron attachment studies have shown that electron attachment to electronically excited molecules can occur with cross sections 10 6 to 10 7 times larger compared to ground state molecules. The study of electron-excited molecule interactions offers many experimental and theoretical challenges and opportunities and is both of fundamental and technological significance. 54 refs., 15 figs

  6. Electron interactions with polar molecules

    International Nuclear Information System (INIS)

    Garrett, W.R.

    1981-01-01

    A description is given of a number of the features of discrete and continuous spectra of electrons interacting with polar molecules. Attention is focused on the extent to which theoretical predictions concerning cross sections, resonances, and bound states are strongly influenced by the various approximations that are so ubiquitous in the treatment of such problems. Similarly, threshold scattering and photodetachment processes are examined for the case of weakly bound dipole states whose higher members overlap the continuum

  7. Electron-molecule interactions and their applications

    CERN Document Server

    Christophorou, L G

    1984-01-01

    Electron-Molecule Interactions and Their Applications, Volume 2 provides a balanced and comprehensive account of electron-molecule interactions in dilute and dense gases and liquid media. This book consists of six chapters. Chapter 1 deals with electron transfer reactions, while Chapter 2 discusses electron-molecular positive-ion recombination. The electron motion in high-pressure gases and electron-molecule interactions from single- to multiple-collision conditions is deliberated in Chapter 3. In Chapter 4, knowledge on electron-molecule interactions in gases is linked to that on similar proc

  8. Modelling of energetic molecule-surface interactions

    International Nuclear Information System (INIS)

    Kerford, M.

    2000-09-01

    This thesis contains the results of molecular dynamics simulations of molecule-surface interactions, looking particularly at fullerene molecules and carbon surfaces. Energetic impacts of fullerene molecules on graphite create defect craters. The relationship between the parameters of the impacting molecule and the parameters of the crater axe examined and found to be a function of the energy and velocity of the impacting molecule. Less energetic fullerene molecules can be scattered from a graphite surface and the partitioning of energy after a scattering event is investigated. It is found that a large fraction of the kinetic energy retained after impact is translational energy, with a small fraction of rotational energy and a number of vibrational modes. At impact energies where the surface is not broken and at normal incidence, surface waves axe seen to occur. These waves axe used to develop a method of desorbing molecules from a graphite surface without damage to either the surface or the molecules being desorbed. A number of fullerene molecules are investigated and ways to increase the desorption yield are examined. It is found that this is a successful technique for desorbing large numbers of intact molecules from graphite. This technique could be used for desorbing intact molecules into a gas phase for mass spectrometric analysis. (author)

  9. Interactions of electrons with biologically important molecules

    International Nuclear Information System (INIS)

    Pisklova, K.; Papp, P.; Stano, M.

    2012-01-01

    For the study of interactions of low-energy electrons with the molecules in the gas phase, the authors used electron-molecule cross-beam apparatus. The experiment is carried out in high vacuum, where molecules of the tested compound are inducted through a capillary. For purposes of this experiment the sample was electrically heated to 180 Deg C., giving a bundle of GlyGly molecules into the gas phase. The resulting signals can be evaluated in two different modes: mass spectrum - at continuous electron energy (e.g. 100 eV) they obtained the signal of intensity of the ions according to their mass to charge ratio; ionization and resonance spectra - for selected ion mass when the authors received the signal of intensity of the ions, depending on the energy of interacting electron.

  10. Proteinaceous molecules mediating Bifidobacterium-host interactions

    Directory of Open Access Journals (Sweden)

    Lorena Ruiz

    2016-08-01

    Full Text Available Bifidobacteria are commensal microoganisms found in the gastrointestinal tract.Several strains have been attributed beneficial traits at local and systemic levels, through pathogen exclusion or immune modulation, among other benefits. This has promoted a growing industrial and scientific interest in bifidobacteria as probiotic supplements. However, the molecular mechanisms mediating this cross-talk with the human host remain unknown. High-throughput technologies, from functional genomics to transcriptomics, proteomics and interactomics coupled to the development of both in vitro and in vivo models to study the dynamics of the intestinal microbiota and their effects on host cells, have eased the identification of key molecules in these interactions. Numerous secreted or surface-associated proteins or peptides have been identified as potential mediators of bifidobacteria-host interactions and molecular cross-talk, directly participating in sensing environmental factors, promoting intestinal colonization or mediating a dialogue with mucosa-associated immune cells. On the other hand, bifidobacteria induce the production of proteins in the intestine, by epithelial or immune cells, and other gut bacteria, which are key elements in orchestrating interactions among bifidobacteria, gut microbiota and host cells. This review aims to give a comprehensive overview on proteinaceous molecules described and characterized to date, as mediators of the dynamic interplay between bifidobacteria and the human host, providing a framework to identify knowledge gaps and future research needs.

  11. Single-molecule magnets ``without'' intermolecular interactions

    Science.gov (United States)

    Wernsdorfer, W.; Vergnani, L.; Rodriguez-Douton, M. J.; Cornia, A.; Neugebauer, P.; Barra, A. L.; Sorace, L.; Sessoli, R.

    2012-02-01

    Intermolecular magnetic interactions (dipole-dipole and exchange) affect strongly the magnetic relaxation of crystals of single-molecule magnets (SMMs), especially at low temperature, where quantum tunneling of the magnetization (QTM) dominates. This leads to complex many-body problems [l]. Measurements on magnetically diluted samples are desirable to clearly sort out the behaviour of magnetically-isolated SMMs and to reveal, by comparison, the effect of intermolecular interactions. Here, we diluted a Fe4 SMM into a diamagnetic crystal lattice, affording arrays of independent and iso-oriented magnetic units. We found that the resonant tunnel transitions are much sharper, the tunneling efficiency changes significantly, and two-body QTM transitions disappear. These changes have been rationalized on the basis of a dipolar shuffling mechanism and of transverse dipolar fields, whose effect has been analyzed using a multispin model. Our findings directly prove the impact of intermolecular magnetic couplings on the SMM behaviour and disclose the magnetic response of truly-isolated giant spins in a diamagnetic crystalline environment.[4pt] [1] W. Wernsdorfer, at al, PRL 82, 3903 (1999); PRL 89, 197201 (2002); Nature 416, 406 (2002); IS Tupitsyn, PCE Stamp, NV Prokof'ev, PRB 69, 132406 (2004).

  12. Structure formation in bis(terpyridine) derivative adlayers: molecule-substrate versus molecule-molecule interactions.

    Science.gov (United States)

    Hoster, Harry E; Roos, Matthias; Breitruck, Achim; Meier, Christoph; Tonigold, Katrin; Waldmann, Thomas; Ziener, Ulrich; Landfester, Katharina; Behm, R Jürgen

    2007-11-06

    The influence of the substrate and the deposition conditions-vapor deposition versus deposition from solution-on the structures formed upon self-assembly of deposited bis(terpyridine) derivative (2,4'-BTP) monolayers on different hexagonal substrates, including highly oriented pyrolytic graphite (HOPG), Au(111), and (111)-oriented Ag thin films, was investigated by high-resolution scanning tunneling microscopy and by model calculations of the intermolecular energies and the lateral corrugation of the substrate-adsorbate interaction. Similar quasi-quadratic network structures with almost the same lattice constants obtained on all substrates are essentially identical to the optimum configuration expected from an optimization of the adlayer structure with C-H...N-type bridging bonds as a structure-determining factor, which underlines a key role of the intermolecular interactions in adlayer order. Slight distortions from the optimum values to form commensurate adlayer structures on the metal substrates and the preferential orientation of the adlayer with respect to the substrate are attributed to the substrate-adsorbate interactions, specifically, the lateral corrugation in the substrate-adsorbate interaction upon lateral displacement and rotation of the adsorbed BTP molecules. The fact that similar adlayer structures are obtained on HOPG under ultrahigh vacuum conditions (solid|gas interface) and on HOPG in trichlorobenzene (solid|liquid interface) indicates that the intermolecular interactions are not severely affected by the solvent.

  13. Dressed molecules in resonantly interacting ultracold atomic Fermi gases

    NARCIS (Netherlands)

    Falco, G.M.; Stoof, H.T.C.

    2007-01-01

    We present a detailed analysis of the two-channel atom-molecule effective Hamiltonian for an ultracold two-component homogeneous Fermi gas interacting near a Feshbach resonance. We particularly focus on the two-body and many-body properties of the dressed molecules in such a gas. An exact result

  14. Interaction of ultrashort pulses with molecules and solids: Physics ...

    Indian Academy of Sciences (India)

    2014-07-26

    energy materials. Abstract. The interaction of ultrashort laser pulses with molecules and solids is an extremely complex area of science research encompassing the fields of physics, chemistry, and materials science. The physics ...

  15. Controlling single-molecule junction conductance by molecular interactions

    Science.gov (United States)

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  16. Muon, positron and antiproton interactions with atoms and molecules

    Energy Technology Data Exchange (ETDEWEB)

    Armour, Edward A G, E-mail: edward.armour@nottingham.ac.u [School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD (United Kingdom)

    2010-04-01

    In this paper, a description is given of some interesting processes involving the interaction of a muon, a positron, or an antiproton with atoms and molecules. The process involving a muon is the resonant formation of the muonic molecular ion, dt{mu}, in the muon catalyzed fusion cycle. In the case of a positron, the process considered is positron annihilation in low-energy positron scattering by the hydrogen molecule. The antiproton is considered as the nucleus of an antihydrogen atom interacting with simple atoms. Attention is given to antiproton annihilation through the strong interaction. An outline is given of proposed tests of fundamental physics to be carried out using antihydrogen.

  17. The interaction of low-energy electrons with fructose molecules

    Science.gov (United States)

    Chernyshova, I. V.; Kontrosh, E. E.; Markush, P. P.; Shpenik, O. B.

    2017-11-01

    Using a hypocycloidal electronic spectrometer, the interactions of low energy electrons (0-8.50 eV) with fructose molecules, namely, electron scattering and dissociative attachment, are studied. The results of these studies showed that the fragmentation of fructose molecules occurs effectively even at an electron energy close to zero. In the total electron-scattering cross section by molecules, resonance features (at energies 3.10 and 5.00 eV) were first observed near the formation thresholds of light ion fragments OH- and H-. The correlation of the features observed in the cross sections of electron scattering and dissociative attachment is analyzed.

  18. The role of the ion-molecule and molecule-molecule interactions in the formation of the two-ion average force interaction potential

    CERN Document Server

    Ajrian, E A; Sidorenko, S N

    2002-01-01

    The effect of the ion-molecule and intermolecular interactions on the formation of inter-ion average force potentials is investigated within the framework of a classical ion-dipole model of electrolyte solutions. These potentials are shown to possess the Coulomb asymptotics at large distances while in the region of mean distances they reveal creation and disintegration of solvent-shared ion pairs. The calculation results provide a qualitatively authentic physical picture which is experimentally observed in strong electrolytes solutions. In particular, an increased interaction between an ion and a molecule enhances formation of ion pairs in which the ions are separated by one solvent molecule

  19. Reciprocal carbonyl-carbonyl interactions in small molecules and proteins.

    Science.gov (United States)

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

    2017-07-19

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

  20. Spin interactions in InAs quantum dots and molecules

    Energy Technology Data Exchange (ETDEWEB)

    Doty, M.F.; Ware, M.E.; Stinaff, E.A.; Scheibner, M.; Bracker, A.S.; Ponomarev, I.V.; Badescu, S.C.; Reinecke, T.L.; Gammon, D. [Naval Research Lab, Washington, DC 20375 (United States); Korenev, V.L. [A.F. Ioffe Physical Technical Institute, St. Petersburg 194021 (Russian Federation)

    2006-12-15

    Spin interactions between particles in quantum dots or quantum dot molecules appear as fine structure in the photoluminescence spectra. Using the understanding of exchange interactions that has been developed from single dot spectra, we analyze the spin signatures of coupled quantum dots separated by a wide barrier such that inter-dot interactions are negligible. We find that electron-hole exchange splitting is directly evident. In dots charged with an excess hole, an effective hole-hole interaction can be turned on through tunnel coupling. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  1. Multiply excited molecules produced by photon and electron interactions

    International Nuclear Information System (INIS)

    Odagiri, T.; Kouchi, N.

    2006-01-01

    The photon and electron interactions with molecules resulting in the formation of multiply excited molecules and the subsequent decay are subjects of great interest because the independent electron model and Born-Oppenheimer approximation are much less reliable for the multiply excited states of molecules than for the ground and lower excited electronic states. We have three methods to observe and investigate multiply excited molecules: 1) Measurements of the cross sections for the emission of fluorescence emitted by neutral fragments in the photoexcitation of molecules as a function of incident photon energy [1-3], 2) Measurements of the electron energy-loss spectra tagged with the fluorescence photons emitted by neutral fragments [4], 3) Measurements of the cross sections for generating a pair of photons in absorption of a single photon by a molecule as a function of incident photon energy [5-7]. Multiply excited states degenerate with ionization continua, which make a large contribution in the cross section curve involving ionization processes. The key point of our methods is hence that we measure cross sections free from ionization. The feature of multiply excited states is noticeable in such a cross section curve. Recently we have measured: i) the cross sections for the emission of the Lyman- fluorescence in the photoexcitation of CH 4 as a function of incident photon energy in the range 18-51 eV, ii) the electron energy-loss spectrum of CH 4 tagged with the Lyman-photons at 80 eV incident electron energy and 10 electron scattering angle in the range of the energy loss 20-45 eV, in order to understand the formation and decay of the doubly excited methane in photon and electron interactions. [8] The results are summarized in this paper and the simultaneous excitation of two electrons by electron interaction is compared with that by photon interaction in terms of the oscillator strength. (authors)

  2. Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Riley, Kevin Eugene; Hobza, Pavel

    2012-01-01

    Roč. 8, č. 11 (2012), s. 4285-4292 ISSN 1549-9618 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : halogenated molecules * noncovalent interactions * benchmark calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.389, year: 2012

  3. Modulation of intermolecular interactions in single-molecule magnets

    Science.gov (United States)

    Heroux, Katie Jeanne

    Polynuclear manganese clusters exhibiting interesting magnetic and quantum properties have been an area of intense research since the discovery of the first single-molecule magnet (SMM) in 1993. These molecules, below their blocking temperature, function as single-domain magnetic particles which exhibit classical macroscale magnetic properties as well as quantum mechanical phenomena such as quantum tunnelling of magnetization (QTM) and quantum phase interference. The union of classical and quantum behavior in these nanomaterials makes SMMs ideal candidates for high-density information storage and quantum computing. However, environmental coupling factors (nuclear spins, phonons, neighboring molecules) must be minimized if such applications are ever to be fully realized. The focus of this work is making small structural changes in well-known manganese SMMs in order to drastically enhance the overall magnetic and quantum properties of the system. Well-isolated molecules of high crystalline quality should lead to well-defined energetic and spectral properties as well. An advantage of SMMs over bulk magnetic materials is that they can be chemically altered from a "bottom-up" approach providing a synthetic tool for tuning magnetic properties. This systematic approach is utilized in the work presented herein by incorporating bulky ligands and/or counterions to "isolate" the magnetic core of [Mn4] dicubane SMMs. Reducing intermolecular interactions in the crystal lattice (neighboring molecules, solvate molecules, dipolar interactions) is an important step toward developing viable quantum computing devices. Detailed bulk magnetic studies as well as single crystal magnetization hysteresis and high-frequency EPR studies on these sterically-isolated complexes show enhanced, and sometimes even unexpected, quantum dynamics. The importance of intra- and intermolecular interactions remains a common theme throughout this work, extending to other SMMs of various topology including

  4. Determination of lateral interactions between NO molecules on Rh(111)

    International Nuclear Information System (INIS)

    Hagelaar, J H A; Flipse, C F J; Jansen, A P J

    2007-01-01

    In this study, the STM was used to locally study the adsorption of NO on a Rh(111) single crystal. Three new structures were identified. At 200 K, patches of the (4 x 2)-2NO and an unreported (2 x 2)-2NO structure were found at about 0.50ML coverage. Higher exposure gave rise to a (2 x 2)-3NO structure with all molecules adsorbed in the hcp sites. At 5K, a (4 x 4)-1NO structure was observed. The large separation between the molecules can only arise from repulsive interactions over a distance of at least four times the lattice constant (11 A). Here the interaction is estimated to be of the order of ∼10K or ∼0.1 kJ/mol. Dynamic Monte Carlo simulations taking into account adsorption, diffusion and pairwise interactions between adsorbates were used to fit the lateral interaction for the next-next nearest neighbor to the patched STM topograph at 200K for 0.50ML coverage. The value was determined to be 2 kJ/mol. Using pairwise interactions only (2 x 2)-3NO structure could not be explained. It might therefore be necessary to include three-particle interactions. Recent DFT calculations support this idea by showing attractive three-particle interactions

  5. Low-energy positron interactions with atoms and molecules

    International Nuclear Information System (INIS)

    Surko, C M; Gribakin, G F; Buckman, S J

    2005-01-01

    This paper is a review of low-energy positron interactions with atoms and molecules. Processes of interest include elastic scattering, electronic and vibrational excitation, ionization, positronium formation and annihilation. An overview is presented of the currently available theoretical and experimental techniques to study these phenomena, including the use of trap-based positron beam sources to study collision processes with improved energy resolution. State-resolved measurements of electronic and vibrational excitation cross sections and measurement of annihilation rates in atoms and molecules as a function of incident positron energy are discussed. Where data are available, comparisons are made with analogous electron scattering cross sections. Resonance phenomena, common in electron scattering, appear to be less common in positron scattering. Possible exceptions include the sharp onsets of positron-impact electronic and vibrational excitation of selected molecules. Recent energy-resolved studies of positron annihilation in hydrocarbons containing more than a few carbon atoms provide direct evidence that vibrational Feshbach resonances underpin the anomalously large annihilation rates observed for many polyatomic species. We discuss open questions regarding this process in larger molecules, as well as positron annihilation in smaller molecules where the theoretical picture is less clear. (topical review)

  6. Reactive oxygen species, essential molecules, during plant-pathogen interactions.

    Science.gov (United States)

    Camejo, Daymi; Guzmán-Cedeño, Ángel; Moreno, Alexander

    2016-06-01

    Reactive oxygen species (ROS) are continually generated as a consequence of the normal metabolism in aerobic organisms. Accumulation and release of ROS into cell take place in response to a wide variety of adverse environmental conditions including salt, temperature, cold stresses and pathogen attack, among others. In plants, peroxidases class III, NADPH oxidase (NOX) locates in cell wall and plasma membrane, respectively, may be mainly enzymatic systems involving ROS generation. It is well documented that ROS play a dual role into cells, acting as important signal transduction molecules and as toxic molecules with strong oxidant power, however some aspects related to its function during plant-pathogen interactions remain unclear. This review focuses on the principal enzymatic systems involving ROS generation addressing the role of ROS as signal molecules during plant-pathogen interactions. We described how the chloroplasts, mitochondria and peroxisomes perceive the external stimuli as pathogen invasion, and trigger resistance response using ROS as signal molecule. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  7. Small molecule inhibitors of bromodomain-acetyl-lysine interactions.

    Science.gov (United States)

    Brand, Michael; Measures, Angelina R; Measures, Angelina M; Wilson, Brian G; Cortopassi, Wilian A; Alexander, Rikki; Höss, Matthias; Hewings, David S; Rooney, Timothy P C; Paton, Robert S; Conway, Stuart J

    2015-01-16

    Bromodomains are protein modules that bind to acetylated lysine residues. Their interaction with histone proteins suggests that they function as "readers" of histone lysine acetylation, a component of the proposed "histone code". Bromodomain-containing proteins are often found as components of larger protein complexes with roles in fundamental cellular process including transcription. The publication of two potent ligands for the BET bromodomains in 2010 demonstrated that small molecules can inhibit the bromodomain-acetyl-lysine protein-protein interaction. These molecules display strong phenotypic effects in a number of cell lines and affect a range of cancers in vivo. This work stimulated intense interest in developing further ligands for the BET bromodomains and the design of ligands for non-BET bromodomains. Here we review the recent progress in the field with particular attention paid to ligand design, the assays employed in early ligand discovery, and the use of computational approaches to inform ligand design.

  8. Small molecule inhibitors target the tissue transglutaminase and fibronectin interaction.

    Directory of Open Access Journals (Sweden)

    Bakhtiyor Yakubov

    Full Text Available Tissue transglutaminase (TG2 mediates protein crosslinking through generation of ε-(γ-glutamyl lysine isopeptide bonds and promotes cell adhesion through interaction with fibronectin (FN and integrins. Cell adhesion to the peritoneal matrix regulated by TG2 facilitates ovarian cancer dissemination. Therefore, disruption of the TG2-FN complex by small molecules may inhibit cell adhesion and metastasis. A novel high throughput screening (HTS assay based on AlphaLISA™ technology was developed to measure the formation of a complex between His-TG2 and the biotinylated FN fragment that binds TG2 and to discover small molecules that inhibit this protein-protein interaction. Several hits were identified from 10,000 compounds screened. The top candidates selected based on >70% inhibition of the TG2/FN complex formation were confirmed by using ELISA and bioassays measuring cell adhesion, migration, invasion, and proliferation. In conclusion, the AlphaLISA bead format assay measuring the TG2-FN interaction is robust and suitable for HTS of small molecules. One compound identified from the screen (TG53 potently inhibited ovarian cancer cell adhesion to FN, cell migration, and invasion and could be further developed as a potential inhibitor for ovarian cancer dissemination.

  9. Collision of hydrogen molecules interacting with two grapheme sheets

    Directory of Open Access Journals (Sweden)

    Malivuk-Gak Dragana

    2017-01-01

    Full Text Available It have been performed the computational experiments with two hydrogen molecules and two graphene sheets. Hydrogen - hydrogen and hydrogen - carbon interactions are described by Lennard - Jones potential. Equations of motion of the wave packet centre are solved numerically. The initial molecule velocity was determined by temperature and collisions occur in central point between two sheets. The molecules after collision stay near or get far away of graphene sheets. Then one can find what temperatures, graphene sheet sizes and their distances are favourable for hydrogen storage. It is found that quantum corrections of the molecule classical trajectories are not significant here. Those investigations of possibility of hydrogen storage by physisorption are of interest for improvement of the fuel cell systems. The main disadvantages of computational experiments are: (1 it cannot compute with very large number of C atoms, (2 it is assumed that carbon atoms are placed always in their equilibrium positions and (3 the changes of wave packet width are not considered.

  10. Rotational dependence of Fermi-type resonance interactions in molecules

    Science.gov (United States)

    Mikhailov, Vladimir M.; Smirnov, M. A.

    1997-03-01

    In Pasadena, (Milliken Lab., USA, 1930) F. Rossetti has observed in Raman spectrum of carbon-dioxide molecule the full symmetric vibration of carbon dioxide appeared as the group of four near lying lines instead of the waited single line. The true interpretation of this enigmatic effect (in that time) was given by E. Fermi -- accidental degeneration of the first excited state of the full symmetric vibration in carbon dioxide. It was the first example of the event observed later in various organic molecules. This event was named as resonance Fermi. The rotational dependence of Fermi type resonance interactions in quasirigid molecules in dominant approximation can be selected in an expansion of the effective vibration-rotation Hamiltonian Hvib- roteff by the operator H(g)(Fermi) equals H30 plus (Sigma) nH3n(g). Let us consider in detail the problem of the construction of the effective vibration-rotational Hamiltonian HVR yields Heff from the point of view of various ordering schemes (grouping) of the vibrational-rotational interactions with sequential analysis of the choice of the convenient grouping adequate to the spectroscopic problem.

  11. Analysis of DNA interactions using single-molecule force spectroscopy.

    Science.gov (United States)

    Ritzefeld, Markus; Walhorn, Volker; Anselmetti, Dario; Sewald, Norbert

    2013-06-01

    Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

  12. Quasiparticle Approach to Molecules Interacting with Quantum Solvents.

    Science.gov (United States)

    Lemeshko, Mikhail

    2017-03-03

    Understanding the behavior of molecules interacting with superfluid helium represents a formidable challenge and, in general, requires approaches relying on large-scale numerical simulations. Here, we demonstrate that experimental data collected over the last 20 years provide evidence that molecules immersed in superfluid helium form recently predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001]. Most important, casting the many-body problem in terms of angulons amounts to a drastic simplification and yields effective molecular moments of inertia as straightforward analytic solutions of a simple microscopic Hamiltonian. The outcome of the angulon theory is in good agreement with experiment for a broad range of molecular impurities, from heavy to medium-mass to light species. These results pave the way to understanding molecular rotation in liquid and crystalline phases in terms of the angulon quasiparticle.

  13. Manipulating molecule-substrate exchange interactions via graphene

    Science.gov (United States)

    Bhandary, Sumanta; Eriksson, Olle; Sanyal, Biplab

    2013-03-01

    Organometallic molecules with a 3d metal center carrying a spin offers many interesting properties, e.g., existence of multiple spin states. A recent interest has been in understanding the magnetic exchange interaction between these organometallic molecules and magnetic substrates both from experiments and theory. In this work, we will show by calculations based on density functional theory how the exchange interaction is mediated via graphene in a geometry containing iron porphyrin(FeP)/graphene/Ni(111). The exchange interaction varies from a ferromagnetic to an antiferromagnetic one depending on the lattice site and type of defect in the graphene lattice along with the switching of spin state of Fe in FeP between S=1 and S=2, which should be detectable by x-ray magnetic circular dichroism experiments. This scenario of complex magnetic couplings with large magnetic moments may offer a unique spintronic logic device. We acknowledge financial support from the Swedish Research Council, KAW foundation and the ERC(project 247062 - ASD).

  14. Interaction between a "processed" ovalbumin peptide and Ia molecules

    DEFF Research Database (Denmark)

    Buus, S; Colon, S; Smith, C

    1986-01-01

    The binding of 125I-labeled immunogenic peptides to purified Ia molecules in detergent solution was examined by equilibrium dialysis. We used the chicken ovalbumin peptide ovalbumin-(323-339)-Tyr, which is immunogenic in the BALB/c mouse and restricted to I-Ad. 125I-labeled ovalbumin-(323-339)-Tyr......-Ak but not to I-Ek, I-Ad, or I-Ed. Thus, a specific interaction between Ia and antigen that correlates with the major histocompatibility complex restriction was demonstrated, strongly arguing in favor of a determinant selection hypothesis for such restriction....

  15. Coherent interaction of single molecules and plasmonic nanowires

    Science.gov (United States)

    Gerhardt, Ilja; Grotz, Bernhard; Siyushev, Petr; Wrachtrup, Jörg

    2017-09-01

    Quantum plasmonics opens the option to integrate complex quantum optical circuitry onto chip scale devices. In the past, often external light sources were used and nonclassical light was coupled in and out of plasmonic structures, such as hole arrays or waveguide structures. Another option to launch single plasmonic excitations is the coupling of single emitters in the direct proximity of, e.g., a silver or gold nanostructure. Here, we present our attempts to integrate the research of single emitters with wet-chemically grown silver nanowires. The emitters of choice are single organic dye molecules under cryogenic conditions, which are known to act as high-brightness and extremely narrow-band single photon sources. Another advantage is their high optical nonlinearity, such that they might mediate photon-photon interactions on the nanoscale. We report on the coupling of a single molecule fluorescence emission through the wire over the length of several wavelengths. The transmission of coherently emitted photons is proven by an extinction type experiment. As for influencing the spectral properties of a single emitter, we are able to show a remote change of the line-width of a single terrylene molecule, which is in close proximity to the nanowire.

  16. Spin interactions in Graphene-Single Molecule Magnets Hybrids

    Science.gov (United States)

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Aña; Luis, Fernando; Rauschenbach, Stephan; Dressel, Martin; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2014-03-01

    Graphene is a potential component of novel spintronics devices owing to its long spin diffusion length. Besides its use as spin-transport channel, graphene can be employed for the detection and manipulation of molecular spins. This requires an appropriate coupling between the sheets and the single molecular magnets (SMM). Here, we present a comprehensive characterization of graphene-Fe4 SMM hybrids. The Fe4 clusters are anchored non-covalently to the graphene following a diffusion-limited assembly and can reorganize into random networks when subjected to slightly elevated temperature. Molecules anchored on graphene sheets show unaltered static magnetic properties, whilst the quantum dynamics is profoundly modulated. Interaction with Dirac fermions becomes the dominant spin-relaxation channel, with observable effects produced by graphene phonons and reduced dipolar interactions. Coupling to graphene drives the spins over Villain's threshold, allowing the first observation of strongly-perturbative tunneling processes. Preliminary spin-transport experiments at low-temperature are further presented.

  17. Interactions of molecules and the properties of crystals

    Science.gov (United States)

    McConnell, Thomas Daniel Leigh

    In this thesis the basic theory of the lattice dynamics of molecular crystals is considered, with particular reference to the specific case of linear molecules. The objective is to carry out a critical investigation of a number of empirical potentials as models for real systems. Suitable coordinates are introduced, in particular vibrational coordinates which are used to describe the translational and rotational modes of the free molecule. The Taylor expansion of the intermolecular potential is introduced and its terms considered, in particular the (first-order) equilibrium conditions for such a system and the (second-order) lattice vibrations. The elastic properties are also considered, in particular with reference to the specific case of rhombohedral crystals. The compressibility and a number of conditions for elastic stability are introduced. The total intermolecular interaction potential is divided into three components using perturbation methods, the electrostatic energy, the repulsion energy and the dispersion energy. A number of models are introduced for these various components. The induction energy is neglected. The electrostatic interaction is represented by atomic multipole and molecular multipole models. The repulsion and dispersion energies are modelled together in a central interaction potential, either the Lennard-Jones atom-atom potential or the anisotropic Berne-Pechukas molecule-molecule potential. In each case, the Taylor expansion coefficients, used to calculate the various molecular properties, are determined. An algorithm is described which provides a relatively simple method for calculating cartesian tensors, which are found in the Taylor expansion coefficients of the multipolar potentials. This proves to be particularly useful from a computational viewpoint, both in terms of programming and calculating efficiency. The model system carbonyl sulphide is introduced and its lattice properties are described. Suitable parameters for potentials used

  18. Multiplex single-molecule interaction profiling of DNA barcoded proteins

    Science.gov (United States)

    Gu, Liangcai; Li, Chao; Aach, John; Hill, David E.; Vidal, Marc; Church, George M.

    2014-01-01

    In contrast with advances in massively parallel DNA sequencing1, high-throughput protein analyses2-4 are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule (SM) protein detection achieved using optical methods5 is limited by the number of spectrally nonoverlapping chromophores. Here, we introduce a single molecular interaction-sequencing (SMI-Seq) technology for parallel protein interaction profiling leveraging SM advantages. DNA barcodes are attached to proteins collectively via ribosome display6 or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide (PAA) thin film to construct a random SM array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies)7 and analyzed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimeter. Furthermore, protein interactions can be measured based on the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor (GPCR) and antibody binding profiling, were demonstrated. SMI-Seq enables “library vs. library” screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity. PMID:25252978

  19. HYDROGEN MOLECULE INTERACTION WITH CpCr(CO3 CATALYST

    Directory of Open Access Journals (Sweden)

    T. Spataru

    2013-12-01

    Full Text Available The hydrogen molecule interaction with CpCr (CO3 catalyst has been studied using the B3LYP, B86 functionals and the 6-311++G** , LACV3P basis sets. The best results in the testing calculations of the analyzed reaction have been obtained by using the B86/6-311++G** DFT version giving quite good agreement between experimental and theoretical calculated enthalpies. The dispersion corrected DFT Grimme’s and Head-Gordon and coworkers’functionals have been attempted without any improvement of the results. The free energies of the initial reactants, transition states, intermediate compounds and fi nal products of the typical six-ring bond modifi cation mechanism have been calculated. The energy barriersof the reaction pathways are too high in the DFT approximation.

  20. A study on interaction of DNA molecules and carbon nanotubes for an effective ejection of the molecules

    International Nuclear Information System (INIS)

    Wu, N.; Wang, Q.

    2012-01-01

    The ejection of DNA molecules from carbon nanotubes is reported from interaction energy perspectives by molecular dynamics simulations. The critical ejection energy, which is to be applied to a DNA molecule for a successful ejection from a carbon nanotube, is investigated based on a study on the friction and binding energy between the DNA molecule and the tube. An effective ejection is realized by subjecting a kinetic energy on the DNA molecule that is larger than the solved critical ejection energy. In addition, the relationship between ejection energies and sizes of DNA molecules and carbon nanotubes is investigated. -- Highlights: ► Report the ejection of DNA molecules from CNTs from interaction energy perspectives. ► Develop a methodology for the critical energy of an effective ejection of a DNA molecule from a CNT. ► Present the relationship between critical ejection energies and sizes of DNA molecules and CNTs. ► Provide a general guidance on the ejection of encapsulated molecules from CNTs.

  1. Fundamental properties of molecules on surfaces. Molecular switching and interaction of magnetic molecules with superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Hatter, Nino

    2016-12-14

    In this thesis, we investigate individual molecular switches and metal-organic complexes on surfaces with scanning tunneling microscopy (STM) and spectroscopy (STS) at low temperatures. One focus addresses the switching ability and mechanism of diarylethene on Ag(111). The other focus lies on resolving and tuning magnetic interactions of individual molecules with superconductors. 4,4'-(4,4'-(perfluorocyclopent-1-ene-1,2-diyl)bis (5-methylthiophene-4,2-diyl)dip yridine (PDTE) is a prototypical photochromic switch. We can induce a structural change of individual PDTE molecules on Ag(111) with the STM tip. This change is accompanied by a reduction of the energy gap between the occupied and unoccupied molecular orbitals. Density functional theory (DFT) calculations reveal that the induced switching corresponds to a ring-closing reaction from an open isomer in a flat adsorption configuration to a ring-closed isomer with its methyl groups in a cis configuration. The final product is thermodynamically stabilized by strong dispersion interactions with the surface. A linear dependence of the switching threshold with the tip-sample distance with a minimal threshold of 1.4 V is found, which we assign to a combination of an electric-field induced process and a tunneling-electron contribution. DFT calculations suggest a large activation barrier for a ring-closing reaction from the open flat configuration into the closed cis configuration. The interaction of magnetic molecules with superconductors is studied on manganese phthalocyanine (MnPc) adsorbed on Pb(111). We find triplets of Shiba states inside the superconducting gap. Different adsorption sites of MnPc provide a large variety of exchange coupling strengths, which lead to a collective energy shift of the Shiba triplets. We can assign the splitting of the Shiba states to be an effect of magnetic anisotropy in the system. A quantum phase transition from a ''Kondo screened'' to a &apos

  2. DNA-psoralen interaction: a single molecule experiment.

    Science.gov (United States)

    Rocha, M S; Viana, N B; Mesquita, O N

    2004-11-15

    By attaching one end of a single lambda-DNA molecule to a microscope coverslip and the other end to a polystyrene microsphere trapped by an optical tweezers, we can study the entropic elasticity of the lambda-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particularly interested in the effects of the photosensitive drug psoralen on the elasticity of the DNA molecule. We have illuminated the sample with different light sources, studying how the different wavelengths affect the psoralen-DNA linkage. To do this, we measure the persistence length of individual DNA-psoralen complexes.

  3. Interaction Between Hydrogen Molecules and a Closed Nanotube

    Directory of Open Access Journals (Sweden)

    Tarasov Egor

    2016-01-01

    Full Text Available The present paper assesses the state of low-energy molecules in the vicinity of the crystal structure of a closed nanotube. It is proposed to use the continuum description of the impact energy from carbon graphene structures. In this approach, a closed tube consists of an open part and two fullerene hemispheres. Calculations revealed that adsorption of gas molecules by surface crystals is not the case of capturing by a part of the nano-object surface, but that of involvement of molecules in a complex orbital motion around the particle.

  4. The formation and interactions of cold and ultracold molecules: new challenges for interdisciplinary physics

    Energy Technology Data Exchange (ETDEWEB)

    Dulieu, O [Laboratoire Aime Cotton, CNRS, Bat. 505, Univ Paris-Sud 11, F-91405 Orsay Cedex (France); Gabbanini, C [Istituto per i processi chimico-fisici del C.N.R., Via Moruzzi 1, 56124 Pisa (Italy)], E-mail: olivier.dulieu@lac.u-psud.fr, E-mail: carlo@ipcf.cnr.it

    2009-08-15

    Progress on research in the field of molecules at cold and ultracold temperatures is reported in this review. It covers extensively the experimental methods to produce, detect and characterize cold and ultracold molecules including association of ultracold atoms, deceleration by external fields and kinematic cooling. Confinement of molecules in different kinds of traps is also discussed. The basic theoretical issues related to the knowledge of the molecular structure, the atom-molecule and molecule-molecule mutual interactions, and to their possible manipulation and control with external fields, are reviewed. A short discussion on the broad area of applications completes the review.

  5. Rotation-vibrational spectra of diatomic molecules and nuclei with Davidson interactions

    CERN Document Server

    Rowe, D J

    1998-01-01

    Complete rotation-vibrational spectra and electromagnetic transition rates are obtained for Hamiltonians of diatomic molecules and nuclei with Davidson interactions. Analytical results are derived by dynamical symmetry methods for diatomic molecules and a liquid-drop model of the nucleus. Numerical solutions are obtained for a many-particle nucleus with quadrupole Davidson interactions within the framework of the microscopic symplectic model. (author)

  6. Dispersion interaction between an atom and linear molecule

    International Nuclear Information System (INIS)

    Carvalho, I.L. de

    1987-01-01

    The Jacobi-Csanak method is adapted to the calculation of the dipole-dipole, dipole-quadrupole, quadrupole-dipole, and quadrupole-quadrupole terms of the dispersion energy of an atom-linear molecule system. The angle-dependent parts of the Born amplitudes for the linear molecule are represented by real spherical harmonics. The dispersion energy is finite at all distances and reproduces the usual expression in the asymptotic region (R≥4.7 (angstrom)). In the intermediary region (2.4(angstrom) ≤ R [pt

  7. Studying small molecule-aptamer interactions using MicroScale Thermophoresis (MST).

    Science.gov (United States)

    Entzian, Clemens; Schubert, Thomas

    2016-03-15

    Aptamers are potent and versatile binding molecules recognizing various classes of target molecules. Even challenging targets such as small molecules can be identified and bound by aptamers. Studying the interaction between aptamers and drugs, antibiotics or metabolites in detail is however difficult due to the lack of sophisticated analysis methods. Basic binding parameters of these small molecule-aptamer interactions such as binding affinity, stoichiometry and thermodynamics are elaborately to access using the state of the art technologies. The innovative MicroScale Thermophoresis (MST) is a novel, rapid and precise method to characterize these small molecule-aptamer interactions in solution at microliter scale. The technology is based on the movement of molecules through temperature gradients, a physical effect referred to as thermophoresis. The thermophoretic movement of a molecule depends - besides on its size - on charge and hydration shell. Upon the interaction of a small molecule and an aptamer, at least one of these parameters is altered, leading to a change in the movement behavior, which can be used to quantify molecular interactions independent of the size of the target molecule. The MST offers free choice of buffers, even measurements in complex bioliquids are possible. The dynamic affinity range covers the pM to mM range and is therefore perfectly suited to analyze small molecule-aptamer interactions. This section describes a protocol how quantitative binding parameters for aptamer-small molecule interactions can be obtained by MST. This is demonstrated by mapping down the binding site of the well-known ATP aptamer DH25.42 to a specific region at the adenine of the ATP molecule. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Interaction of ultrashort pulses with molecules and solids: Physics

    Indian Academy of Sciences (India)

    2014-07-26

    Jul 26, 2014 ... The physics of interaction has been fairly understood over the last couple of decades and, consequently, several applications have been envisaged from these interactions in the fields of photonics, lithography, biomedicine, sensing, telecommunications etc. In the present article we describe three different ...

  9. Synthetic models related to DNA-intercalating molecules. Interactions between 8-alkoxypsoralen and adenine

    International Nuclear Information System (INIS)

    Decout, J.L.; Lhomme, J.

    1983-01-01

    To investigate the interactions and the photoreactions between furocoumarins and adenine, compounds in which a psoralen molecule is linked by different polymethylene bridges have been synthesised. Ring-ring intramolecular interactions are observed by UV spectroscopy. Thermodynamic parameters of these hydrophobic interactions are determined by the study of the variation of the hypochromic effect with temperature. (author)

  10. Isotope effects in interstellar molecules by chemical hyperfine interaction

    International Nuclear Information System (INIS)

    Haberkorn, R.; Michel-Beyerle, M.E.

    1977-01-01

    If free radicals recombine on grain surfaces, not only the different masses of isotopes but also their differing nuclear spin moments (e.g. 12 C/ 13 C, 14 N/ 15 N, 17 O/ 18 O) may imply variations in the recombination probability due to hyperfine interaction. This mechanism has not been accounted for so far. (orig.) [de

  11. Interaction of ultrashort pulses with molecules and solids: Physics ...

    Indian Academy of Sciences (India)

    ent applications resulting from such interactions in photonics and ... nonlinear optical (NLO) properties, figures-of-merit and, consequently, identify ..... ings and other photonic components in fibres, (c) creation of nanoaquarium for dynamic ... is to utilize the plasmonic nanostructures of Ag, Cu, and alloys prepared by ultrafast.

  12. Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu [Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390 (United States)

    2015-12-07

    We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence of a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.

  13. Electric dipole moment of diatomic molecules by configuration interaction. IV.

    Science.gov (United States)

    Green, S.

    1972-01-01

    The theory of basis set dependence in configuration interaction calculations is discussed, taking into account a perturbation model which is valid for small changes in the self-consistent field orbitals. It is found that basis set corrections are essentially additive through first order. It is shown that an error found in a previously published dipole moment calculation by Green (1972) for the metastable first excited state of CO was indeed due to an inadequate basis set as claimed.

  14. Molecular simulation of polar molecules interaction with MOFs family materials

    International Nuclear Information System (INIS)

    De Toni, M.

    2012-01-01

    The topic of this thesis is the adsorption of simple molecular fluids in nano-porous materials. Many industrial processes are based on this phenomenon, including ionic exchange, selective separation and heterogeneous catalysis. I used molecular simulation to study the adsorption properties of polar molecules of industrial interest (CO 2 and H 2 O) in a new class of crystalline microporous hybrid organic-inorganic materials called Metal-Organic Frameworks (MOFs). They have exceptional adsorption properties due to their topological variety and their versatility, allowed by the large range of possibilities offered by organic and coordination chemistry and functionalizations. I first studied the adsorption of CO 2 in a family of materials called IRMOFs, which share the same topology but have different porous volume, in order to characterize the effect of confinement on their adsorption performance. In particular, a general behavior has been highlighted: the critical temperature decreases when the confinement increases. Then, I looked at a recently synthesized cationic MOF called Zn2(CBTACN). After having localized the extra-framework halogen anions in the unit cell of the material, something which was not possible experimentally, I characterized CO 2 adsorption in this system first as a pure gas and then as a component of different mixtures. Finally, I was interested in the hydrothermal stability of MOFs, a crucial issue for their use in industrial applications. I observed the hydration mechanism of system that is analogous to the MOF-5 (IRMOF-0h) and shed light on some collaborative effects of the attack of water that were unknown to in the literature. (author)

  15. Flavonoids as Important Molecules of Plant Interactions with the Environment

    Directory of Open Access Journals (Sweden)

    Justyna Mierziak

    2014-10-01

    Full Text Available Flavonoids are small molecular secondary metabolites synthesized by plants with various biological activities. Due to their physical and biochemical properties, they are capable of participating in plants’ interactions with other organisms (microorganisms, animals and other plants and their reactions to environmental stresses. The majority of their functions result from their strong antioxidative properties. Although an increasing number of studies focus on the application of flavonoids in medicine or the food industry, their relevance for the plants themselves also deserves extensive investigations. This review summarizes the current knowledge on the functions of flavonoids in the physiology of plants and their relations with the environment.

  16. Ion-molecule interactions in crossed-beams

    International Nuclear Information System (INIS)

    Hansen, S.G.

    1980-09-01

    Interactions of the ions N + , F + , and CO 2 + with H 2 and/or its isotopes were examined using the crossed-beam technique in the low ( + ( 3 P) + H 2 → NH + + H, complex formation dominates up to 1.9 eV and a substantial interaction occurs between all collision partners up to 3.6 eV. The distribution of N + scattered nonreactively from H 2 also showed a long-lived complex channel below 1.9 eV. The reaction F + ( 3 P) + H 2 →FH + + H proceeded by a direct reaction mechanism at 0.20 to 1.07 eV. The reaction CO 2 + + D 2 → DCO 2 + + D gives asymmetric product distributions at 0.27 eV and above, indicating a direct reaction mechanism. Results indicated that there are probably barriers in the exit channels for DCO 2 + , DCO + , and D 2 O + products. The electronic state distributions of the N + , F + , and CO 2 + beams was investigated using beam attenuation and total luminescence techniques

  17. Interaction of He+2 ions with hydrogen molecules

    International Nuclear Information System (INIS)

    Afrosimov, V.V.; Leiko, G.A.; Panov, M.N.

    1980-01-01

    Cross sections for all elementary reactions involving a change in charge state in He +2 -H 2 collisions have been measured for He +2 kinetic energies in the range E=1.2--100 keV. Measurements were carried out by distinguishing an individual collision by a coincidence method and by simultaneously analyzing the charge states of the fast and slow particles. Furthermore, in the same event, the electronic states of the particles after the collision were determined by analyzing the kinetic energies of the resulting ions. The elementary reactions involving the formation of He + ions in the ground and excited states were studied. The reactions involving transitions in the hydrogen molecule to the 1ssigma/sub g/ and 2psigma/sub u/ states of H 2 + ions, and reactions in which wto protons are formed, were also studied. At E>15 keV, the largest cross section is that corresponding to one-electron capture: He +2 +H 2 →He + +H 2 + (this cross section is sigma=8.3 x 10 -16 cm 2 at E=50 keV). In this reaction, 90--98% of the He + ions are formed in excited states with principal quantum number n=2. At E + ion predominates, accompanied by the simultaneous dissociation of the H 2 + ion: He +2 +H 2 →He + (1s)+H + H+H0+e - . The cross section for this exothermic capture with dissociation (the energy released is ΔEapprox. =+36.3--3.8 eV) increases with decreasing energy E. At E>15 keV, an endothermic pathway is predominant: →He + (2s,2p)+H + +H+0+e - (the energy expended, ΔE, is more than 3.2 eV). The existence of two capture reactions with dissociation - exothermic and endothermic - leads to a minimum in the cross section for this reaction, at Eapprox. =15 keV. Ionization reactions and ionization with dissociation have the smallest cross sections

  18. A MOLECULAR DYNAMICS STUDY ON SLOW ION INTERACTIONS WITH THE POLYCYCLIC AROMATIC HYDROCARBON MOLECULE ANTHRACENE

    NARCIS (Netherlands)

    Postma, J.; Hoekstra, Ronnie; Tielens, A. G. G. M.; Schlathölter, Thomas

    2014-01-01

    Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on

  19. Interactions of the humoral pattern recognition molecule PTX3 with the complement system

    DEFF Research Database (Denmark)

    Doni, Andrea; Garlanda, Cecilia; Bottazzi, Barbara

    2012-01-01

    The innate immune system comprises a cellular and a humoral arm. The long pentraxin PTX3 is a fluid phase pattern recognition molecule, which acts as an essential component of the humoral arm of innate immunity. PTX3 has antibody-like properties including interactions with complement components....... PTX3 interacts with C1q, ficolin-1 and ficolin-2 as well as mannose-binding lectin, recognition molecules in the classical and lectin complement pathways. The formation of these heterocomplexes results in cooperative pathogen recognition and complement activation. Interactions with C4b binding protein...

  20. Interactions Between Charged Macroions Mediated by Molecules with Rod-like Charged Structures

    Directory of Open Access Journals (Sweden)

    Bohinc, K.

    2014-03-01

    Full Text Available A short review of recent theoretical advances in studies of the interaction between highly charged systems embedded in a solution of rod-like molecules is presented. The system is theoretically described by the functional density theory, where the correlations within the rod-like molecules are accounted for. We show that for sufficiently long molecules and large surface charge densities, an attractive force between like-charged surfaces arises due to the spatially distributed charges within the molecules. The added salt has an influence on the condition for the attractive force between like-charged surfaces. The theoretical results are compared with Monte Carlo simulations. Many phenomena motivate the study of the interaction between like-charged surfaces (DNA condensation, virus aggregation, yeast flocculation, cohesion of cement paste.

  1. Probing Enzyme-Surface Interactions via Protein Engineering and Single-Molecule Techniques

    Science.gov (United States)

    2017-06-26

    SECURITY CLASSIFICATION OF: The overall objective of this research was to exploit protein engineering and fluorescence single-molecule methods to...enhance our understanding of the interaction of proteins and surfaces. Given this objective, the specific aims of this research were to: 1) exploit the...incorporation of unnatural amino acids in proteins to introduce single-molecule probes (i.e., fluorophores for fluorescence resonance energy transfer

  2. Interaction of VUV-photons with molecules. Spectroscopy and dynamics of molecular superexcited states

    International Nuclear Information System (INIS)

    Hatano, Y.

    2002-01-01

    Complete text of publication follows. A survey is given of recent progress in experimental studies of the interaction of VUV-photons with molecules, i.e., those of photoabsorption, photoionization, and photodissociation of molecules in the excitation photon energy range of 10-50 eV, with a particular emphasis placed on current understanding of the spectroscopy and dynamics of formed molecular superexcited states. These studies are of great importance in understanding the interaction of ionizing radiation with matter. Molecules studied are ranged from simple diatomic and triatomic molecules to polyatomic molecules such as hydrocarbons. Most of the observed molecular superexcited states are assigned to high Rydber states which are vibrationally, doubly, or inner-core excited and converge to each of ion states. Non-Rydberg superexcited states are also observed. Dissociation into neutral fragments in comparison with ionization is of unexpectedly great importance in the observed decay of each of these state-assigned superexcited molecules. Dissociation dynamics as well as its products of superexcited states are remarkably different from those of lower excited states below about ionization thresholds. Some remarks are also presented of molecules in the condensed phase

  3. Interactions between nitrogen molecules and barium atoms on Ru (0001) surface

    International Nuclear Information System (INIS)

    Zhao Xinxin; Mi Yiming; Xu Hongxia; Wang Lili; Ren Li; Tao Xiangming; Tan Mingqiu

    2011-01-01

    We had performed first principles calculations on interactions between nitrogen molecules and barium atoms on Ru (0001) surface using density function theory methods. It was shown that effects of barium atoms weakened the bond strength of nitrogen molecules. The bond length of nitrogen molecule increases from 0.113 nm on Ru (001)-N 2 to 0.120 nm on Ru (001)-N 2 /Ba surface. While stretch vibrational frequency of nitrogen molecule decreased from 2222 cm -1 and charge transfer toward nitrogen molecule increased from 0.3 e to 1.1 e. Charge was mainly translated from 6 s orbitals of barium atoms to 4 d orbitals of substrate, which enhanced the hybridization between 4 d and 2 π orbitals and increased the dipole moment of 5 σ and d π orbitals of nitrogen molecule. The molecular dipole moment of nitrogen molecule was increased by -0.136 e Anstrom. It was suggested that barium had some characters to be an electronic promoter on the process of activating nitrogen molecules on Ru (0001) surface. (authors)

  4. Tuning the hybridization bandgap by meta-molecules with in-unit interaction

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yongqiang; Li, Yunhui, E-mail: liyunhui@tongji.edu.cn; Wu, Qian; Jiang, Haitao; Zhang, Yewen; Chen, Hong [Key Laboratory of Advanced Micro-Structured Materials, Ministry of Education, School of Physics Science and Engineering, Tongji University, Shanghai 200092 (China)

    2015-09-07

    In this paper, we demonstrate that the hybridization bandgap (HBG) can be tuned conveniently by deep subwavelength meta-molecules with in-unit interaction. Spontaneous-emission-cancellation-like (SEC-like) effect is realized in a meta-molecule by introducing the destructive interference of two detuned meta-atoms. The meta-atoms consisting of subwavelength zero-index-metamaterial-based resonators are side-coupled to a microstrip. Compared to conventional HBG configurations, the presence of in-unit interaction between meta-atoms provides more flexibility in tuning the bandgap properties, keeping the device volume almost unchanged. Both numerical simulations and microwave experiments confirm that the width, depth, and spectrum shape of HBG can be tuned by simply introducing SEC-like interaction into the meta-molecule. Due to these features, our design may be promising to be applied in microwave or optics communications systems with strict limitation of device volume and flexible bandgap properties.

  5. Concentration-related response potentiometric titrations to study the interaction of small molecules with large biomolecules.

    Science.gov (United States)

    Hamidi-Asl, Ezat; Daems, Devin; De Wael, Karolien; Van Camp, Guy; Nagels, Luc J

    2014-12-16

    In the present paper, the utility of a special potentiometric titration approach for recognition and calculation of biomolecule/small-molecule interactions is reported. This approach is fast, sensitive, reproducible, and inexpensive in comparison to the other methods for the determination of the association constant values (Ka) and the interaction energies (ΔG). The potentiometric titration measurement is based on the use of a classical polymeric membrane indicator electrode in a solution of the small-molecule ligand. The biomolecule is used as a titrant. The potential is measured versus a reference electrode and transformed into a concentration-related signal over the entire concentration interval, also at low concentrations, where the millivolt (y-axis) versus log canalyte (x-axis) potentiometric calibration curve is not linear. In the procedure, Ka is calculated for the interaction of cocaine with a cocaine binding aptamer and with an anticocaine antibody. To study the selectivity and cross-reactivity, other oligonucleotides and aptamers are tested, as well as other small ligand molecules such as tetrakis(4-chlorophenyl)borate, metergoline, lidocaine, and bromhexine. The calculated Ka compared favorably to the value reported in the literature using surface plasmon resonance. The potentiometric titration approach called "concentration-related response potentiometry" is used to study molecular interaction for seven macromolecular target molecules and four small-molecule ligands.

  6. Efficient Isothermal Titration Calorimetry Technique Identifies Direct Interaction of Small Molecule Inhibitors with the Target Protein.

    Science.gov (United States)

    Gal, Maayan; Bloch, Itai; Shechter, Nelia; Romanenko, Olga; Shir, Ofer M

    2016-01-01

    Protein-protein interactions (PPI) play a critical role in regulating many cellular processes. Finding novel PPI inhibitors that interfere with specific binding of two proteins is considered a great challenge, mainly due to the complexity involved in characterizing multi-molecular systems and limited understanding of the physical principles governing PPIs. Here we show that the combination of virtual screening techniques, which are capable of filtering a large library of potential small molecule inhibitors, and a unique secondary screening by isothermal titration calorimetry, a label-free method capable of observing direct interactions, is an efficient tool for finding such an inhibitor. In this study we applied this strategy in a search for a small molecule capable of interfering with the interaction of the tumor-suppressor p53 and the E3-ligase MDM2. We virtually screened a library of 15 million small molecules that were filtered to a final set of 80 virtual hits. Our in vitro experimental assay, designed to validate the activity of mixtures of compounds by isothermal titration calorimetry, was used to identify an active molecule against MDM2. At the end of the process the small molecule (4S,7R)-4-(4-chlorophenyl)-5-hydroxy-2,7-dimethyl-N-(6-methylpyridin-2-yl)-4,6,7,8 tetrahydrIoquinoline-3-carboxamide was found to bind MDM2 with a dissociation constant of ~2 µM. Following the identification of this single bioactive compound, spectroscopic measurements were used to further characterize the interaction of the small molecule with the target protein. 2D NMR spectroscopy was used to map the binding region of the small molecule, and fluorescence polarization measurement confirmed that it indeed competes with p53.

  7. Structural requirements for the interaction between class II MHC molecules and peptide antigens

    DEFF Research Database (Denmark)

    Sette, A; Buus, S; Appella, E

    1990-01-01

    of binding, it is possible to define certain structural features of peptides that are associated with the capacity to bind to a particular MHC specificity (IA(d) or IE(d)); 3) IA(d) and IE(d) molecules recognize different and independent structures on the antigen molecule; 4) only about 10% of the single...... IA(d) and IE(d) molecules and their peptide ligands, we found that some structural characteristics apply to both antigen-MHC interactions. In particular, we found: 1) each MHC molecule is capable of binding many unrelated peptides through the same peptide-binding site; 2) despite this permissiveness...... amino acid substitutions tested on two IA(d)- and IE(d)-binding peptides had significant effect on their MHC-binding capacities, while over 80% of these substitutions significantly impaired T cell recognition of the Ia-peptide complex; 5) based on the segregation between residues that are crucial for T...

  8. Single-Molecule Sensing with Nanopore Confinement: from Chemical Reactions to Biological Interactions.

    Science.gov (United States)

    Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

    2018-03-25

    The nanopore can generate an electrochemical confinement for single-molecule sensing which help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this concept, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Investigation into interaction of CO/sub 2/ molecules with zeolites by infrared spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ignat' eva, L A; Levshin, L V; Chukin, G D; Efimenko, L V; Kozlova, T I [Moskovskij Gosudarstvennyj Univ. (USSR). Kafedra Optiki

    1975-07-01

    Interaction of CO/sub 2/ molecules with zeolites, particularly with SrNaJ was studied by infrared-spectroscopy. To obtain infrared-spectra the zeolites were pressed into tablets and were calcinated at 500 deg. In the spectra the bands of chemisorbed CO/sub 2/ absorption were found in the range 1300 - 1600 cm/sup -1/. The CO/sub 2/ molecule was found to be strongly deformed due to chemisorption. In terms of electronic structure of the zeolite crystalline skeleton several types of CO/sub 2/ molecules interaction with different active zeolites were found. The position of the high-frequency band of CO/sub 2/ absorption in zeolites spectra was found to be a linear function of electrostatic field of the cations.

  10. Exploring Biomolecular Interactions Through Single-Molecule Force Spectroscopy and Computational Simulation

    OpenAIRE

    Yang, Darren

    2016-01-01

    Molecular interactions between cellular components such as proteins and nucleic acids govern the fundamental processes of living systems. Technological advancements in the past decade have allowed the characterization of these molecular interactions at the single-molecule level with high temporal and spatial resolution. Simultaneously, progress in computer simulation has enabled theoretical research at the atomistic level, assisting in the interpretation of experimental results. This thesi...

  11. Interactively Applying the Variational Method to the Dihydrogen Molecule: Exploring Bonding and Antibonding

    Science.gov (United States)

    Cruzeiro, Vinícius Wilian D.; Roitberg, Adrian; Polfer, Nicolas C.

    2016-01-01

    In this work we are going to present how an interactive platform can be used as a powerful tool to allow students to better explore a foundational problem in quantum chemistry: the application of the variational method to the dihydrogen molecule using simple Gaussian trial functions. The theoretical approach for the hydrogen atom is quite…

  12. Methylobacterium-plant interaction genes regulated by plant exudate and quorum sensing molecules

    Directory of Open Access Journals (Sweden)

    Manuella Nóbrega Dourado

    2013-12-01

    Full Text Available Bacteria from the genus Methylobacterium interact symbiotically (endophytically and epiphytically with different plant species. These interactions can promote plant growth or induce systemic resistance, increasing plant fitness. The plant colonization is guided by molecular communication between bacteria-bacteria and bacteria-plants, where the bacteria recognize specific exuded compounds by other bacteria (e.g. homoserine molecules and/or by the plant roots (e.g. flavonoids, ethanol and methanol, respectively. In this context, the aim of this study was to evaluate the effect of quorum sensing molecules (N-acyl-homoserine lactones and plant exudates (including ethanol in the expression of a series of bacterial genes involved in Methylobacterium-plant interaction. The selected genes are related to bacterial metabolism (mxaF, adaptation to stressful environment (crtI, phoU and sss, to interactions with plant metabolism compounds (acdS and pathogenicity (patatin and phoU. Under in vitro conditions, our results showed the differential expression of some important genes related to metabolism, stress and pathogenesis, thereby AHL molecules up-regulate all tested genes, except phoU, while plant exudates induce only mxaF gene expression. In the presence of plant exudates there is a lower bacterial density (due the endophytic and epiphytic colonization, which produce less AHL, leading to down regulation of genes when compared to the control. Therefore, bacterial density, more than plant exudate, influences the expression of genes related to plant-bacteria interaction.

  13. High-intensity X-rays interaction with matter processes in plasmas, clusters, molecules and solids

    CERN Document Server

    Hau-Riege, Stefan P

    2012-01-01

    Filling the need for a book bridging the effect of matter on X-ray radiation and the interaction of x-rays with plasmas, this monograph provides comprehensive coverage of the topic. As such, it presents and explains such powerful new X-ray sources as X-ray free-electron lasers, as well as short pulse interactions with solids, clusters, molecules, and plasmas, and X-ray matter interactions as a diagnostic tool. Equally useful for researchers and practitioners working in the field.

  14. Mode selectivity in cluster-molecule interactions: Ni13 + D2

    International Nuclear Information System (INIS)

    Jellinek, J.; Guevenc, Z.B.

    1991-01-01

    Results of a detailed quasiclassical simulation study of the Ni 13 + D 2 collision system are presented. The dissociative adsorption of the molecule as well as its scattering from the cluster are analyzed as functions of the initial rovibrational molecular state, collision energy and structure of the cluster. Mode-specific features of the reactive and nonreactive channels of the cluster-molecule interaction are displayed and discussed. Evidence for resonances and for a strong cluster structure-reactivity correlation is presented. 13 refs., 6 figs

  15. Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

    Science.gov (United States)

    Gu, Liangcai; Li, Chao; Aach, John; Hill, David E; Vidal, Marc; Church, George M

    2014-11-27

    In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by the number of spectrally non-overlapping chromophores. Here we introduce a single-molecular-interaction sequencing (SMI-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide thin film to construct a random single-molecule array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies) and analysed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimetre. Furthermore, protein interactions can be measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor and antibody-binding profiling, are demonstrated. SMI-seq enables 'library versus library' screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity.

  16. Biophysics of DNA-Protein Interactions From Single Molecules to Biological Systems

    CERN Document Server

    Williams, Mark C

    2011-01-01

    This book presents a concise overview of current research on the biophysics of DNA-protein interactions. A wide range of new and classical methods are presented by authors investigating physical mechanisms by which proteins interact with DNA. For example, several chapters address the mechanisms by which proteins search for and recognize specific binding sites on DNA, a process critical for cellular function. Single molecule methods such as force spectroscopy as well as fluorescence imaging and tracking are described in these chapters as well as other parts of the book that address the dynamics of protein-DNA interactions. Other important topics include the mechanisms by which proteins engage DNA sequences and/or alter DNA structure. These simple but important model interactions are then placed in the broader biological context with discussion of larger protein-DNA complexes . Topics include replication forks, recombination complexes, DNA repair interactions, and ultimately, methods to understand the chromatin...

  17. Density functional study the interaction of oxygen molecule with defect sites of graphene

    Energy Technology Data Exchange (ETDEWEB)

    Qi Xuejun [State Key Laboratory of Coal Combustion, Wuhan 430074 (China); Guo Xin, E-mail: guoxin@mail.hust.edu.cn [State Key Laboratory of Coal Combustion, Wuhan 430074 (China); Zheng Chuguang [State Key Laboratory of Coal Combustion, Wuhan 430074 (China)

    2012-10-15

    Highlights: Black-Right-Pointing-Pointer The defect sites existed on the graphite surface create active sites and enhance the reactivity of carbonaceous material. Black-Right-Pointing-Pointer Oxygen molecule more favor chemisorbed on the graphene surface contains defect sites than the perfect surface. Black-Right-Pointing-Pointer The single active oxygen atom adsorbed on the defect surfaces, it completely insert into the surface. - Abstract: The present article reports a theoretical study of oxygen interacted with graphene surface containing defect sites on the atomic level by employing the density functional theory combined with the graphene cluster model. It was founded that oxygen molecule prefers to be chemisorbed on the graphene surface containing defect sites compared to the perfect surface. The adsorption energy of O{sub 2} on the double defect site is about 2.5 times as large as that on the perfect graphene surface. Moreover, the oxygen molecule interacts with S-W defect site gives rise to stable epoxy structure, which pulling the carbon atom outward from the original site in the direction perpendicular to the surface. If the oxygen molecule is adsorbed on the single vacancy site, two C-O bonds are formed on the graphene surface. However, when the oxygen molecule is chemisorbed on the double vacancy site, the oxygen atoms substitute the missing carbon atom's position in the carbon plane and form a hexagonal structure on the graphene network. The results indicate that single active oxygen atom approaches the defect site, it's completely adsorbed in the plane and high energy is released. In all cases, the interaction of an oxygen atom with defect surface involves an exothermic process. The defect site creates active sites on the surface of graphene and produces catalytic effects during the process of oxidation of carbonaceous materials.

  18. Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules.

    Science.gov (United States)

    Mondal, Saptarsi; Chaterjee, Soumit; Halder, Ritaban; Jana, Biman; Singh, Prashant Chandra

    2017-08-17

    Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.

  19. Trapping and interactions of an ultracold gas of Cs2 molecules

    International Nuclear Information System (INIS)

    Mark, M.; Kraemer, T.; Herbig, J.; Waldburger, P.; Naegerl, H.C.; Chin, C.; Grimm, R.

    2005-01-01

    Full text: We investigate dynamics and interactions of Cs 2 dimers in a CO2-laser dipole trap. Starting with a Bose-Einstein condensate (BEC) of 2.2 x 10 5 Cs atoms, we create ultracold molecules in a single, weakly bound quantum state by sweeping the magnetic field across a narrow Feshbach resonance. When the molecules are created in free space, the conversion efficiency exceeds 30 %, yielding up to 50000 molecules. In our trapping experiments, about 6000 ultracold Cs 2 dimers are prepared in the optical trap at a temperature of 200 nK. We transfer the trapped molecules from the initial molecular state to other molecular states by following avoided crossings. We find two magnetically tunable resonances in collisions between the molecules for one of the molecular states. We interpret these Feshbach-liKEX resonances as being induced by Cs 4 bound states near the molecular scattering continuum. Further, we have discovered a new molecular state with very large orbital angular momentum of l = 8. This state is very weakly coupled to one of the initial molecular states. We use the associated avoided crossing as a molecular beam splitter to realize a molecular Ramsey-type interferometer. Refs. 2 (author)

  20. Temperature-dependent interaction potential between NF3 molecules and thermophysical properties of gaseous NF3

    International Nuclear Information System (INIS)

    Damyanova, M; Balabanova, E; Hohm, U

    2014-01-01

    A temperature-dependent effective intermolecular interaction potential is applied to describe the interaction between two nitrogen fluoride (NF 3 ) molecules in gas phase. To this end, a spherically-symmetric (n-6) Lennard-Jones temperature-dependent potential (LJTDP) is used. The (n-6) LJTDP takes into account the influence of vibrational excitation of the molecules on the potential parameters, namely, the equilibrium distance r m and the potential well depth ε. The potential parameters at T = 0 K were obtained from the very small amount of existing thermophysical equilibrium and transport properties of low-density NF 3 gas. Fitting formulae are tabulated for a fast and reliable prediction of the thermophysical properties and potential parameters in the temperature range between 200 K and 1200 K. A comparison is also presented between our estimates for some thermophysical properties of the NF 3 gas with the available experimental and calculated data.

  1. Inelastic transitions of atoms and molecules induced by van der Waals interaction with a surface

    International Nuclear Information System (INIS)

    Baudon, J.; Hamamda, M.; Boustimi, M.; Bocvarski, V.; Taillandier-Loize, T.; Dutier, G.; Perales, F.; Ducloy, M.

    2012-01-01

    Inelastic processes occuring in thermal-velocity metastable atoms and molecules passing at a mean distance (1–100 nm) are investigated. These processes are caused by the quadrupolar part of the van der Waals interaction: fine-structure transitions in atoms (Ar ∗ , Kr ∗ ), rovibrational transitions in N 2 ∗ ( 3 Σ u + ), transitions among magnetic sub-levels in the presence of a magnetic field.

  2. Nature of chalcogen hor ellipsis chalcogen contact interactions in organic donor-molecule salts

    Energy Technology Data Exchange (ETDEWEB)

    Novoa, J.J.; Whangbo, Myung-Hwan (North Carolina State Univ., Raleigh, NC (USA). Dept. of Chemistry); Williams, J.M. (Argonne National Lab., IL (USA))

    1990-01-01

    The nature of chalcogen{hor ellipsis}chalcogen contact interactions in organic donor-molecule salts was examined by performing ab initio SCF-MO/MP2 calculations on H{sub 2}X{hor ellipsis}XH{sub 2}(X = O, S, SE, Te) and MM2 calculations on donor dimers (TXF){sub 2} (X = S, SE, Te) and (BEDX-TTF){sub 2} (X = O, S). 14 refs., 4 figs., 4 tabs.

  3. Confined Catalysis in the g-C3N4/Pt(111) Interface: Feasible Molecule Intercalation, Tunable Molecule-Metal Interaction, and Enhanced Reaction Activity of CO Oxidation.

    Science.gov (United States)

    Wang, Shujiao; Feng, Yingxin; Yu, Ming'an; Wan, Qiang; Lin, Sen

    2017-09-27

    The deposition of a two-dimensional (2D) atomic nanosheet on a metal surface has been considered as a new route for tuning the molecule-metal interaction and surface reactivity in terms of the confinement effect. In this work, we use first-principles calculations to systematically explore a novel nanospace constructed by placing a 2D graphitic carbon nitride (g-C 3 N 4 ) nanosheet over a Pt(111) surface. The confined catalytic activity in this nanospace is investigated using CO oxidation as a model reaction. With the inherent triangular pores in the g-C 3 N 4 overlayer being taken advantage of, molecules such as CO and O 2 can diffuse to adsorb on the Pt(111) surface underneath the g-C 3 N 4 overlayer. Moreover, the mechanism of intercalation is also elucidated, and the results reveal that the energy barrier depends mainly on the properties of the molecule and the channel. Importantly, the molecule-catalyst interaction can be tuned by the g-C 3 N 4 overlayer, considerably reducing the adsorption energy of CO on Pt(111) and leading to enhanced reactivity in CO oxidation. This work will provide important insight for constructing a promising nanoreactor in which the following is observed: The molecule intercalation is facile; the molecule-metal interaction is efficiently tuned; the metal-catalyzed reaction is promoted.

  4. Structural Analysis of ‘key’ Interactions in Functional RNA Molecules

    KAUST Repository

    Chawla, Mohit

    2018-04-01

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

  5. Structural Analysis of ‘key’ Interactions in Functional RNA Molecules

    KAUST Repository

    Chawla, Mohit

    2018-01-01

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

  6. STITCH 2: an interaction network database for small molecules and proteins

    DEFF Research Database (Denmark)

    Kuhn, Michael; Szklarczyk, Damian; Franceschini, Andrea

    2010-01-01

    Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug......-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other...... chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74,000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/....

  7. Strength of interactions between immobilized dye molecules and sol-gel matrices.

    Science.gov (United States)

    Ismail, Fanya; Schoenleber, Monika; Mansour, Rolan; Bastani, Behnam; Fielden, Peter; Goddard, Nicholas J

    2011-02-21

    In this paper we present a new theory to re-examine the immobilization technique of dye doped sol-gel films, define the strength and types of possible bonds between the immobilized molecule and sol-gel glass, and show that the immobilized molecule is not free inside the pores as was previously thought. Immobilizing three different pH sensitive dyes with different size and functional groups inside the same sol-gel films revealed important information about the nature of the interaction between the doped molecule and the sol-gel matrix. The samples were characterized by means of ultraviolet-visible spectrophotometer (UV-VIS), thermal gravimetric analysis (TGA), mercury porosimetry (MP), nuclear magnetic resonance spectroscopy ((29)Si NMR) and field-emission environmental scanning electron microscopy (ESEM-FEG). It was found that the doped molecule itself has a great effect on the strength and types of the bonds. A number of factors were identified, such as number and types of the functional groups, overall charge, size, pK(a) and number of the silanol groups which surround the immobilized molecule. These results were confirmed by the successful immobilization of bromocresol green (BCG) after a completely polymerized sol-gel was made. The sol-gel consisted of 50% tetraethoxysilane (TEOS) and 50% methyltriethoxysilane (MTEOS) (w/w). Moreover, the effect of the immobilized molecule on the structure of the sol-gel was studied by means of a leaky waveguide (LW) mode for doped films made before and after polymerization of the sol-gel.

  8. Single NdPc{sub 2} molecules on surfaces. Adsorption, interaction, and molecular magnetism

    Energy Technology Data Exchange (ETDEWEB)

    Fahrendorf, Sarah

    2013-01-24

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc{sub 2}) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc{sub 2}) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc{sub 2} molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the

  9. Single NdPc2 molecules on surfaces. Adsorption, interaction, and molecular magnetism

    International Nuclear Information System (INIS)

    Fahrendorf, Sarah

    2013-01-01

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc 2 ) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc 2 ) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc 2 molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the spin

  10. EVAPORATION: a new vapour pressure estimation methodfor organic molecules including non-additivity and intramolecular interactions

    Directory of Open Access Journals (Sweden)

    S. Compernolle

    2011-09-01

    Full Text Available We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects, a method to predict (subcooled liquid pure compound vapour pressure p0 of organic molecules that requires only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: aldehydes, ketones, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA.

  11. Ligand-regulated peptides: a general approach for modulating protein-peptide interactions with small molecules.

    Science.gov (United States)

    Binkowski, Brock F; Miller, Russell A; Belshaw, Peter J

    2005-07-01

    We engineered a novel ligand-regulated peptide (LiRP) system where the binding activity of intracellular peptides is controlled by a cell-permeable small molecule. In the absence of ligand, peptides expressed as fusions in an FKBP-peptide-FRB-GST LiRP scaffold protein are free to interact with target proteins. In the presence of the ligand rapamycin, or the nonimmunosuppressive rapamycin derivative AP23102, the scaffold protein undergoes a conformational change that prevents the interaction of the peptide with the target protein. The modular design of the scaffold enables the creation of LiRPs through rational design or selection from combinatorial peptide libraries. Using these methods, we identified LiRPs that interact with three independent targets: retinoblastoma protein, c-Src, and the AMP-activated protein kinase. The LiRP system should provide a general method to temporally and spatially regulate protein function in cells and organisms.

  12. Interaction between vegetable oil based plasticizer molecules and polyvinyl chloride, and their plasticization effect

    Science.gov (United States)

    Haryono, Agus; Triwulandari, Evi; Jiang, Pingping

    2017-01-01

    Plasticizer molecules are low molecular weight compounds that are widely used in polymer industries especially in polyvinyl chloride (PVC) resin. As an additive in PVC resin, the important role of plasticizer molecules is to improve the flexibility and processability of PVC by lowering the glass transition temperature (Tg). However, the commercial plasticizer like di(2-ethylhexyl)phthalate (DEHP) is known to cause liver cancer, at least in laboratory rats. DEHP can leach out from PVC into blood, certain drug solutions and fatty foods, which has been detected in the bloodstream of patients undergoing transfusion. Vegetable oil based plasticizers have some attractive properties such as non-toxic, bio-degradable, good heat and light stability, renewable resources, and environmentally friendly. Here we discussed the main results and development of vegetable oil based plasticizer, and especially palm oil based plasticizer. The interaction between plasticizer and polymer was discussed from the properties of the plasticized polymeric material.

  13. Interplay of radiative and nonradiative transitions in surface hopping with radiation-molecule interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bajo, Juan José [Departamento de Química-Física I, Universidad Complutense de Madrid, 28040 Madrid (Spain); Granucci, Giovanni, E-mail: giovanni.granucci@unipi.it; Persico, Maurizio [Università di Pisa, Dipartimento di Chimica e Chimica Industriale, via Risorgimento 35, 56126 Pisa (Italy)

    2014-01-28

    We implemented a method for the treatment of field induced transitions in trajectory surface hopping simulations, in the framework of the local diabatization scheme, especially suited for on-the-fly dynamics. The method is applied to a simple one-dimensional model with an avoided crossing and compared with quantum wavepacket dynamics. The results show the importance of introducing a proper decoherence correction to surface hopping, in order to obtain meaningful results. Also the energy conservation policy of standard surface hopping must be revised: in fact, the quantum wavepacket energetics is well reproduced if energy absorption/emission is allowed for in the hops determined by radiation-molecule coupling. To our knowledge, this is the first time the issues of decoherence and energy conservation have been analyzed in depth to devise a mixed quantum-classical method for dynamics with molecule-field interactions.

  14. Stability of metal organic frameworks and interaction of small gas molecules in these materials

    Science.gov (United States)

    Tan, Kui

    The work in this dissertation combines spectroscopy ( in-situ infrared absorption and Raman), powder X-ray diffraction and DFT calculations to study the stability of metal organic frameworks materials (MOFs) in the presence of water vapor and other corrosive gases (e.g., SO 2, NO2 NO), and the interaction and competitive co-adsorption of several gases within MOFs by considering two types of prototypical MOFs: 1) a MOF with saturated metal centers based on paddlewheel secondary building units: M(bdc)(ted)0.5 [M=Cu, Zn, Ni, Co, bdc = 1,4-benzenedicarboxylate, ted = triethylenediamine], and 2) a MOF with unsaturated metal centers: M2(dobdc) [M=Mg2+, Zn2+, Ni2+, Co2+ and dobdc = 2,5-dihydroxybenzenedicarboxylate]. We find that the stability of MOFs to water vapor critically depends on their structure and the specific metal cation in the building units. For M(bdc)(ted)0.5, the metal-bdc bond is the most vulnerable for Cu(bdc)(ted)0.5, while the metal-ted bond is first attacked for the Zn and Co analogs. In contrast, Ni(bdc)(ted)0.5 remains stable under the same conditions. For M2(dobdc), or MOF-74, the weak link is the dobdc-metal bond. The water molecule is dissociatively adsorbed at the metal-oxygen group with OH adsorption directly on the metal center and H adsorption on the bridging O of the phenolate group in the dobdc linker. Other technologically important molecules besides water, such as NO, NO2, SO2, tend to poison M2(dobdc) through dissociative or molecular adsorption onto the open metal sites. A high uptake SO2 capacity was measured in M(bdc)(ted)0.5, attributed to multipoint interactions between the guest SO2 molecule and the MOF host. In the case of competitive co-adsorption between CO2 and other small molecules, we find that binding energy alone is not a good indicator of molecular site occupation within the MOF (i.e., it cannot successfully predict and evaluate the displacement of CO2 by other molecules). Instead, we show that the kinetic barrier for the

  15. Spin-interaction effects for ultralong-range Rydberg molecules in a magnetic field

    Science.gov (United States)

    Hummel, Frederic; Fey, Christian; Schmelcher, Peter

    2018-04-01

    We investigate the fine and spin structure of ultralong-range Rydberg molecules exposed to a homogeneous magnetic field. Each molecule consists of a 87Rb Rydberg atom the outer electron of which interacts via spin-dependent s - and p -wave scattering with a polarizable 87Rb ground-state atom. Our model includes also the hyperfine structure of the ground-state atom as well as spin-orbit couplings of the Rydberg and ground-state atom. We focus on d -Rydberg states and principal quantum numbers n in the vicinity of 40. The electronic structure and vibrational states are determined in the framework of the Born-Oppenheimer approximation for varying field strengths ranging from a few up to hundred Gauss. The results show that the interplay between the scattering interactions and the spin couplings gives rise to a large variety of molecular states in different spin configurations as well as in different spatial arrangements that can be tuned by the magnetic field. This includes relatively regularly shaped energy surfaces in a regime where the Zeeman splitting is large compared to the scattering interaction but small compared to the Rydberg fine structure, as well as more complex structures for both weaker and stronger fields. We quantify the impact of spin couplings by comparing the extended theory to a spin-independent model.

  16. Self-interaction corrections applied to Mg-porphyrin, C{sub 60}, and pentacene molecules

    Energy Technology Data Exchange (ETDEWEB)

    Pederson, Mark R. [Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Baruah, Tunna; Basurto, Luis [Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968 (United States); Kao, Der-you [Department of Mechanical and Aerospace Engineering, George Washington University, Washington, DC 20052 (United States)

    2016-04-28

    We have applied a recently developed method to incorporate the self-interaction correction through Fermi orbitals to Mg-porphyrin, C{sub 60}, and pentacene molecules. The Fermi-Löwdin orbitals are localized and unitarily invariant to the Kohn-Sham orbitals from which they are constructed. The self-interaction-corrected energy is obtained variationally leading to an optimum set of Fermi-Löwdin orbitals (orthonormalized Fermi orbitals) that gives the minimum energy. A Fermi orbital, by definition, is dependent on a certain point which is referred to as the descriptor position. The degree to which the initial choice of descriptor positions influences the variational approach to the minimum and the complexity of the energy landscape as a function of Fermi-orbital descriptors is examined in detail for Mg-porphyrin. The applications presented here also demonstrate that the method can be applied to larger molecular systems containing a few hundred electrons. The atomization energy of the C{sub 60} molecule within the Fermi-Löwdin-orbital self-interaction-correction approach is significantly improved compared to local density approximation in the Perdew-Wang 92 functional and generalized gradient approximation of Perdew-Burke-Ernzerhof functionals. The eigenvalues of the highest occupied molecular orbitals show qualitative improvement.

  17. Self-interaction corrections applied to Mg-porphyrin, C60, and pentacene molecules

    International Nuclear Information System (INIS)

    Pederson, Mark R.; Baruah, Tunna; Basurto, Luis; Kao, Der-you

    2016-01-01

    We have applied a recently developed method to incorporate the self-interaction correction through Fermi orbitals to Mg-porphyrin, C 60 , and pentacene molecules. The Fermi-Löwdin orbitals are localized and unitarily invariant to the Kohn-Sham orbitals from which they are constructed. The self-interaction-corrected energy is obtained variationally leading to an optimum set of Fermi-Löwdin orbitals (orthonormalized Fermi orbitals) that gives the minimum energy. A Fermi orbital, by definition, is dependent on a certain point which is referred to as the descriptor position. The degree to which the initial choice of descriptor positions influences the variational approach to the minimum and the complexity of the energy landscape as a function of Fermi-orbital descriptors is examined in detail for Mg-porphyrin. The applications presented here also demonstrate that the method can be applied to larger molecular systems containing a few hundred electrons. The atomization energy of the C 60 molecule within the Fermi-Löwdin-orbital self-interaction-correction approach is significantly improved compared to local density approximation in the Perdew-Wang 92 functional and generalized gradient approximation of Perdew-Burke-Ernzerhof functionals. The eigenvalues of the highest occupied molecular orbitals show qualitative improvement.

  18. A theoretical and experimental investigation of the interaction between gas molecules and cryogenic surfaces

    International Nuclear Information System (INIS)

    Varlam, M.; Steflea, D.; Chiriloaie, N.

    1992-01-01

    The cryo-pumping performance of a cryo-surface subjected to the impingement of low-pressure, thermal-velocity air flow is experimentally and theoretically investigated. Our purpose is to determine the angular dependence of capture coefficients for gas molecules incident on a cryogenic surface under conditions closely approximating those prevailing in cryo-pumped high vacuum chambers. The classical model for the interaction of gas atoms and the solid surface - the 'soft-tube' model - is developed and the basic assumption are examined. Starting from this theory we have calculated the capture coefficient of the Ag - N system and these values are discussed in terms of principal parameters considered. Despite the many simplifying assumptions, this model has the important attribute that it yields closed-form expressions for the capture coefficient of gas molecules. The molecular beam technique offers a direct experimental method for determining the capture coefficient for molecules with given angles of incidence by measuring the incident and reflected molecular fluxes. An experimental setup is also designed and the method for determining these coefficients is proposed. (Author)

  19. Hypertonic saline impedes tumor cell-endothelial cell interaction by reducing adhesion molecule and laminin expression.

    LENUS (Irish Health Repository)

    Shields, Conor J

    2012-02-03

    BACKGROUND: Hypertonic saline infusion dampens inflammatory responses and suppresses neutrophil-endothelial interaction by reducing adhesion molecule expression. This study tested the hypothesis that hypertonic saline attenuates tumor cell adhesion to the endothelium through a similar mechanism. METHODS: Human colon cancer cells (LS174T) were transfected with green fluorescent protein and exposed to lipopolysaccharide, tumor necrosis factor-alpha, and interleukin-6 under hypertonic and isotonic conditions for 1 and 4 hours. Confluent human umbilical vein endothelial cells were similarly exposed. Cellular apoptosis and expression of adhesion molecules and laminin were measured by flow cytometry. Tumor cell adhesion to endothelium and laminin was assessed with fluorescence microscopy. Data are represented as mean +\\/- standard error of mean, and an ANOVA test was performed to gauge statistical significance, with P <.05 considered significant. RESULTS: Hypertonic exposure significantly reduced tumor cell adhesion despite the presence of the perioperative cell stressors (42 +\\/- 2.9 vs 172.5 +\\/- 12.4, P <.05), attenuated tumor cell beta-1 integrin (14.43 vs 23.84, P <.05), and endothelial cell laminin expression (22.78 +\\/- 2.2 vs 33.74 +\\/- 2.4, P <.05), but did not significantly alter cell viability. CONCLUSION: Hypertonic saline significantly attenuates tumor cell adhesion to endothelium by inhibiting adhesion molecule and laminin expression. This may halt the metastatic behavior of tumor cells shed at surgery.

  20. Single Molecule Science for Personalized Nanomedicine: Atomic Force Microscopy of Biopolymer-Protein Interactions

    Science.gov (United States)

    Hsueh, Carlin

    Nanotechnology has a unique and relatively untapped utility in the fields of medicine and dentistry at the level of single-biopolymer and -molecule diagnostics. In recent years atomic force microscopy (AFM) has garnered much interest due to its ability to obtain atomic-resolution of molecular structures and probe biophysical behaviors of biopolymers and proteins in a variety of biologically significant environments. The work presented in this thesis focuses on the nanoscale manipulation and observation of biopolymers to develop an innovative technology for personalized medicine while understanding complex biological systems. These studies described here primarily use AFM to observe biopolymer interactions with proteins and its surroundings with unprecedented resolution, providing a better understanding of these systems and interactions at the nanoscale. Transcriptional profiling, the measure of messenger RNA (mRNA) abundance in a single cell, is a powerful technique that detects "behavior" or "symptoms" at the tissue and cellular level. We have sought to develop an alternative approach, using our expertise in AFM and single molecule nanotechnology, to achieve a cost-effective high throughput method for sensitive detection and profiling of subtle changes in transcript abundance. The technique does not require amplification of the mRNA sample because the AFM provides three-dimensional views of molecules with unprecedented resolution, requires minimal sample preparation, and utilizes a simple tagging chemistry on cDNA molecules. AFM images showed collagen polymers in teeth and of Drebrin-A remodeling of filamentous actin structure and mechanics. AFM was used to image collagen on exposed dentine tubules and confirmed tubule occlusion with a desensitizing prophylaxis paste by Colgate-Palmolive. The AFM also superseded other microscopy tools in resolving F-actin helix remodeling and possible cooperative binding by a neuronal actin binding protein---Drebrin-A, an

  1. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, Ted Alfred [Univ. of California, Berkeley, CA (United States)

    2002-01-01

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  2. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    International Nuclear Information System (INIS)

    Laurence, Ted Alfred

    2002-01-01

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  3. A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules.

    Science.gov (United States)

    Demirel, Habibe Cansu; Dogan, Tunca; Tuncbag, Nurcan

    2018-05-31

    Protein-protein interactions (PPIs) are the key components in many cellular processes including signaling pathways, enzymatic reactions and epigenetic regulation. Abnormal interactions of some proteins may be pathogenic and cause various disorders including cancer and neurodegenerative diseases. Although inhibiting PPIs with small molecules is a challenging task, it gained an increasing interest because of its strong potential for drug discovery and design. The knowledge of the interface as well as the structural and chemical characteristics of the PPIs and their roles in the cellular pathways are necessary for a rational design of small molecules to modulate PPIs. In this study, we review the recent progress in the field and detail the physicochemical properties of PPIs including binding hot spots with a focus on structural methods. Then, we review recent approaches for structural prediction of PPIs. Finally, we revisit the concept of targeting PPIs in a systems biology perspective and we refer to the non-structural approaches, usually employed when the structural information is not present. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  4. Plasma-neutral gas interaction in a tokamak divertor: effects of hydrogen molecules and plasma recombination

    International Nuclear Information System (INIS)

    Krasheninnikov, S.I.; Pigarov, A.Yu.; Soboleva, T.K.; Sigmar, D.J.

    1997-01-01

    We investigate the influence of hydrogen molecules on plasma recombination using a collisional-radiative model for multispecies hydrogen plasmas and tokamak detached divertor parameters. The rate constant found for molecular activated recombination of a plasma can be as high as 2 x 10 -10 cm 3 /s, confirming our pervious estimates. We investigate the effects of hydrogen molecules and plasma recombination on self-consistent plasma-neutral gas interactions in the recycling region of a tokamak divertor. We treat the plasma flow in a fluid approximation retaining the effects of plasma recombination and employing a Knudsen neutral transport model for a 'gas box' divertor geometry. For the model of plasma-neutral interactions we employ we find: (a) molecular activated recombination is a dominant channel of divertor plasma recombination; and (b) plasma recombination is a key element leading to a decrease in the plasma flux onto the target and substantial plasma pressure drop which are the main features of detached divertor regimes. (orig.)

  5. An immersion calorimetric study of the interactions between some organic molecules and functionalized carbon nanotube surfaces

    International Nuclear Information System (INIS)

    Castillejos-López, E.; Bachiller-Baeza, B.; Guerrero-Ruiz, A.; Rodriguez-Ramos, I.

    2013-01-01

    Highlights: ► The interaction of organic chemicals with the surface of modified CNTs was studied. ► Specific π–π interactions between graphitic CNTs and toluene have been considered. ► Confinement effects in CNTs increase the adsorption strength of aromatic compounds. ► Methanol molecules form H-bonds with the oxygen functional groups on CNT surfaces. - Abstract: The interaction of organic chemicals with the surface of carbon nanotubes has been studied by immersion calorimetry revealing significant differences in the properties when these materials are modified thermally or chemically. Therefore, multiwall carbon nanotubes have been synthesized using a chemical vapour deposition procedure and subsequently aliquots were treated with HNO 3 at reflux, maintaining the reaction during different times, in order to incorporate oxygen surface groups, or were treated at 2873 K under inert atmosphere. The aim of this thermal treatment is to eliminate structural defects of the carbon nanostructures and to graphitize the amorphous carbon phases. These features were confirmed by high-resolution transmission electron microscopy. The immersion in organic compounds, including toluene, methanol and methylcyclohexane, of all these carbon nanotubes samples reveals that the surface properties are remarkably modified. Thus, the formation of different types of interaction, depending on the surface, gives place to changes in the immersion enthalpies

  6. Investigation of the Hydantoin Monomer and its Interaction with Water Molecules

    Science.gov (United States)

    Gruet, Sébastien; Perez, Cristobal; Schnell, Melanie

    2017-06-01

    Hydantoin (Imidazolidine-2,4-dione, C_3H_4N_2O_2) is a five-membered heterocyclic compound of astrobiological interest. This molecule has been detected in carbonaceous chondrites [1], and its formation can rise from the presence of glycolic acid and urea, two prebiotic molecules [2]. The hydrolysis of hydantoin under acidic conditions can also produce glycine [3], an amino acid actively searched for in the interstellar medium. Spectroscopic data of hydantoin is very limited and mostly dedicated to the solid phase. The high resolution study in gas phase is restricted to the work recently published by Ozeki et al. reporting the pure rotational spectra of the ground state and two vibrational states of the molecule in the millimeter-wave region (90-370 GHz)[4]. Using chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy, we recorded the jet-cooled rotational spectra of hydantoin with water between 2 to 8 GHz. We observed the ground state of hydantoin monomer and several water complexes with one or two water molecules. All the observed species exhibit a hyperfine structure due to the two nitrogen atoms present in the molecule, which were fully resolved and analyzed. Additional experiments with a ^{18}O enriched water sample were realized to determine the oxygen-atom positions of the water monomers. These experiments yielded accurate structural information on the preferred water binding sites. The observed complexes and the interactions that hold them together, mainly strong directional hydrogen bonds, will be presented and discussed. [1] Shimoyama, A. and Ogasawara, R., Orig. Life Evol. Biosph., 32, 165-179, 2002. DOI:10.1023/A:1016015319112. [2] Menor-Salván, C. and Marín-Yaseli, M.R., Chem. Soc. Rev., 41(16), 5404-5415, 2012. DOI:10.1039/c2cs35060b. [3] De Marcellus P., Bertrand M., Nuevo M., Westall F. and Le Sergeant d'Hendecourt L., Astrobiology. 11(9), 847-854, 2011. DOI:10.1089/ast.2011.0677. [4] Ozeki, H., Miyahara R., Ihara H., Todaka S., Kobayashi

  7. Phospholipid monolayer coated microfabricated electrodes to model the interaction of molecules with biomembranes

    Energy Technology Data Exchange (ETDEWEB)

    Coldrick, Zachary [Centre for Self-Organising Molecular Systems (SOMS), School of Chemistry, University of Leeds, Leeds, LS2 9JT (United Kingdom)], E-mail: eenzc@leeds.ac.uk; Steenson, Paul [School of Electronic Engineering, University of Leeds, Leeds, LS2 9JT (United Kingdom); Millner, Paul [Institute of Membrane and Systems Biology, University of Leeds, Leeds, LS2 9JT (United Kingdom); Davies, Matthew [Health and Safety Laboratories, Buxton, SK17 9JN (United Kingdom); Nelson, Andrew [Centre for Self-Organising Molecular Systems (SOMS), School of Chemistry, University of Leeds, Leeds, LS2 9JT (United Kingdom)

    2009-09-01

    The hanging mercury (Hg) drop electrode (HMDE) has a classical application as a tool to study adsorption and desorption processes of surface organic films due to its: (a) atomically smooth surface and, (b) hydrophobicity at its potential of zero charge. In this study we report on a replacement of the HMDE for studying supported organic layers in the form of platinum (Pt) working electrodes fabricated using lithography techniques on which a thin film of Hg is electrodeposited. These wafer-based Pt/Hg electrodes are characterised and compared to the HMDE using rapid cyclic voltammetry (RCV) and show similar capacitance-potential profiles while being far more mechanically stable and consuming considerably less Hg over their lifetime of several months. The electrodes have been used to support self-assembled phospholipid monolayers which are dynamic surface coatings with unique dielectric properties. The issue of surface contamination has been solved by regenerating the electrode surface prior to phospholipid coating by application of extreme cathodic potentials more negative than -2.6 V (vs. Ag/AgCl). The phospholipid coated electrodes presented in this paper mimic one half of a phospholipid bilayer and exhibit interactions with the biomembrane active drug molecules chlorpromazine, and quinidine. The magnitudes of these interactions have been assessed by recording changes in the capacitance-potential profiles in real time using RCV at 40 V s{sup -1} over potential ranges >1 V. A method for electrode coating with phospholipids with the electrodes fitted in a flow cell device has been developed. This has enabled sequential rapid cleaning/coating/interaction cycles for the purposes of drug screening and/or on-line monitoring for molecules of interest.

  8. Phospholipid monolayer coated microfabricated electrodes to model the interaction of molecules with biomembranes

    International Nuclear Information System (INIS)

    Coldrick, Zachary; Steenson, Paul; Millner, Paul; Davies, Matthew; Nelson, Andrew

    2009-01-01

    The hanging mercury (Hg) drop electrode (HMDE) has a classical application as a tool to study adsorption and desorption processes of surface organic films due to its: (a) atomically smooth surface and, (b) hydrophobicity at its potential of zero charge. In this study we report on a replacement of the HMDE for studying supported organic layers in the form of platinum (Pt) working electrodes fabricated using lithography techniques on which a thin film of Hg is electrodeposited. These wafer-based Pt/Hg electrodes are characterised and compared to the HMDE using rapid cyclic voltammetry (RCV) and show similar capacitance-potential profiles while being far more mechanically stable and consuming considerably less Hg over their lifetime of several months. The electrodes have been used to support self-assembled phospholipid monolayers which are dynamic surface coatings with unique dielectric properties. The issue of surface contamination has been solved by regenerating the electrode surface prior to phospholipid coating by application of extreme cathodic potentials more negative than -2.6 V (vs. Ag/AgCl). The phospholipid coated electrodes presented in this paper mimic one half of a phospholipid bilayer and exhibit interactions with the biomembrane active drug molecules chlorpromazine, and quinidine. The magnitudes of these interactions have been assessed by recording changes in the capacitance-potential profiles in real time using RCV at 40 V s -1 over potential ranges >1 V. A method for electrode coating with phospholipids with the electrodes fitted in a flow cell device has been developed. This has enabled sequential rapid cleaning/coating/interaction cycles for the purposes of drug screening and/or on-line monitoring for molecules of interest.

  9. Positron-molecule interactions and corresponding positron attachment to molecules. As a basis for positron emission tomography (PET)

    International Nuclear Information System (INIS)

    Tachikawa, Masanori; Kimura, Mineo; Pichl, Lukas

    2007-01-01

    Through positron and electron interactions, they annihilate emitting primarily two gamma rays with 180-degree opposite directions. Positron spectroscopy using the characteristics of these gamma rays has been employed for analyzing various properties of material as well as for positron emission tomography (PET). However, its fundamental physics of positron-electron interactions and resulting features of emitting gamma rays are not well understood. By obtaining better understanding of positron interactions, it should become possible to provide the firm bases for positron spectroscopy in finer accuracy and quality. Here, we propose a significant mechanism for positron annihilation through positron attachment process, which may help increase the quality of positron spectroscopy. (author)

  10. Interaction of small molecule inhibitors of HIV-1 entry with CCR5

    International Nuclear Information System (INIS)

    Seibert, Christoph; Ying Weiwen; Gavrilov, Svetlana; Tsamis, Fotini; Kuhmann, Shawn E.; Palani, Anandan; Tagat, Jayaram R.; Clader, John W.; McCombie, Stuart W.; Baroudy, Bahige M.; Smith, Steven O.; Dragic, Tatjana; Moore, John P.; Sakmar, Thomas P.

    2006-01-01

    The CC-chemokine receptor 5 (CCR5) is the major coreceptor for macrophage-tropic (R5) HIV-1 strains. Several small molecule inhibitors of CCR5 that block chemokine binding and HIV-1 entry are being evaluated as drug candidates. Here we define how CCR5 antagonists TAK-779, AD101 (SCH-350581) and SCH-C (SCH-351125), which inhibit HIV-1 entry, interact with CCR5. Using a mutagenesis approach in combination with a viral entry assay to provide a direct functional read out, we tested predictions based on a homology model of CCR5 and analyzed the functions of more than 30 amino acid residues. We find that a key set of aromatic and aliphatic residues serves as a hydrophobic core for the ligand binding pocket, while E283 is critical for high affinity interaction, most likely by acting as the counterion for a positively charged nitrogen atom common to all three inhibitors. These results provide a structural basis for understanding how specific antagonists interact with CCR5, and may be useful for the rational design of new, improved CCR5 ligands

  11. Intercellular adhesion molecule-1 augments myoblast adhesion and fusion through homophilic trans-interactions.

    Science.gov (United States)

    Pizza, Francis X; Martin, Ryan A; Springer, Evan M; Leffler, Maxwell S; Woelmer, Bryce R; Recker, Isaac J; Leaman, Douglas W

    2017-07-11

    The overall objective of the study was to identify mechanisms through which intercellular adhesion molecule-1 (ICAM-1) augments the adhesive and fusogenic properties of myogenic cells. Hypotheses were tested using cultured myoblasts and fibroblasts, which do not constitutively express ICAM-1, and myoblasts and fibroblasts forced to express full length ICAM-1 or a truncated form lacking the cytoplasmic domain of ICAM-1. ICAM-1 mediated myoblast adhesion and fusion were quantified using novel assays and cell mixing experiments. We report that ICAM-1 augments myoblast adhesion to myoblasts and myotubes through homophilic trans-interactions. Such adhesive interactions enhanced levels of active Rac in adherent and fusing myoblasts, as well as triggered lamellipodia, spreading, and fusion of myoblasts through the signaling function of the cytoplasmic domain of ICAM-1. Rac inhibition negated ICAM-1 mediated lamellipodia, spreading, and fusion of myoblasts. The fusogenic property of ICAM-1-ICAM-1 interactions was restricted to myogenic cells, as forced expression of ICAM-1 by fibroblasts did not augment their fusion to ICAM-1+ myoblasts/myotubes. We conclude that ICAM-1 augments myoblast adhesion and fusion through its ability to self-associate and initiate Rac-mediated remodeling of the actin cytoskeleton.

  12. Exchange Interactions on the Highest-Spin Reported Molecule: the Mixed-Valence Fe42 Complex

    Science.gov (United States)

    Aravena, Daniel; Venegas-Yazigi, Diego; Ruiz, Eliseo

    2016-04-01

    The finding of high-spin molecules that could behave as conventional magnets has been one of the main challenges in Molecular Magnetism. Here, the exchange interactions, present in the highest-spin molecule published in the literature, Fe42, have been analysed using theoretical methods based on Density Functional Theory. The system with a total spin value S = 45 is formed by 42 iron centres containing 18 high-spin FeIII ferromagnetically coupled and 24 diamagnetic low-spin FeII ions. The bridging ligands between the two paramagnetic centres are two cyanide ligands coordinated to the diamagnetic FeII cations. Calculations were performed using either small Fe4 or Fe3 models or the whole Fe42 complex, showing the presence of two different ferromagnetic couplings between the paramagnetic FeIII centres. Finally, Quantum Monte Carlo simulations for the whole system were carried out in order to compare the experimental and simulated magnetic susceptibility curves from the calculated exchange coupling constants with the experimental one. This comparison allows for the evaluation of the accuracy of different exchange-correlation functionals to reproduce such magnetic properties.

  13. Room temperature ionic liquids interacting with bio-molecules: an overview of experimental and computational studies

    Science.gov (United States)

    Benedetto, Antonio; Ballone, Pietro

    2016-03-01

    We briefly review experimental and computational studies of room temperature ionic liquids (RTILs) interacting with important classes of biomolecules, including phospholipids, peptides and proteins, nucleic acids and carbohydrates. Most of these studies have been driven by the interest for RTILs applications as solvents. Thus, available experimental data cover primarily thermodynamic properties such as the reciprocal solubility of RTILs and bio-molecules, as well as phase boundaries. Less extensive data are also available on transport properties such as diffusion and viscosity of homogeneous binary (RTILs/biomolecules) and ternary (RTIL/biomolecules/water) solutions. Most of the structural information at the atomistic level, of interest especially for biochemical, pharmaceutical and nanotechnology applications, has been made available by molecular dynamics simulations. Major exceptions to this statement are represented by the results from NMR and circular dichroism spectroscopy, by selected neutron and X-ray scattering data, and by recent neutron reflectometry measurements on lipid bilayers on surfaces, hydrated by water-RTIL solutions. A final section of our paper summarizes new developments in the field of RTILs based on amino acids, that combine in themselves the two main aspects of our discussion, i.e. ionic liquids and bio-molecules.

  14. Interaction of epitaxial silicene with overlayers formed by exposure to Al atoms and O2 molecules.

    Science.gov (United States)

    Friedlein, R; Van Bui, H; Wiggers, F B; Yamada-Takamura, Y; Kovalgin, A Y; de Jong, M P

    2014-05-28

    As silicene is not chemically inert, the study and exploitation of its electronic properties outside of ultrahigh vacuum environments require the use of insulating capping layers. In order to understand if aluminum oxide might be a suitable encapsulation material, we used high-resolution synchrotron photoelectron spectroscopy to study the interactions of Al atoms and O2 molecules, as well as the combination of both, with epitaxial silicene on thin ZrB2(0001) films grown on Si(111). The deposition of Al atoms onto silicene, up to the coverage of about 0.4 Al per Si atoms, has little effect on the chemical state of the Si atoms. The silicene-terminated surface is also hardly affected by exposure to O2 gas, up to a dose of 4500 L. In contrast, when Al-covered silicene is exposed to the same dose, a large fraction of the Si atoms becomes oxidized. This is attributed to dissociative chemisorption of O2 molecules by Al atoms at the surface, producing reactive atomic oxygen species that cause the oxidation. It is concluded that aluminum oxide overlayers prepared in this fashion are not suitable for encapsulation since they do not prevent but actually enhance the degradation of silicene.

  15. A Synthetic Biology Project - Developing a single-molecule device for screening drug-target interactions.

    Science.gov (United States)

    Firman, Keith; Evans, Luke; Youell, James

    2012-07-16

    This review describes a European-funded project in the area of Synthetic Biology. The project seeks to demonstrate the application of engineering techniques and methodologies to the design and construction of a biosensor for detecting drug-target interactions at the single-molecule level. Production of the proteins required for the system followed the principle of previously described "bioparts" concepts (a system where a database of biological parts - promoters, genes, terminators, linking tags and cleavage sequences - is used to construct novel gene assemblies) and cassette-type assembly of gene expression systems (the concept of linking different "bioparts" to produce functional "cassettes"), but problems were quickly identified with these approaches. DNA substrates for the device were also constructed using a cassette-system. Finally, micro-engineering was used to build a magnetoresistive Magnetic Tweezer device for detection of single molecule DNA modifying enzymes (motors), while the possibility of constructing a Hall Effect version of this device was explored. The device is currently being used to study helicases from Plasmodium as potential targets for anti-malarial drugs, but we also suggest other potential uses for the device. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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

    KAUST Repository

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

    2016-01-01

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

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

    KAUST Repository

    Conboy, Gary

    2016-04-26

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

  18. Rovibrational Interaction and Vibrational Constants of the Symmetric Top Molecule 14NF3

    Directory of Open Access Journals (Sweden)

    Hamid Najib

    2013-01-01

    Full Text Available Several accurate experimental values of the and rotation-vibration interaction parameters and , , and vibrational constants have been extracted from the most recent high-resolution Fourier transform infrared, millimeter wave, and centimeter wave investigations in the spectra of the oblate symmetric top molecule 14NF3. The band-centres used are those of the four fundamental, the overtones, the combination, and hot bands identified in the region between 400 cm−1 and 2000 cm−1. Comparison of our constants with the ones measured previously, by infrared spectroscopy at low resolution, reveals orders of magnitude higher accuracy of the new values. The agreement between our values and those determined by ab initio calculations employing the TZ2Pf basis is excellent.

  19. Hot spot-based design of small-molecule inhibitors for protein-protein interactions.

    Science.gov (United States)

    Guo, Wenxing; Wisniewski, John A; Ji, Haitao

    2014-06-01

    Protein-protein interactions (PPIs) are important targets for the development of chemical probes and therapeutic agents. From the initial discovery of the existence of hot spots at PPI interfaces, it has been proposed that hot spots might provide the key for developing small-molecule PPI inhibitors. However, there has been no review on the ways in which the knowledge of hot spots can be used to achieve inhibitor design, nor critical examination of successful examples. This Digest discusses the characteristics of hot spots and the identification of druggable hot spot pockets. An analysis of four examples of hot spot-based design reveals the importance of this strategy in discovering potent and selective PPI inhibitors. A general procedure for hot spot-based design of PPI inhibitors is outlined. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Physical manipulation of single-molecule DNA using microbead and its application to analysis of DNA-protein interaction

    International Nuclear Information System (INIS)

    Kurita, Hirofumi; Yasuda, Hachiro; Takashima, Kazunori; Katsura, Shinji; Mizuno, Akira

    2009-01-01

    We carried out an individual DNA manipulation using an optical trapping for a microbead. This manipulation system is based on a fluorescent microscopy equipped with an IR laser. Both ends of linear DNA molecule were labeled with a biotin and a thiol group, respectively. Then the biotinylated end was attached to a microbead, and the other was immobilized on a thiol-linkable glass surface. We controlled the form of an individual DNA molecule by moving the focal point of IR laser, which trapped the microbead. In addition, we applied single-molecule approach to analyze DNA hydrolysis. We also used microchannel for single-molecule observation of DNA hydrolysis. The shortening of DNA in length caused by enzymatic hydrolysis was observed in real-time. The single-molecule DNA manipulation should contribute to elucidate detailed mechanisms of DNA-protein interactions

  1. Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

    Science.gov (United States)

    Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

    2008-02-19

    Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

  2. Third version of a program for calculating the static interaction potential between an electron and a diatomic molecule

    International Nuclear Information System (INIS)

    Raseev, G.

    1980-01-01

    This program calculates the one-centre expansion of a two-centre wave function of a diatomic molecule and also the multipole expansion of its static interaction with a point charge. It is an extension to some classes of open-shell targets of the previous versions and it provides both the wave function and the potential in a form suitable for use in an electron-molecule scattering program. (orig./HSI)

  3. Effect of Dipolar Interactions on the Magnetization of Single-Molecule Magnets in a cubic lattice

    Science.gov (United States)

    Alcantara Ortigoza, Marisol

    2005-03-01

    Since the one-body tunnel picture of single-molecule magnets (SMM) is not always sufficient to explain the fine structure of experimental hysteresis loops, the effect of intermolecular dipolar interactions has been investigated on an ensemble of 100 3D-systems of 5X5X4 particles, each with spin S = 5, arranged in a cubic lattice. We have solved the Landau-Lifshitz-Gilbert equation for several values of the damping constant, the field sweep rate and the lattice constant. We find that the smaller the damping constant is, the stronger the maximum field needs to be to produce hysteresis. Furthermore, the shape of the hysteresis loops also depends on the damping constant. We also find that the system magnetizes and demagnetizes faster with decreasing sweep rates, resulting in smaller hysteresis loops. Variations of the lattice constant within realistic values (1.5nm and 2.5nm) show that the dipolar interaction plays an important role in magnetic hysteresis by controlling the relaxation process. Examination of temperature dependencies (0.1K and 0.7K) of the above will be presented and compared with recent experimental data on SMM.

  4. Extracellular Protein Interactions Mediated by the Neural Cell Adhesion Molecule, NCAM: Heterophilic Interactions Between NCAM and Cell Adhesion Molecules, Extracellular Matrix Proteins, and Viruses

    DEFF Research Database (Denmark)

    Nielsen, Janne; Kulahin, Nikolaj; Walmod, Peter

    2008-01-01

    interactions, thereby modulating a range of biological processes. This review summarizes interactions between NCAM and other CAMs and ECM proteins. Additionally, the role of NCAM as a receptor for rabies virus, and its implications in rabies infections is briefly described. Interactions between NCAM and its...

  5. Segmental Interactions between Polymers and Small Molecules in Batteries and Biofuel Purification

    Science.gov (United States)

    Balsara, Nitash

    2015-03-01

    Polymers such as poly(ethylene oxide) (PEO) and poly(dimethyl siloxane) (PDMS) have the potential to play an important role in the emerging clean energy landscape. Mixtures of PEO and lithium salts are the most widely studied non-flammable electrolyte for rechargeable lithium batteries. PDMS membranes are ideally suited for purifying bioethanol and biobutanol from fermentation broths. The ability of PEO and PDMS to function in these applications depends on segmental interactions between the polymeric host and small molecule guests. One experimental approach for studying these interactions is X-ray absorption spectroscopy (XAS). Models for interpreting XAS spectra of amorphous mixtures and charged species such as salts must quantify the effect of segmental interactions on the electronic structure of the atoms of interest (e.g. sulfur). This combination of experiment and theory is used to determine the species formed in during charging and discharging lithium-sulfur batteries; the theoretical specific energy of lithium-sulfur batteries is a factor of four larger than that of current lithium-ion batteries. Selective transport of alcohols in PDMS-containing membranes is controlled by the size, shape, and connectivity of sub-nanometer cavities or free volume that form and disappear spontaneously as the chain segments undergo Brownian motion. We demonstrate that self-assembly of PDMS-containing block copolymers can be used to control segmental relaxation, which, in turn, affects free volume. Positron annihilation was used to determine the size distribution of free volume cavities in the PDMS-containing block copolymers. The effect of this artificial free volume on selective permeation of alcohols formed by fermentation of sugars derived from lignocellulosic biomass is studied. Molecular dynamics simulations are needed to understand the relationship between self-assembly, free volume, and transport in block copolymers.

  6. Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions.

    Science.gov (United States)

    Götz, Markus; Wortmann, Philipp; Schmid, Sonja; Hugel, Thorsten

    2018-01-30

    Single-molecule Förster resonance energy transfer (smFRET) has become a widely used biophysical technique to study the dynamics of biomolecules. For many molecular machines in a cell proteins have to act together with interaction partners in a functional cycle to fulfill their task. The extension of two-color to multi-color smFRET makes it possible to simultaneously probe more than one interaction or conformational change. This not only adds a new dimension to smFRET experiments but it also offers the unique possibility to directly study the sequence of events and to detect correlated interactions when using an immobilized sample and a total internal reflection fluorescence microscope (TIRFM). Therefore, multi-color smFRET is a versatile tool for studying biomolecular complexes in a quantitative manner and in a previously unachievable detail. Here, we demonstrate how to overcome the special challenges of multi-color smFRET experiments on proteins. We present detailed protocols for obtaining the data and for extracting kinetic information. This includes trace selection criteria, state separation, and the recovery of state trajectories from the noisy data using a 3D ensemble Hidden Markov Model (HMM). Compared to other methods, the kinetic information is not recovered from dwell time histograms but directly from the HMM. The maximum likelihood framework allows us to critically evaluate the kinetic model and to provide meaningful uncertainties for the rates. By applying our method to the heat shock protein 90 (Hsp90), we are able to disentangle the nucleotide binding and the global conformational changes of the protein. This allows us to directly observe the cooperativity between the two nucleotide binding pockets of the Hsp90 dimer.

  7. Interactive session: alpha emitters, fashion or reality? radionuclides and molecules availability

    International Nuclear Information System (INIS)

    Zimmermann, R.

    2015-01-01

    Full text of publication follows. This introduction to the interactive session will simply be based on statements related to the future of therapy in nuclear medicine with some emphasis on the use of alpha-emitters. Some hypotheses will be developed on topics such as 'How will look nuclear medicine in 2025?', 'Do we have enough information to support the use of alpha in therapy?' 'Does it make sense to develop alpha-labelled molecules without long term financial commitment?', 'Will sufficient amounts of radionuclides available when the drugs will be ready for marketing?', 'Do we know enough about alpha emitters toxicity?', 'Is personalized medicine really the solution of the future of health care?', 'How can we convince authorities about the advantages of alpha labelled molecules?', 'Is the development of alpha RIT more expensive or more difficult than beta RIT?', 'Where are all the beta-emitter under development gone?', 'With alpha-emitters, are we speaking about 2025 or 2050?', 'Will Xofigo be a success?', 'What will be the real role of pharmaceutical companies in radiotherapy?', 'Who are the most afraid about radioactivity, the patients or the authorities?'. The speaker will provide his own opinion about each topic. Will you agree or not with him? What is your opinion? (author)

  8. Ethylene glycol monolayer protected nanoparticles: synthesis, characterization, and interactions with biological molecules.

    Science.gov (United States)

    Zheng, Ming; Li, Zhigang; Huang, Xueying

    2004-05-11

    The usefulness of the hybrid materials of nanoparticles and biological molecules on many occasions depends on how well one can achieve a rational design based on specific binding and programmable assembly. Nonspecific binding between nanoparticles and biomolecules is one of the major barriers for achieving their utilities in a biological system. In this paper, we demonstrate a new approach to eliminate nonspecific interactions between nanoparticles and biological molecules by shielding the nanoparticle with a monolayer of ethylene glycol. A direct synthesis of di-, tri-, and tetra(ethylene glycol)-protected gold nanoparticles (Au-S-EGn, n = 2, 3, and 4) was achieved under the condition that the water content was optimized in the range of 9-18% in the reaction mixture. With controlled ratio of [HAuCl4]/[EGn-SH] at 2, the synthesized particles have an average diameter of 3.5 nm and a surface plasma resonance band around 510 nm. Their surface structures were confirmed by 1H NMR spectra. These gold nanoparticles are bonded with a uniform monolayer with defined lengths of 0.8, 1.2, and 1.6 nm for Au-S-EG2, Au-S-EG3, and Au-S-EG4, respectively. They have great stabilities in aqueous solutions with a high concentration of electrolytes as well as in organic solvents. Thermogravimetric analysis revealed that the ethylene glycol monolayer coating is ca. 14% of the total nanoparticle weight. Biological binding tests by using ion-exchange chromatography and gel electrophoresis demonstrated that these Au-S-EGn (n = 2, 3, or 4) nanoparticles are free of any nonspecific bindings with various proteins, DNA, and RNA. These types of nanoparticles provide a fundamental starting material for designing hybrid materials composed of metallic nanoparticles and biomolecules.

  9. Interaction of Proliferating Cell Nuclear Antigen With DNA at the Single Molecule Level

    KAUST Repository

    Raducanu, Vlad-Stefan

    2016-05-01

    Proliferating cell nuclear antigen (PCNA) is a key factor involved in Eukaryotic DNA replication and repair, as well as other cellular pathways. Its importance comes mainly from two aspects: the large numbers of interacting partners and the mechanism of facilitated diffusion along the DNA. The large numbers of interacting partners makes PCNA a necessary factor to consider when studying DNA replication, either in vitro or in vivo. The mechanism of facilitated diffusion along the DNA, i.e. sliding along the duplex, reduces the six degrees of freedom of the molecule, three degrees of freedom of translation and three degrees of freedom of rotation, to only two, translation along the duplex and rotational tracking of the helix. Through this mechanism PCNA can recruit its partner proteins and localize them to the right spot on the DNA, maybe in the right spatial orientation, more effectively and in coordination with other proteins. Passive loading of the closed PCNA ring on the DNA without free ends is a topologically forbidden process. Replication factor C (RFC) uses energy of ATP hydrolysis to mechanically open the PCNA ring and load it on the dsDNA. The first half of the introduction gives overview of PCNA and RFC and the loading mechanism of PCNA on dsDNA. The second half is dedicated to a diffusion model and to an algorithm for analyzing PCNA sliding. PCNA and RFC were successfully purified, simulations and a mean squared displacement analysis algorithm were run and showed good stability and experimental PCNA sliding data was analyzed and led to parameters similar to the ones in literature.

  10. Suppression of Magnetic Quantum Tunneling in a Chiral Single-Molecule Magnet by Ferromagnetic Interactions.

    Science.gov (United States)

    Lippert, Kai-Alexander; Mukherjee, Chandan; Broschinski, Jan-Philipp; Lippert, Yvonne; Walleck, Stephan; Stammler, Anja; Bögge, Hartmut; Schnack, Jürgen; Glaser, Thorsten

    2017-12-18

    Single-molecule magnets (SMMs) retain a magnetization without applied magnetic field for a decent time due to an energy barrier U for spin-reversal. Despite the success to increase U, the difficult to control magnetic quantum tunneling often leads to a decreased effective barrier U eff and a fast relaxation. Here, we demonstrate the influence of the exchange coupling on the tunneling probability in two heptanuclear SMMs hosting the same spin-system with the same high spin ground state S t = 21/2. A chirality-induced symmetry reduction leads to a switch of the Mn III -Mn III exchange from antiferromagnetic in the achiral SMM [Mn III 6 Cr III ] 3+ to ferromagnetic in the new chiral SMM RR [Mn III 6 Cr III ] 3+ . Multispin Hamiltonian analysis by full-matrix diagonalization demonstrates that the ferromagnetic interactions in RR [Mn III 6 Cr III ] 3+ enforce a well-defined S t = 21/2 ground state with substantially less mixing of M S substates in contrast to [Mn III 6 Cr III ] 3+ and no tunneling pathways below the top of the energy barrier. This is experimentally verified as U eff is smaller than the calculated energy barrier U in [Mn III 6 Cr III ] 3+ due to tunneling pathways, whereas U eff equals U in RR [Mn III 6 Cr III ] 3+ demonstrating the absence of quantum tunneling.

  11. A program for calculating and plotting soft x-ray optical interaction coefficients for molecules

    International Nuclear Information System (INIS)

    Thomas, M.M.; Davis, J.C.; Jacobsen, C.J.; Perera, R.C.C.

    1989-08-01

    Comprehensive tables for atomic scattering factor components, f1 and f2, were compiled by Henke et al. for the extended photon region 50 - 10000 eV. Accurate calculations of optical interaction coefficients for absorption, reflection and scattering by material systems (e.g. filters, multi-layers, etc...), which have widespread application, can be based simply upon the atomic scattering factors for the elements comprising the material, except near the absorption threshold energies. These calculations based upon the weighted sum of f1 and f2 for each atomic species present can be very tedious if done by hand. This led us to develop a user friendly program to perform these calculations on an IBM PC or compatible computer. By entering the chemical formula, density and thickness of up to six molecules, values of the f1, f2, mass absorption transmission efficiencies, attenuation lengths, mirror reflectivities and complex indices of refraction can be calculated and plotted as a function of energy or wavelength. This program will be available distribution. 7 refs., 1 fig

  12. Control of the interaction strength of photonic molecules by nanometer precise 3D fabrication.

    Science.gov (United States)

    Rawlings, Colin D; Zientek, Michal; Spieser, Martin; Urbonas, Darius; Stöferle, Thilo; Mahrt, Rainer F; Lisunova, Yuliya; Brugger, Juergen; Duerig, Urs; Knoll, Armin W

    2017-11-28

    Applications for high resolution 3D profiles, so-called grayscale lithography, exist in diverse fields such as optics, nanofluidics and tribology. All of them require the fabrication of patterns with reliable absolute patterning depth independent of the substrate location and target materials. Here we present a complete patterning and pattern-transfer solution based on thermal scanning probe lithography (t-SPL) and dry etching. We demonstrate the fabrication of 3D profiles in silicon and silicon oxide with nanometer scale accuracy of absolute depth levels. An accuracy of less than 1nm standard deviation in t-SPL is achieved by providing an accurate physical model of the writing process to a model-based implementation of a closed-loop lithography process. For transfering the pattern to a target substrate we optimized the etch process and demonstrate linear amplification of grayscale patterns into silicon and silicon oxide with amplification ratios of ∼6 and ∼1, respectively. The performance of the entire process is demonstrated by manufacturing photonic molecules of desired interaction strength. Excellent agreement of fabricated and simulated structures has been achieved.

  13. Inter-molecule interaction for magnetic property of vanadyl tetrakis(thiadiazole) porphyrazine film on Au(1 1 1)

    Science.gov (United States)

    Hou, Jie; Wang, Yu; Eguchi, Keitaro; Nanjo, Chihiro; Takaoka, Tsuyoshi; Sainoo, Yasuyuki; Awaga, Kunio; Komeda, Tadahiro

    2018-05-01

    We report scanning tunneling microscope (STM) observation of vanadyl tetrakis(thiadiazole) porphyrazine (VOTTDPz) molecules, which is a family molecule of phthalocyanine (Pc) but without Csbnd H termination in the perimeter, deposited on Au(1 1 1) surface. Well-ordered film corresponding to 4 × 4 superstructure with respect to Au(1 1 1) surface is formed, in which the centers of the molecules are separated by 1.12 nm, which is much smaller than that observed for a VOPc molecule on Au(1 1 1), due to the absence of Csbnd H termination. At the same time, the azimuthal angles of neighboring molecules rotate with each other by 30°. A contrast variation of bright and dark molecules is observed, which are interpreted as O-up and O-down molecules, respectively, based on the density functional theory simulation. Spin-polarized local density of states calculation shows spin-polarized V 3d state, which is delocalized over the ring. Spin detection is executed by measuring Kondo resonance in the tunneling spectroscopy near the Fermi level, which is caused by the interaction of an isolated spin and conduction electron of the substrate. We detected asymmetric and weak Kondo peak for out-of-plane outer magnetic field of 0 T, which becomes strong and symmetric peak at 5 T, which is understood by the shift of the spin center of the Kondo resonance from V 3d to delocalized π state in ring with the magnetic field.

  14. Quantum chemical analysis explains hemagglutinin peptide-MHC Class II molecule HLA-DRβ1*0101 interactions

    International Nuclear Information System (INIS)

    Cardenas, Constanza; Villaveces, Jose Luis; Bohorquez, Hugo; Llanos, Eugenio; Suarez, Carlos; Obregon, Mateo; Patarroyo, Manuel Elkin

    2004-01-01

    We present a new method to explore interactions between peptides and major histocompatibility complex (MHC) molecules using the resultant vector of the three principal multipole terms of the electrostatic field expansion. Being that molecular interactions are driven by electrostatic interactions, we applied quantum chemistry methods to better understand variations in the electrostatic field of the MHC Class II HLA-DRβ1*0101-HA complex. Multipole terms were studied, finding strong alterations of the field in Pocket 1 of this MHC molecule, and weak variations in other pockets, with Pocket 1 >> Pocket 4 > Pocket 9 ∼ Pocket 7 > Pocket 6. Variations produced by 'ideal' amino acids and by other occupying amino acids were compared. Two types of interactions were found in all pockets: a strong unspecific one (global interaction) and a weak specific interaction (differential interaction). Interactions in Pocket 1, the dominant pocket for this allele, are driven mainly by the quadrupole term, confirming the idea that aromatic rings are important in these interactions. Multipolar analysis is in agreement with experimental results, suggesting quantum chemistry methods as an adequate methodology to understand these interactions

  15. The interaction of linear and ring forms of DNA molecules with nanodiamonds synthesized by detonation

    International Nuclear Information System (INIS)

    Purtov, K V; Burakova, L P; Puzyr, A P; Bondar, V S

    2008-01-01

    Nanodiamonds synthesized by detonation have been found not to immobilize the ring form of pUC19 plasmid DNA. Linear pUC19 molecules with blunt ends, prepared by restriction of the initial ring form of pUC19 DNA, and linear 0.25-10 kb DNA fragments are adsorbed on nanodiamonds. The amount of adsorbed linear DNA molecules depends on the size of the molecules and the size of the nanodiamond clusters

  16. Electric dipole moment of diatomic molecules by configuration interaction. V - Two states of /2/Sigma/+/ symmetry in CN.

    Science.gov (United States)

    Green, S.

    1972-01-01

    Previous accurate dipole moment calculation techniques are modified to be applicable to higher excited states of symmetry. The self-consistent fields and configuration interactions are calculated for the X(2)Sigma(+) and B(2)Sigma(+) states of CN. Spin hyperfine constants and spin density at the nucleus are considered in the context of one-electron operator properties. The values of the self-consistent field and configuration interaction for the spin density are compared with experimental values for several diatomic molecules.

  17. Elementary electron-molecule interactions and negative ion resonances at subexcitation energies and their significance in gaseous dielectrics

    International Nuclear Information System (INIS)

    Christophorou, L.G.

    1977-01-01

    Recent knowledge on low-energy (mostly approximately less than 10 eV) electron-molecule interaction processes in dilute and in dense gases is synthesized, discussed, and related to the breakdown strength of gaseous dielectrics. Optimal design of multicomponent gaseous insulators can be made on the basis of such knowledge

  18. Interaction of slow electrons with high-pressure gases ('Quasi-liquids'): synthesis of our knowledge on slow electron-molecule interactions. Progress report

    International Nuclear Information System (INIS)

    McCorkle, D.L.; Christophorou, L.G.

    1985-01-01

    A crucial step in our efforts to develop not only a coherent picture of radiation interaction with matter, but also to understand radiation effects and mechanisms, as well as the effects of chemical pollutants and toxic compounds, is to relate the often abundant knowledge on isolated molecules (low pressure gases) to that on liquids or solids. To understand the roles of the physical and chemical properties of molecules in biological reactions, we must know how these isolated-molecule properties change as molecules are embedded in gradually thicker and thicker (denser and denser) gaseous and, finally, liquid environments. The work initiated by us both at the Physics Department of The University of Tennessee and at the Oak Ridge National Laboratory addresses itself to this question. At both places, high pressure (40 to approx.8000 kPa) electron swarm experiments are currently in operation yielding information as to the effects of the density and nature of the environment on fundamental electron-molecule interaction processes at densities intermediate to those corresponding to low pressure gases and liquids, and the gradual transition from isolated molecule to condensed phase behavior

  19. [Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data].

    Science.gov (United States)

    Gonzalez, E; Lino, J; Deriabina, A; Herrera, J N F; Poltev, V I

    2013-01-01

    To elucidate details of the DNA-water interactions we performed the calculations and systemaitic search for minima of interaction energy of the systems consisting of one of DNA bases and one or two water molecules. The results of calculations using two force fields of molecular mechanics (MM) and correlated ab initio method MP2/6-31G(d, p) of quantum mechanics (QM) have been compared with one another and with experimental data. The calculations demonstrated a qualitative agreement between geometry characteristics of the most of local energy minima obtained via different methods. The deepest minima revealed by MM and QM methods correspond to water molecule position between two neighbor hydrophilic centers of the base and to the formation by water molecule of hydrogen bonds with them. Nevertheless, the relative depth of some minima and peculiarities of mutual water-base positions in' these minima depend on the method used. The analysis revealed insignificance of some differences in the results of calculations performed via different methods and the importance of other ones for the description of DNA hydration. The calculations via MM methods enable us to reproduce quantitatively all the experimental data on the enthalpies of complex formation of single water molecule with the set of mono-, di-, and trimethylated bases, as well as on water molecule locations near base hydrophilic atoms in the crystals of DNA duplex fragments, while some of these data cannot be rationalized by QM calculations.

  20. pH dependence of the interaction between immunogenic peptides and MHC class II molecules. Evidence for an acidic intracellular compartment being the organelle of interaction

    DEFF Research Database (Denmark)

    Mouritsen, S; Buus, Anette Stryhn; Petersen, B L

    1992-01-01

    and most notably in the endosome-lysosome compartment in which Ag processing is thought to occur. Thus, Ag processing and interaction with MHC class II molecules can potentially happen in the very same compartment. This yet undefined acidic compartment would have to contain proteolytic enzymes and MHC...

  1. Alteration of RNA splicing by small molecule inhibitors of the interaction between NHP2L1 and U4

    Science.gov (United States)

    Diouf, Barthelemy; Lin, Wenwei; Goktug, Asli; Grace, Christy R. R.; Waddell, Michael Brett; Bao, Ju; Shao, Youming; Heath, Richard J.; Zheng, Jie J.; Shelat, Anang A.; Relling, Mary V.; Chen, Taosheng; Evans, William E.

    2018-01-01

    Splicing is an important eukaryotic mechanism for expanding the transcriptome and proteome, influencing a number of biological processes. Understanding its regulation and identifying small molecules that modulate this process remains a challenge. We developed an assay based on time-resolved FRET (TR-FRET) to detect the interaction between the protein NHP2L1 and U4 RNA, which are two key components of the spliceosome. We used this assay to identify small molecules that interfere with this interaction in a high-throughput screening (HTS) campaign. Topotecan and other camptothecin derivatives were among the top hits. We confirmed that topotecan disrupts the interaction between NHP2L1 and U4 by binding to U4 and inhibits RNA splicing. Our data reveal new functions of known drugs which could facilitate the development of therapeutic strategies to modify splicing and alter gene function. PMID:28985478

  2. Resonance reactions and enhancement of weak interactions in collisions of cold molecules

    International Nuclear Information System (INIS)

    Flambaum, V. V.; Ginges, J. S. M.

    2006-01-01

    With the creation of ultracold atoms and molecules, a new type of chemistry - 'resonance' chemistry - emerges: chemical reactions can occur when the energy of colliding atoms and molecules matches a bound state of the combined molecule (Feshbach resonance). This chemistry is rather similar to reactions that take place in nuclei at low energies. In this paper we suggest some problems for future experimental and theoretical work related to the resonance chemistry of ultracold molecules. Molecular Bose-Einstein condensates are particularly interesting because in this system collisions and chemical reactions are extremely sensitive to weak fields; also, a preferred reaction channel may be enhanced due to a finite number of final states. The sensitivity to weak fields arises due to the high density of narrow compound resonances and the macroscopic number of molecules with kinetic energy E=0 (in the ground state of a mean-field potential). The high sensitivity to the magnetic field may be used to measure the distribution of energy intervals, widths, and magnetic moments of compound resonances and study the onset of quantum chaos. A difference in the production rate of right-handed and left-handed chiral molecules may be produced by external electric E and magnetic B fields and the finite width Γ of the resonance (correlation ΓE·B). The same effect may be produced by the parity-violating energy difference in chiral molecules

  3. (CryoTransmission Electron Microscopy of Phospholipid Model Membranes Interacting with Amphiphilic and Polyphilic Molecules

    Directory of Open Access Journals (Sweden)

    Annette Meister

    2017-10-01

    Full Text Available Lipid membranes can incorporate amphiphilic or polyphilic molecules leading to specific functionalities and to adaptable properties of the lipid bilayer host. The insertion of guest molecules into membranes frequently induces changes in the shape of the lipid matrix that can be visualized by transmission electron microscopy (TEM techniques. Here, we review the use of stained and vitrified specimens in (cryoTEM to characterize the morphology of amphiphilic and polyphilic molecules upon insertion into phospholipid model membranes. Special emphasis is placed on the impact of novel synthetic amphiphilic and polyphilic bolalipids and polymers on membrane integrity and shape stability.

  4. Improving the first hyperpolarizability of anthracene through interaction with HX molecules (Xdbnd F, Cl, Br): A theoretical study

    Science.gov (United States)

    Abdolmaleki, Ahmad; Dadsetani, Mehrdad; Zabardasti, Abedin

    2018-05-01

    The variations in nonlinear optical activity (NLO) of anthracene (C14H10) was investigated via intermolecular interactions between C14H10 and HX molecules (Xdbnd F, Cl and Br) using B3LYP-D3 method at 6-311++G(d,p) basis set. The stabilization of those complexes was investigated via vibrational analysis, quantum theory of atoms in molecules, molecular electrostatic potential, natural bond orbitals and symmetry-adapted perturbation theory (SAPT) analysis. Furthermore, the optical spectra and the first hyperpolarizabilities of C14H10⋯HX complexes were computed. The adsorption of hydrogen halide through C14H10⋯HX complex formation, didn't change much the linear optical activities of C14H10 molecule, but the magnitude of the first hyperpolarizability of the C14H10⋯HX complexes to be as much as that of urea.

  5. Electrostatic similarities between protein and small molecule ligands facilitate the design of protein-protein interaction inhibitors.

    Directory of Open Access Journals (Sweden)

    Arnout Voet

    Full Text Available One of the underlying principles in drug discovery is that a biologically active compound is complimentary in shape and molecular recognition features to its receptor. This principle infers that molecules binding to the same receptor may share some common features. Here, we have investigated whether the electrostatic similarity can be used for the discovery of small molecule protein-protein interaction inhibitors (SMPPIIs. We have developed a method that can be used to evaluate the similarity of electrostatic potentials between small molecules and known protein ligands. This method was implemented in a software called EleKit. Analyses of all available (at the time of research SMPPII structures indicate that SMPPIIs bear some similarities of electrostatic potential with the ligand proteins of the same receptor. This is especially true for the more polar SMPPIIs. Retrospective analysis of several successful SMPPIIs has shown the applicability of EleKit in the design of new SMPPIIs.

  6. Separation and Characterization of DNA Molecules and Intermolecular Interactions in Pressure-Driven Micro Flow

    Science.gov (United States)

    Friedrich, Sarah; Wang, Tza-Huei

    Pressure-driven flow in micron-sized diameter capillaries can be used to separate DNA molecules by size in a technique called Free Solution Hydrodynamic Separation. By coupling this technique with Cylindrical Illumination Confocal Spectroscopy, we have developed a highly sensitive and quantitative platform capable of separating DNA molecules by length over a large dynamic range (25 bp to 48 kbp) in a single run using only picoliters or femtograms of a DNA sample. The optical detection volume completely spans the capillary cross section, enabling highly efficient single molecule detection for enhanced sensitivity and quantification accuracy via single molecule counting. Because each DNA molecule generates its own fluorescent burst, these burst profiles can be further analyzed to individually characterize each DNA molecule's shape as it passes through the detection region. We exploit these burst profiles to visualize fluctuations in conformation under shear flow in microcapillaries, and utilizing combined mobility shift analysis, explore the complex relationship between molecular properties including length and conformation, hydrodynamic mobility, solution conditions including ion species and concentrations, and separation conditions including flow rate and capillary diameter.

  7. Photo-cross-linked small-molecule microarrays as chemical genomic tools for dissecting protein-ligand interactions.

    Science.gov (United States)

    Kanoh, Naoki; Asami, Aya; Kawatani, Makoto; Honda, Kaori; Kumashiro, Saori; Takayama, Hiroshi; Simizu, Siro; Amemiya, Tomoyuki; Kondoh, Yasumitsu; Hatakeyama, Satoru; Tsuganezawa, Keiko; Utata, Rei; Tanaka, Akiko; Yokoyama, Shigeyuki; Tashiro, Hideo; Osada, Hiroyuki

    2006-12-18

    We have developed a unique photo-cross-linking approach for immobilizing a variety of small molecules in a functional-group-independent manner. Our approach depends on the reactivity of the carbene species generated from trifluoromethylaryldiazirine upon UV irradiation. It was demonstrated in model experiments that the photogenerated carbenes were able to react with every small molecule tested, and they produced multiple conjugates in most cases. It was also found in on-array immobilization experiments that various small molecules were immobilized, and the immobilized small molecules retained their ability to interact with their binding proteins. With this approach, photo-cross-linked microarrays of about 2000 natural products and drugs were constructed. This photo-cross-linked microarray format was found to be useful not merely for ligand screening but also to study the structure-activity relationship, that is, the relationship between the structural motif (or pharmacophore) found in small molecules and its binding affinity toward a protein, by taking advantage of the nonselective nature of the photo-cross-linking process.

  8. Theoretical investigation of interaction of sorbitol molecules with alcohol dehydrogenase in aqueous solution using molecular dynamics simulation.

    Science.gov (United States)

    Bahrami, Homayoon; Zahedi, Mansour; Moosavi-Movahedi, Ali Akbar; Azizian, Homa; Amanlou, Massoud

    2011-03-01

    The nature of protein-sorbitol-water interaction in solution at the molecular level, has been investigated using molecular dynamics simulations. In order to do this task, two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.9 M) and another in the absence of sorbitol. The results show that the sorbitol molecules cluster and move toward the protein, and form hydrogen bonds with protein. Also, coating by sorbitol reduces the conformational fluctuations of the protein compared to the sorbitol-free system. Thus, it is concluded that at moderate concentration of sorbitol solution, sorbitol molecules interact with ADH via many H-bonds that prevent the protein folding. In fact, at more concentrated sorbitol solution, water and sorbitol molecules accumulate around the protein surface and form a continuous space-filling network to reduce the protein flexibility. Namely, in such solution, sorbitol molecules can stabilize a misfolded state of ADH, and prevent the protein from folding to its native structure.

  9. Molecular self assembly and chiral recognition of copper octacyanophthalocyanine on Au(111): Interplay of intermolecular and molecule-substrate interactions.

    Science.gov (United States)

    Sk, Rejaul; Dhara, Barun; Miller, Joel; Deshpande, Aparna

    Submolecular resolution scanning tunneling microscopy (STM) of copper octacyanophthalocyanine, CuPc(CN)8, at 77 K demonstrates that these achiral molecules form a two dimensional (2D) tetramer-based self-assembly upon evaporation onto an atomically flat Au(111) substrate. They assemble in two different structurally chiral configurations upon adsorption on Au(111). Scanning tunneling spectroscopy (STS),acquired at 77 K, unveils the HOMO and LUMO energy levels of this self-assembly. Voltage dependent STM images show that each molecule in both the structurally chiral configurations individually becomes chiral by breaking the mirror symmetry due to the enhanced intermolecular dipolar coupling interaction at the LUMO energy while the individual molecules remain achiral at the HOMO energy and within the HOMO-LUMO gap. At the LUMO energy, the handedness of the each chiral molecule is decided by the direction of the dipolar coupling interaction in the tetramer unit cell. This preference for LUMO energy indicates that this chirality is purely electronic in nature and it manifests on top of the organizational chirality that is present in the self-assembly independent of the orbital energy. Supported by IISER Pune and DAE-BRNS, India (Project No. 2011/20/37C/17/BRNS).

  10. Raman scattering signatures of the unusual vibronic interaction of molecules in liquid helium-3

    Energy Technology Data Exchange (ETDEWEB)

    Tehver, I., E-mail: imbi.tehver@ut.ee [Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu (Estonia); Benedek, G. [Donostia International Physics Center (DIPC) and University of the Basque Country (EHU), Paseo de Lardizabal 4, 20018 Donostia/San Sebastian (Spain); Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Via Cozzi 53, 20125 Milano (Italy); Hizhnyakov, V. [Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu (Estonia)

    2015-10-16

    Highlights: • Theory of resonance Raman scattering (RRS) of molecules in {sup 3}He liquid is proposed. • Fermi excitations give essential contribution to RRS. • RRS spectra of glyoxal molecule in {sup 3}He droplets are calculated. - Abstract: Light scattering in quantum liquid helium-3 may involve a unique mechanism – the creation and annihilation of atom excitations across the Fermi level. The density of states of particle–hole excitations in the low-energy limit is strongly enhanced as compared to that of collective excitations of phonons in helium-3. This makes possible to directly observe Fermi excitations in the resonant Raman scattering (RRS) by {sup 3}He droplets doped by impurity molecules. The RRS spectra essentially depend on the excitation frequency. In case of excitation in the anti-Stokes side of absorption the first order RRS is directly determined by the particle–hole excitations in the vicinity of the impurity molecule and the contribution of phonons mainly given by the localized spherical vibration. The calculations are made for a {sup 3}He droplet doped by a glyoxal molecule.

  11. Direct Determination of Chitosan–Mucin Interactions Using a Single-Molecule Strategy: Comparison to Alginate–Mucin Interactions

    Directory of Open Access Journals (Sweden)

    Kristin E. Haugstad

    2015-01-01

    Full Text Available Aqueous chitosan possesses attractive interaction capacities with various molecular groups that can be involved in hydrogen bonds and electrostatic and hydrophobic interactions. In the present paper, we report on the direct determination of chitosan–mucin molecular pair interactions at various solvent conditions as compared to alginate–mucin interactions. Two chitosans of high molecular weight with different degrees of acetylation—thus possessing different solubility profiles in aqueous solution as a function of pH and two alginates with different fractions of α-guluronic acid were employed. The interaction properties were determined through a direct unbinding assay at the single-molecular pair level using an atomic force microscope. When probed against immobilized mucin, both chitosans and alginates revealed unbinding profiles characteristic of localized interactions along the polymers. The interaction capacities and estimated parameters of the energy landscapes of the pairwise chitosan–mucin and alginate–mucin interactions are discussed in view of possible contributions from various fundamental forces. Signatures arising both from an electrostatic mechanism and hydrophobic interaction are identified in the chitosan–mucin interaction properties. The molecular nature of the observed chitosan–mucin and alginate–mucin interactions indicates that force spectroscopy provides fundamental insights that can be useful in understanding the surface binding properties of other potentially mucoadhesive polymers.

  12. Interaction of spin and vibrations in transport through single-molecule magnets

    Directory of Open Access Journals (Sweden)

    Falk May

    2011-10-01

    Full Text Available We study electron transport through a single-molecule magnet (SMM and the interplay of its anisotropic spin with quantized vibrational distortions of the molecule. Based on numerical renormalization group calculations we show that, despite the longitudinal anisotropy barrier and small transverse anisotropy, vibrational fluctuations can induce quantum spin-tunneling (QST and a QST-Kondo effect. The interplay of spin scattering, QST and molecular vibrations can strongly enhance the Kondo effect and induce an anomalous magnetic field dependence of vibrational Kondo side-bands.

  13. Interaction of an immunodominant epitope with Ia molecules in T-cell activation

    DEFF Research Database (Denmark)

    Adorini, L; Sette, A; Buus, S

    1988-01-01

    The amino acid sequence corresponding to residues 107-116 of hen egg-white lysozyme (HEL) has been identified as containing an immunodominant T-cell epitope recognized in association with the I-Ed molecule. The immunodominance of this epitope in HEL-primed H-2d mice was demonstrated by analysis o......-120)-peptide was found to be immunogenic in H-2d mice. Thus, a single semiconservative substitution drastically reduces binding capacity and abolishes immunogenicity, suggesting that a strict correlation exists between binding of a peptide to Ia molecules and its immunogenicity....

  14. Molecule-surface interaction processes of relevance to gas blanket type fusion device divertor design

    Energy Technology Data Exchange (ETDEWEB)

    Snowdon, K.J. [Newcastle Univ. (United Kingdom). Dept. of Physics; Tawara, H.

    1997-01-01

    The mechanisms which may lead to the departure of molecular species from surfaces exposed to low energy (0.1-100 eV) particle or photon and electron irradiation are reviewed. Where possible, the charge and electronic state, angular, translational and internal energy distributions of the departing molecules are described and the physical origin of the nature of those distributions identified. The consequences, for the departing molecules, of certain material choices become apparent from such an analysis. Such information may help guide the choice of appropriate materials for plasma facing components of gas-blanket type divertors such as that recently proposed for the International Thermonuclear Experimental Reactor (ITER). (author). 71 refs.

  15. Interaction of spin and vibrations in transport through single-molecule magnets.

    Science.gov (United States)

    May, Falk; Wegewijs, Maarten R; Hofstetter, Walter

    2011-01-01

    We study electron transport through a single-molecule magnet (SMM) and the interplay of its anisotropic spin with quantized vibrational distortions of the molecule. Based on numerical renormalization group calculations we show that, despite the longitudinal anisotropy barrier and small transverse anisotropy, vibrational fluctuations can induce quantum spin-tunneling (QST) and a QST-Kondo effect. The interplay of spin scattering, QST and molecular vibrations can strongly enhance the Kondo effect and induce an anomalous magnetic field dependence of vibrational Kondo side-bands.

  16. Multiphoton interactions in molecules with picosecond laser pulses. Progress report, July 15, 1985-July 14, 1986

    International Nuclear Information System (INIS)

    Kwok, H.S.

    1986-01-01

    The phenomena of superexcitation is discussed for C 2 F 5 Cl. This phenomena, which was first observed for SF 6 , is the excitation of very high levels of molecules by ultrashort pulses. For the same fluence, picosecond pulses were found to deposit more energy into the molecule than longer duration pulses. A second experimental result is discussed. The effect of collisions and pulse duration on the absorption spectrum of C 3 F 7 I. In this experiment it is observed that the linewidth decreases with pulse length. A red shift is observed with increased pressure. 2 refs., 2 figs

  17. Domain-based small molecule binding site annotation

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2006-03-01

    Full Text Available Abstract Background Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule binding site protein sequence annotation is sparse. The Small Molecule Interaction Database (SMID, a database of protein domain-small molecule interactions, was created using structural data from the Protein Data Bank (PDB. More importantly it provides a means to predict small molecule binding sites on proteins with a known or unknown structure and unlike prior approaches, removes large numbers of false positive hits arising from transitive alignment errors, non-biologically significant small molecules and crystallographic conditions that overpredict ion binding sites. Description Using a set of co-crystallized protein-small molecule structures as a starting point, SMID interactions were generated by identifying protein domains that bind to small molecules, using NCBI's Reverse Position Specific BLAST (RPS-BLAST algorithm. SMID records are available for viewing at http://smid.blueprint.org. The SMID-BLAST tool provides accurate transitive annotation of small-molecule binding sites for proteins not found in the PDB. Given a protein sequence, SMID-BLAST identifies domains using RPS-BLAST and then lists potential small molecule ligands based on SMID records, as well as their aligned binding sites. A heuristic ligand score is calculated based on E-value, ligand residue identity and domain entropy to assign a level of confidence to hits found. SMID-BLAST predictions were validated against a set of 793 experimental small molecule interactions from the PDB, of which 472 (60% of predicted interactions identically matched the experimental small molecule and of these, 344 had greater than 80% of the binding site residues correctly identified. Further, we estimate that 45% of predictions which were not observed in the PDB validation set may be true positives. Conclusion By

  18. Surface-supported Ag islands stabilized by a quantum size effect: Their interaction with small molecules relevant to ethylene epoxidation

    Energy Technology Data Exchange (ETDEWEB)

    Shao, Dahai [Iowa State Univ., Ames, IA (United States)

    2013-05-15

    This dissertation focuses on how QSE-stabilized, surface-supported Ag nanoclusters will interact with ethylene or oxygen. Experiments are performed to determine whether the QSE-mediated Ag islands react differently toward adsorption of ethylene or oxygen, or whether the adsorption of these small molecules will affect the QSE-mediated stability of Ag islands. Studies of the interaction of oxygen with Ag/Si(111)-7×7 were previously reported, but these studies were performed at a low Ag coverage where 3D Ag islands were not formed. So the study of such a system at a higher Ag coverage will be a subject of this work. The interaction of ethylene with Ag/Si(111)-7×7, as well as the interaction of oxygen with Ag/NiAl(110) are also important parts of this study.

  19. The semiclassical approximation in the local theory of resonance inelastic interaction of slow electrons with molecules

    International Nuclear Information System (INIS)

    Kazansky, A.K.

    1984-01-01

    The semiclassical approach is developed to calculate the cross sections of vibrational excitation and dissociative attachment for diatomic molecules within the framework of the 'boomerang model'. The formulae obtained reveal the energy dependence of the cross sections on the parameters of the system. Numerical calculations for N 2 , CO, H 2 , HD and D 2 confirm the high accuracy of the method. (author)

  20. Interaction of intense electromagnetic fields with SF6 molecules and clusters in supersonic expansion

    International Nuclear Information System (INIS)

    Airoldi, V.J.T.

    1987-01-01

    A method of measuring SF 6 cluster formation and inhibition in pulsed supersonic expansion in the presence of intense electromagnetic radiation is presented. The characterization of the expansion of SF 6 molecules was done and, the extension of the collision region was determined. An improved unidimensional theory of supersonic expansion showed good agreement with the experimental results. The spectra of multiphoton absorption of SF 6 molecules in supersonic jet and the average energy absorved by each molecule were determined. The absorption spectra of molecule in the collision region present absorption maxima different from those obtained in the collisionless region. The results, if compared with the literature data, show good agreement, with a small difference in the spetra corresponding to the collisionless region. This difference was observed, for the first time in the multiphoton absorption and is attribuited to cluster formation in the jet. A new technique for measuring cluster formation in the supersonic jet, based on determination of the spatial distribution of the energy of molecules in the jet after passing through a skimmer located in the collision region is shown. The inhibition of cluster formation, due to the incidence of intense electromagnetic radiation from a CO 2 -TEA pulsed laser in the initial collision region of the jet, causes a second expansion in the skimmer. The results obtained show that this method can lead to a new isotope separation process. All the parts of the experimental set up, for example, high vacuum system, pulsed valve and pyroelectric detector, were developed and constructed specially for the experiment. (Author) [pt

  1. Mouse CD23 regulates monocyte activation through an interaction with the adhesion molecule CD11b/CD18.

    Science.gov (United States)

    Lecoanet-Henchoz, S; Plater-Zyberk, C; Graber, P; Gretener, D; Aubry, J P; Conrad, D H; Bonnefoy, J Y

    1997-09-01

    CD23 is expressed on a variety of hemopoietic cells. Recently, we have reported that blocking CD23 interactions in a murine model of arthritis resulted in a marked improvement of disease severity. Here, we demonstrate that CD11b, the alpha chain of the beta 2 integrin adhesion molecule complex CD11b/CD18 expressed on monocytes interacts with CD23. Using a recombinant fusion protein (ZZ-CD23), murine CD23 was shown to bind to peritoneal macrophages and peripheral blood cells isolated from mice as well as the murine macrophage cell line, RAW. The interactions between mouse ZZ-CD23 and CD11b/CD18-expressing cells were significantly inhibited by anti-CD11b monoclonal antibodies. A functional consequence was then demonstrated by inducing an up-regulation of interleukin-6 (IL-6) production following ZZ-CD23 incubation with monocytes. The addition of Fab fragments generated from the monoclonal antibody CD11b impaired this cytokine production by 50%. Interestingly, a positive autocrine loop was identified as IL-6 was shown to increase CD23 binding to macrophages. These results demonstrate that similar to findings using human cells, murine CD23 binds to the surface adhesion molecule, CD11b, and these interactions regulate biological activities of murine myeloid cells.

  2. Exploring in vivo cholesterol-mediated interactions between activated EGF receptors in plasma membrane with single-molecule optical tracking

    International Nuclear Information System (INIS)

    Lin, Chien Y.; Huang, Jung Y.; Lo, Leu-Wei

    2016-01-01

    The first step in many cellular signaling processes occurs at various types of receptors in the plasma membrane. Membrane cholesterol can alter these signaling pathways of living cells. However, the process in which the interaction of activated receptors is modulated by cholesterol remains unclear. In this study, we measured single-molecule optical trajectories of epidermal growth factor receptors moving in the plasma membranes of two cancerous cell lines and one normal endothelial cell line. A stochastic model was developed and applied to identify critical information from single-molecule trajectories. We discovered that unliganded epidermal growth factor receptors may reside nearby cholesterol-riched regions of the plasma membrane and can move into these lipid domains when subjected to ligand binding. The amount of membrane cholesterol considerably affects the stability of correlated motion of activated epidermal growth factor receptors. Our results provide single-molecule evidence of membrane cholesterol in regulating signaling receptors. Because the three cell lines used for this study are quite diverse, our results may be useful to shed light on the mechanism of cholesterol-mediated interaction between activated receptors in live cells

  3. Utilizing Biotinylated Proteins Expressed in Yeast to Visualize DNA–Protein Interactions at the Single-Molecule Level

    Directory of Open Access Journals (Sweden)

    Huijun Xue

    2017-10-01

    Full Text Available Much of our knowledge in conventional biochemistry has derived from bulk assays. However, many stochastic processes and transient intermediates are hidden when averaged over the ensemble. The powerful technique of single-molecule fluorescence microscopy has made great contributions to the understanding of life processes that are inaccessible when using traditional approaches. In single-molecule studies, quantum dots (Qdots have several unique advantages over other fluorescent probes, such as high brightness, extremely high photostability, and large Stokes shift, thus allowing long-time observation and improved signal-to-noise ratios. So far, however, there is no convenient way to label proteins purified from budding yeast with Qdots. Based on BirA–Avi and biotin–streptavidin systems, we have established a simple method to acquire a Qdot-labeled protein and visualize its interaction with DNA using total internal reflection fluorescence microscopy. For proof-of-concept, we chose replication protein A (RPA and origin recognition complex (ORC as the proteins of interest. Proteins were purified from budding yeast with high biotinylation efficiency and rapidly labeled with streptavidin-coated Qdots. Interactions between proteins and DNA were observed successfully at the single-molecule level.

  4. Theoretical studies on CH+ ion molecule using configuration interaction method and its spectroscopic properties

    International Nuclear Information System (INIS)

    Machado, F.B.C.

    1985-01-01

    The use of the configuration (CI) method for the calculation of very accurate potential energy curves and dipole moment functions, and then their use in the comprehension of spectroscopic properties of diatomic molecules is presented. The spectroscopic properties of CH + and CD + such as: vibrational levels, spectroscopic constants, averaged dipole moments for all vibrational levels, radiative transition probabilities for emission and absorption, and radiative lifetimes are verificated. (M.J.C.) [pt

  5. Small Molecule Binding, Docking, and Characterization of the Interaction between Pth1 and Peptidyl-tRNA

    Directory of Open Access Journals (Sweden)

    Mary C. Hames

    2013-11-01

    Full Text Available Bacterial Pth1 is essential for viability. Pth1 cleaves the ester bond between the peptide and nucleotide of peptidyl-tRNA generated from aborted translation, expression of mini-genes, and short ORFs. We have determined the shape of the Pth1:peptidyl-tRNA complex using small angle neutron scattering. Binding of piperonylpiperazine, a small molecule constituent of a combinatorial synthetic library common to most compounds with inhibitory activity, was mapped to Pth1 via NMR spectroscopy. We also report computational docking results, modeling piperonylpiperazine binding based on chemical shift perturbation mapping. Overall these studies promote Pth1 as a novel antibiotic target, contribute to understanding how Pth1 interacts with its substrate, advance the current model for cleavage, and demonstrate feasibility of small molecule inhibition.

  6. Molecular properties of metal difluorides and their interactions with CO2 and H2O molecules: a DFT investigation.

    Science.gov (United States)

    Arokiyanathan, Agnes Lincy; Lakshmipathi, Senthilkumar

    2017-11-18

    A computational study of metal difluorides (MF 2 ; M = Ca to Zn) and their interactions with carbon dioxide and water molecules was performed. The structural parameter values obtained and the results of AIM analysis and energy decomposition analysis indicated that the Ca-F bond is weaker and less ionic than the bonds in the transition metal difluorides. A deformation density plot revealed the stablizing influence of the Jahn-Teller effect in nonlinear MF 2 molecules (e.g., where M= Sc, Ti, Cr). An anaysis of the metal K-edge peaks of the difluorides showed that shifts in the edge energy were due to the combined effects of the ionicity, effective nuclear charge, and the spin state of the metal. The interactions of CO 2 with ScF 2 (Scc3 geometry) and TiF 2 (Tic2 geometry) caused CO 2 to shift from its usual linear geometry to a bent geometry (η 2 (C=O) binding mode), while it retained its linear geometry (η 1 (O) binding mode) when it interacted with the other metal difluorides. Energy decomposition analysis showed that, among the various geometries considered, the Scc3 and Tic2 geometries possessed the highest interaction energies and orbital interaction energies. Heavier transition metal difluorides showed stronger affinities for H 2 O, whereas the lighter transition metal (Sc and Ti) difluorides preferred CO 2 . Overall, the results of this study suggest that fluorides of lighter transition metals with partially filled d orbitals (e.g., Sc and Ti) could be used for CO 2 capture under moist conditions. Graphical abstract Interaction of metal difluorides with carbon dioxide and water.

  7. Electrostatic interactions between immunoglobulin (IgG) molecules and a charged sorbent

    NARCIS (Netherlands)

    Bremer, M.G.E.G.; Duval, J.; Norde, Willem; Lyklema, J.

    2004-01-01

    The influence of electrostatic interactions on the adsorption of IgG is examined both theoretically and experimentally. The long-range interaction between IgG and the charged sorbent surface is treated in terms of the DLVO theory taking into account the possibility of charge- and potential

  8. Regulation of drug-metabolizing enzymes in infectious and inflammatory disease: implications for biologics-small molecule drug interactions.

    Science.gov (United States)

    Mallick, Pankajini; Taneja, Guncha; Moorthy, Bhagavatula; Ghose, Romi

    2017-06-01

    Drug-metabolizing enzymes (DMEs) are primarily down-regulated during infectious and inflammatory diseases, leading to disruption in the metabolism of small molecule drugs (smds), which are increasingly being prescribed therapeutically in combination with biologics for a number of chronic diseases. The biologics may exert pro- or anti-inflammatory effect, which may in turn affect the expression/activity of DMEs. Thus, patients with infectious/inflammatory diseases undergoing biologic/smd treatment can have complex changes in DMEs due to combined effects of the disease and treatment. Areas covered: We will discuss clinical biologics-SMD interaction and regulation of DMEs during infection and inflammatory diseases. Mechanistic studies will be discussed and consequences on biologic-small molecule combination therapy on disease outcome due to changes in drug metabolism will be highlighted. Expert opinion: The involvement of immunomodulatory mediators in biologic-SMDs is well known. Regulatory guidelines recommend appropriate in vitro or in vivo assessments for possible interactions. The role of cytokines in biologic-SMDs has been documented. However, the mechanisms of drug-drug interactions is much more complex, and is probably multi-factorial. Studies aimed at understanding the mechanism by which biologics effect the DMEs during inflammation/infection are clinically important.

  9. Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Das, Priyadip; Duanias-Assaf, Tal; Reches, Meital

    2017-03-06

    The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

  10. Effects of ionizing radiation on cell-matrix interactions at the single molecule level

    Energy Technology Data Exchange (ETDEWEB)

    Lauer, Florian

    2015-04-20

    Single molecule microscopy is a technology that allows for accurate assessment of the location and motion of single fluorescent molecules, even in the context of observations on living biological samples. In the present thesis, a flexible analysis tool for single molecule data as obtained in biological experiments was established. The development of a tool to faithfully detect and localize diffraction-limited images of individual fluorescent probes was necessary since data acquired under cell cultivation conditions that account for a three-dimensional microenvironment as experienced physiologically by cells in native tissue poses a challenge not faced ordinarily. After design, implementation, quantitative tests using simulations for comparisons and verification, and evaluation of the different steps of the analysis procedure including local background estimation, local noise estimation, de-noising approaches, detection, localization, and post-processing, analysis capabilities were utilized to evaluate the impact of x-ray irradiation on the plasma membrane architecture of U2OS human osteosarcoma cells as assessed by tracking individual fluorescent lipid-mimetic dye molecules diffusing in the outer membrane leaflet. It was shown that lateral diffusion in the plasma membrane is well described as two-phase anomalous subdiffusion and presence of 3D extracellular matrix leads to lower anomalous exponents of the fast fraction in comparison to monolayer cell culture. Interestingly, even high single-dose (25 Gy) treatments known to induce membrane-mediated apoptosis in tumor microvessel endothelium via membrane viscosity enhancing ceramide generation were not observed to alter membrane architecture in U2OS cells which can be related to amplifying, feedback-driven redox-signaling in the endothelium absent in U2OS. In summary, the sensitive and accurate framework developed in this thesis to assess minute changes of plasma membrane located dynamic processes did not uncover a

  11. Effects of ionizing radiation on cell-matrix interactions at the single molecule level

    International Nuclear Information System (INIS)

    Lauer, Florian

    2015-01-01

    Single molecule microscopy is a technology that allows for accurate assessment of the location and motion of single fluorescent molecules, even in the context of observations on living biological samples. In the present thesis, a flexible analysis tool for single molecule data as obtained in biological experiments was established. The development of a tool to faithfully detect and localize diffraction-limited images of individual fluorescent probes was necessary since data acquired under cell cultivation conditions that account for a three-dimensional microenvironment as experienced physiologically by cells in native tissue poses a challenge not faced ordinarily. After design, implementation, quantitative tests using simulations for comparisons and verification, and evaluation of the different steps of the analysis procedure including local background estimation, local noise estimation, de-noising approaches, detection, localization, and post-processing, analysis capabilities were utilized to evaluate the impact of x-ray irradiation on the plasma membrane architecture of U2OS human osteosarcoma cells as assessed by tracking individual fluorescent lipid-mimetic dye molecules diffusing in the outer membrane leaflet. It was shown that lateral diffusion in the plasma membrane is well described as two-phase anomalous subdiffusion and presence of 3D extracellular matrix leads to lower anomalous exponents of the fast fraction in comparison to monolayer cell culture. Interestingly, even high single-dose (25 Gy) treatments known to induce membrane-mediated apoptosis in tumor microvessel endothelium via membrane viscosity enhancing ceramide generation were not observed to alter membrane architecture in U2OS cells which can be related to amplifying, feedback-driven redox-signaling in the endothelium absent in U2OS. In summary, the sensitive and accurate framework developed in this thesis to assess minute changes of plasma membrane located dynamic processes did not uncover a

  12. Identification of Small Molecule Translesion Synthesis Inhibitors That Target the Rev1-CT/RIR Protein-Protein Interaction.

    Science.gov (United States)

    Sail, Vibhavari; Rizzo, Alessandro A; Chatterjee, Nimrat; Dash, Radha C; Ozen, Zuleyha; Walker, Graham C; Korzhnev, Dmitry M; Hadden, M Kyle

    2017-07-21

    Translesion synthesis (TLS) is an important mechanism through which proliferating cells tolerate DNA damage during replication. The mutagenic Rev1/Polζ-dependent branch of TLS helps cancer cells survive first-line genotoxic chemotherapy and introduces mutations that can contribute to the acquired resistance so often observed with standard anticancer regimens. As such, inhibition of Rev1/Polζ-dependent TLS has recently emerged as a strategy to enhance the efficacy of first-line chemotherapy and reduce the acquisition of chemoresistance by decreasing tumor mutation rate. The TLS DNA polymerase Rev1 serves as an integral scaffolding protein that mediates the assembly of the active multiprotein TLS complexes. Protein-protein interactions (PPIs) between the C-terminal domain of Rev1 (Rev1-CT) and the Rev1-interacting region (RIR) of other TLS DNA polymerases play an essential role in regulating TLS activity. To probe whether disrupting the Rev1-CT/RIR PPI is a valid approach for developing a new class of targeted anticancer agents, we designed a fluorescence polarization-based assay that was utilized in a pilot screen for small molecule inhibitors of this PPI. Two small molecule scaffolds that disrupt this interaction were identified, and secondary validation assays confirmed that compound 5 binds to Rev1-CT at the RIR interface. Finally, survival and mutagenesis assays in mouse embryonic fibroblasts and human fibrosarcoma HT1080 cells treated with cisplatin and ultraviolet light indicate that these compounds inhibit mutagenic Rev1/Polζ-dependent TLS in cells, validating the Rev1-CT/RIR PPI for future anticancer drug discovery and identifying the first small molecule inhibitors of TLS that target Rev1-CT.

  13. Interaction of Proliferating Cell Nuclear Antigen With DNA at the Single Molecule Level

    KAUST Repository

    Raducanu, Vlad-Stefan

    2016-01-01

    Proliferating cell nuclear antigen (PCNA) is a key factor involved in Eukaryotic DNA replication and repair, as well as other cellular pathways. Its importance comes mainly from two aspects: the large numbers of interacting partners

  14. Cross Talk between H2O2 and Interacting Signal Molecules under Plant Stress Response

    Science.gov (United States)

    Saxena, Ina; Srikanth, Sandhya; Chen, Zhong

    2016-01-01

    It is well established that oxidative stress is an important cause of cellular damage. During stress conditions, plants have evolved regulatory mechanisms to adapt to various environmental stresses. One of the consequences of stress is an increase in the cellular concentration of reactive oxygen species, which is subsequently converted to H2O2. H2O2 is continuously produced as the byproduct of oxidative plant aerobic metabolism. Organelles with a high oxidizing metabolic activity or with an intense rate of electron flow, such as chloroplasts, mitochondria, or peroxisomes are major sources of H2O2 production. H2O2 acts as a versatile molecule because of its dual role in cells. Under normal conditions, H2O2 immerges as an important factor during many biological processes. It has been established that it acts as a secondary messenger in signal transduction networks. In this review, we discuss potential roles of H2O2 and other signaling molecules during various stress responses. PMID:27200043

  15. Interaction of multicharged ions with molecules (CO2, C60) by coincident electron spectroscopy

    International Nuclear Information System (INIS)

    Moretto-Capelle, P.; Bordenave-Montesquieu, D.; Bordenave-Montesquieu, A.

    2001-01-01

    First results for the investigation of electron capture processes in collisions between multicharged ions and molecule targets using electron spectroscopy in coincidence with charged fragments, are presented. It is shown that a much more detailed investigation of the capture reaction can be achieved using molecular instead of heavy atomic targets provided that an analysis of the target dissociation is made. The collisional systems 18 O 8+ +Ar, CO 2 and C 60 have been studied at 80 keV. Non coincident electron spectra as well as first results of double or triple coincidence experiments are discussed. Kinetic energy distributions of the C n + fragments (n=1 to 8) produced in multiple capture processes from C 60 target are given. A detailed investigation of the double capture process with CO 2 molecule allows the measurement of kinetic energy release distributions (KERD) which characterize the dissociation of CO 2 2+ molecular ions; our results are found to be very similar to those measured in double photoionisation experiments. (orig.)

  16. Discovery of a small-molecule inhibitor of Dvl-CXXC5 interaction by computational approaches

    Science.gov (United States)

    Ma, Songling; Choi, Jiwon; Jin, Xuemei; Kim, Hyun-Yi; Yun, Ji-Hye; Lee, Weontae; Choi, Kang-Yell; No, Kyoung Tai

    2018-05-01

    The Wnt/β-catenin signaling pathway plays a significant role in the control of osteoblastogenesis and bone formation. CXXC finger protein 5 (CXXC5) has been recently identified as a negative feedback regulator of osteoblast differentiation through a specific interaction with Dishevelled (Dvl) protein. It was reported that targeting the Dvl-CXXC5 interaction could be a novel anabolic therapeutic target for osteoporosis. In this study, complex structure of Dvl PDZ domain and CXXC5 peptide was simulated with molecular dynamics (MD). Based on the structural analysis of binding modes of MD-simulated Dvl PDZ domain with CXXC5 peptide and crystal Dvl PDZ domain with synthetic peptide-ligands, we generated two different pharmacophore models and applied pharmacophore-based virtual screening to discover potent inhibitors of the Dvl-CXXC5 interaction for the anabolic therapy of osteoporosis. Analysis of 16 compounds selected by means of a virtual screening protocol yielded four compounds that effectively disrupted the Dvl-CXXC5 interaction in the fluorescence polarization assay. Potential compounds were validated by fluorescence spectroscopy and nuclear magnetic resonance. We successfully identified a highly potent inhibitor, BMD4722, which directly binds to the Dvl PDZ domain and disrupts the Dvl-CXXC5 interaction. Overall, CXXC5-Dvl PDZ domain complex based pharmacophore combined with various traditional and simple computational methods is a promising approach for the development of modulators targeting the Dvl-CXXC5 interaction, and the potent inhibitor BMD4722 could serve as a starting point to discover or design more potent and specific the Dvl-CXXC5 interaction disruptors.

  17. Discovery of a small-molecule inhibitor of Dvl-CXXC5 interaction by computational approaches.

    Science.gov (United States)

    Ma, Songling; Choi, Jiwon; Jin, Xuemei; Kim, Hyun-Yi; Yun, Ji-Hye; Lee, Weontae; Choi, Kang-Yell; No, Kyoung Tai

    2018-04-07

    The Wnt/β-catenin signaling pathway plays a significant role in the control of osteoblastogenesis and bone formation. CXXC finger protein 5 (CXXC5) has been recently identified as a negative feedback regulator of osteoblast differentiation through a specific interaction with Dishevelled (Dvl) protein. It was reported that targeting the Dvl-CXXC5 interaction could be a novel anabolic therapeutic target for osteoporosis. In this study, complex structure of Dvl PDZ domain and CXXC5 peptide was simulated with molecular dynamics (MD). Based on the structural analysis of binding modes of MD-simulated Dvl PDZ domain with CXXC5 peptide and crystal Dvl PDZ domain with synthetic peptide-ligands, we generated two different pharmacophore models and applied pharmacophore-based virtual screening to discover potent inhibitors of the Dvl-CXXC5 interaction for the anabolic therapy of osteoporosis. Analysis of 16 compounds selected by means of a virtual screening protocol yielded four compounds that effectively disrupted the Dvl-CXXC5 interaction in the fluorescence polarization assay. Potential compounds were validated by fluorescence spectroscopy and nuclear magnetic resonance. We successfully identified a highly potent inhibitor, BMD4722, which directly binds to the Dvl PDZ domain and disrupts the Dvl-CXXC5 interaction. Overall, CXXC5-Dvl PDZ domain complex based pharmacophore combined with various traditional and simple computational methods is a promising approach for the development of modulators targeting the Dvl-CXXC5 interaction, and the potent inhibitor BMD4722 could serve as a starting point to discover or design more potent and specific the Dvl-CXXC5 interaction disruptors.

  18. Quenching points of dimeric single-molecule magnets: Exchange interaction effects

    International Nuclear Information System (INIS)

    Florez, J.M.; Nunez, Alvaro S.; Vargas, P.

    2010-01-01

    We study the quenched energy-splitting (Δ E ) of a single-molecule magnet (SMM) conformed by two exchange coupled giant-spins. An assessment of two nontrivial characteristics of this quenching is presented: (i) The quenching-points of a strongly exchange-coupled dimer differ from the ones of their respective giant-spin modeled SMM and such a difference can be well described by using the Solari-Kochetov extra phase; (ii) the dependence on the exchange coupling of the magnetic field values at the quenching-points when Δ E passes from monomeric to dimeric behavior. The physics behind these exchange-modified points, their relation with the Δ E -oscillations experimentally obtained by the Landau-Zener method and with the diabolical-plane of a SMM, is discussed.

  19. Quenching points of dimeric single-molecule magnets: Exchange interaction effects

    Energy Technology Data Exchange (ETDEWEB)

    Florez, J.M., E-mail: juanmanuel.florez@alumnos.usm.c [Departamento de Fisica, Universidad Tecnica Federico Santa Maria, P.O. Box 110-V, Valparaiso (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.c [Departamento de Fisica, Facultad de Ciencias Fisicas y Matematicas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Vargas, P., E-mail: patricio.vargas@usm.c [Departamento de Fisica, Universidad Tecnica Federico Santa Maria, P.O. Box 110-V, Valparaiso (Chile)

    2010-11-15

    We study the quenched energy-splitting ({Delta}{sub E}) of a single-molecule magnet (SMM) conformed by two exchange coupled giant-spins. An assessment of two nontrivial characteristics of this quenching is presented: (i) The quenching-points of a strongly exchange-coupled dimer differ from the ones of their respective giant-spin modeled SMM and such a difference can be well described by using the Solari-Kochetov extra phase; (ii) the dependence on the exchange coupling of the magnetic field values at the quenching-points when {Delta}{sub E} passes from monomeric to dimeric behavior. The physics behind these exchange-modified points, their relation with the {Delta}{sub E}-oscillations experimentally obtained by the Landau-Zener method and with the diabolical-plane of a SMM, is discussed.

  20. Ab initio study of low-energy electrons interacting with HCN molecules

    International Nuclear Information System (INIS)

    Jain, A.; Norcross, D.W.

    1984-01-01

    Our earlier study of low-energy electron scattering with HCN molecules is further improved by treating exchange exactly (in a separable exchange approximation 2 ) in Σ, π and Δ symmetries: the 3.8 eV π resonance is shifted towards lower energy (2.56 eV, the experimental position is around 2.26 eV 3 ), while in Σ and the Δ symmetries the difference is within 15%. We also study possible negative ion states of HCN by calculating potential energy curves with respect to C-H and C-N stretches. For example, there is evidence of an avoiding crossing between a 1Σ + and a 2Σ + state (C-H stretch) of HCN -

  1. Studying the molecular mechanisms of radiation damage : low-energy electron interactions with biomolecules and medically relevant molecules

    International Nuclear Information System (INIS)

    Tanzer, K.

    2015-01-01

    Since it was discovered in the year 2000 that secondary electrons with energies below 20 eV, which are the most abundant secondary species produced upon the interaction of ionizing radiation with biological tissue, can induce severe damages in the DNA such as single and double strand breaks, the interest for the study of the interaction of electrons with essential molecules of the human body has grown immensely. Double strand breaks can lead to cancer and are therefore a substantial threat to human health, however, the radiation research community is not sure how these strand breaks are formed upon interaction with ionizing radiation. The fact that even electrons with energies well below the ionization threshold can induce great damage in biological molecules via a resonant process called dissociative electron attachment (DEA), has even furthered the interest in these electron interactions, as it was shown to be a very efficient decomposition mechanism. A variety of studies, such as DEA studies to components of the DNA, for example, have been undertaken so far to shed more light on the role electrons play in the radiation damage of biomolecules. In this thesis two nucleobases, adenine and hypoxanthine, have been studied by observing their response towards low-energy electrons. It has been found that these nucleobases behave in a similar manner upon low-energy electron interaction, as do other nucleobases, that have been studied previously. The loss of hydrogen is suspected to act as a precursor for the decomposition of the DNA and the nucleobases can also undergo ring cleavage, which will induce substantial damage in the DNA. Furthermore, the search for improved and more efficient methods for the treatment of cancer is as important as ever, considering the ever-rising number of cancer deaths. Radiotherapy has proven to be one of the best treatments for tumors, but was found to be ineffective in hypoxic - oxygen deprived - tumors. Compounds called radiosensitizers

  2. Small molecule inhibitors of ERCC1-XPF protein-protein interaction synergize alkylating agents in cancer cells.

    Science.gov (United States)

    Jordheim, Lars Petter; Barakat, Khaled H; Heinrich-Balard, Laurence; Matera, Eva-Laure; Cros-Perrial, Emeline; Bouledrak, Karima; El Sabeh, Rana; Perez-Pineiro, Rolando; Wishart, David S; Cohen, Richard; Tuszynski, Jack; Dumontet, Charles

    2013-07-01

    The benefit of cancer chemotherapy based on alkylating agents is limited because of the action of DNA repair enzymes, which mitigate the damage induced by these agents. The interaction between the proteins ERCC1 and XPF involves two major components of the nucleotide excision repair pathway. Here, novel inhibitors of this interaction were identified by virtual screening based on available structures with use of the National Cancer Institute diversity set and a panel of DrugBank small molecules. Subsequently, experimental validation of the in silico screening was undertaken. Top hits were evaluated on A549 and HCT116 cancer cells. In particular, the compound labeled NSC 130813 [4-[(6-chloro-2-methoxy-9-acridinyl)amino]-2-[(4-methyl-1-piperazinyl)methyl

  3. Magnetic field manipulation of spin current in a single-molecule magnet tunnel junction with two-electron Coulomb interaction

    Science.gov (United States)

    Zhang, Chao; Yao, Hui; Nie, Yi-Hang; Liang, Jiu-Qing; Niu, Peng-Bin

    2018-04-01

    In this work, we study the generation of spin-current in a single-molecule magnet (SMM) tunnel junction with Coulomb interaction of transport electrons and external magnetic field. In the absence of field the spin-up and -down currents are symmetric with respect to the initial polarizations of molecule. The existence of magnetic field breaks the time-reversal symmetry, which leads to unsymmetrical spin currents of parallel and antiparallel polarizations. Both the amplitude and polarization direction of spin current can be controlled by the applied magnetic field. Particularly when the magnetic field increases to a certain value the spin-current with antiparallel polarization is reversed along with the magnetization reversal of the SMM. The two-electron occupation indeed enhances the transport current compared with the single-electron process. However the increase of Coulomb interaction results in the suppression of spin-current amplitude at the electron-hole symmetry point. We propose a scheme to compensate the suppression with the magnetic field.

  4. Natural products mediating ecological interactions in Antarctic benthic communities: a mini-review of the known molecules.

    Science.gov (United States)

    Núñez-Pons, L; Avila, C

    2015-07-01

    Out of the many bioactive compounds described from the oceans, only a small fraction have been studied for their ecological significance. Similarly, most chemically mediated interactions are not well understood, because the molecules involved remain unrevealed. In Antarctica, this gap in knowledge is even more acute in comparison to tropical or temperate regions, even though polar organisms are also prolific producers of chemical defenses, and pharmacologically relevant products are being reported from the Southern Ocean. The extreme and unique marine environments surrounding Antarctica along with the numerous unusual interactions taking place in benthic communities are expected to select for novel functional secondary metabolites. There is an urgent need to comprehend the evolutionary role of marine derived substances in general, and particularly at the Poles, since molecules of keystone significance are vital in species survival, and therefore, in structuring the communities. Here we provide a mini-review on the identified marine natural products proven to have an ecological function in Antarctic ecosystems. This report recapitulates some of the bibliography from original Antarctic reviews, and updates the new literature in the field from 2009 to the present.

  5. Interactions of molecules with surfaces. Progress report, 1 February 1985-31 January 1986

    International Nuclear Information System (INIS)

    Greene, E.F.

    1986-01-01

    The angular distributions of beams of Ne and Ar atoms scattered nearly elastically from LiF (100) at 294 K show structure that is obscured by inelastic scattering when the whole range of velocities leaving the crystal is recorded. Increased fluxes of neutral species in beams from an effusive source of alkali halide vapor observed when a beam of electrons is coaxial with the neutral beam are shown to be well accounted for by a model involving electron stimulated desorption of alkali atoms. A simple model is proposed for the compensation observed for changes of the preexponential factor and activation energy in rate coefficients for the desorption of molecules from surfaces undergoing surface phase transitions. The isomerization of perfluoroDewarbenzene to perfluorobenzene can be produced in yields of 10% after single energetic collisions with a surface of polytetrafluoroethylene. The yield of ions produced when a beam of Na atoms strikes a Si(111) surface is increased over the equilibrium value observed for thermal beams by a factor of 10 or more when the kinetic energy of the incoming atoms is increased to 14 eV. The yield is sensitive to the dynamics of electron exchange between the surface and the ion. 12 refs., 1 fig

  6. Interaction of silicon nanoparticles with the molecules of bovine serum albumin in aqueous solutions

    International Nuclear Information System (INIS)

    Anenkova, K A; Sergeeva, I A; Petrova, G P; Fedorova, K V; Osminkina, L A; Timoshenko, Viktor Yu

    2011-01-01

    Using the method of photon-correlation spectroscopy, the coefficient of translational diffusion D t and the hydrodynamic radius R of the particles in aqueous solutions of the bovine serum albumin, containing silicon nanoparticles, are determined. The character of the dependence of these parameters on the concentration of the protein indicates the absence of interaction between the studied particles in the chosen range of albumin concentrations 0.2 - 1.0 mg mL -1 . (optical technologies in biophysics and medicine)

  7. Interactive measurement and characterization of DNA molecules by analysis of AFM images

    Czech Academy of Sciences Publication Activity Database

    Marek, J.; Demjénová, E.; Tomori, Z.; Janáček, Jiří; Zolotová, I.; Valle, F.; Favre, M.; Dietler, G.

    2005-01-01

    Roč. 63, č. 2 (2005), s. 87-93 ISSN 1552-4922 Grant - others:VEGA(SK) 5048; VEGA(SK) 2185; CZ-SK(CZ) KONTAKT 139; Swiss National Science Foundation(CH) 2100-063746.00/1 Institutional research plan: CEZ:AV0Z5011922 Keywords : DNA * atomic force microscopy * interactive image analysis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.115, year: 2005

  8. Interactions of carbon dioxide with model organic molecules: A comparative theoretical study

    Science.gov (United States)

    Trung, Nguyen Tien; Nguyen, Minh Tho

    2013-08-01

    Interaction energies obtained using CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ computations including both ZPE and BSSE corrections range from -2.9 to -14.2 kJ mol-1. While formic acid forms the most stable complex with CO2, formaldehyde yields the least stable complex. Lewis acid-base interaction such as C-N⋯C(CO2), Cdbnd O⋯C(CO2), which overcomes C-H⋯O blue-shifting hydrogen bond, plays a significant role in stabilizing most complexes. However, the strength of (HCOOH, CO2) is mainly determined by O-H⋯O red-shifting hydrogen bond. The C-H⋯O blue-shifting hydrogen bond is revealed upon complexation of CH3OH, HCHO, HCOOH, CH3COCH3 and HCOOCH3 with CO2. Remarkably, existence of weak hydrogen bonded C-H⋯O interaction is not found in the (CH3OCH3, CO2) and (CH3NH2, CO2) pairs.

  9. International Conference on the Interaction of atoms, molecules and plasmas with intense ultrashort laser pulses. Book of abstracts

    International Nuclear Information System (INIS)

    2006-01-01

    International Conference on the Interaction of atoms, molecules and plasmas with intense ultrashort laser pulses was held in Hungary in 2006. This conference which joined the ULTRA COST activity ('Laser-matter interactions with ultra-short pulses, high-frequency pulses and ultra-intense pulses. From attophysics to petawatt physics') and the XTRA ('Ultrashort XUV Pulses for Time-Resolved and Non-Linear Applications') Marie-Curie Research Training Network, intends to offer a possibility to the members of both of these activities to exchange ideas on recent theoretical and experimental results on the interaction of ultrashort laser pulses with matter giving a broad view from theoretical models to practical and technical applications. Ultrashort laser pulses reaching extra high intensities open new windows to obtain information about molecular and atomic processes. These pulses are even able to penetrate into atomic scalelengths not only by generating particles of ultrahigh energy but also inside the spatial and temporal atomic scalelengths. New regimes of laser-matter interaction were opened in the last decade with an increasing number of laboratories and researchers in these fields. (S.I.)

  10. Assessing Specific Oligonucleotides and Small Molecule Antibiotics for the Ability to Inhibit the CRD-BP-CD44 RNA Interaction

    Science.gov (United States)

    Thomsen, Dana; Lee, Chow H.

    2014-01-01

    Studies on Coding Region Determinant-Binding Protein (CRD-BP) and its orthologs have confirmed their functional role in mRNA stability and localization. CRD-BP is present in extremely low levels in normal adult tissues, but it is over-expressed in many types of aggressive human cancers and in neonatal tissues. Although the exact role of CRD-BP in tumour progression is unclear, cumulative evidence suggests that its ability to physically associate with target mRNAs is an important criterion for its oncogenic role. CRD-BP has high affinity for the 3′UTR of the oncogenic CD44 mRNA and depletion of CRD-BP in cells led to destabilization of CD44 mRNA, decreased CD44 expression, reduced adhesion and disruption of invadopodia formation. Here, we further characterize the CRD-BP-CD44 RNA interaction and assess specific antisense oligonucleotides and small molecule antibiotics for their ability to inhibit the CRD-BP-CD44 RNA interaction. CRD-BP has a high affinity for binding to CD44 RNA nts 2862–3055 with a Kd of 645 nM. Out of ten antisense oligonucleotides spanning nts 2862–3055, only three antisense oligonucleotides (DD4, DD7 and DD10) were effective in competing with CRD-BP for binding to 32P-labeled CD44 RNA. The potency of DD4, DD7 and DD10 in inhibiting the CRD-BP-CD44 RNA interaction in vitro correlated with their ability to specifically reduce the steady-state level of CD44 mRNA in cells. The aminoglycoside antibiotics neomycin, paramomycin, kanamycin and streptomycin effectively inhibited the CRD-BP-CD44 RNA interaction in vitro. Assessing the potential inhibitory effect of aminoglycoside antibiotics including neomycin on the CRD-BP-CD44 mRNA interaction in cells proved difficult, likely due to their propensity to non-specifically bind nucleic acids. Our results have important implications for future studies in finding small molecules and nucleic acid-based inhibitors that interfere with protein-RNA interactions. PMID:24622399

  11. Analysis of vibronic interactions in the molecules of cross-conjugated ketones

    Directory of Open Access Journals (Sweden)

    Kompaneez V.V.

    2017-01-01

    Full Text Available We have done quantitative analysis of vibronic parameters of two cross-conjugated δ-dimethylaminoketones. The research shows the influence of С-N and C=O bonds in the rings, and the radicals with nitro compounds on the vibronic parameters of characteristic bands, which describe the state (vibrations, types of deformation under excitation of the phenyl ring and the polyene bridge. Results described impact of the substituent’s nature on the parameters of intra- and intermolecular interactions presents for the studied compounds.

  12. Controlling the formation process and atomic structures of single pyrazine molecular junction by tuning the strength of the metal-molecule interaction.

    Science.gov (United States)

    Kaneko, Satoshi; Takahashi, Ryoji; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

    2017-04-12

    The formation process and atomic structures were investigated for single pyrazine molecular junctions sandwiched by three different Au, Ag, and Cu electrodes using a mechanically controllable break junction technique in ultrahigh vacuum conditions at 300 K. We demonstrated that the formation process of the single-molecule junction crucially depended on the choice of the metal electrodes. While single-molecule junction showing two distinct conductance states were found for the Au electrodes, only the single conductance state was evident for the Ag electrodes, and there was no junction formation for the Cu electrodes. These results suggested that metal-molecule interaction dominates the formation process and probability of the single-molecule junction. In addition to the metal-molecule interaction, temperature affected the formation process of the single-molecule junction. The single pyrazine molecular junction formed between Au electrodes exhibited significant temperature dependence where the junction-formation probability was about 8% at 300 K, while there was no junction-formation at 100 K. Instead of the junction formation, an Au atomic wire was formed at the low temperature. This study provides insight into the tuning of the junction-forming process for single-molecule junctions, which is needed to construct device structures on a single molecule scale.

  13. Origin of the Strong Interaction between Polar Molecules and Copper(II) Paddle-Wheels in Metal Organic Frameworks.

    Science.gov (United States)

    Ongari, Daniele; Tiana, Davide; Stoneburner, Samuel J; Gagliardi, Laura; Smit, Berend

    2017-07-20

    The copper paddle-wheel is the building unit of many metal organic frameworks. Because of the ability of the copper cations to attract polar molecules, copper paddle-wheels are promising for carbon dioxide adsorption and separation. They have therefore been studied extensively, both experimentally and computationally. In this work we investigate the copper-CO 2 interaction in HKUST-1 and in two different cluster models of HKUST-1: monocopper Cu(formate) 2 and dicopper Cu 2 (formate) 4 . We show that density functional theory methods severely underestimate the interaction energy between copper paddle-wheels and CO 2 , even including corrections for the dispersion forces. In contrast, a multireference wave function followed by perturbation theory to second order using the CASPT2 method correctly describes this interaction. The restricted open-shell Møller-Plesset 2 method (ROS-MP2, equivalent to (2,2) CASPT2) was also found to be adequate in describing the system and used to develop a novel force field. Our parametrization is able to predict the experimental CO 2 adsorption isotherms in HKUST-1, and it is shown to be transferable to other copper paddle-wheel systems.

  14. Interaction of epitaxial silicene with overlayers formed by exposure to Al atoms and O{sub 2} molecules

    Energy Technology Data Exchange (ETDEWEB)

    Friedlein, R.; Yamada-Takamura, Y. [Japan Advanced Institute of Science and Technology, School of Materials Science, Nomi, Ishikawa 923-1292 (Japan); Van Bui, H.; Wiggers, F. B.; Kovalgin, A. Y.; Jong, M. P. de, E-mail: M.P.deJong@utwente.nl [MESA Institute for Nanotechnology, University of Twente, 7500 AE Enschede (Netherlands)

    2014-05-28

    As silicene is not chemically inert, the study and exploitation of its electronic properties outside of ultrahigh vacuum environments require the use of insulating capping layers. In order to understand if aluminum oxide might be a suitable encapsulation material, we used high-resolution synchrotron photoelectron spectroscopy to study the interactions of Al atoms and O{sub 2} molecules, as well as the combination of both, with epitaxial silicene on thin ZrB{sub 2}(0001) films grown on Si(111). The deposition of Al atoms onto silicene, up to the coverage of about 0.4 Al per Si atoms, has little effect on the chemical state of the Si atoms. The silicene-terminated surface is also hardly affected by exposure to O{sub 2} gas, up to a dose of 4500 L. In contrast, when Al-covered silicene is exposed to the same dose, a large fraction of the Si atoms becomes oxidized. This is attributed to dissociative chemisorption of O{sub 2} molecules by Al atoms at the surface, producing reactive atomic oxygen species that cause the oxidation. It is concluded that aluminum oxide overlayers prepared in this fashion are not suitable for encapsulation since they do not prevent but actually enhance the degradation of silicene.

  15. CHIPMUNK: A Virtual Synthesizable Small-Molecule Library for Medicinal Chemistry, Exploitable for Protein-Protein Interaction Modulators.

    Science.gov (United States)

    Humbeck, Lina; Weigang, Sebastian; Schäfer, Till; Mutzel, Petra; Koch, Oliver

    2018-03-20

    A common issue during drug design and development is the discovery of novel scaffolds for protein targets. On the one hand the chemical space of purchasable compounds is rather limited; on the other hand artificially generated molecules suffer from a grave lack of accessibility in practice. Therefore, we generated a novel virtual library of small molecules which are synthesizable from purchasable educts, called CHIPMUNK (CHemically feasible In silico Public Molecular UNiverse Knowledge base). Altogether, CHIPMUNK covers over 95 million compounds and encompasses regions of the chemical space that are not covered by existing databases. The coverage of CHIPMUNK exceeds the chemical space spanned by the Lipinski rule of five to foster the exploration of novel and difficult target classes. The analysis of the generated property space reveals that CHIPMUNK is well suited for the design of protein-protein interaction inhibitors (PPIIs). Furthermore, a recently developed structural clustering algorithm (StruClus) for big data was used to partition the sub-libraries into meaningful subsets and assist scientists to process the large amount of data. These clustered subsets also contain the target space based on ChEMBL data which was included during clustering. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Toward Small-Molecule Inhibition of Protein-Protein Interactions: General Aspects and Recent Progress in Targeting Costimulatory and Coinhibitory (Immune Checkpoint) Interactions.

    Science.gov (United States)

    Bojadzic, Damir; Buchwald, Peter

    2018-05-30

    Protein-protein interactions (PPIs) that are part of the costimulatory and coinhibitory (immune checkpoint) signaling are critical for adequate T cell response and are important therapeutic targets for immunomodulation. Biologics targeting them have already achieved considerable clinical success in the treatment of autoimmune diseases or transplant recipients (e.g., abatacept, belatacept, and belimumab) as well as cancer (e.g., ipilimumab, nivolumab, pembrolizumab, atezolizumab, durvalumab, and avelumab). In view of such progress, there have been only relatively limited efforts toward developing small-molecule PPI inhibitors (SMPPIIs) targeting these cosignaling interactions, possibly because they, as all other PPIs, are difficult to target by small molecules and were not considered druggable. Nevertheless, substantial progress has been achieved during the last decade. SMPPIIs proving the feasibility of such approaches have been identified through various strategies for a number of cosignaling interactions including CD40-CD40L, OX40-OX40L, BAFFR-BAFF, CD80-CD28, and PD-1-PD-L1s. Here, after an overview of the general aspects and challenges of SMPPII-focused drug discovery, we review them briefly together with relevant structural, immune-signaling, physicochemical, and medicinal chemistry aspects. While so far only a few of these SMPPIIs have shown activity in animal models (DRI-C21045 for CD40-D40L, KR33426 for BAFFR-BAFF) or reached clinical development (RhuDex for CD80-CD28, CA-170 for PD-1-PD-L1), there is proof-of-principle evidence for the feasibility of such approaches in immunomodulation. They can result in products that are easier to develop/manufacture and are less likely to be immunogenic or encounter postmarket safety events than corresponding biologics, and, contrary to them, can even become orally bioavailable. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Fibronectin type III (FN3) modules of the neuronal cell adhesion molecule L1 interact directly with the fibroblast growth factor (FGF) receptor

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Li, Shizhong; Hinsby, Anders Mørkeberg

    2008-01-01

    The neuronal cell adhesion molecule (CAM) L1 promotes axonal outgrowth, presumably through an interaction with the fibroblast growth factor receptor (FGFR). The present study demonstrates a direct interaction between L1 fibronectin type III (FN3) modules I-V and FGFR1 immunoglobulin (Ig) modules II...

  18. Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a Coulomb and van der Waals model.

    Science.gov (United States)

    Wahlberg, Nanna; Madsen, Anders Ø; Mikkelsen, Kurt V

    2018-06-09

    The nucleation processes of acetaminophen on poly(methyl methacrylate) and poly(vinyl acetate) have been investigated and the mechanisms of the processes are studied. This is achieved by a combination of theoretical models and computational investigations within the framework of a modified QM/MM method; a Coulomb-van der Waals model. We have combined quantum mechanical computations and electrostatic models at the atomistic level for investigating the stability of different orientations of acetaminophen on the polymer surfaces. Based on the Coulomb-van der Waals model, we have determined the most stable orientation to be a flat orientation, and the strongest interaction is seen between poly(vinyl acetate) and the molecule in a flat orientation in vacuum.

  19. Ab Initio Density Functional Theory Investigation of the Interaction between Carbon Nanotubes and Water Molecules during Water Desalination Process

    Directory of Open Access Journals (Sweden)

    Loay A. Elalfy

    2013-01-01

    Full Text Available Density functional theory calculations using B3LYP/3-21G level of theory have been implemented on 6 carbon nanotubes (CNTs structures (3 zigzag and 3 armchair CNTs to study the energetics of the reverse osmosis during water desalination process. Calculations of the band gap, interaction energy, highest occupied molecular orbital, lowest unoccupied molecular orbital, electronegativity, hardness, and pressure of the system are discussed. The calculations showed that the water molecule that exists inside the CNT is about 2-3 Å away from its wall. The calculations have proven that the zigzag CNTs are more efficient for reverse osmosis water desalination process than armchair CNTs as the reverse osmosis process requires pressure of approximately 200 MPa for armchair CNTs, which is consistent with the values used in molecular dynamics simulations, while that needed when using zigzag CNTs was in the order of 60 MPa.

  20. Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome.

    Science.gov (United States)

    Lewis, Jacob S; Spenkelink, Lisanne M; Schauer, Grant D; Hill, Flynn R; Georgescu, Roxanna E; O'Donnell, Michael E; van Oijen, Antoine M

    2017-10-03

    The replisome, the multiprotein system responsible for genome duplication, is a highly dynamic complex displaying a large number of different enzyme activities. Recently, the Saccharomyces cerevisiae minimal replication reaction has been successfully reconstituted in vitro. This provided an opportunity to uncover the enzymatic activities of many of the components in a eukaryotic system. Their dynamic behavior and interactions in the context of the replisome, however, remain unclear. We use a tethered-bead assay to provide real-time visualization of leading-strand synthesis by the S. cerevisiae replisome at the single-molecule level. The minimal reconstituted leading-strand replisome requires 24 proteins, forming the CMG helicase, the Pol ε DNA polymerase, the RFC clamp loader, the PCNA sliding clamp, and the RPA single-stranded DNA binding protein. We observe rates and product lengths similar to those obtained from ensemble biochemical experiments. At the single-molecule level, we probe the behavior of two components of the replication progression complex and characterize their interaction with active leading-strand replisomes. The Minichromosome maintenance protein 10 (Mcm10), an important player in CMG activation, increases the number of productive replication events in our assay. Furthermore, we show that the fork protection complex Mrc1-Tof1-Csm3 (MTC) enhances the rate of the leading-strand replisome threefold. The introduction of periods of fast replication by MTC leads to an average rate enhancement of a factor of 2, similar to observations in cellular studies. We observe that the MTC complex acts in a dynamic fashion with the moving replisome, leading to alternating phases of slow and fast replication.

  1. Interaction of ions, atoms, and small molecules with quantized vortex lines in superfluid (4)He.

    Science.gov (United States)

    Mateo, David; Eloranta, Jussi; Williams, Gary A

    2015-02-14

    The interaction of a number of impurities (H2, Ag, Cu, Ag2, Cu2, Li, He3 (+), He(*) ((3)S), He2 (∗) ((3)Σu), and e(-)) with quantized rectilinear vortex lines in superfluid (4)He is calculated by using the Orsay-Trento density functional theory (DFT) method at 0 K. The Donnelly-Parks (DP) potential function binding ions to the vortex is combined with DFT data, yielding the impurity radius as well as the vortex line core parameter. The vortex core parameter at 0 K (0.74 Å) obtained either directly from the vortex line geometry or through the DP potential fitting is smaller than previously suggested but is compatible with the value obtained from re-analysis of the Rayfield-Reif experiment. All of the impurities have significantly higher binding energies to vortex lines below 1 K than the available thermal energy, where the thermally assisted escape process becomes exponentially negligible. Even at higher temperatures 1.5-2.0 K, the trapping times for larger metal clusters are sufficiently long that the previously observed metal nanowire assembly in superfluid helium can take place at vortex lines. The binding energy of the electron bubble is predicted to decrease as a function of both temperature and pressure, which allows adjusting the trap depth for either permanent trapping or to allow thermally assisted escape. Finally, a new scheme for determining the trapping of impurities on vortex lines by optical absorption spectroscopy is outlined and demonstrated for He(*).

  2. An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions.

    Directory of Open Access Journals (Sweden)

    Garima Tiwari

    Full Text Available Inhibitors of PDZ-peptide interactions have important implications in a variety of biological processes including treatment of cancer and Parkinson's disease. Even though experimental studies have reported characterization of peptidomimetic inhibitors of PDZ-peptide interactions, the binding modes for most of them have not been characterized by structural studies. In this study we have attempted to understand the structural basis of the small molecule-PDZ interactions by in silico analysis of the binding modes and binding affinities of a set of 38 small molecules with known K(i or K(d values for PDZ2 and PDZ3 domains of PSD-95 protein. These two PDZ domains show differential selectivity for these compounds despite having a high degree of sequence similarity and almost identical peptide binding pockets. Optimum binding modes for these ligands for PDZ2 and PDZ3 domains were identified by using a novel combination of semi-flexible docking and explicit solvent molecular dynamics (MD simulations. Analysis of the binding modes revealed most of the peptidomimectic ligands which had high K(i or K(d moved away from the peptide binding pocket, while ligands with high binding affinities remained in the peptide binding pocket. The differential specificities of the PDZ2 and PDZ3 domains primarily arise from differences in the conformation of the loop connecting βB and βC strands, because this loop interacts with the N-terminal chemical moieties of the ligands. We have also computed the MM/PBSA binding free energy values for these 38 compounds with both the PDZ domains from multiple 5 ns MD trajectories on each complex i.e. a total of 228 MD trajectories of 5 ns length each. Interestingly, computational binding free energies show good agreement with experimental binding free energies with a correlation coefficient of approximately 0.6. Thus our study demonstrates that combined use of docking and MD simulations can help in identification of potent inhibitors

  3. From the depletion attraction to the bridging attraction: the effect of solvent molecules on the effective colloidal interactions.

    Science.gov (United States)

    Chen, Jie; Kline, Steven R; Liu, Yun

    2015-02-28

    Depletion attraction induced by non-adsorbing polymers or small particles in colloidal solutions has been widely used as a model colloidal interaction to understand aggregation behavior and phase diagrams, such as glass transitions and gelation. However, much less attention has been paid to study the effective colloidal interaction when small particles/molecules can be reversibly attracted to large colloidal particles. At the strong attraction limit, small particles can introduce bridging attraction as it can simultaneously attach to neighbouring large colloidal particles. We use Baxter's multi-component method for sticky hard sphere systems with the Percus-Yevick approximation to study the bridging attraction and its consequence to phase diagrams, which are controlled by the concentration of small particles and their interaction with large particles. When the concentration of small particles is very low, the bridging attraction strength increases very fast with the increase of small particle concentration. The attraction strength eventually reaches a maximum bridging attraction (MBA). Adding more small particles after the MBA concentration keeps decreasing the attraction strength until reaching a concentration above which the net effect of small particles only introduces an effective repulsion between large colloidal particles. These behaviors are qualitatively different from the concentration dependence of the depletion attraction on small particles and make phase diagrams very rich for bridging attraction systems. We calculate the spinodal and binodal regions, the percolation lines, the MBA lines, and the equivalent hard sphere interaction line for bridging attraction systems and have proposed a simple analytic solution to calculate the effective attraction strength using the concentrations of large and small particles. Our theoretical results are found to be consistent with experimental results reported recently.

  4. Physisorption of three amine terminated molecules (TMBDA, BDA, TFBDA) on the Au(111) Surface: The Role of van der Waals Interaction

    Science.gov (United States)

    Aminpour, Maral; Le, Duy; Rahman, Talat S.

    2012-02-01

    Recently, the electronic properties and alignment of tetramethyl-1,4-benzenediamine (TMBDA), 1,4-benzenediamine (BDA) and tetrafluro-1,4-benzenediamine (TFBDA) molecules were studied experimentally. Discrepancies were found for both the binding energy and the molecule tilt angle with respect to the surface, when results were compared with density functional theory calculations [1]. We have included the effect of vdW interactions both between the molecules and the Au(111) surface and find binding energies which are in very good agreement with experiments. We also find that at low coverages each of these molecules would adsorb almost parallel to the surface. N-Au bond lengths and charge redistribution on adsorption of the molecules are also analyzed. Our calculations are based on DFT using vdW-DF exchange correlation functionals. For BDA (since we are aware of experimental data), we show that for higher coverage, inclusion of intermolecular van der Waals interaction leads to tilting of the molecules with respect to the surface and formation of line structures. Our results demonstrate the central role played by intermolecular interaction in pattern formation on this surface.[4pt] [1] M. Dell'Angela et al, Nano Lett. 2010, 10, 2470; M. Kamenetska et al, J. Phys. Chem. C, 2011, 115, 12625

  5. Molecular characterization of the gerbil C5a receptor and identification of a transmembrane domain V amino acid that is crucial for small molecule antagonist interaction.

    Science.gov (United States)

    Waters, Stephen M; Brodbeck, Robbin M; Steflik, Jeremy; Yu, Jianying; Baltazar, Carolyn; Peck, Amy E; Severance, Daniel; Zhang, Lu Yan; Currie, Kevin; Chenard, Bertrand L; Hutchison, Alan J; Maynard, George; Krause, James E

    2005-12-09

    Anaphylatoxin C5a is a potent inflammatory mediator associated with pathogenesis and progression of several inflammation-associated disorders. Small molecule C5a receptor (C5aR) antagonist development is hampered by species-specific receptor biology and the associated inability to use standard rat and mouse in vivo models. Gerbil is one rodent species reportedly responsive to small molecule C5aR antagonists with human C5aR affinity. We report the identification of the gerbil C5aR cDNA using a degenerate primer PCR cloning strategy. The nucleotide sequence revealed an open reading frame encoding a 347-amino acid protein. The cloned receptor (expressed in Sf9 cells) bound recombinant human C5a with nanomolar affinity. Alignment of the gerbil C5aR sequence with those from other species showed that a Trp residue in transmembrane domain V is the only transmembrane domain amino acid unique to small molecule C5aR antagonist-responsive species (i.e. gerbil, human, and non-human primate). Site-directed mutagenesis was used to generate human and mouse C5aRs with a residue exchange of this Trp residue. Mutation of Trp to Leu in human C5aR completely eliminated small molecule antagonist-receptor interaction. In contrast, mutation of Leu to Trp in mouse C5aR enabled small molecule antagonist-receptor interaction. This crucial Trp residue is located deeper within transmembrane domain V than residues reportedly involved in C5a- and cyclic peptide C5a antagonist-receptor interaction, suggesting a novel interaction site(s) for small molecule antagonists. These data provide insight into the basis for small molecule antagonist species selectivity and further define sites critical for C5aR activation and function.

  6. Single-molecule pull-down (SiMPull) for new-age biochemistry: methodology and biochemical applications of single-molecule pull-down (SiMPull) for probing biomolecular interactions in crude cell extracts.

    Science.gov (United States)

    Aggarwal, Vasudha; Ha, Taekjip

    2014-11-01

    Macromolecular interactions play a central role in many biological processes. Protein-protein interactions have mostly been studied by co-immunoprecipitation, which cannot provide quantitative information on all possible molecular connections present in the complex. We will review a new approach that allows cellular proteins and biomolecular complexes to be studied in real-time at the single-molecule level. This technique is called single-molecule pull-down (SiMPull), because it integrates principles of conventional immunoprecipitation with the powerful single-molecule fluorescence microscopy. SiMPull is used to count how many of each protein is present in the physiological complexes found in cytosol and membranes. Concurrently, it serves as a single-molecule biochemical tool to perform functional studies on the pulled-down proteins. In this review, we will focus on the detailed methodology of SiMPull, its salient features and a wide range of biological applications in comparison with other biosensing tools. © 2014 WILEY Periodicals, Inc.

  7. Effect of finite Coulomb interaction on full counting statistics of electronic transport through single-molecule magnet

    Energy Technology Data Exchange (ETDEWEB)

    Xue Haibin, E-mail: xhb98326110@163.co [Institute of Theoretical Physics, Shanxi University, Taiyuan, Shanxi 030006 (China); Nie, Y.-H., E-mail: nieyh@sxu.edu.c [Institute of Theoretical Physics, Shanxi University, Taiyuan, Shanxi 030006 (China); Li, Z.-J.; Liang, J.-Q. [Institute of Theoretical Physics, Shanxi University, Taiyuan, Shanxi 030006 (China)

    2011-01-17

    We study the full counting statistics (FCS) in a single-molecule magnet (SMM) with finite Coulomb interaction U. For finite U the FCS, differing from U{yields}{infinity}, shows a symmetric gate-voltage-dependence when the coupling strengths with two electrodes are interchanged, which can be observed experimentally just by reversing the bias-voltage. Moreover, we find that the effect of finite U on shot noise depends on the internal level structure of the SMM and the coupling asymmetry of the SMM with two electrodes as well. When the coupling of the SMM with the incident-electrode is stronger than that with the outgoing-electrode, the super-Poissonian shot noise in the sequential tunneling regime appears under relatively small gate-voltage and relatively large finite U, and dose not for U{yields}{infinity}; while it occurs at relatively large gate-voltage for the opposite coupling case. The formation mechanism of super-Poissonian shot noise can be qualitatively attributed to the competition between fast and slow transport channels.

  8. Effect of finite Coulomb interaction on full counting statistics of electronic transport through single-molecule magnet

    International Nuclear Information System (INIS)

    Xue Haibin; Nie, Y.-H.; Li, Z.-J.; Liang, J.-Q.

    2011-01-01

    We study the full counting statistics (FCS) in a single-molecule magnet (SMM) with finite Coulomb interaction U. For finite U the FCS, differing from U→∞, shows a symmetric gate-voltage-dependence when the coupling strengths with two electrodes are interchanged, which can be observed experimentally just by reversing the bias-voltage. Moreover, we find that the effect of finite U on shot noise depends on the internal level structure of the SMM and the coupling asymmetry of the SMM with two electrodes as well. When the coupling of the SMM with the incident-electrode is stronger than that with the outgoing-electrode, the super-Poissonian shot noise in the sequential tunneling regime appears under relatively small gate-voltage and relatively large finite U, and dose not for U→∞; while it occurs at relatively large gate-voltage for the opposite coupling case. The formation mechanism of super-Poissonian shot noise can be qualitatively attributed to the competition between fast and slow transport channels.

  9. Stromal interaction molecule 1 (STIM1) silencing inhibits tumor growth and promotes cell cycle arrest and apoptosis in hypopharyngeal carcinoma.

    Science.gov (United States)

    Sun, Yuanhao; Cui, Xiaobo; Wang, Jun; Wu, Shuai; Bai, Yunfei; Wang, Yaping; Wang, Boqian; Fang, Jugao

    2015-05-01

    As an important pathway maintaining the balance of intracellular calcium (Ca(2+)), store-operated Ca(2+) entry (SOCE) is critical for cellular functions. Stromal interaction molecule 1 (STIM1), a key component of SOCE, plays a dual role as an endoplasmic reticulum Ca(2+) receptor and an SOCE exciter. Aberrant expression of STIM1 could be discovered in several human cancer cells. However, the role of STIM1 in regulating human hypopharyngeal carcinoma still remains unclear. Real-time polymerase chain reaction (PCR) was used to detect expression of STIM1 in human hypopharyngeal carcinoma cell line FaDu. STIM1 on FaDu cells was knocked down by lentiviral transduction method. The biological impacts after knocking down of STIM1 on FaDu cells were investigated in vitro and in vivo. The result of real-time PCR showed that STIM1 was expressed in FaDu cells. Lentiviral transduction efficiently downregulated the expression of STIM1 in FaDu cells at both mRNA and protein levels. Significant downregulation of STIM1 on FaDu cells inhibited cell proliferation, induced cell cycle arrest in G0/G1 phase, promoted cell apoptosis, and restrained cell growth rate. The antigrowth effect of STIM1 silencing was also discovered in FaDu hypopharyngeal tumor model. Our findings indicate that STIM1 is likely to become a new therapeutic target for hypopharyngeal carcinoma treatment.

  10. UNIQUAC interaction parameters for molecules with -OH groups on adjacent carbon atoms in aqueous solution determined by molecular mechanics - glycols, glycerol and glucose

    DEFF Research Database (Denmark)

    Jonsdottir, Svava Osk; Klein, R. A.

    1997-01-01

    UNIQUAC interaction parameters have been determined, using molecular mechanics calculations, for 1,2-ethanediol, 1,2-propanediol, glycerol and glucose with water in aqueous solution. Conformational space for individual pairs of molecules was explored using a stochastic method, the Boltzmann Jump...

  11. Electronic structure of CoPc adsorbed on Ag(100): Evidence for molecule-substrate interaction mediated by Co 3d orbitals

    Czech Academy of Sciences Publication Activity Database

    Salomon, E.; Amsalem, P.; Marom, N.; Vondráček, Martin; Kronik, L.; Koch, N.; Angot, T.

    2013-01-01

    Roč. 87, č. 7 (2013), "075407-1"-"075407-9" ISSN 1098-0121 R&D Projects: GA MŠk(CZ) LG12003 Institutional support: RVO:68378271 Keywords : cobalt-phthalocyanine * molecule-substrate interaction * photoemission spectroscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.664, year: 2013

  12. Interaction of slow electrons with high-pressure gases (Quasi-liquids). Synthesis of our knowledge on slow electron-molecule interactions. Progress report for year ending June 15, 1984

    International Nuclear Information System (INIS)

    McCorkle, D.L.; Christophorou, L.G.

    1984-01-01

    A crucial step in efforts to develop not only a coherent picture of radiation interaction with matter, but also to understand radiation effects and mechanisms, as well as the effects of chemical pollutants and toxic compounds, is to relate the often abundant knowledge on isolated molecules (low pressure gases) to that on liquids or solids. To understand the roles of the physical and chemical properties of molecules in biological reactions, the way these isolated-molecule properties change as molecules are embedded in gradually thicker and thicker (denser and denser) gaseous and, finally, liquid environments must be known. The work reported here, carried out both at the Physics Department of the University of Tennessee and at the Oak Ridge National Laboratory addresses itself to this question. At both places, high pressure (40 to approx. 8000 kPa) electron swarm experiments are currently in operation yielding the first information as to the effects of the density and nature of the environment on fundamental electron-molecule interaction processes at densities intermediate to those corresponding to low pressure gases and liquids, and the gradual transition from isolated molecule to condensed phase behavior. Basic physical data on the electronic states of atmospheric halocarbons in general, and of polycyclic aromatic hydrocarbons in particular were also studied. Such data are of special significance because of the occurrence of these molecules in the atmosphere, and are presently lacking

  13. Multireference configuration interaction study on spectroscopic properties of low-lying electronic states of As2 molecule

    International Nuclear Information System (INIS)

    Wang Jie-Min; Liu Qiang

    2013-01-01

    The potential energy curves (PECs) of four electronic states (X 1 Σ g + , e 3 Δ u , a 3 Σ u − , and d 3 Π g ) of an As 2 molecule are investigated employing the complete active space self-consistent field (CASSCF) method followed by the valence internally contracted multireference configuration interaction (MRCI) approach in conjunction with the correlation-consistent aug-cc-pV5Z basis set. The effect on PECs by the relativistic correction is taken into account. The way to consider the relativistic correction is to employ the second-order Douglas-Kroll Hamiltonian approximation. The correction is made at the level of a cc-pV5Z basis set. The PECs of the electronic states involved are extrapolated to the complete basis set limit. With the PECs, the spectroscopic parameters (T e , R e , ω e , ω e x e , ω e y e , α e , β e , γ e , and B e ) of these electronic states are determined and compared in detail with those reported in the literature. Excellent agreement is found between the present results and the experimental data. The first 40 vibrational states are studied for each electronic state when the rotational quantum number J equals zero. In addition, the vibrational levels, inertial rotation and centrifugal distortion constants of d 3 Π g electronic state are reported which are in excellent agreement with the available measurements. Comparison with the experimental data shows that the present results are both reliable and accurate. (atomic and molecular physics)

  14. Free molecule flow analysis of the interaction of skimming hardware components and background gas with free jets

    International Nuclear Information System (INIS)

    Raghuraman, P.; Bossel, U.

    1974-01-01

    Under conditions typical for the extraction of nozzle beams from free jets the rarefied flow pattern in the expansion chamber containing skimming hardware components and background gas is studied using a free molecule solution to the Boltzmann equation

  15. Molecules in the cold environment of a supersonic free-jet beam: from spectroscopy of neutral-neutral interactions to a test of Bell's inequality

    International Nuclear Information System (INIS)

    Koperski, J; Fry, E S

    2006-01-01

    The supersonic free-jet expansion technique has been used in different fields of research in physics, physical chemistry and chemistry to study vibrational and rotational molecular structures in ground and excited electronic energy states as well as in cold chemistry to study chemical reactions in a unique environment. The supersonic beam technique, as a widely used method in laser spectroscopy of molecules, exploits a source of monokinetic, rotationally and vibrationally cold molecules, that are very weakly bound in their ground electronic states (van der Waals molecules). In experiments at Jagiellonian University the supersonic free-jet beam serves as a source of ground-state van der Waals objects in studies of neutral-neutral interactions between group 12 metal (M = Zn, Cd, Hg) and noble gas (NG) atoms. Recently, the method has been applied as a source of entangled 199 Hg atom pairs in order to test Bell's inequality in an experiment at Texas A and M University

  16. The effect of water molecules on the thiol collector interaction on the galena (PbS) and sphalerite (ZnS) surfaces: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Long, Xianhao [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Chen, Ye, E-mail: fby18@126.com [College of Resources and Metallurgy, Guangxi University, Nanning 530004 (China); Chen, Jianhua, E-mail: jhchen@gxu.edu.cn [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); College of Resources and Metallurgy, Guangxi University, Nanning 530004 (China); Xu, Zhenghe; Liu, Qingxia [Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2V4 (Canada); Du, Zheng [National Supercomputing Center in Shenzhen, Shenzhen 518055 (China)

    2016-12-15

    Highlights: • Water adsorption has a greater effect on the electron distribution of ZnS surface than PbS surface. • Water adsorption decreases the reactivity of ZnS surface atoms but improves that of PbS. • Thiol collectors cannot interact with the hydrated ZnS surface. • The hydration has little influence on the interaction of thiol collectors with PbS surface. - Abstracts: In froth flotation the molecular interaction between reagents and mineral surfaces take place at the solid liquid interface. In this paper, the effect of water molecule on the three typical thiol collectors (xanthate, dithiocarbomate and dithiophosphate) interactions at the galena (PbS) and sphalerite (ZnS) surfaces has been studied adopting density functional theory (DFT). The results suggests that the presence of water molecule shows a greater influence on the electron distribution of ZnS surface than PbS surface, and reduce the reactivity of ZnS surface atoms but improves the reactivity of PbS surface atoms during the reaction with xanthate. Water adsorption could also reduce the covalent binding between Zn and S atoms but have little influence on Pb-S bond. In the presence of water, xanthate, dithiocarbomate (DTC) and dithiophosphate (DTP) could not adsorb on the sphalerite surface. And for galena (PbS) surface, the interaction of DTP is the strongest, then the DTC and the interaction of xanthate is the weakest. These results agree well with the flotation practice.

  17. Quantum electrodynamics with nonrelativistic sources. V. Electromagnetic field correlations and intermolecular interactions between molecules in either ground or excited states

    International Nuclear Information System (INIS)

    Power, E.A.; Thirunamachandran, T.

    1993-01-01

    Spatial correlations between electromagnetic fields arising from neutral sources with electric-dipole transition moments are calculated using nonrelativistic quantum electrodynamics in the multipolar formalism. Expressions for electric-electric, magnetic-magnetic, and electric-magnetic correlation functions at two points r and r' are given for a source molecule in either a ground or an excited state. In contrast to the electric-electric and magnetic-magnetic cases there are no electric-magnetic correlations for a ground-state molecule. For an excited molecule the downward transitions contribute additional terms which have modulating factors depending on (r-r')/λ. From these correlation functions electric and magnetic energy densities are found by setting r=r'. These energy densities are then used in a response formalism to calculate intermolecular energy shifts. In the case of two ground-state molecules this leads to the Casimir-Polder potential. However, for a pair of molecules, one or both excited, there are additional terms arising from downward transitions. An important feature of these energies is that they exhibit an R -2 dependence for large intermolecular separations R. This dependence is interpreted in terms of the Poynting vector, which itself can be obtained by setting r=r' in the electric-magnetic correlation function

  18. Interaction of VLA-5 Molecule With Rheumatoid Articular Cartilage Surface : An Electron Microscopic Evidence of Expression of VLA-5 on Pannus Invading Cells

    OpenAIRE

    Ishikawa, Hitoshi; Hirata, Souichirou; Saura, Ryuuichi; Andoh, Yoshihiro; Mizuno, Kosaku

    1998-01-01

    Pannus is made up mainly of fibroblasts, macrophages and lymphocytes. VLA-5 positive cells are present in the pannus in large numbers. It is likely that the tissue distribution of infiltrated cells derived from post-capillary venules is influenced by the ECM of the pannus and the ability of these cells to interact with the ECM through surface receptor expression. VLA-5 molecules are the predominant (31 integrins expressed by synovial pannus. Since the VLA integrins function as fibronectin rec...

  19. Positron-attachment to small molecules: Vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach

    Energy Technology Data Exchange (ETDEWEB)

    Tachikawa, Masanori [Quantum Chemistry Division, Graduate School of NanoBioScience, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama 236-0027 (Japan)

    2015-12-31

    To theoretically demonstrate the binding of a positron to small polarized molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic - single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential.

  20. Interaction of plant cell signaling molecules, salicylic acid and jasmonic acid, with the mitochondria of Helicoverpa armigera.

    Science.gov (United States)

    Akbar, S M D; Sharma, H C; Jayalakshmi, S K; Sreeramulu, K

    2012-02-01

    The cotton bollworm, Helicoverpa armigera is a polyphagous pest in Asia, Africa, and the Mediterranean Europe. Salicylic acid (SA) and jasmonic acid (JA) are the cell signaling molecules produced in response to insect attack in plants. The effect of these signaling molecules was investigated on the oxidative phosphorylation and oxidative stress of H. armigera. SA significantly inhibited the state III and state IV respiration, respiratory control index (RCI), respiratory complexes I and II, induced mitochondrial swelling, and cytochrome c release in vitro. Under in vivo conditions, SA induced state IV respiration as well as oxidative stress in time- and dose-dependent manner, and also inhibited the larval growth. In contrast, JA did not affect the mitochondrial respiration and oxidative stress. SA affected the growth and development of H. armigera, in addition to its function as signaling molecules involved in both local defense reactions at feeding sites and the induction of systemic acquired resistance in plants.

  1. Receptor-like Molecules on Human Intestinal Epithelial Cells Interact with an Adhesion Factor from Lactobacillus reuteri.

    Science.gov (United States)

    Matsuo, Yosuke; Miyoshi, Yukihiro; Okada, Sanae; Satoh, Eiichi

    2012-01-01

    A surface protein of Lactobacillus reuteri, mucus adhesion-promoting protein (MapA), is considered to be an adhesion factor. MapA is expressed in L. reuteri strains and adheres to piglet gastric mucus, collagen type I, and human intestinal epithelial cells such as Caco-2. The aim of this study was to identify molecules that mediate the attachment of MapA from L. reuteri to the intestinal epithelial cell surface by investigating the adhesion of MapA to receptor-like molecules on Caco-2 cells. MapA-binding receptor-like molecules were detected in Caco-2 cell lysates by 2D-PAGE. Two proteins, annexin A13 (ANXA13) and paralemmin (PALM), were identified by MALDI TOF-MS. The results of a pull-down assay showed that MapA bound directly to ANXA13 and PALM. Fluorescence microscopy studies confirmed that MapA binding to ANXA13 and PALM was colocalized on the Caco-2 cell membrane. To evaluate whether ANXA13 and PALM are important for MapA adhesion, ANXA13 and PALM knockdown cell lines were established. The adhesion of MapA to the abovementioned cell lines was reduced compared with that to wild-type Caco-2 cells. These knockdown experiments established the importance of these receptor-like molecules in MapA adhesion.

  2. The yeast three-hybrid system as an experimental platform to identify proteins interacting with small signaling molecules in plant cells: Potential and limitations

    Directory of Open Access Journals (Sweden)

    Stéphanie eCottier

    2011-12-01

    Full Text Available Chemical genetics is a powerful scientific strategy that utilizes small bioactive molecules as experimental tools to unravel biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that can be used to dissect functions of biological systems. Once the bioactivity of a natural or synthetic compound has been critically evaluated the challenge remains to identify its molecular target and mode of action, which usually is a time consuming and labor-intensive process. To facilitate this task, we decided to implement the yeast three-hybrid (Y3H technology as a general experimental platform to scan the whole Arabidopsis proteome for targets of small signaling molecules. The Y3H technology is based on the yeast two-hybrid system and allows direct cloning of proteins that interact in vivo with a synthetic hybrid ligand, which comprises the biologically active molecule of interest covalently linked to methotrexate (Mtx. In yeast nucleus the hybrid ligand connects two fusion proteins: the Mtx part binding to dihydrofolate reductase fused to a DNA binding domain (encoded in the yeast strain, and the bioactive molecule part binding to its potential protein target fused to a DNA activating domain (encoded on a cDNA expression vector. During cDNA library screening, the formation of this ternary, transcriptional activator complex leads to reporter gene activation in yeast cells, and thereby allows selection of the putative targets of small bioactive molecules of interest. Here we present the strategy and experimental details for construction and application of a Y3H platform, including chemical synthesis of different hybrid ligands, construction of suitable cDNA libraries, the choice of yeast strains, and appropriate screening conditions. Based on the results obtained and the current literature we discussed the perspectives and limitations of the Y3H approach for identifying targets of small bioactive molecules.

  3. A viral, transporter associated with antigen processing (TAP)-independent, high affinity ligand with alternative interactions endogenously presented by the nonclassical human leukocyte antigen E class I molecule.

    Science.gov (United States)

    Lorente, Elena; Infantes, Susana; Abia, David; Barnea, Eilon; Beer, Ilan; García, Ruth; Lasala, Fátima; Jiménez, Mercedes; Mir, Carmen; Morreale, Antonio; Admon, Arie; López, Daniel

    2012-10-12

    The transporter associated with antigen processing (TAP) enables the flow of viral peptides generated in the cytosol by the proteasome and other proteases to the endoplasmic reticulum, where they complex with nascent human leukocyte antigen (HLA) class I. Later, these peptide-HLA class I complexes can be recognized by CD8(+) lymphocytes. Cancerous cells and infected cells in which TAP is blocked, as well as individuals with unusable TAP complexes, are able to present peptides on HLA class I by generating them through TAP-independent processing pathways. Here, we identify a physiologically processed HLA-E ligand derived from the D8L protein in TAP-deficient vaccinia virus-infected cells. This natural high affinity HLA-E class I ligand uses alternative interactions to the anchor motifs previously described to be presented on nonclassical HLA class I molecules. This octameric peptide was also presented on HLA-Cw1 with similar binding affinity on both classical and nonclassical class I molecules. In addition, this viral peptide inhibits HLA-E-mediated cytolysis by natural killer cells. Comparison between the amino acid sequences of the presenting HLA-E and HLA-Cw1 alleles revealed a shared structural motif in both HLA class molecules, which could be related to their observed similar cross-reactivity affinities. This motif consists of several residues located on the floor of the peptide-binding site. These data expand the role of HLA-E as an antigen-presenting molecule.

  4. Theoretical study of the interaction of N2 with water molecules. (H2O)/sub n/:N2, n = 1--8

    International Nuclear Information System (INIS)

    Curtiss, L.A.; Eisgruber, C.L.

    1984-01-01

    Ab initio molecular orbital calculations including correlation energy have been carried out on the interaction of a single H 2 O molecule with N 2 . The potential energy surface for H 2 O:N 2 is found to have a minimum corresponding to a HOH xxx N 2 structure with a weak ( -1 ) hydrogen bond. A second, less stable, configuration corresponding to a H 2 O xxx N 2 structure with N 2 bonded side on to the oxygen of H 2 O was found to be either a minimum or a saddle point in the potential energy surface depending on the level of calculation. The minimal STO-3G basis set was used to investigate the interaction of up to eight H 2 O molecules with N 2 . Two types of clusters, one containing only HOH xxx N 2 interactions and the other containing both HOH xxxN 2 and H 2 O xxx N 2 interactions, were investigated for [N 2 :(H 2 O)/sub n/, n = 2--8

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

    Science.gov (United States)

    Malina, Halina Z

    2011-01-19

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

  6. Improved Limits on Axionlike-Particle-Mediated P , T -Violating Interactions between Electrons and Nucleons from Electric Dipole Moments of Atoms and Molecules

    Science.gov (United States)

    Stadnik, Y. V.; Dzuba, V. A.; Flambaum, V. V.

    2018-01-01

    In the presence of P , T -violating interactions, the exchange of axionlike particles between electrons and nucleons in atoms and molecules induces electric dipole moments (EDMs) of atoms and molecules. We perform calculations of such axion-exchange-induced atomic EDMs using the relativistic Hartree-Fock-Dirac method including electron core polarization corrections. We present analytical estimates to explain the dependence of these induced atomic EDMs on the axion mass and atomic parameters. From the experimental bounds on the EDMs of atoms and molecules, including Cs 133 , Tl 205 , Xe 129 , Hg 199 , Yb 171 F 19 , Hf 180 F+ 19 , and Th 232 O 16 , we constrain the P , T -violating scalar-pseudoscalar nucleon-electron and electron-electron interactions mediated by a generic axionlike particle of arbitrary mass. Our limits improve on existing laboratory bounds from other experiments by many orders of magnitude for ma≳10-2 eV . We also place constraints on C P violation in certain types of relaxion models.

  7. Affinity imaging mass spectrometry (AIMS): high-throughput screening for specific small molecule interactions with frozen tissue sections.

    Science.gov (United States)

    Yoshimi, T; Kawabata, S; Taira, S; Okuno, A; Mikawa, R; Murayama, S; Tanaka, K; Takikawa, O

    2015-11-07

    A novel screening system, using affinity imaging mass spectrometry (AIMS), has been developed to identify protein aggregates or organ structures in unfixed human tissue. Frozen tissue sections are positioned on small (millimetre-scale) stainless steel chips and incubated with an extensive library of small molecules. Candidate molecules showing specific affinity for the tissue section are identified by imaging mass spectrometry (IMS). As an example application, we screened over a thousand compounds against Alzheimer's disease (AD) brain tissue and identified several compounds with high affinity for AD brain sections containing tau deposits compared to age-matched controls. It should also be possible to use AIMS to isolate chemical compounds with affinity for tissue structures or components that have been extensively modified by events such as oxidation, phosphorylation, acetylation, aggregation, racemization or truncation, for example, due to aging. It may also be applicable to biomarker screening programs.

  8. Ureaplasma diversum Genome Provides New Insights about the Interaction of the Surface Molecules of This Bacterium with the Host.

    Directory of Open Access Journals (Sweden)

    Lucas M Marques

    Full Text Available Whole genome sequencing and analyses of Ureaplasma diversum ATCC 49782 was undertaken as a step towards understanding U. diversum biology and pathogenicity. The complete genome showed 973,501 bp in a single circular chromosome, with 28.2% of G+C content. A total of 782 coding DNA sequences (CDSs, and 6 rRNA and 32 tRNA genes were predicted and annotated. The metabolic pathways are identical to other human ureaplasmas, including the production of ATP via hydrolysis of the urea. Genes related to pathogenicity, such as urease, phospholipase, hemolysin, and a Mycoplasma Ig binding protein (MIB-Mycoplasma Ig protease (MIP system were identified. More interestingly, a large number of genes (n = 40 encoding surface molecules were annotated in the genome (lipoproteins, multiple-banded antigen like protein, membrane nuclease lipoprotein and variable surface antigens lipoprotein. In addition, a gene encoding glycosyltransferase was also found. This enzyme has been associated with the production of capsule in mycoplasmas and ureaplasma. We then sought to detect the presence of a capsule in this organism. A polysaccharide capsule from 11 to 17 nm of U. diversum was observed trough electron microscopy and using specific dyes. This structure contained arabinose, xylose, mannose, galactose and glucose. In order to understand the inflammatory response against these surface molecules, we evaluated the response of murine macrophages J774 against viable and non-viable U. diversum. As with viable bacteria, non-viable bacteria were capable of promoting a significant inflammatory response by activation of Toll like receptor 2 (TLR2, indicating that surface molecules are important for the activation of inflammatory response. Furthermore, a cascade of genes related to the inflammasome pathway of macrophages was also up-regulated during infection with viable organisms when compared to non-infected cells. In conclusion, U. diversum has a typical ureaplasma genome and

  9. Ureaplasma diversum Genome Provides New Insights about the Interaction of the Surface Molecules of This Bacterium with the Host.

    Science.gov (United States)

    Marques, Lucas M; Rezende, Izadora S; Barbosa, Maysa S; Guimarães, Ana M S; Martins, Hellen B; Campos, Guilherme B; do Nascimento, Naíla C; Dos Santos, Andrea P; Amorim, Aline T; Santos, Verena M; Farias, Sávio T; Barrence, Fernanda  C; de Souza, Lauro M; Buzinhani, Melissa; Arana-Chavez, Victor E; Zenteno, Maria E; Amarante-Mendes, Gustavo P; Messick, Joanne B; Timenetsky, Jorge

    2016-01-01

    Whole genome sequencing and analyses of Ureaplasma diversum ATCC 49782 was undertaken as a step towards understanding U. diversum biology and pathogenicity. The complete genome showed 973,501 bp in a single circular chromosome, with 28.2% of G+C content. A total of 782 coding DNA sequences (CDSs), and 6 rRNA and 32 tRNA genes were predicted and annotated. The metabolic pathways are identical to other human ureaplasmas, including the production of ATP via hydrolysis of the urea. Genes related to pathogenicity, such as urease, phospholipase, hemolysin, and a Mycoplasma Ig binding protein (MIB)-Mycoplasma Ig protease (MIP) system were identified. More interestingly, a large number of genes (n = 40) encoding surface molecules were annotated in the genome (lipoproteins, multiple-banded antigen like protein, membrane nuclease lipoprotein and variable surface antigens lipoprotein). In addition, a gene encoding glycosyltransferase was also found. This enzyme has been associated with the production of capsule in mycoplasmas and ureaplasma. We then sought to detect the presence of a capsule in this organism. A polysaccharide capsule from 11 to 17 nm of U. diversum was observed trough electron microscopy and using specific dyes. This structure contained arabinose, xylose, mannose, galactose and glucose. In order to understand the inflammatory response against these surface molecules, we evaluated the response of murine macrophages J774 against viable and non-viable U. diversum. As with viable bacteria, non-viable bacteria were capable of promoting a significant inflammatory response by activation of Toll like receptor 2 (TLR2), indicating that surface molecules are important for the activation of inflammatory response. Furthermore, a cascade of genes related to the inflammasome pathway of macrophages was also up-regulated during infection with viable organisms when compared to non-infected cells. In conclusion, U. diversum has a typical ureaplasma genome and metabolism, and

  10. Synthetic strategies for controlling inter- and intramolecular interactions: Applications in single-molecule fluorescence imaging, bioluminescence imaging, and palladium catalysis

    Science.gov (United States)

    Conley, Nicholas R.

    The field of synthetic organic chemistry has reached such maturity that, with sufficient effort and resources, the synthesis of virtually any small molecule which exhibits reasonable stability at room temperature can be realized. While representing a monumental achievement for the field, the ability to exert precise control over molecular structure is just a means to an end, and it is frequently the responsibility of the synthetic chemist to determine which molecules should actually be synthesized. For better or worse, there exists no competitive free market in academia for new molecules, and as a result, the decision of which compounds should be synthesized is seldom driven by the forces of supply and demand; rather, it is guided by the synthetic chemist's interest in an anticipated structure-function relationship or in the properties of a previously unstudied class of molecules. As a consequence, there exists a pervasive need for chemists with synthetic expertise in fields (e.g., molecular imaging) and subdisciplines of chemistry (e.g., physical chemistry) in which the identification of promising synthetic targets dramatically outpaces the synthetic output in that field or subdiscipline, and ample opportunities are available for synthetic chemists who choose to pursue such cross-disciplinary research. This thesis describes synthetic efforts that leverage these opportunities to realize applications in biological imaging and in palladium catalysis. In Part I, the synthesis and characterization of three novel luminophores and their imaging applications are discussed. The first is a molecular beacon that utilizes a fluorophorefluorophore pair which exhibits H-dimer quenching in the closed conformation. This probe offers several advantages over conventional fluorophore-quencher molecular beacons in the detection of oligonucleotides, both in bulk and at the single-molecule level. Secondly, a fluorescent, Cy3-Cy5 covalent heterodimer is reported, which on account of the

  11. Novel fusion protein approach for efficient high-throughput screening of small molecule-mediating protein-protein interactions in cells and living animals.

    Science.gov (United States)

    Paulmurugan, Ramasamy; Gambhir, Sanjiv S

    2005-08-15

    Networks of protein interactions execute many different intracellular pathways. Small molecules either synthesized within the cell or obtained from the external environment mediate many of these protein-protein interactions. The study of these small molecule-mediated protein-protein interactions is important in understanding abnormal signal transduction pathways in a variety of disorders, as well as in optimizing the process of drug development and validation. In this study, we evaluated the rapamycin-mediated interaction of the human proteins FK506-binding protein (FKBP12) rapamycin-binding domain (FRB) and FKBP12 by constructing a fusion of these proteins with a split-Renilla luciferase or a split enhanced green fluorescent protein (split-EGFP) such that complementation of the reporter fragments occurs in the presence of rapamycin. Different linker peptides in the fusion protein were evaluated for the efficient maintenance of complemented reporter activity. This system was studied in both cell culture and xenografts in living animals. We found that peptide linkers with two or four EAAAR repeat showed higher protein-protein interaction-mediated signal with lower background signal compared with having no linker or linkers with amino acid sequences GGGGSGGGGS, ACGSLSCGSF, and ACGSLSCGSFACGSLSCGSF. A 9 +/- 2-fold increase in signal intensity both in cell culture and in living mice was seen compared with a system that expresses both reporter fragments and the interacting proteins separately. In this fusion system, rapamycin induced heterodimerization of the FRB and FKBP12 moieties occurred rapidly even at very lower concentrations (0.00001 nmol/L) of rapamycin. For a similar fusion system employing split-EGFP, flow cytometry analysis showed significant level of rapamycin-induced complementation.

  12. 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.

  13. Interaction Research on the Antiviral Molecule Dufulin Targeting on Southern Rice Black Streaked Dwarf Virus P9-1 Nonstructural Protein

    Directory of Open Access Journals (Sweden)

    Zhenchao Wang

    2015-03-01

    Full Text Available ern rice black streaked dwarf virus (SRBSDV causes severe harm to rice production. Unfortunately, studies on effective antiviral drugs against SRBSDV and interaction mechanism of antiviral molecule targeting on SRBSDV have not been reported. This study found dufulin (DFL, an ideal anti-SRBSDV molecule, and investigated the interactions of DFL targeting on the nonstructural protein P9-1. The biological sequence information and bonding characterization of DFL to four kinds of P9-1 protein were described with fluorescence titration (FT and microscale thermophoresis (MST assays. The sequence analysis indicated that P9-1 had highly-conserved C- and N-terminal amino acid residues and a hypervariable region that differed from 131 aa to 160 aa. Consequently, wild-type (WT-His-P9-1, 23 C-terminal residues truncated (TR-ΔC23-His-P9-1, 6 N-terminal residues truncated (TR-ΔN6-His-P9-1, and Ser138 site-directed (MU-138-His-P9-1 mutant proteins were expressed. The FT and MST assay results indicated that DFL bounded to WT-His-P9-1 with micromole affinity and the 23 C-terminal amino acids were the potential targeting site. This system, which combines a complete sequence analysis, mutant protein expression, and binding action evaluating system, could further advance the understanding of the interaction abilities between antiviral drugs and their targets.

  14. A Functional Analysis on the Interspecies Interaction between Mouse LFA-1 and Human Intercellular Adhesion Molecule-1 at the Cell Level

    Directory of Open Access Journals (Sweden)

    David Núñez

    2017-12-01

    Full Text Available The interaction between intercellular adhesion molecules (ICAM and the integrin leukocyte function-associated antigen-1 (LFA-1 is crucial for the regulation of several physiological and pathophysiological processes like cell-mediated elimination of tumor or virus infected cells, cancer metastasis, or inflammatory and autoimmune processes. Using purified proteins it was reported a species restriction for the interaction of ICAM-1 and LFA-1, being mouse ICAM-1 able to interact with human LFA-1 but not human ICAM-1 with mouse LFA-1. However, in vivo results employing tumor cells transfected with human ICAM-1 suggest that functionally mouse LFA-1 can recognize human ICAM-1. In order to clarify the interspecies cross-reactivity of the ICAM-1/LFA-1 interaction, we have performed functional studies analyzing the ability of human soluble ICAM-1 and human/mouse LFA-1 derived peptides to inhibit cell aggregation and adhesion as well as cell-mediated cytotoxicity in both mouse and human systems. In parallel, the affinity of the interaction between mouse LFA-1-derived peptides and human ICAM-1 was determined by calorimetry assays. According to the results obtained, it seems that human ICAM-1 is able to interact with mouse LFA-1 on intact cells, which should be taking into account when using humanized mice and xenograft models for the study of immune-related processes.

  15. A Functional Analysis on the Interspecies Interaction between Mouse LFA-1 and Human Intercellular Adhesion Molecule-1 at the Cell Level.

    Science.gov (United States)

    Núñez, David; Comas, Laura; Lanuza, Pilar M; Sánchez-Martinez, Diego; Pérez-Hernández, Marta; Catalán, Elena; Domingo, María Pilar; Velázquez-Campoy, Adrián; Pardo, Julián; Gálvez, Eva M

    2017-01-01

    The interaction between intercellular adhesion molecules (ICAM) and the integrin leukocyte function-associated antigen-1 (LFA-1) is crucial for the regulation of several physiological and pathophysiological processes like cell-mediated elimination of tumor or virus infected cells, cancer metastasis, or inflammatory and autoimmune processes. Using purified proteins it was reported a species restriction for the interaction of ICAM-1 and LFA-1, being mouse ICAM-1 able to interact with human LFA-1 but not human ICAM-1 with mouse LFA-1. However, in vivo results employing tumor cells transfected with human ICAM-1 suggest that functionally mouse LFA-1 can recognize human ICAM-1. In order to clarify the interspecies cross-reactivity of the ICAM-1/LFA-1 interaction, we have performed functional studies analyzing the ability of human soluble ICAM-1 and human/mouse LFA-1 derived peptides to inhibit cell aggregation and adhesion as well as cell-mediated cytotoxicity in both mouse and human systems. In parallel, the affinity of the interaction between mouse LFA-1-derived peptides and human ICAM-1 was determined by calorimetry assays. According to the results obtained, it seems that human ICAM-1 is able to interact with mouse LFA-1 on intact cells, which should be taking into account when using humanized mice and xenograft models for the study of immune-related processes.

  16. Disruption of focal adhesion kinase and p53 interaction with small molecule compound R2 reactivated p53 and blocked tumor growth

    International Nuclear Information System (INIS)

    Golubovskaya, Vita M; Ho, Baotran; Zheng, Min; Magis, Andrew; Ostrov, David; Morrison, Carl; Cance, William G

    2013-01-01

    Focal Adhesion Kinase (FAK) is a 125 kDa non-receptor kinase that plays a major role in cancer cell survival and metastasis. We performed computer modeling of the p53 peptide containing the site of interaction with FAK, predicted the peptide structure and docked it into the three-dimensional structure of the N-terminal domain of FAK involved in the complex with p53. We screened small molecule compounds that targeted the site of the FAK-p53 interaction and identified compounds (called Roslins, or R compounds) docked in silico to this site. By different assays in isogenic HCT116p53 + / + and HCT116 p53 - / - cells we identified a small molecule compound called Roslin 2 (R2) that bound FAK, disrupted the binding of FAK and p53 and decreased cancer cell viability and clonogenicity in a p53-dependent manner. In addition, dual-luciferase assays demonstrated that the R2 compound increased p53 transcriptional activity that was inhibited by FAK using p21, Mdm-2, and Bax-promoter targets. R2 also caused increased expression of p53 targets: p21, Mdm-2 and Bax proteins. Furthermore, R2 significantly decreased tumor growth, disrupted the complex of FAK and p53, and up-regulated p21 in HCT116 p53 + / + but not in HCT116 p53 - / - xenografts in vivo. In addition, R2 sensitized HCT116p53 + / + cells to doxorubicin and 5-fluorouracil. Thus, disruption of the FAK and p53 interaction with a novel small molecule reactivated p53 in cancer cells in vitro and in vivo and can be effectively used for development of FAK-p53 targeted cancer therapy approaches

  17. 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.

  18. Method for accurate determination of dissociation constants of optical ratiometric systems: chemical probes, genetically encoded sensors, and interacting molecules.

    Science.gov (United States)

    Pomorski, Adam; Kochańczyk, Tomasz; Miłoch, Anna; Krężel, Artur

    2013-12-03

    Ratiometric chemical probes and genetically encoded sensors are of high interest for both analytical chemists and molecular biologists. Their high sensitivity toward the target ligand and ability to obtain quantitative results without a known sensor concentration have made them a very useful tool in both in vitro and in vivo assays. Although ratiometric sensors are widely used in many applications, their successful and accurate usage depends on how they are characterized in terms of sensing target molecules. The most important feature of probes and sensors besides their optical parameters is an affinity constant toward analyzed molecules. The literature shows that different analytical approaches are used to determine the stability constants, with the ratio approach being most popular. However, oversimplification and lack of attention to detail results in inaccurate determination of stability constants, which in turn affects the results obtained using these sensors. Here, we present a new method where ratio signal is calibrated for borderline values of intensities of both wavelengths, instead of borderline ratio values that generate errors in many studies. At the same time, the equation takes into account the cooperativity factor or fluorescence artifacts and therefore can be used to characterize systems with various stoichiometries and experimental conditions. Accurate determination of stability constants is demonstrated utilizing four known optical ratiometric probes and sensors, together with a discussion regarding other, currently used methods.

  19. Interaction of multicharged ions with molecules (CO{sub 2}, C{sub 60}) by coincident electron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Moretto-Capelle, P.; Bordenave-Montesquieu, D.; Bordenave-Montesquieu, A. [Universite Paul Sabatier, Toulouse (France). Lab. CAR-IRSAMC

    2001-07-01

    First results for the investigation of electron capture processes in collisions between multicharged ions and molecule targets using electron spectroscopy in coincidence with charged fragments, are presented. It is shown that a much more detailed investigation of the capture reaction can be achieved using molecular instead of heavy atomic targets provided that an analysis of the target dissociation is made. The collisional systems {sup 18}O{sup 8+}+Ar, CO{sub 2} and C{sub 60} have been studied at 80 keV. Non coincident electron spectra as well as first results of double or triple coincidence experiments are discussed. Kinetic energy distributions of the C{sub n}{sup +} fragments (n=1 to 8) produced in multiple capture processes from C{sub 60} target are given. A detailed investigation of the double capture process with CO{sub 2} molecule allows the measurement of kinetic energy release distributions (KERD) which characterize the dissociation of CO{sub 2}{sup 2+} molecular ions; our results are found to be very similar to those measured in double photoionisation experiments. (orig.)

  20. Tuning dispersion correction in DFT-D2 for metal-molecule interactions: A tailored reparameterization strategy for the adsorption of aromatic systems on Ag(1 1 1)

    Science.gov (United States)

    Schiavo, Eduardo; Muñoz-García, Ana B.; Barone, Vincenzo; Vittadini, Andrea; Casarin, Maurizio; Forrer, Daniel; Pavone, Michele

    2018-02-01

    Common local and semi-local density functionals poorly describe the molecular physisorption on metal surfaces due to the lack of dispersion interactions. In the last decade, several correction schemes have been proposed to amend this fundamental flaw of Density Functional Theory. Using the prototypical case of aromatic molecules adsorbed on Ag(1 1 1), we discuss the accuracy of different dispersion-correction methods and present a reparameterization strategy for the simple and effective DFT-D2. For the adsorption of different aromatic systems on the same metallic substrate, good results at feasible computational costs are achieved by means of a fitting procedure against MP2 data.

  1. Filamin A Modulates Store-Operated Ca2+ Entry by Regulating STIM1 (Stromal Interaction Molecule 1)-Orai1 Association in Human Platelets.

    Science.gov (United States)

    Lopez, Jose J; Albarrán, Letizia; Jardín, Isaac; Sanchez-Collado, Jose; Redondo, Pedro C; Bermejo, Nuria; Bobe, Regis; Smani, Tarik; Rosado, Juan A

    2018-02-01

    Here, we provide evidence for the role of FLNA (filamin A) in the modulation of store-operated calcium entry (SOCE). SOCE is a major mechanism for calcium influx controlled by the intracellular Ca 2+ stores. On store depletion, the endoplasmic reticulum calcium sensor STIM1 (stromal interaction molecule 1) redistributes into puncta at endoplasmic reticulum/plasma membrane junctions, a process supported by the cytoskeleton, where it interacts with the calcium channels; however, the mechanism for fine-tuning SOCE is not completely understood. Our results demonstrate that STIM1 interacts with FLNA on calcium store depletion in human platelets. The interaction is dependent on the phosphorylation of FLNA at Ser 2152 by the cAMP-dependent protein kinase. Impairment of FLNA phosphorylation and knockdown of FLNA expression using siRNA increased SOCE in platelets. Similarly, SOCE was significantly greater in FLNA-deficient melanoma M2 cells than in the FLNA-expressing M2 subclone A7. Expression of FLNA in M2 cells attenuated SOCE, an effect prevented when the cells were transfected with the nonphosphorylatable FLNA S2152A mutant. Transfection of M2 cells with the STIM1(K684,685E) mutant reduced the STIM1-FLNA interaction. In platelets, attenuation of FLNA expression using siRNA resulted in enhanced association of STIM1 with the cytoskeleton, greater STIM1-Orai1 interaction, and SOCE. Introduction of an anti-FLNA (2597-2647) antibody attenuated the STIM1-FLNA interaction and enhanced thrombin-induced platelet aggregation. Our results indicate that FLNA modulates SOCE and then the correct platelet function, by fine-tuning the distribution of STIM1 in the cytoskeleton and the interaction with Orai1 channels. © 2017 American Heart Association, Inc.

  2. Enhancing the blocking temperature in single-molecule magnets by incorporating 3d-5d exchange interactions

    DEFF Research Database (Denmark)

    Pedersen, Kasper Søndergaard; Schau-Magnussen, Magnus; Bendix, Jesper

    2010-01-01

    We report the first single-molecule magnet (SMM) to incorporate the [Os(CN)(6)](3-) moiety. The compound (1) has a trimeric, cyanide-bridged Mn(III)-Os(III)-Mn(III) skeleton in which Mn(III) designates a [Mn(5-Brsalen)(MeOH)](+) unit (5-Brsalen=N,N'-ethylenebis(5-bromosalicylideneiminato)). X......-ray crystallographic experiments reveal that 1 is isostructural with the Mn(III)-Fe(III)-Mn(III) analogue (2). Both compounds exhibit a frequency-dependent out-of-phase ¿''(T) alternating current (ac) susceptibility signal that is suggestive of SMM behaviour. From the Arrhenius expression, the effective barrier for 1...... for the design of a new generation of SMMs with enhanced SMM properties....

  3. Van der Waals interaction between a molecule and a spherical cavity in a metal: Nonlocality and anisotropy effects

    International Nuclear Information System (INIS)

    Labani, B.; Boustimi, M.; Baudon, J.

    1997-01-01

    The electric response field of a small spherical metallic cavity to a molecule characterized by fluctuating dipolar and quadrupolar moments is built from spherical tensor theory. The electric susceptibility of the field gradient between the two points inside the metallic cavity is formulated by a general expression of the van der Waals energy between the two partners. The induction contribution is introduced by using the field gradient susceptibilities of the cavity at zero frequency. In order to illustrate the nonlocal effects as well as the importance of the curvature of the metallic cavity on the magnitude of the physisorption energy, we present numerical results for typical systems (HF, HCl on Ag, Al, and Cu). copyright 1997 The American Physical Society

  4. ESR study on the interaction between carbon blacks and oxygen molecules; ESR ho ni yoru carbon black to sanso bunshi tono sogo sayo no kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    Okazaki, M.; Toriyama, K.; Konishi, Y. [National Industrial Research Institute of Nagoya, Nagoya (Japan)

    2000-02-24

    Interaction between carbon blacks and oxygen molecules has been studied by means of electron spin resonance (ESR) spectroscopy. The ESR spectra of the carbon blacks appears at the g-value of free spin, which are contributed by both isolated electrons and conduction electrons. Upon introducing oxygen to the system the ESR linewidth was broadened in proportion to the partial pressure of oxygen. In case of lampblack (LB 101, Degussa) the interaction was not so strong that it took a tong time at 77K for the linewidth to reach the maxmum value. In case of gassblack (P 140 V, Degussa), on the other hand, the oxygen was easily adsorbed at 298K and the linewidth at 77K became its maximum immediately after cooling. The number of unpaired electrons decreased when the system was kept at 298 K and the decrease was prominent for the local spins. These phenomena have been explained with a simple band model for the electron. (author)

  5. Stability of defects in monolayer MoS_2 and their interaction with O_2 molecule: A first-principles study

    International Nuclear Information System (INIS)

    Zhao, B.; Shang, C.; Qi, N.; Chen, Z.Y.; Chen, Z.Q.

    2017-01-01

    Highlights: • Defects can exist steadily in monolayer MoS_2 and break surface chemical inertness. • Activated surfaces are beneficial to the adsorption of O_2 through the introduction of defect levels. • Adsorbed O_2 on defective surface can dissociate with low activation energy barrier. • Defective system may be a potential substrate to design MoS_2-based gas sensor or catalysts. - Abstract: The stability of various defects in monolayer MoS_2, as well as their interactions with free O_2 molecules were investigated by density functional theory (DFT) calculations coupled with the nudged elastic band (NEB) method. The defects including S vacancy (monosulfur and disulfue vacancies), antisite defect (Mo_S) and external Mo atom can exist steadily in monolayer MoS_2, and introduce defect levels in these defective systems, which breaks the surface chemical inertness and significantly enhances the adsorption capacity for free O_2. The adsorption energy calculations and electronic properties analysis suggest that there is a strong interaction between O_2 molecule and defective system. The adsorbed O_2 on the defective surface can dissociate with a lower activation energy barrier, which produce two active oxygen atoms. Especially, two Mo atoms can occupy one Mo lattice site, and adsorbed O_2 on the top of the Mo atom can then dissociate directly with the lowest activation energy barrier. Hence, our work may provide useful information to design MoS_2-based gas sensor or catalysts.

  6. The spherical-harmonics representation for the interaction between diatomic molecules: The general case and applications to COsbnd CO and COsbnd HF

    Science.gov (United States)

    Barreto, Patricia R. P.; Cruz, Ana Claudia P. S.; Barreto, Rodrigo L. P.; Palazzetti, Federico; Albernaz, Alessandra F.; Lombardi, Andrea; Maciel, Glauciete S.; Aquilanti, Vincenzo

    2017-07-01

    The spherical-harmonics expansion is a mathematically rigorous procedure and a powerful tool for the representation of potential energy surfaces of interacting molecular systems, determining their spectroscopic and dynamical properties, specifically in van der Waals clusters, with applications also to classical and quantum molecular dynamics simulations. The technique consists in the construction (by ab initio or semiempirical methods) of the expanded potential interaction up to terms that provide the generation of a number of leading configurations sufficient to account for faithful geometrical representations. This paper reports the full general description of the method of the spherical-harmonics expansion as applied to diatomic-molecule - diatomic-molecule systems of increasing complexity: the presentation of the mathematical background is given for providing both the application to the prototypical cases considered previously (O2sbnd O2, N2sbnd N2, and N2sbnd O2 systems) and the generalization to: (i) the COsbnd CO system, where a characteristic feature is the lower symmetry order with respect to the cases studied before, requiring a larger number of expansion terms necessary to adequately represent the potential energy surface; and (ii) the COsbnd HF system, which exhibits the lowest order of symmetry among this class of aggregates and therefore the highest number of leading configurations.

  7. 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.

  8. Self-interaction error in density functional theory: a mean-field correction for molecules and large systems

    International Nuclear Information System (INIS)

    Ciofini, Ilaria; Adamo, Carlo; Chermette, Henry

    2005-01-01

    Corrections to the self-interaction error which is rooted in all standard exchange-correlation functionals in the density functional theory (DFT) have become the object of an increasing interest. After an introduction reminding the origin of the self-interaction error in the DFT formalism, and a brief review of the self-interaction free approximations, we present a simple, yet effective, self-consistent method to correct this error. The model is based on an average density self-interaction correction (ADSIC), where both exchange and Coulomb contributions are screened by a fraction of the electron density. The ansatz on which the method is built makes it particularly appealing, due to its simplicity and its favorable scaling with the size of the system. We have tested the ADSIC approach on one of the classical pathological problem for density functional theory: the direct estimation of the ionization potential from orbital eigenvalues. A large set of different chemical systems, ranging from simple atoms to large fullerenes, has been considered as test cases. Our results show that the ADSIC approach provides good numerical values for all the molecular systems, the agreement with the experimental values increasing, due to its average ansatz, with the size (conjugation) of the systems

  9. The Independent Gradient Model: A New Approach for Probing Strong and Weak Interactions in Molecules from Wave Function Calculations.

    Science.gov (United States)

    Lefebvre, Corentin; Khartabil, Hassan; Boisson, Jean-Charles; Contreras-García, Julia; Piquemal, Jean-Philip; Hénon, Eric

    2018-03-19

    Extraction of the chemical interaction signature from local descriptors based on electron density (ED) is still a fruitful field of development in chemical interpretation. In a previous work that used promolecular ED (frozen ED), the new descriptor, δg , was defined. It represents the difference between a virtual upper limit of the ED gradient (∇ρIGM , IGM=independent gradient model) that represents a noninteracting system and the true ED gradient (∇ρ ). It can be seen as a measure of electron sharing brought by ED contragradience. A compelling feature of this model is to provide an automatic workflow that extracts the signature of interactions between selected groups of atoms. As with the noncovalent interaction (NCI) approach, it provides chemists with a visual understanding of the interactions present in chemical systems. ∇ρIGM is achieved simply by using absolute values upon summing the individual gradient contributions that make up the total ED gradient. Hereby, we extend this model to relaxed ED calculated from a wave function. To this end, we formulated gradient-based partitioning (GBP) to assess the contribution of each orbital to the total ED gradient. We highlight these new possibilities across two prototypical examples of organic chemistry: the unconventional hexamethylbenzene dication, with a hexa-coordinated carbon atom, and β-thioaminoacrolein. It will be shown how a bond-by-bond picture can be obtained from a wave function, which opens the way to monitor specific interactions along reaction paths. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. 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).

  11. 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.

  12. Landau-Zener tunneling in the presence of weak intermolecular interactions in a crystal of Mn4 single-molecule magnets

    Science.gov (United States)

    Wernsdorfer, W.; Bhaduri, S.; Vinslava, A.; Christou, G.

    2005-12-01

    A Mn4 single-molecule magnet (SMM), with a well-isolated spin ground state of S=9/2 , is used as a model system to study Landau-Zener (LZ) tunneling in the presence of weak intermolecular dipolar and exchange interactions. The anisotropy constants D and B are measured with minor hysteresis loops. A transverse field is used to tune the tunnel splitting over a large range. Using the LZ and inverse LZ method, it is shown that these interactions play an important role in the tunnel rates. Three regions are identified: (i) at small transverse fields, tunneling is dominated by single tunnel transitions, (ii) at intermediate transverse fields, the measured tunnel rates are governed by reshuffling of internal fields, and (iii) at larger transverse fields, the magnetization reversal starts to be influenced by the direct relaxation process, and many-body tunnel events may occur. The hole digging method is used to study the next-nearest-neighbor interactions. At small external fields, it is shown that magnetic ordering occurs which does not quench tunneling. An applied transverse field can increase the ordering rate. Spin-spin cross-relaxations, mediated by dipolar and weak exchange interactions, are proposed to explain additional quantum steps.

  13. Attractive and repulsive interactions among methanol molecules in supercritical state investigated by Raman spectroscopy and perturbed hard-sphere theory.

    Science.gov (United States)

    Saitow, Ken-ichi; Sasaki, Jungo

    2005-03-08

    , inhomogeneous width, and local density. The density fluctuation in the vicinity of a vibrating molecule is compared to the fluctuation of bulk density, which is obtained from the thermodynamic calculation.

  14. Interactions of Histone Acetyltransferase p300 with the Nuclear Proteins Histone and HMGB1, As Revealed by Single Molecule Atomic Force Spectroscopy.

    Science.gov (United States)

    Banerjee, S; Rakshit, T; Sett, S; Mukhopadhyay, R

    2015-10-22

    One of the important properties of the transcriptional coactivator p300 is histone acetyltransferase (HAT) activity that enables p300 to influence chromatin action via histone modulation. p300 can exert its HAT action upon the other nuclear proteins too--one notable example being the transcription-factor-like protein HMGB1, which functions also as a cytokine, and whose accumulation in the cytoplasm, as a response to tissue damage, is triggered by its acetylation. Hitherto, no information on the structure and stability of the complexes between full-length p300 (p300FL) (300 kDa) and the histone/HMGB1 proteins are available, probably due to the presence of unstructured regions within p300FL that makes it difficult to be crystallized. Herein, we have adopted the high-resolution atomic force microscopy (AFM) approach, which allows molecularly resolved three-dimensional contour mapping of a protein molecule of any size and structure. From the off-rate and activation barrier values, obtained using single molecule dynamic force spectroscopy, the biochemical proposition of preferential binding of p300FL to histone H3, compared to the octameric histone, can be validated. Importantly, from the energy landscape of the dissociation events, a model for the p300-histone and the p300-HMGB1 dynamic complexes that HAT forms, can be proposed. The lower unbinding forces of the complexes observed in acetylating conditions, compared to those observed in non-acetylating conditions, indicate that upon acetylation, p300 tends to weakly associate, probably as an outcome of charge alterations on the histone/HMGB1 surface and/or acetylation-induced conformational changes. To our knowledge, for the first time, a single molecule level treatment of the interactions of HAT, where the full-length protein is considered, is being reported.

  15. 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.

  16. Role of electrostatic interactions on the transport of druglike molecules in hydrogel-based articular cartilage mimics

    DEFF Research Database (Denmark)

    Ye, Fengbin; Baldursdottir, Stefania G.; Hvidt, Søren

    2016-01-01

    In the field of drug delivery to the articular cartilage, it is advantageous to apply artificial tissue models as surrogates of cartilage for investigating drug transport and release properties. In this study, artificial cartilage models consisting of 0.5% (w/v) agarose gel containing 0.5% (w...... to the pure agarose gel. The decrease in apparent diffusivity of the cationic compounds was not caused by a change in the gel structure since a similar reduction in apparent diffusivity was not observed for the net negatively charged protein α-lactalbumin. The apparent diffusivity of the cationic compounds...... the electrostatic nature of their interactions. The results obtained from the UV imaging diffusion studies are important for understanding the effect of drug physicochemical properties on the transport in articular cartilage. The extracted information may be useful in the development of hydrogels for in vitro...

  17. Interaction of uranium(VI) towards glutathione. An example to study different functional groups in one molecule

    International Nuclear Information System (INIS)

    Frost, L.; Geipel, G.; Viehweger, K.; Bernhard, G.

    2011-01-01

    Glutathione, the most abundant thiol compound of the cell, has a great binding potential towards heavy metal ions. Hence it might influence the distribution of actinides on a cellular level. The unknown strength of the interaction of uranium(VI) with glutathione at physiologically relevant pH is subject of this paper and was studied with UV-vis spectroscopy and time-resolved laserinduced fluorescence spectroscopy (TRLFS). The complex stability constant of UO 2 H 2 GS + , logβ 121 0 , was calculated to be 39.09±0.15 and 39.04±0.02 in case of UV-vis spectroscopy and TRLFS respectively. Therefore the average formation constant for UO 2 2+ +H 2 GS - = UO 2 H 2 GS + can be assigned to be log K 0 11 = 19.83±0.15. Furthermore it was demonstrated that derivatization of the ligand associated with an enhancement of the ligand's spectroscopic properties can be used for the determination of complex stability constants and to assess the coordination chemistry in more detail. Using UV-vis spectroscopy, the stability constant of the complex between UO 2 2+ and glutathione pyruvate S-conjugate, a well absorbing ligand in contrast to glutathione, was calculated to be > 39.24±0.08. Furthermore the interaction of UO 2 2+ with glutathione derivatized with the fluorescent label monobromobimane was examined with femtosecond laser fluorescence spectroscopy. Thereby the stability constant of the 1: 1 complex was determined to be > 39.35±0.02. Although the thiol group of glutathione was blocked a strong coordination was found. Thus a significant involvement of the thiol group in the coordination of U(VI) can be excluded. (orig.)

  18. irGPU.proton.Net: Irregular strong charge interaction networks of protonatable groups in protein molecules--a GPU solver using the fast multipole method and statistical thermodynamics.

    Science.gov (United States)

    Kantardjiev, Alexander A

    2015-04-05

    A cluster of strongly interacting ionization groups in protein molecules with irregular ionization behavior is suggestive for specific structure-function relationship. However, their computational treatment is unconventional (e.g., lack of convergence in naive self-consistent iterative algorithm). The stringent evaluation requires evaluation of Boltzmann averaged statistical mechanics sums and electrostatic energy estimation for each microstate. irGPU: Irregular strong interactions in proteins--a GPU solver is novel solution to a versatile problem in protein biophysics--atypical protonation behavior of coupled groups. The computational severity of the problem is alleviated by parallelization (via GPU kernels) which is applied for the electrostatic interaction evaluation (including explicit electrostatics via the fast multipole method) as well as statistical mechanics sums (partition function) estimation. Special attention is given to the ease of the service and encapsulation of theoretical details without sacrificing rigor of computational procedures. irGPU is not just a solution-in-principle but a promising practical application with potential to entice community into deeper understanding of principles governing biomolecule mechanisms. © 2015 Wiley Periodicals, Inc.

  19. Reconstruction of calmodulin single-molecule FRET states, dye interactions, and CaMKII peptide binding by MultiNest and classic maximum entropy

    Science.gov (United States)

    DeVore, Matthew S.; Gull, Stephen F.; Johnson, Carey K.

    2013-08-01

    We analyzed single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.

  20. Reconstruction of Calmodulin Single-Molecule FRET States, Dye-Interactions, and CaMKII Peptide Binding by MultiNest and Classic Maximum Entropy.

    Science.gov (United States)

    Devore, Matthew S; Gull, Stephen F; Johnson, Carey K

    2013-08-30

    We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca 2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.

  1. Interactions between protein molecules and the virus removal membrane surface: Effects of immunoglobulin G adsorption and conformational changes on filter performance.

    Science.gov (United States)

    Hamamoto, Ryo; Ito, Hidemi; Hirohara, Makoto; Chang, Ryongsok; Hongo-Hirasaki, Tomoko; Hayashi, Tomohiro

    2018-03-01

    Membrane fouling commonly occurs in all filter types during virus filtration in protein-based biopharmaceutical manufacturing. Mechanisms of decline in virus filter performance due to membrane fouling were investigated using a cellulose-based virus filter as a model membrane. Filter performance was critically dependent on solution conditions; specifically, ionic strength. To understand the interaction between immunoglobulin G (IgG) and cellulose, sensors coated with cellulose were fabricated for surface plasmon resonance and quartz crystal microbalance with energy dissipation measurements. The primary cause of flux decline appeared to be irreversible IgG adsorption on the surface of the virus filter membrane. In particular, post-adsorption conformational changes in the IgG molecules promoted further irreversible IgG adsorption, a finding that could not be adequately explained by DLVO theory. Analyses of adsorption and desorption and conformational changes in IgG molecules on cellulose surfaces mimicking cellulose-based virus removal membranes provide an effective approach for identifying ways of optimizing solution conditions to maximize virus filter performance. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:379-386, 2018. © 2017 American Institute of Chemical Engineers.

  2. Hsp90α forms a stable complex at the cilium neck for the interaction of signalling molecules in IGF-1 receptor signalling.

    Science.gov (United States)

    Wang, Hongzhong; Zou, Xinle; Wei, Zhuang; Wu, Yuan; Li, Rongxia; Zeng, Rong; Chen, Zhengjun; Liao, Kan

    2015-01-01

    The primary cilium is composed of an axoneme that protrudes from the cell surface, a basal body beneath the membrane and a transition neck in between. It is a sensory organelle on the plasma membrane, involved in mediating extracellular signals. In the transition neck region of the cilium, the microtubules change from triplet to doublet microtubules. This region also contains the transition fibres that crosslink the axoneme with the membrane and the necklace proteins that regulate molecules being transported into and out of the cilium. In this protein-enriched, complex area it is important to maintain the correct assembly of all of these proteins. Here, through immunofluorescent staining and protein isolation, we identify the molecular chaperone Hsp90α clustered at the periciliary base. At the transition neck region, phosphorylated Hsp90α forms a stable ring around the axoneme. Heat shock treatment causes Hsp90α to dissipate and induces resorption of cilia. We further identify that Hsp90α at the transition neck region represents a signalling platform on which IRS-1 interacts with intracellular downstream signalling molecules involved in IGF-1 receptor signalling. © 2015. Published by The Company of Biologists Ltd.

  3. Deciphering the perturbation effect of urea on the supramolecular host-guest interaction of biologically active hydrophobic molecule inside the nanocavity of cyclodextrins

    Energy Technology Data Exchange (ETDEWEB)

    Maity, Banibrata; Chatterjee, Aninda; Ahmed, Sayeed Ashique; Seth, Debabrata, E-mail: debabrata@iitp.ac.in

    2017-03-15

    The present work articulates the supramolecular interaction and the formation of host-guest complex between the biologically active hydrophobic coumarin derivative and cyclodextrins by using several spectroscopic, calorimetric and microscopic techniques. All the studies clearly revealed that in presence of cyclodextrins (CDs), coumarin forms 1:1 stoichiometric complex. From all the study, we have found that with gradual increasing the cavity diameter of the hosts, the binding efficiency of the complexes gradually increases. The small population of the non emissive twisted intramolecular charge transfer (TICT) state of coumarin molecule turns into highly emissive in presence of γ-CD owing to its greater cavity diameter. The emissive TICT band is not found in β-CD complex due to its comparative small hydrophilic exterior and less polar environment. The present finding also interpret the perturbation effect of urea on host-guest complexes. In the presence of urea, the TICT emissive band of γ-CD is completely diminished. From, {sup 1}H NMR study it was observed that –NEt{sub 2} moiety of 7-DCCAE molecule is deeply buried inside the hydrophobic cavity of the CDs and forms host-guest complexes. Isothermal titration calorimetry measurement also indicates the formation of 1:1 host-guest complexes.

  4. Relaxed electric dipole moments of polar molecules interacting with a slow positron: H{sub 2}O and CH{sub 3}X (X=F, Cl, Br)

    Energy Technology Data Exchange (ETDEWEB)

    Assafrao, Denise; Mohallem, Jose R, E-mail: rachid@fisica.ufmg.b [Laboratorio de Atomos e Moleculas Especiais, Departamento de FIsica, ICEx, Universidade Federal de Minas Gerais, PO Box 702, 30123-970, Belo Horizonte, MG (Brazil)

    2010-08-14

    The variation in the electric dipole moments of H{sub 2}O, CH{sub 3}F, CH{sub 3}Cl and CH{sub 3}Br as their geometries relax due to interaction with a positron is evaluated. The results are in good agreement with a recently observed empirical dependence of the positron binding energy on molecular properties (Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 235203). For binding energies larger than 100 meV relaxation could alter significantly the analysis of the binding, but it is in the prospect of generating effective potentials for positron scattering by molecules that the effect can be more important.

  5. Electronic excitation of molecules in solution calculated using the symmetry-adapted cluster–configuration interaction method in the polarizable continuum model

    International Nuclear Information System (INIS)

    Fukuda, Ryoichi; Ehara, Masahiro

    2015-01-01

    The effects from solvent environment are specific to the electronic states; therefore, a computational scheme for solvent effects consistent with the electronic states is necessary to discuss electronic excitation of molecules in solution. The PCM (polarizable continuum model) SAC (symmetry-adapted cluster) and SAC-CI (configuration interaction) methods are developed for such purposes. The PCM SAC-CI adopts the state-specific (SS) solvation scheme where solvent effects are self-consistently considered for every ground and excited states. For efficient computations of many excited states, we develop a perturbative approximation for the PCM SAC-CI method, which is called corrected linear response (cLR) scheme. Our test calculations show that the cLR PCM SAC-CI is a very good approximation of the SS PCM SAC-CI method for polar and nonpolar solvents

  6. Rotationally adiabatic pair interactions of para- and ortho-hydrogen with the halogen molecules F2, Cl2, and Br2.

    Science.gov (United States)

    Berg, Matthias; Accardi, Antonio; Paulus, Beate; Schmidt, Burkhard

    2014-08-21

    The present work is concerned with the weak interactions between hydrogen and halogen molecules, i.e., the interactions of pairs H2-X2 with X = F, Cl, Br, which are dominated by dispersion and quadrupole-quadrupole forces. The global minimum of the four-dimensional (4D) coupled cluster with singles and doubles and perturbative triples (CCSD(T)) pair potentials is always a T shaped structure where H2 acts as the hat of the T, with well depths (De) of 1.3, 2.4, and 3.1 kJ/mol for F2, Cl2, and Br2, respectively. MP2/AVQZ results, in reasonable agreement with CCSD(T) results extrapolated to the basis set limit, are used for detailed scans of the potentials. Due to the large difference in the rotational constants of the monomers, in the adiabatic approximation, one can solve the rotational Schrödinger equation for H2 in the potential of the X2 molecule. This yields effective two-dimensional rotationally adiabatic potential energy surfaces where pH2 and oH2 are point-like particles. These potentials for the H2-X2 complexes have global and local minima for effective linear and T-shaped complexes, respectively, which are separated by 0.4-1.0 kJ/mol, where oH2 binds stronger than pH2 to X2, due to higher alignment to minima structures of the 4D-pair potential. Further, we provide fits of an analytical function to the rotationally adiabatic potentials.

  7. Stability of defects in monolayer MoS{sub 2} and their interaction with O{sub 2} molecule: A first-principles study

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, B. [Hubei Nuclear Solid Physics Key Laboratory, Department of Physics, Wuhan University, Wuhan, 430072 (China); Shang, C. [Wuhan National High Magnetic Field Center, Huazhong University of Science and Technology, Wuhan, 430074 (China); Qi, N. [Hubei Nuclear Solid Physics Key Laboratory, Department of Physics, Wuhan University, Wuhan, 430072 (China); Chen, Z.Y. [School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning, 437100 (China); Chen, Z.Q., E-mail: chenzq@whu.edu.cn [Hubei Nuclear Solid Physics Key Laboratory, Department of Physics, Wuhan University, Wuhan, 430072 (China)

    2017-08-01

    Highlights: • Defects can exist steadily in monolayer MoS{sub 2} and break surface chemical inertness. • Activated surfaces are beneficial to the adsorption of O{sub 2} through the introduction of defect levels. • Adsorbed O{sub 2} on defective surface can dissociate with low activation energy barrier. • Defective system may be a potential substrate to design MoS{sub 2}-based gas sensor or catalysts. - Abstract: The stability of various defects in monolayer MoS{sub 2}, as well as their interactions with free O{sub 2} molecules were investigated by density functional theory (DFT) calculations coupled with the nudged elastic band (NEB) method. The defects including S vacancy (monosulfur and disulfue vacancies), antisite defect (Mo{sub S}) and external Mo atom can exist steadily in monolayer MoS{sub 2}, and introduce defect levels in these defective systems, which breaks the surface chemical inertness and significantly enhances the adsorption capacity for free O{sub 2}. The adsorption energy calculations and electronic properties analysis suggest that there is a strong interaction between O{sub 2} molecule and defective system. The adsorbed O{sub 2} on the defective surface can dissociate with a lower activation energy barrier, which produce two active oxygen atoms. Especially, two Mo atoms can occupy one Mo lattice site, and adsorbed O{sub 2} on the top of the Mo atom can then dissociate directly with the lowest activation energy barrier. Hence, our work may provide useful information to design MoS{sub 2}-based gas sensor or catalysts.

  8. Size effects of solvent molecules on the phase behavior and effective interaction of colloidal systems with the bridging attraction

    International Nuclear Information System (INIS)

    Chen, Jie; Wang, Xuewu; Kline, Steven R; Liu, Yun

    2016-01-01

    There has been much recent research interest towards understanding the phase behavior of colloidal systems interacting with a bridging attraction, where the small solvent particles and large solute colloidal particles can be reversibly associated with each other. These systems show interesting phase behavior compared to the more widely studied depletion attraction systems. Here, we use Baxter’s two-component sticky hard sphere model with a Percus–Yevick closure to solve the Ornstein–Zernike equation and study the size effect on colloidal systems with bridging attractions. The spinodal decomposition regions, percolation transition boundaries and binodal regions are systematically investigated as a function of the relative size of the small solvent and large solute particles as well as the attraction strength between the small and large particles. In the phase space determined by the concentrations of small and large particles, the spinodal and binodal regions form isolated islands. The locations and shapes of the spinodal and binodal regions sensitively depend on the relative size of the small and large particles and the attraction strength between them. The percolation region shrinks by decreasing the size ratio, while the binodal region slightly expands with the decrease of the size ratio. Our results are very important in understanding the phase behavior for a bridging attraction colloidal system, a model system that provides insight into oppositely charged colloidal systems, protein phase behavior, and colloidal gelation mechanisms. (paper)

  9. Size effects of solvent molecules on the phase behavior and effective interaction of colloidal systems with the bridging attraction.

    Science.gov (United States)

    Chen, Jie; Wang, Xuewu; Kline, Steven R; Liu, Yun

    2016-11-16

    There has been much recent research interest towards understanding the phase behavior of colloidal systems interacting with a bridging attraction, where the small solvent particles and large solute colloidal particles can be reversibly associated with each other. These systems show interesting phase behavior compared to the more widely studied depletion attraction systems. Here, we use Baxter's two-component sticky hard sphere model with a Percus-Yevick closure to solve the Ornstein-Zernike equation and study the size effect on colloidal systems with bridging attractions. The spinodal decomposition regions, percolation transition boundaries and binodal regions are systematically investigated as a function of the relative size of the small solvent and large solute particles as well as the attraction strength between the small and large particles. In the phase space determined by the concentrations of small and large particles, the spinodal and binodal regions form isolated islands. The locations and shapes of the spinodal and binodal regions sensitively depend on the relative size of the small and large particles and the attraction strength between them. The percolation region shrinks by decreasing the size ratio, while the binodal region slightly expands with the decrease of the size ratio. Our results are very important in understanding the phase behavior for a bridging attraction colloidal system, a model system that provides insight into oppositely charged colloidal systems, protein phase behavior, and colloidal gelation mechanisms.

  10. Relative importance of driving force and electrostatic interactions in the reduction of multihaem cytochromes by small molecules.

    Science.gov (United States)

    Quintas, Pedro O; Cepeda, Andreia P; Borges, Nuno; Catarino, Teresa; Turner, David L

    2013-06-01

    Multihaem cytochromes are essential to the energetics of organisms capable of bioremediation and energy production. The haems in several of these cytochromes have been discriminated thermodynamically and their individual rates of reduction by small electron donors were characterized. The kinetic characterization of individual haems used the Marcus theory of electron transfer and assumed that the rates of reduction of each haem by sodium dithionite depend only on the driving force, while electrostatic interactions were neglected. To determine the relative importance of these factors in controlling the rates, we studied the effect of ionic strength on the redox potential and the rate of reduction by dithionite of native Methylophilus methylotrophus cytochrome c″ and three mutants at different pH values. We found that the main factor determining the rate is the driving force and that Marcus theory describes this satisfactorily. This validates the method of the simultaneous fitting of kinetic and thermodynamic data in multihaem cytochromes and opens the way for further investigation into the mechanisms of these proteins. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Small molecule inhibitors uncover synthetic genetic interactions of human flap endonuclease 1 (FEN1 with DNA damage response genes.

    Directory of Open Access Journals (Sweden)

    Thomas A Ward

    Full Text Available Flap endonuclease 1 (FEN1 is a structure selective endonuclease required for proficient DNA replication and the repair of DNA damage. Cellularly active inhibitors of this enzyme have previously been shown to induce a DNA damage response and, ultimately, cell death. High-throughput screens of human cancer cell-lines identify colorectal and gastric cell-lines with microsatellite instability (MSI as enriched for cellular sensitivity to N-hydroxyurea series inhibitors of FEN1, but not the PARP inhibitor olaparib or other inhibitors of the DNA damage response. This sensitivity is due to a synthetic lethal interaction between FEN1 and MRE11A, which is often mutated in MSI cancers through instabilities at a poly(T microsatellite repeat. Disruption of ATM is similarly synthetic lethal with FEN1 inhibition, suggesting that disruption of FEN1 function leads to the accumulation of DNA double-strand breaks. These are likely a result of the accumulation of aberrant replication forks, that accumulate as a consequence of a failure in Okazaki fragment maturation, as inhibition of FEN1 is toxic in cells disrupted for the Fanconi anemia pathway and post-replication repair. Furthermore, RAD51 foci accumulate as a consequence of FEN1 inhibition and the toxicity of FEN1 inhibitors increases in cells disrupted for the homologous recombination pathway, suggesting a role for homologous recombination in the resolution of damage induced by FEN1 inhibition. Finally, FEN1 appears to be required for the repair of damage induced by olaparib and cisplatin within the Fanconi anemia pathway, and may play a role in the repair of damage associated with its own disruption.

  12. 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 ...

  13. Single molecule force spectroscopy for in-situ probing oridonin inhibited ROS-mediated EGF-EGFR interactions in living KYSE-150 cells.

    Science.gov (United States)

    Pi, Jiang; Jin, Hua; Jiang, Jinhuan; Yang, Fen; Cai, Huaihong; Yang, Peihui; Cai, Jiye; Chen, Zheng W

    2017-05-01

    As the active anticancer component of Rabdosia Rubescens, oridonin has been proved to show strong anticancer activity in cancer cells, which is also found to be closely related to its specific inhibition effects on the EGFR tyrosine kinase activity. In this study, atomic force microscopy based single molecule force spectroscopy (AFM-SMFS) was used for real-time and in-situ detection of EGF-EGFR interactions in living esophageal cancer KYSE-150 cells to evaluate the anticancer activity of oridonin for the first time. Oridonin was found to induce apoptosis and also reduce EGFR expression in KYSE-150 cells. AFM-SMFS results demonstrated that oridonin could inhibit the binding between EGF and EGFR in KYSE-150 cells by decreasing the unbinding force and binding probability for EGF-EGFR complexes, which was further proved to be closely associated with the intracellular ROS level. More precise mechanism studies based on AFM-SMFS demonstrated that oridonin treatment could decrease the energy barrier width, increase the dissociation off rate constant and decrease the activation energy of EGF-EGFR complexes in ROS dependent way, suggesting oridonin as a strong anticancer agent targeting EGF-EGFR interactions in cancer cells through ROS dependent mechanism. Our results not only suggested oridonin as a strong anticancer agent targeting EGF-EGFR interactions in ROS dependent mechanism, but also highlighted AFM-SMFS as a powerful technique for pharmacodynamic studies by detecting ligand-receptor interactions, which was also expected to be developed into a promising tool for the screening and mechanism studies of drugs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Deuterium-labelled N-acyl-l-homoserine lactones (AHLs) - inter-kingdom signalling molecules - synthesis, structural studies, and interactions with model lipid membranes

    Energy Technology Data Exchange (ETDEWEB)

    Jakubczyk, Dorota [Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe (Germany); Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany); Barth, Christoph; Anastassacos, Frances; Koelsch, Patrick; Schepers, Ute [Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany); Kubas, Adam; Fink, Karin [Institute of Nanotechnology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany); Brenner-Weiss, Gerald [Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany); Braese, Stefan [Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe (Germany)

    2012-04-15

    N-Acyl-l-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechanism of those interactions. Precise structural studies are required to analyse the different AHL isomers as only one form is biologically most active. Theoretical studies combined with experimental infrared and Raman spectroscopic data are therefore undertaken to characterise the obtained compounds. To mimic interactions between AHL and cell membranes, we studied the insertion of AHL in supported lipid bilayers, using vibrational sum-frequency-generation spectroscopy. Deuterium-labelled AHLs were thus synthesized. Starting from readily available deuterated fatty acids, a two-step procedure towards deuterated N-acyl-l-homoserine lactones with varying chain lengths is described. This included the acylation of Meldrum's acid followed by amidation. Additionally, the detailed analytical evaluation of the products is presented herein. (orig.)

  15. Deuterium-labelled N-acyl-l-homoserine lactones (AHLs) - inter-kingdom signalling molecules - synthesis, structural studies, and interactions with model lipid membranes

    International Nuclear Information System (INIS)

    Jakubczyk, Dorota; Barth, Christoph; Anastassacos, Frances; Koelsch, Patrick; Schepers, Ute; Kubas, Adam; Fink, Karin; Brenner-Weiss, Gerald; Braese, Stefan

    2012-01-01

    N-Acyl-l-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechanism of those interactions. Precise structural studies are required to analyse the different AHL isomers as only one form is biologically most active. Theoretical studies combined with experimental infrared and Raman spectroscopic data are therefore undertaken to characterise the obtained compounds. To mimic interactions between AHL and cell membranes, we studied the insertion of AHL in supported lipid bilayers, using vibrational sum-frequency-generation spectroscopy. Deuterium-labelled AHLs were thus synthesized. Starting from readily available deuterated fatty acids, a two-step procedure towards deuterated N-acyl-l-homoserine lactones with varying chain lengths is described. This included the acylation of Meldrum's acid followed by amidation. Additionally, the detailed analytical evaluation of the products is presented herein. (orig.)

  16. Double-edged swords as cancer therapeutics: novel, orally active, small molecules simultaneously inhibit p53-MDM2 interaction and the NF-κB pathway.

    Science.gov (United States)

    Zhuang, Chunlin; Miao, Zhenyuan; Wu, Yuelin; Guo, Zizhao; Li, Jin; Yao, Jianzhong; Xing, Chengguo; Sheng, Chunquan; Zhang, Wannian

    2014-02-13

    Simultaneous inactivation of p53 and hyperactivation of nuclear factor-κB (NF-κB) is a common occurrence in human cancer. Currently, antitumor agents are being designed to selectively activate p53 or inhibit NF-κB. However, there is no concerted effort yet to deliberately design inhibitors that can simultaneously do both. This paper provided a proof-of-concept study that p53-MDM2 interaction and NF-κB pathway can be simultaneously targeted by a small-molecule inhibitor. A series of pyrrolo[3,4-c]pyrazole derivatives were rationally designed and synthesized as the first-in-class inhibitors of p53-MDM2 interaction and NF-κB pathway. Most of the compounds were identified to possess nanomolar p53-MDM2 inhibitory activity. Compounds 5q and 5s suppressed NF-κB activation through inhibition of IκBα phosphorylation and elevation of the cytoplasmic levels of p65 and phosphorylated IKKα/β. Biochemical assay for the kinases also supported the fact that pyrrolo[3,4-c]pyrazole compounds directly targeted the NF-κB pathway. In addition, four compounds (5j, 5q, 5s, and 5u) effectively inhibited tumor growth in the A549 xenograft model. Further pharmacokinetic study revealed that compound 5q exhibited excellent oral bioavailability (72.9%).

  17. An exploration of the effect and interaction mechanism of bisphenol A on waste sludge hydrolysis with multi-spectra, isothermal titration microcalorimetry and molecule docking.

    Science.gov (United States)

    Hou, Guangying; Zhang, Rui; Hao, Xiaoyan; Liu, Chunguang

    2017-07-05

    An increasing amount of bisphenol A (BPA) is being produced and used, then discharged into sewage treatment plants and accumulated in sludge or soil, when the sludge is used as fertilizer. Accumulation of BPA in sludge or soil causes poisoning to the enzyme, which affects the biological treatment of sludge and the circulation and conversion of materials in soil. In this research, effect of BPA on sludge hydrolysis is studied from the respect of concentration and components of soluble organic matter in sludge, using three-dimensional fluorescence spectra. In order to illuminate the interaction mechanism, toxic effect of BPA on α-Amylase (a model of hydrolase in sludge) is investigated with multi-spectra, isothermal titration microcalorimetry and molecule docking at the molecular level. Results show that the secondary structure of α-Amylase and the microenvironment of amino acid residue in α-Amylase are changed. The molecular docking study and ITC results show that hydrophobic bond and hydrogen bond exist in the interaction between BPA and α-Amylase. Based on the above analysis and enzyme activity assay, sludge hydrolysis is inhibited due to the denaturation of α-Amylase with BPA exposure. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Interaction of HmC1q with leech microglial cells: involvement of C1qBP-related molecule in the induction of cell chemotaxis

    Directory of Open Access Journals (Sweden)

    Tahtouh Muriel

    2012-02-01

    Full Text Available Abstract Background In invertebrates, the medicinal leech is considered to be an interesting and appropriate model to study neuroimmune mechanisms. Indeed, this non-vertebrate animal can restore normal function of its central nervous system (CNS after injury. Microglia accumulation at the damage site has been shown to be required for axon sprouting and for efficient regeneration. We characterized HmC1q as a novel chemotactic factor for leech microglial cell recruitment. In mammals, a C1q-binding protein (C1qBP alias gC1qR, which interacts with the globular head of C1q, has been reported to participate in C1q-mediated chemotaxis of blood immune cells. In this study, we evaluated the chemotactic activities of a recombinant form of HmC1q and its interaction with a newly characterized leech C1qBP that acts as its potential ligand. Methods Recombinant HmC1q (rHmC1q was produced in the yeast Pichia pastoris. Chemotaxis assays were performed to investigate rHmC1q-dependent microglia migration. The involvement of a C1qBP-related molecule in this chemotaxis mechanism was assessed by flow cytometry and with affinity purification experiments. The cellular localization of C1qBP mRNA and protein in leech was investigated using immunohistochemistry and in situ hybridization techniques. Results rHmC1q-stimulated microglia migrate in a dose-dependent manner. This rHmC1q-induced chemotaxis was reduced when cells were preincubated with either anti-HmC1q or anti-human C1qBP antibodies. A C1qBP-related molecule was characterized in leech microglia. Conclusions A previous study showed that recruitment of microglia is observed after HmC1q release at the cut end of axons. Here, we demonstrate that rHmC1q-dependent chemotaxis might be driven via a HmC1q-binding protein located on the microglial cell surface. Taken together, these results highlight the importance of the interaction between C1q and C1qBP in microglial activation leading to nerve repair in the medicinal

  19. Interaction of HmC1q with leech microglial cells: involvement of C1qBP-related molecule in the induction of cell chemotaxis.

    Science.gov (United States)

    Tahtouh, Muriel; Garçon-Bocquet, Annelise; Croq, Françoise; Vizioli, Jacopo; Sautière, Pierre-Eric; Van Camp, Christelle; Salzet, Michel; Nagnan-le Meillour, Patricia; Pestel, Joël; Lefebvre, Christophe

    2012-02-22

    In invertebrates, the medicinal leech is considered to be an interesting and appropriate model to study neuroimmune mechanisms. Indeed, this non-vertebrate animal can restore normal function of its central nervous system (CNS) after injury. Microglia accumulation at the damage site has been shown to be required for axon sprouting and for efficient regeneration. We characterized HmC1q as a novel chemotactic factor for leech microglial cell recruitment. In mammals, a C1q-binding protein (C1qBP alias gC1qR), which interacts with the globular head of C1q, has been reported to participate in C1q-mediated chemotaxis of blood immune cells. In this study, we evaluated the chemotactic activities of a recombinant form of HmC1q and its interaction with a newly characterized leech C1qBP that acts as its potential ligand. Recombinant HmC1q (rHmC1q) was produced in the yeast Pichia pastoris. Chemotaxis assays were performed to investigate rHmC1q-dependent microglia migration. The involvement of a C1qBP-related molecule in this chemotaxis mechanism was assessed by flow cytometry and with affinity purification experiments. The cellular localization of C1qBP mRNA and protein in leech was investigated using immunohistochemistry and in situ hybridization techniques. rHmC1q-stimulated microglia migrate in a dose-dependent manner. This rHmC1q-induced chemotaxis was reduced when cells were preincubated with either anti-HmC1q or anti-human C1qBP antibodies. A C1qBP-related molecule was characterized in leech microglia. A previous study showed that recruitment of microglia is observed after HmC1q release at the cut end of axons. Here, we demonstrate that rHmC1q-dependent chemotaxis might be driven via a HmC1q-binding protein located on the microglial cell surface. Taken together, these results highlight the importance of the interaction between C1q and C1qBP in microglial activation leading to nerve repair in the medicinal leech.

  20. The Caenorhabditis elegans NF2/Merlin Molecule NFM-1 Nonautonomously Regulates Neuroblast Migration and Interacts Genetically with the Guidance Cue SLT-1/Slit.

    Science.gov (United States)

    Josephson, Matthew P; Aliani, Rana; Norris, Megan L; Ochs, Matthew E; Gujar, Mahekta; Lundquist, Erik A

    2017-02-01

    During nervous system development, neurons and their progenitors migrate to their final destinations. In Caenorhabditis elegans, the bilateral Q neuroblasts and their descendants migrate long distances in opposite directions, despite being born in the same posterior region. QR on the right migrates anteriorly and generates the AQR neuron positioned near the head, and QL on the left migrates posteriorly, giving rise to the PQR neuron positioned near the tail. In a screen for genes required for AQR and PQR migration, we identified an allele of nfm-1, which encodes a molecule similar to vertebrate NF2/Merlin, an important tumor suppressor in humans. Mutations in NF2 lead to neurofibromatosis type II, characterized by benign tumors of glial tissues. Here we demonstrate that in C. elegans, nfm-1 is required for the ability of Q cells and their descendants to extend protrusions and to migrate, but is not required for direction of migration. Using a combination of mosaic analysis and cell-specific expression, we show that NFM-1 is required nonautonomously, possibly in muscles, to promote Q lineage migrations. We also show a genetic interaction between nfm-1 and the C. elegans Slit homolog slt-1, which encodes a conserved secreted guidance cue. Our results suggest that NFM-1 might be involved in the generation of an extracellular cue that promotes Q neuroblast protrusion and migration that acts with or in parallel to SLT-1 In vertebrates, NF2 and Slit2 interact in axon pathfinding, suggesting a conserved interaction of NF2 and Slit2 in regulating migratory events. Copyright © 2017 by the Genetics Society of America.

  1. 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.

  2. 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)

  3. Protein Scaffolding for Small Molecule Catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Baker, David [Univ. of Washington, Seattle, WA (United States)

    2014-09-14

    We aim to design hybrid catalysts for energy production and storage that combine the high specificity, affinity, and tunability of proteins with the potent chemical reactivities of small organometallic molecules. The widely used Rosetta and RosettaDesign methodologies will be extended to model novel protein / small molecule catalysts in which one or many small molecule active centers are supported and coordinated by protein scaffolding. The promise of such hybrid molecular systems will be demonstrated with the nickel-phosphine hydrogenase of DuBois et. al.We will enhance the hydrogenase activity of the catalyst by designing protein scaffolds that incorporate proton relays and systematically modulate the local environment of the catalyticcenter. In collaboration with DuBois and Shaw, the designs will be experimentally synthesized and characterized.

  4. 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.

  5. 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.

  6. 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.

  7. 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:

  8. RNAi pathways in Mucor: A tale of proteins, small RNAs and functional diversity.

    Science.gov (United States)

    Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M

    2016-05-01

    The existence of an RNA-mediated silencing mechanism in the opportunistic fungal pathogen Mucor circinelloides was first described in the early 2000. Since then, Mucor has reached an outstanding position within the fungal kingdom as a model system to achieve a deeper understanding of regulation of endogenous functions by the RNA interference (RNAi) machinery. M. circinelloides combines diverse components of its RNAi machinery to carry out functions not only limited to the defense against invasive nucleic acids, but also to regulate expression of its own genes by producing different classes of endogenous small RNA molecules (esRNAs). The recent discovery of a novel RNase that participates in a new RNA degradation pathway adds more elements to the gene silencing-mediated regulation. This review focuses on esRNAs in M. circinelloides, the different pathways involved in their biogenesis, and their roles in regulating specific physiological and developmental processes in response to environmental signals, highlighting the complexity of silencing-mediated regulation in fungi. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Energy dependence of effective atomic numbers for photon energy absorption and photon interaction: Studies of some biological molecules in the energy range 1 keV-20 MeV

    DEFF Research Database (Denmark)

    Manohara, S.R.; Hanagodimath, S.M.; Gerward, Leif

    2008-01-01

    Effective atomic numbers for photon energy absorption, Z(PEA,eff), and for photon interaction, Z(PI,eff), have been calculated by a direct method in the photon-energy region from 1 keV to 20 MeV for biological molecules, such as fatty acids (lauric, myristic, palmitic, stearic, oleic, linoleic......, linolenic, arachidonic, and arachidic acids), nucleotide bases (adenine, guanine, cytosine, uracil, and thymine), and carbohydrates (glucose, sucrose, raffinose, and starch). The Z(PEA, eff) and Z(PI, eff) values have been found to change with energy and composition of the biological molecules. The energy...

  10. Exotic helium molecules

    International Nuclear Information System (INIS)

    Portier, M.

    2007-12-01

    We study the photo-association of an ultracold cloud of magnetically trapped helium atoms: pairs of colliding atoms interact with one or two laser fields to produce a purely long range 4 He 2 (2 3 S 1 -2 3 P 0 ) molecule, or a 4 He 2 (2 3 S 1 -2 3 S 1 ) long range molecule. Light shifts in one photon photo-association spectra are measured and studied as a function of the laser polarization and intensity, and the vibrational state of the excited molecule. They result from the light-induced coupling between the excited molecule, and bound and scattering states of the interaction between two metastable atoms. Their analysis leads to the determination of the scattering length a = (7.2 ± 0.6) ruling collisions between spin polarized atoms. The two photon photo-association spectra show evidence of the production of polarized, long-range 4 He 2 (2 3 S 1 -2 3 S 1 ) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime τ = (1.4 ± 0.3) μs is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

  11. 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 ...

  12. Effect of conformational propensity of peptide antigens in their interaction with MHC class II molecules. Failure to document the importance of regular secondary structures

    DEFF Research Database (Denmark)

    Sette, A; Lamont, A; Buus, S

    1989-01-01

    the binding capacity, but no correlation was found between their effect and their alpha-helical, beta-sheet, or beta-turn conformational propensity as calculated by the Chou and Fasman algorithm. In summary, all the data presented herein suggest that, at least in the case of OVA 323-336 and IAd......, the propensity of the antigen molecule to form secondary structures such as alpha-helices, beta-sheets, or beta-turns does not correlate with its capacity to bind MHC molecules....

  13. Single-Molecule Manipulation of Double-Stranded DNA Using Optical Tweezers: Interaction Studies of DNA with RecA and YOYO-1

    NARCIS (Netherlands)

    Bennink, Martin L.; Scharer, Orlando D.; Kanaar, Ronald; Sakata-Sogawa, Kumiko; Schins, J.M.; Kanger, Johannes S.; de Grooth, B.G.; Greve, Jan

    1999-01-01

    By using optical tweezers and a specially designed flow cell with an integrated glass micropipette, we constructed a setup similar to that of Smith et al. (Science 271:795-799, 1996) in which an individual double-stranded DNA (dsDNA) molecule can be captured between two polystyrene beads. The first

  14. The electronic spectrum of CUONg(4) (Ng = Ne, Ar, Kr, Xe): New insights in the interaction of the CUO molecule with noble gas matrices

    NARCIS (Netherlands)

    Tecmer, P.; van Lingen, H.; Gomes, A.S.P.; Visscher, L.

    2012-01-01

    The electronic spectrum of the CUO molecule was investigated with the IHFSCC-SD (intermediate Hamiltonian Fock-space coupled cluster with singles and doubles) method and with TD-DFT (time-dependent density functional theory) employing the PBE and PBE0 exchange-correlation functionals. The importance

  15. Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk

    NARCIS (Netherlands)

    Hu, Xinli; Deutsch, Aaron J; Lenz, Tobias L; Onengut-Gumuscu, Suna; Han, Buhm; Chen, Wei-Min; Howson, Joanna M M; Todd, John A; de Bakker, Paul I W; Rich, Stephen S; Raychaudhuri, Soumya

    Variation in the human leukocyte antigen (HLA) genes accounts for one-half of the genetic risk in type 1 diabetes (T1D). Amino acid changes in the HLA-DR and HLA-DQ molecules mediate most of the risk, but extensive linkage disequilibrium complicates the localization of independent effects. Using

  16. Interaction of protons with the C{sub 60} molecule: calculation of deposited energies and electronic stopping cross sections (v{sub {<=}}5 au)

    Energy Technology Data Exchange (ETDEWEB)

    Moretto-Capelle, P. [Laboratoire CAR, IRSAMC, UMR 5589 CNRS, Universite Paul Sabatier, Toulouse (France)]. E-mail: pmc@irsamc.ups-tlse.fr; Bordenave-Montesquieu, D.; Rentenier, A.; Bordenave-Montesquieu, A. [Laboratoire CAR, IRSAMC, UMR 5589 CNRS, Universite Paul Sabatier, Toulouse (France)

    2001-09-28

    The energy deposited by a proton in a C{sub 60} molecule is calculated over a broad collision velocity range from 0.1 to 5 au, using the free-electron gas model of Lindhard and Winther (1964 Mat. Fys. Medd. K Dan. Vidensk. Selsk. 34) and the C{sub 60} electron density distribution calculated by Puska and Nieminen. The energy lost by the proton is maximum near 1.8 au collision velocity in contrast with the saturation found in the low-velocity regime, in the 0.25-0.5 au velocity range, by Kunert and Schmidt. From the impact parameter dependence we deduce the distributions of deposited energies, the averaged energy losses and the C{sub 60} electronic stopping cross sections. It is found that the C{sub 60} molecule behaves as a carbon foil giving very similar absolute stopping cross sections per atom. (author). Letter-to-the-editor.

  17. Strong interaction between dye molecule and electromagnetic field localized around 1 Nm3 at gaps of nanoparticle dimers by plasmon resonance

    Science.gov (United States)

    Itoh, Tamitake; Yamamoto, Yuko S.

    2017-11-01

    Electronic transition rates of a molecule located at a crevasse or a gap of a plasmonic nanoparticle (NP) dimer are largely enhanced up to the factor of around 106 due to electromagnetic (EM) coupling between plasmonic and molecular electronic resonances. The coupling rate is determined by mode density of the EM fields at the crevasse and the oscillator strength of the local electronic resonance of a molecule. The enhancement by EM coupling at a gap of plasmonic NP dimer enables us single molecule (SM) Raman spectroscopy. Recently, this type of research has entered a new regime wherein EM enhancement effects cannot be treated by conventional theorems, namely EM mechanism. Thus, such theorems used for the EM enhancement effect should be re-examined. We here firstly summarize EM mechanism by using surface-enhanced Raman scattering (SERS), which is common in EM enhancement phenomena. Secondly, we focus on recent two our studies on probing SM fluctuation by SERS within the spatial resolution of sub-nanometer scales. Finally, we discuss the necessity of re-examining the EM mechanism with respect to two-fold breakdowns of the weak coupling assumption: the breakdown of Kasha's rule induced by the ultra-fast plasmonic de-excitation and the breakdown of the weak coupling by EM coupling rates exceeding both the plasmonic and molecular excitonic dephasing rates.

  18. Molecular electrostatic potential and "atoms-in-molecules" analyses of the interplay between π-hole and lone pair···π/X-H···π/metal···π interactions.

    Science.gov (United States)

    Bauzá, Antonio; Seth, Saikat Kumar; Frontera, Antonio

    2018-04-05

    Using ab initio calculations, we analyze the interplay between π-hole interactions involving the nitro group of 1,4-dinitrobenzene and lone pair···π (lp···π), C-H···π or metal(M)···π noncovalent interactions. Moreover, we have also used 1,4-phenylenebis(phosphine dioxide) for comparison purposes. Interesting cooperativity effects are found when π-hole (F···N,P) and lp···π/C-H···π/M···π interactions coexist in the same supramolecular assembly. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods (RI-MP2/def2-TZVP). A charge density analysis using the Bader's theory of "atoms in molecules" is carried out to characterize the interactions and to analyze their strengthening or weakening depending on the variation of charge density at critical points. The importance of electrostatic effects on the mutual influence of the interaction is studied by means of molecular electrostatic potential calculations. By taking advantage of these computational tools, the present study examines interplay of these interactions. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  19. Highly parallel translation of DNA sequences into small molecules.

    Directory of Open Access Journals (Sweden)

    Rebecca M Weisinger

    Full Text Available A large body of in vitro evolution work establishes the utility of biopolymer libraries comprising 10(10 to 10(15 distinct molecules for the discovery of nanomolar-affinity ligands to proteins. Small-molecule libraries of comparable complexity will likely provide nanomolar-affinity small-molecule ligands. Unlike biopolymers, small molecules can offer the advantages of cell permeability, low immunogenicity, metabolic stability, rapid diffusion and inexpensive mass production. It is thought that such desirable in vivo behavior is correlated with the physical properties of small molecules, specifically a limited number of hydrogen bond donors and acceptors, a defined range of hydrophobicity, and most importantly, molecular weights less than 500 Daltons. Creating a collection of 10(10 to 10(15 small molecules that meet these criteria requires the use of hundreds to thousands of diversity elements per step in a combinatorial synthesis of three to five steps. With this goal in mind, we have reported a set of mesofluidic devices that enable DNA-programmed combinatorial chemistry in a highly parallel 384-well plate format. Here, we demonstrate that these devices can translate DNA genes encoding 384 diversity elements per coding position into corresponding small-molecule gene products. This robust and efficient procedure yields small molecule-DNA conjugates suitable for in vitro evolution experiments.

  20. 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:

  1. Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction.

    Science.gov (United States)

    Markowitz, Joseph; Chen, Ijen; Gitti, Rossi; Baldisseri, Donna M; Pan, Yongping; Udan, Ryan; Carrier, France; MacKerell, Alexander D; Weber, David J

    2004-10-07

    The binding of S100B to p53 down-regulates wild-type p53 tumor suppressor activity in cancer cells such as malignant melanoma, so a search for small molecules that bind S100B and prevent S100B-p53 complex formation was undertaken. Chemical databases were computationally searched for potential inhibitors of S100B, and 60 compounds were selected for testing on the basis of energy scoring, commercial availability, and chemical similarity clustering. Seven of these compounds bound to S100B as determined by steady state fluorescence spectroscopy (1.0 microM model of one such inhibitor, pentamidine, bound to Ca(2+)-loaded S100B was calculated using intermolecular NOE data between S100B and the drug, and indicates that pentamidine binds into the p53 binding site on S100B defined by helices 3 and 4 and loop 2 (termed the hinge region).

  2. Benchmarking semiempirical and DFT methods for the interaction of thiophene and diethyl sulfide molecules with a Ti(OH)4(H2O) cluster.

    Science.gov (United States)

    Vorontsov, Alexander V; Smirniotis, Panagiotis G

    2017-08-01

    Semiempirical methods pm6 and pm7 as well as density functional theory functionals exchange LSDA, exchange-correlation PW91 and PBE, hybrid B3LYP1 and PBE0 were compared for energy and geometry of thiophene, diethyl sulfide (DES) molecules and their binding to a frozen Ti(OH) 4 (H 2 O) complex having one coordinatively unsaturated Ti 5C site representing small fragment of TiO 2 anatase (001) surface. PBE0/6-31G(d) with DFT-D3 dispersion correction was the best method for description of thiophene and DES molecules geometries as comparison with experimental data demonstrated. Semiempirical methods pm6 and pm7 resulted in only three of four possible binding configurations of thiophene with the Ti(OH) 4 (H 2 O) complex while pm7 described correctly the enthalpy and all configurations of DES binding with the Ti(OH) 4 (H 2 O) complex. SBKJC pseudopotential and LSDA with and without dispersion correction produced flawed results for many configurations. PBE0 and PBE with and without dispersion correction and PW91 with 6-31G(d) basis set systematically produced dependable results for thiophene and DES binding to the Ti(OH) 4 (H 2 O) complex. PBE0-D3/6-31G(d), B3LYP1-D3/6-31G(d), and PBE-D3/6-31G(d) gave best match of binding energy for thiophene while PBE0/6-31G(d) gave best match of DES binding energy as comparison with CCSD(T) energy demonstrated. On the basis of the superior results obtained with PBE0/6-31G(d), it is the recommended method for modeling of adsorption over TiO 2 surfaces. Such a conclusion is in agreement with recent literature.

  3. Biochemical investigations of the mechanism of action of small molecules ZL006 and IC87201 as potential inhibitors of the nNOS-PDZ/PSD-95-PDZ interactions

    DEFF Research Database (Denmark)

    Bach, Anders

    2015-01-01

    ZL006 and IC87201 have been presented as efficient inhibitors of the nNOS/PSD-95 protein-protein interaction and shown great promise in cellular experiments and animal models of ischemic stroke and pain. Here, we investigate the proposed mechanism of action of ZL006 and IC87201 using biochemical...... by interacting with the β-finger of nNOS-PDZ. Our findings have implications for further medicinal chemistry efforts of ZL006, IC87201 and analogues, and challenge the general and widespread view on their mechanism of action....

  4. Analysis of the interactions between difluoroacetylene and one or two hydrogen fluoride molecules based on calculated spin–spin coupling constants

    DEFF Research Database (Denmark)

    Provasi, Patricio F.; Caputo, María Cristina; Sauer, Stephan P. A.

    2012-01-01

    A theoretical study of FCCF:(HF)n complexes, with n = 1 and 2, has been carried out by means of ab initio computational methods. Two types of complexes are formed: those with FH···p interactions and those with FH···FC hydrogen bonds. The indirect spin–spin coupling constants have been calculated ...

  5. Influence of the Debye length on the interaction of a small molecule-modified Au nanoparticle with a surface-bound bioreceptor.

    Science.gov (United States)

    Bukar, Natalia; Zhao, Sandy Shuo; Charbonneau, David M; Pelletier, Joelle N; Masson, Jean-Francois

    2014-05-18

    We report that a shorter Debye length and, as a consequence, decreased colloidal stability are required for the molecular interaction of folic acid-modified Au nanoparticles (Au NPs) to occur on a surface-bound receptor, human dihydrofolate reductase (hDHFR). The interaction measured using surface plasmon resonance (SPR) sensing was optimal in a phosphate buffer at pH 6 and ionic strength exceeding 300 mM. Under these conditions, the aggregation constant of the Au NPs was approximately 10(4) M(-1) s(-1) and the Debye length was below 1 nm, on the same length scale as the size of the folate anion (approximately 0.8 nm). Longer Debye lengths led to poorer SPR responses, revealing a reduced affinity of the folic acid-modified Au NPs for hDHFR. While high colloidal stability of Au NPs is desired in most applications, these conditions may hinder molecular interactions due to Debye lengths exceeding the size of the ligand and thus preventing close interactions with the surface-bound molecular receptor.

  6. Role of Magnetic Exchange Interactions in the Magnetization Relaxation of {3d-4f} Single-Molecule Magnets: A Theoretical Perspective.

    Science.gov (United States)

    Singh, Saurabh Kumar; Beg, Mohammad Faizan; Rajaraman, Gopalan

    2016-01-11

    Combined density functional and ab initio calculations are performed on two isomorphous tetranuclear {Ni3 (III) Ln(III) } star-type complexes [Ln=Gd (1), Dy (2)] to shed light on the mechanism of magnetic exchange in 1 and the origin of the slow magnetization relaxation in complex 2. DFT calculations correctly reproduce the sign and magnitude of the J values compared to the experiments for complex 1. Acute ∢Ni-O-Gd bond angles present in 1 instigate a significant interaction between the 4fxyz orbital of the Gd(III) ion and 3d${{_{x{^{2}}- y{^{2}}}}}$ orbital of the Ni(II) ions, leading to rare and strong antiferromagnetic Ni⋅⋅⋅Gd interactions. Calculations reveal the presence of a strong next-nearest-neighbour Ni⋅⋅⋅Ni antiferromagnetic interaction in complex 1 leading to spin frustration behavior. CASSCF+RASSI-SO calculations performed on complex 2 suggest that the octahedral environment around the Dy(III) ion is neither strong enough to stabilize the mJ |±15/2〉 as the ground state nor able to achieve a large ground-state-first-excited-state gap. The ground-state Kramers doublet for the Dy(III) ion is found to be the mJ |±13/2〉 state with a significant transverse anisotropy, leading to very strong quantum tunneling of magnetization (QTM). Using the POLY_ANISO program, we have extracted the JNiDy interaction as -1.45 cm(-1) . The strong Ni⋅⋅⋅Dy and next-nearest-neighbour Ni⋅⋅⋅Ni interactions are found to quench the QTM to a certain extent, resulting in zero-field SMM behavior for complex 2. The absence of any ac signals at zero field for the structurally similar [Dy(AlMe4 )3 ] highlights the importance of both the Ni⋅⋅⋅Dy and the Ni⋅⋅⋅Ni interactions in the magnetization relaxation of complex 2. To the best of our knowledge, this is the first time that the roles of both the Ni⋅⋅⋅Dy and Ni⋅⋅⋅Ni interactions in magnetization relaxation of a {3d-4f} molecular magnet have been established. © 2016

  7. ΔM/sub j/ transitions in homonuclear molecule scattering off corrugated surfaces. Square and rectangular lattice symmetry and purely repulsive interaction

    International Nuclear Information System (INIS)

    Proctor, T.R.; Kouri, D.J.; Gerber, R.B.

    1984-01-01

    In this paper, we present the first formal and computational studies of Δm/sub j/ transitions occurring in homonuclear molecule-corrugated surface collisions. The model potential is a pairwise additive one which correctly incorporates the fact that Δm/sub j/ transitions occur only for corrugated surfaces (provided the quantization axis is chosen to be the average surface normal). The principal results are: (a) Δm/sub j/ transitions are extremely sensitive to lattice symmetry; (b) strong selection rules obtain for specular scattering; (c) the magnitude of Δm/sub j/ -transition probabilities are strongly sensitive to surface corrugation; (d) the Δm/sub j/ transitions depend strongly on diffraction peak; (e) the ratio of molecular length to lattice dimension (r/a) has a strong influence on the magnitude of Δm/sub j/ -transition probabilities [with the probabilities increasing as (r/a) increases]; (f) Δm/sub j/ rainbows are predicted to occur as a function of the (r/a) ratio increases; (g) Δm/sub j/ transitions and the Δm/sub j/ rainbow are expected to accompany Δj-rotational rainbows; (h) such magnetic transition rainbows accompanying Δj rainbows are suggested as an explanation of recent experimental observations of quenching of NO polarization for larger Δj transitions in NO/Ag(111) scattering

  8. Site-directed mutational analysis of structural interactions of low molecule compounds binding to the N-terminal 8 kDa domain of DNA polymerase β

    International Nuclear Information System (INIS)

    Murakami, Shizuka; Kamisuki, Shinji; Takata, Kei-ichi; Kasai, Nobuyuki; Kimura, Seisuke; Mizushina, Yoshiyuki; Ohta, Keisuke; Sugawara, Fumio; Sakaguchi, Kengo

    2006-01-01

    We previously reported the mode of inhibition of DNA polymerase β (pol. β) by long chain fatty acids and a bile acid, involving binding analyses to the N-terminal 8-kDa DNA binding domain. Here we describe a site-directed mutational analysis in which the key amino acids (L11, K35, H51, K60, L77, and T79), which are direct interaction sites in the domain, were substituted with K, A, A, A, K, and A, respectively. And their pol. β interactions with a C24-long chain fatty acid, nervonic acid (NA), and a bile acid, lithocholic acid (LCA), were investigated by gel mobility shift assay and NMR spectroscopy. In the case of K35A, there was complete loss of DNA binding activity while K60A hardly has any activity. In contrast the other mutations had no appreciable effects. Thus, K35 and K60 are key amino acid sites for binding to template DNA. The DNA binding activities of L11K, H51A, and T79A as well as the wild type were inhibited by NA to the same extent. T79A demonstrated a disturbed interaction with LCA. 1 H- 15 N HSQC NMR analysis indicated that despite their many similarities, the wild-type and the mutant proteins displayed some significant chemical shift differences. Not only were the substituted amino acid residues three-dimensionally shifted, but some amino acids which are positioned far distant from the key amino acids showed a shift. These results suggest that the interaction surface was significantly distorted with the result that LCA could not bind to the domain. These findings confirm our previous biochemical and 3D structural proposals concerning inhibition by NA and LCA

  9. Intracomplex {pi}-{pi} stacking interaction between adjacent phenanthroline molecules in complexes with rare-earth nitrates: Crystal and molecular structures of bis(1,10-Phenanthroline)trinitratoytterbium and bis(1,10-Phenanthroline)trinitratolanthanum

    Energy Technology Data Exchange (ETDEWEB)

    Sadikov, G. G., E-mail: sadgg@igic.ras.ru; Antsyshkina, A. S.; Rodnikova, M. N.; Solonina, I. A. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

    2009-01-15

    Crystals of the compounds Yb(NO{sub 3}){sub 3}(Phen){sub 2} and La(NO{sub 3}){sub 3}(Phen){sub 2} (Phen = 1,10-phenanthroline) are investigated using X-ray diffraction. It is established that there exist two different crystalline modifications: the main modification (phase 1) is characteristic of all members of the isostructural series, and the second modification (phase 2) is observed only for the Eu, Er, and Yb elements. It is assumed that the stability and universality of main phase 1 are associated with the occurrence of the nonbonded {pi}-{pi} stacking interactions between the adjacent phenanthroline ligands in the complexes. The indication of the interactions is a distortion of the planar shape of the Phen molecule (the folding of the metallocycle along the N-N line with a folding angle of 11{sup o}-13{sup o} and its 'boomerang' distortion). The assumption regarding the {pi}-{pi} stacking interaction is very consistent with the shape of the ellipsoids of atomic thermal vibrations, as well as with the data obtained from thermography and IR spectroscopy. An analysis of the structures of a number of rare-earth compounds has demonstrated that the intracomplex {pi}-{pi} stacking interactions directly contribute to the formation of supramolecular associates in the crystals, such as molecular dimers, supramolecules, chain and layered ensembles, and framework systems.

  10. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions ...

  11. Physics of Complex Polymeric Molecules

    Science.gov (United States)

    Kelly, Joshua Walter

    The statistical physics of complex polymers with branches and circuits is the topic of this dissertation. An important motivation are large, single-stranded (ss) RNA molecules. Such molecules form complex ``secondary" and ``tertiary" structures that can be represented as branched polymers with circuits. Such structures are in part directly determined by the nucleotide sequence and in part subject to thermal fluctuations. The polymer physics literature on molecules in this class has mostly focused on randomly branched polymers without circuits while there has been minimal research on polymers with specific structures and on polymers that contain circuits. The dissertation is composed of three parts: Part I studies branched polymers with thermally fluctuating structure confined to a potential well as a simple model for the encapsidation of viral RNA. Excluded volume interactions were ignored. In Part II, I apply Flory theory to the study of the encapsidation of viral ss RNA molecules with specific branched structures, but without circuits, in the presence of excluded volume interaction. In Part III, I expand on Part II and consider complex polymers with specific structure including both branching and circuits. I introduce a method based on the mathematics of Laplacian matrices that allows me to calculate density profiles for such molecules, which was not possible within Flory theory.

  12. Ion-molecule interactions in crossed-beams. [N/sup +/-H/sub 2/; F/sup +/-H; CO/sub 2//sup +/-D/sub 2/

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, S.G.

    1980-09-01

    Interactions of the ions N/sup +/, F/sup +/, and CO/sub 2//sup +/ with H/sub 2/ and/or its isotopes were examined using the crossed-beam technique in the low (< 4 eV) initial relative energy. For the reaction N/sup +/(/sup 3/P) + H/sub 2/ ..-->.. NH/sup +/ + H, complex formation dominates up to 1.9 eV and a substantial interaction occurs between all collision partners up to 3.6 eV. The distribution of N/sup +/ scattered nonreactively from H/sub 2/ also showed a long-lived complex channel below 1.9 eV. The reaction F/sup +/(/sup 3/P) + H/sub 2/ ..-->..FH/sup +/ + H proceeded by a direct reaction mechanism at 0.20 to 1.07 eV. The reaction CO/sub 2//sup +/ + D/sub 2/ ..-->.. DCO/sub 2//sup +/ + D gives asymmetric product distributions at 0.27 eV and above, indicating a direct reaction mechanism. Results indicated that there are probably barriers in the exit channels for DCO/sub 2//sup +/, DCO/sup +/, and D/sub 2/O/sup +/ products. The electronic state distributions of the N/sup +/, F/sup +/, and CO/sub 2//sup +/ beams was investigated using beam attenuation and total luminescence techniques.

  13. Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules

    International Nuclear Information System (INIS)

    Cao, Siqin; Sheong, Fu Kit; Huang, Xuhui

    2015-01-01

    Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute

  14. Role of α-globin H helix in the building of tetrameric human hemoglobin: interaction with α-hemoglobin stabilizing protein (AHSP) and heme molecule.

    Science.gov (United States)

    Domingues-Hamdi, Elisa; Vasseur, Corinne; Fournier, Jean-Baptiste; Marden, Michael C; Wajcman, Henri; Baudin-Creuza, Véronique

    2014-01-01

    Alpha-Hemoglobin Stabilizing Protein (AHSP) binds to α-hemoglobin (α-Hb) or α-globin and maintains it in a soluble state until its association with the β-Hb chain partner to form Hb tetramers. AHSP specifically recognizes the G and H helices of α-Hb. To investigate the degree of interaction of the various regions of the α-globin H helix with AHSP, this interface was studied by stepwise elimination of regions of the α-globin H helix: five truncated α-Hbs α-Hb1-138, α-Hb1-134, α-Hb1-126, α-Hb1-123, α-Hb1-117 were co-expressed with AHSP as two glutathione-S-transferase (GST) fusion proteins. SDS-PAGE and Western Blot analysis revealed that the level of expression of each truncated α-Hb was similar to that of the wild type α-Hb except the shortest protein α-Hb1-117 which displayed a decreased expression. While truncated GST-α-Hb1-138 and GST-α-Hb1-134 were normally soluble; the shorter globins GST-α-Hb1-126 and GST-α-Hb1-117 were obtained in very low quantities, and the truncated GST-α-Hb1-123 provided the least material. Absorbance and fluorescence studies of complexes showed that the truncated α-Hb1-134 and shorter forms led to modified absorption spectra together with an increased fluorescence emission. This attests that shortening the H helix leads to a lower affinity of the α-globin for the heme. Upon addition of β-Hb, the increase in fluorescence indicates the replacement of AHSP by β-Hb. The CO binding kinetics of different truncated AHSPWT/α-Hb complexes showed that these Hbs were not functionally normal in terms of the allosteric transition. The N-terminal part of the H helix is primordial for interaction with AHSP and C-terminal part for interaction with heme, both features being required for stability of α-globin chain.

  15. αMβ2-integrin-intercellular adhesion molecule-1 interactions drive the flow-dependent trafficking of Guillain-Barré syndrome patient derived mononuclear leukocytes at the blood-nerve barrier in vitro

    Science.gov (United States)

    Yosef, Nejla; Ubogu, Eroboghene E.

    2012-01-01

    The mechanisms of hematogenous leukocyte trafficking at the human blood-nerve barrier (BNB) are largely unknown. Intercellular adhesion molecule-1 (ICAM-1) has been implicated in the pathogenesis of Guillain-Barré syndrome (GBS). We developed a cytokine-activated human in vitro BNB model using primary endoneurial endothelial cells. Endothelial treatment with 10 U/mL tissue necrosis factor-α and 20 U/mL interferon-γ resulted in de novo expression of proinflammatory chemokines CCL2, CXCL9, CXCL11 and CCL20, with increased expression of CXCL2-3, CXCL8 and CXCL10 relative to basal levels. Cytokine treatment induced/ enhanced ICAM-1, E- and P-selectin, vascular cell adhesion molecule-1 and the alternatively spliced pro-adhesive fibronectin variant, fibronectin connecting segment-1 expression in a time-dependent manner, without alterations in junctional adhesion molecule-A expression. Lymphocytes and monocytes from untreated GBS patients express ICAM-1 counterligands, αM- and αL-integrin, with differential regulation of αM-integrin expression compared to healthy controls. Under flow conditions that mimic capillary hemodynamics in vivo, there was a >3-fold increase in total GBS patient and healthy control mononuclear leukocyte adhesion/ migration at the BNB following cytokine treatment relative to the untreated state. Function neutralizing monoclonal antibodies against human αM-integrin (CD11b) and ICAM-1 reduced untreated GBS patient mononuclear leukocyte trafficking at the BNB by 59% and 64.2% respectively. Monoclonal antibodies against αL-integrin (CD11a) and human intravenous immunoglobulin reduced total leukocyte adhesion/migration by 22.8% and 17.6% respectively. This study demonstrates differential regulation of αM-integrin on circulating mononuclear cells in GBS, as well as an important role for αM-integrin-ICAM-1 interactions in pathogenic GBS patient leukocyte trafficking at the human BNB in vitro. PMID:22552879

  16. ψ(3S) and Υ(5S) Originating in Heavy Meson Molecules: A Coupled Channel Analysis Based on an Effective Vector Quark–Quark Interaction

    International Nuclear Information System (INIS)

    Matsuda, Y.; Sakai, M.; Hirano, M.

    2013-01-01

    In our previous coupled channel analysis based on the Cornell effective quark–quark interaction, it was indicated that the ψ(3S) solution corresponding to ψ(4040) originates from a D ∗ D¯ ∗ channel state. In this article, we report on a simultaneous analysis of the ψ - and Υ-family states. The most conspicuous outcome is a finding that the Υ(5S) solution corresponding to Υ(10860) originates from a B ∗ B¯ ∗ channel state, very much like ψ(3S). Some other characteristics of the result, including the induced very large S–D mixing and relation of some of the solutions with newly observed heavy quarkonia-like states are discussed. (author)

  17. Single molecule detection, thermal fluctuation and life

    Science.gov (United States)

    YANAGIDA, Toshio; ISHII, Yoshiharu

    2017-01-01

    Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines. PMID:28190869

  18. Nuclei quadrupole coupling constants in diatomic molecule

    International Nuclear Information System (INIS)

    Ivanov, A.I.; Rebane, T.K.

    1993-01-01

    An approximate relationship between the constants of quadrupole interaction of nuclei in a two-atom molecule is found. It enabled to establish proportionality of oscillatory-rotation corrections to these constants for both nuclei in the molecule. Similar results were obtained for the factors of electrical dipole-quadrupole screening of nuclei. Applicability of these relationships is proven by the example of lithium deuteride molecule. 4 refs., 1 tab

  19. A Mott-like State of Molecules

    International Nuclear Information System (INIS)

    Duerr, S.; Volz, T.; Syassen, N.; Bauer, D. M.; Hansis, E.; Rempe, G.

    2006-01-01

    We prepare a quantum state where each site of an optical lattice is occupied by exactly one molecule. This is the same quantum state as in a Mott insulator of molecules in the limit of negligible tunneling. Unlike previous Mott insulators, our system consists of molecules which can collide inelastically. In the absence of the optical lattice these collisions would lead to fast loss of the molecules from the sample. To prepare the state, we start from a Mott insulator of atomic 87Rb with a central region, where each lattice site is occupied by exactly two atoms. We then associate molecules using a Feshbach resonance. Remaining atoms can be removed using blast light. Our method does not rely on the molecule-molecule interaction properties and is therefore applicable to many systems

  20. Spectroscopy and Chemistry of Cold Molecules

    Science.gov (United States)

    Momose, Takamasa

    2012-06-01

    Molecules at low temperatures are expected to behave quite differently from those at high temperatures because pronounced quantum effects emerge from thermal averages. Even at 10 K, a significant enhancement of reaction cross section is expected due to tunneling and resonance effects. Chemistry at this temperature is very important in order to understand chemical reactions in interstellar molecular clouds. At temperatures lower than 1 K, collisions and intermolecular interactions become qualitatively different from those at high temperatures because of the large thermal de Broglie wavelength of molecules. Collisions at these temperatures must be treated as the interference of molecular matter waves, but not as hard sphere collisions. A Bose-Einstein condensate is a significant state of matter as a result of coherent matter wave interaction. Especially, dense para-H_2 molecules are predicted to become a condensate even around 1 K. A convenient method to investigate molecules around 1 K is to dope molecules in cold matrices. Among various matrices, quantum hosts such as solid para-H_2 and superfluid He nano-droplets have been proven to be an excellent host for high-resolution spectroscopy. Rovibrational motion of molecules in these quantum hosts is well quantized on account of the weak interactions and the softness of quantum environment. The linewidths of infrared spectra of molecules in the quantum hosts are extremely narrow compared with those in other matrices. The sharp linewidths allow us to resolve fine spectral structures originated in subtle interactions between guest and host molecules. In this talk, I will describe how the splitting and lineshape of high-resolution spectra of molecules in quantum hosts give us new information on the static and dynamical interactions of molecules in quantum medium. The topics include dynamical response of superfluid environment upon rotational excitation, and possible superfluid phase of para-H_2 clusters. I will also

  1. Study of two examples of non linear interaction of a laser wave with matter: laser-induced damage of dielectrics and non linear optical properties of organometallic molecules in solution

    International Nuclear Information System (INIS)

    Gaudry, Jean-Baptiste

    2000-01-01

    This research thesis reports the study of two mechanisms of non linear interaction of a laser wave with matter. More particularly, it reports the experimental investigation of non linear optical properties of organometallic molecules in solution, as well as the damage of perfect silica under laser irradiation by using simulation codes. As far as optical properties are concerned, the author highlights the influence of the electronic configuration of the metal present in the organometallic compound, and the influence of the ligand on the second-order non-linear response. As far as the simulation is concerned, some experimental results have been reproduced. This work can be useful for the investigation of the extrinsic damage of imperfect materials, and for the design of experiments of transient measurements of excited silica [fr

  2. Single-molecule dynamics in nanofabricated traps

    Science.gov (United States)

    Cohen, Adam

    2009-03-01

    The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

  3. Biochemical evaluation of interactions between synergistic molecules and phase I enzymes involved in insecticide resistance in B- and Q-type Bemisia tabaci (Hemiptera: Aleyrodidae).

    Science.gov (United States)

    Panini, Michela; Tozzi, Francesco; Zimmer, Christoph T; Bass, Chris; Field, Linda; Borzatta, Valerio; Mazzoni, Emanuele; Moores, Graham

    2017-09-01

    Metabolic resistance is an important consideration in the whitefly Bemisia tabaci, where an esterase-based mechanism has been attributed to pyrethroid resistance and over-expression of the cytochrome P450, CYP6CM1, has been correlated to resistance to imidacloprid and other neonicotinoids. In vitro interactions between putative synergists and CYP6CM1, B and Q-type esterases were investigated, and structure-activity relationship analyses allowed the identification of chemical structures capable of acting as inhibitors of esterase and oxidase activities. Specifically, methylenedioxyphenyl (MDP) moieties with a polyether chain were preferable for optimum inhibition of B-type esterase, whilst corresponding dihydrobenzofuran structures were potent for the Q-esterase variation. Potent inhibition of CYP6CM1 resulted from structures which contained an alkynyl chain with a terminal methyl group. Synergist candidates could be considered for field control of B. tabaci, especially to abrogate neonicotinoid resistance. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  4. Acid–base interaction between carbon black and polyurethane molecules with different amine values: Dispersion stability of carbon black suspension for use in lithium ion battery cathodes

    International Nuclear Information System (INIS)

    Kil, Ki Chun; Kim, Gu Yeon; Cho, Chae-Woong; Lim, Myung Duk; Kim, Kijun; Jeong, Kyung-Min; Lee, Jinuk; Paik, Ungyu

    2013-01-01

    The dispersion properties of carbon black (CB) slurries as well as the accompanying electrochemical properties of Li(Ni 1/3 Co 1/3 Mn 1/3 )O 2 (NCM) electrodes were investigated by controlling the amine value of polyurethane-based dispersants. The increase in amine value of dispersants leads to an increase in adsorption level on CB surface due to a strong acid/base interaction between dispersants and CB particles, providing the improvement of steric repulsion between particles at the solid–liquid interface. This results in the enhancement of the dispersion stability of CB and the related microstructure of the electrodes. Electrochemical experiments indicated that the rate capabilities and cycle performance of the electrodes are in good agreement with dispersion properties of CB slurries. However, it was found that the excessive addition of the dispersant was deleterious to electrochemical properties because the non-adsorbed dispersants act as an electronic conduction barrier between solid phases. Therefore, it is suggested that the amine value of dispersant and tailored amount of dispersant addition can be key roles for obtaining the optimized dispersion stability of CB and the corresponding excellent electrochemical properties of the cathode

  5. Comparison of arsenic acid with phosphoric acid in the interaction with a water molecule and an alkali/alkaline-earth metal cation.

    Science.gov (United States)

    Park, Sung Woo; Kim, Chang Woo; Lee, Ji Hyun; Shim, Giwoong; Kim, Kwang S

    2011-10-20

    Recently, Wolfe-Simon has discovered a bacterium which is able to survive using arsenic(V) rather than phosphorus(V) in its DNA. Thus it is important to investigate some important structural and chemical similarities and dissimilarities between phosphate and arsenate. We compared the monohydrated structures and the alkali/alkaline-earth metal (Na(+), K(+), Mg(2+) and Ca(2+)) complexes of the arsenic acid/anions with those of the phosphoric acid/anions [i.e., H(m)PO(4)(-(3-m)) vs H(m)AsO(4)(-(3-m)) (m = 1-3)]. We carried out geometry optimization along with harmonic frequency calculations using ab initio calculations. Despite the increased van der Waals radius of As, the hydrated structures of both P and As systems show very close similarity (within 0.25 Å in the P/As···O(water) distance and within a few kJ/mol in binding energy) because of the increased induction energies by more polar arsenic acid/anons and slightly increased dispersion energy by a larger size of the As atom. In the metal complexes, the arsenic acid has a slightly larger binding distance (by 0.07-1.0 Å) and weaker binding energy because the As(V) ion has a slightly larger radius than the P(V) ion, and the electrostatic interaction is the dominating feature in these systems.

  6. Exotic helium molecules; Molecules exotiques d'helium

    Energy Technology Data Exchange (ETDEWEB)

    Portier, M

    2007-12-15

    We study the photo-association of an ultracold cloud of magnetically trapped helium atoms: pairs of colliding atoms interact with one or two laser fields to produce a purely long range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}P{sub 0}) molecule, or a {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) long range molecule. Light shifts in one photon photo-association spectra are measured and studied as a function of the laser polarization and intensity, and the vibrational state of the excited molecule. They result from the light-induced coupling between the excited molecule, and bound and scattering states of the interaction between two metastable atoms. Their analysis leads to the determination of the scattering length a = (7.2 {+-} 0.6) ruling collisions between spin polarized atoms. The two photon photo-association spectra show evidence of the production of polarized, long-range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime {tau} = (1.4 {+-} 0.3) {mu}s is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

  7. Exotic helium molecules; Molecules exotiques d'helium

    Energy Technology Data Exchange (ETDEWEB)

    Portier, M

    2007-12-15

    We study the photo-association of an ultracold cloud of magnetically trapped helium atoms: pairs of colliding atoms interact with one or two laser fields to produce a purely long range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}P{sub 0}) molecule, or a {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) long range molecule. Light shifts in one photon photo-association spectra are measured and studied as a function of the laser polarization and intensity, and the vibrational state of the excited molecule. They result from the light-induced coupling between the excited molecule, and bound and scattering states of the interaction between two metastable atoms. Their analysis leads to the determination of the scattering length a = (7.2 {+-} 0.6) ruling collisions between spin polarized atoms. The two photon photo-association spectra show evidence of the production of polarized, long-range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime {tau} = (1.4 {+-} 0.3) {mu}s is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

  8. Effect of electron beam radio-sterilization on cyclo olefin copolymers and its impact on the interactions with other active molecules

    International Nuclear Information System (INIS)

    Barakat, H.

    2013-01-01

    The aim of this work was to study the effect of electron beam radio-sterilization on cyclo olefins copolymers (COC) used as pharmaceutical storage materials, as well as to investigate its impact on the interaction with pharmaceuticals formulations. Due to the analytical methodology used which has dealt with different techniques of characterization such as size exclusion chromatography, reversed phase high performance liquid chromatography, Fourier transformed infrared spectroscopy, atomic force microscopy and contact angle measurements, we have been able to put into evidence different kinds of modifications both in the bulk and on the surface of the sterilized material and also after ageing. The principal modification of material's bulk, observed at the recommended dose for sterilization (25 kGy), was polymer chains scissions, accompanied with creation of low molecular weight compounds, that are potentials migrants that are likely to affect the safe use of COC. Indeed, some of these compounds have been found with a relatively important concentration in the solutions where sterilized COC has been stored, especially in aqueous solutions. However, the preliminary study of toxicity has shown the absence of cytotoxicity of the extractable by-products obtained at the sterilization dose. Surface modifications of radio-sterilized COC are of two types: a physical one, with an increase of the surface's roughness and a chemical one with the formation of polar oxidation products; these two modifications result in an increase of surface's wettability that may be important. However, in some cases such as for aged samples, these modifications are relatively weak even at doses higher than the one recommended for sterilization, which can explain the absence of the effect of radiation on the behavior of COC concerning drug solutions. Indeed, no variation of drug sorption has been observed between irradiated aged COC and no-irradiated aged COC. (author)

  9. Structural Basis of the Interaction of a Trypanosoma cruzi Surface Molecule Implicated in Oral Infection with Host Cells and Gastric Mucin

    Science.gov (United States)

    Cortez, Cristian; Yoshida, Nobuko; Bahia, Diana; Sobreira, Tiago J.P.

    2012-01-01

    Host cell invasion and dissemination within the host are hallmarks of virulence for many pathogenic microorganisms. As concerns Trypanosoma cruzi, which causes Chagas disease, the insect vector-derived metacyclic trypomastigotes (MT) initiate infection by invading host cells, and later blood trypomastigotes disseminate to diverse organs and tissues. Studies with MT generated in vitro and tissue culture-derived trypomastigotes (TCT), as counterparts of insect-borne and bloodstream parasites, have implicated members of the gp85/trans-sialidase superfamily, MT gp82 and TCT Tc85-11, in cell invasion and interaction with host factors. Here we analyzed the gp82 structure/function characteristics and compared them with those previously reported for Tc85-11. One of the gp82 sequences identified as a cell binding site consisted of an α-helix, which connects the N-terminal β-propeller domain to the C-terminal β-sandwich domain where the second binding site is nested. In the gp82 structure model, both sites were exposed at the surface. Unlike gp82, the Tc85-11 cell adhesion sites are located in the N-terminal β-propeller region. The gp82 sequence corresponding to the epitope for a monoclonal antibody that inhibits MT entry into target cells was exposed on the surface, upstream and contiguous to the α-helix. Located downstream and close to the α-helix was the gp82 gastric mucin binding site, which plays a central role in oral T. cruzi infection. The sequences equivalent to Tc85-11 laminin-binding sites, which have been associated with the parasite ability to overcome extracellular matrices and basal laminae, was poorly conserved in gp82, compatible with its reduced capacity to bind laminin. Our study indicates that gp82 is structurally suited for MT to initiate infection by the oral route, whereas Tc85-11, with its affinity for laminin, would facilitate the parasite dissemination through diverse organs and tissues. PMID:22860068

  10. Quantitative real-time PCR as a sensitive protein-protein interaction quantification method and a partial solution for non-accessible autoactivator and false-negative molecule analysis in the yeast two-hybrid system.

    Science.gov (United States)

    Maier, Richard H; Maier, Christina J; Hintner, Helmut; Bauer, Johann W; Onder, Kamil

    2012-12-01

    Many functional proteomic experiments make use of high-throughput technologies such as mass spectrometry combined with two-dimensional polyacrylamide gel electrophoresis and the yeast two-hybrid (Y2H) system. Currently there are even automated versions of the Y2H system available that can be used for proteome-wide research. The Y2H system has the capacity to deliver a profusion of Y2H positive colonies from a single library screen. However, subsequent analysis of these numerous primary candidates with complementary methods can be overwhelming. Therefore, a method to select the most promising candidates with strong interaction properties might be useful to reduce the number of candidates requiring further analysis. The method described here offers a new way of quantifying and rating the performance of positive Y2H candidates. The novelty lies in the detection and measurement of mRNA expression instead of proteins or conventional Y2H genetic reporters. This method correlates well with the direct genetic reporter readouts usually used in the Y2H system, and has greater sensitivity for detecting and quantifying protein-protein interactions (PPIs) than the conventional Y2H system, as demonstrated by detection of the Y2H false-negative PPI of RXR/PPARG. Approximately 20% of all proteins are not suitable for the Y2H system, the so-called autoactivators. A further advantage of this method is the possibility to evaluate molecules that usually cannot be analyzed in the Y2H system, exemplified by a VDR-LXXLL motif peptide interaction. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Nanodevices for generating power from molecules and batteryless sensing

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yinmin; Wang, Xianying; Hamza, Alex V.

    2017-01-03

    A nanoconverter or nanosensor is disclosed capable of directly generating electricity through physisorption interactions with molecules that are dipole containing organic species in a molecule interaction zone. High surface-to-volume ratio semiconductor nanowires or nanotubes (such as ZnO, silicon, carbon, etc.) are grown either aligned or randomly-aligned on a substrate. Epoxy or other nonconductive polymers are used to seal portions of the nanowires or nanotubes to create molecule noninteraction zones. By correlating certain molecule species to voltages generated, a nanosensor may quickly identify which species is detected. Nanoconverters in a series parallel arrangement may be constructed in planar, stacked, or rolled arrays to supply power to nano- and micro-devices without use of external batteries. In some cases breath, from human or other life forms, contain sufficient molecules to power a nanoconverter. A membrane permeable to certain molecules around the molecule interaction zone increases specific molecule nanosensor selectivity response.

  12. Photoelectron spectroscopy of heavy atoms and molecules

    International Nuclear Information System (INIS)

    White, M.G.

    1979-07-01

    The importance of relativistic interactions in the photoionization of heavy atoms and molecules has been investigated by the technique of photoelectron spectroscopy. In particular, experiments are reported which illustrate the effects of the spin-orbit interaction in the neutral ground state, final ionic states and continuum states of the photoionization target

  13. Hybrid molecule/superconductor assemblies

    International Nuclear Information System (INIS)

    McDevitt, J.T.; Haupt, S.G.; Riley, D.R.; Zhao, J.; Zhou, J.P., Jones, C.

    1993-01-01

    The fabrication of electronic devices from molecular materials has attracted much attention recently. Schottky diodes, molecular transistors, metal-insulator-semiconductor diodes, MIS field effect transistors and light emitting diodes have all been prepared utilizing such substances. The active elements in these devices have been constructed by depositing the molecular phase onto the surface of a metal, semiconductor or insulating substrate. With the recent discovery of high temperature superconductivity, new opportunities now exist for the study of molecule/superconductor interactions as well as for the construction of novel hybrid molecule/superconductor devices. In this paper, methods for preparing the initial two composite molecule/semiconductor devices will be reported. Consequently, light sensors based on dye-coated superconductor junctions as well as molecular switches fashioned from conductive polymer coated superconductor junctions as well as molecular switches fashioned from conductive polymer coated superconductor microbridges will be discussed. Moreover, molecule/superconductor energy and electron transfer phenomena will be illustrated also for the first time

  14. 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)

  15. Current status and future perspectives of electron interactions with molecules, clusters, surfaces, and interfaces [Workshop on Fundamental challenges in electron-driven chemistry; Workshop on Electron-driven processes: Scientific challenges and technological opportunities

    Energy Technology Data Exchange (ETDEWEB)

    Becker, Kurt H.; McCurdy, C. William; Orlando, Thomas M.; Rescigno, Thomas N.

    2000-09-01

    This report is based largely on presentations and discussions at two workshops and contributions from workshop participants. The workshop on Fundamental Challenges in Electron-Driven Chemistry was held in Berkeley, October 9-10, 1998, and addressed questions regarding theory, computation, and simulation. The workshop on Electron-Driven Processes: Scientific Challenges and Technological Opportunities was held at Stevens Institute of Technology, March 16-17, 2000, and focused largely on experiments. Electron-molecule and electron-atom collisions initiate and drive almost all the relevant chemical processes associated with radiation chemistry, environmental chemistry, stability of waste repositories, plasma-enhanced chemical vapor deposition, plasma processing of materials for microelectronic devices and other applications, and novel light sources for research purposes (e.g. excimer lamps in the extreme ultraviolet) and in everyday lighting applications. The life sciences are a rapidly advancing field where the important role of electron-driven processes is only now beginning to be recognized. Many of the applications of electron-initiated chemical processes require results in the near term. A large-scale, multidisciplinary and collaborative effort should be mounted to solve these problems in a timely way so that their solution will have the needed impact on the urgent questions of understanding the physico-chemical processes initiated and driven by electron interactions.

  16. Physics of atoms and molecules

    International Nuclear Information System (INIS)

    Bransden, B.H.; Joachain, C.J.

    1983-01-01

    This book presents a unified account of the physics of atoms and molecules at a level suitable for second- and third-year undergraduate students of physics and physical chemistry. Following a brief historical introduction to the subject the authors outline the ideas and approximation methods of quantum mechanics to be used later in the book. Six chapters look at the structure of atoms and the interactions between atoms and electromagnetic radiation. The authors then move on to describe the structure of molecules and molecular spectra. Three chapters deal with atomic collisions, the scattering of electrons by atoms and the scattering of atoms by atoms. The concluding chapter considers a few of the many important applications of atomic physics within astrophysics, laser technology, and nuclear fusion. Problems are given at the end of each chapter, with hints at the solutions in an appendix. Other appendices include various special topics and derivations together with useful tables of units. (author)

  17. 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 ...

  18. 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 ...

  19. 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:

  20. Single molecule conductance

    NARCIS (Netherlands)

    Willems, R.

    2008-01-01

    This thesis represents an excursion into the world of molecular electronics, i.e. the field of research trying to use individual (organic) molecules as electronic components; in this work various experimental methods have been explored to connect individual molecules to metallic contacts and

  1. Molecules in stars

    International Nuclear Information System (INIS)

    Tsuji, T.

    1986-01-01

    Recently, research related to molecules in stars has rapidly expanded because of progress in related fields. For this reason, it is almost impossible to cover all the topics related to molecules in stars. Thus, here the authors focus their attention on molecules in the atmospheres of cool stars and do not cover in any detail topics related to circumstellar molecules originating from expanding envelopes located far from the stellar surface. However, the authors do discuss molecules in quasi-static circumstellar envelopes (a recently discovered new component of circumstellar envelopes) located near the stellar surface, since molecular lines originating from such envelopes show little velocity shift relative to photospheric lines, and hence they directly affect the interpretation and analysis of stellar spectra

  2. Molecular Wring Resonances in Chain Molecules

    DEFF Research Database (Denmark)

    Bohr, Henrik; Brunak, Søren; Bohr, Jakob

    1997-01-01

    It is shown that the eigenfrequency of collective twist excitations in chain molecules can be in the megahertz and gigahertz range. Accordingly, resonance states can be obtained at specific frequencies, and phenomena that involve structural properties can take place. Chain molecules can alter the...... their conformation and their ability to function, and a breaking of the chain can result. It is suggested that this phenomenon forms the basis for effects caused by the interaction of microwaves and biomolecules, e.g. microwave assisted hydrolysis of chain molecules....

  3. 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....

  4. Single-Molecule Electronics with Cross- Conjugated Molecules: Quantum Interference, IETS and Non-Equilibrium "Temperatures"

    DEFF Research Database (Denmark)

    Jørgensen, Jacob Lykkebo

    Abstract The idea of using single-molecules as components in electronic devices is fas- cinating. For this idea to come into fruition, a number of technical and theo- retical challenges must be overcome. In this PhD thesis, the electron-phonon interaction is studied for a special class of molecules......, which is characterised by destructive quantum interference. The molecules are cross-conjugated, which means that the two parts of the molecules are conjugated to a third part, but not to each other. This gives rise to an anti-resonance in the trans- mission. In the low bias and low temperature regime......-conjugated molecules. We nd that the vibrational modes that would be expected to dominate, following the propensity, rules are very weak. Instead, other modes are found to be the dominant ones. We study this phenomenon for a number of cross-conjugated molecules, and link these ndings to the anti...

  5. 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.

  6. Dissociation in small molecules

    International Nuclear Information System (INIS)

    Dehmer, P.M.

    1982-01-01

    The study of molecular dissociation processes is one of the most interesting areas of modern spectroscopy owing to the challenges presented bt even the simplest of diatomic molecules. This paper reviews the commonly used descriptions of molecular dissociation processes for diatomic molecules, the selection rules for predissociation, and a few of the principles to be remembered when one is forced to speculate about dissociation mechanisms in a new molecule. Some of these points will be illustrated by the example of dissociative ionization in O 2

  7. Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Sony Malhotra

    Full Text Available Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets.

  8. Electronic states and nature of bonding of the molecule NiGe by all electron ab initio Hartree–Fock (HF) and configuration interaction (CI) calculations and mass spectrometric equilibrium experiments

    DEFF Research Database (Denmark)

    Shim, Irene; Kingcade, Joseph E.; Gingerich, Karl A.

    1988-01-01

    -lying electronic states of the NiGe molecule have all been characterized by the symmetry of the hole in the 3d shell of Ni. The dissociation energy of the NiGe molecule has been determined from our high temperature mass spectrometric equilibrium data in combination with the theoretical results as D [open circle] 0...... =286.8±10.9 kJ mol−1. The standard heat of formation of the NiGe molecule has been obtained as DeltaH [open circle] f,298 =514±12 kJ mol−1. The Journal of Chemical Physics is copyrighted by The American Institute of Physics....

  9. 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...

  10. Molecules to Materials

    Indian Academy of Sciences (India)

    evolved as a new line of thinking wherein a single molecule or perhaps a collection .... In photonic communication processes, laser light has to be modulated and .... The author wishes to thank G Rajaram for a critical reading of the manuscript.

  11. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    overall absorption spectrum of a molecule is a superposition of many such sharp lines .... dilute solution of the enzyme and the substrate over few drops of silicone oil placed ..... Near-field Scanning Optical Microscopy (NSOM): Development.

  12. 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.

  13. Molecule of the Month

    Indian Academy of Sciences (India)

    Molecule of the Month - Adamantane - A Plastic Piece of Diamond. J Chandrasekhar. Volume 16 Issue 12 ... Keywords. Adamantane; diamondoid systems; plastic crystals. ... Resonance – Journal of Science Education | News. © 2017 Indian ...

  14. Intersystem crossing in complex molecules

    International Nuclear Information System (INIS)

    Pappalardo, R.G.

    1980-01-01

    The general question of singlet-triplet intersystem crossing is addressed in the context of large organic molecules, i.e., ''complex'' molecules capable of self-relaxation in the absence of collisions. Examples of spectral properties of such molecules in the vapor phase are discussed, relying on extensive Russian literature in this area. Formal expressions for the relaxation rate in the electronic excited states are derived on the basis of the formalism of collision theory, and are applied to the specific case of intersystem crossing. The derivation of the ''energy-gap'' law for triplet-singlet conversion in aromatic hydrocarbons is briefly outlined. The steep rise of internal conversion rates as a function of excess excitation energy, and its competition with the intersystem crossing process, are reviewed for the case of naphthalene vapor. A general expression for the spin-orbit interaction Hamiltonian in molecular systems is outlined. Experimental observations on singlet-triplet conversion rates and the factors that can drastically affect such rates are discussed, with emphasis on the ''in- ternal'' and ''external'' heavy-atom effects. Basic relations of ESR spectroscopy and magnetophotoselection are reviewed. Technological implications of the singlet-triplet crossing in complex molecules are discussed in the context of chelate lasers, dye lasers and luminescent displays. Effects related to singlet-triplet crossing, and generally to excited-state energy-transfer in biological systems, are exemplified by the role of aromatic amino-acids in the phosphorescence of proteins, by some recent studies of energy-transfer in models of biomembranes, and by the clustering of triplet-energy donor-acceptor pairs in micelles

  15. Stability of matter-antimatter molecules

    International Nuclear Information System (INIS)

    Wong, Cheuk-Yin; Lee, Teck-Ghee

    2011-01-01

    Highlights: → We examine stability of matter-antimatter molecules with four constituents. → The binding of matter-antimatter molecules is a common phenomenon. → Molecules have bound states if ratio of constituent masses greater than ∼4. → We evaluate molecular binding energies and annihilation lifetimes. - Abstract: We examine the stability of matter-antimatter molecules by reducing the four-body problem into a simpler two-body problem with residual interactions. We find that matter-antimatter molecules with constituents (m 1 + ,m 2 - ,m-bar 2 + ,m-bar 1 - ) possess bound states if their constituent mass ratio m 1 /m 2 is greater than about 4. This stability condition suggests that the binding of matter-antimatter molecules is a rather common phenomenon. We evaluate the binding energies and eigenstates of matter-antimatter molecules (μ + e - )-(e + μ - ),(π + e - )-(e + π - ),(K + e - )-(e + K - ),(pe - )-(e + p-bar),(pμ - )-(μ + p-bar), and (K + μ - ) - (μ + K - ), which satisfy the stability condition. We estimate the molecular annihilation lifetimes in their s states.

  16. Multi-Excitonic Quantum Dot Molecules

    Science.gov (United States)

    Scheibner, M.; Stinaff, E. A.; Doty, M. F.; Ware, M. E.; Bracker, A. S.; Gammon, D.; Ponomarev, I. V.; Reinecke, T. L.; Korenev, V. L.

    2006-03-01

    With the ability to create coupled pairs of quantum dots, the next step towards the realization of semiconductor based quantum information processing devices can be taken. However, so far little knowledge has been gained on these artificial molecules. Our photoluminescence experiments on single InAs/GaAs quantum dot molecules provide the systematics of coupled quantum dots by delineating the spectroscopic features of several key charge configurations in such quantum systems, including X, X^+,X^2+, XX, XX^+ (with X being the neutral exciton). We extract general rules which determine the formation of molecular states of coupled quantum dots. These include the fact that quantum dot molecules provide the possibility to realize various spin configurations and to switch the electron hole exchange interaction on and off by shifting charges inside the molecule. This knowledge will be valuable in developing implementations for quantum information processing.

  17. Electron-molecule collisions

    International Nuclear Information System (INIS)

    Shimamura, I.; Takayanagi, K.

    1984-01-01

    The study of collision processes plays an important research role in modern physics. Many significant discoveries have been made by means of collision experiments. Based on theoretical, experimental, and computational studies, this volume presents an overview detailing the basic processes of electron-molecule collisions. The editors have collected papers-written by a group of international experts-that consider a diverse range of phenomena occurring in electronmolecule collisions. The volume discusses first the basic formulation for scattering problems and then gives an outline of the physics of electron-molecule collisions. The main topics covered are rotational transitions, vibrational transitions, dissociation of molecules in slow collisions, the electron-molecule collision as a spectroscopic tool for studying molecular electronic structures, and experimental and computational techniques for determining the cross sections. These well-referenced chapters are self-contained and can be read independently or consecutively. Authoritative and up-to-date, Electron-Molecule Collisions is a useful addition to the libraries of students and researchers in the fields of atomic, molecular, and chemical physics, and physical chemistry

  18. Hidden charm molecules in a finite volume

    International Nuclear Information System (INIS)

    Albaladejo, M.; Hidalgo-Duque, C.; Nieves, J.; Oset, E.

    2014-01-01

    In the present paper we address the interaction of charmed mesons in hidden charm channels in a finite box. We use the interaction from a recent model based on heavy quark spin symmetry that predicts molecules of hidden charm in the infinite volume. The energy levels in the box are generated within this model, and several methods for the analysis of these levels ("inverse problem") are investigated. (author)

  19. 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.

  20. Protection of a PWR nuclear power stations against corrosion using hydrogen molecules to capture oxygen molecules

    International Nuclear Information System (INIS)

    Nahili, M.

    2004-01-01

    A protection method for the primary loops metals of nuclear power plants from corrosion was investigated. Hydrogen molecules were added to the primary circuit to eliminate oxygen molecules produced by radiolysis of coolant at the reactor core. The hydrogen molecules were produced by electrolyses of water and then added when the coolant water was passing through the primary coolant circuit. Thermodynamical process and the protection methods from corrosion were discussed, the discussion emphasized on the removal of oxygen molecules as one of the protection methods, and compared with other methods. The amount of hydrogen molecules needed for complete removal of oxygen was estimated in two cases: in the case without passing the water through the oxygen removal system, and in the case of passing water through the system. A pressurized water reactor VVER was chosen to be investigated in this study. The amount of hydrogen molecules was estimated so as to eliminate completely the oxygen molecules from coolant water. The estimated value was found to be less than the permissible range for coolant water for such type of reactors. A simulation study for interaction mechanism between hydrogen and oxygen molecules as water flowing in a tube similar to that of coolant water was performed with different water flow velocities. The interaction between the molecules of hydrogen and oxygen was described. The gas diffusion at the surface of the tube was found to play a major role in the interaction. A mathematical model was found to give full description of the change of oxygen concentration through the tube, as well as, to calculate the length of the tube where the concentration of oxygen reduced to few order of magnitude. (Author)

  1. 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

  2. Single molecule microscopy and spectroscopy: concluding remarks.

    Science.gov (United States)

    van Hulst, Niek F

    2015-01-01

    Chemistry is all about molecules: control, synthesis, interaction and reaction of molecules. All too easily on a blackboard, one draws molecules, their structures and dynamics, to create an insightful picture. The dream is to see these molecules in reality. This is exactly what "Single Molecule Detection" provides: a look at molecules in action at ambient conditions; a breakthrough technology in chemistry, physics and biology. Within the realms of the Royal Society of Chemistry, the Faraday Discussion on "Single Molecule Microscopy and Spectroscopy" was a very appropriate topic for presentation, deliberation and debate. Undoubtedly, the Faraday Discussions have a splendid reputation in stimulating scientific debates along the traditions set by Michael Faraday. Interestingly, back in the 1830's, Faraday himself pursued an experiment that led to the idea that atoms in a compound were joined by an electrical component. He placed two opposite electrodes in a solution of water containing a dissolved compound, and observed that one of the elements of the compound accumulated on one electrode, while the other was deposited on the opposite electrode. Although Faraday was deeply opposed to atomism, he had to recognize that electrical forces were responsible for the joining of atoms. Probably a direct view on the atoms or molecules in his experiment would have convinced him. As such, Michael Faraday might have liked the gathering at Burlington House in September 2015 (). Surely, with the questioning eyes of his bust on the 1st floor corridor, the non-believer Michael Faraday has incited each passer-by to enter into discussion and search for deeper answers at the level of single molecules. In these concluding remarks, highlights of the presented papers and discussions are summarized, complemented by a conclusion on future perspectives.

  3. Systematic studies of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher derivative methods: Applications to asymmetric and symmetric top and linear polyatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Clabo, D.A. Jr.

    1987-04-01

    Inclusion of the anharmonicity normal mode vibrations (i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface) is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules.

  4. Systematic studies of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher derivative methods: Applications to asymmetric and symmetric top and linear polyatomic molecules

    International Nuclear Information System (INIS)

    Clabo, D.A. Jr.

    1987-04-01

    Inclusion of the anharmonicity normal mode vibrations [i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface] is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules

  5. Neutral molecules in tokamak edge plasma - role of vibrationally excited hydrogen molecules

    International Nuclear Information System (INIS)

    Cadez, I.; Cercek, M.; Pelicon, P.; Razpet, A.

    2003-01-01

    The role of neutral molecules in edge plasma is discussed with special emphasis on the vibrationally excited hydrogen. Neutral molecules are formed mostly by surface processes on the walls and then released to the edge plasma where they take part in volumetric reactions with other particles. Typically these molecules are formed in excited states and data are needed for their reactions on the wall and in the volume. Processes in edge plasma determine particle and energy flux what is especially critical issue in tokamak divertor region. Various cross sections and reaction rates are needed for modelling edge plasma and its interaction with walls. (author)

  6. 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:

  7. Electrons in Molecules

    Indian Academy of Sciences (India)

    structure and properties (includingreactivt'ty) - both static (independent of time) and ... Furthermore, since the energy of H2 + in the ground state must be lower than that of .... (Figure 2b); note also that dp is positive in parts of the antibinding regions behind the two ... But, now both the sizes and shapes of molecules enter into.

  8. 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.

  9. OMG: Open molecule generator

    NARCIS (Netherlands)

    Peironcely, J.E.; Rojas-Chertó, M.; Fichera, D.; Reijmers, T.; Coulier, L.; Faulon, J.-L.; Hankemeier, T.

    2012-01-01

    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

  10. Molecule-based magnets

    Indian Academy of Sciences (India)

    Administrator

    Employing self-assembly methods, it is possible to engineer a bulk molecular material ... synthesis of molecular magnets in 1986, a large variety of them have been synthesized, which can be catego- ... maintained stably per organic molecule, stabilization of a ..... rotating freely under an applied field because it is a magne-.

  11. 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:

  12. 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.

  13. OMG: Open Molecule Generator

    Directory of Open Access Journals (Sweden)

    Peironcely Julio E

    2012-09-01

    Full Text Available Abstract 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.

  14. Capillary condensation of short-chain molecules.

    Science.gov (United States)

    Bryk, Paweł; Pizio, Orest; Sokolowski, Stefan

    2005-05-15

    A density-functional study of capillary condensation of fluids of short-chain molecules confined to slitlike pores is presented. The molecules are modeled as freely jointed tangent spherical segments with a hard core and with short-range attractive interaction between all the segments. We investigate how the critical parameters of capillary condensation of the fluid change when the pore width decreases and eventually becomes smaller than the nominal linear dimension of the single-chain molecule. We find that the dependence of critical parameters for a fluid of dimers and of tetramers on pore width is similar to that of the monomer fluid. On the other hand, for a fluid of chains consisting of a larger number of segments we observe an inversion effect. Namely, the critical temperature of capillary condensation decreases with increasing pore width for a certain interval of values of the pore width. This anomalous behavior is also influenced by the interaction between molecules and pore walls. We attribute this behavior to the effect of conformational changes of molecules upon confinement.

  15. Mechanism of action and efficacy of RX-111, a thieno[2,3-c]pyridine derivative and small molecule inhibitor of protein interaction with glycosaminoglycans (SMIGs), in delayed-type hypersensitivity, TNBS-induced colitis and experimental autoimmune encephalomyelitis

    Czech Academy of Sciences Publication Activity Database

    Harris, N.; Koppel, J.; Zsila, F.; Juhás, Štefan; Ilková, G.; Kogan, F. Y.; Lahmy, O.; Wildbaum, G.; Karin, N.; Zhuk, R.; Gregor, P.

    2016-01-01

    Roč. 65, č. 4 (2016), s. 285-294 ISSN 1023-3830 Institutional support: RVO:67985904 Keywords : small molecule drug * glycosaminoglycan * heparin binding protein * heparan sulfate * inflammation * autoimmune disease Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.659, year: 2016

  16. Free and binary rotation of polyatomic molecules

    International Nuclear Information System (INIS)

    Konyukhov, V K

    2003-01-01

    A modification of the quantum-mechanical theory of rotation of polyatomic molecules (binary rotation) is proposed, which is based on the algebra and representations of the SO(4) group and allows the introduction of the concept of parity, as in atomic spectroscopy. It is shown that, if an asymmetric top molecule performing binary rotation finds itself in a spatially inhomogeneous electric field, its rotational levels acquire the additional energy due to the quadrupole moment. The existence of the rotational states of polyatomic molecules that cannot transfer to the free rotation state is predicted. In particular, the spin isomers of a water molecule, which corresponds to such states, can have different absolute values of the adsorption energy due to the quadrupole interaction of the molecule with a surface. The difference in the adsorption energies allows one to explain qualitatively the behaviour of the ortho- and para-molecules of water upon their adsorption on the surface of solids in accordance with experimental data. (laser applications and other topics in quantum electronics)

  17. Cold guided beams of polar molecules

    International Nuclear Information System (INIS)

    Motsch, Michael

    2010-01-01

    This thesis reports on experiments characterizing cold guided beams of polar molecules which are produced by electrostatic velocity filtering. This filtering method exploits the interaction between the polar molecules and the electric field provided by an electrostatic quadrupole guide to extract efficiently the slow molecules from a thermal reservoir. For molecules with large and linear Stark shifts such as deuterated ammonia (ND 3 ) or formaldehyde (H 2 CO), fluxes of guided molecules of 10 10 -10 11 molecules/s are produced. The velocities of the molecules in these beams are in the range of 10-200 m/s and correspond to typical translational temperatures of a few Kelvin. The maximum velocity of the guided molecules depends on the Stark shift, the molecular mass, the geometry of the guide, and the applied electrode voltage. Although the source is operated in the near-effusive regime, the number density of the slowest molecules is sensitive to collisions. A theoretical model, taking into account this velocity-dependent collisional loss of molecules in the vicinity of the nozzle, reproduces the density of the guided molecules over a wide pressure range. A careful adjustment of pressure allows an increase in the total number of molecules, whilst yet minimizing losses due to collisions of the sought-for slow molecules. This is an important issue for future applications. Electrostatic velocity filtering is suited for different molecular species. This is demonstrated by producing cold guided beams of the water isotopologs H 2 O, D 2 O, and HDO. Although these are chemically similar, they show linear and quadratic Stark shifts, respectively, when exposed to external electric fields. As a result, the flux of HDO is larger by one order of magnitude, and the flux of the individual isotopologs shows a characteristic dependence on the guiding electric field. The internal-state distribution of guided molecules is studied with a newly developed diagnostic method: depletion

  18. 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.

  19. Simulations of the Static Friction Due to Adsorbed Molecules

    OpenAIRE

    He, Gang; Robbins, Mark O.

    2001-01-01

    The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent with macroscopic friction laws. Crystalline alignment, sliding direction, and the number of adsorbed molecules are not controlled in most experiments and are shown to have little effect on the friction. Temperature, molecular geometry and interaction potenti...

  20. Theoretical model for ultracold molecule formation via adaptive feedback control

    OpenAIRE

    Poschinger, Ulrich; Salzmann, Wenzel; Wester, Roland; Weidemueller, Matthias; Koch, Christiane P.; Kosloff, Ronnie

    2006-01-01

    We investigate pump-dump photoassociation of ultracold molecules with amplitude- and phase-modulated femtosecond laser pulses. For this purpose a perturbative model for the light-matter interaction is developed and combined with a genetic algorithm for adaptive feedback control of the laser pulse shapes. The model is applied to the formation of 85Rb2 molecules in a magneto-optical trap. We find for optimized pulse shapes an improvement for the formation of ground state molecules by more than ...

  1. Single molecule force spectroscopy: methods and applications in biology

    International Nuclear Information System (INIS)

    Shen Yi; Hu Jun

    2012-01-01

    Single molecule measurements have transformed our view of biomolecules. Owing to the ability of monitoring the activity of individual molecules, we now see them as uniquely structured, fluctuating molecules that stochastically transition between frequently many substrates, as two molecules do not follow precisely the same trajectory. Indeed, it is this discovery of critical yet short-lived substrates that were often missed in ensemble measurements that has perhaps contributed most to the better understanding of biomolecular functioning resulting from single molecule experiments. In this paper, we give a review on the three major techniques of single molecule force spectroscopy, and their applications especially in biology. The single molecular study of biotin-streptavidin interactions is introduced as a successful example. The problems and prospects of the single molecule force spectroscopy are discussed, too. (authors)

  2. Single-Molecule Interfacial Electron Transfer

    Energy Technology Data Exchange (ETDEWEB)

    Lu, H. Peter [Bowling Green State Univ., Bowling Green, OH (United States). Dept. of Chemistry and Center for Photochemical Sciences

    2017-11-28

    This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static and dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO2 and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO2 nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO2 nanoparticle surfaces by using ultrafast single-molecule

  3. Quantum Mechanical Study of Atoms and Molecules

    Science.gov (United States)

    Sahni, R. C.

    1961-01-01

    This paper, following a brief introduction, is divided into five parts. Part I outlines the theory of the molecular orbital method for the ground, ionized and excited states of molecules. Part II gives a brief summary of the interaction integrals and their tabulation. Part III outlines an automatic program designed for the computation of various states of molecules. Part IV gives examples of the study of ground, ionized and excited states of CO, BH and N2 where the program of automatic computation and molecular integrals have been utilized. Part V enlists some special problems of Molecular Quantum Mechanics are being tackled at New York University.

  4. Abrupt relaxation in high-spin molecules

    International Nuclear Information System (INIS)

    Chang, C.-R.; Cheng, T.C.

    2000-01-01

    Mean-field model suggests that the rate of resonant quantum tunneling in high-spin molecules is not only field-dependent but also time-dependent. The relaxation-assisted resonant tunneling in high-spin molecules produces an abrupt magnetization change during relaxation. When the applied field is very close to the resonant field, a time-dependent interaction field gradually shifts the energies of different collective spin states, and magnetization tunneling is observed as two energies of the spin states coincide

  5. 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.

  6. Superexcited states of molecules

    International Nuclear Information System (INIS)

    Nakamura, Hiroki; Takagi, Hidekazu.

    1990-01-01

    The report addresses the nature and major features of molecule's superexcited states, focusing on their involvement in dynamic processes. It also outlines the quantum defect theory which allows various processes involving these states to be treated in a unified way. The Rydberg state has close relation with an ionized state with a positive energy. The quantum defect theory interprets such relation. Specifically, the report first describes the quantum defect theory focusing on its basic principle. The multi-channel quantum defect theory is then outlined centering on how to describe a Rydberg-type superexcited state. Description of a dissociative double-electron excited state is also discussed. The quantum defect theory is based on the fact that the physics of the motion of a Rydberg electron vary with the region in the electron's coordinate space. Finally, various molecular processes that involve a superexcited state are addressed focusing on autoionization, photoionization, dissociative recombination and bonding ionization of diatomic molecules. (N.K.)

  7. 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.

  8. 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.

  9. Interstellar molecules and masers

    International Nuclear Information System (INIS)

    Nguyen-Q-Rieu; Guibert, J.

    1978-01-01

    The study of dense and dark clouds, in which hydrogen is mostly in molecular form, became possible since the discovery of interstellar molecules, emitting in the centimeter and millimeter wavelengths. The molecular lines are generally not in local thermal equilibrium (LTE). Their intensity can often be explained by invoking a population inversion mechanism. Maser emission lines due to OH, H 2 O and SiO molecules are among the most intense molecular lines. The H 2 CO molecule, detected in absorption in front of the cold cosmic background radiation of 2.7 K, illustrates the inverse phenomenon, the antimaser absorption. For a radio transition of frequency v, the inversion rate Δn (relative population difference between the upper and lower level) as well as the maser gain can be determined from the radio observations. In the case of the OH lines in the 2 PIsub(3/2), J=3/2 state, the inversion rates approximately 1 to 2% derived from the observations, are comparable with those obtained in the laboratory. The determination of the excitation mechanisms of the masers, through the statistical equilibrium and radiative transfer equations, implies the knowledge of collisional and radiative transition probabilities. A pumping model, which can satisfactorily explain the radio observations of some interstellar OH clouds, will be discussed [fr

  10. Excitonic Behavior of Rhodamine Dimers: A Single-Molecule Study

    NARCIS (Netherlands)

    Hernando Campos, J.; van der Schaaf, Martijn; van Dijk, E.M.H.P.; Sauer, Markus; Garcia Parajo, M.F.; van Hulst, N.F.

    2003-01-01

    The optical behavior of a dimer of tetramethylrhodamine-5-isothiocyanate has been investigated by means of single-molecule measurements. Bulk absorption and fluorescence spectra show the existence of two populations of the dimer molecule that exhibit distinct excitonic interactions (strong and weak

  11. Infrared, Raman and laser fluorescence studies on large molecules

    International Nuclear Information System (INIS)

    Venkateswaran, Sugandhi

    2000-01-01

    In the present thesis, infrared and Raman spectroscopic studies on large molecules, molecular assemblies and crystalline solids, as a function of temperature, pressure and added materials have been carried out. Spectral changes observed in our studies are interpreted in terms of intermolecular interaction, phase transition and conformational changes taking place in the molecules studied

  12. A density functional study on the adsorption of hydrogen molecule

    Indian Academy of Sciences (India)

    An all-electron scalar relativistic calculation on the adsorption of hydrogen molecule onto small copper clusters has been performed by using density functional theory with the generalized gradient approximation (GGA) at PW91 level. Our results reveal that after adsorption of H2 molecule, the Cu-Cu interaction is ...

  13. A radial distribution function-based open boundary force model for multi-centered molecules

    KAUST Repository

    Neumann, Philipp; Eckhardt, Wolfgang; Bungartz, Hans-Joachim

    2014-01-01

    We derive an expression for radial distribution function (RDF)-based open boundary forcing for molecules with multiple interaction sites. Due to the high-dimensionality of the molecule configuration space and missing rotational invariance, a

  14. Adsorption of small gas molecules on B36 nanocluster

    Indian Academy of Sciences (India)

    B36 cluster; Adsorption; Density functional theory; Gas molecules. 1. Introduction ... tural and chemical properties of boron clusters by com- putational methods and ..... systems in which the interaction is physical adsorption. (R>2 Å) are the ...

  15. Attosecond electron dynamics in molecules and liquids

    Science.gov (United States)

    WöRner, Hans Jakob

    The ultrafast motion of electrons and holes following light-matter interaction is fundamental to a broad range of chemical and biophysical processes. In this lecture, I will discuss some of our recent experiments that measure the atomic-scale motion of charge with attosecond temporal resolution (1 as = 10-18s). The first experiment is carried out on isolated, spatially oriented molecules in the gas phase. Using high-harmonic spectroscopy, we resolve the migration of an electron hole across the molecule with a resolution of 100 as and simultaneously demonstrate extensive control over charge migration. In the second class of experiments, we use an attosecond pulse train synchronized with a near-infrared laser pulse to temporally resolve the process of photoemission from molecules in the gas phase and from a liquid-water microjet, resolving electron transport through liquid water on the attosecond time scale.

  16. Collision data involving hydro-carbon molecules

    International Nuclear Information System (INIS)

    Tawara, H.; Itikawa, Y.; Nishimura, H.; Tanaka, H.; Nakamura, Y.

    1990-07-01

    Hydro-carbon molecules are abundantly produced when graphites are used as internal wall materials of hydrogen plasmas and strongly influence properties of low temperature plasmas near the edges as well as those of high temperature plasmas at the center. In this report, following simple description of the production mechanisms of hydro-carbon molecules under the interactions between graphite and hydrogen plasma, the present status of collision data for hydro-carbon molecules by electron impact is discussed and the relevant data are summarized in a series of figures and tables. It should also be noted that, in addition to fusion plasmas, these hydrocarbon data compiled here are quite useful in other applications such as plasma chemistry and material processing. (author)

  17. Spin fine structure of optically excited quantum dot molecules

    Science.gov (United States)

    Scheibner, M.; Doty, M. F.; Ponomarev, I. V.; Bracker, A. S.; Stinaff, E. A.; Korenev, V. L.; Reinecke, T. L.; Gammon, D.

    2007-06-01

    The interaction between spins in coupled quantum dots is revealed in distinct fine structure patterns in the measured optical spectra of InAs/GaAs double quantum dot molecules containing zero, one, or two excess holes. The fine structure is explained well in terms of a uniquely molecular interplay of spin-exchange interactions, Pauli exclusion, and orbital tunneling. This knowledge is critical for converting quantum dot molecule tunneling into a means of optically coupling not just orbitals but also spins.

  18. Quark chemistry: charmonium molecules

    International Nuclear Information System (INIS)

    De Rujula, A.; Jaffe, R.L.

    1977-01-01

    The theoretical and experimental evidence for two quark-two antiquark hadrons is reviewed. Concentration is placed on predictions for S-wave ''charmonium molecules,'' built of a c anti c charmonium pair and a light quark-antiquark pair. Their spectrum and quantum numbers are predicted and an estimate of their decay couplings and their prediction in monochromatic pion decays from charmonium resonances produced in e + e - -annihilation is given. Some S-wave charmonium resonances should be detectable in these decays, but typical branching ratios are only at the 1% level. 19 references

  19. Quantum design rules for single molecule logic gates.

    Science.gov (United States)

    Renaud, N; Hliwa, M; Joachim, C

    2011-08-28

    Recent publications have demonstrated how to implement a NOR logic gate with a single molecule using its interaction with two surface atoms as logical inputs [W. Soe et al., ACS Nano, 2011, 5, 1436]. We demonstrate here how this NOR logic gate belongs to the general family of quantum logic gates where the Boolean truth table results from a full control of the quantum trajectory of the electron transfer process through the molecule by very local and classical inputs practiced on the molecule. A new molecule OR gate is proposed for the logical inputs to be also single metal atoms, one per logical input.

  20. Full Alignment of Molecules Using Elliptically Polarized Light

    DEFF Research Database (Denmark)

    Larsen, Jakob Juul; Hald, Kasper; Seideman, Tamar

    When a molecule with an anisotropic polarizability is placed in a strong nonresonant laser field the interaction occurs through the induced dipole moment. The outcome is that the molecule experiences an angular dependent potential energy. It is now well established that a linearly polarized laser...... field can be used to align molecules along their axis of highest polarizability. Here we demonstrate, theoretically and experimentally, that an elliptically polarized laser field can be used to simultaneously force two axes of a molecule into alignment through the same mechanism. Due to the rigidity...

  1. Tuning the conductance of carbon nanotubes with encapsulated molecules

    International Nuclear Information System (INIS)

    Meunier, Vincent; Sumpter, Bobby G

    2007-01-01

    It was recently shown that a molecule encapsulated inside a carbon nanotube can be used to devise a novel type of non-volatile memory element. At the heart of the mechanism for storing and reading information is the new concept of a molecular gate where the molecule acts as a passive gate that hinders the flow of electrons for a given position relative to the nanotube host. By systematically exploring the effects of encapsulation of an acceptor molecule in a series of carbon nanotubes, we show that the reliability of the memory mechanism is very sensitive to the interaction between the nanotube host and the molecule guest

  2. 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

  3. 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.

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

    KAUST Repository

    Yoo, Hyejin; Furumaki, Shu; Yang, Jaesung; Lee, Ji-Eun; Chung, Heejae; Oba, Tatsuya; Kobayashi, Hiroyuki; Rybtchinski, Boris; Wilson, Thea M.; Wasielewski, Michael R.; Vacha, Martin; Kim, Dongho

    2012-01-01

    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.

  5. A multi-reference singles and doubles configuration interaction determination in the dissociation energy and vibrational levels of the BeF molecules in the X2Σ + state

    International Nuclear Information System (INIS)

    Machado, F.B.C.; Ornellas, F.R.

    1988-10-01

    An accurate potential energy curve for the BeF molecule in the X 2 Σ + state is calculated within the MRSDCI approach. Vibrational level spacings and the dissociation energy are reported. Agreement with the available experimental spacings is 15 cm -1 on the average. The theoretically computed D o , 5.92 eV, favors the experimental value of 5.85 eV over the higher value of 6.26 eV. Arguments are also presented that show why the value obtained by the Birge-Sponer linear extrapolation is accidentally a good one. (author) [pt

  6. 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...

  7. Friction mediated by redox-active supramolecular connector molecules.

    Science.gov (United States)

    Bozna, B L; Blass, J; Albrecht, M; Hausen, F; Wenz, G; Bennewitz, R

    2015-10-06

    We report on a friction study at the nanometer scale using atomic force microscopy under electrochemical control. Friction arises from the interaction between two surfaces functionalized with cyclodextrin molecules. The interaction is mediated by connector molecules with (ferrocenylmethyl)ammonium end groups forming supramolecular complexes with the cyclodextrin molecules. With ferrocene connector molecules in solution, the friction increases by a factor of up to 12 compared to control experiments without connector molecules. The electrochemical oxidation of ferrocene to ferrocenium causes a decrease in friction owing to the lower stability of ferrocenium-cyclodextrin complex. Upon switching between oxidative and reduction potentials, a change in friction by a factor of 1.2-1.8 is observed. Isothermal titration calorimetry reveals fast dissociation and rebinding kinetics and thus an equilibrium regime for the friction experiments.

  8. Small Talk: Children's Everyday `Molecule' Ideas

    Science.gov (United States)

    Jakab, Cheryl

    2013-08-01

    This paper reports on 6-11-year-old children's `sayings and doings' (Harré 2002) as they explore molecule artefacts in dialectical-interactive teaching interviews (Fleer, Cultural Studies of Science Education 3:781-786, 2008; Hedegaard et al. 2008). This sociocultural study was designed to explore children's everyday awareness of and meaning-making with cultural molecular artefacts. Our everyday world is populated with an ever increasing range of molecular or nanoworld words, symbols, images, and games. What do children today say about these artefacts that are used to represent molecular world entities? What are the material and social resources that can influence a child's everyday and developing scientific ideas about `molecules'? How do children interact with these cognitive tools when given expert assistance? What meaning-making is afforded when children are socially and materially assisted in using molecular tools in early chemical and nanoworld thinking? Tool-dependent discursive studies show that provision of cultural artefacts can assist and direct developmental thinking across many domains of science (Schoultz et al., Human Development 44:103-118, 2001; Siegal 2008). Young children's use of molecular artefacts as cognitive tools has not received much attention to date (Jakab 2009a, b). This study shows 6-11-year-old children expressing everyday ideas of molecular artefacts and raising their own questions about the artefacts. They are seen beginning to domesticate (Erneling 2010) the words, symbols, and images to their own purposes when given the opportunity to interact with such artefacts in supported activity. Discursive analysis supports the notion that using `molecules' as cultural tools can help young children to begin `putting on molecular spectacles' (Kind 2004). Playing with an interactive game (ICT) is shown to be particularly helpful in assisting children's early meaning-making with representations of molecules, atoms, and their chemical symbols.

  9. Single-Molecule Plasmon Sensing: Current Status and Future Prospects.

    Science.gov (United States)

    Taylor, Adam B; Zijlstra, Peter

    2017-08-25

    Single-molecule detection has long relied on fluorescent labeling with high quantum-yield fluorophores. Plasmon-enhanced detection circumvents the need for labeling by allowing direct optical detection of weakly emitting and completely nonfluorescent species. This review focuses on recent advances in single molecule detection using plasmonic metal nanostructures as a sensing platform, particularly using a single particle-single molecule approach. In the past decade two mechanisms for plasmon-enhanced single-molecule detection have been demonstrated: (1) by plasmonically enhancing the emission of weakly fluorescent biomolecules, or (2) by monitoring shifts of the plasmon resonance induced by single-molecule interactions. We begin with a motivation regarding the importance of single molecule detection, and advantages plasmonic detection offers. We describe both detection mechanisms and discuss challenges and potential solutions. We finalize by highlighting the exciting possibilities in analytical chemistry and medical diagnostics.

  10. Small molecule-guided thermoresponsive supramolecular assemblies

    KAUST Repository

    Rancatore, Benjamin J.; Mauldin, Clayton E.; Frechet, Jean; Xu, Ting

    2012-01-01

    Small organic molecules with strong intermolecular interactions have a wide range of desirable optical and electronic properties and rich phase behaviors. Incorporating them into block copolymer (BCP)-based supramolecules opens new routes to generate functional responsive materials. Using oligothiophene- containing supramolecules, we present systematic studies of critical thermodynamic parameters and kinetic pathway that govern the coassemblies of BCP and strongly interacting small molecules. A number of potentially useful morphologies for optoelectronic materials, including a nanoscopic network of oligothiophene and nanoscopic crystalline lamellae, were obtained by varying the assembly pathway. Hierarchical coassemblies of oligothiophene and BCP, rather than macrophase separation, can be obtained. Crystallization of the oligothiophene not only induces chain stretching of the BCP block the oligothiophene is hydrogen bonded to but also changes the conformation of the other BCP coil block. This leads to an over 70% change in the BCP periodicity (e.g., from 31 to 53 nm) as the oligothiophene changes from a melt to a crystalline state, which provides access to a large BCP periodicity using fairly low molecular weight BCP. The present studies have demonstrated the experimental feasibility of generating thermoresponsive materials that convert heat into mechanical energy. Incorporating strongly interacting small molecules into BCP supramolecules effectively increases the BCP periodicity and may also open new opportunities to tailor their optical properties without the need for high molecular weight BCP. © 2012 American Chemical Society.

  11. Small molecule-guided thermoresponsive supramolecular assemblies

    KAUST Repository

    Rancatore, Benjamin J.

    2012-10-23

    Small organic molecules with strong intermolecular interactions have a wide range of desirable optical and electronic properties and rich phase behaviors. Incorporating them into block copolymer (BCP)-based supramolecules opens new routes to generate functional responsive materials. Using oligothiophene- containing supramolecules, we present systematic studies of critical thermodynamic parameters and kinetic pathway that govern the coassemblies of BCP and strongly interacting small molecules. A number of potentially useful morphologies for optoelectronic materials, including a nanoscopic network of oligothiophene and nanoscopic crystalline lamellae, were obtained by varying the assembly pathway. Hierarchical coassemblies of oligothiophene and BCP, rather than macrophase separation, can be obtained. Crystallization of the oligothiophene not only induces chain stretching of the BCP block the oligothiophene is hydrogen bonded to but also changes the conformation of the other BCP coil block. This leads to an over 70% change in the BCP periodicity (e.g., from 31 to 53 nm) as the oligothiophene changes from a melt to a crystalline state, which provides access to a large BCP periodicity using fairly low molecular weight BCP. The present studies have demonstrated the experimental feasibility of generating thermoresponsive materials that convert heat into mechanical energy. Incorporating strongly interacting small molecules into BCP supramolecules effectively increases the BCP periodicity and may also open new opportunities to tailor their optical properties without the need for high molecular weight BCP. © 2012 American Chemical Society.

  12. 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.

  13. Lanthanide single molecule magnets

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jinkui; Zhang, Peng [Chinese Academy of Sciences, Changchun (China). Changchun Inst. of Applied Chemistry

    2015-10-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures - an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and explore new directions.

  14. Lanthanide single molecule magnets

    CERN Document Server

    Tang, Jinkui

    2015-01-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs, and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures – an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and...

  15. Molecules in the Spotlight

    Energy Technology Data Exchange (ETDEWEB)

    Cryan, James

    2010-01-26

    SLAC has just unveiled the world's first X-ray laser, the LCLS. This machine produces pulses of X-rays that are ten billion times brighter than those from conventional sources. One of the goals of this machine is to make movies of chemical reactions, including reactions necessary for life and reactions that might power new energy technologies. This public lecture will show the first results from the LCLS. As a first target, we have chosen nitrogen gas, the main component of the air we breathe. Using the unprecedented power of the LCLS X-rays as a blasting torch, we have created new forms of this molecule and with unique electronic arrangements. Please share with us the first insights from this new technology.

  16. Magnetic field modification of ultracold molecule-molecule collisions

    International Nuclear Information System (INIS)

    Tscherbul, T V; Suleimanov, Yu V; Aquilanti, V; Krems, R V

    2009-01-01

    We present an accurate quantum mechanical study of molecule-molecule collisions in the presence of a magnetic field. The work focuses on the analysis of elastic scattering and spin relaxation in collisions of O 2 ( 3 Σ g - ) molecules at cold (∼0.1 K) and ultracold (∼10 -6 K) temperatures. Our calculations show that magnetic spin relaxation in molecule-molecule collisions is extremely efficient except at magnetic fields below 1 mT. The rate constant for spin relaxation at T=0.1 K and a magnetic field of 0.1 T is found to be as large as 6.1x10 -11 cm -3 s -1 . The magnetic field dependence of elastic and inelastic scattering cross sections at ultracold temperatures is dominated by a manifold of Feshbach resonances with the density of ∼100 resonances per Tesla for collisions of molecules in the absolute ground state. This suggests that the scattering length of ultracold molecules in the absolute ground state can be effectively tuned in a very wide range of magnetic fields. Our calculations demonstrate that the number and properties of the magnetic Feshbach resonances are dramatically different for molecules in the absolute ground and excited spin states. The density of Feshbach resonances for molecule-molecule scattering in the low-field-seeking Zeeman state is reduced by a factor of 10.

  17. Molecules to Materials

    Indian Academy of Sciences (India)

    In Part 1 of this series of articles the historical background of the development of molecular materials was presented. The subtle interactions exploited in their design and the various methods of fabrication were reviewed. Part 2 provided an overview ofliquid crystals and molecular semiconductors, conductors and.

  18. Host–Pathogen Interactions

    NARCIS (Netherlands)

    Smits, M.A.; Schokker, D.J.

    2011-01-01

    The outcome of an infection is determined by numerous interactions between hosts and pathogens occurring at many different biological levels, ranging from molecule to population. To develop new control strategies for infectious diseases in livestock species, appropriate methodologies are needed

  19. Organic Molecules in Meteorites

    Science.gov (United States)

    Martins, Zita

    2015-08-01

    Carbonaceous meteorites are primitive samples from the asteroid belt, containing 3-5wt% organic carbon. The exogenous delivery of organic matter by carbonaceous meteorites may have contributed to the organic inventory of the early Earth. The majority (>70%) of the meteoritic organic material consist of insoluble organic matter (IOM) [1]. The remaining meteoritic organic material (meteorites contain soluble organic molecules with different abundances and distributions, which may reflect the extension of aqueous alteration or thermal metamorphism on the meteorite parent bodies. Extensive aqueous alteration on the meteorite parent body may result on 1) the decomposition of α-amino acids [5, 6]; 2) synthesis of β- and γ-amino acids [2, 6-9]; 3) higher relative abundances of alkylated polycyclic aromatic hydrocarbons (PAHs) [6, 10]; and 4) higher L-enantiomer excess (Lee) value of isovaline [6, 11, 12].The soluble organic content of carbonaceous meteorites may also have a contribution from Fischer-Tropsch/Haber-Bosch type gas-grain reactions after the meteorite parent body cooled to lower temperatures [13, 14].The analysis of the abundances and distribution of the organic molecules present in meteorites helps to determine the physical and chemical conditions of the early solar system, and the prebiotic organic compounds available on the early Earth.[1] Cody and Alexander (2005) GCA 69, 1085. [2] Cronin and Chang (1993) in: The Chemistry of Life’s Origin. pp. 209-258. [3] Martins and Sephton (2009) in: Amino acids, peptides and proteins in organic chemistry. pp. 1-42. [4] Martins (2011) Elements 7, 35. [5] Botta et al. (2007) MAPS 42, 81. [6] Martins et al. (2015) MAPS, in press. [7] Cooper and Cronin (1995) GCA 59, 1003. [8] Glavin et al. (2006) MAPS. 41, 889. [9] Glavin et al. (2011) MAPS 45, 1948. [10] Elsila et al. (2005) GCA 5, 1349. [11] Glavin and Dworkin (2009) PNAS 106, 5487. [12] Pizzarello et al. (2003) GCA 67, 1589. [13] Chan et al. (2012) MAPS. 47, 1502

  20. Dynamic Colloidal Molecules Maneuvered by Light-Controlled Janus Micromotors.

    Science.gov (United States)

    Gao, Yirong; Mou, Fangzhi; Feng, Yizheng; Che, Shengping; Li, Wei; Xu, Leilei; Guan, Jianguo

    2017-07-12

    In this work, we propose and demonstrate a dynamic colloidal molecule that is capable of moving autonomously and performing swift, reversible, and in-place assembly dissociation in a high accuracy by manipulating a TiO 2 /Pt Janus micromotor with light irradiation. Due to the efficient motion of the TiO 2 /Pt Janus motor and the light-switchable electrostatic interactions between the micromotor and colloidal particles, the colloidal particles can be captured and assembled one by one on the fly, subsequently forming into swimming colloidal molecules by mimicking space-filling models of simple molecules with central atoms. The as-demonstrated dynamic colloidal molecules have a configuration accurately controlled and stabilized by regulating the time-dependent intensity of UV light, which controls the stop-and-go motion of the colloidal molecules. The dynamic colloidal molecules are dissociated when the light irradiation is turned off due to the disappearance of light-switchable electrostatic interaction between the motor and the colloidal particles. The strategy for the assembly of dynamic colloidal molecules is applicable to various charged colloidal particles. The simulated optical properties of a dynamic colloidal molecule imply that the results here may provide a novel approach for in-place building functional microdevices, such as microlens arrays, in a swift and reversible manner.

  1. Role of glial cell line-derived neurotrophic factor (GDNF)-neural cell adhesion molecule (NCAM) interactions in induction of neurite outgrowth and identification of a binding site for NCAM in the heel region of GDNF

    DEFF Research Database (Denmark)

    Nielsen, Janne; Gotfryd, Kamil; Li, Shizhong

    2009-01-01

    NCAM-induced neurite outgrowth by being independent of NCAM polysialylation. Additionally, we investigated the structural basis for GDNF-NCAM interactions and find that NCAM Ig3 is necessary for GDNF binding. Furthermore, we identify within the heel region of GDNF a binding site for NCAM...

  2. Thermodynamic parameters for polyether adducts with neutral molecules

    International Nuclear Information System (INIS)

    Spencer, J.N.; Zafar, A.I.; Ganunis, T.F.

    1992-01-01

    Using calorimetry, thermodynamic parameters for the interaction of neutral molecules with polyether adducts are determined. When compared to its analogous acyclic ether, no macrocyclic effect is observed for 12-crown-4. The ether's collective oxygen atoms' action determines interaction with acetonitrile and malononitrile, with dimethyltin dichloride having a specific oxygen-binding site. 14 refs., 1 tab

  3. Tunnelling of a molecule

    International Nuclear Information System (INIS)

    Jarvis, P.D.; Bulte, D.P.

    1998-01-01

    A quantum-mechanical description of tunnelling is presented for a one-dimensional system with internal oscillator degrees of freedom. The 'charged diatomic molecule' is frustrated on encountering a barrier potential by its centre of charge not being coincident with its centre of mass, resulting in transitions amongst internal states. In an adiabatic limit, the tunnelling of semiclassical coherent-like oscillator states is shown to exhibit the Hartman and Bueuttiker-Landauer times t H and t BL , with the time dependence of the coherent state parameter for the tunnelled state given by α(t) = α e -iω(t+Δt) , Δt = t H - it BL . A perturbation formalism is developed, whereby the exact transfer matrix can be expanded to any desired accuracy in a suitable limit. An 'intrinsic' time, based on the oscillator transition rate during tunnelling, transmission or reflection, is introduced. In simple situations the resulting intrinsic tunnelling time is shown to vanish to lowest order. In the general case a particular (nonzero) parametrisation is inferred, and its properties discussed in comparison with the literature on tunnelling times for both wavepackets and internal clocks. Copyright (1998) CSIRO Australia

  4. Single molecule tracking

    Science.gov (United States)

    Shera, E. Brooks

    1988-01-01

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photones are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions.

  5. Investigation of polyelectrolyte desorption by single molecule force spectroscopy

    International Nuclear Information System (INIS)

    Friedsam, C; Seitz, M; Gaub, H E

    2004-01-01

    Single molecule force spectroscopy has evolved into a powerful method for the investigation of intra- and intermolecular interactions at the level of individual molecules. Many examples, including the investigation of the dynamic properties of complex biological systems as well as the properties of covalent bonds or intermolecular transitions within individual polymers, are reported in the literature. The technique has recently been extended to the systematic investigation of desorption processes of individual polyelectrolyte molecules adsorbed on generic surfaces. The stable covalent attachment of polyelectrolyte molecules to the AFM-tip provides the possibility of performing long-term measurements with the same set of molecules and therefore allows the in situ observation of the impact of environmental changes on the adsorption behaviour of individual molecules. Different types of interactions, e.g. electrostatic or hydrophobic interactions, that determine the adsorption process could be identified and characterized. The experiments provided valuable details that help to understand the nature and the properties of non-covalent interactions, which is helpful with regard to biological systems as well as for technical applications. Apart from this, desorption experiments can be utilized to characterize the properties of surfaces or polymer coatings. Therefore they represent a versatile tool that can be further developed in terms of various aspects

  6. Theoretical Investigations Regarding Single Molecules

    DEFF Research Database (Denmark)

    Pedersen, Kim Georg Lind

    Neoclassical Valence Bond Theory, Quantum Transport, Quantum Interference, Kondo Effect, and Electron Pumping. Trap a single organic molecule between two electrodes and apply a bias voltage across this "molecular junction". When electrons pass through the molecule, the different electron paths can...... interfere destructively or constructively. Destructive interference effects in electron transport could potentially improve thermo-electrics, organic logic circuits and energy harvesting. We have investigated destructive interference in off-resonant transport through organic molecules, and have found a set...

  7. Biofuels: from microbes to molecules

    National Research Council Canada - National Science Library

    Lu, Xuefeng

    2014-01-01

    .... The production of different biofuel molecules including hydrogen, methane, ethanol, butanol, higher chain alcohols, isoprenoids and fatty acid derivatives, from genetically engineered microbes...

  8. Labelled molecules, modern research implements

    International Nuclear Information System (INIS)

    Pichat, L.; Langourieux, Y.

    1974-01-01

    Details of the synthesis of carbon 14- and tritium-labelled molecules are examined. Although the methods used are those of classical organic chemistry the preparation of carbon 14-labelled molecules differs in some respects, most noticeably in the use of 14 CO 2 which requires very special handling techniques. For the tritium labelling of organic molecules the methods are somewhat different, very often involving exchange reactions. The following are described in turn: the so-called Wilzbach exchange method; exchange by catalysis in solution; catalytic hydrogenation with tritium; reductions with borotritides. Some applications of labelled molecules in organic chemistry, biochemistry and pharmacology are listed [fr

  9. 1,4-Bis(5-(naphthalen-1-yl)thiophen-2-yl)naphthalene, a small molecule, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular Lens epithelium-derived growth factor.

    Science.gov (United States)

    Gu, Wan-gang; Ip, Denis Tsz-Ming; Liu, Si-jie; Chan, Joseph H; Wang, Yan; Zhang, Xuan; Zheng, Yong-tang; Wan, David Chi-Cheong

    2014-04-25

    Translocation of viral integrase (IN) into the nucleus is a critical precondition of integration during the life cycle of HIV, a causative agent of Acquired Immunodeficiency Syndromes (AIDS). As the first discovered cellular factor to interact with IN, Lens epithelium-derived growth factor (LEDGF/p75) plays an important role in the process of integration. Disruption of the LEDGF/p75-IN interaction has provided a great interest for anti-HIV agent discovery. In this work, we reported that one small molecular compound, 1,4-bis(5-(naphthalen-1-yl)thiophen-2-yl)naphthalene(Compound 15), potently inhibit the IN-LEDGF/p75 interaction and affect the HIV-1 IN nuclear distribution at 1 μM. The putative binding mode of Compound 15 was constructed by a molecular docking simulation to provide structural insights into the ligand-binding mechanism. Compound 15 suppressed viral replication by measuring p24 antigen production in HIV-1IIIB acute infected C8166 cells with EC50 value of 11.19 μM. Compound 15 might supply useful structural information for further anti-HIV agent discovery. Copyright © 2014. Published by Elsevier Ireland Ltd.

  10. Growing interstellar molecules with ion-molecule reactions

    International Nuclear Information System (INIS)

    Bohme, D.K.

    1989-01-01

    Laboratory measurements of gas-phase ion-molecule reactions continue to provide important insights into the chemistry of molecular growth in interstellar environments. It is also true that the measurements are becoming more demanding as larger molecules capture our interest. While some of these measurements are motivated by current developments in chemical models of interstellar environments or by new molecular observations by astronomers, others explore novel chemistry which can lead to predictions of new interstellar molecules. Here the author views the results of some recent measurements, taken in the Ion Chemistry Laboratory at York University with the SIFT technique, which address some of the current needs of modellers and observers and which also provide some new fundamental insight into molecular growth, particularly when it occurs in the presence of large molecules such as PAH molecules which are now thought to have a major influence on the chemistry of interstellar environments in which they are present

  11. Organization of central synapses by adhesion molecules.

    Science.gov (United States)

    Tallafuss, Alexandra; Constable, John R L; Washbourne, Philip

    2010-07-01

    Synapses are the primary means for transmitting information from one neuron to the next. They are formed during the development of the nervous system, and the formation of appropriate synapses is crucial for the establishment of neuronal circuits that underlie behavior and cognition. Understanding how synapses form and are maintained will allow us to address developmental disorders such as autism, mental retardation and possibly also psychological disorders. A number of biochemical and proteomic studies have revealed a diverse and vast assortment of molecules that are present at the synapse. It is now important to untangle this large array of proteins and determine how it assembles into a functioning unit. Here we focus on recent reports describing how synaptic cell adhesion molecules interact with and organize the presynaptic and postsynaptic specializations of both excitatory and inhibitory central synapses. © The Authors (2010). Journal Compilation © Federation of European Neuroscience Societies and Blackwell Publishing Ltd.

  12. Energy redistribution in diatomic molecules on surfaces

    International Nuclear Information System (INIS)

    Asscher, M.; Somorjai, G.A.

    1984-04-01

    Translational and internal degrees of freedom of a scattered beam of NO molecules from a Pt(111) single crystal surface were measured as a function of scattering angle and crystal temperature in the range 450 to 1250K. None of the three degrees of freedom were found to fully accommodate to the crystal temperature, the translational degree being the most accommodated and the rotational degree of freedom the least. A precursor state model is suggested to account for the incomplete accommodation of translational and vibrational degrees of freedom as a function of crystal temperature and incident beam energy. The vibrational accommodation is further discussed in terms of a competition between desorption and vibrational excitation processes, thus providing valuable information on the interaction between vibrationally excited molecules and surfaces. Energy transfer into rotational degrees of freedom is qualitatively discussed

  13. Theory of Charged Quantum Dot Molecules

    Science.gov (United States)

    Ponomarev, I. V.; Scheibner, M.; Stinaff, E. A.; Bracker, A. S.; Doty, M. F.; Ware, M. E.; Gammon, D.; Reinecke, T. L.; Korenev, V. L.

    2006-03-01

    Recent optical spectroscopy of excitonic molecules in coupled quantum dots (CQDs) tuned by electric field reveal a richer diversity in spectral line patterns than in their single quantum dot counterparts. We developed a theoretical model that allows us to classify energies and intensities of various PL transitions. In this approach the electric field induced resonance tunneling of the electron and hole states occurs at different biases due to the inherent asymmetry of CQDs. The truncated many-body basis configurations for each molecule are constructed from antisymmetrized products of single-particle states, where the electron occupies only one ground state level in single QD and the hole can occupy two lowest levels of CQD system. The Coulomb interaction between particles is treated with perturbation theory. As a result the observed PL spectral lines can be described with a small number of parameters. The theoretical predictions account well for recent experiments.

  14. Photochemical dynamics of surface oriented molecules

    International Nuclear Information System (INIS)

    Ho, W.

    1992-01-01

    The period 8/01/91-7/31/92 is the first year of a new project titled ''Photochemical Dynamics of Surface Oriented Molecules'', initiated with DOE Support. The main objective of this project is to understand the dynamics of elementary chemical reactions by studying photochemical dynamics of surface-oriented molecules. In addition, the mechanisms of photon-surface interactions need to be elucidated. The strategy is to carry out experiments to measure the translational energy distribution, as a function of the angle from the surface normal, of the photoproducts by time-of-flight (TOF) technique by varying the photon wavelength, intensity, polarization, and pulse duration. By choosing adsorbates with different bonding configuration, the effects of adsorbate orientation on surface photochemical dynamics can be studied

  15. Automated imaging system for single molecules

    Science.gov (United States)

    Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel

    2012-09-18

    There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

  16. 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.

  17. Computer systems for annotation of single molecule fragments

    Science.gov (United States)

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  18. Interaction of the carbon monoxide-releasing molecule Ru(CO)3Cl(glycinate) (CORM-3) with Salmonella enterica serovar Typhimurium: in situ measurements of carbon monoxide binding by integrating cavity dual-beam spectrophotometry.

    Science.gov (United States)

    Rana, Namrata; McLean, Samantha; Mann, Brian E; Poole, Robert K

    2014-12-01

    Carbon monoxide (CO) is a toxic gas that binds to haems, but also plays critical signalling and cytoprotective roles in mammalian systems; despite problems associated with systemic delivery by inhalation of the gas, it may be employed therapeutically. CO delivered to cells and tissues by CO-releasing molecules (CO-RMs) has beneficial and toxic effects not mimicked by CO gas; CO-RMs are also attractive candidates as novel antimicrobial agents. Salmonella enterica serovar Typhimurium is an enteropathogen causing gastroenteritis in humans. Recent studies have implicated haem oxygenase-1 (HO-1), the protein that catalyses the degradation of haem into biliverdin, free iron and CO, in the host immune response to Salmonella infection. In several studies, CO administration via CO-RMs elicited many of the protective roles of HO-1 induction and so we investigated the effects of a well-characterized water-soluble CO-RM, Ru(CO)3Cl(glycinate) (CORM-3), on Salmonella. CORM-3 exhibits toxic effects at concentrations significantly lower than those reported to cause toxicity to RAW 264.7 macrophages. We demonstrated here, through oxyhaemoglobin assays, that CORM-3 did not release CO spontaneously in phosphate buffer, buffered minimal medium or very rich medium. CORM-3 was, however, accumulated to high levels intracellularly (as shown by inductively coupled plasma MS) and released CO inside cells. Using growing Salmonella cultures without prior concentration, we showed for the first time that sensitive dual-beam integrating cavity absorption spectrophotometry can detect directly the CO released from CORM-3 binding in real-time to haems of the bacterial electron transport chain. The toxic effects of CO-RMs suggested potential applications as adjuvants to antibiotics in antimicrobial therapy. © 2014 The Authors.

  19. ZL006, a small molecule inhibitor of PSD-95/nNOS interaction, does not induce antidepressant-like effects in two genetically predisposed rat models of depression and control animals.

    Directory of Open Access Journals (Sweden)

    Sandra Tillmann

    Full Text Available N-methyl-D-aspartate receptor (NMDA-R antagonists and nitric oxide inhibitors have shown promising efficacy in depression but commonly induce adverse events. To circumvent these, a more indirect disruption of the nitric oxide synthase/postsynaptic density protein 95 kDa complex at the NMDA-R has been proposed. This disruption can be achieved using small molecule inhibitors such as ZL006, which has attracted attention as ischemic stroke therapy in rodents and has been proposed as a potential novel treatment for depression. Based on this, our aim was to translate these findings to animal models of depression to elucidate antidepressant-like properties in more detail. In the present study, we administered ZL006 to two established animal models of depression and control rodents. Following treatment, we measured locomotion in the Open Field and depressive-like behavior in the Forced Swim Test and Tail Suspension Test. Our experimental designs included the use of different species (rats, mice, strains (Flinders Sensitive Line rats, Flinders Resistant Line rats, Wistar Kyoto rats, Wistar Hanover rats, Sprague Dawley rats, B6NTac mice, routes of administration (intraperitoneal, intracerebroventricular, times of administration (single injection, repeated injections, treatment regimens (acute, sustained, and doses (5, 10, 15, 50 mg/kg. ZL006 did not affect behavior in any of the described settings. On a molecular level, ZL006 significantly reduced total nitrate/nitrite concentrations in the cerebellum, supporting that it is capable of reducing nitric oxide metabolites in the brain. Future studies using different experimental parameters are needed to further investigate the behavioral profile of ZL006.

  20. Mechanism of action and efficacy of RX-111, a thieno[2,3-c]pyridine derivative and small molecule inhibitor of protein interaction with glycosaminoglycans (SMIGs), in delayed-type hypersensitivity, TNBS-induced colitis and experimental autoimmune encephalomyelitis.

    Science.gov (United States)

    Harris, Nicholas; Koppel, Juraj; Zsila, Ferenc; Juhas, Stefan; Il'kova, Gabriela; Kogan, Faina Yurgenzon; Lahmy, Orly; Wildbaum, Gizi; Karin, Nathan; Zhuk, Regina; Gregor, Paul

    2016-04-01

    Elucidate the mechanism of action of the small molecule inhibitor of protein binding to glycosaminoglycans, RX-111 and assay its anti-inflammatory activity in animal models of inflammatory disease. The glycosaminoglycan, heparin, was used in the mechanism of action study of RX-111. Human T lymphocytes and umbilical vein endothelial cells were used to assay the in vitro activity of RX-111. Mouse and rat models of disease were used to assay the anti-inflammatory activity of RX-111 in vivo. Circular dichroism and UV/Vis absorption spectroscopy were used to study the binding of RX-111 to the glycosaminoglycan, heparin. T lymphocyte rolling on endothelial cells under shear flow was used to assay RX-111 activity in vitro. Delayed-type hypersensitivity (DTH) and tri-nitrobenzene sulfonic acid (TNBS)-induced colitis in mice and experimental autoimmune encephalomyelitis (EAE) in rats were used to assay anti-inflammatory activity of RX-111 in vivo. RX-111 was shown to bind directly to heparin. It inhibited leukocyte rolling on endothelial cells under shear flow and reduced inflammation in the mouse model of DTH. RX-111 was efficacious in the mouse model of inflammatory bowel disease, TNBS-induced colitis and the rat model of multiple sclerosis, EAE. RX-111 exercises its broad spectrum anti-inflammatory activity by a singular mechanism of action, inhibition of protein binding to the cell surface GAG, heparan sulfate. RX-111 and related thieno[2,3-c]pyridine derivatives are potential therapeutics for the treatment of inflammatory and autoimmune diseases.

  1. Spectral simulations of polar diatomic molecules immersed in He clusters: application to the ICl (X) molecule

    International Nuclear Information System (INIS)

    Villarreal, P; Lara-Castells, M P de; Prosmiti, R; Delgado-Barrio, G; Lopez-Duran, D; Gianturco, F A; Jellinek, J

    2007-01-01

    A recently developed quantum-chemistry-like methodology to study molecules solvated in atomic clusters is applied to the ICl (iodine chloride) polar diatomic molecule immersed in clusters of He atoms. The atoms of the solvent clusters are treated as the 'electrons' and the solvated molecule as a structured 'nucleus' of the combined solvent-solute system. The helium-helium and helium-dopant interactions are represented by parametrized two-body and ab initio three-body potentials, respectively. The ground-state wavefunctions are used to compute the infrared (IR) spectra of the solvated molecule. In agreement with the experimental observations, the computed spectra exhibit considerable differences depending on whether the solvent cluster is comprised of bosonic ( 4 He) or fermionic ( 3 He) atoms. The source of these differences is attributed to the different spin-statistics of the solvent clusters. The bosonic versus fermionic nature of the solvent is reflected in the IR absorption selection rules. Only P and R branches with single state transitions appear in the spectrum when the molecule is solvated in a bosonic cluster. On the other hand, when the solvent represents a fermionic environment, quasi-degenerate multiplets of spin states contribute to each branch and, in addition, the Q-branch becomes also allowed. Combined, these two factors explain the more congested nature of the spectrum in the fermionic case

  2. Molecular studies on di-sodium tartrate molecule

    Science.gov (United States)

    Divya, P.; Jayakumar, S.; George, Preethamary; Shubashree, N. S.; Ahmed. M, Anees

    2015-06-01

    Structural characterization is important for the development of new material. The acoustical parameters such as Free Length, Internal Pressure have been measured from ultrasonic velocity, density for di sodium tartrate an optically active molecule at different temperatures using ultrasonic interferometer of frequency (2MHZ). The ultrasonic velocity increases with increase in concentration there is an increase in solute-solvent interaction. The stability constant had been calculated. SEM with EDAX studies has been done for Di-sodium tartrate an optically active molecule.

  3. Chemoreactomic analysis of thiamine disulfide, thiamine hydrochloride, and benfotiamine molecules

    OpenAIRE

    O. A. Gromova; I. Yu. Torshin; L. V. Stakhovskaya; L. E. Fedotova

    2017-01-01

    Objective: to analyze the interactions that could indicate the potential pharmacological properties of the molecules of thiamin, thiamine disulfide, and others.Material and methods. The investigators simulated the properties of thiamine disulfide (bistiamin) versus those of the reference molecules of thiamin hydrochloride and benfotiamine. The study was performed using chemoreactomic simulation that is the newest area in post-genome pharmacology.Results and discussion. Chemoreactomic analysis...

  4. Elastic scattering of low energy electrons by hydrogen molecule

    International Nuclear Information System (INIS)

    Freitas, L.C.G.; Mu-Tao, L.; Botelho, L.F.

    1987-01-01

    The coherent version of the Renormalized Multiple-Centre Potential Model (RMPM) has been extended to treat the elastic scattering of low energy electrons by H2 molecule. The intramolecular Multiple Scattering (MS) effect has also been included. The comparison against the experimental data shows that the inclusion of the MS improves significantly with experiment. The extension of the present method to study electron-polyatomic molecule interaction is also discussed. (author) [pt

  5. Single molecules and single nanoparticles as windows to the nanoscale

    Science.gov (United States)

    Caldarola, Martín; Orrit, Michel

    2018-05-01

    Since the first optical detection of single molecules, they have been used as nanometersized optical sensors to explore the physical properties of materials and light-matter interaction at the nanoscale. Understanding nanoscale properties of materials is fundamental for the development of new technology that requires precise control of atoms and molecules when the quantum nature of matter cannot be ignored. In the following lines, we illustrate this journey into nanoscience with some experiments from our group.

  6. 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...

  7. Enzyme Molecules in Solitary Confinement

    Directory of Open Access Journals (Sweden)

    Raphaela B. Liebherr

    2014-09-01

    Full Text Available Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

  8. Organizing and addressing magnetic molecules.

    Science.gov (United States)

    Gatteschi, Dante; Cornia, Andrea; Mannini, Matteo; Sessoli, Roberta

    2009-04-20

    Magnetic molecules ranging from simple organic radicals to single-molecule magnets (SMMs) are intensively investigated for their potential applications in molecule-based information storage and processing. The goal of this Article is to review recent achievements in the organization of magnetic molecules on surfaces and in their individual probing and manipulation. We stress that the inherent fragility and redox sensitivity of most SMM complexes, combined with the noninnocent role played by the substrate, ask for a careful evaluation of the structural and electronic properties of deposited molecules going beyond routine methods for surface analysis. Detailed magnetic information can be directly obtained using X-ray magnetic circular dichroism or newly emerging scanning probe techniques with magnetic detection capabilities.

  9. Ion-Molecule Reaction Dynamics.

    Science.gov (United States)

    Meyer, Jennifer; Wester, Roland

    2017-05-05

    We review the recent advances in the investigation of the dynamics of ion-molecule reactions. During the past decade, the combination of single-collision experiments in crossed ion and neutral beams with the velocity map ion imaging detection technique has enabled a wealth of studies on ion-molecule reactions. These methods, in combination with chemical dynamics simulations, have uncovered new and unexpected reaction mechanisms, such as the roundabout mechanism and the subtle influence of the leaving group in anion-molecule nucleophilic substitution reactions. For this important class of reactions, as well as for many fundamental cation-molecule reactions, the information obtained with crossed-beam imaging is discussed. The first steps toward understanding micro-solvation of ion-molecule reaction dynamics are presented. We conclude with the presentation of several interesting directions for future research.

  10. Finding optimal interaction interface alignments between biological complexes

    KAUST Repository

    Cui, Xuefeng; Naveed, Hammad; Gao, Xin

    2015-01-01

    Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which

  11. Real-Time, Label-Free Detection of Biomolecular Interactions in Sandwich Assays by the Oblique-Incidence Reflectivity Difference Technique

    Directory of Open Access Journals (Sweden)

    Yung-Shin Sun

    2014-12-01

    Full Text Available One of the most important goals in proteomics is to detect the real-time kinetics of diverse biomolecular interactions. Fluorescence, which requires extrinsic tags, is a commonly and widely used method because of its high convenience and sensitivity. However, in order to maintain the conformational and functional integrality of biomolecules, label-free detection methods are highly under demand. We have developed the oblique-incidence reflectivity difference (OI-RD technique for label-free, kinetic measurements of protein-biomolecule interactions. Incorporating the total internal refection geometry into the OI-RD technique, we are able to detect as low as 0.1% of a protein monolayer, and this sensitivity is comparable with other label-free techniques such as surface plasmon resonance (SPR. The unique advantage of OI-RD over SPR is no need for dielectric layers. Moreover, using a photodiode array as the detector enables multi-channel detection and also eliminates the over-time signal drift. In this paper, we demonstrate the applicability and feasibility of the OI-RD technique by measuring the kinetics of protein-protein and protein-small molecule interactions in sandwich assays.

  12. Manipulating ultracold polar molecules with microwave radiation: The influence of hyperfine structure

    International Nuclear Information System (INIS)

    Aldegunde, J.; Hutson, Jeremy M.; Ran Hong

    2009-01-01

    We calculate the microwave spectra of ultracold 40 K 87 Rb alkali-metal dimers, including hyperfine interactions and in the presence of electric and magnetic fields. We show that microwave transitions may be used to transfer molecules between different hyperfine states, but only because of the presence of nuclear quadrupole interactions. Hyperfine splittings may also complicate the use of ultracold molecules for quantum computing. The spectrum of molecules oriented in electric fields may be simplified dramatically by applying a simultaneous magnetic field.

  13. Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA.

    Science.gov (United States)

    Velagapudi, Sai Pradeep; Luo, Yiling; Tran, Tuan; Haniff, Hafeez S; Nakai, Yoshio; Fallahi, Mohammad; Martinez, Gustavo J; Childs-Disney, Jessica L; Disney, Matthew D

    2017-03-22

    RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.

  14. 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.

  15. Investigating single molecule adhesion by atomic force spectroscopy.

    Science.gov (United States)

    Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

    2015-02-27

    Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

  16. Single Molecule Electronics and Devices

    Science.gov (United States)

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

    The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

  17. Quantum theory of anharmonic effects in molecules

    CERN Document Server

    Kazakov, Konstantin V

    2012-01-01

    Presented in a clear and straightforward analysis, this book explores quantum mechanics and the application of quantum mechanics to interpret spectral phenomena. Specifically, the book discusses the relation between spectral features in mid or rear infrared regions, or in Raman scattering spectrum, and interactions between molecules or molecular species such as molecular ions, and their respective motions in gaseous or crystalline conditions. Beginning with an overview of conventional methods and problems which arise in molecular spectroscopy, the second half of the book suggests original t

  18. Thermally induced charge current through long molecules

    Science.gov (United States)

    Zimbovskaya, Natalya A.; Nitzan, Abraham

    2018-01-01

    In this work, we theoretically study steady state thermoelectric transport through a single-molecule junction with a long chain-like bridge. Electron transmission through the system is computed using a tight-binding model for the bridge. We analyze dependences of thermocurrent on the bridge length in unbiased and biased systems operating within and beyond the linear response regime. It is shown that the length-dependent thermocurrent is controlled by the lineshape of electron transmission in the interval corresponding to the HOMO/LUMO transport channel. Also, it is demonstrated that electron interactions with molecular vibrations may significantly affect the length-dependent thermocurrent.

  19. Aging-From molecules to populations

    DEFF Research Database (Denmark)

    Sander, Miriam; Avlund, Kirsten; Lauritzen, Martin

    2008-01-01

    of human aging. To foster interactions and collaboration between diverse scientists interested in the biochemical, physiological, epidemiological and psychosocial aspects of aging, The University of Copenhagen Faculty of Health Sciences recently organized and co-sponsored a workshop entitled Aging......-From Molecules to Populations. The following questions about human aging were discussed at the workshop: What is the limit of human life expectancy? What are the key indicators of human aging? What are the key drivers of human aging? Which genes have the greatest impact on human aging? How similar is aging...

  20. The (e,2e) reaction in molecules

    International Nuclear Information System (INIS)

    Dey, S.; Dixon, A.; Teubner, P.J.O.; Weigold, E.

    1975-01-01

    The aplication of the (e,2e) technique is discussed in the framework of (e,2e) on molecular hydrogen. It is shown that the technique is sufficiently sensitive to distinguish between simple wavefunctions and those containing configuration interactions. By comparing the data on H 2 and D 2 is shown that the Born-Oppenheimer approximation is confirmed to an accuracy of about 3 per cent. The data is also used to contrast other methods of determining electron momentum distributions in molecules. Data on methane, carbon monoxide and molecular nitrogen is also presented. (author)

  1. Small Molecule TH-39 Potentially Targets Hec1/Nek2 Interaction and Exhibits Antitumor Efficacy in K562 Cells via G0/G1 Cell Cycle Arrest and Apoptosis Induction.

    Science.gov (United States)

    Zhu, Yongxia; Wei, Wei; Ye, Tinghong; Liu, Zhihao; Liu, Li; Luo, Yong; Zhang, Lidan; Gao, Chao; Wang, Ningyu; Yu, Luoting

    2016-01-01

    Cancer is still a major public health issue worldwide, and new therapeutics with anti-tumor activity are still urgently needed. The anti-tumor activity of TH-39, which shows potent anti-proliferative activity against K562 cells with an IC50 of 0.78 µM, was investigated using immunoblot, co-immunoprecipitation, the MTT assay, and flow cytometry. Mechanistically, TH-39 may disrupt the interaction between Hec1 and Nek2 in K562 cells. Moreover, TH-39 inhibited cell proliferation in a concentration- and time-dependent manner by influencing the morphology of K562 cells and inducing G0/G1 phase arrest. G0/G1 phase arrest was associated with down-regulation of CDK2-cyclin E complex and CDK4/6-cyclin D complex activities. Furthermore, TH-39 also induced cell apoptosis, which was associated with activation of caspase-3, down-regulation of Bcl-2 expression and up-regulation of Bax. TH-39 could also decrease mitochondrial membrane potential (Δψm) and increase reactive oxygen species (ROS) accumulation in K562 cells. The results indicated that TH-39 might induce apoptosis via the ROS-mitochondrial apoptotic pathway. This study highlights the potential therapeutic efficacy of the anti-cancer compound TH-39 in treatment-resistant chronic myeloid leukemia. © 2016 The Author(s) Published by S. Karger AG, Basel.

  2. Conducting single-molecule magnet materials.

    Science.gov (United States)

    Cosquer, Goulven; Shen, Yongbing; Almeida, Manuel; Yamashita, Masahiro

    2018-05-11

    Multifunctional molecular materials exhibiting electrical conductivity and single-molecule magnet (SMM) behaviour are particularly attractive for electronic devices and related applications owing to the interaction between electronic conduction and magnetization of unimolecular units. The preparation of such materials remains a challenge that has been pursued by a bi-component approach of combination of SMM cationic (or anionic) units with conducting networks made of partially oxidized (or reduced) donor (or acceptor) molecules. The present status of the research concerning the preparation of molecular materials exhibiting SMM behaviour and electrical conductivity is reviewed, describing the few molecular compounds where both SMM properties and electrical conductivity have been observed. The evolution of this research field through the years is discussed. The first reported compounds are semiconductors in spite being able to present relatively high electrical conductivity, and the SMM behaviour is observed at low temperatures where the electrical conductivity of the materials is similar to that of an insulator. During the recent years, a breakthrough has been achieved with the coexistence of high electrical conductivity and SMM behaviour in a molecular compound at the same temperature range, but so far without evidence of a synergy between these properties. The combination of high electrical conductivity with SMM behaviour requires not only SMM units but also the regular and as far as possible uniform packing of partially oxidized molecules, which are able to provide a conducting network.

  3. Photoexcitation circular dichroism in chiral molecules

    Science.gov (United States)

    Beaulieu, S.; Comby, A.; Descamps, D.; Fabre, B.; Garcia, G. A.; Géneaux, R.; Harvey, A. G.; Légaré, F.; Mašín, Z.; Nahon, L.; Ordonez, A. F.; Petit, S.; Pons, B.; Mairesse, Y.; Smirnova, O.; Blanchet, V.

    2018-05-01

    Chiral effects appear in a wide variety of natural phenomena and are of fundamental importance in science, from particle physics to metamaterials. The standard technique of chiral discrimination—photoabsorption circular dichroism—relies on the magnetic properties of a chiral medium and yields an extremely weak chiral response. Here, we propose and demonstrate an orders of magnitude more sensitive type of circular dichroism in neutral molecules: photoexcitation circular dichroism. This technique does not rely on weak magnetic effects, but takes advantage of the coherent helical motion of bound electrons excited by ultrashort circularly polarized light. It results in an ultrafast chiral response and the efficient excitation of a macroscopic chiral density in an initially isotropic ensemble of randomly oriented chiral molecules. We probe this excitation using linearly polarized laser pulses, without the aid of further chiral interactions. Our time-resolved study of vibronic chiral dynamics opens a way to the efficient initiation, control and monitoring of chiral chemical change in neutral molecules at the level of electrons.

  4. Spin tunneling in magnetic molecules

    Science.gov (United States)

    Kececioglu, Ersin

    In this thesis, we will focus on spin tunneling in a family of systems called magnetic molecules such as Fe8 and Mn12. This is comparatively new, in relation to other tunneling problems. Many issues are not completely solved and/or understood yet. The magnetic molecule Fe 8 has been observed to have a rich pattern of degeneracies in its magnetic spectrum. We focus on these degeneracies from several points of view. We start with the simplest anisotropy Hamiltonian to describe the Fe 8 molecule and extend our discussion to include higher order anisotropy terms. We give analytical expressions as much as we can, for the degeneracies in the semi-classical limit in both cases. We reintroduce jump instantons to the instanton formalism. Finally, we discuss the effect of the environment on the molecule. Our results, for all different models and techniques, agree well with both experimental and numerical results.

  5. Experimental decoherence in molecule interferometry

    International Nuclear Information System (INIS)

    Hackermueller, L.; Hornberger, K.; Stibor, A.; Zeilinger, A.; Arndt, M.; Kiesewetter, G.

    2005-01-01

    Full text: We present three mechanisms of decoherence that occur quite naturally in matter wave interferometer with large molecules. One way molecules can lose coherence is through collision with background gas particles. We observe a loss of contrast with increasing background pressure for various types of gases. We can understand this phenomenon quantitatively with a new model for collisional decoherence which corrects older models by a factor of 2 π;. The second experiment studies the thermal emission of photons related to the high internal energy of the interfering molecules. When sufficiently many or sufficiently short photons are emitted inside the interferometer, the fringe contrast is lost. We can continuously vary the temperature of the molecules and compare the loss of contrast with a model based on decoherence theory. Again we find good quantitative agreement. A third mechanism that influences our interference pattern is dephasing due to vibrations of the interference gratings. By adding additional vibrations we study this effect in more detail. (author)

  6. Photoionization of atoms and molecules

    International Nuclear Information System (INIS)

    Samson, J.A.R.

    1976-01-01

    A literature review on the present state of knowledge in photoionization is presented. Various experimental techniques that have been developed to study photoionization, such as fluorescence and photoelectron spectroscopy, mass spectroscopy, are examined. Various atoms and molecules were chosen to illustrate these techniques, specifically helium and xenon atoms and hydrogen molecules. Specialized photoionization such as in positive and negative ions, excited states, and free radicals is also treated. Absorption cross sections and ionization potentials are also discussed

  7. Low pressure tritiation of molecules

    International Nuclear Information System (INIS)

    Moran, T.F.; Powers, J.C.; Lively, M.O.

    1980-01-01

    A method is described of tritiating sensitive biological molecules by depositing molecules of the substance to be tritiated on a supporting substrate in an evacuated vacuum chamber near, but not in the path of, an electron beam which traverses the chamber, admitting tritium gas into the chamber, and subjecting the tritium to the electron beam. Vibrationally excited tritium gas species are generated which collide and react with the substance thus incorporating tritium atoms into the substance. (U.K.)

  8. Synthesis of single-molecule nanocars.

    Science.gov (United States)

    Vives, Guillaume; Tour, James M

    2009-03-17

    The drive to miniaturize devices has led to a variety of molecular machines inspired by macroscopic counterparts such as molecular motors, switches, shuttles, turnstiles, barrows, elevators, and nanovehicles. Such nanomachines are designed for controlled mechanical motion and the transport of nanocargo. As researchers miniaturize devices, they can consider two complementary approaches: (1) the "top-down" approach, which reduces the size of macroscopic objects to reach an equivalent microscopic entity using photolithography and related techniques and (2) the "bottom-up" approach, which builds functional microscopic or nanoscopic entities from molecular building blocks. The top-down approach, extensively used by the semiconductor industry, is nearing its scaling limits. On the other hand, the bottom-up approach takes advantage of the self-assembly of smaller molecules into larger networks by exploiting typically weak molecular interactions. But self-assembly alone will not permit complex assembly. Using nanomachines, we hope to eventually consider complex, enzyme-like directed assembly. With that ultimate goal, we are currently exploring the control of nanomachines that would provide a basis for the future bottom-up construction of complex systems. This Account describes the synthesis of a class of molecular machines that resemble macroscopic vehicles. We designed these so-called nanocars for study at the single-molecule level by scanning probe microscopy (SPM). The vehicles have a chassis connected to wheel-terminated axles and convert energy inputs such as heat, electric fields, or light into controlled motion on a surface, ultimately leading to transport of nanocargo. At first, we used C(60) fullerenes as wheels, which allowed the demonstration of a directional rolling mechanism of a nanocar on a gold surface by STM. However, because of the low solubility of the fullerene nanocars and the incompatibility of fullerenes with photochemical processes, we developed new

  9. Evolutionary game theory: molecules as players.

    Science.gov (United States)

    Bohl, Katrin; Hummert, Sabine; Werner, Sarah; Basanta, David; Deutsch, Andreas; Schuster, Stefan; Theissen, Günter; Schroeter, Anja

    2014-12-01

    In this and an accompanying paper we review the use of game theoretical concepts in cell biology and molecular biology. This review focuses on the subcellular level by considering viruses, genes, and molecules as players. We discuss in which way catalytic RNA can be treated by game theory. Moreover, genes can compete for success in replication and can have different strategies in interactions with other genetic elements. Also transposable elements, or "jumping genes", can act as players because they usually bear different traits or strategies. Viruses compete in the case of co-infecting a host cell. Proteins interact in a game theoretical sense when forming heterodimers. Finally, we describe how the Shapley value can be applied to enzymes in metabolic pathways. We show that game theory can be successfully applied to describe and analyse scenarios at the molecular level resulting in counterintuitive conclusions.

  10. Small molecule annotation for the Protein Data Bank.

    Science.gov (United States)

    Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

    2014-01-01

    The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors. © The Author(s) 2014. Published by Oxford University Press.

  11. Thermal ion-molecule reactions in oxygen-containing molecules

    International Nuclear Information System (INIS)

    Kumakura, Minoru

    1981-02-01

    The energetics of ions and the thermal ion-molecule reactions in oxygen-containing molecules have been studied with a modified time-of-flight mass spectrometer. It was found that the translational energy of ion can be easily obtained from analysis of the decay curve using the time-of-flight mass spectrometer. The condensation-elimination reactions proceeded via cross- and homo-elimination mechanism in which the nature of intermediate-complex could be correlated with the nature of reactant ion. It was elucidated that behavior of poly-atomic oxygen-containing ions on the condensation-elimination reactions is considerably influenced by their oxonium ion structures having functional groups. In addition, the rate constants of the condensation-elimination reactions have affected with the energy state of reactant ion and the dipole moment and/or the polarizability of neutral molecule. It was clarified that the rate constants of the ion-molecule clustering reactions in poly-atomic oxygen-containing molecules such as cyclic ether of six member rings are very large and the cluster ions are stable owing to the large number of vibrational degree of freedom in the cluster ions. (author)

  12. EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

    Science.gov (United States)

    Carr, Lincoln D.; Ye, Jun

    2009-05-01

    , controllability, tunable interactions, no disorder, etc). First, they are more easily manipulated because of the strong response of their electric dipole moment to external electric fields, DC or AC. The electric dipole moment also creates the new aspect of long range interactions. Second, they have a rich internal structure, with vibrational and rotational states, fine or hyperfine structure, and Ω- or Λ-doublets. This internal structure allows for wonderful new possibilities in areas such as precision measurement and exquisite control of system dynamics. Therefore, although this focus issue contains a few articles on homonuclear molecules, more complex molecules such as benzene, and even a contribution on atomic chromium, which has a significant magnetic dipole moment, our main focus is on the heteronuclear polar case. This focus issue explores both direct and indirect cooling of mainly polar molecules, and the theory to support and inspire these advances. Thirty-eight research groups have contributed original work, and there are two review articles to complement these advances: the first covers cold and ultracold molecules broadly from few body to many body physics, including foundational theory, the technology to make them, and their scientific applications. The second is on the search for time variation of fundamental constants. The former review, which is comprehensive in nature, concludes with a list of open questions. This sets the tone for the focus issue, namely, openness, innovation, and possibility, an emphasis for which New Journal of Physics, an open-access journal of the highest quality, is especially fitted. Focus on Cold and Ultracold Molecules Contents Cold and ultracold molecules: science, technology and applications Lincoln D Carr, David DeMille, Roman V Krems and Jun Ye Ultracold molecules: new probes on the variation of fundamental constants Cheng Chin, V V Flambaum and M G Kozlov Probing the unitarity limit at low laser intensities Philippe Pellegrini and

  13. The Molecule Cloud - compact visualization of large collections of molecules

    Directory of Open Access Journals (Sweden)

    Ertl Peter

    2012-07-01

    Full Text Available Abstract Background Analysis and visualization of large collections of molecules is one of the most frequent challenges cheminformatics experts in pharmaceutical industry are facing. Various sophisticated methods are available to perform this task, including clustering, dimensionality reduction or scaffold frequency analysis. In any case, however, viewing and analyzing large tables with molecular structures is necessary. We present a new visualization technique, providing basic information about the composition of molecular data sets at a single glance. Summary A method is presented here allowing visual representation of the most common structural features of chemical databases in a form of a cloud diagram. The frequency of molecules containing particular substructure is indicated by the size of respective structural image. The method is useful to quickly perceive the most prominent structural features present in the data set. This approach was inspired by popular word cloud diagrams that are used to visualize textual information in a compact form. Therefore we call this approach “Molecule Cloud”. The method also supports visualization of additional information, for example biological activity of molecules containing this scaffold or the protein target class typical for particular scaffolds, by color coding. Detailed description of the algorithm is provided, allowing easy implementation of the method by any cheminformatics toolkit. The layout algorithm is available as open source Java code. Conclusions Visualization of large molecular data sets using the Molecule Cloud approach allows scientists to get information about the composition of molecular databases and their most frequent structural features easily. The method may be used in the areas where analysis of large molecular collections is needed, for example processing of high throughput screening results, virtual screening or compound purchasing. Several example visualizations of large

  14. Influencing the bonding and assembly of a multiterminal molecule on a metal surface

    Energy Technology Data Exchange (ETDEWEB)

    Lukas, Maya; Doessel, Kerrin; Fink, Karin; Fuhr, Olaf [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); DFG Center of Functional Nanostructures (CFN), D-76049 Karlsruhe (Germany); Schramm, Alexandrina; Stroh, Christophe [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); Mayor, Marcel [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); DFG Center of Functional Nanostructures (CFN), D-76049 Karlsruhe (Germany); University of Basel, Department of Chemistry, CH-4056 Basel (Switzerland); Loehneysen, Hilbert von [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); DFG Center of Functional Nanostructures (CFN), D-76049 Karlsruhe (Germany); Karlsruhe Institute of Technology (KIT), Physics Institute and Institute for Solid State Physics, D-76049 Karlsruhe (Germany)

    2011-07-01

    The bond of a molecule to a metallic electrode is known to have a crucial influence on the molecular conductance. As electronic functionalities are integrated into molecules or several subunits are connected to a three-dimensional multiterminal molecule, it is not obvious that a ''well-known'' chemical linker group will lead to the bonding configuration known from simpler molecules. We investigated a series of tripodal molecules on metal surfaces by STM. The chemical linker groups and the complex connecting the three wire-units are varied. We find that the position of molecules on the surface is governed by a subtle balance of intermolecular and molecule-surface interactions, partly in strong contrast to expectations. This emphasizes the need to characterize the nature of molecule-electrode contacts along with the investigation of the electronic conductance.

  15. Layers of Cold Dipolar Molecules in the Harmonic Approximation

    DEFF Research Database (Denmark)

    R. Armstrong, J.; Zinner, Nikolaj Thomas; V. Fedorov, D.

    2012-01-01

    We consider the N-body problem in a layered geometry containing cold polar molecules with dipole moments that are polarized perpendicular to the layers. A harmonic approximation is used to simplify the hamiltonian and bound state properties of the two-body inter-layer dipolar potential are used...... to adjust this effective interaction. To model the intra-layer repulsion of the polar molecules, we introduce a repulsive inter-molecule potential that can be parametrically varied. Single chains containing one molecule in each layer, as well as multi-chain structures in many layers are discussed...... and their energies and radii determined. We extract the normal modes of the various systems as measures of their volatility and eventually of instability, and compare our findings to the excitations in crystals. We find modes that can be classified as either chains vibrating in phase or as layers vibrating against...

  16. Orientation of KRb molecules in a switched electrostatic field

    International Nuclear Information System (INIS)

    Huang Yun-Xia; Xu Shu-Wu; Yang Xiao-Hua

    2013-01-01

    We theoretically investigate the orientation of the cold KRb molecules induced in a switched electrostatic field by numerically solving the full time-dependent Schrödinger equation. The results show that the periodic field-free molecular orientation can be realized for the KRb molecules by rapidly switching off the electrostatic field. Meanwhile, by varying the switching times of the electrostatic field, the adiabatic and nonadiabatic interactions of the molecules with the applied field can be realized. Moreover, the influences of the electrostatic field strength and the rotational temperature to the degree of the molecular orientation are studied. The investigations show that increasing the electrostatic field will increase the degree of the molecular orientation, both in the constant-field regime and in the field-free regime, while the increasing of the rotational temperature of the cold molecules will greatly decrease the degree of the molecular orientation. (atomic and molecular physics)

  17. Quantum Behavior of Water Molecules Confined to Nanocavities in Gemstones.

    Science.gov (United States)

    Gorshunov, Boris P; Zhukova, Elena S; Torgashev, Victor I; Lebedev, Vladimir V; Shakurov, Gil'man S; Kremer, Reinhard K; Pestrjakov, Efim V; Thomas, Victor G; Fursenko, Dimitry A; Dressel, Martin

    2013-06-20

    When water is confined to nanocavities, its quantum mechanical behavior can be revealed by terahertz spectroscopy. We place H2O molecules in the nanopores of a beryl crystal lattice and observe a rich and highly anisotropic set of absorption lines in the terahertz spectral range. Two bands can be identified, which originate from translational and librational motions of the water molecule isolated within the cage; they correspond to the analogous broad bands in liquid water and ice. In the present case of well-defined and highly symmetric nanocavities, the observed fine structure can be explained by macroscopic tunneling of the H2O molecules within a six-fold potential caused by the interaction of the molecule with the cavity walls.

  18. Fabrication and study of hybrid molecule/superconductor assemblies

    International Nuclear Information System (INIS)

    McDevitt, J.T.; Haupt, S.G.; Jurbergs, D.; Riley, D.R.; Zhao, J.; Zhou, J.P.; Lo, K.; Grassi, J.; Jones, C.

    1994-01-01

    The fabrication of electronic devices from molecular materials has attracted much attention recently. Schottky diodes, molecular transistors, metal-insulator-semiconductor diodes, MIS field effect transistors and light emitting diodes have all been prepared utilizing such substances. The active elements in these devices have been constructed by depositing the molecular phase onto the surface of a metal, semiconductor or insulating substrate. With the recent discovery of high temperature superconductivity, new opportunities now exist for the study of molecule/superconductor interactions as well as for the construction of novel hybrid molecule/superconductor devices. In this paper, methods for preparing the first two classes of composite molecule/superconductor devices are reported. Consequently, light sensors based on organic dye-coated superconductor junctions as well as molecular switches fashioned from organic conductive polymer-coated superconductor microbridges are discussed. Moreover, the initial results related to the study of molecule/superconductor energy and electron transfer phenomena are reported

  19. Entanglement of polar symmetric top molecules as candidate qubits.

    Science.gov (United States)

    Wei, Qi; Kais, Sabre; Friedrich, Bretislav; Herschbach, Dudley

    2011-10-21

    Proposals for quantum computing using rotational states of polar molecules as qubits have previously considered only diatomic molecules. For these the Stark effect is second-order, so a sizable external electric field is required to produce the requisite dipole moments in the laboratory frame. Here we consider use of polar symmetric top molecules. These offer advantages resulting from a first-order Stark effect, which renders the effective dipole moments nearly independent of the field strength. That permits use of much lower external field strengths for addressing sites. Moreover, for a particular choice of qubits, the electric dipole interactions become isomorphous with NMR systems for which many techniques enhancing logic gate operations have been developed. Also inviting is the wider chemical scope, since many symmetric top organic molecules provide options for auxiliary storage qubits in spin and hyperfine structure or in internal rotation states. © 2011 American Institute of Physics

  20. Molecule-by-Molecule Writing Using a Focused Electron Beam

    DEFF Research Database (Denmark)

    Van Dorp, Willem F.; Zhang, Xiaoyan; Feringa, Ben L.

    2012-01-01

    atoms also be written with an electron beam? We verify this with focused electron-beam-induced deposition (FEBID), a direct-write technique that has the current record for the smallest feature written by (electron) optical lithography. We show that the deposition of an organometallic precursor...... on graphene can be followed molecule-by-molecule with FEBID. The results show that mechanisms that are inherent to the process inhibit a further increase in control over the process. Hence, our results present the resolution limit of (electron) optical lithography techniques. The writing of isolated...

  1. Far-Infrared Spectroscopy of Weakly Bound Hydrated Cluster Molecules

    DEFF Research Database (Denmark)

    Andersen, Jonas

    The thermodynamic properties of condensed phases, the functionality of many materials and the molecular organization in biological organisms are all governed by the classes of non-covalent interactions that occur already on the microscopic scale between pairs of molecules. A detailed investigation...... of the intermolecular interactions between prototypical molecular assemblies are valuable for accurate descriptions of larger supramolecular systems such as materials, gas hydrates and biological macromolecules. The aim of this PhD dissertation is to investigate intermolecular interactions fora series of medium...... vibrational bands of the cluster molecules in the challenging far-infrared and terahertz spectral regions.A key parameter in the validation of the performance of theoretical predictions for weak non-covalent intermolecular interactions is the dissociation energy D0 that depends heavily on the class of large...

  2. Quantum transport through organic molecules

    International Nuclear Information System (INIS)

    Maiti, Santanu K.

    2007-01-01

    We investigate the electronic transport for the model of benzene-1, 4-dithiolate (BDT) molecule and some other geometric models of benzene molecule attached with two semi-infinite metallic electrodes by the use of Green's function technique. An analytic approach for the electronic transport through the molecular bridges is presented, based on the tight-binding model. Transport of electrons in such molecular bridges is strongly affected by the geometry of the molecules and their coupling strength with the electrodes. Conductance (g) shows resonance peaks associated with the molecular energy eigenstates. In the weak molecule-to-electrodes coupling limit current (I) passing through the molecules shows staircase-like behavior with sharp steps, while, it varies quite continuously in the limit of strong molecular coupling with the applied bias voltage (V). In presence of the transverse magnetic field conductance gives oscillatory behavior with flux φ, threaded by the molecular ring, showing φ 0 ( = ch/e) flux-quantum periodicity. Though conductance changes with the application of transverse magnetic field, but the current-voltage characteristics remain same in presence of this magnetic field for these molecular bridge systems

  3. Dissociation and decay of ultracold sodium molecules

    International Nuclear Information System (INIS)

    Mukaiyama, T.; Abo-Shaeer, J.R.; Xu, K.; Chin, J.K.; Ketterle, W.

    2004-01-01

    The dissociation of ultracold molecules was studied by ramping an external magnetic field through a Feshbach resonance. The observed dissociation energies directly yielded the strength of the atom-molecule coupling. They showed nonlinear dependence on the ramp speed. This was explained by a Wigner threshold law which predicts that the decay rate of the molecules above threshold increases with the density of states. In addition, inelastic molecule-molecule and molecule-atom collisions were characterized

  4. The mechanism of 2-dimensional manipulation of DNA molecules by water and ethanol flows

    International Nuclear Information System (INIS)

    Shen Zigang; Huang Yibo; Li Bin; Zhang Yi

    2007-01-01

    Due to its unique physical and chemical properties, DNA has recently become a promising material for building blocks in nanofabrication. Many researches focus on how to use DNA molecules as a template for nanowires. Molecular Combing technique is one of important methods to manipulate DNA molecules by using a water meniscus and form specific DNA nano-structures on surfaces. In this paper, by employing a modified molecular combing technique, special patterns of DNA molecules was formed, and the interaction between liquid flows or meniscus and DNA molecules was analyzed, and the mechanism of manipulating DNA molecules by liquid was studied. (authors)

  5. Controlling the alignment of neutral molecules by a strong laser field

    DEFF Research Database (Denmark)

    Sakai, H.; Hilligsøe, Karen Marie; Hald, K.

    1999-01-01

    by lowering the initial rotational energy of the molecules or by increasing the laser intensity. The alignment is measured by photodissociating the molecules with a femtosecond laser pulse and detecting the direction of the photofragments by imaging techniques. The strongest degree of alignment observed......A strong nonresonant nanosecond laser pulse is used to align neutral iodine molecules. The technique, applicable to both polar and nonpolar molecules, relies on the interaction between the strong laser field and the induced dipole moment of the molecules. The degree of alignment is enhanced...

  6. Coherent Control of Ground State NaK Molecules

    Science.gov (United States)

    Yan, Zoe; Park, Jee Woo; Loh, Huanqian; Will, Sebastian; Zwierlein, Martin

    2016-05-01

    Ultracold dipolar molecules exhibit anisotropic, tunable, long-range interactions, making them attractive for the study of novel states of matter and quantum information processing. We demonstrate the creation and control of 23 Na40 K molecules in their rovibronic and hyperfine ground state. By applying microwaves, we drive coherent Rabi oscillations of spin-polarized molecules between the rotational ground state (J=0) and J=1. The control afforded by microwave manipulation allows us to pursue engineered dipolar interactions via microwave dressing. By driving a two-photon transition, we are also able to observe Ramsey fringes between different J=0 hyperfine states, with coherence times as long as 0.5s. The realization of long coherence times between different molecular states is crucial for applications in quantum information processing. NSF, AFOSR- MURI, Alfred P. Sloan Foundation, DARPA-OLE

  7. The iodine molecule insights into intra- and intermolecular perturbation in diatomic molecules

    CERN Document Server

    Lukashov, Sergey; Pravilov, Anatoly

    2018-01-01

    This book presents experimental and theoretical spectroscopic studies performed over the last 25 years on the iodine molecule’s excited states and their perturbations. It is going to be of interest to researchers who study intra- and intermolecular perturbations in diatomic molecules and more complex systems. The book offers a detailed treatment of the nonadiabatic perturbations of valence, ion pair and Rydberg states induced by intramolecular as well as intermolecular interactions in collisions or in weakly-bound complexes. It also provides an overview of current instrumentation and techniques as well as theoretical approaches describing intra- and intermolecular perturbations. The authors are experts in the use of spectroscopy for the study of intrinsic and collision-induced perturbations in diatomic iodine. They introduced new methods of two- and three-step optical population of the iodine ion-pair states. The iodine molecule has 23 valence states correlating with three dissociation limits, 20 so-called ...

  8. Capacitive Sensing of Intercalated H2O Molecules Using Graphene

    OpenAIRE

    Olson, Eric J.; Ma, Rui; Sun, Tao; Ebrish, Mona A.; Haratipour, Nazila; Min, Kyoungmin; Aluru, Narayana R.; Koester, Steven J.

    2015-01-01

    Understanding the interactions of ambient molecules with graphene and adjacent dielectrics is of fundamental importance for a range of graphene-based devices, particularly sensors, where such interactions could influence the operation of the device. It is well-known that water can be trapped underneath graphene and its host substrate, however, the electrical effect of water beneath graphene and the dynamics of how it changes with different ambient conditions has not been quantified. Here, usi...

  9. Small molecule fluoride toxicity agonists.

    Science.gov (United States)

    Nelson, James W; Plummer, Mark S; Blount, Kenneth F; Ames, Tyler D; Breaker, Ronald R

    2015-04-23

    Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here, we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Double photoionisation spectra of molecules

    CERN Document Server

    Eland, John

    2017-01-01

    This book contains spectra of the doubly charged positive ions (dications) of some 75 molecules, including the major constituents of terrestrial and planetary atmospheres and prototypes of major chemical groups. It is intended to be a new resource for research in all areas of molecular spectroscopy involving high energy environments, both terrestrial and extra-terrestrial. All the spectra have been produced by photoionisation using laboratory lamps or synchrotron radiation and have been measured using the magnetic bottle time-of-flight technique by coincidence detection of correlated electron pairs. Full references to published work on the same species are given, though for several molecules these are the first published spectra. Double ionisation energies are listed and discussed in relation to the molecular electronic structure of the molecules. A full introduction to the field of molecular double ionisation is included and the mechanisms by which double photoionisation can occur are examined in detail. A p...

  11. Structure and hydrodynamic properties of plectin molecules.

    Science.gov (United States)

    Foisner, R; Wiche, G

    1987-12-05

    Plectin is a cytoskeletal, high molecular weight protein of widespread and abundant occurrence in cultured cells and tissues. To study its molecular structure, the protein was purified from rat glioma C6 cells and subjected to chemical and biophysical analyses. Plectin's polypeptide chains have an apparent molecular weight of 300,000, as shown by one-dimensional sodium dodecyl sulfate/polyacrylamide electrophoresis. Cross-linking of non-denatured plectin in solution with dimethyl suberimidate and electrophoretic analyses on sodium dodecyl sulfate/agarose gels revealed that the predominant soluble plectin species was a molecule of 1200 X 10(3) Mr consisting of four 300 X 10(3) Mr polypeptide chains. Hydrodynamic properties of plectin in solution were obtained by sedimentation velocity centrifugation and high-pressure liquid chromatography analysis yielding a sedimentation coefficient of 10 S and a Stokes radius of 27 nm. The high f/fmin ratio of 4.0 indicated a very elongated shape of plectin molecules and an axial ratio of about 50. Shadowing and negative staining electron microscopy of plectin molecules revealed multiple domains: a rigid rod of 184 nm in length and 2 nm in diameter, and two globular heads of 9 nm diameter at each end of the rod. Circular dichroism spectra suggested a composition of 30% alpha-helix, 9% beta-structure and 61% random coil or aperiodic structure. The rod-like shape, the alpha-helix content as well as the thermal transition within a midpoint of 45 degrees C and the transition enthalpy (168 kJ/mol) of secondary structure suggested a double-stranded, alpha-helical coiled coil rod domain. Based on the available data, we favor a model of native plectin as a dumb-bell-like association of four 300 X 10(3) Mr polypeptide chains. Electron microscopy and turbidity measurements showed that plectin molecules self-associate into various oligomeric states in solutions of nearly physiological ionic strength. These interactions apparently involved

  12. Adsorption property of volatile molecules on ZnO nanowires ...

    Indian Academy of Sciences (India)

    2018-02-02

    Feb 2, 2018 ... 2Centre for Fire Explosive and Environment Safety, Defence Research and Development Organisation, Ministry ... present work, Zn site was chosen as an adsorption site for a ... Virtual NanoLab [18] software was utilized to construct the ..... In reality, there will be plenty of vapour molecules that interact over.

  13. Technetium-aspirin molecule complexes

    International Nuclear Information System (INIS)

    El-Shahawy, A.S.; Mahfouz, R.M.; Aly, A.A.M.; El-Zohry, M.

    1993-01-01

    Technetium-aspirin and technetium-aspirin-like molecule complexes were prepared. The structure of N-acetylanthranilic acid (NAA) has been decided through CNDO calculations. The ionization potential and electron affinity of the NAA molecule as well as the charge densities were calculated. The electronic absorption spectra of Tc(V)-Asp and Tc(V)-ATS complexes have two characteristic absorption bands at 450 and 600 nm, but the Tc(V)-NAA spectrum has one characteristic band at 450 nm. As a comparative study, Mo-ATS complex was prepared and its electronic absorption spectrum is comparable with the Tc-ATS complex spectrum. (author)

  14. Teaching lasers to control molecules

    International Nuclear Information System (INIS)

    Judson, R.S.; Rabitz, H.

    1992-01-01

    We simulate a method to teach a laser pulse sequences to excite specified molecular states. We use a learning procedure to direct the production of pulses based on ''fitness'' information provided by a laboratory measurement device. Over a series of pulses the algorithm learns an optimal sequence. The experimental apparatus, which consists of a laser, a sample of molecules and a measurement device, acts as an analog computer that solves Schroedinger's equation n/Iexactly, in real time. We simulate an apparatus that learns to excite specified rotational states in a diatomic molecule

  15. Model Hamiltonian Calculations of the Nonlinear Polarizabilities of Conjugated Molecules.

    Science.gov (United States)

    Risser, Steven Michael

    This dissertation advances the theoretical knowledge of the nonlinear polarizabilities of conjugated molecules. The unifying feature of these molecules is an extended delocalized pi electron structure. The pi electrons dominate the electronic properties of the molecules, allowing prediction of molecular properties based on the treatment of just the pi electrons. Two separate pi electron Hamiltonians are used in the research. The principal Hamiltonian used is the non-interacting single-particle Huckel Hamiltonian, which replaces the Coulomb interaction among the pi electrons with a mean field interaction. The simplification allows for exact solution of the Hamiltonian for large molecules. The second Hamiltonian used for this research is the interacting multi-particle Pariser-Parr-Pople (PPP) Hamiltonian, which retains explicit Coulomb interactions. This limits exact solutions to molecules containing at most eight electrons. The molecular properties being investigated are the linear polarizability, and the second and third order hyperpolarizabilities. The hyperpolarizabilities determine the nonlinear optical response of materials. These molecular parameters are determined by two independent approaches. The results from the Huckel Hamiltonian are obtained through first, second and third order perturbation theory. The results from the PPP Hamiltonian are obtained by including the applied field directly in the Hamiltonian and determining the ground state energy at a series of field strengths. By fitting the energy to a polynomial in field strength, the polarizability and hyperpolarizabilities are determined. The Huckel Hamiltonian is used to calculate the third order hyperpolarizability of polyenes. These calculations were the first to show the average hyperpolarizability of the polyenes to be positive, and also to show the saturation of the hyperpolarizability. Comparison of these Huckel results to those from the PPP Hamiltonian shows the lack of explicit Coulomb

  16. Molecular dynamics study of water molecule diffusion in oil-paper insulation materials

    International Nuclear Information System (INIS)

    Liao Ruijin; Zhu Mengzhao; Yang Lijun; Zhou Xin; Gong Chunyan

    2011-01-01

    Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.

  17. Molecular dynamics study of water molecule diffusion in oil-paper insulation materials

    Energy Technology Data Exchange (ETDEWEB)

    Liao Ruijin [State Key Laboratory of Power Transmission Equipment and System Security and New Technology, Chongqing University, Chongqing 400044 (China); Zhu Mengzhao, E-mail: xiaozhupost@163.co [State Key Laboratory of Power Transmission Equipment and System Security and New Technology, Chongqing University, Chongqing 400044 (China); Yang Lijun; Zhou Xin; Gong Chunyan [State Key Laboratory of Power Transmission Equipment and System Security and New Technology, Chongqing University, Chongqing 400044 (China)

    2011-03-01

    Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.

  18. Using Synthetic Nanopores for Single-Molecule Analyses: Detecting SNPs, Trapping DNA Molecules, and the Prospects for Sequencing DNA

    Science.gov (United States)

    Dimitrov, Valentin V.

    2009-01-01

    This work focuses on studying properties of DNA molecules and DNA-protein interactions using synthetic nanopores, and it examines the prospects of sequencing DNA using synthetic nanopores. We have developed a method for discriminating between alleles that uses a synthetic nanopore to measure the binding of a restriction enzyme to DNA. There exists…

  19. Nucleic Acids as Information Molecules.

    Science.gov (United States)

    McInerney, Joseph D.

    1996-01-01

    Presents an activity that aims at enabling students to recognize that DNA and RNA are information molecules whose function is to store, copy, and make available the information in biological systems, without feeling overwhelmed by the specialized vocabulary and the minutia of the central dogma. (JRH)

  20. Small Molecule PET-Radiopharmaceuticals

    NARCIS (Netherlands)

    Elsinga, Philip H.; Dierckx, Rudi A. J. O.

    This review describes several aspects required for the development of small molecule PET-tracers. Design and selection criteria are important to consider before starting to develop novel PET-tracers. Principles and latest trends in C-11 and F-18-radiochemistry are summarized. In addition an update